diff --git a/.DS_Store b/.DS_Store index f9edd2d2..bf5be19a 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/Examples/biology/aktsignaling/akt-signaling_metadata.yaml b/Examples/biology/aktsignaling/akt-signaling_metadata.yaml new file mode 100644 index 00000000..0ba86d21 --- /dev/null +++ b/Examples/biology/aktsignaling/akt-signaling_metadata.yaml @@ -0,0 +1,54 @@ +id: "akt-signaling" +name: "akt signaling" +description: "Signaling rates" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["akt", "signaling", "growthfactor", "rtk", "pi3k", "mtorc2", "mtorc1", "s6k"] + +date: + last_tested: 2026-06-29 + +biol_categories: ["other"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf", "molclustpy", "vcell" ] + nfsim_compatible: true + molclustpy_compatible: true + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/akt-signaling.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/aktsignaling/metadata.yaml b/Examples/biology/aktsignaling/metadata.yaml index aef1085d..a4e1c414 100644 --- a/Examples/biology/aktsignaling/metadata.yaml +++ b/Examples/biology/aktsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["akt", "signaling", "growthfactor", "rtk", "pi3k", "mtorc2", "mtorc1", "s6k"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/allostericactivation/allosteric-activation_metadata.yaml b/Examples/biology/allostericactivation/allosteric-activation_metadata.yaml new file mode 100644 index 00000000..e6ec7983 --- /dev/null +++ b/Examples/biology/allostericactivation/allosteric-activation_metadata.yaml @@ -0,0 +1,55 @@ +id: "allosteric-activation" +name: "allosteric activation" +description: "Binding constants" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["allosteric", "activation", "enzyme", "substrate", "activator", "product"] + +date: + last_tested: 2026-06-26 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: [ "ode", "ssa", "nf", "vcell" ] + nfsim_compatible: true + molclustpy_compatible: false + comments: " cannot access local variable 'stdout_str' where it is not associated with a value" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: true + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/allosteric-activation.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/allostericactivation/metadata.yaml b/Examples/biology/allostericactivation/metadata.yaml index 2b92498d..6b745ed3 100644 --- a/Examples/biology/allostericactivation/metadata.yaml +++ b/Examples/biology/allostericactivation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["allosteric", "activation", "enzyme", "substrate", "activator", "product"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/ampksignaling/ampk-signaling_metadata.yaml b/Examples/biology/ampksignaling/ampk-signaling_metadata.yaml new file mode 100644 index 00000000..6c6b13a4 --- /dev/null +++ b/Examples/biology/ampksignaling/ampk-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "ampk-signaling" +name: "ampk signaling" +description: "AMPK signaling: The cellular energy sensor." +contributors: + - name: "Achyudhan" +tags: ["ampk", "signaling", "amp", "lkb1", "ca", "sik", "crtc"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ampk-signaling.bngl" +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/ampksignaling/metadata.yaml b/Examples/biology/ampksignaling/metadata.yaml index 6e5845d2..7de8ec4d 100644 --- a/Examples/biology/ampksignaling/metadata.yaml +++ b/Examples/biology/ampksignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ampk", "signaling", "amp", "lkb1", "ca", "sik", "crtc"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/apoptosiscascade/apoptosis-cascade_metadata.yaml b/Examples/biology/apoptosiscascade/apoptosis-cascade_metadata.yaml new file mode 100644 index 00000000..1a53653d --- /dev/null +++ b/Examples/biology/apoptosiscascade/apoptosis-cascade_metadata.yaml @@ -0,0 +1,26 @@ +id: "apoptosis-cascade" +name: "apoptosis cascade" +description: "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling." +contributors: + - name: "Achyudhan" +tags: ["apoptosis", "cascade", "deathligand", "caspase8", "bid", "mito", "apaf1", "caspase3", "xiap", "smac"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/apoptosis-cascade.bngl" +playground: + visible: false + gallery_categories: ["cell-cycle","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/apoptosiscascade/metadata.yaml b/Examples/biology/apoptosiscascade/metadata.yaml index 213491d5..f5d45b14 100644 --- a/Examples/biology/apoptosiscascade/metadata.yaml +++ b/Examples/biology/apoptosiscascade/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["apoptosis", "cascade", "deathligand", "caspase8", "bid", "mito", "apaf1", "caspase3", "xiap", "smac"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/autoactivationloop/auto-activation-loop_metadata.yaml b/Examples/biology/autoactivationloop/auto-activation-loop_metadata.yaml new file mode 100644 index 00000000..9c0d4eb8 --- /dev/null +++ b/Examples/biology/autoactivationloop/auto-activation-loop_metadata.yaml @@ -0,0 +1,26 @@ +id: "auto-activation-loop" +name: "auto activation loop" +description: "Auto-activation loop: A positive feedback circuit." +contributors: + - name: "Achyudhan" +tags: ["auto", "activation", "loop", "gene", "mrna", "protein", "rbp"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/auto-activation-loop.bngl" +playground: + visible: false + gallery_categories: ["metabolism","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/autoactivationloop/metadata.yaml b/Examples/biology/autoactivationloop/metadata.yaml index 56df9c5d..eb2716f9 100644 --- a/Examples/biology/autoactivationloop/metadata.yaml +++ b/Examples/biology/autoactivationloop/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["auto", "activation", "loop", "gene", "mrna", "protein", "rbp"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/autophagyregulation/autophagy-regulation_metadata.yaml b/Examples/biology/autophagyregulation/autophagy-regulation_metadata.yaml new file mode 100644 index 00000000..7ee958f3 --- /dev/null +++ b/Examples/biology/autophagyregulation/autophagy-regulation_metadata.yaml @@ -0,0 +1,55 @@ +id: "autophagy-regulation" +name: "autophagy-regulation" +description: "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["autophagy", "regulation", "mtor", "ampk", "ulk1", "lc3", "p62"] + +date: + last_tested: 2026-06-30 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: false + vcell_compatible: false + vcell_errors: "Encountered } at line 38" + simulation_methods: ["ode", "ssa",] + nfsim_compatible: false + molclustpy_compatible: false + comments: "IndexError: list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/autophagy-regulation.bngl" + +playground: + visible: false + gallery_categories: ["tutorials"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/autophagyregulation/metadata.yaml b/Examples/biology/autophagyregulation/metadata.yaml index 0c56ed90..3a60963d 100644 --- a/Examples/biology/autophagyregulation/metadata.yaml +++ b/Examples/biology/autophagyregulation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["autophagy", "regulation", "mtor", "ampk", "ulk1", "lc3", "p62"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/bcrsignaling/bcr-signaling_metadata.yaml b/Examples/biology/bcrsignaling/bcr-signaling_metadata.yaml new file mode 100644 index 00000000..205be5ed --- /dev/null +++ b/Examples/biology/bcrsignaling/bcr-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "bcr-signaling" +name: "bcr signaling" +description: "BCR signaling: The B-cell antigen receptor cascade." +contributors: + - name: "Achyudhan" +tags: ["bcr", "signaling", "antigen", "syk", "plcg2", "cd22", "shp1", "calcium"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/bcr-signaling.bngl" +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/bcrsignaling/metadata.yaml b/Examples/biology/bcrsignaling/metadata.yaml index 3ff750bc..4167a329 100644 --- a/Examples/biology/bcrsignaling/metadata.yaml +++ b/Examples/biology/bcrsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["bcr", "signaling", "antigen", "syk", "plcg2", "cd22", "shp1", "calcium"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/betaadrenergicresponse/beta-adrenergic-response_metadata.yaml b/Examples/biology/betaadrenergicresponse/beta-adrenergic-response_metadata.yaml new file mode 100644 index 00000000..e2ddef87 --- /dev/null +++ b/Examples/biology/betaadrenergicresponse/beta-adrenergic-response_metadata.yaml @@ -0,0 +1,55 @@ +id: "beta-adrenergic-response" +name: "beta adrenergic response" +description: "Beta-adrenergic signaling: GPCR pathway and desensitization." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["beta", "adrenergic", "response", "epi", "betar", "gs", "ac", "arr", "camp"] + +date: + last_tested: 2026-06-29 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: [ "ode", "ssa", "nf", "vcell" ] + nfsim_compatible: true + molclustpy_compatible: false + comments: "#IndexError: list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/beta-adrenergic-response.bngl" + +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/betaadrenergicresponse/metadata.yaml b/Examples/biology/betaadrenergicresponse/metadata.yaml index 87ff0a62..c7f9b5dd 100644 --- a/Examples/biology/betaadrenergicresponse/metadata.yaml +++ b/Examples/biology/betaadrenergicresponse/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["beta", "adrenergic", "response", "epi", "betar", "gs", "ac", "arr", "camp"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/bistabletoggleswitch/bistable-toggle-switch_metadata.yaml b/Examples/biology/bistabletoggleswitch/bistable-toggle-switch_metadata.yaml new file mode 100644 index 00000000..c2563d5b --- /dev/null +++ b/Examples/biology/bistabletoggleswitch/bistable-toggle-switch_metadata.yaml @@ -0,0 +1,26 @@ +id: "bistable-toggle-switch" +name: "bistable toggle switch" +description: "Genetic Toggle Switch: Mutual repression circuit." +contributors: + - name: "Achyudhan" +tags: ["bistable", "toggle", "switch", "proml", "promr", "tf_l", "tf_r", "ind_l", "ind_r"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/bistable-toggle-switch.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/bistabletoggleswitch/metadata.yaml b/Examples/biology/bistabletoggleswitch/metadata.yaml index d875c60b..4247db9c 100644 --- a/Examples/biology/bistabletoggleswitch/metadata.yaml +++ b/Examples/biology/bistabletoggleswitch/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["bistable", "toggle", "switch", "proml", "promr", "tf_l", "tf_r", "ind_l", "ind_r"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin_metadata.yaml b/Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin_metadata.yaml new file mode 100644 index 00000000..544b2552 --- /dev/null +++ b/Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin_metadata.yaml @@ -0,0 +1,54 @@ +id: "blood-coagulation-thrombin" +name: "blood coagulation thrombin" +description: "Blood coagulation: Thrombin burst and feedback propagation." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["blood", "coagulation", "thrombin", "signaling"] + +date: + last_tested: 2026-06-26 + +biol_categories: ["signaling"] + +comp_categories: ["tutorial"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: " Encountered TotalRate " + simulation_methods: ["ode", "ssa", "nf"] + nfsim_compatible: true + molclustpy_compatible: true + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: true + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/blood-coagulation-thrombin.bngl" + +playground: + visible: false + gallery_categories: ["immunology", "test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/bloodcoagulationthrombin/metadata.yaml b/Examples/biology/bloodcoagulationthrombin/metadata.yaml index 3df63cac..02ec6533 100644 --- a/Examples/biology/bloodcoagulationthrombin/metadata.yaml +++ b/Examples/biology/bloodcoagulationthrombin/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["blood", "coagulation", "thrombin", "tf", "factorx", "factorv", "prothrombin", "fibrinogen", "at"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/bmpsignaling/bmp-signaling_metadata.yaml b/Examples/biology/bmpsignaling/bmp-signaling_metadata.yaml new file mode 100644 index 00000000..9e806d0a --- /dev/null +++ b/Examples/biology/bmpsignaling/bmp-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "bmp-signaling" +name: "bmp signaling" +description: "BMP-Smad signaling: Developmental gradient relay." +contributors: + - name: "Achyudhan" +tags: ["bmp", "signaling", "noggin", "receptor1", "receptor2", "smad1", "smad4", "smad6"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/bmp-signaling.bngl" +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/bmpsignaling/metadata.yaml b/Examples/biology/bmpsignaling/metadata.yaml index fc124170..757fb27d 100644 --- a/Examples/biology/bmpsignaling/metadata.yaml +++ b/Examples/biology/bmpsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["bmp", "signaling", "noggin", "receptor1", "receptor2", "smad1", "smad4", "smad6"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/brusselatoroscillator/brusselator-oscillator_metadata.yaml b/Examples/biology/brusselatoroscillator/brusselator-oscillator_metadata.yaml new file mode 100644 index 00000000..b550f108 --- /dev/null +++ b/Examples/biology/brusselatoroscillator/brusselator-oscillator_metadata.yaml @@ -0,0 +1,55 @@ +id: "brusselator-oscillator" +name: "brusselator oscillator" +description: "The Brusselator: Auto-catalytic chemical oscillator." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["brusselator", "oscillator", "a", "b", "x", "y"] + +date: + last_tested: 2026-06-29 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: false + comments: "list index out of range, after continue=>1 is removed " + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/brusselator-oscillator.bngl" + +playground: + visible: false + gallery_categories: ["physics", "test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/brusselatoroscillator/metadata.yaml b/Examples/biology/brusselatoroscillator/metadata.yaml index 359484b7..6c895515 100644 --- a/Examples/biology/brusselatoroscillator/metadata.yaml +++ b/Examples/biology/brusselatoroscillator/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["brusselator", "oscillator", "a", "b", "x", "y"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway_metadata.yaml b/Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway_metadata.yaml new file mode 100644 index 00000000..24207580 --- /dev/null +++ b/Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway_metadata.yaml @@ -0,0 +1,26 @@ +id: "calcineurin-nfat-pathway" +name: "calcineurin nfat pathway" +description: "NFAT Signaling: Calcium-dependent nuclear translocation." +contributors: + - name: "Achyudhan" +tags: ["calcineurin", "nfat", "pathway", "ca", "cam", "can", "rcan1"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/calcineurin-nfat-pathway.bngl" +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/calcineurinnfatpathway/metadata.yaml b/Examples/biology/calcineurinnfatpathway/metadata.yaml index 3a2f4b32..e75fb435 100644 --- a/Examples/biology/calcineurinnfatpathway/metadata.yaml +++ b/Examples/biology/calcineurinnfatpathway/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["calcineurin", "nfat", "pathway", "ca", "cam", "can", "rcan1"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/calciumspikesignaling/calcium-spike-signaling_metadata.yaml b/Examples/biology/calciumspikesignaling/calcium-spike-signaling_metadata.yaml new file mode 100644 index 00000000..dfa749da --- /dev/null +++ b/Examples/biology/calciumspikesignaling/calcium-spike-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "calcium-spike-signaling" +name: "calcium spike signaling" +description: "Calcium spikes: Oscillations driven by IP3R and CICR feedback." +contributors: + - name: "Achyudhan" +tags: ["calcium", "spike", "signaling", "plc", "ip3", "ca", "stim1"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/calcium-spike-signaling.bngl" +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/calciumspikesignaling/metadata.yaml b/Examples/biology/calciumspikesignaling/metadata.yaml index b0d87e80..39f13dae 100644 --- a/Examples/biology/calciumspikesignaling/metadata.yaml +++ b/Examples/biology/calciumspikesignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["calcium", "spike", "signaling", "plc", "ip3", "ca", "stim1"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/biology/caspaseactivationloop/caspase-activation-loop_metadata.yaml b/Examples/biology/caspaseactivationloop/caspase-activation-loop_metadata.yaml new file mode 100644 index 00000000..ef671005 --- /dev/null +++ b/Examples/biology/caspaseactivationloop/caspase-activation-loop_metadata.yaml @@ -0,0 +1,55 @@ +id: "caspase-activation-loop" +name: "caspase activation loop" +description: "Caspase activation loop: The executioner feedback system." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["caspase", "activation", "loop", "deathligand", "caspase8", "caspase3", "iap", "flip"] + +date: + last_tested: 2026-07-01 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 0 at line 85" + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: false + comments: "IndexError: list index out of range #false in original metadata.yaml, but runs with nf on bng2 WARNING: Species with more than 20 molecules will be labeled with the Quasi method. " + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/calcium-spike-signaling.bngl" + +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/caspaseactivationloop/metadata.yaml b/Examples/biology/caspaseactivationloop/metadata.yaml index 2c76c8ad..3ea35e90 100644 --- a/Examples/biology/caspaseactivationloop/metadata.yaml +++ b/Examples/biology/caspaseactivationloop/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["caspase", "activation", "loop", "deathligand", "caspase8", "caspase3", "iap", "flip"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/cd40signaling/cd40-signaling_metadata.yaml b/Examples/biology/cd40signaling/cd40-signaling_metadata.yaml new file mode 100644 index 00000000..f86f8d32 --- /dev/null +++ b/Examples/biology/cd40signaling/cd40-signaling_metadata.yaml @@ -0,0 +1,55 @@ +id: "cd40-signaling" +name: "cd40 signaling" +description: "CD40 Signaling: B-cell activation and TRAF-mediated relay." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["cd40", "signaling", "cd40l", "traf", "ikk", "nik", "nfkb", "relb"] + +date: + last_tested: 2026-07-01 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered TotalRate at line 71 " + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: true + comments: "Put action block after end model; #false in original metadata.yaml, but runs with nf on bng2 " + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: true + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cd40-signaling.bngl" + +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/cd40signaling/metadata.yaml b/Examples/biology/cd40signaling/metadata.yaml index 562b1a8c..048509ef 100644 --- a/Examples/biology/cd40signaling/metadata.yaml +++ b/Examples/biology/cd40signaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cd40", "signaling", "cd40l", "traf", "ikk", "nik", "nfkb", "relb"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint_metadata.yaml b/Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint_metadata.yaml new file mode 100644 index 00000000..b56a3efa --- /dev/null +++ b/Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint_metadata.yaml @@ -0,0 +1,55 @@ +id: "cell-cycle-checkpoint" +name: "cell cycle checkpoint" +description: "Cell cycle checkpoint: Mitotic entry switch (CDK1)." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["cell", "cycle", "checkpoint", "cyclin", "cdk", "cdc25", "wee1", "apc", "p21"] + +date: + last_tested: 2026-07-01 + +biol_categories: ["cell cycle"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered ! at line 77" + simulation_methods: ["ode", "ssa"] + nfsim_compatible: false + molclustpy_compatible: false + comments: "#UnboundLocalError: cannot access local variable 'stdout_str' where it is not associated with a value" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cell-cycle-checkpoint.bngl" + +playground: + visible: false + gallery_categories: ["cell-cycle","test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/cellcyclecheckpoint/metadata.yaml b/Examples/biology/cellcyclecheckpoint/metadata.yaml index b4dac77d..9f627cc0 100644 --- a/Examples/biology/cellcyclecheckpoint/metadata.yaml +++ b/Examples/biology/cellcyclecheckpoint/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cell", "cycle", "checkpoint", "cyclin", "cdk", "cdc25", "wee1", "apc", "p21"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling_metadata.yaml b/Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling_metadata.yaml new file mode 100644 index 00000000..d74e9eda --- /dev/null +++ b/Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling_metadata.yaml @@ -0,0 +1,55 @@ +id: "checkpoint-kinase-signaling" +name: "checkpoint kinase signaling" +description: "DNA Checkpoint: ATM/ATR mediated damage sensing." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["checkpoint", "kinase", "signaling", "dna", "atm", "atr", "chk1", "chk2", "p53", "cdc25"] + +date: + last_tested: 2026-07-01 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: "import works but simulation fails: RuntimeException-Application 'NFSim app' has no generated Math" + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: true + comments: "false in original metadata.yaml, but runs with nf on bng2 " + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/checkpoint-kinase-signaling.bngl" + +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/checkpointkinasesignaling/metadata.yaml b/Examples/biology/checkpointkinasesignaling/metadata.yaml index 26666b85..fd3e2ddc 100644 --- a/Examples/biology/checkpointkinasesignaling/metadata.yaml +++ b/Examples/biology/checkpointkinasesignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["checkpoint", "kinase", "signaling", "dna", "atm", "atr", "chk1", "chk2", "p53", "cdc25"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction_metadata.yaml b/Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction_metadata.yaml new file mode 100644 index 00000000..c9e696eb --- /dev/null +++ b/Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction_metadata.yaml @@ -0,0 +1,26 @@ +id: "chemotaxis-signal-transduction" +name: "chemotaxis signal transduction" +description: "Bacterial Chemotaxis: Adaptation through methylation." +contributors: + - name: "Achyudhan" +tags: ["chemotaxis", "signal", "transduction", "attr", "mcp", "chea", "chey", "cheb", "motor"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/chemotaxis-signal-transduction.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/chemotaxissignaltransduction/metadata.yaml b/Examples/biology/chemotaxissignaltransduction/metadata.yaml index d940bb40..c8997ac7 100644 --- a/Examples/biology/chemotaxissignaltransduction/metadata.yaml +++ b/Examples/biology/chemotaxissignaltransduction/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["chemotaxis", "signal", "transduction", "attr", "mcp", "chea", "chey", "cheb", "motor"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/circadianoscillator/circadian-oscillator_metadata.yaml b/Examples/biology/circadianoscillator/circadian-oscillator_metadata.yaml new file mode 100644 index 00000000..bdfce7e3 --- /dev/null +++ b/Examples/biology/circadianoscillator/circadian-oscillator_metadata.yaml @@ -0,0 +1,26 @@ +id: "circadian-oscillator" +name: "circadian oscillator" +description: "title: Vilar Circadian Oscillator Model" +contributors: + - name: "Achyudhan" +tags: ["circadian", "oscillator", "a", "r", "pa", "pr", "mrna_a", "mrna_r"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/circadian-oscillator.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/circadianoscillator/metadata.yaml b/Examples/biology/circadianoscillator/metadata.yaml index 402fd37a..2e49205f 100644 --- a/Examples/biology/circadianoscillator/metadata.yaml +++ b/Examples/biology/circadianoscillator/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["circadian", "oscillator", "a", "r", "pa", "pr", "mrna_a", "mrna_r"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit_metadata.yaml b/Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit_metadata.yaml new file mode 100644 index 00000000..0f7f9c53 --- /dev/null +++ b/Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit_metadata.yaml @@ -0,0 +1,26 @@ +id: "clock-bmal1-gene-circuit" +name: "clock bmal1 gene circuit" +description: "BMAL1-CLOCK: The master activator of the circadian circuit." +contributors: + - name: "Achyudhan" +tags: ["clock", "bmal1", "gene", "circuit", "ror", "reverb", "dna"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/clock-bmal1-gene-circuit.bngl" +playground: + visible: false + gallery_categories: ["cell-cycle","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/clockbmal1genecircuit/metadata.yaml b/Examples/biology/clockbmal1genecircuit/metadata.yaml index 10fe366d..2b730fea 100644 --- a/Examples/biology/clockbmal1genecircuit/metadata.yaml +++ b/Examples/biology/clockbmal1genecircuit/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["clock", "bmal1", "gene", "circuit", "ror", "reverb", "dna"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition_metadata.yaml b/Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition_metadata.yaml new file mode 100644 index 00000000..03f6b71b --- /dev/null +++ b/Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition_metadata.yaml @@ -0,0 +1,55 @@ +id: "competitive-enzyme-inhibition" +name: "competitive enzyme inhibition" +description: "A model of competitive enzyme inhibition." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["competitive", "enzyme", "inhibition", "substrate1", "substrate2", "inhibitor", "product"] + +date: + last_tested: 2026-07-01 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 0 at line 65" + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: false + comments: "#IndexError: list index out of range" + +features: + uses_generate_network: false + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/competitive-enzyme-inhibition.bngl" + +playground: + visible: false + gallery_categories: ["metabolism","test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/competitiveenzymeinhibition/metadata.yaml b/Examples/biology/competitiveenzymeinhibition/metadata.yaml index 59799735..e78aafa3 100644 --- a/Examples/biology/competitiveenzymeinhibition/metadata.yaml +++ b/Examples/biology/competitiveenzymeinhibition/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["competitive", "enzyme", "inhibition", "substrate1", "substrate2", "inhibitor", "product"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/complementactivationcascade/complement-activation-cascade_metadata.yaml b/Examples/biology/complementactivationcascade/complement-activation-cascade_metadata.yaml new file mode 100644 index 00000000..785856ae --- /dev/null +++ b/Examples/biology/complementactivationcascade/complement-activation-cascade_metadata.yaml @@ -0,0 +1,55 @@ +id: "complement-activation-cascade" +name: "complement activation cascade" +description: "Complement System: Pathogen opsonization and the Alternative Pathway." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["complement", "activation", "cascade", "c3", "fb", "c5", "mac", "surf"] + +date: + last_tested: 2026-07-02 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 85" + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: false + comments: "#IndexError: list index out of range" + +features: + uses_generate_network: false + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/complement-activation-cascade.bngl" + +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/complementactivationcascade/metadata.yaml b/Examples/biology/complementactivationcascade/metadata.yaml index 6535786d..c8d7b6f6 100644 --- a/Examples/biology/complementactivationcascade/metadata.yaml +++ b/Examples/biology/complementactivationcascade/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["complement", "activation", "cascade", "c3", "fb", "c5", "mac", "surf"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl b/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl index 11e200ad..47e81ca8 100644 --- a/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl +++ b/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl @@ -30,6 +30,7 @@ begin parameters YAP_tot 500 TEAD_tot 150 NF2_tot 100 + Contact_total 1000 k_contact_pulse 1.0 # Density-dependent activation triggernal rate end parameters @@ -42,7 +43,7 @@ begin molecule types end molecule types begin seed species - Contact(s~low) 1000 + Contact(s~low) Contact_total MST(s~U) MST_tot LATS(s~U) LATS_tot YAP(b,s~U,loc~cyt) YAP_tot diff --git a/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap_metadata.yaml b/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap_metadata.yaml new file mode 100644 index 00000000..0877b07e --- /dev/null +++ b/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap_metadata.yaml @@ -0,0 +1,59 @@ +id: "contact-inhibition-hippo-yap" +name: "contact inhibition hippo yap" +description: "Hippo Pathway: Contact inhibition and YAP regulation." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["contact", "inhibition", "hippo", "yap", "mst", "lats", "tead"] + +date: + last_tested: 2026-07-02 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: true + uses_compartments: false + uses_energy: false + uses_functions: true + comments: "VCell: put actions outside of model NFsim: # CHANGED! WARNING: Species with more than 20 molecules will be labeled with the Quasi method. MCP: if set species concentration to variable instead of 1000" + + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/contact-inhibition-hippo-yap.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/contactinhibitionhippoyap/metadata.yaml b/Examples/biology/contactinhibitionhippoyap/metadata.yaml index 19056567..9588e61f 100644 --- a/Examples/biology/contactinhibitionhippoyap/metadata.yaml +++ b/Examples/biology/contactinhibitionhippoyap/metadata.yaml @@ -1,24 +1,58 @@ id: "contact-inhibition-hippo-yap" name: "contact inhibition hippo yap" description: "Hippo Pathway: Contact inhibition and YAP regulation." + contributors: - name: "Achyudhan" + - name: "Nabil Mardhy" + tags: ["contact", "inhibition", "hippo", "yap", "mst", "lats", "tead"] + +date: + last_tested: 2026-07-02 + category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true bng2_compatible: true - simulation_methods: ["ode"] + bngp_compatible: true + vcell_compatible: true + vcell_errors: "to run put actions outside of model" + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: true uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + source: origin: "ai-generated" original_format: "bngl" original_repository: "bionetgen-web-simulator" source_path: "example-models/contact-inhibition-hippo-yap.bngl" + playground: visible: false gallery_categories: ["test-models"] featured: false difficulty: "advanced" + diff --git a/Examples/biology/cooperativebinding/cooperative-binding_metadata.yaml b/Examples/biology/cooperativebinding/cooperative-binding_metadata.yaml new file mode 100644 index 00000000..1c1047b3 --- /dev/null +++ b/Examples/biology/cooperativebinding/cooperative-binding_metadata.yaml @@ -0,0 +1,54 @@ +id: "cooperative-binding" +name: "cooperative binding" +description: "Cooperative binding: The binding of the first ligand molecule increases" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["cooperative", "binding", "receptor", "ligand", "competitor"] + +date: + last_tested: 2026-07-02 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: "put actions outside of model" + simulation_methods: ["ode", "ssa","nf"] + nfsim_compatible: true + molclustpy_compatible: true + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cooperative-binding.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/cooperativebinding/metadata.yaml b/Examples/biology/cooperativebinding/metadata.yaml index 270f0273..2da7b6f0 100644 --- a/Examples/biology/cooperativebinding/metadata.yaml +++ b/Examples/biology/cooperativebinding/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cooperative", "binding", "receptor", "ligand", "competitor"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/dnadamagerepair/dna-damage-repair_metadata.yaml b/Examples/biology/dnadamagerepair/dna-damage-repair_metadata.yaml new file mode 100644 index 00000000..925a742b --- /dev/null +++ b/Examples/biology/dnadamagerepair/dna-damage-repair_metadata.yaml @@ -0,0 +1,54 @@ +id: "dna-damage-repair" +name: "dna damage repair" +description: "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["dna", "damage", "repair", "mrn", "atm", "chk2", "repaircomplex"] + +date: + last_tested: 2026-07-02 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: "put actions outside of model" + simulation_methods: ["ode", "ssa","nf"] + nfsim_compatible: true + molclustpy_compatible: true + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/dna-damage-repair.bngl" + +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Examples/biology/dnadamagerepair/metadata.yaml b/Examples/biology/dnadamagerepair/metadata.yaml index f916c5bf..29b0b769 100644 --- a/Examples/biology/dnadamagerepair/metadata.yaml +++ b/Examples/biology/dnadamagerepair/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["dna", "damage", "repair", "mrn", "atm", "chk2", "repaircomplex"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/dnamethylationdynamics/dna-methylation-dynamics_metadata.yaml b/Examples/biology/dnamethylationdynamics/dna-methylation-dynamics_metadata.yaml new file mode 100644 index 00000000..884e79e2 --- /dev/null +++ b/Examples/biology/dnamethylationdynamics/dna-methylation-dynamics_metadata.yaml @@ -0,0 +1,55 @@ +id: "dna-methylation-dynamics" +name: "dna methylation dynamics" +description: "DNA Methylation: Maintenance and de novo dynamics." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["dna", "methylation", "dynamics", "cpg", "dnmt1", "tet", "v_maint", "v_erase"] + +date: + last_tested: 2026-07-02 + +biol_categories: ["methylation"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: Encountered "}" at line 29 + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: true + comments: "false in original metadata.yaml but runs with bng2" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/dna-methylation-dynamics.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + diff --git a/Examples/biology/dnamethylationdynamics/metadata.yaml b/Examples/biology/dnamethylationdynamics/metadata.yaml index 197172e8..e2d2cef9 100644 --- a/Examples/biology/dnamethylationdynamics/metadata.yaml +++ b/Examples/biology/dnamethylationdynamics/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["dna", "methylation", "dynamics", "cpg", "dnmt1", "tet", "v_maint", "v_erase"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling_metadata.yaml b/Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling_metadata.yaml new file mode 100644 index 00000000..81a0aaf3 --- /dev/null +++ b/Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling_metadata.yaml @@ -0,0 +1,56 @@ +id: "dr5-apoptosis-signaling" +name: "dr5 apoptosis signaling" +description: "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["dr5", "apoptosis", "signaling", "trail", "fadd", "caspase8", "flip", "death_signal"] + +date: + last_tested: 2026-07-02 + +biol_categories: ["signaling", "cell cycle", "apoptosis"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 78" + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true + molclustpy_compatible: false + comments: "false in original metadata.yaml but runs with bng2; MCP: IndexError: list index out of range" + +Features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: true + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/dr5-apoptosis-signaling.bngl" + +playground: + visible: false + gallery_categories: ["cell-cycle","test-models"] + featured: false + difficulty: "advanced" + + diff --git a/Examples/biology/dr5apoptosissignaling/metadata.yaml b/Examples/biology/dr5apoptosissignaling/metadata.yaml index 47404f0b..4173bdda 100644 --- a/Examples/biology/dr5apoptosissignaling/metadata.yaml +++ b/Examples/biology/dr5apoptosissignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["dr5", "apoptosis", "signaling", "trail", "fadd", "caspase8", "flip", "death_signal"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/dualsitephosphorylation/dual-site-phosphorylation_metadata.yaml b/Examples/biology/dualsitephosphorylation/dual-site-phosphorylation_metadata.yaml new file mode 100644 index 00000000..662fb02c --- /dev/null +++ b/Examples/biology/dualsitephosphorylation/dual-site-phosphorylation_metadata.yaml @@ -0,0 +1,56 @@ +id: "dual-site-phosphorylation" +name: "dual site phosphorylation" +description: "Dual-site phosphorylation: Requires two sequential modifications for activity." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["dual", "site", "phosphorylation", "kinase", "phosphatase", "substrate"] + +date: + last_tested: 2026-07-02 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: "#put actions outside of model, however, does not run simulation: Failed to generate new Math, Reactant Site state!? and its matching Product Site state~on have incompatible Bond Types. " + simulation_methods: ["ode", "ssa","nf"] + nfsim_compatible: false + molclustpy_compatible: false + comments: "NFSim: #true in original metadata.yaml, nf works on bngp but not bng2: You created a reaction (_R2) that deletes a molecule, but you did not use the 'DeleteMolecules' keyword cannot access local variable 'stdout_str' where it is not associated with a value" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: true + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/dual-site-phosphorylation.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + diff --git a/Examples/biology/dualsitephosphorylation/metadata.yaml b/Examples/biology/dualsitephosphorylation/metadata.yaml index b8765241..ba640e06 100644 --- a/Examples/biology/dualsitephosphorylation/metadata.yaml +++ b/Examples/biology/dualsitephosphorylation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["dual", "site", "phosphorylation", "kinase", "phosphatase", "substrate"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch_metadata.yaml b/Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch_metadata.yaml new file mode 100644 index 00000000..6670c916 --- /dev/null +++ b/Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch_metadata.yaml @@ -0,0 +1,55 @@ +id: "e2f-rb-cell-cycle-switch" +name: "e2f rb cell cycle switch" +description: "E2F/Rb Switch: The G1/S transition gate." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["e2f", "rb", "cell", "cycle", "switch", "mitogen", "cycd", "cyce", "p27"] +date: + last_tested: 2026-07-02 + +biol_categories: ["signaling", "cell cycle"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 73" + simulation_methods: ["ode", "ssa"] + nfsim_compatible: false + molclustpy_compatible: false + comments: "NFsim does not support 'continue' option. at line 101; IndexError: list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/e2f-rb-cell-cycle-switch.bngl" + +playground: + visible: false + gallery_categories: ["cell-cycle","test-models"] + featured: false + difficulty: "advanced" + + diff --git a/Examples/biology/e2frbcellcycleswitch/metadata.yaml b/Examples/biology/e2frbcellcycleswitch/metadata.yaml index d7d77db0..d157a497 100644 --- a/Examples/biology/e2frbcellcycleswitch/metadata.yaml +++ b/Examples/biology/e2frbcellcycleswitch/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["e2f", "rb", "cell", "cycle", "switch", "mitogen", "cycd", "cyce", "p27"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/egfrsignalingpathway/egfr-signaling-pathway_metadata.yaml b/Examples/biology/egfrsignalingpathway/egfr-signaling-pathway_metadata.yaml new file mode 100644 index 00000000..a5c8f926 --- /dev/null +++ b/Examples/biology/egfrsignalingpathway/egfr-signaling-pathway_metadata.yaml @@ -0,0 +1,26 @@ +id: "egfr-signaling-pathway" +name: "egfr signaling pathway" +description: "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites." +contributors: + - name: "Achyudhan" +tags: ["egfr", "signaling", "pathway", "egf", "grb2", "shc"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/egfr-signaling-pathway.bngl" +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/egfrsignalingpathway/metadata.yaml b/Examples/biology/egfrsignalingpathway/metadata.yaml index 5e481af7..a0df769e 100644 --- a/Examples/biology/egfrsignalingpathway/metadata.yaml +++ b/Examples/biology/egfrsignalingpathway/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["egfr", "signaling", "pathway", "egf", "grb2", "shc"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/eif2astressresponse/eif2a-stress-response_metadata.yaml b/Examples/biology/eif2astressresponse/eif2a-stress-response_metadata.yaml new file mode 100644 index 00000000..6ab3630a --- /dev/null +++ b/Examples/biology/eif2astressresponse/eif2a-stress-response_metadata.yaml @@ -0,0 +1,26 @@ +id: "eif2a-stress-response" +name: "eif2a stress response" +description: "Integrated Stress Response: eIF2alpha and the translational gate." +contributors: + - name: "Achyudhan" +tags: ["eif2a", "stress", "response", "eif2b", "perk", "gadd34"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/eif2a-stress-response.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/eif2astressresponse/metadata.yaml b/Examples/biology/eif2astressresponse/metadata.yaml index 53b0f096..0a7bd9ac 100644 --- a/Examples/biology/eif2astressresponse/metadata.yaml +++ b/Examples/biology/eif2astressresponse/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["eif2a", "stress", "response", "eif2b", "perk", "gadd34"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/endosomalsortingrab/endosomal-sorting-rab_metadata.yaml b/Examples/biology/endosomalsortingrab/endosomal-sorting-rab_metadata.yaml new file mode 100644 index 00000000..4c4dce10 --- /dev/null +++ b/Examples/biology/endosomalsortingrab/endosomal-sorting-rab_metadata.yaml @@ -0,0 +1,26 @@ +id: "endosomal-sorting-rab" +name: "endosomal sorting rab" +description: "Endosomal Sorting: Rab GTPase conversion and effector recruitment." +contributors: + - name: "Achyudhan" +tags: ["endosomal", "sorting", "rab", "rab5", "rab7", "effector", "v_gef", "v_gap_drive"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/endosomal-sorting-rab.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/endosomalsortingrab/metadata.yaml b/Examples/biology/endosomalsortingrab/metadata.yaml index aea7c211..e4225cbd 100644 --- a/Examples/biology/endosomalsortingrab/metadata.yaml +++ b/Examples/biology/endosomalsortingrab/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["endosomal", "sorting", "rab", "rab5", "rab7", "effector", "v_gef", "v_gap_drive"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/erknucleartranslocation/erk-nuclear-translocation_metadata.yaml b/Examples/biology/erknucleartranslocation/erk-nuclear-translocation_metadata.yaml new file mode 100644 index 00000000..0f7227a6 --- /dev/null +++ b/Examples/biology/erknucleartranslocation/erk-nuclear-translocation_metadata.yaml @@ -0,0 +1,26 @@ +id: "erk-nuclear-translocation" +name: "erk nuclear translocation" +description: "ERK Translocation: Spatial signaling and transcriptional assembly." +contributors: + - name: "Achyudhan" +tags: ["erk", "nuclear", "translocation", "mek", "elk1", "dusp", "transcription_signal"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/erk-nuclear-translocation.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/erknucleartranslocation/metadata.yaml b/Examples/biology/erknucleartranslocation/metadata.yaml index f8f6bc7f..56784f13 100644 --- a/Examples/biology/erknucleartranslocation/metadata.yaml +++ b/Examples/biology/erknucleartranslocation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["erk", "nuclear", "translocation", "mek", "elk1", "dusp", "transcription_signal"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/erstressresponse/er-stress-response_metadata.yaml b/Examples/biology/erstressresponse/er-stress-response_metadata.yaml new file mode 100644 index 00000000..bc29d973 --- /dev/null +++ b/Examples/biology/erstressresponse/er-stress-response_metadata.yaml @@ -0,0 +1,26 @@ +id: "er-stress-response" +name: "er stress response" +description: "Rate Constants" +contributors: + - name: "Achyudhan" +tags: ["er", "stress", "response", "unfoldedprotein", "perk", "eif2a", "chaperone"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/er-stress-response.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/erstressresponse/metadata.yaml b/Examples/biology/erstressresponse/metadata.yaml index 8311e074..e1f6b1e5 100644 --- a/Examples/biology/erstressresponse/metadata.yaml +++ b/Examples/biology/erstressresponse/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["er", "stress", "response", "unfoldedprotein", "perk", "eif2a", "chaperone"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/fgfsignalingpathway/fgf-signaling-pathway_metadata.yaml b/Examples/biology/fgfsignalingpathway/fgf-signaling-pathway_metadata.yaml new file mode 100644 index 00000000..aa68174a --- /dev/null +++ b/Examples/biology/fgfsignalingpathway/fgf-signaling-pathway_metadata.yaml @@ -0,0 +1,26 @@ +id: "fgf-signaling-pathway" +name: "fgf signaling pathway" +description: "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay." +contributors: + - name: "Achyudhan" +tags: ["fgf", "signaling", "pathway", "fgfr", "frs2", "spry", "rasgef", "internalized_rec"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/fgf-signaling-pathway.bngl" +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/fgfsignalingpathway/metadata.yaml b/Examples/biology/fgfsignalingpathway/metadata.yaml index 887672b9..e2f9cb19 100644 --- a/Examples/biology/fgfsignalingpathway/metadata.yaml +++ b/Examples/biology/fgfsignalingpathway/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["fgf", "signaling", "pathway", "fgfr", "frs2", "spry", "rasgef", "internalized_rec"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/gas6axlsignaling/gas6-axl-signaling_metadata.yaml b/Examples/biology/gas6axlsignaling/gas6-axl-signaling_metadata.yaml new file mode 100644 index 00000000..0839095a --- /dev/null +++ b/Examples/biology/gas6axlsignaling/gas6-axl-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "gas6-axl-signaling" +name: "gas6 axl signaling" +description: "GAS6/AXL Signaling: AKT activation and SOCS feedback." +contributors: + - name: "Achyudhan" +tags: ["gas6", "axl", "signaling", "pi3k", "akt", "socs", "survival_burst"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/gas6-axl-signaling.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/gas6axlsignaling/metadata.yaml b/Examples/biology/gas6axlsignaling/metadata.yaml index 8dd37a59..8c205580 100644 --- a/Examples/biology/gas6axlsignaling/metadata.yaml +++ b/Examples/biology/gas6axlsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["gas6", "axl", "signaling", "pi3k", "akt", "socs", "survival_burst"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/geneexpressiontoggle/gene-expression-toggle_metadata.yaml b/Examples/biology/geneexpressiontoggle/gene-expression-toggle_metadata.yaml new file mode 100644 index 00000000..ec1f9c4e --- /dev/null +++ b/Examples/biology/geneexpressiontoggle/gene-expression-toggle_metadata.yaml @@ -0,0 +1,26 @@ +id: "gene-expression-toggle" +name: "gene expression toggle" +description: "Kinetic Parameters" +contributors: + - name: "Achyudhan" +tags: ["gene", "expression", "toggle", "mrna", "protein"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/gene-expression-toggle.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/geneexpressiontoggle/metadata.yaml b/Examples/biology/geneexpressiontoggle/metadata.yaml index 15656a35..c97f2dad 100644 --- a/Examples/biology/geneexpressiontoggle/metadata.yaml +++ b/Examples/biology/geneexpressiontoggle/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["gene", "expression", "toggle", "mrna", "protein"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling_metadata.yaml b/Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling_metadata.yaml new file mode 100644 index 00000000..89ae8595 --- /dev/null +++ b/Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "glioblastoma-egfrviii-signaling" +name: "glioblastoma egfrviii signaling" +description: "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay." +contributors: + - name: "Achyudhan" +tags: ["glioblastoma", "egfrviii", "signaling", "pi3k", "akt", "oncogenic_output", "v_viii_act"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/glioblastoma-egfrviii-signaling.bngl" +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml b/Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml index d5ec0c4a..575bd54a 100644 --- a/Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml +++ b/Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["glioblastoma", "egfrviii", "signaling", "pi3k", "akt", "oncogenic_output", "v_viii_act"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/glycolysisbranchpoint/glycolysis-branch-point_metadata.yaml b/Examples/biology/glycolysisbranchpoint/glycolysis-branch-point_metadata.yaml new file mode 100644 index 00000000..87c7b246 --- /dev/null +++ b/Examples/biology/glycolysisbranchpoint/glycolysis-branch-point_metadata.yaml @@ -0,0 +1,26 @@ +id: "glycolysis-branch-point" +name: "glycolysis branch point" +description: "BioNetGen model: glycolysis branch point" +contributors: + - name: "Achyudhan" +tags: ["glycolysis", "branch", "point", "glucose", "atp", "biomass"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/glycolysis-branch-point.bngl" +playground: + visible: false + gallery_categories: ["metabolism","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/glycolysisbranchpoint/metadata.yaml b/Examples/biology/glycolysisbranchpoint/metadata.yaml index e838ca8e..d127a5af 100644 --- a/Examples/biology/glycolysisbranchpoint/metadata.yaml +++ b/Examples/biology/glycolysisbranchpoint/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["glycolysis", "branch", "point", "glucose", "atp", "biomass"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin_metadata.yaml b/Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin_metadata.yaml new file mode 100644 index 00000000..fca4f32f --- /dev/null +++ b/Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin_metadata.yaml @@ -0,0 +1,26 @@ +id: "gpcr-desensitization-arrestin" +name: "gpcr desensitization arrestin" +description: "GPCR Desensitization: Arrestin-mediated spatial sequestration." +contributors: + - name: "Achyudhan" +tags: ["gpcr", "desensitization", "arrestin", "ligand", "gprotein"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/gpcr-desensitization-arrestin.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/gpcrdesensitizationarrestin/metadata.yaml b/Examples/biology/gpcrdesensitizationarrestin/metadata.yaml index 39524bec..327ca73f 100644 --- a/Examples/biology/gpcrdesensitizationarrestin/metadata.yaml +++ b/Examples/biology/gpcrdesensitizationarrestin/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["gpcr", "desensitization", "arrestin", "ligand", "gprotein"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway_metadata.yaml b/Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway_metadata.yaml new file mode 100644 index 00000000..51e03722 --- /dev/null +++ b/Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway_metadata.yaml @@ -0,0 +1,26 @@ +id: "hedgehog-signaling-pathway" +name: "hedgehog signaling pathway" +description: "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing." +contributors: + - name: "Achyudhan" +tags: ["hedgehog", "signaling", "pathway", "hh", "ptch", "smo", "gli", "sufu"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/hedgehog-signaling-pathway.bngl" +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/hedgehogsignalingpathway/metadata.yaml b/Examples/biology/hedgehogsignalingpathway/metadata.yaml index f54accbe..1200bf9c 100644 --- a/Examples/biology/hedgehogsignalingpathway/metadata.yaml +++ b/Examples/biology/hedgehogsignalingpathway/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["hedgehog", "signaling", "pathway", "hh", "ptch", "smo", "gli", "sufu"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor_metadata.yaml b/Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor_metadata.yaml new file mode 100644 index 00000000..f13499e6 --- /dev/null +++ b/Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor_metadata.yaml @@ -0,0 +1,26 @@ +id: "hematopoietic-growth-factor" +name: "hematopoietic growth factor" +description: "Kinetic Parameters" +contributors: + - name: "Achyudhan" +tags: ["hematopoietic", "growth", "factor", "epo", "epor", "jak2", "stat5"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/hematopoietic-growth-factor.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/hematopoieticgrowthfactor/metadata.yaml b/Examples/biology/hematopoieticgrowthfactor/metadata.yaml index 85835455..587128af 100644 --- a/Examples/biology/hematopoieticgrowthfactor/metadata.yaml +++ b/Examples/biology/hematopoieticgrowthfactor/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["hematopoietic", "growth", "factor", "epo", "epor", "jak2", "stat5"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/hif1adegradationloop/hif1a_degradation_loop_metadata.yaml b/Examples/biology/hif1adegradationloop/hif1a_degradation_loop_metadata.yaml new file mode 100644 index 00000000..af91165a --- /dev/null +++ b/Examples/biology/hif1adegradationloop/hif1a_degradation_loop_metadata.yaml @@ -0,0 +1,26 @@ +id: "hif1a_degradation_loop" +name: "hif1a degradation loop" +description: "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay." +contributors: + - name: "Achyudhan" +tags: ["hif1a", "degradation", "loop", "vhl", "arnt", "v_hydrox"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/hif1a_degradation_loop.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/hif1adegradationloop/metadata.yaml b/Examples/biology/hif1adegradationloop/metadata.yaml index 4df43b3a..c3fafb15 100644 --- a/Examples/biology/hif1adegradationloop/metadata.yaml +++ b/Examples/biology/hif1adegradationloop/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["hif1a", "degradation", "loop", "vhl", "arnt", "v_hydrox"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling_metadata.yaml b/Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling_metadata.yaml new file mode 100644 index 00000000..aa1f3377 --- /dev/null +++ b/Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "hypoxia-response-signaling" +name: "hypoxia response signaling" +description: "Rate Constants" +contributors: + - name: "Achyudhan" +tags: ["hypoxia", "response", "signaling", "oxygensensor", "hif1", "vegf"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/hypoxia-response-signaling.bngl" +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/hypoxiaresponsesignaling/metadata.yaml b/Examples/biology/hypoxiaresponsesignaling/metadata.yaml index 21767de4..1c7eac3a 100644 --- a/Examples/biology/hypoxiaresponsesignaling/metadata.yaml +++ b/Examples/biology/hypoxiaresponsesignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["hypoxia", "response", "signaling", "oxygensensor", "hif1", "vegf"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/il1bsignaling/il1b-signaling_metadata.yaml b/Examples/biology/il1bsignaling/il1b-signaling_metadata.yaml new file mode 100644 index 00000000..034c0d62 --- /dev/null +++ b/Examples/biology/il1bsignaling/il1b-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "il1b-signaling" +name: "il1b signaling" +description: "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation." +contributors: + - name: "Achyudhan" +tags: ["il1b", "signaling", "il1ri", "myd88", "irak", "nfkb"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/il1b-signaling.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/il1bsignaling/metadata.yaml b/Examples/biology/il1bsignaling/metadata.yaml index ee1147e9..0efeda2f 100644 --- a/Examples/biology/il1bsignaling/metadata.yaml +++ b/Examples/biology/il1bsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["il1b", "signaling", "il1ri", "myd88", "irak", "nfkb"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/il6jakstatpathway/il6-jak-stat-pathway_metadata.yaml b/Examples/biology/il6jakstatpathway/il6-jak-stat-pathway_metadata.yaml new file mode 100644 index 00000000..e1ba6f56 --- /dev/null +++ b/Examples/biology/il6jakstatpathway/il6-jak-stat-pathway_metadata.yaml @@ -0,0 +1,26 @@ +id: "il6-jak-stat-pathway" +name: "il6 jak stat pathway" +description: "IL-6 Signaling: gp130 hexamerization and pSTAT3 import." +contributors: + - name: "Achyudhan" +tags: ["il6", "jak", "stat", "pathway", "gp130", "stat3", "socs"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/il6-jak-stat-pathway.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/il6jakstatpathway/metadata.yaml b/Examples/biology/il6jakstatpathway/metadata.yaml index 300dadaf..fdf7b0a4 100644 --- a/Examples/biology/il6jakstatpathway/metadata.yaml +++ b/Examples/biology/il6jakstatpathway/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["il6", "jak", "stat", "pathway", "gp130", "stat3", "socs"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/immunesynapseformation/immune-synapse-formation_metadata.yaml b/Examples/biology/immunesynapseformation/immune-synapse-formation_metadata.yaml new file mode 100644 index 00000000..20632dcd --- /dev/null +++ b/Examples/biology/immunesynapseformation/immune-synapse-formation_metadata.yaml @@ -0,0 +1,26 @@ +id: "immune-synapse-formation" +name: "immune synapse formation" +description: "Kinetic Parameters" +contributors: + - name: "Achyudhan" +tags: ["immune", "synapse", "formation", "tcr", "pmhc", "lck", "zap70"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/immune-synapse-formation.bngl" +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/immunesynapseformation/metadata.yaml b/Examples/biology/immunesynapseformation/metadata.yaml index 2fcd966b..841e97bb 100644 --- a/Examples/biology/immunesynapseformation/metadata.yaml +++ b/Examples/biology/immunesynapseformation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["immune", "synapse", "formation", "tcr", "pmhc", "lck", "zap70"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/inflammasomeactivation/inflammasome-activation_metadata.yaml b/Examples/biology/inflammasomeactivation/inflammasome-activation_metadata.yaml new file mode 100644 index 00000000..f44f5283 --- /dev/null +++ b/Examples/biology/inflammasomeactivation/inflammasome-activation_metadata.yaml @@ -0,0 +1,26 @@ +id: "inflammasome-activation" +name: "inflammasome activation" +description: "Rate Constants" +contributors: + - name: "Achyudhan" +tags: ["inflammasome", "activation", "sensor", "asc", "caspase1", "il1b"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/inflammasome-activation.bngl" +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/inflammasomeactivation/metadata.yaml b/Examples/biology/inflammasomeactivation/metadata.yaml index f52dd1df..bd74a07e 100644 --- a/Examples/biology/inflammasomeactivation/metadata.yaml +++ b/Examples/biology/inflammasomeactivation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["inflammasome", "activation", "sensor", "asc", "caspase1", "il1b"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism_metadata.yaml b/Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism_metadata.yaml new file mode 100644 index 00000000..1ce34294 --- /dev/null +++ b/Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism_metadata.yaml @@ -0,0 +1,26 @@ +id: "inositol-phosphate-metabolism" +name: "inositol phosphate metabolism" +description: "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points." +contributors: + - name: "Achyudhan" +tags: ["inositol", "phosphate", "metabolism", "pip2", "ip3", "ip4", "calcium", "agonist"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/inositol-phosphate-metabolism.bngl" +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/inositolphosphatemetabolism/metadata.yaml b/Examples/biology/inositolphosphatemetabolism/metadata.yaml index 9d7e1c66..bc584c54 100644 --- a/Examples/biology/inositolphosphatemetabolism/metadata.yaml +++ b/Examples/biology/inositolphosphatemetabolism/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["inositol", "phosphate", "metabolism", "pip2", "ip3", "ip4", "calcium", "agonist"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis_metadata.yaml b/Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis_metadata.yaml new file mode 100644 index 00000000..fa15d89f --- /dev/null +++ b/Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis_metadata.yaml @@ -0,0 +1,26 @@ +id: "insulin-glucose-homeostasis" +name: "insulin glucose homeostasis" +description: "Insulin-Glucose: Compartmentalized transport." +contributors: + - name: "Achyudhan" +tags: ["insulin", "glucose", "homeostasis", "ir", "glut4", "pancreas"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/insulin-glucose-homeostasis.bngl" +playground: + visible: false + gallery_categories: ["metabolism","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/insulinglucosehomeostasis/metadata.yaml b/Examples/biology/insulinglucosehomeostasis/metadata.yaml index 01947eb7..fd27e2da 100644 --- a/Examples/biology/insulinglucosehomeostasis/metadata.yaml +++ b/Examples/biology/insulinglucosehomeostasis/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["insulin", "glucose", "homeostasis", "ir", "glut4", "pancreas"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/biology/interferonsignaling/interferon-signaling_metadata.yaml b/Examples/biology/interferonsignaling/interferon-signaling_metadata.yaml new file mode 100644 index 00000000..f1ecc755 --- /dev/null +++ b/Examples/biology/interferonsignaling/interferon-signaling_metadata.yaml @@ -0,0 +1,58 @@ +id: "interferon-signaling" +name: "interferon signaling" +description: "Rate Constants" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["interferon", "signaling", "ifn", "ifnar", "tyk2", "stat1"] +date: + last_tested: 2026-07-07 + +category: "signaling" + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa","nf"] + molclustpy_compatible: true + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/interferon-signaling.bngl" + +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/interferonsignaling/metadata.yaml b/Examples/biology/interferonsignaling/metadata.yaml index f9100964..ffe8e419 100644 --- a/Examples/biology/interferonsignaling/metadata.yaml +++ b/Examples/biology/interferonsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["interferon", "signaling", "ifn", "ifnar", "tyk2", "stat1"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl b/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl index f5d7d1cb..0bb75a6e 100644 --- a/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl +++ b/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl @@ -27,6 +27,7 @@ begin parameters XBP1_mRNA 1000 # The splicing substrate Target_mRNA 800 # RIDD substrate BiP_tot 300 + Unfolded_tot 10 end parameters begin molecule types @@ -34,21 +35,21 @@ begin molecule types BiP(b) Unfolded(b) XBP1(s~u~s) # u: unspliced,s: spliced - RIDD_Target() # Vulnerable mRNA pool + RIDD_Target(s) # Vulnerable mRNA pool end molecule types begin seed species IRE1(b,s~U) IRE1_tot BiP(b) BiP_tot - Unfolded(b) 10 + Unfolded(b) Unfolded_tot XBP1(s~u) XBP1_mRNA - RIDD_Target() Target_mRNA + RIDD_Target(s) Target_mRNA end seed species begin observables # KEY BIOLOGICAL OUTPUTS Molecules ProSurvival_XBP1 XBP1(s~s) # Adaptive output - Molecules RIDD_Drive RIDD_Target() # Destructive output (mRNA decay) + Molecules RIDD_Drive RIDD_Target(s) # Destructive output (mRNA decay) Molecules Active_IRE1 IRE1(s~P) # Signaling sensor status Molecules Stress_Burden Unfolded() # Unbuffered protein load Molecules Chaperone_Bip BiP() # ER capacity index @@ -77,7 +78,7 @@ begin reaction rules IRE1(s~P) + XBP1(s~u) -> IRE1(s~P) + XBP1(s~s) k_xbp1_splice # RIDD: Active IRE1 degrades target mRNAs (Functional Rate) - RIDD_Target() -> 0 v_ridd() + RIDD_Target(s) -> 0 v_ridd() ## ADAPTATION Stage # Spliced XBP1 induces BiP (Hill-driven burst) @@ -90,7 +91,7 @@ begin reaction rules ## RESET Phase IRE1(s~P) -> IRE1(s~U) k_reset XBP1(s~s) -> 0 0.05 - 0 -> RIDD_Target() 0.1 + 0 -> RIDD_Target(s) 0.1 end reaction rules begin actions diff --git a/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress_metadata.yaml b/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress_metadata.yaml new file mode 100644 index 00000000..f4c0e1ac --- /dev/null +++ b/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress_metadata.yaml @@ -0,0 +1,61 @@ +id: "ire1a-xbp1-er-stress" +name: "ire1a xbp1 er stress" +description: "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD)." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["ire1a", "xbp1", "er", "stress", "ire1", "bip", "unfolded", "ridd_target"] +date: + last_tested: 2026-07-07 + +category: "signaling" + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 69" + simulation_methods: ["ode", "ssa"] + molclustpy_compatible: true + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: true + uses_exclude_include_reactants: false + uses_energy: false + uses_functions: true + uses_compartments: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ire1a-xbp1-er-stress.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/ire1axbp1erstress/metadata.yaml b/Examples/biology/ire1axbp1erstress/metadata.yaml index 84193774..dfa43c11 100644 --- a/Examples/biology/ire1axbp1erstress/metadata.yaml +++ b/Examples/biology/ire1axbp1erstress/metadata.yaml @@ -1,24 +1,62 @@ id: "ire1a-xbp1-er-stress" name: "ire1a xbp1 er stress" description: "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD)." + contributors: - name: "Achyudhan" + - name: "Nabil Mardhy" + tags: ["ire1a", "xbp1", "er", "stress", "ire1", "bip", "unfolded", "ridd_target"] +date: + last_tested: 2026-07-07 + category: "signaling" + +biol_categories: ["signaling"] + +comp_categories: ["other"] + compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true bng2_compatible: true - simulation_methods: ["ode"] + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 69" + simulation_methods: ["ode", "ssa"] + molclustpy_compatible: true + uses_energy: false + uses_functions: true uses_compartments: false + nfsim_compatible: true + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: true + uses_exclude_include_reactants: false uses_energy: false uses_functions: true - nfsim_compatible: false + uses_compartments: false + source: origin: "ai-generated" original_format: "bngl" original_repository: "bionetgen-web-simulator" source_path: "example-models/ire1a-xbp1-er-stress.bngl" + playground: visible: false gallery_categories: ["test-models"] featured: false difficulty: "advanced" + + + + diff --git a/Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling_metadata.yaml b/Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling_metadata.yaml new file mode 100644 index 00000000..dc799b5e --- /dev/null +++ b/Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling_metadata.yaml @@ -0,0 +1,59 @@ +id: "jak-stat-cytokine-signaling" +name: "jak stat cytokine signaling" +description: "Rate Constants" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["jak", "stat", "cytokine", "signaling", "receptor"] +date: + last_tested: 2026-07-07 + +category: "signaling" + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 35" + simulation_methods: ["ode", "ssa","nf"] + molclustpy_compatible: true + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + comments: "different simulation results from NFsim and MCP" + +Features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/jak-stat-cytokine-signaling.bngl" + +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/jakstatcytokinesignaling/metadata.yaml b/Examples/biology/jakstatcytokinesignaling/metadata.yaml index 23d44738..31a932a5 100644 --- a/Examples/biology/jakstatcytokinesignaling/metadata.yaml +++ b/Examples/biology/jakstatcytokinesignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["jak", "stat", "cytokine", "signaling", "receptor"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/jnkmapksignaling/jnk-mapk-signaling_metadata.yaml b/Examples/biology/jnkmapksignaling/jnk-mapk-signaling_metadata.yaml new file mode 100644 index 00000000..654c5eaf --- /dev/null +++ b/Examples/biology/jnkmapksignaling/jnk-mapk-signaling_metadata.yaml @@ -0,0 +1,62 @@ +id: "jnk-mapk-signaling" +name: "jnk mapk signaling" +description: "JNK MAPK Signaling: Scaffold-mediated activation and feedback." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["jnk", "mapk", "signaling", "mkk7", "jip1", "v_dephos"] +date: + last_tested: 2026-07-07 + +category: "signaling" + +biol_categories: ["signaling"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: "RuntimeException-Application 'NFSim app' has no generated Math, Failed to generate new Math: not mass action: flattened Kf for reactionRule(r5) is not numeric, exp = '(3.0 * Total_pJNK / (250.0 + Total_pJNK))' MappingException-not mass action: flattened Kf for reactionRule(r5) is not numeric, exp = '(3.0 * Total_pJNK / (250.0 + Total_pJNK))'" + simulation_methods: ["ode", "ssa"] + molclustpy_compatible: false + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + comments: "false in orignal metadata.yaml file, but runs with bng2; mcp: cannot access local variable 'stdout_str' where it is not associated with a value" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_energy: false + uses_functions: true + uses_compartments: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/jak-stat-cytokine-signaling.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/jnkmapksignaling/metadata.yaml b/Examples/biology/jnkmapksignaling/metadata.yaml index 85869abe..83919170 100644 --- a/Examples/biology/jnkmapksignaling/metadata.yaml +++ b/Examples/biology/jnkmapksignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["jnk", "mapk", "signaling", "mkk7", "jip1", "v_dephos"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/kirchannelregulation/kir-channel-regulation_metadata.yaml b/Examples/biology/kirchannelregulation/kir-channel-regulation_metadata.yaml new file mode 100644 index 00000000..b0b68156 --- /dev/null +++ b/Examples/biology/kirchannelregulation/kir-channel-regulation_metadata.yaml @@ -0,0 +1,62 @@ +id: "kir-channel-regulation" +name: "kir channel regulation" +description: "Kir Channel Regulation: PIP2 modulation and G-protein potentiation." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["kir", "channel", "regulation", "pip2", "gbg", "v_opening", "v_gbg_factor"] +date: + last_tested: 2026-07-07 + +category: "signaling" + +biol_categories: ["regulation"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Function 'v_opening can not be added, function v_gbg_factor() not found as a bngl function or as a vcell built-in function" + simulation_methods: ["ode", "ssa"] + molclustpy_compatible: false + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: false # + comments: "Composite Functions (functions that call other functions) cannot have references to observables. " + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_energy: false + uses_functions: true + uses_compartments: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/kir-channel-regulation.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/kirchannelregulation/metadata.yaml b/Examples/biology/kirchannelregulation/metadata.yaml index 006f08f3..3b49b627 100644 --- a/Examples/biology/kirchannelregulation/metadata.yaml +++ b/Examples/biology/kirchannelregulation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["kir", "channel", "regulation", "pip2", "gbg", "v_opening", "v_gbg_factor"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/lacoperonregulation/lac-operon-regulation_metadata.yaml b/Examples/biology/lacoperonregulation/lac-operon-regulation_metadata.yaml new file mode 100644 index 00000000..0414cc81 --- /dev/null +++ b/Examples/biology/lacoperonregulation/lac-operon-regulation_metadata.yaml @@ -0,0 +1,61 @@ +id: "lac-operon-regulation" +name: "lac operon regulation" +description: "Kinetic Parameters" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["lac", "operon", "regulation", "laci", "promoter", "mrna", "betagal", "lactose", "allolactose"] +date: + last_tested: 2026-07-07 + +category: "signaling" + +biol_categories: ["regulation"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 0 at line 53" + simulation_methods: ["ode", "ssa","nf"] + molclustpy_compatible: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + comments: "#IndexError: list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_energy: false + uses_functions: true + uses_compartments: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/lac-operon-regulation.bngl" + +playground: + visible: false + gallery_categories: ["metabolism","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/lacoperonregulation/metadata.yaml b/Examples/biology/lacoperonregulation/metadata.yaml index 4b33871e..01d17bb0 100644 --- a/Examples/biology/lacoperonregulation/metadata.yaml +++ b/Examples/biology/lacoperonregulation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["lac", "operon", "regulation", "laci", "promoter", "mrna", "betagal", "lactose", "allolactose"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling_metadata.yaml b/Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling_metadata.yaml new file mode 100644 index 00000000..f35c9bf7 --- /dev/null +++ b/Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "lipid-mediated-pip3-signaling" +name: "lipid mediated pip3 signaling" +description: "Kinetic Parameters" +contributors: + - name: "Achyudhan" +tags: ["lipid", "mediated", "pip3", "signaling", "pi3k", "pip2", "pten", "pdk1"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/lipid-mediated-pip3-signaling.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/lipidmediatedpip3signaling/metadata.yaml b/Examples/biology/lipidmediatedpip3signaling/metadata.yaml index 49cf3a7e..f18032fc 100644 --- a/Examples/biology/lipidmediatedpip3signaling/metadata.yaml +++ b/Examples/biology/lipidmediatedpip3signaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["lipid", "mediated", "pip3", "signaling", "pi3k", "pip2", "pten", "pdk1"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics_metadata.yaml b/Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics_metadata.yaml new file mode 100644 index 00000000..5acfd08f --- /dev/null +++ b/Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics_metadata.yaml @@ -0,0 +1,26 @@ +id: "l-type-calcium-channel-dynamics" +name: "l type calcium channel dynamics" +description: "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation)." +contributors: + - name: "Achyudhan" +tags: ["l", "type", "calcium", "channel", "dynamics", "ltcc", "voltage", "v_open", "v_inact"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/l-type-calcium-channel-dynamics.bngl" +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/ltypecalciumchanneldynamics/metadata.yaml b/Examples/biology/ltypecalciumchanneldynamics/metadata.yaml index 4b61850a..181dd9ad 100644 --- a/Examples/biology/ltypecalciumchanneldynamics/metadata.yaml +++ b/Examples/biology/ltypecalciumchanneldynamics/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["l", "type", "calcium", "channel", "dynamics", "ltcc", "voltage", "v_open", "v_inact"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/mapksignalingcascade/mapk-signaling-cascade_metadata.yaml b/Examples/biology/mapksignalingcascade/mapk-signaling-cascade_metadata.yaml new file mode 100644 index 00000000..4e63438b --- /dev/null +++ b/Examples/biology/mapksignalingcascade/mapk-signaling-cascade_metadata.yaml @@ -0,0 +1,26 @@ +id: "mapk-signaling-cascade" +name: "mapk signaling cascade" +description: "Rate Constants" +contributors: + - name: "Achyudhan" +tags: ["mapk", "signaling", "cascade", "ligand", "receptor", "mapkkk", "mapkk"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/mapk-signaling-cascade.bngl" +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/mapksignalingcascade/metadata.yaml b/Examples/biology/mapksignalingcascade/metadata.yaml index 798f143a..deecdc0f 100644 --- a/Examples/biology/mapksignalingcascade/metadata.yaml +++ b/Examples/biology/mapksignalingcascade/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["mapk", "signaling", "cascade", "ligand", "receptor", "mapkkk", "mapkk"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/michaelismentenkinetics/metadata.yaml b/Examples/biology/michaelismentenkinetics/metadata.yaml index e494ff51..c008a7be 100644 --- a/Examples/biology/michaelismentenkinetics/metadata.yaml +++ b/Examples/biology/michaelismentenkinetics/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["michaelis", "menten", "kinetics", "e", "s", "p", "generate_network", "simulate", "writesbml"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics_metadata.yaml b/Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics_metadata.yaml new file mode 100644 index 00000000..7d35415a --- /dev/null +++ b/Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics_metadata.yaml @@ -0,0 +1,61 @@ +id: "michaelis-menten-kinetics" +name: "michaelis menten kinetics" +description: "Kinetic Constants" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["michaelis", "menten", "kinetics", "e", "s", "p", "generate_network", "simulate", "writesbml"] + +date: + last_tested: 2026-07-09 + +category: "signaling" +biol_categories: ["kinetics"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + comments: "MCP IndexError: list index out of range bngp Simulation failed: NFsim simulation failed: NFsim completed but output file not found nfsim You created a reaction (Catalysis) that deletes a molecule, but you did not use the DeleteMolecules keyword." + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_energy: false + uses_functions: false + uses_compartments: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/michaelis-menten-kinetics.bngl" + +playground: + visible: false + gallery_categories: ["metabolism","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/mtorc2signaling/metadata.yaml b/Examples/biology/mtorc2signaling/metadata.yaml index 92858154..66231c92 100644 --- a/Examples/biology/mtorc2signaling/metadata.yaml +++ b/Examples/biology/mtorc2signaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["mtorc2", "signaling", "mtor", "sin1", "rictor", "akt", "sgk1", "pip3"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/mtorc2signaling/mtorc2-signaling_metadata.yaml b/Examples/biology/mtorc2signaling/mtorc2-signaling_metadata.yaml new file mode 100644 index 00000000..967b8a4b --- /dev/null +++ b/Examples/biology/mtorc2signaling/mtorc2-signaling_metadata.yaml @@ -0,0 +1,61 @@ +id: "mtorc2-signaling" +name: "mtorc2 signaling" +description: "mTORC2 signaling regulates cell survival and growth via AKT and SGK1." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["mtorc2", "signaling", "mtor", "sin1", "rictor", "akt", "sgk1", "pip3"] + +date: + last_tested: 2026-07-09 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 89" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "MCP IndexError: list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_energy: false + uses_functions: false + uses_compartments: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/mtorc2-signaling.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/mtorsignaling/metadata.yaml b/Examples/biology/mtorsignaling/metadata.yaml index c5e508fe..1d6ef958 100644 --- a/Examples/biology/mtorsignaling/metadata.yaml +++ b/Examples/biology/mtorsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["mtor", "signaling", "rheb", "mtorc1", "s6k", "ampk"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/mtorsignaling/mtor-signaling_metadata.yaml b/Examples/biology/mtorsignaling/mtor-signaling_metadata.yaml new file mode 100644 index 00000000..3347684b --- /dev/null +++ b/Examples/biology/mtorsignaling/mtor-signaling_metadata.yaml @@ -0,0 +1,61 @@ +id: "mtor-signaling" +name: "mtor signaling" +description: "mTOR Signaling Pathway" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["mtor", "signaling", "rheb", "mtorc1", "s6k", "ampk"] + +date: + last_tested: 2026-07-09 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa","nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: "remove actions from model to make it compatible with vcell" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/mtor-signaling.bngl" + +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/myogenicdifferentiation/metadata.yaml b/Examples/biology/myogenicdifferentiation/metadata.yaml index cd2cf720..350f316f 100644 --- a/Examples/biology/myogenicdifferentiation/metadata.yaml +++ b/Examples/biology/myogenicdifferentiation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["myogenic", "differentiation", "myod", "myog", "mef2"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/myogenicdifferentiation/myogenic-differentiation_metadata.yaml b/Examples/biology/myogenicdifferentiation/myogenic-differentiation_metadata.yaml new file mode 100644 index 00000000..3c5a0fab --- /dev/null +++ b/Examples/biology/myogenicdifferentiation/myogenic-differentiation_metadata.yaml @@ -0,0 +1,62 @@ +id: "myogenic-differentiation" +name: "myogenic differentiation" +description: "Myogenic Differentiation" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["myogenic", "differentiation", "myod", "myog", "mef2"] + +date: + last_tested: 2026-07-09 + +category: "signaling" +biol_categories: ["differentiation"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa","nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_energy: false + uses_functions: false + uses_compartments: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/myogenic-differentiation.bngl" + +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/negativefeedbackloop/metadata.yaml b/Examples/biology/negativefeedbackloop/metadata.yaml index cfd8f9cb..08465643 100644 --- a/Examples/biology/negativefeedbackloop/metadata.yaml +++ b/Examples/biology/negativefeedbackloop/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["negative", "feedback", "loop", "gene", "mrna", "protein"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/negativefeedbackloop/negative-feedback-loop_metadata.yaml b/Examples/biology/negativefeedbackloop/negative-feedback-loop_metadata.yaml new file mode 100644 index 00000000..8c06d043 --- /dev/null +++ b/Examples/biology/negativefeedbackloop/negative-feedback-loop_metadata.yaml @@ -0,0 +1,62 @@ +id: "negative-feedback-loop" +name: "negative feedback loop" +description: "Negative Feedback Loop" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["negative", "feedback", "loop", "gene", "mrna", "protein"] + +date: + last_tested: 2026-07-11 + +category: "signaling" +biol_categories: ["feedback_loop"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 0 at line 44" + simulation_methods: ["ode", "ssa","nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "Need fixing 0-> MCP IndexError list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/negative-feedback-loop.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/neurotransmitterrelease/metadata.yaml b/Examples/biology/neurotransmitterrelease/metadata.yaml index 379b27f4..c4af934f 100644 --- a/Examples/biology/neurotransmitterrelease/metadata.yaml +++ b/Examples/biology/neurotransmitterrelease/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["neurotransmitter", "release", "calcium", "snare", "vesicle", "postsynaptic"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/neurotransmitterrelease/neurotransmitter-release_metadata.yaml b/Examples/biology/neurotransmitterrelease/neurotransmitter-release_metadata.yaml new file mode 100644 index 00000000..f4f42f97 --- /dev/null +++ b/Examples/biology/neurotransmitterrelease/neurotransmitter-release_metadata.yaml @@ -0,0 +1,62 @@ +id: "neurotransmitter-release" +name: "neurotransmitter release" +description: "Neurotransmitter Release" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["neurotransmitter", "release", "calcium", "snare", "vesicle", "postsynaptic"] + +date: + last_tested: 2026-07-11 + +category: "signaling" +biol_categories: ["neurotransmitter_release"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/neurotransmitter-release.bngl" + +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/nfkbfeedback/metadata.yaml b/Examples/biology/nfkbfeedback/metadata.yaml index c16ec085..515a3620 100644 --- a/Examples/biology/nfkbfeedback/metadata.yaml +++ b/Examples/biology/nfkbfeedback/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["nfkb", "feedback", "ikb", "ikk", "a20"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/nfkbfeedback/nfkb-feedback_metadata.yaml b/Examples/biology/nfkbfeedback/nfkb-feedback_metadata.yaml new file mode 100644 index 00000000..0e216444 --- /dev/null +++ b/Examples/biology/nfkbfeedback/nfkb-feedback_metadata.yaml @@ -0,0 +1,62 @@ +id: "nfkb-feedback" +name: "nfkb feedback" +description: "TNFalpha-induced NF-kB signaling with IkappaB-alpha feedback." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["nfkb", "feedback", "ikb", "ikk", "a20"] + +date: + last_tested: 2026-07-11 + +category: "signaling" +biol_categories: ["feedback"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered TotalRate at line 64" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + comments: "MCP cannot access local variable stdout_str where it is not associated with a value nfsim ERROR! You created a reaction (_R2) that deletes a molecule, but you did not use the DeleteMolecules keyword." + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: true + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/nfkb-feedback.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/nocgmpsignaling/metadata.yaml b/Examples/biology/nocgmpsignaling/metadata.yaml index 57a0eedb..130ef2bd 100644 --- a/Examples/biology/nocgmpsignaling/metadata.yaml +++ b/Examples/biology/nocgmpsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["no", "cgmp", "signaling", "sgc", "pkg"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/nocgmpsignaling/no-cgmp-signaling_metadata.yaml b/Examples/biology/nocgmpsignaling/no-cgmp-signaling_metadata.yaml new file mode 100644 index 00000000..bc11fa5a --- /dev/null +++ b/Examples/biology/nocgmpsignaling/no-cgmp-signaling_metadata.yaml @@ -0,0 +1,62 @@ +id: "no-cgmp-signaling" +name: "no cgmp signaling" +description: "Nitric Oxide (NO) / cGMP signaling pathway." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["no", "cgmp", "signaling", "sgc", "pkg"] + +date: + last_tested: 2026-07-11 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 65" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "does not run in bngp, runs in bng2, MCP IndexError list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/nfkb-feedback.bngl" + +playground: + visible: false + gallery_categories: "example-models/no-cgmp-signaling.bngl" + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/notchdeltalateralinhibition/metadata.yaml b/Examples/biology/notchdeltalateralinhibition/metadata.yaml index a13eb8da..80f735c7 100644 --- a/Examples/biology/notchdeltalateralinhibition/metadata.yaml +++ b/Examples/biology/notchdeltalateralinhibition/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["notch", "delta", "lateral", "inhibition", "cellnotch", "celldelta"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition_metadata.yaml b/Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition_metadata.yaml new file mode 100644 index 00000000..a086e561 --- /dev/null +++ b/Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition_metadata.yaml @@ -0,0 +1,62 @@ +id: "notch-delta-lateral-inhibition" +name: "notch delta lateral inhibition" +description: "Notch-Delta Lateral Inhibition" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["notch", "delta", "lateral", "inhibition", "cellnotch", "celldelta"] + +date: + last_tested: 2026-07-11 + +category: "signaling" +biol_categories: ["inhibition"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/notch-delta-lateral-inhibition.bngl" + +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/oxidativestressresponse/metadata.yaml b/Examples/biology/oxidativestressresponse/metadata.yaml index 1a6debbc..da850968 100644 --- a/Examples/biology/oxidativestressresponse/metadata.yaml +++ b/Examples/biology/oxidativestressresponse/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["oxidative", "stress", "response", "ros", "keap1", "nrf2", "antioxidant"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/oxidativestressresponse/oxidative-stress-response_metadata.yaml b/Examples/biology/oxidativestressresponse/oxidative-stress-response_metadata.yaml new file mode 100644 index 00000000..2d1124ae --- /dev/null +++ b/Examples/biology/oxidativestressresponse/oxidative-stress-response_metadata.yaml @@ -0,0 +1,62 @@ +id: "oxidative-stress-response" +name: "oxidative stress response" +description: "Oxidative Stress Response (Keap1-Nrf2 Pathway)" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["oxidative", "stress", "response", "ros", "keap1", "nrf2", "antioxidant"] + +date: + last_tested: 2026-07-12 + +category: "signaling" +biol_categories: ["inhibition"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/oxidative-stress-response.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/p38mapksignaling/metadata.yaml b/Examples/biology/p38mapksignaling/metadata.yaml index fe05f690..717f6811 100644 --- a/Examples/biology/p38mapksignaling/metadata.yaml +++ b/Examples/biology/p38mapksignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["p38", "mapk", "signaling", "mkk3", "mapkap2", "v_thermal"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/p38mapksignaling/p38-mapk-signaling_metadata.yaml b/Examples/biology/p38mapksignaling/p38-mapk-signaling_metadata.yaml new file mode 100644 index 00000000..7f4f0055 --- /dev/null +++ b/Examples/biology/p38mapksignaling/p38-mapk-signaling_metadata.yaml @@ -0,0 +1,62 @@ +id: "p38-mapk-signaling" +name: "p38 mapk signaling" +description: "p38 MAPK stress signaling cascade." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["p38", "mapk", "signaling", "mkk3", "mapkap2", "v_thermal"] + +date: + last_tested: 2026-07-12 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: "changed nfsim to true as it runs on bng2, does not run on bngp" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/p38-mapk-signaling.bngl" + +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/p53mdm2oscillator/metadata.yaml b/Examples/biology/p53mdm2oscillator/metadata.yaml index 80360b68..7a4b2a6b 100644 --- a/Examples/biology/p53mdm2oscillator/metadata.yaml +++ b/Examples/biology/p53mdm2oscillator/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["p53", "mdm2", "oscillator", "generate_network"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator_metadata.yaml b/Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator_metadata.yaml new file mode 100644 index 00000000..1c2c6c00 --- /dev/null +++ b/Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator_metadata.yaml @@ -0,0 +1,62 @@ +id: "p53-mdm2-oscillator" +name: "p53 mdm2 oscillator" +description: "BioNetGen model: p53 mdm2 oscillator" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["p53", "mdm2", "oscillator", "generate_network"] + +date: + last_tested: 2026-07-12 + +category: "signaling" +biol_categories: ["oscillator"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 25, column 5" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "MCP list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/p53-mdm2-oscillator.bngl" + +playground: + visible: false + gallery_categories: ["cell-cycle","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/parp1mediateddnarepair/metadata.yaml b/Examples/biology/parp1mediateddnarepair/metadata.yaml index 87599529..b17e58cc 100644 --- a/Examples/biology/parp1mediateddnarepair/metadata.yaml +++ b/Examples/biology/parp1mediateddnarepair/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["parp1", "mediated", "dna", "repair", "par", "nad", "v_parylate"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair_metadata.yaml b/Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair_metadata.yaml new file mode 100644 index 00000000..f6bbcf0a --- /dev/null +++ b/Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair_metadata.yaml @@ -0,0 +1,62 @@ +id: "parp1-mediated-dna-repair" +name: "parp1 mediated dna repair" +description: "PARP1-mediated DNA damage sensing and repair." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["parp1", "mediated", "dna", "repair", "par", "nad", "v_parylate"] + +date: + last_tested: 2026-07-12 + +category: "signaling" +biol_categories: ["dna_repair"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered DeleteMolecules at line 71" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "changed nfsim_compatible to true. MCP There was an issue parsing BNGL file parp1-mediated-dna-repair.bnglFailed to parse action generate_network({overwrite=>1,max_stoich=>{PAR=>20}})" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: true + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/parp1-mediated-dna-repair.bngl" + +playground: + visible: false + gallery_categories: ["cell-cycle","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/phosphorelaychain/metadata.yaml b/Examples/biology/phosphorelaychain/metadata.yaml index ac2f1b98..78f50e6a 100644 --- a/Examples/biology/phosphorelaychain/metadata.yaml +++ b/Examples/biology/phosphorelaychain/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["phosphorelay", "chain", "sensor", "relay", "output"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/phosphorelaychain/phosphorelay-chain_metadata.yaml b/Examples/biology/phosphorelaychain/phosphorelay-chain_metadata.yaml new file mode 100644 index 00000000..cef40e95 --- /dev/null +++ b/Examples/biology/phosphorelaychain/phosphorelay-chain_metadata.yaml @@ -0,0 +1,62 @@ +id: "phosphorelay-chain" +name: "phosphorelay chain" +description: "BioNetGen model: phosphorelay chain" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["phosphorelay", "chain", "sensor", "relay", "output"] + +date: + last_tested: 2026-07-12 + +category: "signaling" +biol_categories: ["phosphorelay"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/phosphorelay-chain.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/plateletactivation/metadata.yaml b/Examples/biology/plateletactivation/metadata.yaml index e834d559..46eb371c 100644 --- a/Examples/biology/plateletactivation/metadata.yaml +++ b/Examples/biology/plateletactivation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["platelet", "activation", "adp", "p2y12", "integrin", "thromboxane"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/plateletactivation/platelet-activation_metadata.yaml b/Examples/biology/plateletactivation/platelet-activation_metadata.yaml new file mode 100644 index 00000000..32383efd --- /dev/null +++ b/Examples/biology/plateletactivation/platelet-activation_metadata.yaml @@ -0,0 +1,62 @@ +id: "platelet-activation" +name: "platelet activation" +description: "BioNetGen model: platelet activation" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["platelet", "activation", "adp", "p2y12", "integrin", "thromboxane"] + +date: + last_tested: 2026-07-12 + +category: "signaling" +biol_categories: ["platelet_activation"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/platelet-activation.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/predatorpreydynamics/metadata.yaml b/Examples/biology/predatorpreydynamics/metadata.yaml index bb813d63..0b72ab91 100644 --- a/Examples/biology/predatorpreydynamics/metadata.yaml +++ b/Examples/biology/predatorpreydynamics/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["predator", "prey", "dynamics"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/predatorpreydynamics/predator-prey-dynamics_metadata.yaml b/Examples/biology/predatorpreydynamics/predator-prey-dynamics_metadata.yaml new file mode 100644 index 00000000..dbece075 --- /dev/null +++ b/Examples/biology/predatorpreydynamics/predator-prey-dynamics_metadata.yaml @@ -0,0 +1,62 @@ +id: "predator-prey-dynamics" +name: "predator prey dynamics" +description: "BioNetGen model: predator prey dynamics" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["predator", "prey", "dynamics"] + +date: + last_tested: 2026-07-12 + +category: "signaling" +biol_categories: ["dynamics"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 0 at line 28" + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "MCP list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/predator-prey-dynamics.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/quorumsensingcircuit/metadata.yaml b/Examples/biology/quorumsensingcircuit/metadata.yaml index 31669387..50a09841 100644 --- a/Examples/biology/quorumsensingcircuit/metadata.yaml +++ b/Examples/biology/quorumsensingcircuit/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["quorum", "sensing", "circuit", "autoinducer", "autoinducer_env", "gene", "protein"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit_metadata.yaml b/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit_metadata.yaml new file mode 100644 index 00000000..b777529a --- /dev/null +++ b/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit_metadata.yaml @@ -0,0 +1,26 @@ +id: "quorum-sensing-circuit" +name: "quorum sensing circuit" +description: "BioNetGen model: quorum sensing circuit" +contributors: + - name: "Achyudhan" +tags: ["quorum", "sensing", "circuit", "autoinducer", "autoinducer_env", "gene", "protein"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/quorum-sensing-circuit.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit_metadta.yaml b/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit_metadta.yaml new file mode 100644 index 00000000..9ec0444e --- /dev/null +++ b/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit_metadta.yaml @@ -0,0 +1,60 @@ +id: "quorum-sensing-circuit" +name: "quorum sensing circuit" +description: "BioNetGen model: quorum sensing circuit" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["quorum", "sensing", "circuit", "autoinducer", "autoinducer_env", "gene", "protein"] + +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["circuit"] +comp_categories: ["other"] + +compatibility: + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 0 at line 35" + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "MCP list index out of range ()" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/quorum-sensing-circuit.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/rabgtpasecycle/metadata.yaml b/Examples/biology/rabgtpasecycle/metadata.yaml index 3147c933..0ddfa738 100644 --- a/Examples/biology/rabgtpasecycle/metadata.yaml +++ b/Examples/biology/rabgtpasecycle/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["rab", "gtpase", "cycle", "gef", "gap", "effector"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/rabgtpasecycle/rab-gtpase-cycle_metadata.yaml b/Examples/biology/rabgtpasecycle/rab-gtpase-cycle_metadata.yaml new file mode 100644 index 00000000..d84a0a51 --- /dev/null +++ b/Examples/biology/rabgtpasecycle/rab-gtpase-cycle_metadata.yaml @@ -0,0 +1,62 @@ +id: "rab-gtpase-cycle" +name: "rab gtpase cycle" +description: "BioNetGen model: rab gtpase cycle" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["rab", "gtpase", "cycle", "gef", "gap", "effector"] + +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["circuit"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/rab-gtpase-cycle.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/ranklranksignaling/metadata.yaml b/Examples/biology/ranklranksignaling/metadata.yaml index 80d8eb10..8bc1bef7 100644 --- a/Examples/biology/ranklranksignaling/metadata.yaml +++ b/Examples/biology/ranklranksignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["rankl", "rank", "signaling", "opg", "nfat", "traf6"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/ranklranksignaling/rankl-rank-signaling_metadata.yaml b/Examples/biology/ranklranksignaling/rankl-rank-signaling_metadata.yaml new file mode 100644 index 00000000..4f69629f --- /dev/null +++ b/Examples/biology/ranklranksignaling/rankl-rank-signaling_metadata.yaml @@ -0,0 +1,61 @@ +id: "rankl-rank-signaling" +name: "rankl rank signaling" +description: "RANKL-RANK-OPG signaling in bone remodeling." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["rankl", "rank", "signaling", "opg", "nfat", "traf6"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: "nfsim false in original but runs with bng2 vcell error when trying to simulate RuntimeException-Application BioNetGen app has no generated Math, Failed to generate new Math: Unable to sort, unknown identifier TRAF6_Complexes UnresolvedException-Unable to sort, unknown identifier TRAF6_Complexes" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/rankl-rank-signaling.bngl" + +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/rasgefgapcycle/metadata.yaml b/Examples/biology/rasgefgapcycle/metadata.yaml index 1eac248b..bbff4ff2 100644 --- a/Examples/biology/rasgefgapcycle/metadata.yaml +++ b/Examples/biology/rasgefgapcycle/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ras", "gef", "gap", "cycle", "sos", "rasgap", "v_gef", "v_gap"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/rasgefgapcycle/ras-gef-gap-cycle_metadata.yaml b/Examples/biology/rasgefgapcycle/ras-gef-gap-cycle_metadata.yaml new file mode 100644 index 00000000..80dae2a4 --- /dev/null +++ b/Examples/biology/rasgefgapcycle/ras-gef-gap-cycle_metadata.yaml @@ -0,0 +1,61 @@ +id: "ras-gef-gap-cycle" +name: "ras gef gap cycle" +description: "Ras-GEF-GAP cycle with explicit nucleotide exchange." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["ras", "gef", "gap", "cycle", "sos", "rasgap", "v_gef", "v_gap"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["cycle"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: "vcell put actions out of model" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ras-gef-gap-cycle.bngl" + +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/repressilatoroscillator/metadata.yaml b/Examples/biology/repressilatoroscillator/metadata.yaml index 4bfd3302..2cb5be37 100644 --- a/Examples/biology/repressilatoroscillator/metadata.yaml +++ b/Examples/biology/repressilatoroscillator/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["repressilator", "oscillator", "genea", "geneb", "genec", "mrna_a", "mrna_b", "mrna_c", "proteina", "proteinb"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/repressilatoroscillator/repressilator-oscillator_metadata.yaml b/Examples/biology/repressilatoroscillator/repressilator-oscillator_metadata.yaml new file mode 100644 index 00000000..326b04c0 --- /dev/null +++ b/Examples/biology/repressilatoroscillator/repressilator-oscillator_metadata.yaml @@ -0,0 +1,61 @@ +id: "repressilator-oscillator" +name: "repressilator oscillator" +description: "BioNetGen model: repressilator oscillator" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["repressilator", "oscillator", "genea", "geneb", "genec", "mrna_a", "mrna_b", "mrna_c", "proteina", "proteinb"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["oscillator"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 0 at line 49" + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "MCP list index out of range ()" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/repressilator-oscillator.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/retinoicacidsignaling/metadata.yaml b/Examples/biology/retinoicacidsignaling/metadata.yaml index e16c8a70..6f758b8a 100644 --- a/Examples/biology/retinoicacidsignaling/metadata.yaml +++ b/Examples/biology/retinoicacidsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["retinoic", "acid", "signaling", "ra", "rarrxr", "corepressor", "targetgene"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/retinoicacidsignaling/retinoic-acid-signaling_metadata.yaml b/Examples/biology/retinoicacidsignaling/retinoic-acid-signaling_metadata.yaml new file mode 100644 index 00000000..241647d7 --- /dev/null +++ b/Examples/biology/retinoicacidsignaling/retinoic-acid-signaling_metadata.yaml @@ -0,0 +1,61 @@ +id: "retinoic-acid-signaling" +name: "retinoic acid signaling" +description: "BioNetGen model: retinoic acid signaling" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["retinoic", "acid", "signaling", "ra", "rarrxr", "corepressor", "targetgene"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: "vcell put actions out of model" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/retinoic-acid-signaling.bngl" + +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml b/Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml index 562b546d..f0c02f24 100644 --- a/Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml +++ b/Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["rho", "gtpase", "actin", "cytoskeleton", "rhoa", "rock", "limk", "cofilin"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton_metadata.yaml b/Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton_metadata.yaml new file mode 100644 index 00000000..a3b84706 --- /dev/null +++ b/Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton_metadata.yaml @@ -0,0 +1,61 @@ +id: "rho-gtpase-actin-cytoskeleton" +name: "rho gtpase actin cytoskeleton" +description: "RhoA-GTPase regulation of the actin cytoskeleton." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["rho", "gtpase", "actin", "cytoskeleton", "rhoa", "rock", "limk", "cofilin"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered TotalRate at line 57" + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: true + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/rho-gtpase-actin-cytoskeleton.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/shp2phosphataseregulation/metadata.yaml b/Examples/biology/shp2phosphataseregulation/metadata.yaml index e48befaa..226532b8 100644 --- a/Examples/biology/shp2phosphataseregulation/metadata.yaml +++ b/Examples/biology/shp2phosphataseregulation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["shp2", "phosphatase", "regulation", "rtk", "substrate", "v_dephos"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation_metadata.yaml b/Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation_metadata.yaml new file mode 100644 index 00000000..77c9f142 --- /dev/null +++ b/Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation_metadata.yaml @@ -0,0 +1,61 @@ +id: "shp2-phosphatase-regulation" +name: "shp2 phosphatase regulation" +description: "SHP2 phosphatase regulation via autoinhibition and SH2 binding." + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["shp2", "phosphatase", "regulation", "rtk", "substrate", "v_dephos"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: "nfsim false in original but runs with bng2 vcell simulation doesn't run has an error, RuntimeException-Application BioNetGen app has no generated Math, Failed to generate new Math Local parameter Active_Substrat math namescope name is Active_Substrate and conflicts with existing global parameter named Active_Substrate. " + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/rho-gtpase-actin-cytoskeleton.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/signalamplificationcascade/metadata.yaml b/Examples/biology/signalamplificationcascade/metadata.yaml index d701b857..d15dff97 100644 --- a/Examples/biology/signalamplificationcascade/metadata.yaml +++ b/Examples/biology/signalamplificationcascade/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["signal", "amplification", "cascade", "ligand", "receptor", "effector", "messenger"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/signalamplificationcascade/signal-amplification-cascade_metadata.yaml b/Examples/biology/signalamplificationcascade/signal-amplification-cascade_metadata.yaml new file mode 100644 index 00000000..78878cf2 --- /dev/null +++ b/Examples/biology/signalamplificationcascade/signal-amplification-cascade_metadata.yaml @@ -0,0 +1,61 @@ +id: "signal-amplification-cascade" +name: "signal amplification cascade" +description: "BioNetGen model: signal amplification cascade" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["signal", "amplification", "cascade", "ligand", "receptor", "effector", "messenger"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["receptor"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 0 at line 35" + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + comments: "need a site inside L()" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/signal-amplification-cascade.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/simpledimerization/metadata.yaml b/Examples/biology/simpledimerization/metadata.yaml index 1748cdde..33c69caa 100644 --- a/Examples/biology/simpledimerization/metadata.yaml +++ b/Examples/biology/simpledimerization/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["simple", "dimerization", "a", "b", "generate_network", "simulate"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/simpledimerization/simple-dimerization_metadata.yaml b/Examples/biology/simpledimerization/simple-dimerization_metadata.yaml new file mode 100644 index 00000000..9a1ded87 --- /dev/null +++ b/Examples/biology/simpledimerization/simple-dimerization_metadata.yaml @@ -0,0 +1,61 @@ +id: "simple-dimerization" +name: "simple dimerization" +description: "BioNetGen model: simple dimerization" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["simple", "dimerization", "a", "b", "generate_network", "simulate"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["receptor"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/simple-dimerization.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/sirepidemicmodel/metadata.yaml b/Examples/biology/sirepidemicmodel/metadata.yaml index 08da27dd..7419cc8e 100644 --- a/Examples/biology/sirepidemicmodel/metadata.yaml +++ b/Examples/biology/sirepidemicmodel/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["sir", "epidemic", "model", "human", "generate_network", "simulate"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/sirepidemicmodel/sir-epidemic-model_metadata.yaml b/Examples/biology/sirepidemicmodel/sir-epidemic-model_metadata.yaml new file mode 100644 index 00000000..697184d9 --- /dev/null +++ b/Examples/biology/sirepidemicmodel/sir-epidemic-model_metadata.yaml @@ -0,0 +1,61 @@ +id: "sir-epidemic-model" +name: "sir epidemic model" +description: "BioNetGen model: sir epidemic model" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["sir", "epidemic", "model", "human", "generate_network", "simulate"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["receptor"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/sir-epidemic-model.bngl" + +playground: + visible: false + gallery_categories: ["ecology","tutorials","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/smadtgfbetasignaling/metadata.yaml b/Examples/biology/smadtgfbetasignaling/metadata.yaml index 5aab150b..e0d594d9 100644 --- a/Examples/biology/smadtgfbetasignaling/metadata.yaml +++ b/Examples/biology/smadtgfbetasignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["smad", "tgf", "beta", "signaling", "tgfb", "tgfbr", "smad2", "smad4"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling_metadata.yaml b/Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling_metadata.yaml new file mode 100644 index 00000000..8e7f0dc9 --- /dev/null +++ b/Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling_metadata.yaml @@ -0,0 +1,61 @@ +id: "smad-tgf-beta-signaling" +name: "smad tgf beta signaling" +description: "BioNetGen model: smad tgf beta signaling" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["smad", "tgf", "beta", "signaling", "tgfb", "tgfbr", "smad2", "smad4"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + comments: "vcell put actions outside of model" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/smad-tgf-beta-signaling.bngl" + +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/sonichedgehoggradient/metadata.yaml b/Examples/biology/sonichedgehoggradient/metadata.yaml index fed2f2fc..011ee069 100644 --- a/Examples/biology/sonichedgehoggradient/metadata.yaml +++ b/Examples/biology/sonichedgehoggradient/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["sonic", "hedgehog", "gradient", "shh", "ptc1", "v_prod"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient_metadata.yaml b/Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient_metadata.yaml new file mode 100644 index 00000000..ada79361 --- /dev/null +++ b/Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient_metadata.yaml @@ -0,0 +1,61 @@ +id: "sonic-hedgehog-gradient" +name: "sonic hedgehog gradient" +description: "BioNetGen model: smad tgf beta signaling" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["sonic", "hedgehog", "gradient", "shh", "ptc1", "v_prod"] +date: + last_tested: 2026-07-13 + +category: "signaling" +biol_categories: ["gradient"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered -> at line 50" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + comments: "MCP cannot access local variable stdout_str where it is not associated with a value nfsim ERROR! You created a reaction (_R4) that deletes a molecule, but you did not use the DeleteMolecules keyword" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/smad-tgf-beta-signaling.bngl" + +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" + + + diff --git a/Examples/biology/stat3mediatedtranscription/metadata.yaml b/Examples/biology/stat3mediatedtranscription/metadata.yaml index 3e8884e2..3492ec7e 100644 --- a/Examples/biology/stat3mediatedtranscription/metadata.yaml +++ b/Examples/biology/stat3mediatedtranscription/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["stat3", "mediated", "transcription", "dna", "pias3", "mrna"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription_metadata.yaml b/Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription_metadata.yaml new file mode 100644 index 00000000..f4999245 --- /dev/null +++ b/Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription_metadata.yaml @@ -0,0 +1,26 @@ +id: "stat3-mediated-transcription" +name: "stat3 mediated transcription" +description: "STAT3-mediated transcription and feedback." +contributors: + - name: "Achyudhan" +tags: ["stat3", "mediated", "transcription", "dna", "pias3", "mrna"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/stat3-mediated-transcription.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/stressresponseadaptation/metadata.yaml b/Examples/biology/stressresponseadaptation/metadata.yaml index 4790cde5..41d5f5d8 100644 --- a/Examples/biology/stressresponseadaptation/metadata.yaml +++ b/Examples/biology/stressresponseadaptation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["stress", "response", "adaptation", "sensor", "adapter", "enzyme"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/stressresponseadaptation/stress-response-adaptation_metadata.yaml b/Examples/biology/stressresponseadaptation/stress-response-adaptation_metadata.yaml new file mode 100644 index 00000000..4e7476af --- /dev/null +++ b/Examples/biology/stressresponseadaptation/stress-response-adaptation_metadata.yaml @@ -0,0 +1,26 @@ +id: "stress-response-adaptation" +name: "stress response adaptation" +description: "BioNetGen model: stress response adaptation" +contributors: + - name: "Achyudhan" +tags: ["stress", "response", "adaptation", "sensor", "adapter", "enzyme"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/stress-response-adaptation.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/synapticplasticityltp/metadata.yaml b/Examples/biology/synapticplasticityltp/metadata.yaml index 3d91589d..66cda84d 100644 --- a/Examples/biology/synapticplasticityltp/metadata.yaml +++ b/Examples/biology/synapticplasticityltp/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["synaptic", "plasticity", "ltp", "glutamate", "nmda", "calcium", "camkii", "ampar", "glusource"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp_metadata.yaml b/Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp_metadata.yaml new file mode 100644 index 00000000..81b75fc8 --- /dev/null +++ b/Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp_metadata.yaml @@ -0,0 +1,26 @@ +id: "synaptic-plasticity-ltp" +name: "synaptic plasticity ltp" +description: "Initial Concentrations" +contributors: + - name: "Achyudhan" +tags: ["synaptic", "plasticity", "ltp", "glutamate", "nmda", "calcium", "camkii", "ampar", "glusource"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/synaptic-plasticity-ltp.bngl" +playground: + visible: false + gallery_categories: ["neuroscience","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/tcellactivation/metadata.yaml b/Examples/biology/tcellactivation/metadata.yaml index 513ad5b8..408392f3 100644 --- a/Examples/biology/tcellactivation/metadata.yaml +++ b/Examples/biology/tcellactivation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["t", "cell", "activation", "tcr", "antigen", "cytokine"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/tcellactivation/t-cell-activation_metadata.yaml b/Examples/biology/tcellactivation/t-cell-activation_metadata.yaml new file mode 100644 index 00000000..de54d6db --- /dev/null +++ b/Examples/biology/tcellactivation/t-cell-activation_metadata.yaml @@ -0,0 +1,26 @@ +id: "t-cell-activation" +name: "t cell activation" +description: "BioNetGen model: t cell activation" +contributors: + - name: "Achyudhan" +tags: ["t", "cell", "activation", "tcr", "antigen", "cytokine"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/t-cell-activation.bngl" +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/tlr3dsrnasensing/metadata.yaml b/Examples/biology/tlr3dsrnasensing/metadata.yaml index 4b66a09e..d99b8398 100644 --- a/Examples/biology/tlr3dsrnasensing/metadata.yaml +++ b/Examples/biology/tlr3dsrnasensing/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["tlr3", "dsrna", "sensing", "trif", "irf3", "sarm"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing_metadata.yaml b/Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing_metadata.yaml new file mode 100644 index 00000000..0e70de8f --- /dev/null +++ b/Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing_metadata.yaml @@ -0,0 +1,26 @@ +id: "tlr3-dsrna-sensing" +name: "tlr3 dsrna sensing" +description: "TLR3-mediated dsRNA sensing and TRIF pathway activation." +contributors: + - name: "Achyudhan" +tags: ["tlr3", "dsrna", "sensing", "trif", "irf3", "sarm"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/tlr3-dsrna-sensing.bngl" +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/tnfinducedapoptosis/metadata.yaml b/Examples/biology/tnfinducedapoptosis/metadata.yaml index d8987ab2..a8811ca0 100644 --- a/Examples/biology/tnfinducedapoptosis/metadata.yaml +++ b/Examples/biology/tnfinducedapoptosis/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["tnf", "induced", "apoptosis", "tnfr", "caspase8", "bid", "caspase3"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis_metadata.yaml b/Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis_metadata.yaml new file mode 100644 index 00000000..88832a4c --- /dev/null +++ b/Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis_metadata.yaml @@ -0,0 +1,26 @@ +id: "tnf-induced-apoptosis" +name: "tnf induced apoptosis" +description: "BioNetGen model: tnf induced apoptosis" +contributors: + - name: "Achyudhan" +tags: ["tnf", "induced", "apoptosis", "tnfr", "caspase8", "bid", "caspase3"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/tnf-induced-apoptosis.bngl" +playground: + visible: false + gallery_categories: ["cell-cycle","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/twocomponentsystem/metadata.yaml b/Examples/biology/twocomponentsystem/metadata.yaml index a39f2d54..4af4b738 100644 --- a/Examples/biology/twocomponentsystem/metadata.yaml +++ b/Examples/biology/twocomponentsystem/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["two", "component", "system", "kinase", "regulator", "target"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/twocomponentsystem/two-component-system_metadata.yaml b/Examples/biology/twocomponentsystem/two-component-system_metadata.yaml new file mode 100644 index 00000000..05d1d0ed --- /dev/null +++ b/Examples/biology/twocomponentsystem/two-component-system_metadata.yaml @@ -0,0 +1,26 @@ +id: "two-component-system" +name: "two component system" +description: "BioNetGen model: two component system" +contributors: + - name: "Achyudhan" +tags: ["two", "component", "system", "kinase", "regulator", "target"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/two-component-system.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/vegfangiogenesis/metadata.yaml b/Examples/biology/vegfangiogenesis/metadata.yaml index e52b50ec..6d64a924 100644 --- a/Examples/biology/vegfangiogenesis/metadata.yaml +++ b/Examples/biology/vegfangiogenesis/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["vegf", "angiogenesis", "vegfr2", "vegfr1", "erk", "endothelial"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/vegfangiogenesis/vegf-angiogenesis_metadata.yaml b/Examples/biology/vegfangiogenesis/vegf-angiogenesis_metadata.yaml new file mode 100644 index 00000000..4596eeac --- /dev/null +++ b/Examples/biology/vegfangiogenesis/vegf-angiogenesis_metadata.yaml @@ -0,0 +1,26 @@ +id: "vegf-angiogenesis" +name: "vegf angiogenesis" +description: "VEGF-mediated signaling in angiogenesis." +contributors: + - name: "Achyudhan" +tags: ["vegf", "angiogenesis", "vegfr2", "vegfr1", "erk", "endothelial"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/vegf-angiogenesis.bngl" +playground: + visible: false + gallery_categories: ["cancer","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/viralsensinginnateimmunity/metadata.yaml b/Examples/biology/viralsensinginnateimmunity/metadata.yaml index 4ad35afa..af7c7c37 100644 --- a/Examples/biology/viralsensinginnateimmunity/metadata.yaml +++ b/Examples/biology/viralsensinginnateimmunity/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["viral", "sensing", "innate", "immunity", "viralrna", "rigi", "mavs", "irf3", "ifnb"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity_metadata.yaml b/Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity_metadata.yaml new file mode 100644 index 00000000..5257f787 --- /dev/null +++ b/Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity_metadata.yaml @@ -0,0 +1,26 @@ +id: "viral-sensing-innate-immunity" +name: "viral sensing innate immunity" +description: "BioNetGen model: viral sensing innate immunity" +contributors: + - name: "Achyudhan" +tags: ["viral", "sensing", "innate", "immunity", "viralrna", "rigi", "mavs", "irf3", "ifnb"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/viral-sensing-innate-immunity.bngl" +playground: + visible: false + gallery_categories: ["immunology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/wntbetacateninsignaling/metadata.yaml b/Examples/biology/wntbetacateninsignaling/metadata.yaml index a0f48d2e..c6665eb4 100644 --- a/Examples/biology/wntbetacateninsignaling/metadata.yaml +++ b/Examples/biology/wntbetacateninsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["wnt", "beta", "catenin", "signaling", "frizzled", "dvl", "dest_complex", "betacatenin", "tcf"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling_metadata.yaml b/Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling_metadata.yaml new file mode 100644 index 00000000..e25d2567 --- /dev/null +++ b/Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "wnt-beta-catenin-signaling" +name: "wnt beta catenin signaling" +description: "Wnt/Beta-Catenin signaling (Canonical pathway)." +contributors: + - name: "Achyudhan" +tags: ["wnt", "beta", "catenin", "signaling", "frizzled", "dvl", "dest_complex", "betacatenin", "tcf"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/wnt-beta-catenin-signaling.bngl" +playground: + visible: false + gallery_categories: ["developmental","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/biology/woundhealingpdgfsignaling/metadata.yaml b/Examples/biology/woundhealingpdgfsignaling/metadata.yaml index 2b160e68..7e743d66 100644 --- a/Examples/biology/woundhealingpdgfsignaling/metadata.yaml +++ b/Examples/biology/woundhealingpdgfsignaling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["wound", "healing", "pdgf", "signaling", "pdgfr", "stat3", "fibroblast"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling_metadata.yaml b/Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling_metadata.yaml new file mode 100644 index 00000000..1de15d83 --- /dev/null +++ b/Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling_metadata.yaml @@ -0,0 +1,26 @@ +id: "wound-healing-pdgf-signaling" +name: "wound healing pdgf signaling" +description: "BioNetGen model: wound healing pdgf signaling" +contributors: + - name: "Achyudhan" +tags: ["wound", "healing", "pdgf", "signaling", "pdgfr", "stat3", "fibroblast"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/wound-healing-pdgf-signaling.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/compartments/compartmentendocytosis/compartment_endocytosis_metadata.yaml b/Examples/compartments/compartmentendocytosis/compartment_endocytosis_metadata.yaml new file mode 100644 index 00000000..f60fae9c --- /dev/null +++ b/Examples/compartments/compartmentendocytosis/compartment_endocytosis_metadata.yaml @@ -0,0 +1,26 @@ +id: "compartment_endocytosis" +name: "compartment endocytosis" +description: "Model: compartment_endocytosis.bngl" +contributors: + - name: "Achyudhan" +tags: ["compartment", "endocytosis", "l", "r", "t"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/compartment_endocytosis.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/compartments/compartmentendocytosis/metadata.yaml b/Examples/compartments/compartmentendocytosis/metadata.yaml index f2450bf9..71324fd8 100644 --- a/Examples/compartments/compartmentendocytosis/metadata.yaml +++ b/Examples/compartments/compartmentendocytosis/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["compartment", "endocytosis", "l", "r", "t"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/compartments/compartmentmembranebound/compartment_membrane_bound_metadata.yaml b/Examples/compartments/compartmentmembranebound/compartment_membrane_bound_metadata.yaml new file mode 100644 index 00000000..cef51319 --- /dev/null +++ b/Examples/compartments/compartmentmembranebound/compartment_membrane_bound_metadata.yaml @@ -0,0 +1,26 @@ +id: "compartment_membrane_bound" +name: "compartment membrane bound" +description: "Model: compartment_membrane_bound.bngl" +contributors: + - name: "Achyudhan" +tags: ["compartment", "membrane", "bound", "p", "lipid", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/compartment_membrane_bound.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/compartments/compartmentmembranebound/metadata.yaml b/Examples/compartments/compartmentmembranebound/metadata.yaml index 17e9bbaf..fd0d93bb 100644 --- a/Examples/compartments/compartmentmembranebound/metadata.yaml +++ b/Examples/compartments/compartmentmembranebound/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["compartment", "membrane", "bound", "p", "lipid", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/compartments/compartmentnestedtransport/compartment_nested_transport_metadata.yaml b/Examples/compartments/compartmentnestedtransport/compartment_nested_transport_metadata.yaml new file mode 100644 index 00000000..fb632d87 --- /dev/null +++ b/Examples/compartments/compartmentnestedtransport/compartment_nested_transport_metadata.yaml @@ -0,0 +1,26 @@ +id: "compartment_nested_transport" +name: "compartment nested transport" +description: "Model: compartment_nested_transport.bngl" +contributors: + - name: "Achyudhan" +tags: ["compartment", "nested", "transport", "s", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/compartment_nested_transport.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/compartments/compartmentnestedtransport/metadata.yaml b/Examples/compartments/compartmentnestedtransport/metadata.yaml index a7614f8c..38835728 100644 --- a/Examples/compartments/compartmentnestedtransport/metadata.yaml +++ b/Examples/compartments/compartmentnestedtransport/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["compartment", "nested", "transport", "s", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport_metadata.yaml b/Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport_metadata.yaml new file mode 100644 index 00000000..2ad5d89f --- /dev/null +++ b/Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport_metadata.yaml @@ -0,0 +1,26 @@ +id: "compartment_nuclear_transport" +name: "compartment nuclear transport" +description: "Model: compartment_nuclear_transport.bngl" +contributors: + - name: "Achyudhan" +tags: ["compartment", "nuclear", "transport", "tf", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/compartment_nuclear_transport.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/compartments/compartmentnucleartransport/metadata.yaml b/Examples/compartments/compartmentnucleartransport/metadata.yaml index 5312e5c3..e8db8b43 100644 --- a/Examples/compartments/compartmentnucleartransport/metadata.yaml +++ b/Examples/compartments/compartmentnucleartransport/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["compartment", "nuclear", "transport", "tf", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange_metadata.yaml b/Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange_metadata.yaml new file mode 100644 index 00000000..e4a080e9 --- /dev/null +++ b/Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange_metadata.yaml @@ -0,0 +1,26 @@ +id: "compartment_organelle_exchange" +name: "compartment organelle exchange" +description: "Model: compartment_organelle_exchange.bngl" +contributors: + - name: "Achyudhan" +tags: ["compartment", "organelle", "exchange", "cargo", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/compartment_organelle_exchange.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/compartments/compartmentorganelleexchange/metadata.yaml b/Examples/compartments/compartmentorganelleexchange/metadata.yaml index 117bb562..c522d3bc 100644 --- a/Examples/compartments/compartmentorganelleexchange/metadata.yaml +++ b/Examples/compartments/compartmentorganelleexchange/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["compartment", "organelle", "exchange", "cargo", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/cs/csdiffiehellman/cs_diffie_hellman_metadata.yaml b/Examples/cs/csdiffiehellman/cs_diffie_hellman_metadata.yaml new file mode 100644 index 00000000..f603d573 --- /dev/null +++ b/Examples/cs/csdiffiehellman/cs_diffie_hellman_metadata.yaml @@ -0,0 +1,26 @@ +id: "cs_diffie_hellman" +name: "cs diffie hellman" +description: "Model: cs_diffie_hellman.bngl" +contributors: + - name: "Achyudhan" +tags: ["cs", "diffie", "hellman", "agent", "target", "dshareda_dt", "dsharedb_dt"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cs_diffie_hellman.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/cs/csdiffiehellman/metadata.yaml b/Examples/cs/csdiffiehellman/metadata.yaml index f2cea06d..73604f8e 100644 --- a/Examples/cs/csdiffiehellman/metadata.yaml +++ b/Examples/cs/csdiffiehellman/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cs", "diffie", "hellman", "agent", "target", "dshareda_dt", "dsharedb_dt"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/cs/cshashfunction/cs_hash_function_metadata.yaml b/Examples/cs/cshashfunction/cs_hash_function_metadata.yaml new file mode 100644 index 00000000..ee2505bf --- /dev/null +++ b/Examples/cs/cshashfunction/cs_hash_function_metadata.yaml @@ -0,0 +1,26 @@ +id: "cs_hash_function" +name: "cs hash function" +description: "Cryptographic Hash Function in BNGL" +contributors: + - name: "Achyudhan" +tags: ["cs", "hash", "function", "b0", "b1", "b2", "b3", "h0", "h1", "h2", "h3"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cs_hash_function.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/cs/cshashfunction/metadata.yaml b/Examples/cs/cshashfunction/metadata.yaml index ab0695d2..6d7957ff 100644 --- a/Examples/cs/cshashfunction/metadata.yaml +++ b/Examples/cs/cshashfunction/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cs", "hash", "function", "b0", "b1", "b2", "b3", "h0", "h1", "h2", "h3"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/cs/cshuffman/cs_huffman_metadata.yaml b/Examples/cs/cshuffman/cs_huffman_metadata.yaml new file mode 100644 index 00000000..451d8ec4 --- /dev/null +++ b/Examples/cs/cshuffman/cs_huffman_metadata.yaml @@ -0,0 +1,26 @@ +id: "cs_huffman" +name: "cs huffman" +description: "Model: cs_huffman.bngl" +contributors: + - name: "Achyudhan" +tags: ["cs", "huffman", "char", "hnode", "generate_network", "simulate"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cs_huffman.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/cs/cshuffman/metadata.yaml b/Examples/cs/cshuffman/metadata.yaml index 3106e7cc..7ce34006 100644 --- a/Examples/cs/cshuffman/metadata.yaml +++ b/Examples/cs/cshuffman/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cs", "huffman", "char", "hnode", "generate_network", "simulate"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/cs/csmontecarlopi/cs_monte_carlo_pi_metadata.yaml b/Examples/cs/csmontecarlopi/cs_monte_carlo_pi_metadata.yaml new file mode 100644 index 00000000..18a002a9 --- /dev/null +++ b/Examples/cs/csmontecarlopi/cs_monte_carlo_pi_metadata.yaml @@ -0,0 +1,26 @@ +id: "cs_monte_carlo_pi" +name: "cs monte carlo pi" +description: "Model: cs_monte_carlo_pi.bngl" +contributors: + - name: "Achyudhan" +tags: ["cs", "monte", "carlo", "pi", "trial", "pi_estimate", "generate_network", "simulate"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cs_monte_carlo_pi.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/cs/csmontecarlopi/metadata.yaml b/Examples/cs/csmontecarlopi/metadata.yaml index 058023f5..d45fb322 100644 --- a/Examples/cs/csmontecarlopi/metadata.yaml +++ b/Examples/cs/csmontecarlopi/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cs", "monte", "carlo", "pi", "trial", "pi_estimate", "generate_network", "simulate"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/cs/cspagerank/cs_pagerank_metadata.yaml b/Examples/cs/cspagerank/cs_pagerank_metadata.yaml new file mode 100644 index 00000000..36137eed --- /dev/null +++ b/Examples/cs/cspagerank/cs_pagerank_metadata.yaml @@ -0,0 +1,26 @@ +id: "cs_pagerank" +name: "cs pagerank" +description: "Model: cs_pagerank.bngl" +contributors: + - name: "Achyudhan" +tags: ["cs", "pagerank", "teleport", "page"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cs_pagerank.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/cs/cspagerank/metadata.yaml b/Examples/cs/cspagerank/metadata.yaml index 74cb2bdf..e61e97c6 100644 --- a/Examples/cs/cspagerank/metadata.yaml +++ b/Examples/cs/cspagerank/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cs", "pagerank", "teleport", "page"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/cs/cspidcontroller/cs_pid_controller_metadata.yaml b/Examples/cs/cspidcontroller/cs_pid_controller_metadata.yaml new file mode 100644 index 00000000..c253be28 --- /dev/null +++ b/Examples/cs/cspidcontroller/cs_pid_controller_metadata.yaml @@ -0,0 +1,26 @@ +id: "cs_pid_controller" +name: "cs pid controller" +description: "PID Controller in BNGL" +contributors: + - name: "Achyudhan" +tags: ["cs", "pid", "controller", "sensor", "accumulator", "leakyerror", "actuator", "disturbance"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cs_pid_controller.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/cs/cspidcontroller/metadata.yaml b/Examples/cs/cspidcontroller/metadata.yaml index 047171bc..c7bc1e70 100644 --- a/Examples/cs/cspidcontroller/metadata.yaml +++ b/Examples/cs/cspidcontroller/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cs", "pid", "controller", "sensor", "accumulator", "leakyerror", "actuator", "disturbance"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/cs/csregexnfa/cs_regex_nfa_metadata.yaml b/Examples/cs/csregexnfa/cs_regex_nfa_metadata.yaml new file mode 100644 index 00000000..5cdc902c --- /dev/null +++ b/Examples/cs/csregexnfa/cs_regex_nfa_metadata.yaml @@ -0,0 +1,26 @@ +id: "cs_regex_nfa" +name: "cs regex nfa" +description: "Model: cs_regex_nfa.bngl" +contributors: + - name: "Achyudhan" +tags: ["cs", "regex", "nfa", "state", "char", "generate_network", "simulate", "setparameter"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/cs_regex_nfa.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/cs/csregexnfa/metadata.yaml b/Examples/cs/csregexnfa/metadata.yaml index 6e59131b..138629c4 100644 --- a/Examples/cs/csregexnfa/metadata.yaml +++ b/Examples/cs/csregexnfa/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["cs", "regex", "nfa", "state", "char", "generate_network", "simulate", "setparameter"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite_metadata.yaml b/Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite_metadata.yaml new file mode 100644 index 00000000..c4b7d7f3 --- /dev/null +++ b/Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite_metadata.yaml @@ -0,0 +1,26 @@ +id: "eco_coevolution_host_parasite" +name: "eco coevolution host parasite" +description: "Model: eco_coevolution_host_parasite.bngl" +contributors: + - name: "Achyudhan" +tags: ["eco", "coevolution", "host", "parasite"] +category: "ecology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/eco_coevolution_host_parasite.bngl" +playground: + visible: false + gallery_categories: ["ecology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ecology/ecocoevolutionhostparasite/metadata.yaml b/Examples/ecology/ecocoevolutionhostparasite/metadata.yaml index 57a5f192..be7d746c 100644 --- a/Examples/ecology/ecocoevolutionhostparasite/metadata.yaml +++ b/Examples/ecology/ecocoevolutionhostparasite/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["eco", "coevolution", "host", "parasite"] category: "ecology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp_metadata.yaml b/Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp_metadata.yaml new file mode 100644 index 00000000..31fad48e --- /dev/null +++ b/Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp_metadata.yaml @@ -0,0 +1,26 @@ +id: "eco_food_web_chaos_3sp" +name: "eco food web chaos 3sp" +description: "Model: eco_food_web_chaos_3sp.bngl" +contributors: + - name: "Achyudhan" +tags: ["eco", "food", "web", "chaos", "3sp", "r", "c", "p", "k_eat_r", "k_eat_c"] +category: "ecology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/eco_food_web_chaos_3sp.bngl" +playground: + visible: false + gallery_categories: ["ecology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ecology/ecofoodwebchaos3sp/metadata.yaml b/Examples/ecology/ecofoodwebchaos3sp/metadata.yaml index 07b284ad..611cf0eb 100644 --- a/Examples/ecology/ecofoodwebchaos3sp/metadata.yaml +++ b/Examples/ecology/ecofoodwebchaos3sp/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["eco", "food", "web", "chaos", "3sp", "r", "c", "p", "k_eat_r", "k_eat_c"] category: "ecology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid_metadata.yaml b/Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid_metadata.yaml new file mode 100644 index 00000000..4a298022 --- /dev/null +++ b/Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid_metadata.yaml @@ -0,0 +1,26 @@ +id: "eco_lotka_volterra_grid" +name: "eco lotka volterra grid" +description: "Model: eco_lotka_volterra_grid.bngl" +contributors: + - name: "Achyudhan" +tags: ["eco", "lotka", "volterra", "grid", "prey", "pred"] +category: "ecology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/eco_lotka_volterra_grid.bngl" +playground: + visible: false + gallery_categories: ["ecology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ecology/ecolotkavolterragrid/metadata.yaml b/Examples/ecology/ecolotkavolterragrid/metadata.yaml index ef56b02b..f38d9996 100644 --- a/Examples/ecology/ecolotkavolterragrid/metadata.yaml +++ b/Examples/ecology/ecolotkavolterragrid/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["eco", "lotka", "volterra", "grid", "prey", "pred"] category: "ecology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/ecology/ecomutualismobligate/eco_mutualism_obligate_metadata.yaml b/Examples/ecology/ecomutualismobligate/eco_mutualism_obligate_metadata.yaml new file mode 100644 index 00000000..0cc5c9c8 --- /dev/null +++ b/Examples/ecology/ecomutualismobligate/eco_mutualism_obligate_metadata.yaml @@ -0,0 +1,26 @@ +id: "eco_mutualism_obligate" +name: "eco mutualism obligate" +description: "Model: eco_mutualism_obligate.bngl" +contributors: + - name: "Achyudhan" +tags: ["eco", "mutualism", "obligate", "a", "b"] +category: "ecology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/eco_mutualism_obligate.bngl" +playground: + visible: false + gallery_categories: ["ecology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ecology/ecomutualismobligate/metadata.yaml b/Examples/ecology/ecomutualismobligate/metadata.yaml index 3292a504..3c309248 100644 --- a/Examples/ecology/ecomutualismobligate/metadata.yaml +++ b/Examples/ecology/ecomutualismobligate/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["eco", "mutualism", "obligate", "a", "b"] category: "ecology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial_metadata.yaml b/Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial_metadata.yaml new file mode 100644 index 00000000..3c50cb8d --- /dev/null +++ b/Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial_metadata.yaml @@ -0,0 +1,26 @@ +id: "eco_rock_paper_scissors_spatial" +name: "eco rock paper scissors spatial" +description: "Model: eco_rock_paper_scissors_spatial.bngl" +contributors: + - name: "Achyudhan" +tags: ["eco", "rock", "paper", "scissors", "spatial", "s", "generate_network"] +category: "ecology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/eco_rock_paper_scissors_spatial.bngl" +playground: + visible: false + gallery_categories: ["ecology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml b/Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml index 7b776bad..0312d08f 100644 --- a/Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml +++ b/Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["eco", "rock", "paper", "scissors", "spatial", "s", "generate_network"] category: "ecology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/energy/energyallosterymwc/energy_allostery_mwc_metadata.yaml b/Examples/energy/energyallosterymwc/energy_allostery_mwc_metadata.yaml new file mode 100644 index 00000000..da31d070 --- /dev/null +++ b/Examples/energy/energyallosterymwc/energy_allostery_mwc_metadata.yaml @@ -0,0 +1,26 @@ +id: "energy_allostery_mwc" +name: "energy allostery mwc" +description: "Model: energy_allostery_mwc.bngl" +contributors: + - name: "Achyudhan" +tags: ["energy", "allostery", "mwc", "p", "l"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/energy_allostery_mwc.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/energy/energyallosterymwc/metadata.yaml b/Examples/energy/energyallosterymwc/metadata.yaml index 212fd97d..9f23ec32 100644 --- a/Examples/energy/energyallosterymwc/metadata.yaml +++ b/Examples/energy/energyallosterymwc/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["energy", "allostery", "mwc", "p", "l"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/energy/energycatalysismm/energy_catalysis_mm_metadata.yaml b/Examples/energy/energycatalysismm/energy_catalysis_mm_metadata.yaml new file mode 100644 index 00000000..d110cc34 --- /dev/null +++ b/Examples/energy/energycatalysismm/energy_catalysis_mm_metadata.yaml @@ -0,0 +1,26 @@ +id: "energy_catalysis_mm" +name: "energy catalysis mm" +description: "Model: energy_catalysis_mm.bngl" +contributors: + - name: "Achyudhan" +tags: ["energy", "catalysis", "mm", "e", "s", "p"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/energy_catalysis_mm.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/energy/energycatalysismm/metadata.yaml b/Examples/energy/energycatalysismm/metadata.yaml index d0943cbe..da066a0c 100644 --- a/Examples/energy/energycatalysismm/metadata.yaml +++ b/Examples/energy/energycatalysismm/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["energy", "catalysis", "mm", "e", "s", "p"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/energy/energycooperativityadh/energy_cooperativity_adh_metadata.yaml b/Examples/energy/energycooperativityadh/energy_cooperativity_adh_metadata.yaml new file mode 100644 index 00000000..a54ed093 --- /dev/null +++ b/Examples/energy/energycooperativityadh/energy_cooperativity_adh_metadata.yaml @@ -0,0 +1,26 @@ +id: "energy_cooperativity_adh" +name: "energy cooperativity adh" +description: "Model: energy_cooperativity_adh.bngl" +contributors: + - name: "Achyudhan" +tags: ["energy", "cooperativity", "adh", "r", "l"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/energy_cooperativity_adh.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/energy/energycooperativityadh/metadata.yaml b/Examples/energy/energycooperativityadh/metadata.yaml index 2bfa8da4..ee2d9e2b 100644 --- a/Examples/energy/energycooperativityadh/metadata.yaml +++ b/Examples/energy/energycooperativityadh/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["energy", "cooperativity", "adh", "r", "l"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/energy/energylinearchain/energy_linear_chain_metadata.yaml b/Examples/energy/energylinearchain/energy_linear_chain_metadata.yaml new file mode 100644 index 00000000..534890c6 --- /dev/null +++ b/Examples/energy/energylinearchain/energy_linear_chain_metadata.yaml @@ -0,0 +1,26 @@ +id: "energy_linear_chain" +name: "energy linear chain" +description: "Model: energy_linear_chain.bngl" +contributors: + - name: "Achyudhan" +tags: ["energy", "linear", "chain", "m", "generate_network"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/energy_linear_chain.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/energy/energylinearchain/metadata.yaml b/Examples/energy/energylinearchain/metadata.yaml index 5b11762e..71b84884 100644 --- a/Examples/energy/energylinearchain/metadata.yaml +++ b/Examples/energy/energylinearchain/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["energy", "linear", "chain", "m", "generate_network"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/energy/energytransportpump/energy_transport_pump_metadata.yaml b/Examples/energy/energytransportpump/energy_transport_pump_metadata.yaml new file mode 100644 index 00000000..a84dc90c --- /dev/null +++ b/Examples/energy/energytransportpump/energy_transport_pump_metadata.yaml @@ -0,0 +1,26 @@ +id: "energy_transport_pump" +name: "energy transport pump" +description: "Model: energy_transport_pump.bngl" +contributors: + - name: "Achyudhan" +tags: ["energy", "transport", "pump", "a", "atp", "adp", "pi", "t"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/energy_transport_pump.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/energy/energytransportpump/metadata.yaml b/Examples/energy/energytransportpump/metadata.yaml index 3c53ea6c..4df923f4 100644 --- a/Examples/energy/energytransportpump/metadata.yaml +++ b/Examples/energy/energytransportpump/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["energy", "transport", "pump", "a", "atp", "adp", "pi", "t"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume_metadata.yaml b/Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume_metadata.yaml new file mode 100644 index 00000000..005ef115 --- /dev/null +++ b/Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume_metadata.yaml @@ -0,0 +1,26 @@ +id: "feature_functional_rates_volume" +name: "feature functional rates volume" +description: "Model: feature_functional_rates_volume.bngl" +contributors: + - name: "Achyudhan" +tags: ["feature", "functional", "rates", "volume", "a", "b", "c"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/feature_functional_rates_volume.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml b/Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml index ebaa1c3d..6dc16ade 100644 --- a/Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml +++ b/Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["feature", "functional", "rates", "volume", "a", "b", "c"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan_metadata.yaml b/Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan_metadata.yaml new file mode 100644 index 00000000..317c0d36 --- /dev/null +++ b/Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan_metadata.yaml @@ -0,0 +1,26 @@ +id: "feature_global_functions_scan" +name: "feature global functions scan" +description: "Model: feature_global_functions_scan.bngl" +contributors: + - name: "Achyudhan" +tags: ["feature", "global", "functions", "scan", "signal", "response", "stimulus"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/feature_global_functions_scan.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml b/Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml index df436d67..820444b3 100644 --- a/Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml +++ b/Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["feature", "global", "functions", "scan", "signal", "response", "stimulus"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit_metadata.yaml b/Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit_metadata.yaml new file mode 100644 index 00000000..77f9952e --- /dev/null +++ b/Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit_metadata.yaml @@ -0,0 +1,26 @@ +id: "feature_local_functions_explicit" +name: "feature local functions explicit" +description: "Model: feature_local_functions_explicit.bngl" +contributors: + - name: "Achyudhan" +tags: ["feature", "local", "functions", "explicit", "s", "p", "e", "mm_rate", "ratelaw"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/feature_local_functions_explicit.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml b/Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml index 2934ef94..f860c4a4 100644 --- a/Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml +++ b/Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["feature", "local", "functions", "explicit", "s", "p", "e", "mm_rate", "ratelaw"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic_metadata.yaml b/Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic_metadata.yaml new file mode 100644 index 00000000..9116a9f6 --- /dev/null +++ b/Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic_metadata.yaml @@ -0,0 +1,26 @@ +id: "feature_symmetry_factors_cyclic" +name: "feature symmetry factors cyclic" +description: "Model: feature_symmetry_factors_cyclic.bngl" +contributors: + - name: "Achyudhan" +tags: ["feature", "symmetry", "factors", "cyclic", "x", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/feature_symmetry_factors_cyclic.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml b/Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml index faa877fc..64a6ff5e 100644 --- a/Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml +++ b/Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["feature", "symmetry", "factors", "cyclic", "x", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss_metadata.yaml b/Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss_metadata.yaml new file mode 100644 index 00000000..d059a7bd --- /dev/null +++ b/Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss_metadata.yaml @@ -0,0 +1,26 @@ +id: "feature_synthesis_degradation_ss" +name: "feature synthesis degradation ss" +description: "Model: feature_synthesis_degradation_ss.bngl" +contributors: + - name: "Achyudhan" +tags: ["feature", "synthesis", "degradation", "ss", "m", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/feature_synthesis_degradation_ss.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml b/Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml index 3486e427..dc51a975 100644 --- a/Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml +++ b/Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["feature", "synthesis", "degradation", "ss", "m", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/generative/gmgameoflife/gm_game_of_life_metadata.yaml b/Examples/generative/gmgameoflife/gm_game_of_life_metadata.yaml new file mode 100644 index 00000000..d46517bb --- /dev/null +++ b/Examples/generative/gmgameoflife/gm_game_of_life_metadata.yaml @@ -0,0 +1,26 @@ +id: "gm_game_of_life" +name: "gm game of life" +description: "Model: gm_game_of_life.bngl" +contributors: + - name: "Achyudhan" +tags: ["gm", "game", "of", "life", "cell"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/gm_game_of_life.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/generative/gmgameoflife/metadata.yaml b/Examples/generative/gmgameoflife/metadata.yaml index 0da07cbf..308fcbbd 100644 --- a/Examples/generative/gmgameoflife/metadata.yaml +++ b/Examples/generative/gmgameoflife/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["gm", "game", "of", "life", "cell"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Examples/generative/gmraymarcher/gm_ray_marcher_metadata.yaml b/Examples/generative/gmraymarcher/gm_ray_marcher_metadata.yaml new file mode 100644 index 00000000..9cc0c23b --- /dev/null +++ b/Examples/generative/gmraymarcher/gm_ray_marcher_metadata.yaml @@ -0,0 +1,26 @@ +id: "gm_ray_marcher" +name: "gm ray marcher" +description: "Ray Marching Renderer in BNGL" +contributors: + - name: "Achyudhan" +tags: ["gm", "ray", "marcher", "ray0", "hit0", "bright0", "sdf0", "sdf1", "sdf2", "sdf3", "speed0"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/gm_ray_marcher.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/generative/gmraymarcher/metadata.yaml b/Examples/generative/gmraymarcher/metadata.yaml index 587cf105..b0769d87 100644 --- a/Examples/generative/gmraymarcher/metadata.yaml +++ b/Examples/generative/gmraymarcher/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["gm", "ray", "marcher", "ray0", "hit0", "bright0", "sdf0", "sdf1", "sdf2", "sdf3", "speed0"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy_metadata.yaml b/Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy_metadata.yaml new file mode 100644 index 00000000..1cc506f7 --- /dev/null +++ b/Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy_metadata.yaml @@ -0,0 +1,26 @@ +id: "genetic_bistability_energy" +name: "genetic bistability energy" +description: "Model: genetic_bistability_energy.bngl" +contributors: + - name: "Achyudhan" +tags: ["genetic", "bistability", "energy", "genea", "geneb", "prota", "protb"] +category: "gene-expression" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/genetic_bistability_energy.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/genetics/geneticbistabilityenergy/metadata.yaml b/Examples/genetics/geneticbistabilityenergy/metadata.yaml index 12a84d89..d8fed248 100644 --- a/Examples/genetics/geneticbistabilityenergy/metadata.yaml +++ b/Examples/genetics/geneticbistabilityenergy/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["genetic", "bistability", "energy", "genea", "geneb", "prota", "protb"] category: "gene-expression" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic_metadata.yaml b/Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic_metadata.yaml new file mode 100644 index 00000000..8fce2c75 --- /dev/null +++ b/Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic_metadata.yaml @@ -0,0 +1,26 @@ +id: "genetic_dna_replication_stochastic" +name: "genetic dna replication stochastic" +description: "Model: genetic_dna_replication_stochastic.bngl" +contributors: + - name: "Achyudhan" +tags: ["genetic", "dna", "replication", "stochastic", "pol", "n", "generate_network"] +category: "gene-expression" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/genetic_dna_replication_stochastic.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/genetics/geneticdnareplicationstochastic/metadata.yaml b/Examples/genetics/geneticdnareplicationstochastic/metadata.yaml index e6d059d1..ae2162a9 100644 --- a/Examples/genetics/geneticdnareplicationstochastic/metadata.yaml +++ b/Examples/genetics/geneticdnareplicationstochastic/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["genetic", "dna", "replication", "stochastic", "pol", "n", "generate_network"] category: "gene-expression" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator_metadata.yaml b/Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator_metadata.yaml new file mode 100644 index 00000000..06e6403c --- /dev/null +++ b/Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator_metadata.yaml @@ -0,0 +1,26 @@ +id: "genetic_goodwin_oscillator" +name: "genetic goodwin oscillator" +description: "Model: genetic_goodwin_oscillator.bngl" +contributors: + - name: "Achyudhan" +tags: ["genetic", "goodwin", "oscillator", "gene", "mrna", "protein", "repressor"] +category: "gene-expression" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/genetic_goodwin_oscillator.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/genetics/geneticgoodwinoscillator/metadata.yaml b/Examples/genetics/geneticgoodwinoscillator/metadata.yaml index cf8138ae..28bd2ce5 100644 --- a/Examples/genetics/geneticgoodwinoscillator/metadata.yaml +++ b/Examples/genetics/geneticgoodwinoscillator/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["genetic", "goodwin", "oscillator", "gene", "mrna", "protein", "repressor"] category: "gene-expression" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics_metadata.yaml b/Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics_metadata.yaml new file mode 100644 index 00000000..f3851c4e --- /dev/null +++ b/Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics_metadata.yaml @@ -0,0 +1,26 @@ +id: "genetic_translation_kinetics" +name: "genetic translation kinetics" +description: "Model: genetic_translation_kinetics.bngl" +contributors: + - name: "Achyudhan" +tags: ["genetic", "translation", "kinetics", "mrna", "rib", "protein"] +category: "gene-expression" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/genetic_translation_kinetics.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/genetics/genetictranslationkinetics/metadata.yaml b/Examples/genetics/genetictranslationkinetics/metadata.yaml index 15006709..b28c10ae 100644 --- a/Examples/genetics/genetictranslationkinetics/metadata.yaml +++ b/Examples/genetics/genetictranslationkinetics/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["genetic", "translation", "kinetics", "mrna", "rib", "protein"] category: "gene-expression" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d_metadata.yaml b/Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d_metadata.yaml new file mode 100644 index 00000000..53619fb0 --- /dev/null +++ b/Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d_metadata.yaml @@ -0,0 +1,26 @@ +id: "genetic_turing_pattern_1d" +name: "genetic turing pattern 1d" +description: "Model: genetic_turing_pattern_1d.bngl" +contributors: + - name: "Achyudhan" +tags: ["genetic", "turing", "pattern", "1d", "a", "b"] +category: "gene-expression" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/genetic_turing_pattern_1d.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/genetics/geneticturingpattern1d/metadata.yaml b/Examples/genetics/geneticturingpattern1d/metadata.yaml index 154c59ef..8e3560f4 100644 --- a/Examples/genetics/geneticturingpattern1d/metadata.yaml +++ b/Examples/genetics/geneticturingpattern1d/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["genetic", "turing", "pattern", "1d", "a", "b"] category: "gene-expression" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Examples/meta/metaformalgametheory/meta_formal_game_theory_metadata.yaml b/Examples/meta/metaformalgametheory/meta_formal_game_theory_metadata.yaml new file mode 100644 index 00000000..ecd50b8e --- /dev/null +++ b/Examples/meta/metaformalgametheory/meta_formal_game_theory_metadata.yaml @@ -0,0 +1,26 @@ +id: "meta_formal_game_theory" +name: "meta formal game theory" +description: "Model: meta_formal_game_theory.bngl" +contributors: + - name: "Achyudhan" +tags: ["meta", "formal", "game", "theory", "hawk", "dove", "pop", "payoffh", "payoffd"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/meta_formal_game_theory.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/meta/metaformalgametheory/metadata.yaml b/Examples/meta/metaformalgametheory/metadata.yaml index f720a4fc..7df39658 100644 --- a/Examples/meta/metaformalgametheory/metadata.yaml +++ b/Examples/meta/metaformalgametheory/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["meta", "formal", "game", "theory", "hawk", "dove", "pop", "payoffh", "payoffd"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock_metadata.yaml b/Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock_metadata.yaml new file mode 100644 index 00000000..ac094f0f --- /dev/null +++ b/Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock_metadata.yaml @@ -0,0 +1,26 @@ +id: "meta_formal_molecular_clock" +name: "meta formal molecular clock" +description: "Model: meta_formal_molecular_clock.bngl" +contributors: + - name: "Achyudhan" +tags: ["meta", "formal", "molecular", "clock", "fasta", "fastb", "slowc", "slowd"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/meta_formal_molecular_clock.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/meta/metaformalmolecularclock/metadata.yaml b/Examples/meta/metaformalmolecularclock/metadata.yaml index 9e4b92f0..e626cf86 100644 --- a/Examples/meta/metaformalmolecularclock/metadata.yaml +++ b/Examples/meta/metaformalmolecularclock/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["meta", "formal", "molecular", "clock", "fasta", "fastb", "slowc", "slowd"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/meta/metaformalpetrinet/meta_formal_petri_net_metadata.yaml b/Examples/meta/metaformalpetrinet/meta_formal_petri_net_metadata.yaml new file mode 100644 index 00000000..33f5e399 --- /dev/null +++ b/Examples/meta/metaformalpetrinet/meta_formal_petri_net_metadata.yaml @@ -0,0 +1,26 @@ +id: "meta_formal_petri_net" +name: "meta formal petri net" +description: "Model: meta_formal_petri_net.bngl" +contributors: + - name: "Achyudhan" +tags: ["meta", "formal", "petri", "net", "p1", "p2", "p3", "p4"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/meta_formal_petri_net.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/meta/metaformalpetrinet/metadata.yaml b/Examples/meta/metaformalpetrinet/metadata.yaml index 64be7824..84e2a8a7 100644 --- a/Examples/meta/metaformalpetrinet/metadata.yaml +++ b/Examples/meta/metaformalpetrinet/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["meta", "formal", "petri", "net", "p1", "p2", "p3", "p4"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/meta/mtarithmeticcompiler/metadata.yaml b/Examples/meta/mtarithmeticcompiler/metadata.yaml index fcaa99bf..d3e51c95 100644 --- a/Examples/meta/mtarithmeticcompiler/metadata.yaml +++ b/Examples/meta/mtarithmeticcompiler/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["mt", "arithmetic", "compiler", "node", "target_add", "target_mult"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler_metadata.yaml b/Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler_metadata.yaml new file mode 100644 index 00000000..c8847813 --- /dev/null +++ b/Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler_metadata.yaml @@ -0,0 +1,26 @@ +id: "mt_arithmetic_compiler" +name: "mt arithmetic compiler" +description: "Model: mt_arithmetic_compiler.bngl" +contributors: + - name: "Achyudhan" +tags: ["mt", "arithmetic", "compiler", "node", "target_add", "target_mult"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/mt_arithmetic_compiler.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/meta/mtbnglinterpreter/metadata.yaml b/Examples/meta/mtbnglinterpreter/metadata.yaml index a1805c1b..705bd4e9 100644 --- a/Examples/meta/mtbnglinterpreter/metadata.yaml +++ b/Examples/meta/mtbnglinterpreter/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["mt", "bngl", "interpreter", "rule", "species", "exec_s1_s2", "generate_network", "simulate"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/meta/mtbnglinterpreter/mt_bngl_interpreter_metadata.yaml b/Examples/meta/mtbnglinterpreter/mt_bngl_interpreter_metadata.yaml new file mode 100644 index 00000000..a7b1f0e0 --- /dev/null +++ b/Examples/meta/mtbnglinterpreter/mt_bngl_interpreter_metadata.yaml @@ -0,0 +1,26 @@ +id: "mt_bngl_interpreter" +name: "mt bngl interpreter" +description: "Model: mt_bngl_interpreter.bngl" +contributors: + - name: "Achyudhan" +tags: ["mt", "bngl", "interpreter", "rule", "species", "exec_s1_s2", "generate_network", "simulate"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/mt_bngl_interpreter.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/meta/mtmusicsequencer/metadata.yaml b/Examples/meta/mtmusicsequencer/metadata.yaml index 54c83493..f940229c 100644 --- a/Examples/meta/mtmusicsequencer/metadata.yaml +++ b/Examples/meta/mtmusicsequencer/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["mt", "music", "sequencer", "v1s", "v1c", "v2s", "v2c", "v3s", "v3c", "mix", "chordphase"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/meta/mtmusicsequencer/mt_music_sequencer_metadata.yaml b/Examples/meta/mtmusicsequencer/mt_music_sequencer_metadata.yaml new file mode 100644 index 00000000..8ed16e82 --- /dev/null +++ b/Examples/meta/mtmusicsequencer/mt_music_sequencer_metadata.yaml @@ -0,0 +1,26 @@ +id: "mt_music_sequencer" +name: "mt music sequencer" +description: "Music Sequencer / Chord Synthesizer in BNGL" +contributors: + - name: "Achyudhan" +tags: ["mt", "music", "sequencer", "v1s", "v1c", "v2s", "v2c", "v3s", "v3c", "mix", "chordphase"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/mt_music_sequencer.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/meta/mtpascaltriangle/metadata.yaml b/Examples/meta/mtpascaltriangle/metadata.yaml index b9ecb732..54d64313 100644 --- a/Examples/meta/mtpascaltriangle/metadata.yaml +++ b/Examples/meta/mtpascaltriangle/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["mt", "pascal", "triangle", "node"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/meta/mtpascaltriangle/mt_pascal_triangle_metadata.yaml b/Examples/meta/mtpascaltriangle/mt_pascal_triangle_metadata.yaml new file mode 100644 index 00000000..4496f70d --- /dev/null +++ b/Examples/meta/mtpascaltriangle/mt_pascal_triangle_metadata.yaml @@ -0,0 +1,26 @@ +id: "mt_pascal_triangle" +name: "mt pascal triangle" +description: "Model: mt_pascal_triangle.bngl" +contributors: + - name: "Achyudhan" +tags: ["mt", "pascal", "triangle", "node"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/mt_pascal_triangle.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/meta/mtquine/metadata.yaml b/Examples/meta/mtquine/metadata.yaml index a86b67e8..a593c099 100644 --- a/Examples/meta/mtquine/metadata.yaml +++ b/Examples/meta/mtquine/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["mt", "quine", "gene", "protein"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/meta/mtquine/mt_quine_metadata.yaml b/Examples/meta/mtquine/mt_quine_metadata.yaml new file mode 100644 index 00000000..e4d32c51 --- /dev/null +++ b/Examples/meta/mtquine/mt_quine_metadata.yaml @@ -0,0 +1,26 @@ +id: "mt_quine" +name: "mt quine" +description: "Model: mt_quine.bngl" +contributors: + - name: "Achyudhan" +tags: ["mt", "quine", "gene", "protein"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/mt_quine.bngl" +playground: + visible: false + gallery_categories: ["cs","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ml/mlgradientdescent/metadata.yaml b/Examples/ml/mlgradientdescent/metadata.yaml index a0498658..0784d0fe 100644 --- a/Examples/ml/mlgradientdescent/metadata.yaml +++ b/Examples/ml/mlgradientdescent/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ml", "gradient", "descent", "posx", "posy", "velx", "vely", "loss"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/ml/mlgradientdescent/ml_gradient_descent_metadata.yaml b/Examples/ml/mlgradientdescent/ml_gradient_descent_metadata.yaml new file mode 100644 index 00000000..baa892da --- /dev/null +++ b/Examples/ml/mlgradientdescent/ml_gradient_descent_metadata.yaml @@ -0,0 +1,26 @@ +id: "ml_gradient_descent" +name: "ml gradient descent" +description: "Gradient Descent Optimizer in BNGL" +contributors: + - name: "Achyudhan" +tags: ["ml", "gradient", "descent", "posx", "posy", "velx", "vely", "loss"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ml_gradient_descent.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ml/mlhopfield/metadata.yaml b/Examples/ml/mlhopfield/metadata.yaml index d9f87567..7e39b276 100644 --- a/Examples/ml/mlhopfield/metadata.yaml +++ b/Examples/ml/mlhopfield/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ml", "hopfield", "neuron", "net1", "net2", "net3", "target1"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/ml/mlhopfield/ml_hopfield_metadata.yaml b/Examples/ml/mlhopfield/ml_hopfield_metadata.yaml new file mode 100644 index 00000000..64f4820d --- /dev/null +++ b/Examples/ml/mlhopfield/ml_hopfield_metadata.yaml @@ -0,0 +1,26 @@ +id: "ml_hopfield" +name: "ml hopfield" +description: "Model: ml_hopfield.bngl" +contributors: + - name: "Achyudhan" +tags: ["ml", "hopfield", "neuron", "net1", "net2", "net3", "target1"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ml_hopfield.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ml/mlkmeans/metadata.yaml b/Examples/ml/mlkmeans/metadata.yaml index 1bf04e30..5b3b958c 100644 --- a/Examples/ml/mlkmeans/metadata.yaml +++ b/Examples/ml/mlkmeans/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ml", "kmeans", "ax", "ay", "bx", "by"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/ml/mlkmeans/ml_kmeans_metadata.yaml b/Examples/ml/mlkmeans/ml_kmeans_metadata.yaml new file mode 100644 index 00000000..5f448210 --- /dev/null +++ b/Examples/ml/mlkmeans/ml_kmeans_metadata.yaml @@ -0,0 +1,26 @@ +id: "ml_kmeans" +name: "ml kmeans" +description: "Model: ml_kmeans.bngl" +contributors: + - name: "Achyudhan" +tags: ["ml", "kmeans", "ax", "ay", "bx", "by"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ml_kmeans.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ml/mlqlearning/metadata.yaml b/Examples/ml/mlqlearning/metadata.yaml index 41d18421..c99f8abb 100644 --- a/Examples/ml/mlqlearning/metadata.yaml +++ b/Examples/ml/mlqlearning/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ml", "q", "learning", "pos", "ql", "qr", "reward", "action"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/ml/mlqlearning/ml_q_learning_metadata.yaml b/Examples/ml/mlqlearning/ml_q_learning_metadata.yaml new file mode 100644 index 00000000..4694bd95 --- /dev/null +++ b/Examples/ml/mlqlearning/ml_q_learning_metadata.yaml @@ -0,0 +1,26 @@ +id: "ml_q_learning" +name: "ml q learning" +description: "Q-Learning Agent in BNGL" +contributors: + - name: "Achyudhan" +tags: ["ml", "q", "learning", "pos", "ql", "qr", "reward", "action"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ml_q_learning.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ml/mlsvm/metadata.yaml b/Examples/ml/mlsvm/metadata.yaml index fbef119f..c0579c82 100644 --- a/Examples/ml/mlsvm/metadata.yaml +++ b/Examples/ml/mlsvm/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ml", "svm", "w1", "w2", "b", "db_dt", "dw1_dt"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/ml/mlsvm/ml_svm_metadata.yaml b/Examples/ml/mlsvm/ml_svm_metadata.yaml new file mode 100644 index 00000000..8c376487 --- /dev/null +++ b/Examples/ml/mlsvm/ml_svm_metadata.yaml @@ -0,0 +1,26 @@ +id: "ml_svm" +name: "ml svm" +description: "Model: ml_svm.bngl" +contributors: + - name: "Achyudhan" +tags: ["ml", "svm", "w1", "w2", "b", "db_dt", "dw1_dt"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ml_svm.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/ml/nnxor/metadata.yaml b/Examples/ml/nnxor/metadata.yaml index d24d9c3c..ad16e4e1 100644 --- a/Examples/ml/nnxor/metadata.yaml +++ b/Examples/ml/nnxor/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["nn", "xor", "input", "hidden", "output", "target", "weightih", "weightho", "dopamine"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/ml/nnxor/nn_xor_metadata.yaml b/Examples/ml/nnxor/nn_xor_metadata.yaml new file mode 100644 index 00000000..09059e30 --- /dev/null +++ b/Examples/ml/nnxor/nn_xor_metadata.yaml @@ -0,0 +1,26 @@ +id: "nn_xor" +name: "nn xor" +description: "Model: nn_xor.bngl" +contributors: + - name: "Achyudhan" +tags: ["nn", "xor", "input", "hidden", "output", "target", "weightih", "weightho", "dopamine"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/nn_xor.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/nfsim/nfsimcoarsegraining/metadata.yaml b/Examples/nfsim/nfsimcoarsegraining/metadata.yaml index f3f98eb2..43f4cdaf 100644 --- a/Examples/nfsim/nfsimcoarsegraining/metadata.yaml +++ b/Examples/nfsim/nfsimcoarsegraining/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["nfsim", "coarse", "graining", "droplet"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining_metadata.yaml b/Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining_metadata.yaml new file mode 100644 index 00000000..73d68642 --- /dev/null +++ b/Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining_metadata.yaml @@ -0,0 +1,26 @@ +id: "nfsim_coarse_graining" +name: "nfsim coarse graining" +description: "Model: nfsim_coarse_graining.bngl" +contributors: + - name: "Achyudhan" +tags: ["nfsim", "coarse", "graining", "droplet"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/nfsim_coarse_graining.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/nfsim/nfsimdynamiccompartments/metadata.yaml b/Examples/nfsim/nfsimdynamiccompartments/metadata.yaml index 59272803..0a928d6d 100644 --- a/Examples/nfsim/nfsimdynamiccompartments/metadata.yaml +++ b/Examples/nfsim/nfsimdynamiccompartments/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["nfsim", "dynamic", "compartments", "cell", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments_metadata.yaml b/Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments_metadata.yaml new file mode 100644 index 00000000..28f1744a --- /dev/null +++ b/Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments_metadata.yaml @@ -0,0 +1,26 @@ +id: "nfsim_dynamic_compartments" +name: "nfsim dynamic compartments" +description: "Model: nfsim_dynamic_compartments.bngl" +contributors: + - name: "Achyudhan" +tags: ["nfsim", "dynamic", "compartments", "cell", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/nfsim_dynamic_compartments.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/nfsim/nfsimhybridparticlefield/metadata.yaml b/Examples/nfsim/nfsimhybridparticlefield/metadata.yaml index 8ea02e90..3a1738aa 100644 --- a/Examples/nfsim/nfsimhybridparticlefield/metadata.yaml +++ b/Examples/nfsim/nfsimhybridparticlefield/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["nfsim", "hybrid", "particle", "field"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field_metadata.yaml b/Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field_metadata.yaml new file mode 100644 index 00000000..77aabbde --- /dev/null +++ b/Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field_metadata.yaml @@ -0,0 +1,56 @@ +id: "nfsim_hybrid_particle_field" +name: "nfsim hybrid particle field" +description: "Model: nfsim_hybrid_particle_field.bngl" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["nfsim", "hybrid", "particle", "field"] + +date: + last_tested: 2026-07-02 + +biol_categories: ["other"] + +comp_categories: ["nfsim"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "ComponentStateDefinition 0 doesn't exist!" + simulation_methods: ["ode", "ssa", "nf"] + nfsim_compatible: true + molclustpy_compatible: true + comments: "false in original metadata.yaml but runs with bng2 and bngp" + +features: + uses_generate_network: true + default_sim_command: "nf" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/nfsim_hybrid_particle_field.bngl" + +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" + + diff --git a/Examples/nfsim/nfsimringclosurepolymer/metadata.yaml b/Examples/nfsim/nfsimringclosurepolymer/metadata.yaml index 4efa9d31..11d51ef4 100644 --- a/Examples/nfsim/nfsimringclosurepolymer/metadata.yaml +++ b/Examples/nfsim/nfsimringclosurepolymer/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["nfsim", "ring", "closure", "polymer", "a", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer_metadata.yaml b/Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer_metadata.yaml new file mode 100644 index 00000000..b90849c7 --- /dev/null +++ b/Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer_metadata.yaml @@ -0,0 +1,26 @@ +id: "nfsim_ring_closure_polymer" +name: "nfsim ring closure polymer" +description: "Model: nfsim_ring_closure_polymer.bngl" +contributors: + - name: "Achyudhan" +tags: ["nfsim", "ring", "closure", "polymer", "a", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/nfsim_ring_closure_polymer.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/physics/phlorenzattractor/metadata.yaml b/Examples/physics/phlorenzattractor/metadata.yaml index a7415cf3..d342a480 100644 --- a/Examples/physics/phlorenzattractor/metadata.yaml +++ b/Examples/physics/phlorenzattractor/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ph", "lorenz", "attractor", "lx", "ly", "lz", "x", "y"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/physics/phlorenzattractor/ph_lorenz_attractor_metadata.yaml b/Examples/physics/phlorenzattractor/ph_lorenz_attractor_metadata.yaml new file mode 100644 index 00000000..3cc0a3d7 --- /dev/null +++ b/Examples/physics/phlorenzattractor/ph_lorenz_attractor_metadata.yaml @@ -0,0 +1,26 @@ +id: "ph_lorenz_attractor" +name: "ph lorenz attractor" +description: "Lorenz Attractor in BNGL" +contributors: + - name: "Achyudhan" +tags: ["ph", "lorenz", "attractor", "lx", "ly", "lz", "x", "y"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ph_lorenz_attractor.bngl" +playground: + visible: false + gallery_categories: ["physics","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/physics/phnbodygravity/metadata.yaml b/Examples/physics/phnbodygravity/metadata.yaml index d1f1cd59..90544359 100644 --- a/Examples/physics/phnbodygravity/metadata.yaml +++ b/Examples/physics/phnbodygravity/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ph", "nbody", "gravity", "body", "r2"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/physics/phnbodygravity/ph_nbody_gravity_metadata.yaml b/Examples/physics/phnbodygravity/ph_nbody_gravity_metadata.yaml new file mode 100644 index 00000000..d948b708 --- /dev/null +++ b/Examples/physics/phnbodygravity/ph_nbody_gravity_metadata.yaml @@ -0,0 +1,26 @@ +id: "ph_nbody_gravity" +name: "ph nbody gravity" +description: "Model: ph_nbody_gravity.bngl" +contributors: + - name: "Achyudhan" +tags: ["ph", "nbody", "gravity", "body", "r2"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ph_nbody_gravity.bngl" +playground: + visible: false + gallery_categories: ["physics","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/physics/phschrodinger/metadata.yaml b/Examples/physics/phschrodinger/metadata.yaml index 44774d6d..4b377b98 100644 --- a/Examples/physics/phschrodinger/metadata.yaml +++ b/Examples/physics/phschrodinger/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ph", "schrodinger", "psi"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/physics/phschrodinger/ph_schrodinger_metadata.yaml b/Examples/physics/phschrodinger/ph_schrodinger_metadata.yaml new file mode 100644 index 00000000..966654d5 --- /dev/null +++ b/Examples/physics/phschrodinger/ph_schrodinger_metadata.yaml @@ -0,0 +1,26 @@ +id: "ph_schrodinger" +name: "ph schrodinger" +description: "Model: ph_schrodinger.bngl" +contributors: + - name: "Achyudhan" +tags: ["ph", "schrodinger", "psi"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ph_schrodinger.bngl" +playground: + visible: false + gallery_categories: ["physics","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/physics/phwaveequation/metadata.yaml b/Examples/physics/phwaveequation/metadata.yaml index 801db30a..b70b2fa0 100644 --- a/Examples/physics/phwaveequation/metadata.yaml +++ b/Examples/physics/phwaveequation/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["ph", "wave", "equation", "node"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/physics/phwaveequation/ph_wave_equation_metadata.yaml b/Examples/physics/phwaveequation/ph_wave_equation_metadata.yaml new file mode 100644 index 00000000..eada84cd --- /dev/null +++ b/Examples/physics/phwaveequation/ph_wave_equation_metadata.yaml @@ -0,0 +1,26 @@ +id: "ph_wave_equation" +name: "ph wave equation" +description: "Model: ph_wave_equation.bngl" +contributors: + - name: "Achyudhan" +tags: ["ph", "wave", "equation", "node"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/ph_wave_equation.bngl" +playground: + visible: false + gallery_categories: ["physics","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/processes/processactintreadmilling/metadata.yaml b/Examples/processes/processactintreadmilling/metadata.yaml index 63e8a9b2..c41e4a7a 100644 --- a/Examples/processes/processactintreadmilling/metadata.yaml +++ b/Examples/processes/processactintreadmilling/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["process", "actin", "treadmilling", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Examples/processes/processactintreadmilling/process_actin_treadmilling_metadata.yaml b/Examples/processes/processactintreadmilling/process_actin_treadmilling_metadata.yaml new file mode 100644 index 00000000..11201c8b --- /dev/null +++ b/Examples/processes/processactintreadmilling/process_actin_treadmilling_metadata.yaml @@ -0,0 +1,26 @@ +id: "process_actin_treadmilling" +name: "process actin treadmilling" +description: "Model: process_actin_treadmilling.bngl" +contributors: + - name: "Achyudhan" +tags: ["process", "actin", "treadmilling", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/process_actin_treadmilling.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/processes/processautophagyflux/metadata.yaml b/Examples/processes/processautophagyflux/metadata.yaml index 7321280b..a500b164 100644 --- a/Examples/processes/processautophagyflux/metadata.yaml +++ b/Examples/processes/processautophagyflux/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["process", "autophagy", "flux", "phagophore", "autophagosome", "lysosome", "autolysosome", "cargo"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/processes/processautophagyflux/process_autophagy_flux_metadata.yaml b/Examples/processes/processautophagyflux/process_autophagy_flux_metadata.yaml new file mode 100644 index 00000000..b2de868f --- /dev/null +++ b/Examples/processes/processautophagyflux/process_autophagy_flux_metadata.yaml @@ -0,0 +1,26 @@ +id: "process_autophagy_flux" +name: "process autophagy flux" +description: "Model: process_autophagy_flux.bngl" +contributors: + - name: "Achyudhan" +tags: ["process", "autophagy", "flux", "phagophore", "autophagosome", "lysosome", "autolysosome", "cargo"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/process_autophagy_flux.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/processes/processcelladhesionstrength/metadata.yaml b/Examples/processes/processcelladhesionstrength/metadata.yaml index b99e7435..53171d26 100644 --- a/Examples/processes/processcelladhesionstrength/metadata.yaml +++ b/Examples/processes/processcelladhesionstrength/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["process", "cell", "adhesion", "strength", "c1", "c2", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength_metadata.yaml b/Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength_metadata.yaml new file mode 100644 index 00000000..b9039871 --- /dev/null +++ b/Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength_metadata.yaml @@ -0,0 +1,26 @@ +id: "process_cell_adhesion_strength" +name: "process cell adhesion strength" +description: "Model: process_cell_adhesion_strength.bngl" +contributors: + - name: "Achyudhan" +tags: ["process", "cell", "adhesion", "strength", "c1", "c2", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/process_cell_adhesion_strength.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/processes/processkineticproofreadingtcr/metadata.yaml b/Examples/processes/processkineticproofreadingtcr/metadata.yaml index 9dad7e95..08c8a989 100644 --- a/Examples/processes/processkineticproofreadingtcr/metadata.yaml +++ b/Examples/processes/processkineticproofreadingtcr/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["process", "kinetic", "proofreading", "tcr", "l"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr_metadata.yaml b/Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr_metadata.yaml new file mode 100644 index 00000000..7f44d36f --- /dev/null +++ b/Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr_metadata.yaml @@ -0,0 +1,26 @@ +id: "process_kinetic_proofreading_tcr" +name: "process kinetic proofreading tcr" +description: "Model: process_kinetic_proofreading_tcr.bngl" +contributors: + - name: "Achyudhan" +tags: ["process", "kinetic", "proofreading", "tcr", "l"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/process_kinetic_proofreading_tcr.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/processes/processquorumsensingswitch/metadata.yaml b/Examples/processes/processquorumsensingswitch/metadata.yaml index 4db1b859..360a9234 100644 --- a/Examples/processes/processquorumsensingswitch/metadata.yaml +++ b/Examples/processes/processquorumsensingswitch/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["process", "quorum", "sensing", "switch", "gene_ai", "ai", "r", "gene_light"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch_metadata.yaml b/Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch_metadata.yaml new file mode 100644 index 00000000..c38ace9e --- /dev/null +++ b/Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch_metadata.yaml @@ -0,0 +1,26 @@ +id: "process_quorum_sensing_switch" +name: "process quorum sensing switch" +description: "Model: process_quorum_sensing_switch.bngl" +contributors: + - name: "Achyudhan" +tags: ["process", "quorum", "sensing", "switch", "gene_ai", "ai", "r", "gene_light"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/process_quorum_sensing_switch.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/signal-processing/spfouriersynthesizer/metadata.yaml b/Examples/signal-processing/spfouriersynthesizer/metadata.yaml index f8fa0acd..2cd43f0b 100644 --- a/Examples/signal-processing/spfouriersynthesizer/metadata.yaml +++ b/Examples/signal-processing/spfouriersynthesizer/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["sp", "fourier", "synthesizer", "s1", "s3", "s5", "s7", "s9", "wave", "c1"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer_metadata.yaml b/Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer_metadata.yaml new file mode 100644 index 00000000..41ed74d6 --- /dev/null +++ b/Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer_metadata.yaml @@ -0,0 +1,26 @@ +id: "sp_fourier_synthesizer" +name: "sp fourier synthesizer" +description: "Fourier Series Synthesizer in BNGL" +contributors: + - name: "Achyudhan" +tags: ["sp", "fourier", "synthesizer", "s1", "s3", "s5", "s7", "s9", "wave", "c1"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/sp_fourier_synthesizer.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/signal-processing/spimageconvolution/metadata.yaml b/Examples/signal-processing/spimageconvolution/metadata.yaml index d9560f02..1f3d6b5e 100644 --- a/Examples/signal-processing/spimageconvolution/metadata.yaml +++ b/Examples/signal-processing/spimageconvolution/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["sp", "image", "convolution", "px", "ex", "sink"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/signal-processing/spimageconvolution/sp_image_convolution_metadata.yaml b/Examples/signal-processing/spimageconvolution/sp_image_convolution_metadata.yaml new file mode 100644 index 00000000..8de4c0d9 --- /dev/null +++ b/Examples/signal-processing/spimageconvolution/sp_image_convolution_metadata.yaml @@ -0,0 +1,26 @@ +id: "sp_image_convolution" +name: "sp image convolution" +description: "Image Convolution Filter in BNGL" +contributors: + - name: "Achyudhan" +tags: ["sp", "image", "convolution", "px", "ex", "sink"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/sp_image_convolution.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/signal-processing/spkalmanfilter/metadata.yaml b/Examples/signal-processing/spkalmanfilter/metadata.yaml index 92045178..debba696 100644 --- a/Examples/signal-processing/spkalmanfilter/metadata.yaml +++ b/Examples/signal-processing/spkalmanfilter/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["sp", "kalman", "filter", "truex", "obs", "estx", "estv", "variance", "innovation"] category: "computer-science" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/signal-processing/spkalmanfilter/sp_kalman_filter_metadata.yaml b/Examples/signal-processing/spkalmanfilter/sp_kalman_filter_metadata.yaml new file mode 100644 index 00000000..9f404bc0 --- /dev/null +++ b/Examples/signal-processing/spkalmanfilter/sp_kalman_filter_metadata.yaml @@ -0,0 +1,26 @@ +id: "sp_kalman_filter" +name: "sp kalman filter" +description: "Kalman Filter in BNGL" +contributors: + - name: "Achyudhan" +tags: ["sp", "kalman", "filter", "truex", "obs", "estx", "estv", "variance", "innovation"] +category: "computer-science" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/sp_kalman_filter.bngl" +playground: + visible: false + gallery_categories: ["ml-signal","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/synbio/synbiobandpassfilter/metadata.yaml b/Examples/synbio/synbiobandpassfilter/metadata.yaml index 7826482d..5ea2079c 100644 --- a/Examples/synbio/synbiobandpassfilter/metadata.yaml +++ b/Examples/synbio/synbiobandpassfilter/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["synbio", "band", "pass", "filter", "i", "a", "r", "out"] category: "synthetic-biology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter_metadata.yaml b/Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter_metadata.yaml new file mode 100644 index 00000000..30dc4922 --- /dev/null +++ b/Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter_metadata.yaml @@ -0,0 +1,26 @@ +id: "synbio_band_pass_filter" +name: "synbio band pass filter" +description: "Model: synbio_band_pass_filter.bngl" +contributors: + - name: "Achyudhan" +tags: ["synbio", "band", "pass", "filter", "i", "a", "r", "out"] +category: "synthetic-biology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/synbio_band_pass_filter.bngl" +playground: + visible: false + gallery_categories: ["synbio","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/synbio/synbiocountermolecular/metadata.yaml b/Examples/synbio/synbiocountermolecular/metadata.yaml index e19dc1ea..2484c02a 100644 --- a/Examples/synbio/synbiocountermolecular/metadata.yaml +++ b/Examples/synbio/synbiocountermolecular/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["synbio", "counter", "molecular", "state", "input"] category: "synthetic-biology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/synbio/synbiocountermolecular/synbio_counter_molecular_metadata.yaml b/Examples/synbio/synbiocountermolecular/synbio_counter_molecular_metadata.yaml new file mode 100644 index 00000000..6960b553 --- /dev/null +++ b/Examples/synbio/synbiocountermolecular/synbio_counter_molecular_metadata.yaml @@ -0,0 +1,26 @@ +id: "synbio_counter_molecular" +name: "synbio counter molecular" +description: "Model: synbio_counter_molecular.bngl" +contributors: + - name: "Achyudhan" +tags: ["synbio", "counter", "molecular", "state", "input"] +category: "synthetic-biology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/synbio_counter_molecular.bngl" +playground: + visible: false + gallery_categories: ["synbio","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/synbio/synbioedgedetector/metadata.yaml b/Examples/synbio/synbioedgedetector/metadata.yaml index 0c782e2b..b61c2040 100644 --- a/Examples/synbio/synbioedgedetector/metadata.yaml +++ b/Examples/synbio/synbioedgedetector/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["synbio", "edge", "detector", "x", "y", "z"] category: "synthetic-biology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/synbio/synbioedgedetector/synbio_edge_detector_metadata.yaml b/Examples/synbio/synbioedgedetector/synbio_edge_detector_metadata.yaml new file mode 100644 index 00000000..ac28fdde --- /dev/null +++ b/Examples/synbio/synbioedgedetector/synbio_edge_detector_metadata.yaml @@ -0,0 +1,26 @@ +id: "synbio_edge_detector" +name: "synbio edge detector" +description: "Model: synbio_edge_detector.bngl" +contributors: + - name: "Achyudhan" +tags: ["synbio", "edge", "detector", "x", "y", "z"] +category: "synthetic-biology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/synbio_edge_detector.bngl" +playground: + visible: false + gallery_categories: ["synbio","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/synbio/synbiologicgatesenzymatic/metadata.yaml b/Examples/synbio/synbiologicgatesenzymatic/metadata.yaml index d03229d1..ffb0d27e 100644 --- a/Examples/synbio/synbiologicgatesenzymatic/metadata.yaml +++ b/Examples/synbio/synbiologicgatesenzymatic/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["synbio", "logic", "gates", "enzymatic", "i1", "i2", "gateand", "gateor", "outand", "outor"] category: "synthetic-biology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic_metadata.yaml b/Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic_metadata.yaml new file mode 100644 index 00000000..c29b8e1c --- /dev/null +++ b/Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic_metadata.yaml @@ -0,0 +1,26 @@ +id: "synbio_logic_gates_enzymatic" +name: "synbio logic gates enzymatic" +description: "Model: synbio_logic_gates_enzymatic.bngl" +contributors: + - name: "Achyudhan" +tags: ["synbio", "logic", "gates", "enzymatic", "i1", "i2", "gateand", "gateor", "outand", "outor"] +category: "synthetic-biology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/synbio_logic_gates_enzymatic.bngl" +playground: + visible: false + gallery_categories: ["synbio","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/synbio/synbiooscillatorsynchronization/metadata.yaml b/Examples/synbio/synbiooscillatorsynchronization/metadata.yaml index 04ac40d1..f4f606f0 100644 --- a/Examples/synbio/synbiooscillatorsynchronization/metadata.yaml +++ b/Examples/synbio/synbiooscillatorsynchronization/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["synbio", "oscillator", "synchronization", "osc1", "osc2", "signal"] category: "synthetic-biology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization_metadata.yaml b/Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization_metadata.yaml new file mode 100644 index 00000000..46fbf624 --- /dev/null +++ b/Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization_metadata.yaml @@ -0,0 +1,26 @@ +id: "synbio_oscillator_synchronization" +name: "synbio oscillator synchronization" +description: "Model: synbio_oscillator_synchronization.bngl" +contributors: + - name: "Achyudhan" +tags: ["synbio", "oscillator", "synchronization", "osc1", "osc2", "signal"] +category: "synthetic-biology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/synbio_oscillator_synchronization.bngl" +playground: + visible: false + gallery_categories: ["synbio","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/wacky/wackyalchemystone/metadata.yaml b/Examples/wacky/wackyalchemystone/metadata.yaml index ed32f38a..4928d6d8 100644 --- a/Examples/wacky/wackyalchemystone/metadata.yaml +++ b/Examples/wacky/wackyalchemystone/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["wacky", "alchemy", "stone", "lead", "gold"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/wacky/wackyalchemystone/wacky_alchemy_stone_metadata.yaml b/Examples/wacky/wackyalchemystone/wacky_alchemy_stone_metadata.yaml new file mode 100644 index 00000000..96bd7935 --- /dev/null +++ b/Examples/wacky/wackyalchemystone/wacky_alchemy_stone_metadata.yaml @@ -0,0 +1,26 @@ +id: "wacky_alchemy_stone" +name: "wacky alchemy stone" +description: "Model: wacky_alchemy_stone.bngl" +contributors: + - name: "Achyudhan" +tags: ["wacky", "alchemy", "stone", "lead", "gold"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/wacky_alchemy_stone.bngl" +playground: + visible: false + gallery_categories: ["synbio","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/wacky/wackyblackhole/metadata.yaml b/Examples/wacky/wackyblackhole/metadata.yaml index c8c34c65..d6de7dc6 100644 --- a/Examples/wacky/wackyblackhole/metadata.yaml +++ b/Examples/wacky/wackyblackhole/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["wacky", "black", "hole", "m", "bh", "k_accrete", "k_evap"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/wacky/wackyblackhole/wacky_black_hole_metadata.yaml b/Examples/wacky/wackyblackhole/wacky_black_hole_metadata.yaml new file mode 100644 index 00000000..f45c016c --- /dev/null +++ b/Examples/wacky/wackyblackhole/wacky_black_hole_metadata.yaml @@ -0,0 +1,26 @@ +id: "wacky_black_hole" +name: "wacky black hole" +description: "Model: wacky_black_hole.bngl" +contributors: + - name: "Achyudhan" +tags: ["wacky", "black", "hole", "m", "bh", "k_accrete", "k_evap"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/wacky_black_hole.bngl" +playground: + visible: false + gallery_categories: ["test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/wacky/wackybouncingball/metadata.yaml b/Examples/wacky/wackybouncingball/metadata.yaml index e68148e0..928192be 100644 --- a/Examples/wacky/wackybouncingball/metadata.yaml +++ b/Examples/wacky/wackybouncingball/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["wacky", "bouncing", "ball", "height", "velocity"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/wacky/wackybouncingball/wacky_bouncing_ball_metadata.yaml b/Examples/wacky/wackybouncingball/wacky_bouncing_ball_metadata.yaml new file mode 100644 index 00000000..87146c6e --- /dev/null +++ b/Examples/wacky/wackybouncingball/wacky_bouncing_ball_metadata.yaml @@ -0,0 +1,26 @@ +id: "wacky_bouncing_ball" +name: "wacky bouncing ball" +description: "Model: wacky_bouncing_ball.bngl" +contributors: + - name: "Achyudhan" +tags: ["wacky", "bouncing", "ball", "height", "velocity"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/wacky_bouncing_ball.bngl" +playground: + visible: false + gallery_categories: ["physics","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/wacky/wackytrafficjamasep/metadata.yaml b/Examples/wacky/wackytrafficjamasep/metadata.yaml index 157fa147..f0832c8f 100644 --- a/Examples/wacky/wackytrafficjamasep/metadata.yaml +++ b/Examples/wacky/wackytrafficjamasep/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["wacky", "traffic", "jam", "asep", "site", "car", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep_metadata.yaml b/Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep_metadata.yaml new file mode 100644 index 00000000..3c39f9cb --- /dev/null +++ b/Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep_metadata.yaml @@ -0,0 +1,26 @@ +id: "wacky_traffic_jam_asep" +name: "wacky traffic jam asep" +description: "Model: wacky_traffic_jam_asep.bngl" +contributors: + - name: "Achyudhan" +tags: ["wacky", "traffic", "jam", "asep", "site", "car", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/wacky_traffic_jam_asep.bngl" +playground: + visible: false + gallery_categories: ["physics","test-models"] + featured: false + difficulty: "advanced" diff --git a/Examples/wacky/wackyzombieinfection/metadata.yaml b/Examples/wacky/wackyzombieinfection/metadata.yaml index 39a91d91..bd497327 100644 --- a/Examples/wacky/wackyzombieinfection/metadata.yaml +++ b/Examples/wacky/wackyzombieinfection/metadata.yaml @@ -6,6 +6,7 @@ contributors: tags: ["wacky", "zombie", "infection", "human"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Examples/wacky/wackyzombieinfection/wacky_zombie_infection_metadata.yaml b/Examples/wacky/wackyzombieinfection/wacky_zombie_infection_metadata.yaml new file mode 100644 index 00000000..81d5a6aa --- /dev/null +++ b/Examples/wacky/wackyzombieinfection/wacky_zombie_infection_metadata.yaml @@ -0,0 +1,26 @@ +id: "wacky_zombie_infection" +name: "wacky zombie infection" +description: "Model: wacky_zombie_infection.bngl" +contributors: + - name: "Achyudhan" +tags: ["wacky", "zombie", "infection", "human"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "ai-generated" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "example-models/wacky_zombie_infection.bngl" +playground: + visible: false + gallery_categories: ["ecology","test-models"] + featured: false + difficulty: "advanced" diff --git a/Published/.DS_Store b/Published/.DS_Store index b9fe5cb2..77f1c569 100644 Binary files a/Published/.DS_Store and b/Published/.DS_Store differ diff --git a/Published/An2009/An2009_aigenerated.md b/Published/An2009/An2009_aigenerated.md new file mode 100644 index 00000000..62069c26 --- /dev/null +++ b/Published/An2009/An2009_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: An 2009 + +## One-sentence summary + +Toll-like receptor 4 signaling from LPS recognition to NF-kB-driven inflammatory gene expression. + +## What the model shows + +This model shows how an LPS stimulus can be assembled on CD14, MD2, and TLR4, then routed through TRAM/TRIF and MAL/MyD88 adaptor arms to activate TAK1, the IKK complex, and NF-kB. It also shows feedback through newly produced A20 and IkB, so the inflammatory response is not simply turned on but is later restrained. + +## Biological story + +An 2009 is best read as a receptor-to-transcription cascade. It begins with microbial LPS recognition, passes through two adaptor routes, and ends with NF-kB-dependent inflammatory outputs that are later restrained by the very genes NF-kB helps induce. + +## Main biological players + +LPS, CD14, MD2, TLR4, TRAM, TRIF, MAL, MyD88, IRAK1, IRAK4, TRAF6, TAK1, IKK complex, NF-kB, IkB, A20, TNF. + +## Mechanism in plain English + +LPS is first captured by MD2 and CD14 and presented to TLR4. TLR4 complexes recruit TRAM/TRIF or MAL/MyD88 adaptors, which gather kinases and adaptor proteins such as IRAK and TRAF6. These assemblies activate TAK1 and then the IKK complex. Active IKK promotes release and activation of NF-kB, allowing NF-kB to enter the nucleus and drive transcription of inflammatory outputs such as TNF and regulatory outputs such as A20 and IkB. A20 and IkB then provide negative feedback by breaking signaling complexes, turning off IKK activity, recapturing NF-kB, or promoting degradation of signaling intermediates. + +## Key modeled events + +- LPS is assembled with CD14 and MD2 before engaging TLR4, so receptor activation depends on coreceptor-mediated ligand presentation. +- TLR4 complexes branch through TRAM/TRIF and MAL/MyD88 adaptor routes, allowing the same stimulus to feed multiple inflammatory signaling arms. +- IKK-driven NF-kB activation is countered by A20 and IkB feedback, so the model can show both signal rise and signal shutoff. + +## What the model measures + +The readouts follow TNF production, activated TAK1, activated IKK, A20 abundance, nuclear/active NF-kB, and NF-kB bound to IkB. A biologist should read the plots as a timed inflammatory signaling response with built-in delayed negative feedback. + +## Expected behavior in plots + +The most informative plots would show an early rise in TAK1 and IKK activity, followed by NF-kB activation and later accumulation of TNF, A20, and IkB. A20 or IkB rising after NF-kB indicates delayed negative feedback rather than a separate stimulus. + +## Caveats + +This summary treats the model as a pathway-level TLR4/NF-kB explanation. It does not claim that every possible TLR4 adaptor, cytokine, or cell-type-specific regulator is represented. diff --git a/Published/An2009/An2009_aigenerated_detailed.md b/Published/An2009/An2009_aigenerated_detailed.md new file mode 100644 index 00000000..e4c19c70 --- /dev/null +++ b/Published/An2009/An2009_aigenerated_detailed.md @@ -0,0 +1,103 @@ +# Detailed Model Explanation: An 2009 TLR4 Signaling + +## 1. Model overview + +This model represents lipopolysaccharide (LPS) assembly with CD14, MD2, and Toll-like receptor 4 (TLR4), followed by parallel TRIF- and MyD88-associated routes to TAK1, IKK, and NF-κB activation. Nuclear NF-κB drives TNF, A20, and IκB expression; A20 dismantles upstream signaling complexes, while IκB recaptures NF-κB and terminates promoter occupancy. + +## 2. BNGL block inventory + +The model has 97 parameters, 31 molecule types, 19 seed species, 41 active reaction rules, 19 molecule-count observables, and 7 actions. It contains no functions, compartments, or anchors; localization and activity are represented by internal states. + +## 3. Parameters, functions, and rate laws + +The parameter namespace is largely process-descriptive: association/dissociation pairs build receptor and adaptor complexes, catalytic constants change activation or transcription states, and `*_Init` names define starting pools. Active rules use mass-action rate laws; several declared zero-valued degradation rates intentionally make activated intermediates persistent except where a separate deactivation rule exists. + +| Parameter group or names | Function in this model | +| --- | --- | +| `LPS_MD2_*`, `LPS_CD14_*`, `CD14_MD2_*`, `LPS_TLR4_*`, `CD14_TLR4_*`, `MD2_TLR4_*`, `TLR4_Complex_Dimer_*` | Association/dissociation constants for ordered construction and dimerization of the ligand-loaded receptor assembly. Only the binding members used by rules contribute to the active forward assembly. | +| `TLR4_TRAM_*`, `TLR4TRAM_TRIF_*`, `RP1_TRIF_*`, `TRIF_TRAF6_*`, `RP1_TRAF6_*`, `TRAF6_TRIF_*` | Control recruitment in the TRAM–TRIF–RIP1/TRAF6 branch downstream of the receptor dimer. | +| `TLR4_MAL_*`, `TLR4MAL_MyD88_*`, `MyD88_IRAK4_*`, `MyD88_IRAK1_*`, `IRAK1_IRAK4_*`, `MyD88IRAK1_TRAF6_*`, `TRAF6_MyD88IRAK1_*` | Define assembly of the MAL–MyD88–IRAK–TRAF6 branch. The active rules build a preassembled MyD88/IRAK complex before receptor recruitment. | +| `TRAF6TRIF_TAK1_Activate`, `MyD88IRAK1TRAF6_TAK1_Activate`, `TAK1_Ikk_Complex_Activate` | Catalytic rates connecting either adaptor branch to TAK1 and then to the IKK complex. | +| `TAK1_Deactivation`, `Ikk_Deactivation`, `TAK1_Degradation`, `Ikk_Degradation_Rate` | Control termination of kinase activity. The two degradation parameters are zero, and `Ikk_Deactivation` is also zero in the supplied parameterization. | +| `Ikk_complex_IkB_Phos`, `IkB_Proteasome23_Degrade`, `IkB_DegradeNFkB`, `NFkB_IkB_Bind`, `NFkB_IkB_Unbind` | Govern IKK-dependent phosphorylation of complexed IκB, proteasome recruitment/release, and cytoplasmic NF-κB inhibition. | +| `NFkB_Translocation_Nucleus`, `NFkB_DNA_A20_*`, `NFkB_DNA_TNF_*`, `NFkB_DNA_IkB_*` | Control nuclear entry and NF-κB engagement of the three explicitly active promoters. | +| `A20_Transcription_Execute`, `TNF_Transcription_Execute`, `IkB_Transcription_Execute`; corresponding `*_Translation_Execute` | Create the three mRNAs from promoter-bound NF-κB and their protein products from translation-enabled transcripts. | +| `A20_MyD88IRAK1TRAF6_Degrade`, `A20_TRAF6TRIFRP1_Degrade`, `A20_IkkAct_Deactivate` | Implement catalytic A20 feedback by breaking either upstream adaptor complex or changing active IKK to inactive. The declared `A20_TRAF6_Bind/Unbind` pair is not used by an active rule. | +| `TNF_Degrade`, `A20_Degrade` | Set output and feedback-protein turnover. | +| `CD14_Init` through `p50_Init`, `IkB_Init`, `NFkB_Inactive_Cytoplasm`, `DNA`, `LPS_Init`, `A20_Init`, `A20_Preconditioned` | Establish receptor/adaptor/enzyme pools, the initial inhibited NF-κB pool, two DNA templates, the post-equilibration LPS dose, and initial A20 status. | +| `p65_p50_Bind`, `p65_p50_Unbind` | Declared but unused: p65 and p50 are represented as sites on NF-κB/IκB rather than separate molecule types. | + +There are no active functions; all context dependence is expressed by rule patterns and ordinary parameters. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `LPS`, `CD14`, `MD2`, `TLR4` | 4; 3; 3; 6 | LPS: `MD2`, `TLR4`, `CD14`, `LPS`; CD14: `TLR4`, `MD2`, `LPS`; MD2: `CD14`, `TLR4`, `LPS`; TLR4: `MAL`, `TRAM`, `TLR4`, `CD14`, `MD2`, `LPS` | None | None | Form the ligand-recognition complex and receptor dimer that exposes the two downstream adaptor routes. | +| `TRAM`, `TRIF` | 2; 5 | TRAM: `TLR4`, `TRIF`; TRIF: `TRAM`, `TRAF6`, `RIP1`, `TRAF4`, `SARM` | None | None | Receptor-proximal and hub adaptors for the TRIF-side signal. | +| `RP1`, `TRAF6` | 4; 8 | RP1: `TRIF`, `TRAF6`, `TAK1`, `p38`; TRAF6: `IRAK1`, `TRIF`, `RP1`, `TAK1`, `TRAF4`, `A20`, `JNK`, `p38` | None | None | RP1 (used as the RIP1-like participant) and TRAF6 assemble the TRIF activation complex; TRAF6 also links the MyD88 route to TAK1 and receives A20 feedback. | +| `MAL`, `MyD88`, `IRAK4`, `IRAK1` | 3; 4; 3; 4 | MAL: `TLR4`, `MyD88`, `SOCS1`; MyD88: `MAL`, `IRAK1`, `IRAK4`, `MyD88s`; IRAK4: `Myd88`, `IRAKM`, `IRAK1`; IRAK1: `IRAK4`, `MyD88`, `Tollip`, `TRAF6` | None | None | Build the alternative receptor-to-TRAF6 complex; note the differently capitalized `Myd88` site on IRAK4. | +| `SARM`, `TRAF4`, `Tollip`, `IRAKM`, `MyD88s` | 1; 3; 1; 1; 2 | SARM: `TRIF`; TRAF4: `TRAF6`, `TAK1`, `TRIF`; Tollip: `IRAK1`; IRAKM: `IRAK4`; MyD88s: `MyD88`, `IRAK1` | None | None | Declared regulatory alternatives whose sites define possible interactions, but none participates in an active rule. | +| `TAK1`, `Ikk_Complex` | 2; 1 | TAK1: `TRAF6`, `Activation`; IKK: `Activation` | `Activation`: `No`, `Yes` | None | Successive kinase switches that carry either upstream branch into IκB control. | +| `NFkB` | 3 | `Transcription`, `Activation`, `Location` | transcription `No/Yes`; activation `No/Yes`; location `Cytoplasm/Nucleus` | None | Encodes free/inhibited status, nuclear transport, and promoter engagement in one molecule. | +| `IkB` | 4 | `Phos`, `p65`, `p50`, `Degrade` | phosphorylation `No/Yes`; degradation mark `No/Yes` | None | Inhibitor bound to NF-κB through two contacts, phosphorylated by IKK and processed through a proteasome-bound degradation state. | +| `Proteasome26s` | 1 | `IkB` | None | None | Binds phosphorylated IκB and participates in NF-κB release. | +| `DNA` | 7 | `A20`, `TNF`, `iNOS`, `IL10`, `IkB`, `c`, `c` | None | None | Shared promoter scaffold; only A20, TNF, and IκB sites are used by active rules. The repeated `c` sites remain unused. | +| `TNFmRNA`, `A20mRNA`, `iNOSmRNA`, `IkBmRNA` | 1 each | `Translation` | `On`, `Off` | None | Transcript switches; TNF, A20, and IκB transcripts are active, whereas iNOS mRNA is declared but unused. | +| `TNF`, `A20` | 1 each | TNF: `TNFr`; A20: `TRAF6` | None | None | TNF is the modeled output; A20 is the induced negative-feedback effector. | +| `Trash`, `Administer` | 1 each | `c` | None | None | Trash is the degradation sink; Administer is declared but unused. | + +## 5. Compartments, anchors, initial species, and setup + +No compartments or anchors are declared. Before stimulation, receptor components and most adaptors/kinases are seeded as large free pools, the shared DNA scaffold begins unoccupied, and NF-κB begins in a cytoplasmic IκB-bound complex. A20 and output transcripts start absent. Although `LPS_Init` is 100, the action sequence temporarily sets free LPS to zero for equilibration and restores that dose only before the response simulation. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–7 assemble the LPS receptor and TRIF-side TAK1 trigger, rules 8–17 build the MyD88-side trigger and its A20-sensitive disassembly, rules 18–23 add expression and IKK control, and rules 24–41 form the NF-κB promoter cycle and its induced negative feedback. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–4 | Reversible | `LPS`, `MD2`, `CD14`, `TLR4` recognition sites | Sequentially creates LPS–MD2, adds CD14, adds TLR4 through its LPS/CD14/MD2 sites, then joins two loaded TLR4 complexes through their receptor-dimer sites, using the corresponding bind/unbind pairs. | Constructs the dimeric stimulus receptor required by both adaptor branches. | +| 5–7 | Reversible then one-way | Dimeric `TLR4.TRAM`; `TRAM.TRIF`; `TRIF.TRAF6`; `TAK1.Activation` | TRAM and TRIF bind reversibly (5–6); when TRAF6 is present on TRIF, rule 7 catalytically changes TAK1 `No→Yes`. | Provides the compact TRIF-side route to TAK1 activation. | +| 8–9 | Reversible | `MyD88.IRAK4/IRAK1`, reciprocal IRAK sites | MyD88 first binds IRAK4, then recruits IRAK1 into the same complex with the named association/dissociation rates. | Preassembles the MyD88 signaling unit before receptor engagement. | +| 10–11 | One-way | `TNFmRNA.Translation=On`, `A20mRNA.Translation=On` | Changes the relevant transcript from `On` to `Off` while creating TNF or A20 at its translation rate. | Produces one protein per transcription-created translation opportunity, rather than making each mRNA continuously catalytic. | +| 12 | One-way | Active `TAK1` | Sends active TAK1 to `Trash` at the declared TAK1 degradation rate, which is zero in this parameterization. | Provides a nominal degradation route that is kinetically disabled. | +| 13–15 | Reversible | Dimeric `TLR4.MAL`; `MAL.MyD88`; `IRAK1.TRAF6` | MAL binds the second TLR4, recruits the preassembled MyD88–IRAK complex, and TRAF6 binds IRAK1. | Completes the MyD88-side TAK1 activation platform. | +| 16 | One-way | Free `A20`; TRAF6-bound `IRAK1` | In A20's presence, the IRAK1–TRAF6 connection is lost at `A20_MyD88IRAK1TRAF6_Degrade`; A20 remains free and the other adaptor bonds are retained. | Interrupts the MyD88 branch upstream of TAK1 without consuming or binding the feedback regulator. | +| 17 | One-way | MyD88/IRAK1-bound `TRAF6`; `TAK1.Activation` | Catalytically changes TAK1 `No→Yes` at the MyD88-branch activation rate. | Converges the second receptor branch on the shared kinase. | +| 18 | One-way | `IkBmRNA.Translation=On` | Changes the transcript to `Off` while creating unphosphorylated, undegraded IκB at its translation rate. | Replenishes the inhibitor once per transcription-created translation opportunity. | +| 19–20 | Reversible | `TRIF.RIP1`, `RP1.TRIF/TRAF6`, `TRAF6.TRIF/RP1` | Adds RP1 to TRIF, then creates two coordinated contacts from TRAF6 to TRIF and RP1. | Builds the higher-order TRIF complex used for A20-sensitive feedback. | +| 21–22 | One-way | Free A20; active IKK or TRIF–RP1–TRAF6 complex | A20 changes IKK `Yes→No` (21) or breaks both TRAF6 contacts to TRIF/RP1 (22); in both cases A20 is carried through as a free catalyst. | Applies reusable negative feedback at both kinase and adaptor levels. | +| 23 | One-way | Active `Ikk_Complex`; NF-κB-bound `IkB.Phos` | Catalytically changes IκB phosphorylation `No→Yes` without breaking its two NF-κB contacts. | Marks the inhibitor in the inactive NF-κB complex for proteasomal processing. | +| 24 | Reversible | Active, non-transcribing `NFkB.Location` | Moves free active NF-κB between cytoplasm and nucleus using nuclear translocation and reverse rates. | Makes promoter access contingent on liberation and nuclear entry. | +| 25–28 | Reversible | Nuclear active `NFkB.Transcription`; DNA `A20`, `TNF`, or `IkB`; IκB sites | NF-κB binds A20, TNF, and IκB promoter sites and changes `Transcription No→Yes` (25,27,28). Rule 26 lets unphosphorylated IκB remove NF-κB from the A20 promoter, changes NF-κB to inactive/cytoplasmic, and creates both IκB contacts. | Initiates three feedback genes and demonstrates promoter stripping by newly made inhibitor. | +| 29 | One-way | Phosphorylated NF-κB-bound IκB; `Proteasome26s.IkB` | Proteasome binding changes IκB's degradation mark `No→Yes`, breaks both IκB–NF-κB contacts, and leaves NF-κB active in cytoplasm. | Releases the NF-κB signal carrier after IKK-dependent inhibitor phosphorylation. | +| 30–31 | One-way | Cytoplasmic active NF-κB; unphosphorylated IκB; proteasome-bound marked IκB | Rule 30 forms the two-contact inactive NF-κB–IκB complex; rule 31 releases proteasome from degradation-marked IκB at the proteasome-processing rate. | Closes the inhibition cycle and recycles proteasome. | +| 32–34 | One-way | Promoter-bound transcribing NF-κB; `DNA.IkB/A20/TNF` | Retains each DNA–NF-κB complex and creates the matching translation-enabled mRNA at its transcription-execution rate. | Converts promoter occupancy into inducible feedback/output transcripts. | +| 35–37 | One-way | `TAK1.Activation`, `Ikk_Complex.Activation` | Rules 35–36 change active TAK1 or IKK to inactive at their deactivation rates; rule 37 uses active TAK1 catalytically to change IKK `No→Yes`. | Couples the kinase stages and supplies their explicit off transitions, although IKK deactivation is parameterized at zero. | +| 38–39 | One-way | `TNF`, `A20` | Sends each protein to `Trash` at its degradation rate. | Limits output and feedback persistence. | +| 40–41 | One-way | IκB; NF-κB bound to DNA `IkB` or `TNF` | IκB strips NF-κB from the indicated promoter, changes it to inactive/cytoplasmic, and forms both inhibitor contacts. | Extends the same shutdown mechanism as rule 26 to the IκB and TNF promoters. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `Activated_TAK1`, `Activated_Ikk_complex` | Molecule count | TAK1 and IKK in activation state `Yes`. | Report convergence of the two adaptor branches and transmission to the inhibitor-processing stage. | +| `NFkB_Active_Cyto`, `NFkB_Active_Nucleus`, `Unbound_Cyto_NFkB` | Molecule count | Free/non-transcribing active NF-κB by location, plus all unbound cytoplasmic NF-κB activation states. | Separate the signaling-competent nuclear pool from a broader cytoplasmic pool. | +| `NFkB_Inactive`, `Inactive_Cyto_NFkB` | Molecule count | NF-κB with at least one bond and the specifically two-contact cytoplasmic IκB complex. | The broad first pattern can count bound contexts beyond the canonical inactive complex. | +| `Phos_IkB_NFkB`, `IkB_Prot26s`, `IkB_Degraded` | Molecule count | Phosphorylated NF-κB–IκB complex, proteasome-bound marked IκB, and all degradation-marked IκB. | Resolve successive stages of inhibitor processing and NF-κB release. | +| `IkB_active`, `NonBoundNonPhos_IkB`, `IkBmRNA_Off` | Molecule count | Undegraded IκB, free unphosphorylated IκB, and translation-disabled IκB transcript. | Distinguish the total usable inhibitor pool from the immediately binding-competent subset. | +| `NFkB_DNA_IkB`, `TNF_NFkB_DNA`, `A20_NFkB_DNA` | Molecule count | NF-κB bound at each active promoter. | Direct readouts of transcriptionally engaged DNA complexes. | +| `TNFmRNA_Off`, `TNF`, `A20` | Molecule count | Translation-disabled TNF transcript and the two produced proteins. | Track the inflammatory output alongside its induced A20 brake. | + +## 8. Actions and simulation workflow + +After network generation, the workflow removes free LPS and integrates the ODE system toward a steady state for 50,000 time units. It then restores LPS to `LPS_Init`, exports SBML and MATLAB representations of that stimulated setup, and simulates the response for 100,000 time units with 500 output steps. + +## 9. Technical caveats and ambiguities + +- Several declared regulators (`SARM`, `TRAF4`, `Tollip`, `IRAKM`, `MyD88s`) and the iNOS/IL10 DNA sites have no active rules, so the executable network is narrower than the molecule declarations suggest. +- The source uses `RP1` while its sites and surrounding labels indicate a RIP1-like role; this explanation preserves the declared molecule name rather than resolving that naming ambiguity. +- `TAK1_Degradation`, `Ikk_Degradation_Rate`, and `Ikk_Deactivation` are zero, making their associated active rules kinetically silent under the supplied parameters. +- NF-κB inhibition is encoded with two IκB contacts. Broad bond-wildcard observables can count any matching bound embedding and should not automatically be equated with unique canonical complexes. +- Nuclear and cytoplasmic labels are NF-κB states rather than BNGL compartments, so transport changes state without spatial volume semantics. diff --git a/Published/An2009/An_2009_metadata.yaml b/Published/An2009/An_2009_metadata.yaml new file mode 100644 index 00000000..24b478ed --- /dev/null +++ b/Published/An2009/An_2009_metadata.yaml @@ -0,0 +1,67 @@ +id: "An_2009" +name: "An 2009" +description: "TLR4 signaling" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +citation: + year: "2009" + pmid: "18835283" + reference: "An & Faeder, 2009" + +tags: ["published", "immunology", "an", "2009", "cd14", "md2", "tlr4", "tram", "trif", "sarm", "traf4", "irak1"] +date: + last_tested: 2026-07-14 + +category: "immunology" +biol_categories: ["immunology"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered ! at line 183" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: false + comments: "nfsim did not run successfully at line 242 I can only handle a site that has 0 or 1 bonds in pattern: O13_P1 You gave me 2 instead for component Activation MCP There was an issue parsing BNGL file NoneAction argument atol not recognized! Check to make sure action is correctly formatted bngp Simulation failed NFsim simulation failed NFsim completed but output file /model.gdat not found" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/An_2009.bngl" + +playground: + visible: true + gallery_categories: ["immunology"] + featured: false + difficulty: "intermediate" + + + diff --git a/Published/An2009/metadata.yaml b/Published/An2009/metadata.yaml index f949b5be..9bd83506 100644 --- a/Published/An2009/metadata.yaml +++ b/Published/An2009/metadata.yaml @@ -4,6 +4,7 @@ description: "TLR4 signaling" tags: ["published", "immunology", "an", "2009", "cd14", "md2", "tlr4", "tram", "trif", "sarm", "traf4", "irak1"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Barua2007/Barua2007_aigenerated.md b/Published/Barua2007/Barua2007_aigenerated.md new file mode 100644 index 00000000..7de7b1f2 --- /dev/null +++ b/Published/Barua2007/Barua2007_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2007 + +## One-sentence summary + +SHP2 regulation by phosphorylated receptor dimers and intracomplex SH2-domain engagement. + +## What the model shows + +This model shows how a pre-dimerized receptor can recruit SHP2 and shift SHP2 from a closed, inhibited form toward an open, receptor-bound, catalytically productive form. The central question is how many receptor contacts SHP2 makes, and how those contacts affect receptor dephosphorylation. + +## Biological story + +Barua 2007 focuses on receptor-scaffold control of SHP2. The biological story is not just receptor phosphorylation, but how receptor geometry and SHP2 domain engagement can relieve autoinhibition and turn a recruited enzyme into an active local phosphatase. + +## Main biological players + +A receptor dimer with phosphorylated sites, SHP2 with C-terminal SH2, N-terminal SH2, and phosphatase domains, plus open and closed SHP2 conformations. + +## Mechanism in plain English + +Phosphorylated receptor sites recruit SHP2. SHP2 can bind through different domains, and once one domain is tethered, other parts of the same SHP2 molecule can engage nearby sites on the same receptor dimer. The model distinguishes simple recruitment from stronger intracomplex engagement. Opening SHP2 exposes catalytic function, allowing SHP2 to remove phosphate groups from receptor sites. + +## Key modeled events + +- Phosphorylated receptor dimers recruit SHP2 through SH2-domain contacts, creating receptor-bound phosphatase complexes. +- SHP2 can transition from a closed inhibited form toward an open form when receptor binding stabilizes active conformations. +- Open SHP2 removes phosphate groups from receptor sites, creating a negative-feedback loop on the receptor scaffold itself. + +## What the model measures + +The readouts distinguish free receptor, receptor bound to SHP2, multiply engaged receptor-SHP2 complexes, open SHP2, and phosphorylated receptor. They show how receptor scaffolding and SHP2 conformational opening control the amount of active phosphatase complex. + +## Expected behavior in plots + +Useful plots would compare phosphorylated receptor, receptor-bound SHP2, and open SHP2. A rise in open or multiply engaged SHP2 together with falling receptor phosphorylation would support the intended feedback mechanism. + +## Caveats + +The model abstracts SHP2 regulation into receptor-binding and conformational states. It should not be read as a complete map of all SHP2 partners or all receptor-family signaling outputs. diff --git a/Published/Barua2007/Barua2007_aigenerated_detailed.md b/Published/Barua2007/Barua2007_aigenerated_detailed.md new file mode 100644 index 00000000..852bd4d1 --- /dev/null +++ b/Published/Barua2007/Barua2007_aigenerated_detailed.md @@ -0,0 +1,68 @@ +# Detailed Model Explanation: Barua 2007 multivalent receptor–SHP2 engagement model + +## 1. Model overview + +This model examines how a pre-dimerized phosphoreceptor recruits an SHP2-like protein through its N-terminal SH2, C-terminal SH2, and catalytic PTP domains. Opening of SHP2 enables multiple same-receptor and cross-dimer contacts, which stabilize distinct binding topologies while allowing the PTP domain to dephosphorylate receptor Y1. + +## 2. BNGL block inventory + +The file contains 24 parameters, 2 molecule types, 2 initial species, 23 rules, 1 observable, and 2 actions. It has no model wrapper, compartments, anchors, or functions; the rules use `exclude_reactants` filters on cytosolic recruitment. + +## 3. Parameters, functions, and rate laws + +Free-solution recruitment uses domain-specific on/off pairs, whereas intracomplex binding multiplies the appropriate on-rate by a topology-specific `chi_r` effective-concentration factor. Catalysis and receptor phosphorylation are one-way processes. + +| Parameter group or names | Function in this model | +| --- | --- | +| `kdim`, `R_dim`, `S_tot` | `kdim` is declared but unused by active rules; `R_dim` and `S_tot` initialize pre-dimerized receptor and free SHP2-like protein. | +| `kopen`, `kclose` | Concerted transition between closed NSH2/PTP and open NSH2/PTP conformations. Closing is much faster than opening. | +| `kon_CSH2/koff_CSH2`, `kon_NSH2/koff_NSH2`, `kon_PTP/koff_PTP` | Cytosolic and intracomplex association/dissociation of each S domain with its receptor target. PTP dissociation is faster than either SH2 dissociation. | +| `kkin_Y1`, `kcat_PTP` | Receptor Y1 phosphorylation within a dimer and PTP-catalyzed Y1 dephosphorylation. | +| `chi_r1`–`chi_r11` | Topology-specific multipliers for second or third contacts made after S is already tethered to the receptor dimer; values distinguish same-receptor from cross-dimer geometries. | + +There are no functions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `R` | 3 | `DD`, `Y1`, `Y2` | `Y1: U, P`; `Y2: P` only | None | Pre-dimerized receptor: `DD` holds the receptor pair, Y2 recruits either SH2 domain, and Y1 is phosphorylated and contacted/dephosphorylated by the PTP domain. | +| `S` | 3 | `NSH2`, `CSH2`, `PTP` | `NSH2: C, O`; `PTP: C, O` | None | SHP2-like regulator whose NSH2 and PTP open together; its three domains can simultaneously engage sites across one or both receptors. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial. Receptor begins as a Y1-unphosphorylated, Y2-phosphorylated dimer at `R_dim`, while S begins free with closed NSH2 and PTP domains at `S_tot`. Thus Y2 docking sites are initially available, but NSH2/PTP recruitment requires the reversible opening transition; receptor Y1 must be phosphorylated by rule 1 before PTP engagement. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–7 create phospho-Y1, open S, recruit individual domains, and catalyze dephosphorylation. Rules 8–17 add a second S–receptor contact, and rules 18–23 close a third contact in already bidentate complexes. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | One-way | Receptor `Y1~U` within a `DD`-linked dimer | Changes `Y1: U → P` at `kkin_Y1`. | Creates the PTP substrate/interaction site while requiring receptor dimerization. | +| 2 | Reversible | Free S `NSH2` and `PTP` | Concertedly changes `NSH2: C ↔ O` and `PTP: C ↔ O` at `kopen/kclose`. | Controls access to the N-terminal SH2 and catalytic domains; CSH2 has no conformational state. | +| 3–5 | Reversible | Receptor Y2 with S CSH2 (rule 3), receptor Y2 with open NSH2 (rule 4), or receptor Y1~P with open PTP (rule 5) | Creates/releases the named single contact at its `kon/koff` pair; `exclude_reactants(2,R)` restricts the incoming S reactant from already containing another receptor. | Supplies three alternative first contacts from cytosol without conflating them with intracomplex closure. | +| 6–7 | One-way | PTP-bound receptor Y1~P | Both change `Y1: P → U` and release the PTP–Y1 bond at `kcat_PTP`; rule 6 yields separate R and S, whereas rule 7 keeps them in one complex through other unspecified bonds. | Catalytically removes phospho-Y1 while preserving multivalent complexes when another receptor contact still connects S. | +| 8, 11 | Reversible | S already tethered through CSH2 (rule 8) or NSH2 (rule 11); the other open SH2 domain and the partner receptor Y2 | Adds/releases the second SH2–Y2 contact using `chi_r1*kon_NSH2` or `chi_r1*kon_CSH2`, with the standard off-rate. | Bridges the two receptor subunits symmetrically through both SH2 domains. | +| 9–10, 12–13 | Reversible | S tethered by CSH2 or NSH2; open PTP; receptor Y1~P on the same receptor or its partner | Adds/releases PTP–Y1 using `chi_r2`/`chi_r3` after CSH2 or `chi_r5`/`chi_r4` after NSH2. | Makes catalytic-domain recruitment sensitive to whether PTP folds back onto the same receptor or spans the dimer. | +| 14–17 | Reversible | S tethered by PTP; free CSH2 or open NSH2; receptor Y2 on the same or partner receptor | Adds/releases the selected SH2–Y2 contact; `chi_r2/3` apply to CSH2 and `chi_r5/4` to NSH2 for same/other receptor geometry. | Builds the same bidentate topologies from a PTP-first route, preserving assembly-order alternatives. | +| 18–19 | Reversible | Both SH2 domains already occupy the two Y2 sites; open PTP and either receptor Y1~P | Adds/releases the third PTP contact with `chi_r6` when Y1 shares the CSH2-bound receptor or `chi_r7` when it shares the NSH2-bound receptor. | Completes tridentate engagement and distinguishes which side of the dimer carries the catalytic contact. | +| 20–23 | Reversible | PTP plus one SH2 already bound; the remaining SH2 domain and open receptor Y2 | Rules 20/21 add NSH2 with `chi_r8/9` when CSH2 and PTP are on the same/different receptors; rules 22/23 add CSH2 with `chi_r10/11` when NSH2 and PTP are on different/same receptors. | Closes the final SH2 contact in every remaining tridentate topology and enforces the thermodynamic geometry relations encoded by the `chi_r` values. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `pYR` | Molecule count | Receptor Y1 in state `P`, whether free or domain-bound | Total PTP-substrate phosphorylation; it reports the balance between rule 1 and rules 6–7 but does not distinguish S-binding topology. | + +## 8. Actions and simulation workflow + +The file generates the full network and runs a non-sparse ODE steady-state simulation to time 1,000 with 100 output steps. No stimulus change or separate equilibration phase is defined. + +## 9. Technical caveats and ambiguities + +- `R` and `S` are abstract names; the SHP2-like interpretation follows domain names and local model context. +- Y2 is permanently phosphorylated, and receptor dimerization is fixed in the seed rather than governed by active rules. +- Several product patterns remain connected without displaying the alternative bond that supplies connectivity; their meaning depends on the surrounding complex match. +- `exclude_reactants` and multiline rule modifiers may be parser-sensitive. +- `kdim` is declared but not used by active rules. diff --git a/Published/Barua2007/Barua_2007_metadata.yaml b/Published/Barua2007/Barua_2007_metadata.yaml new file mode 100644 index 00000000..7b296dea --- /dev/null +++ b/Published/Barua2007/Barua_2007_metadata.yaml @@ -0,0 +1,66 @@ +id: "Barua_2007" +name: "Barua 2007" +description: "Model from Haugh (2006)" +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +citation: + year: "2007" + pmid: "17208977" + reference: "Barua et al., 2007" + +tags: ["published", "barua", "2007", "version", "r", "s"] +date: + last_tested: 2026-07-14 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered exclude_reactants at line 64" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: false + comments: "nfsim false in original but runs with bng2 MCP There was an issue parsing BNGL file: NoneAction argument steady_state not recognized! Check to make sure action is correctly formatted bngp Simulation failed NFsim simulation failed NFsim completed but output file /model.gdat not found" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: true + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Barua_2007.bngl" + +playground: + visible: true + gallery_categories: ["cancer"] + featured: false + difficulty: "intermediate" + + + diff --git a/Published/Barua2007/metadata.yaml b/Published/Barua2007/metadata.yaml index 5eaeff0b..60727ccf 100644 --- a/Published/Barua2007/metadata.yaml +++ b/Published/Barua2007/metadata.yaml @@ -4,6 +4,7 @@ description: "Model from Haugh (2006)" tags: ["published", "barua", "2007", "version", "r", "s"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Barua2009/Barua2009_aigenerated.md b/Published/Barua2009/Barua2009_aigenerated.md new file mode 100644 index 00000000..9cfac4c6 --- /dev/null +++ b/Published/Barua2009/Barua2009_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Barua 2009 + +## One-sentence summary + +SH2B dimerization brings JAK2 kinases together and creates cooperative JAK2 phosphorylation. + +## What the model shows + +This compact model isolates a proposed scaffolding role for SH2B in Janus kinase 2 (JAK2) activation. SH2B binds phosphorylated JAK2 through a Src homology 2 (SH2) domain and uses its dimerization domain to assemble complexes containing two kinases. + +## Biological story + +A phosphorylated JAK2 molecule recruits SH2B. Two SH2B molecules associate, bringing their JAK2 partners into a shared assembly. Proximity permits one JAK2 to phosphorylate the other, so partially activated complexes can accelerate completion of the active pair. + +## Main biological players + +JAK2, its recruitment and phosphorylation states, SH2B, the SH2 interaction region, and the SH2B dimerization domain. + +## Mechanism in plain English + +JAK2 that is already phosphorylated at the recruitment site binds SH2B. SH2B molecules then dimerize through their dedicated dimerization domains. When two JAK2 molecules occupy that scaffold, phosphorylation can occur between them. A complex containing one active kinase converts its inactive partner faster than a complex containing two inactive kinases, representing cooperative amplification. + +## Key modeled events + +- Phosphorylated JAK2 recruits SH2B through the SH2 domain. +- SH2B dimerization joins two JAK2–SH2B units. +- Scaffolded JAK2 molecules phosphorylate one another. +- A partially active pair accelerates phosphorylation of its remaining inactive kinase. + +## What the model measures + +Readouts distinguish phosphorylated JAK2 monomers, one-JAK2/one-SH2B complexes, SH2B dimers with one or two JAK2 molecules, and total active versus inactive JAK2. + +## Expected behavior in plots + +JAK2–SH2B complexes should precede the two-kinase scaffold. As the JSSJ assembly accumulates, inactive JAK2 should fall and active JAK2 should rise more sharply if the cooperative phosphorylation route dominates. + +## Caveats + +The model deliberately omits the cytokine receptor, phosphatases, STAT proteins, trafficking, and gene expression. It tests the SH2B scaffold mechanism rather than reconstructing the full JAK–STAT pathway. diff --git a/Published/Barua2009/Barua2009_aigenerated_detailed.md b/Published/Barua2009/Barua2009_aigenerated_detailed.md new file mode 100644 index 00000000..8a147b8e --- /dev/null +++ b/Published/Barua2009/Barua2009_aigenerated_detailed.md @@ -0,0 +1,63 @@ +# Detailed Model Explanation: Barua 2009 JAK2–SH2B cooperative activation model + +## 1. Model overview + +This model uses SH2B as a dimeric scaffold that recruits two JAK2 molecules through phosphorylated docking sites. Once the two kinases share that scaffold, phosphorylation of the first JAK2 is slow and phosphorylation of the second is tenfold faster, producing cooperative activation. + +## 2. BNGL block inventory + +The file contains 8 parameters, 2 molecule types, 2 initial species, 4 rules, 6 observables, and 2 actions. It has no model wrapper, compartments, anchors, or functions; network generation limits complexes to two JAK2 molecules. + +## 3. Parameters, functions, and rate laws + +The model uses two reversible binding pairs and two context-dependent phosphorylation rates. All kinetics are direct mass action, and the only nonlinearity emerges from assembling the required two-JAK2 complex. + +| Parameter group or names | Function in this model | +| --- | --- | +| `kon_SH2`, `koff_SH2` | Association/dissociation of phosphorylated JAK2 `Y1` with the SH2B `SH2` domain. | +| `kon_dimer`, `koff_dimer` | Association/dissociation of two SH2B `DD` domains, creating the central dimeric scaffold. | +| `kphos_slow`, `kphos_fast` | Phosphorylation of a JAK2 `Y` site when the partner JAK2 is unphosphorylated or already phosphorylated; the latter rate is tenfold higher. | +| `Jtot`, `Stot` | Initial JAK2 and SH2B concentrations. SH2B is present in large excess over JAK2. | + +There are no functions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `S` | 2 | `SH2`, `DD` | None | None | SH2B-like adaptor: `SH2` captures JAK2 `Y1~P`, and `DD` dimerizes two adaptors to hold a JAK2 pair. | +| `J` | 2 | `Y1`, `Y` | `Y1: P` only; `Y: U, P` | None | JAK2-like kinase with a constitutively available phospho-docking site (`Y1`) and a regulated activation site (`Y`). | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial. It starts with free SH2B and JAK2 whose `Y1` docking site is already phosphorylated but whose regulated `Y` site is unphosphorylated. No adaptor dimers or kinase complexes are seeded, so the complete JAK2–SH2B–SH2B–JAK2 assembly must form before either phosphorylation rule can fire. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–2 construct the two-kinase scaffold; rules 3–4 phosphorylate its JAK2 pair in a slow-first, fast-second sequence. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | Reversible | JAK2 `Y1~P` and SH2B `SH2` | Creates/releases the `Y1–SH2` bond at `kon_SH2/koff_SH2`; JAK2 `Y` is unconstrained. | Recruits each kinase to an adaptor without changing kinase activation. | +| 2 | Reversible | Two SH2B `DD` sites | Creates/releases the adaptor `DD–DD` bond at `kon_dimer/koff_dimer`. | Joins two recruited JAK2–SH2B units into the geometry required for cross-activation. | +| 3 | One-way | Complete JAK2–SH2B dimer with both JAK2 `Y~U` | Changes one JAK2 `Y: U → P` at `kphos_slow`, retaining every scaffold bond and leaving the partner unmodified. | Initiates activation slowly in a fully assembled but inactive kinase pair. | +| 4 | One-way | Same complete scaffold with one JAK2 `Y~P` and the other `Y~U` | Changes the remaining JAK2 `Y: U → P` at `kphos_fast`. | Completes activation rapidly once the first phosphorylation has occurred, implementing positive cooperativity. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `J_mono` | Molecule count | All JAK2 with the constitutive `Y1~P` state | Effectively a total-JAK2 check, not a strict monomer count, because `Y1` bonding is unconstrained. | +| `JS`, `JSS`, `JSSJ` | Molecule count | One recruited adaptor, a JAK2-bound SH2B dimer, or any complex containing two JAK2 molecules | Stepwise assembly readouts from initial recruitment to the two-kinase scaffold. | +| `J_active`, `J_inactive` | Molecule count | JAK2 with regulated `Y~P` or `Y~U` | Activation-state partition used to see the slow/fast phosphorylation sequence. | + +## 8. Actions and simulation workflow + +The file generates a network capped at two JAK2 molecules per species and then runs a sparse ODE simulation to time 10,000 with 10,000 output steps. No equilibration or stimulus change precedes the run. + +## 9. Technical caveats and ambiguities + +- `Y1` is declared only in state `P`; the model cannot represent creation or loss of the SH2B docking phosphate. +- `J_mono` is named as a monomer readout but does not require JAK2 to be unbound. +- `JSSJ` detects two JAK2 molecules without constraining either activation state. +- The ODE action uses `atoll` rather than the usual `atol`, which may be parser-sensitive. diff --git a/Published/Barua2009/Barua_2009_metadata.yaml b/Published/Barua2009/Barua_2009_metadata.yaml new file mode 100644 index 00000000..369360e8 --- /dev/null +++ b/Published/Barua2009/Barua_2009_metadata.yaml @@ -0,0 +1,66 @@ +id: "Barua_2009" +name: "Barua 2009" +description: "JAK2-SH2B signaling" +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +citation: + year: "2009" + pmid: "19381268" + reference: "Barua at al., 2009" + +tags: ["published", "barua", "2009", "s", "j"] +date: + last_tested: 2026-07-14 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered exclude_reactants at line 64" + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim false in original but runs with bng2 MCP There was an issue parsing BNGL file: NoneAction argument steady_state not recognized! Check to make sure action is correctly formatted bngp Simulation failed NFsim simulation failed NFsim completed but output file /model.gdat not found" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Barua_2007.bngl" + +playground: + visible: true + gallery_categories: ["cancer"] + featured: false + difficulty: "intermediate" + + + diff --git a/Published/Barua2009/metadata.yaml b/Published/Barua2009/metadata.yaml index 3fb621b2..54672a84 100644 --- a/Published/Barua2009/metadata.yaml +++ b/Published/Barua2009/metadata.yaml @@ -4,6 +4,7 @@ description: "JAK2-SH2B signaling" tags: ["published", "barua", "2009", "s", "j"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Barua2013/Barua2013_aigenerated.md b/Published/Barua2013/Barua2013_aigenerated.md new file mode 100644 index 00000000..08ef711a --- /dev/null +++ b/Published/Barua2013/Barua2013_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2013 + +## One-sentence summary + +Beta-catenin control by the Axin/APC/GSK3/CK1 destruction complex. + +## What the model shows + +This model shows how beta-catenin is captured by a destruction complex, phosphorylated at specific regulatory sites, released or degraded, and replenished by synthesis. It emphasizes how Axin and APC organize beta-catenin with the kinases CK1 and GSK3. + +## Biological story + +Barua 2013 tells a destruction-complex cycle: beta-catenin is recruited to Axin/APC scaffolds, primed and phosphorylated by kinases, removed by degradation, and then replaced by new synthesis. + +## Main biological players + +Beta-catenin, APC, Axin, GSK3 beta, CK1 alpha, and degraded beta-catenin. + +## Mechanism in plain English + +Beta-catenin binds APC and Axin through different interaction surfaces. APC binds Axin, GSK3 binds Axin, and CK1 also binds Axin, assembling a phosphorylation-competent destruction complex. CK1 phosphorylates beta-catenin first, GSK3 phosphorylates additional beta-catenin sites, APC can also be phosphorylated, and phosphatase-like reactions reverse those modifications. Beta-catenin can be synthesized, degraded slowly when not appropriately phosphorylated, or degraded faster after phosphorylation. Degradation releases the associated complex members. + +## Key modeled events + +- Beta-catenin binds APC and Axin, placing it into the destruction-complex environment. +- CK1 and GSK3 phosphorylate beta-catenin in sequence, converting it into a form that is removed more rapidly. +- When beta-catenin is degraded, associated APC or Axin partners are released so the scaffold can participate in another cycle. + +## What the model measures + +The readouts track total live beta-catenin, beta-catenin phosphorylated at CK1 and GSK3 target sites, phosphorylated APC, and beta-catenin bound to Axin. The model shows how destruction-complex assembly controls the balance between beta-catenin persistence and removal. + +## Expected behavior in plots + +Plots should show whether beta-catenin remains mostly live and unmodified or shifts into phosphorylated and degraded forms. Increased beta-catenin-Axin association followed by phosphorylated beta-catenin supports destruction-complex processing. + +## Caveats + +The summary focuses on scaffolded beta-catenin control. It does not imply that the entire Wnt pathway, transcriptional beta-catenin output, or upstream ligand regulation is included. diff --git a/Published/Barua2013/Barua2013_aigenerated_detailed.md b/Published/Barua2013/Barua2013_aigenerated_detailed.md new file mode 100644 index 00000000..58a080c0 --- /dev/null +++ b/Published/Barua2013/Barua2013_aigenerated_detailed.md @@ -0,0 +1,82 @@ +# Detailed Model Explanation: Barua 2013 beta-catenin destruction-complex model + +## 1. Model overview + +This model assembles beta-catenin with APC and the AXIN scaffold, recruits CK1a and GSK3b, and applies the ordered phosphorylations that accelerate beta-catenin degradation. Multivalent intracomplex contacts stabilize the destruction complex, while synthesis, dephosphorylation, degradation marking, and rapid partner release control beta-catenin turnover. + +## 2. BNGL block inventory + +The file contains 25 parameters, 7 molecule types, 7 initial species, 29 rules, 5 observables, and 2 actions. It has no model wrapper, compartments, anchors, or functions and uses `begin species` rather than `begin seed species`. + +## 3. Parameters, functions, and rate laws + +Free association uses interface-specific on/off pairs; the same interactions receive a large `chi` multiplier when they close within an existing complex. Modification, synthesis, degradation marking, and post-degradation release use direct one-way rates. + +| Parameter group or names | Function in this model | +| --- | --- | +| `BCATtot`, `APCtot`, `AXINtot`, `GSKtot`, `CK1atot` | Initial pools. AXIN is tenfold less abundant than APC, GSK3b, or CK1a and therefore acts as the limiting scaffold. | +| `kf1_bap/kr1_bap`, `kf2_bap/kr2_bap` | Beta-catenin binding to APC through ARM59–a15 or ARM34–phospho-a20 interfaces. | +| `kf_ba/kr_ba`, `kf_apa/kr_apa` | Beta-catenin–AXIN and APC–AXIN binding. | +| `kf_ga/kr_ga`, `kf_ca/kr_ca` | Recruitment of GSK3b and CK1a to AXIN. | +| `chi` | Effective-concentration multiplier for association when the candidate sites already occupy one connected complex. | +| `kpb`, `kmpb`; `kp`, `kmp` | Beta-catenin phosphorylation/dephosphorylation and APC a20 phosphorylation/dephosphorylation. | +| `ksb`, `kdb1`, `kdb2` | Constitutive beta-catenin synthesis and slow/fast conversion from live to degraded state; S33/S37 phosphorylation selects the faster route. | +| Literal rate `1000` | Rapid release of APC or AXIN contacts from degradation-marked beta-catenin. | + +There are no functions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `AXIN` | 4 | `rgs`, `gid`, `b`, `e` | None | None | Central scaffold binding APC, GSK3b, beta-catenin, and CK1a through separate interfaces. | +| `APC` | 3 | `a15`, `a20`, `s` | `a20: U, P` | None | Multivalent beta-catenin partner: a15 binds ARM59, phospho-a20 binds ARM34, and `s` binds AXIN. | +| `bCat` | 5 | `s33s37`, `s45`, `ARM34`, `ARM59`, `ss` | `s33s37: U, P`; `s45: U, P`; `ss: l, d` | None | Beta-catenin substrate carrying ordered phosphosites, APC/AXIN-binding ARM regions, and a live/degraded status flag. | +| `GSK3b` | 1 | `a` | None | None | AXIN-recruited kinase associated with beta-catenin S33/S37 and APC a20 phosphorylation. | +| `CK1a` | 1 | `e` | None | None | AXIN-recruited kinase associated with priming beta-catenin at S45. | +| `I` | 0 | None | None | None | Conserved source marker that produces beta-catenin without being consumed. | +| `dead` | 0 | None | None | None | Zero-seeded marker not used by any active rule. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial and begins with free, live beta-catenin unphosphorylated at both regulatory sites, unphosphorylated APC, and free AXIN, GSK3b, and CK1a. A single `I` source marker drives ongoing beta-catenin production; `dead` starts at zero and remains unused. No destruction complexes or degradation-marked beta-catenin are seeded. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–15 assemble free and multivalent destruction-complex contacts. Rules 16–24 carry out ordered phosphorylation, reversal, synthesis, and degradation marking; rules 25–29 rapidly detach partners after beta-catenin enters the degraded state. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–3 | Reversible | Beta-catenin `ARM59` and APC `a15`; rule 1 is free association, rules 2–3 close the contact inside complexes already linked through AXIN or APC a20 | Creates/releases ARM59–a15 at `kf1_bap/kr1_bap`; intracomplex rules multiply only the forward rate by `chi`. | Provides the first APC–beta-catenin interface and lets preassembled complexes gain avidity. | +| 4–5 | Reversible | Beta-catenin `ARM34` and phosphorylated APC `a20`; rule 5 begins from an existing ARM59–a15 contact | Creates/releases ARM34–a20 at `kf2_bap/kr2_bap`, with `chi` on the intracomplex forward step. | Makes APC phosphorylation enable a second, bivalent beta-catenin contact. | +| 6–7 | Reversible | Beta-catenin `ARM34` and AXIN `b`; free in rule 6 and APC-co-confined in rule 7 | Creates/releases ARM34–b at `kf_ba/kr_ba`; rule 7 uses `chi*kf_ba`. | Recruits beta-catenin directly to AXIN and closes APC-mediated loops. | +| 8–10 | Reversible | APC `s` and AXIN `rgs`; APC a20 is unphosphorylated, phosphorylated/free, or phosphorylated/occupied | Creates/releases the scaffold contact at `kf_apa/kr_apa` with no state change. | Allows APC recruitment across every a20 occupancy state rather than coupling scaffold binding to one beta-catenin configuration. | +| 11–13 | Reversible | The same APC–AXIN sites inside preassembled APC–beta-catenin–AXIN complexes with the three a20 states from rules 8–10 | Closes/releases `s–rgs` with `chi*kf_apa/kr_apa`. | Stabilizes multivalent destruction complexes after the components are already co-confined. | +| 14–15 | Reversible | GSK3b `a`–AXIN `gid` or CK1a `e`–AXIN `e` | Creates/releases the kinase–scaffold bond at `kf_ga/kr_ga` or `kf_ca/kr_ca`. | Loads the two kinases onto distinct AXIN sites for local substrate modification. | +| 16–18 | One-way | Beta-catenin plus CK1a (rule 16), S45-phosphorylated beta-catenin plus GSK3b (rule 17), or APC plus GSK3b (rule 18) in the same connected complex | Changes bCat `s45: U → P`, then `s33s37: U → P`, or APC `a20: U → P`; rates `kpb`, `kpb`, and `kp`. Existing bonds persist. | Encodes S45 priming before S33/S37 phosphorylation and creates the phospho-APC binding interface. | +| 19–21 | One-way | Phospho-bCat S45, phospho-bCat S33/S37, or phospho-APC in an AXIN complex | Reverses the respective site `P → U` at `kmpb`, `kmpb`, or `kmp`. | Opposes kinase activity and can destabilize phospho-dependent beta-catenin capture. | +| 22 | One-way | Conserved `I` source marker | Creates free, live, doubly unphosphorylated beta-catenin at `ksb` while retaining `I`. | Maintains constitutive beta-catenin input. | +| 23–24 | One-way | Live beta-catenin with S33/S37 unphosphorylated or phosphorylated | Changes `ss: l → d` at slow `kdb1` or fast `kdb2`. | Makes S33/S37 phosphorylation accelerate entry into the degraded state. | +| 25–27 | One-way | Degraded beta-catenin bound to APC through ARM59–a15 (rules 25–26) or ARM34–phospho-a20 (rule 27) | Breaks the named bond at literal rate `1000`; rule 25/27 separate the displayed partners, while rule 26 leaves them connected through another unspecified contact. | Rapidly strips APC contacts after degradation without always forcing complete complex breakup. | +| 28–29 | One-way | Degraded beta-catenin bound to AXIN through ARM34–b | Breaks ARM34–b at `1000`; rule 28 separates the partners, whereas rule 29 preserves connectivity through another bond. | Releases AXIN for reuse after beta-catenin degradation. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `bcat_tot` | Molecule count | Live beta-catenin (`ss~l`) | Total nondegraded substrate pool. | +| `bCat_pS45`, `bCat_pS33S37` | Molecule count | Live beta-catenin phosphorylated at the named site | Priming and degradation-associated phosphorylation stages. | +| `APC_p20a` | Molecule count | APC with phosphorylated a20, whether free or bound | Availability of the ARM34-binding APC state. | +| `BCat_Axin` | Species count | Complete species containing a live ARM34–AXIN-b bond | Direct beta-catenin recruitment to AXIN; species counting avoids treating a partial pattern as a free molecule count. | + +## 8. Actions and simulation workflow + +The file generates a network capped at one APC, one AXIN, and one beta-catenin per species, then runs a sparse ODE simulation to time 250,000 with 2,500 output steps. The action uses tight tolerances but spells the absolute-tolerance key as `atoll`. + +## 9. Technical caveats and ambiguities + +- One local metadata file describes JAK2–SH2B signaling, but the BNGL clearly implements beta-catenin destruction. +- The beta-catenin seed contains a doubled comma, and `atoll` may be an invalid action key. +- Kinases in rules 16–18 are required only as members of the same connected complex; no catalytic-site bond is specified. +- Rules 26 and 29 rely on an unshown alternative bond to keep products connected. +- Nullary `I`/`dead` syntax and the bounded `max_stoich` map may be parser-sensitive. diff --git a/Published/Barua2013/Barua_2013_metadata.yaml b/Published/Barua2013/Barua_2013_metadata.yaml new file mode 100644 index 00000000..ddf9c307 --- /dev/null +++ b/Published/Barua2013/Barua_2013_metadata.yaml @@ -0,0 +1,66 @@ +id: "Barua_2013" +name: "Barua 2013" +description: "JAK2-SH2B signaling" +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +citation: + year: "2013" + pmid: "24086117" + reference: "Barua & Hlavacek, 2013" + +tags: ["published", "barua", "2009", "s", "j"] +date: + last_tested: 2026-07-15 + +category: "regulation" +biol_categories: ["regulation"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "Encountered I at line 45" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim false in original but runs with bng2 MCP There was an issue parsing BNGL file: Barua_2013.bnglFailed to parse action generate_network({overwrite=>1,max_stoich=>{APC=>1,AXIN=>1,bCat=>1}});" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/Barua_2013.bngl" + +playground: + visible: true + gallery_categories: ["cancer"] + featured: false + difficulty: "intermediate" + + + diff --git a/Published/Barua2013/metadata.yaml b/Published/Barua2013/metadata.yaml index 7f3df0e2..8dd7ff7e 100644 --- a/Published/Barua2013/metadata.yaml +++ b/Published/Barua2013/metadata.yaml @@ -4,6 +4,7 @@ description: "Beta-catenin destruction" tags: ["published", "barua", "2013", "axin", "gsk3b", "apc", "bcat", "ck1a"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/BaruaBCR2012/BaruaBCR2012_aigenerated.md b/Published/BaruaBCR2012/BaruaBCR2012_aigenerated.md new file mode 100644 index 00000000..10cea85e --- /dev/null +++ b/Published/BaruaBCR2012/BaruaBCR2012_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Barua 2012 + +## One-sentence summary + +Antigen and tonic B-cell receptor signaling emerge from competing Lyn/Fyn/Syk activation and Csk–PAG inhibitory control. + +## What the model shows + +This model follows early B-cell receptor (BCR) signaling at detailed receptor-proximal resolution. It distinguishes immunoreceptor tyrosine-based activation motif (ITAM) phosphorylation, Src-family kinase activation and autoinhibition, Syk recruitment, and assembly of the inhibitory Csk–PAG module. + +## Biological story + +Even without antigen, basal kinase activity can produce tonic signaling. Antigen strengthens receptor-proximal encounters, allowing Lyn and Fyn to modify the BCR and one another. Doubly phosphorylated ITAMs recruit Syk, while phosphorylated PAG recruits Csk, which places inhibitory phosphates on Lyn and Fyn. + +## Main biological players + +BCR Igα and Igβ chains, Lyn, Fyn, Syk, C-terminal Src kinase (Csk), and the phosphoprotein associated with glycosphingolipid-enriched microdomains (PAG/Cbp). + +## Mechanism in plain English + +Lyn and Fyn bind receptor ITAMs through unique or Src homology 2 (SH2) domains and phosphorylate Igα and Igβ in stages. Doubly phosphorylated Igβ captures tandem-SH2 Syk, which becomes activated by transphosphorylation. Lyn and Fyn also phosphorylate PAG. PAG uses proline-rich and phosphotyrosine sites to tether the kinases and recruit Csk; Csk then phosphorylates their inhibitory C-terminal tyrosines, opposing activation. + +## Key modeled events + +- Lyn and Fyn associate with BCR ITAMs and phosphorylate Igα and Igβ. +- Doubly phosphorylated Igβ recruits Syk and supports Syk activation. +- Lyn and Fyn phosphorylate one another and PAG within receptor-proximal assemblies. +- PAG recruits Csk, which imposes inhibitory phosphorylation on Lyn and Fyn. +- Constitutive dephosphorylation resets receptor, kinase, PAG, and Syk states. + +## What the model measures + +Readouts follow singly and doubly phosphorylated Igα/Igβ, activated and autoinhibited Lyn/Fyn, activated Syk, and PAG-bound Csk. They allow the positive receptor/Syk arm to be compared directly with inhibitory Src-family kinase control. + +## Expected behavior in plots + +Increasing antigen input should first increase receptor ITAM phosphorylation, followed by active Lyn/Fyn and Syk. PAG–Csk complexes and autoinhibited Src-family kinases should develop as a counter-response; strong inhibitory recruitment should reduce or cap the Syk output despite continued receptor input. + +## Caveats + +The model is detailed for BCR-proximal phosphorylation but stops before calcium, Ras–ERK, NF-κB, and transcriptional responses. Several tyrosine pairs are lumped into single model states. diff --git a/Published/BaruaBCR2012/BaruaBCR2012_aigenerated_detailed.md b/Published/BaruaBCR2012/BaruaBCR2012_aigenerated_detailed.md new file mode 100644 index 00000000..6903f6f8 --- /dev/null +++ b/Published/BaruaBCR2012/BaruaBCR2012_aigenerated_detailed.md @@ -0,0 +1,93 @@ +# Detailed Model Explanation: Barua 2012 B-Cell Receptor Signaling + +## 1. Model overview + +This model resolves early B-cell receptor (BCR) phosphorylation by the Src-family kinases Lyn and Fyn, recruitment and activation of Syk, and negative regulation through the PAG–Csk scaffold. Its central competition is between antigen-strength-scaled kinase amplification and Csk-driven phosphorylation of the inhibitory C-terminal sites of Lyn and Fyn. + +## 2. BNGL block inventory + +The model contains 118 parameters, 6 molecule types, 6 seed species, 76 logical reaction rules (108 physical source lines because continuations are used), 9 molecule-count observables, and 1 network-generation action. It contains no functions, compartments, or anchors. + +## 3. Parameters, functions, and rate laws + +The base constants `p1`–`p25` supply copy numbers and kinetic scales; descriptive aliases then map them to particular binding, phosphorylation, or dephosphorylation processes. Most rules use mass action. The dimensionless signal parameter `c` multiplies antigen-dependent phosphorylation rates and is zero in the supplied file, whereas free-kinase phosphorylation terms remain active. + +| Parameter group or names | Function in this model | +| --- | --- | +| `p1`; `BT`, `LT`, `FT`, `PT`, `CT`, `ST` | Initialize equal total pools of BCR, Lyn, Fyn, PAG, Csk, and Syk from the common copy-number scale. | +| `c`, `p19`, `p20`, `p22`, `p23`, `p25` | Set signal-dependent phosphorylation. `c` gates receptor-associated Lyn/Fyn and Syk reactions; `p25` reduces Fyn catalytic rates relative to the corresponding Lyn rates. | +| `kf1/kr1`, `kf2a,b/kr2a,b`; `kf9/kr9`, `kf10a,b/kr10a,b` | Control Lyn or Fyn binding to unphosphorylated BCR through the unique domain and to singly/doubly phosphorylated Ig-alpha through SH2. | +| `kf3/kr3`, `kf11/kr11` | Close or open intramolecular SH2 contacts with phosphorylated Lyn Y508 or Fyn Y531, creating the autoinhibited conformations. | +| `kp4a`–`kp8c` | Lyn-catalyzed BCR ITAM phosphorylation, Lyn/Fyn activation-loop phosphorylation, and PAG-site phosphorylation in receptor-bound or free contexts. | +| `kp12a`–`kp16c` | Parallel Fyn-catalyzed reactions; `kp16b` is exactly zero, disabling direct Fyn phosphorylation of PAG Y163/Y181 in that context. | +| `kf17/kr17`, `kp18a,b` | Recruit Syk tandem SH2 to doubly phosphorylated Ig-beta and activate receptor-bound Syk by trans-phosphorylation. | +| `kf19*`, `kr19a`, `kf20*`, `kr20b`; `kf21*`, `kr21a`, `kf22*`, `kr22b` | Build one- or two-point Lyn–PAG and Fyn–PAG contacts through SH3–proline-rich and SH2–phosphotyrosine interactions. | +| `kf23/kr23`, `kp24`, `kp25` | Recruit Csk to PAG Y317 and let scaffolded Csk phosphorylate the Lyn/Fyn inhibitory tails. | +| `kdp26a,b`–`kdp31` | Remove phosphate stepwise from BCR ITAMs and from Lyn, Fyn, PAG, and Syk regulatory sites. | + +There are no active functions; algebraic behavior is confined to parameter aliases such as `c*p19` and `c*p19/p25`. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `BCR` | 2 | `Y188_Y199`, `Y196_Y207` | each `0`, `P`, `PP` | None | Represents paired Ig-alpha and Ig-beta ITAM tyrosines; their phosphorylation states select kinase and Syk docking. | +| `Lyn` | 5 | `unique`, `SH3`, `SH2`, `Y397`, `Y508` | Y397/Y508: `0/P` | None | Src-family kinase with receptor/PAG binding domains, an activating loop site, and an inhibitory tail site. | +| `Fyn` | 5 | `unique`, `SH3`, `SH2`, `Y420`, `Y531` | Y420/Y531: `0/P` | None | Parallel Src-family kinase with analogous domains but distinct catalytic scaling and PAG specificity. | +| `PAG` | 5 | `PRS1`, `PRS2`, `Y317`, `Y163_Y181`, `Y387_Y417` | three tyrosine groups: `0/P` | None | Scaffold: PRS1/Y163-Y181 favor Fyn, PRS2/Y387-Y417 favor Lyn, and Y317 recruits Csk. | +| `Csk` | 1 | `SH2` | None | None | Inhibitory kinase recruited by phosphorylated PAG Y317. | +| `Syk` | 2 | `tSH2`, `Y525_Y526` | activation loop `0/P` | None | Binds doubly phosphorylated Ig-beta and becomes activated by trans-phosphorylation. | + +## 5. Compartments, anchors, initial species, and setup + +No spatial structure is declared. All six proteins start as free, unbound pools at the same nominal abundance; both BCR ITAM groups, kinase activation and inhibitory sites, PAG tyrosines, and Syk are initially unphosphorylated. Thus activity must emerge from the enabled phosphorylation reactions, but the default `c=0` suppresses the antigen-scaled receptor-associated pathways. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–23 cover Lyn recruitment, catalytic cross-talk, and PAG phosphorylation; 24–46 provide the corresponding Fyn arm; 47–49 activate Syk; 50–64 assemble the PAG scaffold and Csk inhibition; 65–76 reset all phosphosites. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–3 | Reversible | `BCR.Y188_Y199`; Lyn `unique` or `SH2` | Rule 1 binds unique domain to state `0`; rules 2–3 bind SH2 to `P` and `PP`, respectively, with state-specific off rates. | Recruits Lyn before phosphorylation and stabilizes it on phosphorylated Ig-alpha. | +| 4 | Reversible | Lyn `SH2`, `Y508=P` | Creates an intramolecular SH2–tail bond and reverses it at `kr3`. | Converts inhibitory-tail phosphorylation into physical Lyn autoinhibition. | +| 5–12 | One-way | BCR-bound Lyn `Y397=0/P`; BCR Ig-alpha or Ig-beta ITAM | Rules 5–8 phosphorylate Ig-alpha `0→P→PP`; 9–12 do the same for Ig-beta. Each pair distinguishes inactive versus active Lyn and doubles the first-step rate for two equivalent tyrosines. | Builds Syk docking sites and reinforces receptor signaling; all eight rates are proportional to `c`. | +| 13–16 | One-way | Receptor-bound or free Lyn `Y397` | Rules 13–14 activate BCR-bound Lyn; 15–16 activate free Lyn. In each context inactive or already active Lyn can catalyze `Y397:0→P`. | Supplies both antigen-scaled and basal Lyn activation routes. | +| 17–20 | One-way | Lyn `Y397`; Fyn `Y420`; BCR-bound or free context | Lyn changes Fyn `Y420:0→P`; rules 17–18 require receptor association, whereas 19–20 operate on free kinases. | Couples the two Src-family kinase pools. | +| 21–23 | One-way | Active Lyn; PAG `Y387_Y417`, `Y163_Y181`, `Y317` | Phosphorylates the Lyn docking group first, then the Fyn and Csk docking groups in SH2-tethered contexts. | Lets Lyn construct the PAG platform that eventually recruits its inhibitor. | +| 24–26 | Reversible | `BCR.Y188_Y199`; Fyn `unique` or `SH2` | Mirrors rules 1–3 for Fyn, binding state `0` through `unique` and `P/PP` through SH2. | Recruits Fyn to Ig-alpha across the receptor phosphorylation cycle. | +| 27 | Reversible | Fyn `SH2`, `Y531=P` | Creates or releases the intramolecular inhibitory-tail contact. | Implements Fyn autoinhibition. | +| 28–35 | One-way | BCR-bound Fyn `Y420=0/P`; both BCR ITAM groups | Rules 28–31 phosphorylate Ig-beta and 32–35 phosphorylate Ig-alpha, each `0→P→PP`; rates are antigen-scaled and divided by `p25`. | Provides the weaker parallel Fyn contribution to receptor phosphorylation. | +| 36–39 | One-way | Receptor-bound or free Fyn `Y420` | Activates Fyn `0→P` in receptor-bound (36–37) or free (38–39) contexts. | Combines signal-dependent and basal Fyn activation. | +| 40–43 | One-way | Fyn `Y420`; Lyn `Y397`; receptor-bound or free context | Active or inactive Fyn catalyzes Lyn `Y397:0→P`, with receptor variants proportional to `c`. | Makes Lyn–Fyn cross-activation bidirectional. | +| 44–46 | One-way | Active Fyn; PAG tyrosine groups | Phosphorylates PAG Y387/Y417 (44), Y163/Y181 (45), or Y317 (46); rule 45 uses disabled `kp16b=0`. | Allows Fyn to help construct PAG, except for the explicitly silent middle reaction. | +| 47 | Reversible | Syk `tSH2`; `BCR.Y196_Y207=PP` | Creates the tandem-SH2/Ig-beta bond and releases it at `kr17`. | Selectively recruits Syk to fully phosphorylated Ig-beta. | +| 48–49 | One-way | Receptor-bound Syk `Y525_Y526=0/P` | A neighboring bound Syk changes the target activation loop `0→P`; inactive or active Syk can serve as catalyst. | Amplifies Syk activity on phosphorylated receptor clusters. | +| 50–55 | One-way elementary steps | Lyn `SH3/SH2`; PAG `PRS2/Y387_Y417` | Add or release SH3–PRS2 and SH2–pY387/417 contacts from free or singly tethered states; rule 55 releases the doubly attached complex to free partners. | Resolves cooperative two-point Lyn docking rather than treating PAG binding as one event. | +| 56–61 | One-way elementary steps | Fyn `SH3/SH2`; PAG `PRS1/Y163_Y181` | Analogous steps form and dismantle the two-point Fyn–PAG interaction through PRS1 and phosphorylated Y163/Y181. | Positions Fyn on its preferred region of PAG. | +| 62 | Reversible | Csk `SH2`; `PAG.Y317=P` | Creates the Csk–PAG phosphotyrosine bond. | Recruits the negative-regulatory kinase to the scaffold. | +| 63–64 | One-way | PAG-associated Csk; Lyn `Y508` or Fyn `Y531` | Csk changes the kinase inhibitory tail `0→P` while the scaffold complex is retained. | Closes feedback by promoting the autoinhibited states in rules 4 and 27. | +| 65–68 | One-way | BCR Ig-alpha and Ig-beta ITAM states | Removes phosphate stepwise: `P→0` and `PP→P`; the second transitions use a factor of two. | Resets receptor docking and catalytic states. | +| 69–72 | One-way | Lyn `Y397/Y508`; Fyn `Y420/Y531` | Returns each activation-loop or inhibitory-tail site from `P→0`. | Balances kinase activation and Csk-dependent inhibition. | +| 73–75 | One-way | PAG `Y317`, `Y387_Y417`, `Y163_Y181` | Dephosphorylates each docking-site group independently. | Dismantles Csk and Src-family phosphotyrosine docking opportunities. | +| 76 | One-way | Syk `Y525_Y526` | Changes active Syk `P→0` at `kdp31`. | Terminates the downstream kinase signal. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `Ig_alpha_P`, `Ig_alpha_PP`, `Ig_beta_PP` | Molecule count | Singly/doubly phosphorylated BCR ITAM groups. | Report receptor signal progression; no observable is provided for singly phosphorylated Ig-beta. | +| `Activated_Lyn`, `Activated_Fyn`, `Activated_Syk` | Molecule count | Kinases with phosphorylated activation-loop sites. | Measure catalytic-state abundance regardless of binding context. | +| `Autoinhibited_Lyn`, `Autoinhibited_Fyn` | Molecule count | Inhibitory-tail-phosphorylated kinase whose tail is bonded to SH2. | Require both phosphorylation and the intramolecular closed conformation, not tail phosphorylation alone. | +| `PAG1_Csk` | Molecule count | PAG with phosphorylated Y317 engaged in a bond. | Serves as the readout of assembled Csk negative feedback, although the partner is inferred by the rule set rather than named in the pattern. | + +## 8. Actions and simulation workflow + +The file generates and overwrites the reaction network with textual reaction output enabled; it does not run an ODE trajectory despite the metadata listing ODE compatibility. Because the default antigen-strength parameter is zero, users must change `c` before network generation to enable the receptor-associated phosphorylation and Syk amplification terms. + +## 9. Technical caveats and ambiguities + +- The source uses continued lines, so 108 active physical lines correspond to 76 logical rules; rule numbering here follows complete reactions, not line count. +- `c=0` makes all `c`-scaled phosphorylation rules kinetically silent, leaving basal free-kinase routes and dephosphorylation active. +- `kp16b` is independently zero, so one Fyn-to-PAG phosphorylation route remains disabled even if antigen strength is increased. +- `Autoinhibited_*` requires an internal SH2–tail bond; it is narrower than the total inhibitory-tail-phosphorylated pool. +- Wildcards and omitted components deliberately permit multiple surrounding complexes, so molecule-count observables can include many topologies. diff --git a/Published/BaruaBCR2012/BaruaBCR_2012_metadata.yaml b/Published/BaruaBCR2012/BaruaBCR_2012_metadata.yaml new file mode 100644 index 00000000..9c446a94 --- /dev/null +++ b/Published/BaruaBCR2012/BaruaBCR_2012_metadata.yaml @@ -0,0 +1,66 @@ +id: "BaruaBCR_2012" +name: "Barua 2012" +description: "BCR signaling" +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +citation: + year: "2012" + pmid: "22711887" + reference: "Barua et al., 2012" + +tags: ["published", "immunology", "baruabcr", "2012", "bcr", "lyn", "fyn", "csk", "pag", "syk"] +date: + last_tested: 2026-07-15 + +category: "immunology" +biol_categories: ["immunology"] +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: false + vcell_errors: "ComponentStateDefinition 0 doesn't exist" + simulation_methods: ["ode", "ssa", "nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: false + comments: "nfsim Error in Simulation! Creating space for 262144 copies of a MoleculeType: 'BCR'.There is currently an imposed limit of: 200000 molecules per MoleculeType. MCP ValueError: could not convert string to float p1" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/BaruaBCR_2012.bngl" + +playground: + visible: true + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" + + + diff --git a/Published/BaruaBCR2012/metadata.yaml b/Published/BaruaBCR2012/metadata.yaml index f910fe3e..b3ecb51d 100644 --- a/Published/BaruaBCR2012/metadata.yaml +++ b/Published/BaruaBCR2012/metadata.yaml @@ -4,6 +4,7 @@ description: "BCR signaling" tags: ["published", "immunology", "baruabcr", "2012", "bcr", "lyn", "fyn", "csk", "pag", "syk"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/BaruaFceRI2012/BaruaFceRI2012_aigenerated.md b/Published/BaruaFceRI2012/BaruaFceRI2012_aigenerated.md new file mode 100644 index 00000000..bf943e83 --- /dev/null +++ b/Published/BaruaFceRI2012/BaruaFceRI2012_aigenerated.md @@ -0,0 +1,44 @@ +# Model Explanation: BaruaFceRI 2012 + +## One-sentence summary + +Bivalent ligand crosslinks FcεRI and drives Lyn- and Syk-dependent phosphorylation of receptor chains and the LAT adaptor across raft and non-raft membrane environments. + +## What the model shows + +This model focuses on the first signaling events after aggregation of the high-affinity IgE receptor FcεRI. It connects ligand-mediated receptor crosslinking to phosphorylation of the receptor β and γ chains, recruitment and activation of Syk, and phosphorylation of LAT, while explicitly distinguishing raft-localized from non-raft protein states. + +## Biological story + +A divalent ligand binds FcεRI and can bridge two receptors into a signaling-competent cluster. Lyn associates with receptor complexes and phosphorylates the β and γ receptor chains. Phosphorylated γ recruits Syk, which becomes activated and phosphorylates LAT; phosphorylated LAT can then recruit Grb2. Proteins can exchange between raft and non-raft states, and dephosphorylation of receptor, Syk, and LAT signals counteracts cluster-driven activation. + +## Main biological players + +- **Bivalent ligand and FcεRI:** the stimulus and receptor pair whose crosslinking initiates signaling. +- **Lyn:** a Src-family kinase that associates with receptor complexes and phosphorylates FcεRI chains. +- **Syk:** a kinase recruited to phosphorylated receptor γ chains and activated after binding. +- **LAT and Grb2:** a membrane adaptor and its binding partner downstream of active Syk. +- **Raft and non-raft membrane states:** alternative environments that change where receptor-proximal proteins interact. + +## Mechanism in plain English + +Ligand first binds one FcεRI and then captures a second receptor, producing a crosslinked pair. Lyn can associate with receptor chains in the appropriate membrane environment and add phosphate to the β and γ signaling motifs. Syk recognizes phosphorylated γ, binds the receptor, becomes phosphorylated through Lyn- and Syk-dependent steps, and then phosphorylates LAT. Phosphorylated LAT recruits Grb2 as a downstream signaling complex. Constitutive phosphatase-like removal of phosphate and movement between raft and non-raft states limit how much of each activated species accumulates. + +## Key modeled events + +- Bivalent ligand binds and crosslinks two FcεRI complexes, creating the receptor assemblies that support kinase activity. +- Lyn phosphorylates FcεRI β and γ signaling motifs and thereby creates docking sites for downstream proteins. +- Syk binds phosphorylated receptor γ, becomes activated, and phosphorylates LAT. +- LAT phosphorylation recruits Grb2, while dephosphorylation and raft exchange restrain the pathway. + +## What the model measures + +The principal readouts are phosphorylated FcεRI β, phosphorylated FcεRI γ, activated receptor-bound Syk, and phosphorylated LAT. These measurements follow the signaling sequence from receptor modification through kinase activation to adaptor phosphorylation rather than reporting a distal transcriptional or secretory response. + +## Expected behavior in plots + +Receptor β and γ phosphorylation should appear soon after ligand-driven crosslinking. Activated Syk should depend on phosphorylated γ and therefore follow or overlap the receptor signal, while phosphorylated LAT should appear downstream of active Syk. Raft exchange and distinct membrane versus cytosolic dephosphorylation routes can give Syk and LAT different decay profiles even when receptor phosphorylation has already begun to fall. + +## Caveats + +The modeled volume represents one of approximately 8,000 membrane-raft-scale subvolumes rather than a whole cell, so absolute molecule numbers require the stated scaling interpretation. The model concentrates on early phosphorylation and adaptor recruitment and does not include the full FcεRI response leading to calcium release, degranulation, or cytokine production. Raft localization is represented as a discrete state rather than a spatial membrane domain. diff --git a/Published/BaruaFceRI2012/BaruaFceRI2012_aigenerated_detailed.md b/Published/BaruaFceRI2012/BaruaFceRI2012_aigenerated_detailed.md new file mode 100644 index 00000000..08042d82 --- /dev/null +++ b/Published/BaruaFceRI2012/BaruaFceRI2012_aigenerated_detailed.md @@ -0,0 +1,85 @@ +# Detailed Model Explanation: Barua 2012 FcεRI raft-partitioning model + +## 1. Model overview + +This model examines FcεRI signaling while explicitly distinguishing raft-localized and nonraft molecular states. Ligand-crosslinked receptors recruit Lyn and Syk, drive receptor, Syk, and LAT phosphorylation, and recruit Grb2, while reversible raft partitioning changes encounter rates and protects raft-localized phosphoproteins from dephosphorylation. + +## 2. BNGL block inventory + +The model contains 49 parameters, six molecule types, nine initial species, 50 active reaction rules, and four molecule-count observables. It has no compartments, anchors, functions, or embedded actions; raft localization is encoded as an internal molecular state rather than a BNGL compartment. + +## 3. Parameters, functions, and rate laws + +The model represents one of `N = 8000` raft-sized fractions of a cell, so several copy numbers and association rates are divided or multiplied by `N`. Rules use mass-action kinetics, with algebraic parameters defining raft-entry rates, scaled membrane association, and reduced dephosphorylation inside rafts. + +| Parameter group or names | Function in this model | +| --- | --- | +| `LigT`, `RecT`, `LynT`, `SykT`, `LATT`, `GrbT`, `N` | Set ligand and protein pools in the simulated raft-sized fraction; receptor, Lyn, Syk, LAT, and Grb2 totals are scaled by `N`. | +| `kon`, `kx`, `koff` | Govern first-arm ligand capture, second-arm receptor crosslinking, and bond dissociation. `kx` is multiplied by `N` to represent a membrane-confined second encounter. | +| `kon_h`, `koff_h` | Parameterize monovalent hapten competition, but the hapten species, seed, and rule are commented out and inactive. | +| `lf`, `lr1`, `lr2` | Control Lyn binding to unphosphorylated receptor β through its unique domain or to phosphorylated β through SH2; the SH2 bond has the slower off-rate. | +| `sf`, `sr`; `gf`, `gr` | Set Syk binding to receptor γ phosphotyrosine and Grb2 binding to phosphorylated LAT. | +| `plb1_o/d`, `plb2_o/d`; `plg1_o/d`, `plg2_o/d` | Specify Lyn-mediated β- and γ-site phosphorylation for unique-domain- or SH2-bound Lyn in raft (`o`) and nonraft (`d`) states. Raft catalytic rates are fivefold higher. | +| `pss1`, `pss2`, `psl` | Control Syk transphosphorylation by inactive or activated Syk and phosphorylation of LAT by receptor-bound Syk. | +| `db`, `dg`, `ds`, `dl`, `z` | Set β, γ, Syk, and LAT dephosphorylation outside rafts; raft rules multiply these rates by the protection coefficient `z = 0.1`. | +| `f`, `Tau`, `Phi_r`, `Phi_d`, `Phi_l`, `Phi_t` | Define raft area fraction, mean lifetime, and partition preferences for receptor monomers, receptor dimers, Lyn, and LAT. | +| `r_o`/`r_d`, `rdimer_o`/`rdimer_d`, `l_o`/`l_d`, `t_o`/`t_d` | Derived entry/exit rates for receptor monomers, receptor dimers, Lyn-containing complexes, and LAT. Their different partition coefficients make dimers, Lyn, and LAT favor the raft state more strongly than receptor monomers. | + +There are no active functions; all algebraic scaling is evaluated in the parameter block. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `L` | 2 | two repeated `l` sites | None | None | Bivalent ligand that first binds one FcεRI and then crosslinks a second receptor in the same raft state. | +| `FCR` | 4 | `s`, `a`, `b`, `g` | `s`: nonraft `d`, raft `o`; `b`, `g`: unphosphorylated `Y`, phosphorylated `pY` | None | Lumped FcεRI receptor carrying a ligand site, β and γ signaling sites, and an explicit raft-location state. | +| `Lyn` | 3 | `s`, `U`, `SH2` | `s`: `d`, `o` | None | Src-family kinase that binds receptor β through different domains and phosphorylates neighboring receptors. | +| `Syk` | 2 | `tSH2`, `a` | `a`: `Y`, `pY` | None | Binds phosphorylated receptor γ and undergoes activation-loop transphosphorylation. | +| `LAT` | 2 | `s`, `p` | `s`: `d`, `o`; `p`: `Y`, `pY` | None | Raft-partitioning Syk substrate whose phosphorylation creates a Grb2 docking site. | +| `Grb2` | 1 | `SH2` | None | None | Downstream adaptor recruited to phosphorylated LAT; no later Grb2-mediated reactions are modeled. | + +## 5. Compartments, anchors, initial species, and setup + +No BNGL compartments or anchors are used. Instead, receptor, Lyn, and LAT carry `s~d` or `s~o`, denoting nonraft and raft states, and rules move whole matched complexes between them. Free receptor is initially divided according to the receptor-monomer partition coefficient, whereas Lyn and LAT use their own stronger raft preferences; Syk and Grb2 have no location state. Ligand begins free, and all receptor, Syk, and LAT phosphorylation variables begin unphosphorylated. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–9 assemble receptor and adaptor complexes, rules 10–30 create and remove phosphorylation in state-matched signaling assemblies, and rules 31–50 move free molecules and increasingly complex receptor assemblies between nonraft and raft states. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | Reversible | Receptor `a`; either ligand `l` arm | Creates the first receptor–ligand bond at `kon` and releases it at `koff`, without constraining receptor raft state. | Captures ligand from solution and prepares a singly occupied ligand for crosslinking. | +| 2–3 | Reversible | Second receptor `a`; free ligand arm; matched receptor `s` state | Adds a second receptor at `kx` or removes it at `koff`; rule 2 handles two nonraft receptors and rule 3 two raft receptors. | Produces signaling receptor dimers without allowing a crosslink to span the two modeled membrane states. | +| 4–7 | Reversible | Receptor β; Lyn `U` or `SH2`; matched `s` states | Rules 4/6 recruit Lyn `U` to unphosphorylated β in nonraft/raft states; rules 5/7 recruit Lyn SH2 to phosphorylated β. All use `lf`, with domain-specific release `lr1` or `lr2`. | Loads Lyn through a phosphorylation-dependent switch in binding mode. | +| 8 | Reversible | Receptor γ pY; Syk `tSH2` | Creates or releases the receptor–Syk bond at `sf` and `sr`. | Couples γ phosphorylation to Syk recruitment. | +| 9 | Reversible | LAT pY; Grb2 `SH2` | Creates or releases the LAT–Grb2 bond at `gf` and `gr`. | Makes phosphorylated LAT the terminal adaptor-recruitment output. | +| 10–17 | One-way | Crosslinked receptors; β or γ sites; receptor-bound Lyn `U` or `SH2` | Rules 10–13 phosphorylate β or γ in rafts; rules 14–17 repeat the same unique-domain/SH2 variants outside rafts. Each maps to its matching `plb...` or `plg...` rate, with raft rates fivefold higher. | Encodes faster Lyn catalysis in raft-localized receptor dimers. | +| 18–19 | One-way | Two Syk molecules; target Syk activation site `a` | An unphosphorylated Syk phosphorylates a partner at `pss1` (18), while an already phosphorylated Syk uses the faster `pss2` rate (19). | Generates positive reinforcement in the Syk activation state. | +| 20–21 | One-way | Receptor-bound Syk; LAT `p`; matched receptor/LAT `s` state | Catalytically changes LAT from `Y` to `pY`; rule 20 acts outside rafts and rule 21 inside, both at `psl`. | Transfers receptor/Syk activity to the LAT adaptor layer. | +| 22–25 | One-way | Receptor β or γ phosphosite and receptor `s` state | Rules 22–23 dephosphorylate nonraft β/γ at `db`/`dg`; rules 24–25 act in rafts at `z × db`/`z × dg`. | Gives raft-localized receptor phosphotyrosines tenfold protection from removal. | +| 26–28 | One-way | Syk activation site `a`; optionally receptor γ bond | Rule 26 dephosphorylates receptor-bound nonraft Syk at `ds`, rule 27 raft-bound Syk at `z × ds`, and rule 28 free Syk at `ds`. | Extends raft protection to Syk only while it remains attached to a raft-state receptor. | +| 29–30 | One-way | LAT `p` and `s` | Removes LAT phosphorylation at `dl` outside rafts and `z × dl` inside rafts. | Makes the LAT output longer-lived in the raft state. | +| 31–34 | Reversible | Receptor `s`, β state, and optional one-arm ligand bond | Moves free or singly ligand-bound receptor between `d` and `o` at receptor-monomer rates; rules 31/33 cover β~Y and 32/34 β~pY. | Partitions monomeric receptor independently of its phosphorylation and ligand occupancy. | +| 35–39 | Reversible | Lyn `s`; optionally receptor β and one-arm ligand | Moves free Lyn or a monomeric receptor–Lyn complex between states at `l_o`/`l_d`; rules 36/38 cover unique-domain complexes and 37/39 SH2 complexes, without/with ligand. | Applies Lyn's strong raft preference to the whole complex it occupies. | +| 40–42 | Reversible | Crosslinked receptor dimer; receptor β states | Moves ligand-crosslinked dimers with zero, one, or two phosphorylated β sites between states at `rdimer_o`/`rdimer_d`. | Gives receptor dimers a distinct raft partition coefficient while preserving dimer topology. | +| 43–49 | Reversible | Crosslinked receptor dimer with one or two Lyn molecules; β phosphorylation/binding mode | Moves the complete dimer–Lyn assembly at `l_o`/`l_d`; rules 43–46 cover one Lyn across β-state combinations, and 47–49 cover two Lyn molecules. | Prevents localization changes from breaking signaling complexes and lets Lyn determine their raft preference. | +| 50 | Reversible | LAT `s` | Switches LAT between nonraft and raft states at `t_o`/`t_d`, regardless of phosphorylation or Grb2 occupancy. | Supplies raft-localized LAT substrate for rule 21 and protects its phosphorylated product through rule 30. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `pBeta`, `pGamma` | Molecule count | FcεRI molecules with phosphorylated β or γ, whether the site is bound. | Receptor-site outputs pooled across raft and nonraft states; a receptor phosphorylated at both sites contributes to both readouts. | +| `pSyk` | Molecule count | Phosphorylated Syk specifically while its tandem-SH2 site is receptor-bound. | Excludes free phosphorylated Syk, so it measures active receptor-associated Syk rather than total pSyk. | +| `pLAT` | Molecule count | LAT with its signaling site phosphorylated, bound or free and in either membrane state. | Integrates Syk-dependent production and location-dependent dephosphorylation into one downstream readout. | + +## 8. Actions and simulation workflow + +The BNGL file contains no active actions, so it defines the model but does not itself generate a network or run a trajectory. The metadata lists ODE simulation, implying that an external workflow must generate the network and select integration duration and sampling. + +## 9. Technical caveats and ambiguities + +- Rafts are abstract internal states, not physical compartments; a transition rewrites all explicitly matched members of a complex to the same state. +- The model represents one `1/N` cell fraction, and several rates are deliberately rescaled by `N`; using it as a full-cell model requires coordinated changes rather than only multiplying outputs. +- A hapten parameter pair and hapten reaction are present only in comments. Because no `Hap` molecule type or seed is active, competitive monovalent inhibition is not part of this model instance. +- The source has no actions and is marked incompatible with both BNG2 and NFsim in metadata; its intended ODE workflow requires external orchestration and parser validation. diff --git a/Published/BaruaFceRI2012/BaruaFceRI_2012_metadata.yaml b/Published/BaruaFceRI2012/BaruaFceRI_2012_metadata.yaml new file mode 100644 index 00000000..f79ca8a0 --- /dev/null +++ b/Published/BaruaFceRI2012/BaruaFceRI_2012_metadata.yaml @@ -0,0 +1,30 @@ +id: "BaruaFceRI_2012" +name: "BaruaFceRI 2012" +description: "FcεRI signaling" + +citation: + year: "2012" + pmid: "23284735" + reference: "Barua & Goldstein, 2012" + +tags: ["published", "immunology", "baruafceri", "2012", "r_o", "rdimer_o", "l_o", "t_o", "l", "fcr", "lyn", "syk"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/BaruaFceRI_2012.bngl" +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" diff --git a/Published/BaruaFceRI2012/metadata.yaml b/Published/BaruaFceRI2012/metadata.yaml index 4a4b33e5..9aa3e2a9 100644 --- a/Published/BaruaFceRI2012/metadata.yaml +++ b/Published/BaruaFceRI2012/metadata.yaml @@ -4,6 +4,7 @@ description: "FcεRI signaling" tags: ["published", "immunology", "baruafceri", "2012", "r_o", "rdimer_o", "l_o", "t_o", "l", "fcr", "lyn", "syk"] category: "immunology" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Blinov2006/Blinov2006_aigenerated.md b/Published/Blinov2006/Blinov2006_aigenerated.md new file mode 100644 index 00000000..9f5ab978 --- /dev/null +++ b/Published/Blinov2006/Blinov2006_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Blinov 2006 + +## One-sentence summary + +EGF-driven EGFR aggregation creates phosphotyrosine docking routes that assemble Shc–Grb2–SOS signaling complexes. + +## What the model shows + +This model describes the earliest combinatorial stages of epidermal growth factor receptor (EGFR) signaling. Epidermal growth factor (EGF) binds EGFR, receptors aggregate and phosphorylate one another, and two receptor phosphotyrosines support direct or Shc-mediated recruitment of Grb2 and Son of Sevenless (SOS). + +## Biological story + +Ligand occupancy brings receptors together. Receptor phosphorylation creates distinct docking sites: one can recruit Grb2 directly, while another recruits Shc. Phosphorylated Shc adds a second route to Grb2–SOS assembly, allowing several molecular complexes to carry the same downstream exchange factor. + +## Main biological players + +EGF, EGFR, the Shc adaptor, growth factor receptor-bound protein 2 (Grb2), SOS, receptor tyrosines Y1068 and Y1148, and Shc Y317. + +## Mechanism in plain English + +EGF binds receptor and promotes EGFR aggregation. Neighboring receptors phosphorylate Y1068 and Y1148. Grb2 binds phosphorylated Y1068 through its SH2 domain and recruits SOS through an SH3 interaction. Shc binds phosphorylated Y1148, becomes phosphorylated at Y317, and then captures Grb2–SOS. Dephosphorylation and reversible adaptor binding dismantle these routes. + +## Key modeled events + +- EGF binds EGFR and promotes receptor aggregation. +- Aggregated receptors phosphorylate Y1068 and Y1148. +- Grb2 binds Y1068 directly and recruits SOS. +- Shc binds Y1148, becomes phosphorylated at Y317, and creates an alternate Grb2–SOS platform. +- Dephosphorylation and dissociation turn over receptor and adaptor complexes. + +## What the model measures + +Readouts include receptor dimers, total receptor phosphorylation, Shc phosphorylation, direct receptor–Grb2/SOS complexes, receptor–Shc complexes, Shc–Grb2/SOS complexes, and total EGFR, Shc, Grb2, and SOS pools. + +## Expected behavior in plots + +Receptor dimers and phosphotyrosines should rise before adaptor assemblies. Direct Y1068–Grb2–SOS complexes may appear sooner, while the Shc-mediated route should lag because it requires Shc recruitment and phosphorylation; both should decline as receptor and Shc phosphates turn over. + +## Caveats + +The model ends at SOS recruitment and does not explicitly follow Ras nucleotide exchange, the MAP kinase cascade, receptor internalization, or transcription. diff --git a/Published/Blinov2006/Blinov2006_aigenerated_detailed.md b/Published/Blinov2006/Blinov2006_aigenerated_detailed.md new file mode 100644 index 00000000..5f3f89de --- /dev/null +++ b/Published/Blinov2006/Blinov2006_aigenerated_detailed.md @@ -0,0 +1,82 @@ +# Detailed Model Explanation: Blinov 2006 EGFR phosphotyrosine signaling model + +## 1. Model overview + +This model follows EGF-driven EGFR dimerization and phosphorylation at Y1068 and Y1148, then resolves two routes for recruiting the Sos effector. Sos can arrive directly through Grb2 bound to receptor Y1068 or indirectly through phosphorylated Shc bound at Y1148, with adaptor complexes also able to preassemble in cytosol. + +## 2. BNGL block inventory + +The model contains 48 parameters, 5 molecule types, 6 seed species, 23 rules, 15 observables, and 6 active commands. It has no compartments, anchors, or functions; five derived parameters diagnose detailed-balance cycles but do not drive rules. + +## 3. Parameters, functions, and rate laws + +Most interactions use paired microscopic association/dissociation constants, with separate pairs for different assembly orders even when the final complex is the same. Receptor and adaptor phosphorylation are one-way rules balanced by independent dephosphorylation. + +| Parameter group or names | Function in this model | +| --- | --- | +| `egf_tot`, `egfr_tot`, `Grb2_tot`, `Shc_tot`, `Sos_tot`, `Grb2_Sos_tot` | Initial free molecular pools plus a separately seeded Grb2–Sos pool. | +| `kp1/km1`, `kp2/km2` | EGF–EGFR binding and dimerization of ligand-occupied receptors. | +| `kp3`, `km3` | Phosphorylation of dimerized EGFR at either Y1068 or Y1148 and site-independent receptor dephosphorylation. | +| `kp14`, `km14`, `km16` | Phosphorylation of receptor-bound Shc Y317, dephosphorylation while receptor-bound, and slower cytosolic ShcP dephosphorylation. | +| `kp9/km9`, `kp11/km11`, `kp10/km10` | Direct Y1068 route: recruitment of free Grb2, recruitment of prebound Grb2–Sos, or addition of Sos after Grb2 is receptor-bound. | +| `kp13/km13`, `kp15/km15` | Y1148 binding by unphosphorylated or Y317-phosphorylated Shc. | +| `kp17/km17`, `kp18/km18`, `kp19/km19`, `kp20/km20`, `kp24/km24` | Alternative orders for assembling receptor–ShcP–Grb2 and receptor–ShcP–Grb2–Sos complexes. | +| `kp21/km21`, `kp23/km23`, `kp12/km12`, `kp22/km22` | Cytosolic ShcP/Grb2/Sos preassembly before receptor recruitment. | +| `loop1`–`loop5` | Ratios of equilibrium constants used to check closed thermodynamic cycles; no active rule uses them as rates. | + +There are no functions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `egf` | 1 | `r` | None | None | Ligand that occupies EGFR `l`. | +| `egfr` | 4 | `l`, `r`, `Y1068`, `Y1148` | `Y1068: Y, pY`; `Y1148: Y, pY` | None | Receptor whose `r` site dimerizes; Y1068 recruits Grb2 directly and Y1148 recruits Shc. | +| `Shc` | 2 | `PTB`, `Y317` | `Y317: Y, pY` | None | Adaptor that binds receptor through PTB and, after Y317 phosphorylation, recruits Grb2 through its SH2 site. | +| `Grb2` | 2 | `SH2`, `SH3` | None | None | Bifunctional adaptor: SH2 binds phospho-EGFR or phospho-Shc, while SH3 binds Sos. | +| `Sos` | 1 | `dom` | None | None | Effector recruited exclusively through Grb2 SH3. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial. Free EGF, unphosphorylated EGFR, unphosphorylated Shc, free Grb2, and free Sos are seeded, together with a substantial preassembled Grb2–Sos pool. The active workflow first removes EGF to equilibrate adaptor binding, then restores the ligand before the kinetic phase. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–8 create receptor phosphotyrosines and phosphorylated Shc. Rules 9–18 assemble direct Y1068 and indirect Y1148 routes to Sos at receptor, while rules 19–23 form and turn over the same adaptor combinations away from receptor. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–2 | Reversible | EGF `r`, EGFR `l`, and then two ligand-occupied EGFR `r` sites | Rule 1 creates/releases the ligand bond at `kp1/km1`; rule 2 creates/releases the receptor dimer bond at `kp2/km2`. | Builds the ligand-bound dimer required for receptor transphosphorylation. | +| 3–6 | One-way | Dimerized EGFR Y1068 or Y1148 (rules 3–4), and any phosphorylated receptor site (rules 5–6) | Rules 3/4 change Y1068/Y1148 `Y → pY` at `kp3`; rules 5/6 reverse the respective site at `km3`. | Independently opens and closes the direct Grb2 and Shc docking routes. | +| 7–8 | One-way | Shc PTB-bound to receptor Y1148~pY | Rule 7 changes Shc Y317 `Y → pY` at `kp14`; rule 8 changes receptor-bound Y317 `pY → Y` at `km14`, preserving PTB binding. | Makes receptor-bound Shc competent for Grb2 recruitment and permits local reversal. | +| 9–11 | Reversible | EGFR Y1068~pY, Grb2 SH2/SH3, and Sos | Rule 9 recruits Grb2 with free SH3 (`kp9/km9`); rule 10 recruits prebound Grb2–Sos (`kp11/km11`); rule 11 adds Sos to receptor-bound Grb2 (`kp10/km10`). | Provides two assembly orders for the direct receptor–Grb2–Sos route. | +| 12–13 | Reversible | EGFR Y1148~pY and Shc PTB; Shc Y317 is unphosphorylated in rule 12 or phosphorylated in rule 13 | Creates/releases the receptor–PTB bond using `kp13/km13` or `kp15/km15`. | Allows Shc to arrive before or after Y317 phosphorylation. | +| 14–15 | Reversible | Preformed ShcP–Grb2 or ShcP–Grb2–Sos and receptor Y1148~pY | Adds/removes the receptor–Shc PTB bond at `kp18/km18` or `kp20/km20`, retaining internal adaptor bonds. | Recruits partially or fully assembled indirect signaling complexes as units. | +| 16–18 | Reversible | Receptor-bound ShcP, Grb2 SH2, and Sos/Grb2 SH3 | Rule 16 adds free Grb2 (`kp17/km17`); rule 17 adds prebound Grb2–Sos (`kp24/km24`); rule 18 adds Sos after Grb2 (`kp19/km19`). | Completes the indirect Y1148–Shc–Grb2–Sos route through every modeled assembly order. | +| 19–20 | Reversible | Cytosolic ShcP Y317 and Grb2 SH2, with Grb2 SH3 free or already occupied | Forms ShcP–Grb2 at `kp21/km21` or ShcP–Grb2–Sos at `kp23/km23`. | Creates receptor-free adaptor pools available for rules 14–15. | +| 21 | One-way | Cytosolic ShcP with free PTB | Changes Y317 `pY → Y` at `km16`. | Removes the Grb2 docking state after Shc leaves receptor. | +| 22–23 | Reversible | Grb2 SH3 and Sos, either free (rule 22) or within ShcP–Grb2 (rule 23) | Creates/releases SH3–Sos at `kp12/km12` or `kp22/km22`. | Maintains free Grb2–Sos and completes cytosolic ShcP–Grb2–Sos by an alternative order. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `Dimers` | Molecule count | EGFR–EGFR complexes | Receptor dimer abundance; pattern matches may scale with embeddings in larger complexes. | +| `RP` | Molecule count | Sum of Y1068~pY and Y1148~pY receptor patterns | Total phosphotyrosine-site signal; a receptor phosphorylated at both sites can contribute twice. | +| `R_Grb2`, `R_G_S` | Molecule count | Direct Y1068 complexes with Grb2 alone or Grb2–Sos | Occupancy of the direct Sos-recruitment branch. | +| `R_Shc`, `R_ShcP` | Molecule count | Y1148-bound unphosphorylated or phosphorylated Shc | Progress through receptor recruitment and Shc activation. | +| `Shc_Grb`, `Shc_Grb_Sos`, `ShcP` | Molecule count | Phospho-Shc complexes or total phospho-Shc, without requiring receptor | Cytosolic plus receptor-associated adaptor assembly state. | +| `R_S_G_S`, `Sos_act` | Molecule count | Complete indirect receptor–ShcP–Grb2–Sos complex; `Sos_act` sums direct and indirect receptor-bound Sos | Detailed indirect endpoint and combined receptor-associated Sos output. | +| `Efgr_total`, `Shc_total`, `Sos_total`, `Grb2_total` | Molecule count | All molecules of each named type | Pool-conservation checks; `Efgr_total` retains the source spelling. | + +## 8. Actions and simulation workflow + +The workflow generates a network, removes free EGF, and performs a long sparse ODE steady-state equilibration. It then restores EGF, writes SBML, and runs a 120-time-unit kinetic ODE simulation with 120 output steps and tight tolerances. + +## 9. Technical caveats and ambiguities + +- Metadata immunology/BCR tags conflict with the EGFR–Shc–Grb2–Sos source model. +- `RP` sums two site patterns and can double-count doubly phosphorylated receptors. +- `loop1`–`loop5` diagnose detailed-balance consistency but do not enforce or alter rates. +- Pattern observables can count multiple embeddings in one complex. +- Sparse-solver options are reported as parser-sensitive in local compatibility notes. diff --git a/Published/Blinov2006/Blinov_2006_metadata.yaml b/Published/Blinov2006/Blinov_2006_metadata.yaml new file mode 100644 index 00000000..f2b7f844 --- /dev/null +++ b/Published/Blinov2006/Blinov_2006_metadata.yaml @@ -0,0 +1,65 @@ +id: "Blinov_2006" +name: "Blinov 2006" +description: "Phosphotyrosine signaling" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2006" + pmid: "16233948" + reference: "Blinov et al., 2006" + +tags: ["published", "immunology", "baruabcr", "2012", "bcr", "lyn", "fyn", "csk", "pag", "syk"] +date: + last_tested: 2026-07-16 + +category: "immunology" +biol_categories: ["immunology"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered = at line 67" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim false in original but runs with bngp2 if lower numbers of molecules MCP cannot access local variable stdout_str where it is not associated with a value (after removing sparse)" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Blinov_2006.bngl" + +playground: + visible: true + gallery_categories: ["cell-cycle"] + featured: false + difficulty: "intermediate" + + + diff --git a/Published/Blinov2006/metadata.yaml b/Published/Blinov2006/metadata.yaml index 87175063..fd722792 100644 --- a/Published/Blinov2006/metadata.yaml +++ b/Published/Blinov2006/metadata.yaml @@ -4,6 +4,7 @@ description: "Phosphotyrosine signaling" tags: ["published", "blinov", "2006", "egf", "egfr", "shc", "grb2", "sos"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Blinovegfr/Blinov_egfr_metadata.yaml b/Published/Blinovegfr/Blinov_egfr_metadata.yaml new file mode 100644 index 00000000..5a208480 --- /dev/null +++ b/Published/Blinovegfr/Blinov_egfr_metadata.yaml @@ -0,0 +1,40 @@ +id: "Blinov_egfr" +name: "Blinov egfr" +description: "EGFR signaling model" + +citation: + year: "2006" + pmid: "16233948" + reference: "Blinov et al., 2006" + +tags: ["published", "nfsim", "blinov", "egfr", "egf", "grb2", "shc", "simulate_nf"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: true + nfsim_compatible: true + uses_cbngl_compartments: false + uses_vcell_compartments: true + uses_energy: false + uses_functions: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: true + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_generate_network: false + default_sim_command: simulate_nf +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/growth-factor-signaling/Blinov_egfr.bngl" +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" diff --git a/Published/Blinovegfr/Blinovegfr_aigenerated.md b/Published/Blinovegfr/Blinovegfr_aigenerated.md new file mode 100644 index 00000000..84142869 --- /dev/null +++ b/Published/Blinovegfr/Blinovegfr_aigenerated.md @@ -0,0 +1,43 @@ +# Model Explanation: Blinov egfr + +## One-sentence summary + +EGF-driven EGFR dimerization creates two phosphorylated receptor docking sites and recruits Shc for receptor-associated phosphorylation. + +## What the model shows + +This compact epidermal growth factor receptor (EGFR) model isolates the earliest steps between extracellular EGF binding and adaptor phosphorylation. It is useful for comparing ligand occupancy, receptor dimer formation, phosphorylation of EGFR Y1068 and Y1173, and phosphorylation of the cytoplasmic adaptor Shc without adding a larger downstream kinase cascade. + +## Biological story + +Extracellular EGF binds membrane-localized EGFR and enables ligand-bound receptors to dimerize. Dimerization permits phosphorylation at Y1068 and Y1173. Phosphorylated Y1173 recruits Shc from the cytoplasm, after which Shc can be phosphorylated while receptor-bound and can later return to an unphosphorylated cytoplasmic form. Receptor and adaptor phosphatase activity continually opposes these activating steps. + +## Main biological players + +- **EGF:** the extracellular ligand that initiates receptor assembly. +- **EGFR:** the membrane receptor whose dimerization exposes Y1068 and Y1173 to phosphorylation. +- **Shc:** a cytoplasmic adaptor recruited to phosphorylated Y1173 and modified after recruitment. +- **Grb2:** a declared adaptor with SH2 and SOS-associated regions, although it does not participate in the active mechanism summarized here. + +## Mechanism in plain English + +EGF binds EGFR at the cell membrane, and two ligand-occupied receptors associate through their transmembrane regions. The dimerized receptors acquire phosphorylation at Y1068 and Y1173, while rapid dephosphorylation continuously removes both marks. Unphosphorylated Shc binds phosphorylated Y1173 and becomes phosphorylated in the receptor complex; phosphorylated Shc can also rebind Y1173, but with different binding kinetics. Once free in the cytoplasm, phosphorylated Shc is gradually dephosphorylated, limiting the duration of the adaptor signal. + +## Key modeled events + +- Extracellular EGF binds membrane EGFR and creates ligand-occupied receptors. +- Ligand-bound EGFR molecules dimerize, enabling phosphorylation of Y1068 and Y1173. +- Shc is recruited specifically through phosphorylated Y1173 and becomes phosphorylated while associated with EGFR. +- Receptor and Shc dephosphorylation oppose signaling and restore unmodified forms. + +## What the model measures + +The readouts track total membrane EGFR, extracellular EGF, total cytoplasmic Shc, receptor dimers, phosphorylation at EGFR Y1068 and Y1173, the combined abundance of both receptor phosphosites, and phosphorylated cytoplasmic Shc. Together these measurements separate ligand availability, receptor assembly, receptor activation, and adaptor activation. + +## Expected behavior in plots + +EGF engagement should be followed by accumulation of EGFR dimers and then phosphorylation at Y1068 and Y1173. Because both receptor sites are opposed by the same strong dephosphorylation process, their signals may be transient or remain low unless dimer formation continues. Shc phosphorylation should depend most directly on phosphorylated Y1173 and may lag behind the receptor phosphosite signal; free phosphorylated Shc should subsequently decline as it is dephosphorylated in the cytoplasm. + +## Caveats + +The model stops at Shc phosphorylation and does not propagate the signal into Ras, MAPK, PI3K, or transcriptional responses. Grb2 is named as a possible pathway component but is neither initially supplied nor used in the modeled events. Compartment placement distinguishes extracellular ligand, membrane receptor complexes, and cytoplasmic Shc, but it is not a spatial diffusion model. diff --git a/Published/Blinovegfr/Blinovegfr_aigenerated_detailed.md b/Published/Blinovegfr/Blinovegfr_aigenerated_detailed.md new file mode 100644 index 00000000..0fff9566 --- /dev/null +++ b/Published/Blinovegfr/Blinovegfr_aigenerated_detailed.md @@ -0,0 +1,75 @@ +# Detailed Model Explanation: Blinov EGFR signaling model + +## 1. Model overview + +This compact model follows extracellular EGF binding, membrane EGFR dimerization, phosphorylation of EGFR Y1068 and Y1173, and recruitment and phosphorylation of cytosolic Shc. It is a spatially constrained rule-based model intended for direct network-free simulation rather than a comprehensive EGFR pathway. + +## 2. BNGL block inventory + +The model contains three compartments, four molecule types, two anchors, three seed species, ten reaction rules, eight molecule-count observables, and one network-free simulation action. The parameter and function blocks are present but empty; all kinetic constants are written directly on the rules. + +## 3. Parameters, functions, and rate laws + +There is no named parameter namespace. Each rule uses a numeric mass-action rate, with two values for reversible association/state-change rules and one value for irreversible phosphorylation or dephosphorylation. + +| Parameter group or names | Function in this model | +| --- | --- | +| EGF–EGFR binding rates `0.003`, `0.06` | Set ligand capture and release at the receptor extracellular domain. | +| EGFR dimerization rates `0.001`, `0.01` | Set formation and dissociation of the transmembrane-domain bond between two ligand-occupied receptors. | +| EGFR phosphorylation rate `0.01` | Independently converts Y1068 or Y1173 from unphosphorylated to phosphorylated, but only for dimerized receptors. | +| EGFR dephosphorylation rate `4.505` | Removes phosphorylation from either Y1068 or Y1173 regardless of dimer occupancy. | +| Shc recruitment rates `0.045`/`0.6` and `4.5e-4`/`0.3` | Recruit unphosphorylated or phosphorylated Shc, respectively, to EGFR pY1173. The hundredfold lower on-rate for phosphorylated Shc makes its rebinding much weaker. | +| Shc state-change rates `3.0`, `0.03`; cytosolic dephosphorylation `0.005` | Drive Shc toward phosphorylation while receptor-bound, allow the reverse bound-state transition, and slowly reset released cytosolic Shc. | + +There are no active functions; no rate depends on an observable or a computed expression. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `EGFR` | 4 | `ecd`, `tmd`, `y1068`, `y1173` | `y1068`, `y1173`: `u`, `p` | Anchored to `M` | Membrane receptor whose extracellular site binds EGF, transmembrane site dimerizes, and two tyrosines report receptor activation. | +| `EGF` | 1 | `rb` | None | Allowed in `EC` and `M` | Soluble ligand that starts extracellularly and becomes membrane-localized as part of an EGFR complex. | +| `Shc` | 2 | `sh3`, `Y773` | `Y773`: `u`, `p` | None; seeded in `Cyt` | Cytosolic adaptor recruited to EGFR pY1173 and phosphorylated while receptor-bound. | +| `Grb2` | 2 | `sh2`, `sos` | None | None | Declared downstream adaptor, but it has no seed, rule, or observable and therefore does not participate in this model instance. | + +## 5. Compartments, anchors, initial species, and setup + +`EC` and `Cyt` are three-dimensional compartments and `M` is a two-dimensional membrane; all have unit size, with no explicit parent hierarchy. EGFR is constrained to the membrane, while EGF may occur extracellularly or in a membrane complex. The initial pools are 680 extracellular EGF molecules, 602 unbound and unphosphorylated membrane EGFR molecules, and 150 unphosphorylated cytosolic Shc molecules; Grb2 has no initial population. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–2 assemble ligand-bound EGFR dimers, rules 3–6 turn over the two receptor phosphotyrosines, and rules 7–10 couple EGFR pY1173 to Shc recruitment and phosphorylation. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | Reversible | EGF `rb`; EGFR `ecd` and free `tmd` | Creates or releases an EGF–EGFR extracellular-domain bond at `0.003` forward and `0.06` reverse; the complex is membrane-localized. | Supplies ligand-occupied receptors that are eligible for dimerization. | +| 2 | Reversible | Two ligand-bound EGFR molecules; each `tmd` | Creates or releases a bond between the two transmembrane sites at `0.001` and `0.01`. Distinct reactant labels ensure two receptor instances are joined. | Forms the signaling-competent EGFR dimer. | +| 3, 6 | One-way | EGFR Y1173 (rule 3) or Y1068 (rule 6) | Changes the selected site from `p` to `u` at `4.505`, without requiring dimerization. | Rapidly terminates receptor phosphosite occupancy. | +| 4–5 | One-way | Dimerized EGFR `tmd`; Y1068 (rule 4) or Y1173 (rule 5) | Changes the selected site from `u` to `p` at `0.01` while preserving the dimer bond. | Converts receptor dimerization into two independent phosphorylation outputs. | +| 7 | Reversible | EGFR pY1173; unphosphorylated Shc `sh3`/Y773 | Creates or releases the pY1173–Shc recruitment bond at `0.045` and `0.6`. | Brings inactive Shc to activated receptor. | +| 8 | Reversible | EGFR-bound Shc Y773 | Changes Y773 between `u` and `p` while leaving Shc attached, with phosphorylation favored by rates `3.0` versus `0.03`. | Makes receptor occupancy catalytically activate Shc. | +| 9 | One-way | Free cytosolic Shc pY773 | Changes Y773 from `p` to `u` at `0.005`. | Slowly resets phosphorylated Shc after it leaves the receptor. | +| 10 | Reversible | EGFR pY1173; phosphorylated Shc `sh3` | Recruits or releases already-phosphorylated Shc at `4.5e-4` and `0.3`. | Allows Shc product rebinding but makes it less favorable than recruitment of inactive Shc. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `EGFR_tot` | Molecule count | All membrane EGFR molecules. | Conserved receptor-pool readout across free, ligand-bound, dimerized, and Shc-bound forms. | +| `EGF_EC` | Molecule count | EGF molecules located in the extracellular compartment. | Falls when EGF becomes part of a membrane-localized receptor complex and rises on release. | +| `Shc_cyt` | Molecule count | Shc molecules located in the cytosol. | Excludes receptor-bound membrane Shc and therefore reports the free adaptor pool. | +| `Dimers` | Molecule count | Membrane EGFR molecules whose `tmd` site is bonded. | Counts receptor molecules in dimers, so one EGFR dimer contributes two matched EGFR molecules rather than one complex. | +| `Y1068_phosp`, `Y1173_phosp` | Molecule count | EGFR phosphorylated at the named site, whether that site is bound or free. | Site-specific receptor outputs; a doubly phosphorylated receptor contributes to both observables. | +| `Total_phosp` | Molecule count | Sum of matches to EGFR pY1068 and EGFR pY1173. | Counts phosphorylated sites rather than uniquely phosphorylated receptors; a receptor phosphorylated at both sites contributes twice. | +| `ShcP_Cyt` | Molecule count | Cytosolic Shc phosphorylated at Y773. | Measures released phospho-Shc, not the receptor-bound phosphorylated pool. | + +## 8. Actions and simulation workflow + +The model is simulated directly with NFsim for 120 time units, recording 240 steps. It does not explicitly generate a reaction network, equilibrate, change parameters, or export structures before the network-free trajectory. + +## 9. Technical caveats and ambiguities + +- The metadata says `uses_functions: true`, but the active functions block is empty; the model uses only literal numeric rates. +- The README and metadata disagree about BNG2 compatibility, while the model also uses compartments, anchors, match-once labels, and `simulate_nf`; execution should be checked with the intended BioNetGen/NFsim version. +- Grb2 is declared but absent from seeds and rules, so the model stops at Shc phosphorylation rather than continuing into a Grb2/SOS branch. +- The site name `Shc.Y773` is retained as written; its biological residue mapping is not independently established by the local files. diff --git a/Published/Blinovegfr/metadata.yaml b/Published/Blinovegfr/metadata.yaml index bf601496..63d04861 100644 --- a/Published/Blinovegfr/metadata.yaml +++ b/Published/Blinovegfr/metadata.yaml @@ -4,6 +4,7 @@ description: "EGFR signaling model" tags: ["published", "nfsim", "blinov", "egfr", "egf", "grb2", "shc", "simulate_nf"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: true diff --git a/Published/Blinovran/Blinov_ran_metadata.yaml b/Published/Blinovran/Blinov_ran_metadata.yaml new file mode 100644 index 00000000..b16f6cff --- /dev/null +++ b/Published/Blinovran/Blinov_ran_metadata.yaml @@ -0,0 +1,24 @@ +id: "Blinov_ran" +name: "Blinov ran" +description: "Ran GTPase cycle" +tags: ["published", "nfsim", "blinov", "ran", "c", "rcc1", "simulate_nf"] +category: "regulation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["nf"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/Blinov_ran.bngl" +playground: + visible: false + gallery_categories: ["cell-cycle"] + featured: false + difficulty: "advanced" diff --git a/Published/Blinovran/metadata.yaml b/Published/Blinovran/metadata.yaml index 2143b98a..ca17ab5f 100644 --- a/Published/Blinovran/metadata.yaml +++ b/Published/Blinovran/metadata.yaml @@ -4,6 +4,7 @@ description: "Ran GTPase cycle" tags: ["published", "nfsim", "blinov", "ran", "c", "rcc1", "simulate_nf"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["nf"] uses_compartments: true diff --git a/Published/Chattaraj2021/Chattaraj2021_aigenerated.md b/Published/Chattaraj2021/Chattaraj2021_aigenerated.md new file mode 100644 index 00000000..72914e0e --- /dev/null +++ b/Published/Chattaraj2021/Chattaraj2021_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Chattaraj 2021 + +## One-sentence summary + +Multivalent Nephrin-Nck-NWASP clustering as a model of heterotypic biomolecular condensate formation. + +## What the model shows + +This model shows how three multivalent signaling molecules can assemble into clusters through repeated binding interactions. It is tied to the idea that condensate formation depends on binding affinities and the availability of multiple interaction sites. + +## Biological story + +Chattaraj 2021 is about multivalency and phase-like assembly. Nephrin, Nck, and NWASP create clusters because each molecule can make several simultaneous contacts, allowing small complexes to grow cooperatively. + +## Main biological players + +Nephrin, Nck, NWASP, and their repeated binding modules. + +## Mechanism in plain English + +Nephrin provides multiple binding sites for Nck. Nck provides domains that connect Nephrin to NWASP. NWASP contributes additional multivalent sites, allowing small complexes to grow into larger heterogeneous clusters. Binding and unbinding rates determine whether the system remains mostly dispersed or shifts toward larger assemblies. + +## Key modeled events + +- Nephrin recruits Nck through repeated binding modules, creating multivalent receptor-proximal assemblies. +- Nck links Nephrin to NWASP, and NWASP adds more interaction sites that enlarge clusters. +- Binding affinity and the number of available sites determine whether molecules remain dispersed or form larger condensate-like clusters. + +## What the model measures + +The readouts track free molecules and clustered complexes. The model shows how multivalency and affinity can create a threshold-like transition into condensate-like signaling assemblies. + +## Expected behavior in plots + +Plots should distinguish dispersed molecules from clustered assemblies. A sharp increase in large complexes or clustered material indicates crossing into a condensate-like regime. + +## Caveats + +The model addresses clustering logic and solubility-product behavior; it does not by itself prove liquid-like material properties or downstream actin remodeling outcomes. diff --git a/Published/Chattaraj2021/Chattaraj2021_aigenerated_detailed.md b/Published/Chattaraj2021/Chattaraj2021_aigenerated_detailed.md new file mode 100644 index 00000000..ba02fa4a --- /dev/null +++ b/Published/Chattaraj2021/Chattaraj2021_aigenerated_detailed.md @@ -0,0 +1,69 @@ +# Detailed Model Explanation: Chattaraj 2021 multivalent Nephrin–Nck–NWASP clustering model + +## 1. Model overview + +This model studies heterotypic clustering of a trivalent Nephrin scaffold, a four-interface Nck adaptor, and a hexavalent NWASP partner. Condensate-like connectivity emerges solely from reversible, equal-affinity site binding, allowing valency and starting stoichiometry to determine cluster formation. + +## 2. BNGL block inventory + +The model contains 6 parameters, 3 molecule types, 3 free seed species, 11 molecule-count observables, and 21 reversible rules. It has no compartments, anchors, functions, or simulation actions; one XML-export action follows the model block. + +## 3. Parameters, functions, and rate laws + +The namespace separates the Nephrin–Nck interface (`12`) from the Nck–NWASP interface (`23`). Both interfaces are assigned the same dissociation constant and off-rate, so their derived on-rates are also equal. + +| Parameter group or names | Function in this model | +| --- | --- | +| `kd_12`, `kd_23` | Dissociation constants for Nephrin-pY/Nck-SH2 and Nck-S/NWASP-p binding, respectively; both are set to 3500, eliminating affinity as a difference between the two edge types. | +| `koff_12`, `koff_23` | Unbinding rates for the two edge types; both are 1000. | +| `kon_12 = koff_12/kd_12`, `kon_23 = koff_23/kd_23` | Derived association rates. The same ratio for both families makes site count, concentration, and network topology—not kinetic asymmetry—the source of different clustering behavior. | + +There are no functions or conditional rate laws. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `Nephrin` | 3 | `pY1`, `pY2`, `pY3` | None | None | Trivalent upstream scaffold; each phosphotyrosine-like site can bind one Nck SH2 domain. | +| `Nck` | 4 | `S1`, `S2`, `S3`, `Sh2` | None | None | Central adaptor: `Sh2` binds Nephrin, while three S sites independently bind NWASP, allowing Nck to bridge the other two molecule classes. | +| `NWASP` | 6 | `p1`–`p6` | None | None | Hexavalent downstream partner whose six proline-rich sites can each bind any Nck S site, providing the greatest branching capacity. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial and begins with only free molecules: 300 Nephrin, 900 Nck, and 450 NWASP. This 1:3:1.5 ratio supplies exactly three Nck molecules per Nephrin and two Nck molecules per NWASP on average, while the available sites permit much larger crosslinked assemblies. No phosphorylation reactions occur; the `pY` and `p` names denote already available binding sites. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–18 enumerate the complete 3-by-6 matrix of Nck S-site/NWASP p-site contacts. Rules 19–21 connect each Nephrin pY site to the single Nck SH2 site, making Nck the bridge between Nephrin-rich and NWASP-rich portions of a cluster. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–3 | Reversible | Nck `S1`, `S2`, or `S3`, respectively; NWASP `p1` | Creates or releases one Nck-S–NWASP-p1 bond using `kon_23`/`koff_23`. | Gives NWASP site p1 access to all three equivalent Nck S interfaces. | +| 4–6 | Reversible | Nck `S3`, `S2`, or `S1`, respectively; NWASP `p2` | Creates/releases the corresponding bond with the same `kon_23`/`koff_23` pair. | Completes the three Nck choices for NWASP p2; source numbering orders the S variants differently but does not change their kinetics. | +| 7–9 | Reversible | NWASP `p3`; Nck `S2`, `S1`, or `S3` in rules 7, 8, and 9, respectively | Adds/removes one p3 contact at `kon_23`/`koff_23`. | Extends the identical-affinity interaction matrix to the third NWASP site while preserving the source's nonnumerical S-site ordering. | +| 10–12 | Reversible | Nck `S1`–`S3`, respectively; NWASP `p4` | Adds/removes one Nck–p4 bond at the shared rates. | Provides the fourth independently occupiable NWASP branch. | +| 13–15 | Reversible | Nck `S1`–`S3`, respectively; NWASP `p5` | Adds/removes one Nck–p5 bond at the shared rates. | Provides the fifth branch and increases the number of possible cluster topologies. | +| 16–18 | Reversible | NWASP `p6`; Nck `S1`, `S3`, and `S2`, respectively | Adds/removes one p6 contact using `kon_23`/`koff_23`. | Completes the 18-rule Nck–NWASP interaction matrix; all 6 NWASP sites can bind all 3 Nck S sites. | +| 19–21 | Reversible | Nephrin `pY1`, `pY2`, or `pY3`, respectively; Nck `Sh2` | Creates/releases one pY–SH2 bond using `kon_12`/`koff_12`. | Recruits Nck to any of Nephrin's three sites, enabling an Nck molecule to connect Nephrin to NWASP through its still-independent S sites. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `tot_Nephrin`, `tot_Nck`, `tot_NWASP` | Molecule count | Every molecule of each type | Conservation checks for the three fixed pools. | +| `free_Nephrin`, `free_Nck`, `free_NWASP` | Molecule count | Molecules with all declared sites unbound | Strict monomer/free-pool readouts; partial occupancy excludes a molecule from the corresponding free count. | +| `fully_bound_Nephrin`, `fully_bound_Nck`, `fully_bound_NWASP` | Molecule count | Molecules with every site occupied | Measures saturation of each valency class rather than cluster size. Fully bound Nck requires all three S sites and Sh2 to be occupied. | +| `cluster_neph_nck_nw` | Molecule count | Connected complexes containing Nephrin, Nck, and NWASP | Reports ternary network formation, but pattern embeddings may count a large complex more than once when it contains multiple matching molecules. | +| `cluster_nck_nw` | Molecule count | Connected complexes containing Nck and NWASP, whether or not Nephrin is also present | Broader Nck–NWASP association readout; ternary clusters can contribute because Nephrin is not excluded. | + +## 8. Actions and simulation workflow + +The source does not generate a network or run ODE, stochastic, or network-free simulation. Its only action writes an XML representation, so quantitative time courses or equilibrium scans must be supplied by an external workflow. + +## 9. Technical caveats and ambiguities + +- The metadata description says “NFkB oscillations,” but the BNGL and comments unambiguously describe Nephrin–Nck–NWASP clustering; the metadata description is inconsistent. +- All sites within an interface family share identical rates, so the model intentionally omits site-specific affinity or cooperativity. +- Molecule-count cluster observables count pattern matches, not necessarily unique physical condensates. +- The rules model reversible connectivity but no explicit phase, volume, diffusion, or excluded-volume physics; “condensation” is inferred from multivalent cluster behavior. +- The active file exports XML only despite metadata listing ODE compatibility. diff --git a/Published/Chattaraj2021/Chattaraj_2021_metadata.yaml b/Published/Chattaraj2021/Chattaraj_2021_metadata.yaml new file mode 100644 index 00000000..e3c8917f --- /dev/null +++ b/Published/Chattaraj2021/Chattaraj_2021_metadata.yaml @@ -0,0 +1,67 @@ +id: "Chattaraj_2021" +name: "Chattaraj 2021" +description: "NFkB oscillations" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2021" + pmid: "34236318" + reference: "Chattaraj et al., 2021" + +tags: ["published", "chattaraj", "2021", "nephrin", "nck", "nwasp", "writexml"] +date: + last_tested: 2026-07-19 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: false + bngp_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: false + comments: "MCP XML file couldn't be generated nfsim gets stuck while loading file" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: true + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Chattaraj_2021.bngl" + +playground: + visible: false + gallery_categories: ["neuroscience"] + featured: false + difficulty: "advanced" + + + + + + diff --git a/Published/Chattaraj2021/metadata.yaml b/Published/Chattaraj2021/metadata.yaml index 4a2b65f1..daef4c49 100644 --- a/Published/Chattaraj2021/metadata.yaml +++ b/Published/Chattaraj2021/metadata.yaml @@ -4,6 +4,7 @@ description: "NFkB oscillations" tags: ["published", "chattaraj", "2021", "nephrin", "nck", "nwasp", "writexml"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT_metadata.yaml b/Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT_metadata.yaml new file mode 100644 index 00000000..d8f96459 --- /dev/null +++ b/Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT_metadata.yaml @@ -0,0 +1,24 @@ +id: "Cheemalavagu_JAK_STAT" +name: "Cheemalavagu 2024" +description: "JAK-STAT signaling" +tags: ["published", "literature", "signaling", "cheemalavagu", "jak", "stat", "l1", "il6r", "gp130", "l2", "il10r1", "il10r2", "jak1", "jak2"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/literature/Cheemalavagu_JAK_STAT.bngl" +playground: + visible: true + gallery_categories: ["immunology"] + featured: false + difficulty: "intermediate" diff --git a/Published/CheemalavaguJAKSTAT/metadata.yaml b/Published/CheemalavaguJAKSTAT/metadata.yaml index b1aa6a3a..deb08d40 100644 --- a/Published/CheemalavaguJAKSTAT/metadata.yaml +++ b/Published/CheemalavaguJAKSTAT/metadata.yaml @@ -4,6 +4,7 @@ description: "JAK-STAT signaling" tags: ["published", "literature", "signaling", "cheemalavagu", "jak", "stat", "l1", "il6r", "gp130", "l2", "il10r1", "il10r2", "jak1", "jak2"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/ChylekFceRI2014/ChylekFceRI2014_aigenerated.md b/Published/ChylekFceRI2014/ChylekFceRI2014_aigenerated.md new file mode 100644 index 00000000..b9fc4122 --- /dev/null +++ b/Published/ChylekFceRI2014/ChylekFceRI2014_aigenerated.md @@ -0,0 +1,45 @@ +# Model Explanation: Chylek 2014 (FceRI) + +## One-sentence summary + +Transient exposure of two haptens on DNP-BSA controls FcεRI crosslinking and launches a Lyn/Fyn/Syk network that activates LAT–PLCγ1 and PI3K lipid signaling while PAG1–Csk and phosphatases provide restraint. + +## What the model shows + +This detailed early FcεRI signaling model connects dynamic antigen accessibility to receptor aggregation, Src-family kinase regulation, Syk activation, adaptor-complex assembly, and phosphoinositide conversion. It is designed to distinguish how receptor-chain phosphosites, Lyn and Fyn, PAG1–Csk inhibition, LAT scaffolding, and PI3K/PLCγ1 branches contribute to the proximal response. + +## Biological story + +The ligand DNP-BSA carries two virtual haptens that fluctuate between buried and exposed states. Only exposed haptens bind IgE–FcεRI, and simultaneous exposure allows one ligand to crosslink two receptors. Lyn and Fyn associate with aggregated receptors, phosphorylate receptor β and γ chains, and activate Syk. Active Syk and Fyn then build LAT-, Grb2-, Gab2-, Grap2-, Lcp2-, PI3K-, Btk-, and PLCγ1-containing complexes. In parallel, phosphorylated PAG1 recruits Csk, which adds inhibitory phosphates to Lyn and Fyn, and multiple dephosphorylation processes reset the network. + +## Main biological players + +- **DNP-BSA and IgE–FcεRI:** fluctuating bivalent antigen and receptor complexes whose crosslinking initiates signaling. +- **Lyn, Fyn, Syk, PAG1, and Csk:** activating kinases, scaffold, and inhibitory kinase that control receptor-proximal phosphorylation. +- **LAT, PLCγ1, Grb2, Gab2, Grap2, and Lcp2:** adaptor network that connects activated Syk to downstream enzymes. +- **PI3K, Btk, and the PIP2/PIP3 lipid pools:** lipid-signaling branch that supports PLCγ1 recruitment and activation. +- **SHIP/Inpp5d:** phosphoinositide phosphatase recruited to a phosphorylated receptor β-chain site. + +## Mechanism in plain English + +Hapten exposure allows DNP-BSA to bind one receptor and then crosslink a second. Lyn and Fyn dock through receptor-binding domains or phosphorylated receptor sites, acquire activating phosphates, and phosphorylate the receptor β and γ motifs. Doubly phosphorylated γ recruits Syk, which is further activated and phosphorylates LAT. LAT phosphosites recruit PLCγ1 and Grb2/Gab2 or Grap2/Lcp2 assemblies; Gab2 recruits PI3K, which converts PIP2 into PIP3, allowing Btk recruitment and Btk-dependent PLCγ1 phosphorylation. Active PLCγ1 binds PIP2 and generates IP3 and DAG. PAG1 recruits Csk to phosphorylate the inhibitory tails of Lyn and Fyn, while SHIP and other dephosphorylation reactions reduce receptor, kinase, adaptor, and lipid signals. + +## Key modeled events + +- DNP-BSA haptens switch between buried and exposed states, making receptor binding and crosslinking dynamically conditional on antigen accessibility. +- Lyn and Fyn phosphorylate FcεRI β and γ motifs, and phosphorylated γ recruits and activates Syk. +- Syk phosphorylates LAT, allowing PLCγ1 and multi-adaptor complexes to assemble around distinct LAT sites. +- Gab2 recruits PI3K, PIP3 recruits Btk, and Btk activates PLCγ1 to generate IP3 and DAG from PIP2. +- PAG1-bound Csk, SHIP, and dephosphorylation reactions oppose Src-family kinase, receptor, adaptor, and lipid activation. + +## What the model measures + +Readouts include phosphorylation of LAT, the FcεRI β and γ chains, Syk, Gab2, PLCγ1, PAG1, and the Syk activation loop; recruitment of PI3K, Btk, SHIP, and PLCγ1-containing complexes; PIP2, PIP3, PI(3,4)P2, IP3, and ligand crosslinks; Lyn and Fyn binding or autoinhibited conformations; and the number of ligand haptens that are exposed. This combination connects antigen availability to receptor activation, scaffold assembly, and lipid second-messenger production. + +## Expected behavior in plots + +The exposed-hapten measurements should control how rapidly free ligand is converted into receptor crosslinks. Receptor β/γ phosphorylation should precede Syk activation and LAT phosphorylation, with LAT-associated PI3K and PLCγ1 complexes appearing downstream. PIP3 and Btk recruitment should support PLCγ1 Y783 phosphorylation, after which IP3 should rise as PIP2 is consumed. PAG1 phosphorylation, Csk recruitment, Lyn/Fyn inhibitory conformations, and SHIP binding should develop as counter-signals that limit the amplitude or duration of receptor and lipid-pathway readouts. + +## Caveats + +The antigen is represented with two virtual haptens and the receptor includes only one of its two γ chains, simplifying actual FcεRI stoichiometry. Several pairs of nearby tyrosines are lumped into single modeled states, so the corresponding measurements do not resolve individual residues. The model focuses on early phosphorylation and lipid signaling and does not extend to calcium dynamics, degranulation, or cytokine production. diff --git a/Published/ChylekFceRI2014/ChylekFceRI2014_aigenerated_detailed.md b/Published/ChylekFceRI2014/ChylekFceRI2014_aigenerated_detailed.md new file mode 100644 index 00000000..af17f9f9 --- /dev/null +++ b/Published/ChylekFceRI2014/ChylekFceRI2014_aigenerated_detailed.md @@ -0,0 +1,120 @@ +# Detailed Model Explanation: Chylek 2014 FcεRI signaling model + +## 1. Model overview + +This model follows early FcεRI signaling from transient exposure of two ligand haptens and receptor crosslinking through parallel Lyn- and Fyn-dependent kinase branches. It couples receptor and Syk phosphorylation to PAG1–CSK feedback, LAT adaptor assembly, PI3K/PIP3 signaling, PLCG1 activation, and INPP5D-mediated lipid turnover. + +## 2. BNGL block inventory + +The model contains 114 active parameter lines, 23 molecule types, 19 seed species, 133 reaction rules, and 32 molecule-count observables. It defines no functions, compartments, anchors, or embedded actions. + +## 3. Parameters, functions, and rate laws + +Rates are mass-action constants expressed for molecule-number simulation in a 2% cell fraction; bimolecular constants are divided by Avogadro's number and the simulated cell or extracellular volume. Parameter families distinguish binding (`kf`/`kr`), catalytic phosphorylation (`kp` or `kc`), dephosphorylation (`kdp`/`dp`), and lipid interconversion. + +| Parameter group or names | Function in this model | +| --- | --- | +| `NA`, `celldensity`, `Fx`, `ECFvol`, `simECFvol`, `Cellvol`, `simCellvol` | Define extracellular and cellular volumes and convert concentration-based association constants for the simulated 2% fraction. | +| `ProteinTot`, `SimProteinTot`, `LigTot`, `SimLigTot` | Set common starting abundances for most proteins and for the bivalent ligand after fractional-cell scaling. | +| `lambda_p`, `lambda_m`, `kfl`, `kxl`, `krl` | Control buried-to-exposed hapten switching, ligand capture, receptor crosslinking, and dissociation. `kfl` is zero here, making receptor engagement dependent on an external stimulus protocol. | +| `kfRecLyn1/2`, `krRecLyn1/2`, `kfLynIn`, `krLynIn` | Govern Lyn binding through its unique or SH2 domain and intramolecular sequestration of SH2 by phosphorylated Y508. | +| `kpLynB1/2`, `kpLynG1/2`, `kfRecSyk`/`krRecSyk`, `kpLynSyk1/2`, `kpSykSyk0/P` | Set Lyn-dependent receptor phosphorylation, Syk docking and Y346 phosphorylation, and Syk activation-loop transphosphorylation. The paired rates distinguish unique-domain versus SH2-bound Lyn and inactive versus activated Syk. | +| `kfPagLynSH3`, `kfPagLynSH3_2`, `krPagLynSH3`, `kfPagLynSH2`, `kfPagLynSH2_2`, `krPagLyn2point`, `kpLynPag` | Control one- and two-point Lyn attachment to PAG1 and Lyn-dependent phosphorylation of PAG1 docking sites. Tethered second-site capture uses a fast first-order rate. | +| `kfCskPag`/`krCskPag`, `kpCskLyn` | Recruit CSK to PAG1 pY317 and install inhibitory Lyn Y508 phosphorylation. | +| Fyn analogues of the receptor, intramolecular, PAG1, and CSK parameters; `eff` | Reproduce the Lyn branch for Fyn. Fyn catalytic rates toward receptor, Syk, and PAG1 are divided by `eff = 5`, while binding rates inherit Lyn values; CSK targets Fyn Y531. | +| `kfSykLat`/`krSykLat`, `kpSykLat1/2` | Govern transient Syk–LAT encounters and phosphorylation of LAT Y136/Y175, with activated Syk using the faster catalytic rate. | +| `KD_LatPlcg`, `kfLatPlcg`/`krLatPlcg`; `kfLatGrb2`/`krLatGrb2`; `kfLatGrap2`/`krLatGrap2` | Set recruitment of PLCG1, GRB2, and GRAP2 to their LAT phosphotyrosine sites; the PLCG1 on-rate is derived from its dissociation constant. | +| `KD_Grb2Gab2`, `kfGrb2Gab2`/`krGrb2Gab2`, `kfGrap2Lcp2`/`krGrap2Lcp2`, `KD_Lcp2Plcg1`, `kfLcp2Plcg1`/`krLcp2Plcg1` | Assemble the GRB2–GAB2 and GRAP2–LCP2–PLCG1 adaptor branches. The source declares the GRB2/GAB2 constant and associated rates twice; later definitions may override earlier ones depending on parser behavior. | +| `kfFynGab2`/`krFynGab2`, `kpFynGab2`, `kfGab2Pi3k`/`krGab2Pi3k` | Control Fyn phosphorylation of GAB2 Y441 and PI3K recruitment to that phosphosite. | +| `kfPi3kPip2`/`krPi3kPip2`, `kpPi3k`, `kfBtkPip3`/`krBtkPip3`, `kfBtkPlcg`/`krBtkPlcg`, `kpBtkPlcg` | Convert PI45P2 to PI345P3, recruit BTK to PI345P3, and let BTK phosphorylate PLCG1 Y783. | +| `kfPlcgPip2`, `krPlcgPip2`, `kcPlcgP`, `kcPlcg0` | Parameterize PLCG1 access to PI45P2 and catalysis by phosphorylated or unphosphorylated PLCG1; no active reaction rules consume these constants in this file. | +| `kfShipRec`/`krShipRec`, `kfShipPip3`/`krShipPip3`, `kdpShipPip3`, `kfShipPip2`/`krShipPip2` | Govern INPP5D recruitment to receptor pY224, binding and removal of PI345P3, and a declared but unused PI34P2-binding pair. | +| `kPten`, `kfP5`, `krP5` | Control background PI345P3-to-PI45P2 conversion and reversible PI4P/PI45P2 interconversion. | +| `p`, `dp` | Apply uniform nonspecific phosphorylation and dephosphorylation to receptor, kinase, scaffold, adaptor, and PLCG1 sites. | + +There are no active functions; algebraic relationships such as Fyn's `1/eff` catalytic scaling and affinity-derived on-rates are resolved in the parameter namespace. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `Lig` | 2 | two repeated `hap` sites | Each `hap`: buried `b`, exposed `e` | None | Bivalent ligand whose independently exposed haptens capture and crosslink receptors. | +| `Rec` | 5 | two repeated `fab`, `b_Y218`, `b_Y224`, `g_Y65_Y76` | Each Y variable: `0`, `P` | None | Lumped FcεRI/IgE receptor unit with two ligand-binding sites and β/γ-chain signaling phosphosites. | +| `Lyn` | 5 | `U`, `SH3`, `SH2`, `Y397`, `Y508` | Both Y sites: `0`, `P` | None | Src-family kinase recruited to receptor and PAG1; Y508 supports modeled intramolecular inhibition. | +| `Fyn` | 6 | `U`, `SH3`, `SH2`, `PTK`, `Y420`, `Y531` | Both Y sites: `0`, `P` | None | Parallel Src-family kinase that also phosphorylates GAB2; Y531 supports autoinhibitory closure. | +| `Syk` | 4 | `tSH2`, `Y346`, `PTK`, `Y519_Y520` | Both Y variables: `0`, `P` | None | Binds phosphorylated receptor γ sites and propagates activation to LAT after transphosphorylation. | +| `Pag1` | 5 | `PRS1`, `Y165_Y183`, `PRS2`, `Y317`, `Y386_Y409` | Three Y variables: `0`, `P` | None | Multisite scaffold that captures Fyn/Lyn and CSK to form kinase-specific inhibitory complexes. | +| `Csk` | 1 | `SH2` | None | None | PAG1-recruited kinase that phosphorylates inhibitory Lyn Y508 or Fyn Y531. | +| `Lat` | 2 | `Y136`, `Y175` | Both: `0`, `P` | None | Syk substrate whose two phosphosites recruit PLCG1 or adaptor proteins. | +| `Plcg1` | 4 | `SH2`, `SH3`, `PLC`, `Y783` | `Y783`: `0`, `P` | None | LAT/LCP2-associated effector activated by BTK phosphorylation in the implemented rules. | +| `Grb2`, `Grap2` | 2 each | Grb2: `SH2`, `cSH3`; Grap2: `SH2`, `SH3` | None | None | Adaptors linking LAT Y175 to GAB2–PI3K or LCP2–PLCG1, respectively. | +| `Gab2` | 2 | `PRS`, `Y441` | `Y441`: `0`, `P` | None | GRB2-bound scaffold phosphorylated by Fyn to recruit PI3K. | +| `Lcp2` | 2 | `RxxK`, `PRS` | None | None | GRAP2-linked adaptor that offers a second PLCG1 recruitment site. | +| `Pi3k` | 2 | `p85_SH2`, `PI3Kc` | None | None | Binds GAB2 pY441 and catalyzes PI45P2 conversion to PI345P3. | +| `Btk` | 2 | `PH`, `PTK` | None | None | Recruited by PI345P3 and phosphorylates PLCG1 Y783. | +| `Inpp5d` | 3 | `SH2`, `IPP`, `C2` | None | None | Receptor-recruited lipid phosphatase that consumes PI345P3. | +| `PI34P2`, `PI45P2`, `PI345P3` | 1 each | `bind` | None | None | Explicit phosphoinositide pools; PI45P2 is the PI3K substrate, PI345P3 recruits BTK, and PI34P2 is declared as a potential product/readout but is not generated by an active rule. | +| `PI4P`, `IP3`, `DAG`, `Sink` | 0 each | None | None | None | PI4P exchanges with PI45P2; Sink enables background PI345P3 removal. IP3 and DAG are declared output species but are not produced by active rules. | + +## 5. Compartments, anchors, initial species, and setup + +The model has no explicit compartments or anchors, so membrane-associated receptors, adaptors, and lipids are represented through molecule identity and bonds rather than localization syntax. Ligand begins with both haptens buried, and the receptor, kinases, adaptors, and enzymes begin free and unphosphorylated at a shared scaled protein abundance. PI45P2, PI4P, and Sink are initially present at that same scale; PI345P3, PI34P2, IP3, and DAG have no seed pools and can appear only if rules produce them—of these, only PI345P3 is actively generated. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–22 expose ligand, crosslink receptors, and activate the Lyn/Syk core. Rules 23–69 implement parallel PAG1-based Lyn and Fyn feedback; rules 70–105 build LAT, PI3K, BTK, PLCG1, and INPP5D branches, followed by nonspecific phosphosite turnover in rules 106–133. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | Reversible | Either ligand `hap` site | Switches one hapten between buried and exposed states at `lambda_p` and `lambda_m`. | Gates receptor accessibility without creating or destroying ligand. | +| 2–5 | One-way | Exposed ligand haptens; receptor `fab` sites | Rules 2–3 capture a receptor through an exposed hapten in the two possible state contexts, rule 4 adds a second receptor to the other exposed hapten, and rule 5 releases a hapten–receptor bond. | Produces the receptor dimers that initiate signaling; with `kfl = 0`, capture is disabled until externally enabled. | +| 6–11 | One-way | Receptor b_Y218; Lyn `U`, `SH2`, Y508 | Rules 6–9 separately form and release unique-domain binding to unphosphorylated receptor or SH2 binding to pY218. Rules 10–11 close and reopen the intramolecular SH2–pY508 bond. | Controls Lyn recruitment and inhibitory sequestration as explicit directional steps. | +| 12–17 | One-way | Crosslinked receptors; receptor Y218, Y224, Y65_Y76; Lyn bound through `U` or `SH2` | Rules 12/13 phosphorylate Y218, 14/15 Y224, and 16/17 the lumped γ-chain site; the first member uses the unique-domain rate and the second the faster SH2-bound rate. | Writes the receptor phosphotyrosines needed for kinase retention, Syk binding, and INPP5D recruitment. | +| 18–20 | Mixed | Receptor pY65_Y76; Syk `tSH2`/Y346; receptor-bound Lyn | Rule 18 reversibly recruits Syk. Rules 19–20 phosphorylate Syk Y346 via unique-domain- or SH2-bound Lyn. | Loads and primes Syk on the phosphorylated receptor γ site. | +| 21–22 | One-way | Two receptor-bound Syk molecules; target Syk Y519_Y520 | One Syk changes the partner's activation-loop variable from `0` to `P`; unphosphorylated Syk uses `kpSykSyk0`, activated Syk the doubled `kpSykSykP`. | Makes receptor crosslinking support cooperative Syk activation. | +| 23–28 | One-way | Lyn `SH3`/`SH2`; PAG1 `PRS2`/Y386_Y409 | Forms either PAG1 contact from solution or rapidly adds it after the other contact has tethered Lyn; separate rules release the SH3 bond or both contacts. | Creates a two-point Lyn–PAG1 complex with avidity-like tethered capture. | +| 29–36 | One-way | PAG1 Y386_Y409, Y165_Y183, Y317; PAG1-bound Lyn | Lyn phosphorylates the three PAG1 variables across one- and two-point occupancy contexts: rule 29 targets Y386_Y409, 30–32 target Y165_Y183, and 33–36 target Y317. | Builds Lyn docking and CSK recruitment sites on the negative-feedback scaffold. | +| 37–40 | Mixed | PAG1 pY317; CSK `SH2`; PAG1-bound Lyn Y508 | Rule 37 reversibly recruits CSK. Rules 38–40 phosphorylate Lyn Y508 in three permitted Lyn–PAG1 topologies. | Converts the Lyn–PAG1 complex into a CSK-dependent inhibitory circuit. | +| 41–46 | One-way | Receptor b_Y218; Fyn `U`, `SH2`, Y531 | Mirrors rules 6–11 for Fyn: directional receptor association/dissociation through `U` or `SH2`, followed by intramolecular SH2–pY531 closure and reopening. | Gives Fyn an independently represented recruitment and autoinhibition cycle. | +| 47–54 | One-way | Crosslinked receptors; receptor Y218/Y224/Y65_Y76; Syk Y346; receptor-bound Fyn | Rules 47–52 phosphorylate the three receptor variables through unique-domain or SH2-bound Fyn; rules 53–54 phosphorylate Syk Y346 in those two contexts. All Fyn catalytic rates are Lyn rates divided by `eff`. | Supplies a slower parallel route for receptor and Syk phosphorylation. | +| 55–60 | One-way | Fyn `SH3`/`SH2`; PAG1 `PRS1`/Y165_Y183 | Forms one- or two-point Fyn–PAG1 attachments, adds the second contact from a tethered state, and releases one or both contacts. | Builds the Fyn-specific half of the PAG1 scaffold using sites distinct from Lyn's. | +| 61–66 | One-way | PAG1 Y386_Y409/Y317; PAG1-bound Fyn | Rules 61–63 phosphorylate Y386_Y409 and rules 64–66 phosphorylate Y317 across three Fyn-binding topologies at the `eff`-reduced PAG1 rate. | Lets Fyn prepare the common CSK docking module despite its distinct PAG1 contacts. | +| 67–69 | One-way | PAG1 pY317; CSK; Fyn Y531 | CSK changes Fyn Y531 from `0` to `P` in three one- or two-point Fyn–PAG1 arrangements. | Closes the Fyn negative-feedback loop through its inhibitory tyrosine. | +| 70–78 | One-way | Receptor-bound Syk `PTK`; LAT Y136 or Y175 | Rules 70–73 bind, release, or phosphorylate Y136; rules 75–78 repeat this for Y175. Activated Syk uses `kpSykLat2`, whereas unactivated Syk uses `kpSykLat1`; rule 74 separately recruits PLCG1 to pY136. | Converts Syk activation into two differentiated LAT docking sites and begins PLCG1 recruitment. | +| 74, 79–83 | Reversible | LAT pY136/pY175; PLCG1 `SH2`; GRB2/GRAP2 `SH2`; GAB2 `PRS`; LCP2 `RxxK`/`PRS`; PLCG1 `SH3` | Rule 74 binds PLCG1 to pY136. Rules 79–80 competitively recruit GRB2 or GRAP2 to pY175; 81 links GRAP2 to LCP2, 82 links GRB2 to GAB2, and 83 links LCP2 to PLCG1. | Splits LAT output into PLCG1, GAB2–PI3K, and LCP2-supported PLCG1 assemblies. | +| 84–87 | One-way | Fyn `PTK`; LAT–GRB2–GAB2 complex; GAB2 Y441 | Rules 84–85 create a transient Fyn–GAB2 catalytic contact from two Fyn recruitment contexts; rule 86 releases unchanged GAB2, while rule 87 releases it with Y441 phosphorylated. | Makes the assembled GRB2/GAB2 branch competent to recruit PI3K. | +| 88 | Reversible | GAB2 pY441; PI3K `p85_SH2` | Creates or releases the GAB2–PI3K bond. | Couples Fyn-dependent adaptor phosphorylation to lipid kinase recruitment. | +| 89–92 | One-way | Recruited PI3K `PI3Kc`; PI45P2 | PI3K binds PI45P2 (89), can release it unchanged (90), or catalyze PI345P3 production while retaining (91) or deleting (92) the matched substrate copy. | Generates the PIP3-like signal while using alternative BNGL product semantics to manage the lipid pool. | +| 93–96 | Mixed | PI345P3; BTK `PH`/`PTK`; recruited PLCG1 Y783 | PI345P3 reversibly recruits BTK. BTK then forms a transient PLCG1 contact, releases unchanged substrate, or releases PLCG1 with Y783 phosphorylated. | Links PI3K lipid production to PLCG1 activation. | +| 97–102 | Mixed | Receptor pY224; INPP5D `SH2`/`IPP`/`C2`; PI345P3; Sink | Rules 97–99 recruit and release INPP5D through two receptor-context routes, with C2-tethered capture accelerated 100-fold. Rules 100–101 bind then delete PI345P3; rule 102 provides slower sink-mediated deletion. | Opposes PI3K by consuming PI345P3 through receptor-coupled and background routes. | +| 103–105 | One-way | PI345P3, PI45P2, PI4P | Rule 103 converts PI345P3 to PI45P2 while deleting the reactant; rules 104–105 interconvert PI4P and PI45P2. | Replenishes and drains the PI45P2 substrate pool independently of receptor complexes. | +| 106–111 | One-way | Receptor Y218, Y224, Y65_Y76 | Consecutive `p`/`dp` rule pairs add or remove phosphorylation at each receptor variable. | Supplies basal receptor-site turnover outside Lyn/Fyn-containing crosslinks. | +| 112–119 | One-way | Lyn Y508, Fyn Y531, Syk Y346/Y519_Y520 | Consecutive phosphorylation/dephosphorylation pairs turn over the inhibitory Src-family sites and both Syk sites. | Maintains resting enzyme-state flux alongside the scaffold-specific catalytic routes. | +| 120–133 | One-way | PAG1 Y317/Y165_Y183/Y386_Y409; GAB2 Y441; LAT Y136/Y175; PLCG1 Y783 | Seven consecutive `p`/`dp` pairs independently turn over these downstream phosphosites. | Produces basal occupancy and decay for feedback, adaptor, scaffold, and effector readouts. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `Rec_pY218`, `Rec_pY224`, `Rec_pY65_Y76` | Molecule count | Receptor units phosphorylated at each β- or γ-chain variable, regardless of bond occupancy. | Site-specific receptor activation measures; one multisite receptor contributes to every matching readout. | +| `Syk_pY346`, `Syk_pY519_520`, `Lyn_pY508`, `Fyn_pY508` | Molecule count | Syk priming/activation-loop states and inhibitory Src-family phosphorylation. | Distinguishes Syk activation stages and kinase inhibitory-site occupancy. Despite its name, `Fyn_pY508` actually matches Fyn Y531. | +| `Lat_pY136`, `Lat_pY175`, `Gab2_pY441`, `Plcg1_pY783`, `Pag_Y165`, `Pag_Y409` | Molecule count | Phosphorylated scaffold, adaptor, effector, and PAG1 lumped sites. | Reports propagation and feedback, including phosphorylation produced by both specific and nonspecific rules. | +| `LynUbound`, `LynSH2bound`, `Shipbound`, `Btk_recruited` | Molecule count | Lyn with occupied unique or SH2 domains, receptor-bound INPP5D, and PIP3-bound BTK. | Recruitment-state readouts; a Lyn bound at both domains contributes to both Lyn observables. | +| `LynIn`, `FynIn` | Molecule count | Closed intramolecular SH2–inhibitory-pY bonds in Lyn or Fyn. | Directly measures the modeled autoinhibited conformations rather than phosphorylation alone. | +| `Lat_Plc`, `Plc_pip2`, `PI3K_recruited` | Molecule count | LAT–PLCG1, PLCG1–PI45P2, and complete LAT–GRB2–GAB2–PI3K complexes. | `Lat_Plc` and `PI3K_recruited` are active assembly readouts; `Plc_pip2` remains zero because no active rule binds PLCG1 to PI45P2. | +| `PI345P3`, `PI34P2`, `PI45P2`, `IP3` | Molecule count | Counts of the named lipid or soluble-product species in any allowed binding state. | PI345P3 and PI45P2 are dynamic; PI34P2 and IP3 lack active production rules and therefore remain absent from the specified setup. | +| `LigFree`, `LigTotal` | Molecule count | All ligand molecules with unconstrained hapten states/bonds; both patterns are broad. | These patterns do not explicitly require an unbound ligand, so `LigFree` is not a strict free-ligand measure and may track the same total embeddings as `LigTotal`. | +| `Crosslinks` | Molecule count | Ligands using both exposed haptens to bind two receptors. | Measures receptor-crosslinking embeddings rather than necessarily unique connected components. | +| `DNP_exposed_0_of_2`, `DNP_exposed_1_of_2`, `DNP_exposed_2_of_2` | Molecule count | Ligands with zero, one, or two exposed haptens, allowing either bound or free sites. | Partitions ligand by accessibility state; repeated identical `hap` sites can introduce embedding multiplicity, especially in the one-exposed-state pattern. | + +## 8. Actions and simulation workflow + +No action commands are embedded, so loading the model alone neither generates a network nor runs a trajectory. The metadata identifies ODE simulation, but an external workflow must first enable ligand capture by changing the zero-valued `kfl`, then generate the reaction network and integrate the desired basal/stimulated time course. + +## 9. Technical caveats and ambiguities + +- The file contains parser-sensitive features: repeated identical sites, `DeleteMolecules`, wildcard bonds, and duplicate parameter declarations. The metadata consequently marks it as not BNG2-compatible even though ODE is listed as the intended simulation method. +- `KD_Grb2Gab2`, `krGrb2Gab2`, and `kfGrb2Gab2` are declared twice with different dissociation-rate definitions; effective behavior depends on how the parser resolves duplicate names. +- Several declared mechanisms are incomplete in the active rules: PLCG1 lipid hydrolysis constants are unused, and no rules create IP3, DAG, or PI34P2. Those observables should not be interpreted as functioning pathway outputs in this version. +- Some names are misleading or lumped: `Fyn_pY508` observes Y531, `Pag_Y165` covers Y165/Y183, and `Pag_Y409` covers Y386/Y409. +- Molecule observables count pattern matches; repeated ligand/receptor sites and multivalent assemblies can yield embedding counts rather than unique ligand or complex counts. diff --git a/Published/ChylekFceRI2014/ChylekFceRI_2014_metadata.yaml b/Published/ChylekFceRI2014/ChylekFceRI_2014_metadata.yaml new file mode 100644 index 00000000..f722452b --- /dev/null +++ b/Published/ChylekFceRI2014/ChylekFceRI_2014_metadata.yaml @@ -0,0 +1,39 @@ +id: "ChylekFceRI_2014" +name: "Chylek 2014 (FceRI)" +description: "FceRI signaling" + +citation: + year: "2014" + pmid: "24782869" + reference: "Chylek et al., 2014" +tags: ["published", "immunology", "chylekfceri", "2014", "lig", "rec", "lyn", "fyn", "syk", "pag1", "csk", "lat"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + nfsim_compatible: true + uses_cbngl_compartments: false + uses_vcell_compartments: false + uses_energy: false + uses_functions: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: true + uses_deletes_molecules: true + uses_exclude_include_reactants: false + uses_generate_network: false + default_sim_command: null +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/ChylekFceRI_2014.bngl" +playground: + visible: false + gallery_category: "immunology" + featured: false + difficulty: "advanced" diff --git a/Published/ChylekFceRI2014/metadata.yaml b/Published/ChylekFceRI2014/metadata.yaml index de4078e3..40a877e7 100644 --- a/Published/ChylekFceRI2014/metadata.yaml +++ b/Published/ChylekFceRI2014/metadata.yaml @@ -4,6 +4,7 @@ description: "FceRI signaling" tags: ["published", "immunology", "chylekfceri", "2014", "lig", "rec", "lyn", "fyn", "syk", "pag1", "csk", "lat"] category: "immunology" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/ChylekTCR2014/ChylekTCR2014_aigenerated.md b/Published/ChylekTCR2014/ChylekTCR2014_aigenerated.md new file mode 100644 index 00000000..b2ff694d --- /dev/null +++ b/Published/ChylekTCR2014/ChylekTCR2014_aigenerated.md @@ -0,0 +1,43 @@ +# Model Explanation: Chylek 2014 (TCR) + +## One-sentence summary + +TCR and CD28 co-engagement organizes Lck, Fyn, ZAP-70, phosphatases, and LAT-associated adaptors into an early phosphorylation network with both activating and inhibitory feedback. + +## What the model shows + +This model examines phosphorylation-site dynamics during early T-cell receptor (TCR) signaling. Three bivalent ligand types selectively crosslink CD28, TCR, or one of each, allowing comparison of pure co-stimulation, pure receptor engagement, and coupled TCR–CD28 signaling as the complexes recruit kinases, phosphatases, and LAT-associated adaptor proteins. + +## Biological story + +Ligands cluster CD28 and/or TCR, bringing Lck and Itk to CD28 and Fyn to TCR. Lck phosphorylates multiple TCR-chain tyrosines, creating docking sites for ZAP-70 and the phosphatase PTPN6. Activated ZAP-70 phosphorylates LAT and LCP2, enabling assembly of PLCγ1-, GRAP2-, NCK-, and WAS-containing complexes. PAG1–Csk and PTPN6-associated pathways oppose Src-family kinase activity and remove phosphate from several adaptor proteins, creating a dynamic balance rather than an irreversible activation cascade. + +## Main biological players + +- **TCR, CD28, and three ligand classes:** receptor/co-receptor inputs that can be engaged separately or together. +- **Lck, Fyn, Itk, and ZAP-70:** receptor-proximal kinases that establish and propagate phosphotyrosine signals. +- **PTPN6, PAG1, Csk, DOK1, and DOK2:** inhibitory or resetting regulators of kinase and adaptor phosphorylation. +- **LAT, PLCγ1, GRAP2, LCP2, NCK, and WAS:** downstream scaffolds and effectors that assemble after receptor activation. + +## Mechanism in plain English + +Crosslinking positions TCR and CD28 so their associated kinases can modify specific receptor-chain tyrosines. These phosphorylated sites recruit ZAP-70 and PTPN6, while CD28-associated Lck also activates Itk and helps phosphorylate bound ZAP-70. Active ZAP-70 modifies LAT at sites that separately recruit PLCγ1 and GRAP2; GRAP2 brings in LCP2, which supports NCK, WAS, and additional PLCγ1 assembly. Fyn can also reach WAS through receptor- or scaffold-associated complexes. At the same time, PAG1 recruits Csk to phosphorylate the inhibitory Lck tail, and PTPN6 removes activating phosphates from Lck, PAG1, DOK proteins, and other signaling components. + +## Key modeled events + +- Distinct ligands crosslink CD28 alone, TCR alone, or a TCR–CD28 pair, changing which kinases are brought into proximity. +- Lck phosphorylates several TCR-chain sites that recruit ZAP-70 or PTPN6 and thereby branch the signal into activation and negative regulation. +- Activated ZAP-70 phosphorylates LAT and LCP2, enabling assembly of PLCγ1-, GRAP2-, NCK-, and WAS-containing complexes. +- PAG1–Csk and PTPN6 pathways inhibit Lck and dephosphorylate adaptor proteins, shaping site-specific signal duration. + +## What the model measures + +The measurements emphasize phosphorylation of six TCR-chain tyrosine groups; activation-associated sites on ZAP-70, Lck, Itk, PTPN6, WAS, PAG1, DOK1, DOK2, PLCγ1, and LAT; the inhibitory Lck tail; and selected NCK complexes with TCR or LCP2. These readouts are designed to compare early site-specific phosphorylation and scaffold assembly rather than a later cellular phenotype. + +## Expected behavior in plots + +TCR phosphosites should respond most strongly when a ligand engages TCR, whereas CD28-containing complexes should enhance Lck and Itk recruitment and alter phosphorylation of ZAP-70 and downstream adaptors. ZAP-70 phosphorylation should precede or accompany LAT Y191 and PLCγ1 phosphorylation, while NCK–TCR and NCK–LCP2 complexes report two different routes into WAS-associated signaling. Inhibitory Lck Y505, PTPN6 phosphorylation, and PAG1-dependent feedback may rise alongside activation and shorten or reshape the peaks at Lck Y424 and the TCR sites. + +## Caveats + +This is an early signaling model centered on phosphosite kinetics and scaffold assembly; it does not extend to calcium, MAPK, transcription, or T-cell functional outcomes. Ligand classes are abstract tools for controlling TCR and CD28 crosslinking rather than a complete antigen-presentation model. Some related residues are lumped into single modeled sites, so a plotted signal may represent more than one biochemical tyrosine. diff --git a/Published/ChylekTCR2014/ChylekTCR2014_aigenerated_detailed.md b/Published/ChylekTCR2014/ChylekTCR2014_aigenerated_detailed.md new file mode 100644 index 00000000..a3b79c40 --- /dev/null +++ b/Published/ChylekTCR2014/ChylekTCR2014_aigenerated_detailed.md @@ -0,0 +1,117 @@ +# Detailed Model Explanation: Chylek 2014 TCR signaling model + +## 1. Model overview + +This model follows early T-cell receptor signaling initiated by three bivalent ligands that crosslink TCR, CD28, or one of each. It connects receptor-proximal LCK/FYN activity to ZAP70, LAT–LCP2 signalosome assembly, PLCG1 and WAS phosphorylation, while PTPN6 and the PAG1–CSK module provide opposing phosphatase and inhibitory-kinase control. + +## 2. BNGL block inventory + +The model contains 99 parameters, 20 molecule types, 20 seed species, 129 reaction rules, and 20 molecule-count observables. It has no functions, compartments, anchors, or embedded simulation actions. + +## 3. Parameters, functions, and rate laws + +Association constants are converted from concentration-based units using Avogadro's number and a simulated cell or extracellular volume representing 2% of a cell. Most rules use mass-action rates; paired `kf`/`kr` names govern binding, `kp` names govern phosphorylation, and `kdp` names govern dephosphorylation. + +| Parameter group or names | Function in this model | +| --- | --- | +| `NA`, `celldensity`, `Fx`, `ECFvol`, `simECFvol`, `Cellvol`, `simCellvol` | Establish the molecule-number and volume scaling used to convert bimolecular rate constants and initial copy numbers into the simulated 2% cell fraction. | +| `Ligtot`, `Proteintot`, `TCRtot`, `CD28tot` | Set the initial pools: each ligand class receives `Ligtot`, most signaling proteins receive `Proteintot`, and TCR and CD28 have distinct receptor totals. | +| `kfl`, `kfl_m`, `krl` | Control first-arm ligand capture, second-arm crosslinking, and ligand release. Both association rates are zero in this file because the accompanying RNF protocol is expected to set them when stimulation begins. | +| `kfLckCd28`/`krLckCd28`, `kfItkCd28`/`krItkCd28`, `kfTcrFyn`/`krTcrFyn`, `kfTcrNck`, `kfWasNck`/`krWasNck` | Govern constitutive or receptor-supported recruitment of LCK and ITK to CD28, FYN and NCK to TCR, and WAS to NCK. | +| `kfZapTcr`, `krZapTcr`, `kfZapCd3e`, `krZapCd3e`, `kfPtpTcr`, `krPtpTcr` | Set binding of ZAP70 and PTPN6 to phosphorylated TCR-chain sites; ZAP70 leaves the CD3ε-like sites forty times faster than the ζ-like sites. | +| `kpLckTcrz1`, `kpLckTcrz2`, `kpLckCd3e1`, `kpLckCd3e2`, `kpLckCd3g`, `kpLckCd3d` | Specify site-resolved LCK phosphorylation of the six TCR tyrosine variables exposed by a TCR–CD28 crosslink. | +| `act`, `kpLckLck1/2`, `kpLckItk1/2`, `kpLckPtp1/2`, `kpLckZap` | Control LCK-dependent phosphorylation of another LCK, ITK, PTPN6, and receptor-bound ZAP70. The `*2` variants are multiplied by `act`, representing enhanced catalysis by LCK lacking inhibitory Y505 phosphorylation. | +| `kfLckPtp`/`krLckPtp`, `kfLckPtp2`/`krLckPtp2`, `kdpLck192`, `kdpLck394` | Govern PTPN6 association with the two LCK phosphoforms and removal of phosphorylation from LCK Y192 and Y424. | +| `kfPagCsk`/`krPagCsk`, `kfPagLck`/`krPagLck`, `kpLckPag`, `kpCskLck` | Build the PAG1–LCK–CSK inhibitory module: LCK creates the CSK docking site and CSK phosphorylates inhibitory LCK Y505. | +| `kfPagPtp`, `kfPagPtp_cyt`, `cyt`, `krPagPtp`, `kdpPag` | Control PTPN6 capture by PAG1 and PAG1 dephosphorylation. The cytosolic encounter rate is reduced by the factor `cyt`; TCR-tethered encounters use the full rate. | +| `kfDok1Ptp`/`krDok1Ptp`, `kdpDok1`, `kfDok2Ptp`/`krDok2Ptp`, `kdpDok2` | Set recruitment of PTPN6 to the DOK adaptors and catalytic removal of their phosphotyrosines. | +| `kpWas`, `kfWasFyn`/`krWasFyn` | Control FYN access to NCK-bound WAS and phosphorylation of WAS Y291 in receptor- or LAT/LCP2-associated assemblies. | +| `kfZapLat132`, `kfZapLat191`, `krZapLat`, `kpZapLat2` | Describe transient ZAP70–LAT enzyme/substrate encounters and phosphorylation of LAT Y132 and Y191; Y191 capture is threefold faster. | +| `kfPlcgLat`/`krPlcgLat`, `kfLatGrap`/`krLatGrap`, `kfGrapLcp`/`krGrapLcp`, `kfNckLcp`/`krNckLcp` | Assemble the LAT–PLCG1 branch and the LAT–GRAP2–LCP2–NCK branch through phosphotyrosine and adaptor interactions. | +| `kfZapLcp`/`krZapLcp`, `kpZapLcp2`, `kfPlcgLcp`/`krPlcgLcp`, `kfLcpItk`/`krLcpItk`, `kpPlcg` | Control ZAP70 phosphorylation of the two LCP2 sites, LCP2 recruitment of PLCG1 and ITK, and ITK-mediated phosphorylation of PLCG1 Y783. | +| `kp1`–`kp4`, `kdp1`–`kdp5` | Provide low-level site-specific basal phosphorylation and dephosphorylation for receptors, kinases, adaptors, and effectors, allowing nonzero resting-state phosphoprotein populations. | + +There are no active functions; all rates are parameters or simple parameter products written directly on rules. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `Lig1`, `Lig2`, `Lig3` | 2 each | Lig1: two `aCD28`; Lig2: `aCD28`, `aCD3`; Lig3: two `aCD3` | None | None | Bivalent stimuli that selectively crosslink two CD28 molecules, a CD28–TCR pair, or two TCR molecules. | +| `TCR` | 9 | `epitope`, `Y149_D`, `Y171_G`, `Y111`, `Y123`, `fynbind`, `PRS_E`, `Y188_E`, `Y199_E` | Each named Y site: `0`, `P` | None | Receptor hub carrying six independently tracked phosphotyrosines plus ligand-, FYN-, and NCK-binding sites. | +| `CD28` | 3 | `epitope`, `PRS1`, `PRS2` | None | None | Costimulatory receptor whose two proline-rich sites recruit LCK and ITK. | +| `LCK` | 5 | `SH2`, `SH3`, `Y192`, `Y424`, `Y505` | Y sites: `0`, `P` | None | Receptor-proximal kinase; Y424 reports activation-loop phosphorylation, whereas Y505 supports CSK-mediated inhibition and intracomplex rate asymmetry. | +| `ITK` | 4 | `SH3`, `SH2`, `PTK`, `Y512` | `Y512`: `0`, `P` | None | CD28-recruited kinase that is activated by LCK and phosphorylates PLCG1 when positioned on LCP2. | +| `ZAP70` | 3 | `SH2`, `PTK`, `Y493` | `Y493`: `0`, `P` | None | Binds phosphorylated TCR sites and, when activated, phosphorylates LAT and LCP2. | +| `PTPN6` | 3 | `SH2`, `PTP`, `Y566` | `Y566`: `0`, `P` | None | SH2-recruited phosphatase that removes phosphorylation from LCK, PAG1, DOK1, and DOK2. | +| `PAG1` | 2 | `Y163`, `Y317` | Both: `0`, `P` | None | Scaffold coupling LCK to CSK and PTPN6, thereby linking kinase activity to inhibitory feedback. | +| `CSK` | 1 | `SH2` | None | None | Binds PAG1 pY317 and installs inhibitory LCK Y505 phosphorylation. | +| `DOK1`, `DOK2` | 1 each | `Y449`; `Y299` | Each: `0`, `P` | None | Phosphorylated adaptor substrates used to represent PTPN6-dependent dephosphorylation outputs. | +| `FYN` | 2 | `unique`, `PTK` | None | None | TCR-associated kinase that phosphorylates WAS in NCK-linked receptor or signalosome complexes. | +| `NCK` | 3 | `SH3_1`, `SH3_3`, `SH2` | None | None | Bridges TCR or phosphorylated LCP2 to WAS, connecting receptor signaling to the WAS branch. | +| `WAS` | 2 | `PRS`, `Y291` | `Y291`: `0`, `P` | None | NCK-bound effector phosphorylated by FYN in two alternative signaling assemblies. | +| `LAT` | 2 | `Y132`, `Y191` | Both: `0`, `P` | None | ZAP70 substrate whose phosphosites separately recruit PLCG1 and GRAP2. | +| `PLCG1` | 3 | `SH2`, `SH3`, `Y783` | `Y783`: `0`, `P` | None | Effector recruited to LAT and LCP2 and activated by ITK-dependent Y783 phosphorylation. | +| `GRAP2` | 2 | `SH2`, `SH3` | None | None | Adaptor linking LAT pY191 to LCP2. | +| `LCP2` | 4 | `RxxK`, `Y113_Y128`, `PRS`, `Y145` | Both Y variables: `0`, `P` | None | Signalosome scaffold that recruits NCK, PLCG1, and ITK after ZAP70 phosphorylation. | + +## 5. Compartments, anchors, initial species, and setup + +The model is spatially implicit: it declares neither compartments nor anchors. All three ligand classes begin free at the same scaled abundance, while TCR and CD28 begin unbound and unphosphorylated; the ligand association switches are initially zero, so these pools cannot crosslink receptors until an external RNF protocol changes `kfl` and `kfl_m`. Every intracellular signaling protein begins free, and all tracked tyrosines start in state `0`; most share a common scaled protein pool, deliberately giving equal starting abundance rather than protein-specific copy numbers. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–25 create ligand-selected receptor assemblies and load or activate proximal enzymes. Rules 26–85 propagate signals through LCK/PTPN6 feedback, WAS, LAT, LCP2, and PLCG1; rules 86–129 superimpose basal phosphosite turnover on that induced network. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–2 | Reversible | Lig1 `aCD28` arms; CD28 `epitope` | Rule 1 captures one CD28 at `kfl`; rule 2 captures a second CD28 with the intracomplex-scaled `kfl_m`; both arms release at `krl`. | Creates CD28 homodimers that juxtapose CD28-bound kinases. | +| 3–4 | Reversible | Lig3 `aCD3` arms; TCR `epitope` | Sequentially binds one then two TCRs, using `kfl` and `kfl_m` for the first and second arms and `krl` for release. | Creates TCR homodimers capable of receptor-proximal signaling. | +| 5–8 | Reversible | Lig2 `aCD28`/`aCD3`; CD28 and TCR `epitope` | Rules 5–6 bind CD28 first and then TCR; rules 7–8 take the reverse order. The first arm uses `kfl`, the crosslinking arm `kfl_m`, and either bond can reverse at `krl`. | Builds the heterotypic TCR–CD28 complex required by the model's LCK-driven TCR phosphorylation rules. | +| 9–11 | Reversible | LCK `SH3`–CD28 `PRS1`; ITK `SH3`–CD28 `PRS2`; FYN `unique`–TCR `fynbind` | Creates or releases each recruitment bond with its named association/dissociation pair. | Prepositions three kinases on the two receptor types before or during crosslinking. | +| 12–13 | Mixed | NCK `SH3_1`; TCR `PRS_E`, conditioned on `Y188_E` | Rule 12 reversibly recruits NCK only while Y188_E is unphosphorylated. Rule 13 forces rapid NCK release after Y188_E becomes phosphorylated, at `1e5 × krWasNck`. | Makes phosphorylation of the adjacent TCR site a switch that disassembles the receptor-bound NCK branch. | +| 14–17 | Reversible | ZAP70 `SH2`; TCR pY111, pY123, pY199_E, or pY188_E | Each phosphotyrosine recruits ZAP70. Rules 14–15 use the slower-off ζ-site pair; rules 16–17 use the faster-off CD3ε-site pair. | Converts individual TCR phosphosites into alternative ZAP70 docking sites with different residence times. | +| 18–19 | Reversible | PTPN6 `SH2`; TCR pY149_D or pY171_G | Forms or releases an SH2–phosphotyrosine bond at the common `kfPtpTcr`/`krPtpTcr` rates. | Recruits the negative-regulatory phosphatase to two receptor-chain sites. | +| 20–25 | One-way | CD28-bound LCK with unphosphorylated Y505; Lig2-linked TCR Y188_E, Y199_E, Y149_D, Y171_G, Y111, or Y123 | Rules 20–25 phosphorylate the six TCR sites, respectively, without consuming or rebinding LCK; each uses its site-specific `kpLck...` rate. | Writes the receptor phosphotyrosine code that recruits ZAP70, PTPN6, and other downstream partners. | +| 26–29 | One-way | Two ligand-crosslinked CD28 molecules bearing LCK or ITK; LCK Y505 and partner LCK Y424 or ITK Y512 | Rules 26/28 use Y505-phosphorylated LCK and the `*1` rate; rules 27/29 use Y505-unphosphorylated LCK and the `act`-enhanced `*2` rate. Targets are LCK Y424 (26–27) and ITK Y512 (28–29). | Allows CD28 clustering to activate LCK in trans and ITK, with stronger catalysis assigned to the uninhibited LCK form. | +| 30–33 | One-way | CD28-bound LCK Y505~0; TCR-bound ZAP70 at pY111, pY123, pY188_E, or pY199_E | LCK changes ZAP70 Y493 from `0` to `P` at `kpLckZap` while both enzymes remain receptor-linked. | Activates ZAP70 at any of its four modeled receptor docking sites. | +| 34–37 | One-way | CD28-bound LCK; TCR-bound PTPN6 at pY149_D or pY171_G | LCK phosphorylates PTPN6 Y566; rules 34/36 use the basal LCK rate and 35/37 the `act`-multiplied rate according to LCK Y505 state. | Activates receptor-recruited PTPN6 as a delayed counterweight to proximal kinase output. | +| 38–39 | Reversible | PTPN6 pY566; LCK `SH2` with Y192~0 or Y192~P | PTPN6 binds LCK through SH2–pY566 recognition; Y192 phosphorylation switches to the lower-association/higher-dissociation parameter pair. | Creates an additional LCK–PTPN6 complex whose stability depends on LCK Y192. | +| 40–43 | Mixed | PAG1 Y163/Y317; LCK `SH2`, Y505; CSK `SH2` | PAG1 pY163 recruits LCK (41), LCK phosphorylates PAG1 Y317 (42), pY317 recruits CSK (40), and assembled CSK phosphorylates LCK Y505 (43). Binding is reversible; phosphorylation is one-way. | Implements PAG1-scaffolded negative feedback that converts LCK recruitment into LCK inhibition. | +| 44–48 | One-way | Active PTPN6 associated through TCR or LCK; LCK Y192/Y424 | Rules 44–45 remove Y192 phosphorylation in the two TCR-docking contexts. Rules 46–47 remove Y424 in those contexts, while rule 48 removes Y424 from an SH2-linked LCK–PTPN6 pair. | Directly suppresses LCK regulatory phosphorylation through receptor-recruited PTPN6. | +| 49–53 | One-way | PTPN6 `PTP`; PAG1 pY163; optionally TCR-bound PTPN6 | Rules 49–51 form the catalytic complex from two TCR-tethered arrangements or a slower cytosolic encounter; rule 52 releases unchanged substrate, whereas rule 53 releases PAG1 with Y163 dephosphorylated. | Lets PTPN6 erase its own PAG1 recruitment site, limiting the inhibitory scaffold. | +| 54–57 | One-way | PTPN6 `PTP`; DOK1 pY449; TCR pY149_D/pY171_G | Two receptor-tethered capture routes (54–55) feed either noncatalytic release (56) or Y449 dephosphorylation (57). | Represents DOK1 as a phosphatase substrate downstream of PTPN6 recruitment. | +| 58–61 | One-way | PTPN6 `PTP`; DOK2 pY299; TCR pY149_D/pY171_G | Mirrors the DOK1 sequence: two tethered capture routes, unchanged release, or catalytic conversion of DOK2 Y299 to `0`. | Extends the PTPN6 substrate branch to DOK2 with its own kinetic constants. | +| 62–66 | Mixed | WAS `PRS`/Y291; NCK `SH3_3`; FYN `PTK`; receptor- or LCP2-bound assemblies | Rule 62 reversibly recruits WAS to NCK. Rule 63 phosphorylates Y291 when FYN and NCK occupy opposite TCRs in a Lig3 crosslink. Rules 64–66 form, catalyze, or abort the analogous FYN–WAS encounter on the LAT–GRAP2–LCP2–NCK scaffold. | Provides two topology-dependent routes from FYN to WAS activation. | +| 67–72 | One-way | Active, receptor-bound ZAP70 `PTK`; LAT Y132 or Y191 | Rules 67–69 bind, release, or phosphorylate Y132; rules 70–72 do the same for Y191. Only ZAP70 pY493 performs the catalytic step. | Transfers receptor activation onto the two LAT docking sites. | +| 73–76 | Reversible | LAT pY132/pY191; PLCG1 `SH2`; GRAP2 `SH2`; GRAP2 `SH3`; LCP2 `RxxK`; LCP2 pY113_Y128; NCK `SH2` | Sequentially recruits PLCG1 to LAT Y132, GRAP2 to LAT Y191, LCP2 to GRAP2, and NCK to phosphorylated LCP2. | Builds the branched LAT signalosome that brings PLCG1 and the NCK/WAS arm into a shared downstream structure. | +| 77–79 | One-way | Receptor-bound ZAP70 `PTK`; GRAP2-linked LCP2 Y113_Y128 | ZAP70 transiently binds LCP2 (77), can dissociate without change (78), or, if Y493 is phosphorylated, releases after changing the lumped Y113/Y128 variable to `P` (79). | Creates the NCK docking site on LCP2. | +| 80–81 | Reversible | PLCG1 `SH3`–LCP2 `PRS`; ITK `SH2`–LCP2 pY145 | Forms the two adaptor-enzyme links using their respective rate pairs. | Positions PLCG1 and ITK together on LCP2 for PLCG1 activation. | +| 82–84 | One-way | Receptor-bound ZAP70 `PTK`; GRAP2-linked LCP2 Y145 | The three-step encounter binds ZAP70, permits unchanged release, or changes Y145 from `0` to `P` when ZAP70 Y493 is phosphorylated. | Generates the ITK docking site needed for the PLCG1 activation complex. | +| 85 | One-way | LCP2-bound PLCG1 Y783 and ITK | ITK changes PLCG1 Y783 from `0` to `P` at `kpPlcg` while both remain attached to LCP2. | Produces the terminal PLCG1 phosphorylation readout of the modeled LAT/LCP2 branch. | +| 86–97 | One-way | Six TCR sites: Y149_D, Y171_G, Y111, Y123, Y199_E, Y188_E | Consecutive pairs add and remove phosphorylation at each site using `kp1` and the assigned `kdp1` or `kdp4`. | Establishes receptor-site turnover even without ligand-driven kinase assemblies. | +| 98–107 | One-way | LCK Y192/Y424/Y505; PTPN6 Y566; ZAP70 Y493 | Consecutive add/remove pairs apply the appropriate `kp2` or `kp1` and site-specific `kdp` values. | Sets resting-state turnover for the proximal enzymes and their activating or inhibitory sites. | +| 108–119 | One-way | LAT Y132/Y191; ITK Y512; PLCG1 Y783; LCP2 Y113_Y128/Y145 | Consecutive add/remove pairs independently turn over each downstream phosphosite. | Prevents these readouts from being exclusively dependent on assembled catalytic complexes and supplies basal occupancy. | +| 120–129 | One-way | PAG1 Y163/Y317; DOK1 Y449; DOK2 Y299; WAS Y291 | Consecutive phosphorylation/dephosphorylation pairs independently turn over the five sites. | Maintains resting flux through the feedback, phosphatase-substrate, and WAS branches. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `TCR_pY149_D`, `TCR_pY171_G`, `TCR_pY111`, `TCR_pY123`, `TCR_pY188_E`, `TCR_pY199_E` | Molecule count | TCR molecules phosphorylated at each of the six named sites, whether the site is bound or free. | Site-resolved receptor activation readouts; a TCR phosphorylated at several sites contributes once to each applicable observable. | +| `ZAP70_pY493`, `LCK_pY424`, `LCK_pY192`, `LCK_pY505`, `ITK_pY512`, `PTPN6_pY566` | Molecule count | Each kinase or phosphatase carrying the indicated phosphotyrosine. | Separates activating and regulatory enzyme states; notably, LCK Y505 is the model's inhibitory-site readout rather than a generic activity measure. | +| `LAT_pY191`, `PLCG1_pY783`, `WAS_pY291` | Molecule count | Phosphorylated downstream scaffold or effector molecules. | Reports transmission into the LAT/PLCG1 and NCK/WAS branches, including both induced and basal phosphorylation. | +| `PAG1_pY163`, `DOK1_pY449`, `DOK2_pY299` | Molecule count | Phosphorylated negative-regulatory scaffold/adaptor sites. | Tracks substrates coupled to PTPN6 and PAG1 feedback rather than direct receptor output. | +| `NCK_TCR` | Molecule count | TCR–NCK bonds between TCR `PRS_E` and NCK `SH3_1`. | Counts matched receptor–NCK embeddings; phosphorylation-driven release at TCR Y188_E reduces this readout. | +| `NCK_LCP2` | Molecule count | LCP2–NCK bonds at phosphorylated LCP2 Y113_Y128 and NCK SH2. | Reports relocation of NCK into the LAT/LCP2 signalosome; complexes with multiple matching embeddings could contribute more than once. | + +## 8. Actions and simulation workflow + +The BNGL file defines the molecular network but contains no active actions, so it does not generate or simulate that network by itself. Its comments and zero ligand-on rates indicate an external RNF workflow that equilibrates the basal system, changes `kfl` and `kfl_m` to apply ligand, and then performs the intended time course; the metadata identifies ODE as the supported simulation method. + +## 9. Technical caveats and ambiguities + +- The model represents only a 2% fraction of a cell and assigns one common initial copy-number pool to most signaling proteins; these are scaling choices, not claims of equal full-cell abundance. +- Several variables lump multiple biological residues (`Y113_Y128`) or encode chain identity in abbreviated names (`Y149_D`, `Y171_G`, `Y188_E`, `Y199_E`). Their model roles are explicit, but the summary does not expand those labels beyond the local evidence. +- The stimulus is inert when this file is loaded alone because both ligand association parameters are zero. Reproducing the intended response requires the external parameter-changing protocol described in the comments. +- Molecule-count observables match BNGL patterns and may count embeddings rather than unique physical complexes, especially for multivalent assemblies. diff --git a/Published/ChylekTCR2014/ChylekTCR_2014_metadata.yaml b/Published/ChylekTCR2014/ChylekTCR_2014_metadata.yaml new file mode 100644 index 00000000..441bf241 --- /dev/null +++ b/Published/ChylekTCR2014/ChylekTCR_2014_metadata.yaml @@ -0,0 +1,30 @@ +id: "ChylekTCR_2014" +name: "Chylek 2014 (TCR)" +description: "TCR signaling" + +citation: + year: "2014" + pmid: "25147952" + reference: "Chylek et al., 2014" + +tags: ["published", "immunology", "chylektcr", "2014", "lig1", "lig2", "lig3", "tcr", "cd28", "lck", "itk", "zap70"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/ChylekTCR_2014.bngl" +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" diff --git a/Published/ChylekTCR2014/metadata.yaml b/Published/ChylekTCR2014/metadata.yaml index f91b3980..01ad40b7 100644 --- a/Published/ChylekTCR2014/metadata.yaml +++ b/Published/ChylekTCR2014/metadata.yaml @@ -4,6 +4,7 @@ description: "TCR signaling" tags: ["published", "immunology", "chylektcr", "2014", "lig1", "lig2", "lig3", "tcr", "cd28", "lck", "itk", "zap70"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Dembo1978/blbr_dembo1978_metadata.yaml b/Published/Dembo1978/blbr_dembo1978_metadata.yaml new file mode 100644 index 00000000..7d15d028 --- /dev/null +++ b/Published/Dembo1978/blbr_dembo1978_metadata.yaml @@ -0,0 +1,23 @@ +id: "Dembo_1978" +name: "Dembo 1978" +description: "BLBR dembo 1978" +tags: ["published", "physics", "dembo", "1978"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "physics" + featured: false + difficulty: "intermediate" diff --git a/Published/Dembo1978/metadata.yaml b/Published/Dembo1978/metadata.yaml index 766b339a..9d3c8965 100644 --- a/Published/Dembo1978/metadata.yaml +++ b/Published/Dembo1978/metadata.yaml @@ -4,6 +4,7 @@ description: "BLBR dembo 1978" tags: ["published", "physics", "dembo", "1978"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Dolan2015/Dolan2015.bngl b/Published/Dolan2015/Dolan2015.bngl deleted file mode 100644 index ba40671b..00000000 --- a/Published/Dolan2015/Dolan2015.bngl +++ /dev/null @@ -1,3020 +0,0 @@ -# combined model, p53 (Carole) and NHEJ - -# parameters -begin parameters - -kp53mRNAsyn 0.06 # Rate of p53 mRNA Synthesis -kp53mRNAdeg 0.006 # Rate of p53 mRNA Degradation -kp53syn 0.36 # Rate of p53 Synthesis -kp53deg 4.95e-5 # Rate of p53 Degradation -kp53degMDM2dep 0.0495 # Rate of p53 Degradation-MDM2 Dependant -kp53phos 0.36 # Rate of p53 Phosphorylation -kp53dphos 30 # Rate of p53 Dephosphorylation -kMDM2mRNAsyn 0.006 # Rate of MDM2 mRNA Synthesis -kMDM2mRNAdeg 0.006 # Rate of MDM2 mRNA Degradation -kMDM2syn 0.0297 # Rate of MDM2 Synthesis -kMDM2deg 0.02598 # Rate of MDM2 Degradation -kMDM2pdeg 0.024 # Rate of Phosphorylated MDM2 Degradation -kMDM2phos 120 # Rate of MDM2 Phosphorylation -kMDM2dphos 30 # Rate of p53 Dephosphorylation -kp53MDM2bind 0.0693 # Rate of p53 MDM2 Binding -kp53MDM2dis 0.0000693 # Rate of p53 MDM2 Dissociation -kp21mRNAsyn 0.0000036 # Rate of p21 mRNA Synthesis (p53) -kp21mRNAsynp 0.00036 # Rate of p21 mRNA Synthesis (Phosphorylated p53) -kp21mRNAdeg 0.00144 # Rate of p21 mRNA Degradation -kp21synstep1 0.024 # Rate of p21 Synthesis Step 1 -kp21synstep2 0.0024 # Rate of p21 Synthesis Step 2 -kp21synstep3 0.0024 # Rate of p21 Synthesis Step 3 -kp21deg 0.0114 # Rate of p21 Degradation -kGADD45act 0.00024 # Rate of GADD45 Activation/Production -kGADD45deg 0.0006 # Rate of GADD45 Degradation -kp38phos 0.48 # Rate of p38 Phosphorylation -kp38dphos 6 # Rate of p38 Dephosphorylation -kROSgen 1.5 # Rate of ROS Generation by p38 - -kIR 80 - -kROS 50 # Constant rate of ROS production -kdROS 5 # ROS degradation rate -kdam1 0.000006 # Rate of simple damage production by ROS -kdam2 0.000006 # Rate of complex damage production by ROS -kdku1 0.5 # Rate of Ku dissociation from a simple break -kdku2 0.5 # Rate of Ku dissociation from a complex break -kdku3 5 # Rate of oxidised Ku dissociation from a simple break -kdku4 5 # Rate of oxidised Ku dissociation from a complex break -kdnapk1 0.033 # Rate of DNAPK simple break complex formation -kdnapk2 0.0017 # Rate of DNAPK complex break complex formation -kddnapk1 0.02 # Rate of DNAPK simple break complex dissociation -kddnapk2 0.02 # Rate of DNAPK complex break complex dissociation -kdnapkphos1 0.28 # Rate pd DNAPK phosphorylation in a DNAPK complex of a simple break -kdnapkphos2 0.28 # Rate pd DNAPK phosphorylation in a DNAPK complex of a complex break -kliIV1 0.00071 # Rate of LigaseIV binding to a simple break complex -kliIV2 0.00046 # Rate of LigaseIV binding to a complex break complex -kdliIV1 0.0001 # Rate of LigaseIV dissociation from a simple break complex -kdliIV2 0.0001 # Rate of LigaseIV dissociation from a complex break complex -kfixIV1 0.0285 # Rate of DNA repair by LigaseIV of a simple break -kfixIV2 0.0285 # Rate of DNA repair by LigaseIV of a complex break -kPARP1 0.000077 # Rate of PARP binding to simple break -kPARP2 0.000065 # Rate of PARP binding to complex break -kdPARP1 0.02 # Rate of PARP dissociation from a simple break -kdPARP2 0.02 # Rate of PARP dissociation from a complex break -kliIII1 0.0015 # Rate of LigaseIII binding to a simple break -kliIII2 0.00024 # Rate of LigaseIII binding to a complex break -kdliIII1 0.0001 # Rate of LigaseIII dissociation from a simple break -kdliIII2 0.0001 # Rate of LigaseIII dissociation from a complex break -kfixIII1 0.0006 # Rate of DNA accurate repair by LigaseIII for a simple break -kfixIII2 0.0006 # Rate of DNA accurate repair by LigaseIII for a complex break -kfixIII3 0.0009 # Rate of DNA inaccurate repair by LigaseIII for a simple break -kfixIII4 0.0009 # Rate of dna inaccurate repair by LigaseIII for a complex break -kATMact 0.0012 # Rate of ATM Activation -kATMinact 0.03 # Rate of ATM Inactivation -kh2axp1 0.1 # Phosphorylation of h2ax via ATM -kh2axp2 0.5 # Phosphorylation of h2ax via DNA-PKcs -kh2axu 0.01 # Dephosphorylation of h2ax -kh2axfoc 0.5 # Creation of damage foci -kfocback 0.03 # Resolution of damage foci -kh2axfull 0.1 # Creation of complete damage foci -kfocfin 0.03 # Resolution of complete damage foci - -kox 0.000025 # Rate of oxidisation of Ku -kred 0.002 # Rate of reduction of Ku -ksen 100 # Activation of senescent state - -end parameters - - -# molecules -begin molecule types - -Time() -T() -P() -E() -IR() -D() -p53_mRNA() -p53(Site1~u~p) -MDM2(Site1~u~p) -MDM2_mRNA() -p21_mRNA() -p21(step~1~2~3) -p38(Site1~u~p) -GADD45() -Sink() - -ATM(state~0~1~2~3~4~5~6~7~8~9~10~11~12~13~14~15~16~17~18~19~20~21~22~23~24~25~26~27~28~29~30~31~32~33~34~35~36~37~38~39~40~41~42~43~44~45~46~47~48~49~50,h2ax) - -DNA1(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA2(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA3(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA4(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA5(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA6(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA7(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA8(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA9(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA10(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA11(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA12(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA13(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA14(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA15(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA16(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA17(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA18(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA19(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA20(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA21(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA22(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA23(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA24(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA25(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA26(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA27(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA28(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA29(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA30(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA31(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA32(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA33(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA34(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA35(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA36(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA37(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA38(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA39(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA40(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA41(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA42(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA43(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA44(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA45(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA46(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA47(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA48(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA49(site~ok~sdsb~cdsb,h2ax~u~p~foc) -DNA50(site~ok~sdsb~cdsb,h2ax~u~p~foc) -ROS() -Ku(dna,cs,cys~red~ox) -DNAPKcs(ku,liIV,psite~u~p) -LiIII(PARP) -LiIV(cs) -PARP(dna,liIII) -I() - -Sen(int~1~10~PLUS~MINUS,State~normal~sen) - -end molecule types - -# species -begin species - -Time() 0 -P() 1 -T() 1 -E() 1 -IR() 0 -D() 10 -p53_mRNA() 10 -p53(Site1~u) 5 -MDM2_mRNA() 10 -MDM2(Site1~u) 5 -p53(Site1!1~u).MDM2(Site1!1~u) 95 -p21_mRNA() 1 -p21(step~1) 0 -p38(Site1~u) 100 -$Sink() 0 - -ATM(state~0,h2ax) 200 - -DNA1(site~ok,h2ax~u) 1 -DNA2(site~ok,h2ax~u) 1 -DNA3(site~ok,h2ax~u) 1 -DNA4(site~ok,h2ax~u) 1 -DNA5(site~ok,h2ax~u) 1 -DNA6(site~ok,h2ax~u) 1 -DNA7(site~ok,h2ax~u) 1 -DNA8(site~ok,h2ax~u) 1 -DNA9(site~ok,h2ax~u) 1 -DNA10(site~ok,h2ax~u) 1 -DNA11(site~ok,h2ax~u) 1 -DNA12(site~ok,h2ax~u) 1 -DNA13(site~ok,h2ax~u) 1 -DNA14(site~ok,h2ax~u) 1 -DNA15(site~ok,h2ax~u) 1 -DNA16(site~ok,h2ax~u) 1 -DNA17(site~ok,h2ax~u) 1 -DNA18(site~ok,h2ax~u) 1 -DNA19(site~ok,h2ax~u) 1 -DNA20(site~ok,h2ax~u) 1 -DNA21(site~ok,h2ax~u) 1 -DNA22(site~ok,h2ax~u) 1 -DNA23(site~ok,h2ax~u) 1 -DNA24(site~ok,h2ax~u) 1 -DNA25(site~ok,h2ax~u) 1 -DNA26(site~ok,h2ax~u) 1 -DNA27(site~ok,h2ax~u) 1 -DNA28(site~ok,h2ax~u) 1 -DNA29(site~ok,h2ax~u) 1 -DNA30(site~ok,h2ax~u) 1 -DNA31(site~ok,h2ax~u) 1 -DNA32(site~ok,h2ax~u) 1 -DNA33(site~ok,h2ax~u) 1 -DNA34(site~ok,h2ax~u) 1 -DNA35(site~ok,h2ax~u) 1 -DNA36(site~ok,h2ax~u) 1 -DNA37(site~ok,h2ax~u) 1 -DNA38(site~ok,h2ax~u) 1 -DNA39(site~ok,h2ax~u) 1 -DNA40(site~ok,h2ax~u) 1 -DNA41(site~ok,h2ax~u) 1 -DNA42(site~ok,h2ax~u) 1 -DNA43(site~ok,h2ax~u) 1 -DNA44(site~ok,h2ax~u) 1 -DNA45(site~ok,h2ax~u) 1 -DNA46(site~ok,h2ax~u) 1 -DNA47(site~ok,h2ax~u) 1 -DNA48(site~ok,h2ax~u) 1 -DNA49(site~ok,h2ax~u) 1 -DNA50(site~ok,h2ax~u) 1 -ROS() 0 -Ku(dna,cs,cys~red) 450 -Ku(dna,cs,cys~ox) 50 -DNAPKcs(ku,liIV,psite~u) 250 -LiIII(PARP) 300 -LiIV(cs) 300 -PARP(dna,liIII) 500 -I() 1 - -Sen(int~1,State~normal) 1 - - -end species - -# observables -begin observables - -Molecules Time Time() -Molecules p53 p53() -Molecules p53_Bound p53(Site1!1~u).MDM2(Site1!1~u) -Molecules p53_Phos p53(Site1~p) -Molecules p53_Unphos p53(Site1~u) -Molecules p21 p21(step~3) -Molecules p38p p38(Site1~p) -Molecules p38u p38(Site1~u) -Molecules ROS ROS() -Molecules p53_mRNA p53_mRNA() -Molecules MDM2_Phos MDM2(Site1~p) -Molecules MDM2_Unphos MDM2(Site1~u) -Molecules MDM2_mRNA MDM2_mRNA() -Molecules p21_mRNA p21_mRNA() -Molecules GADD45 GADD45() - - -Molecules ATM0 ATM(state~0) -Molecules ATM1 ATM(state~1) -Molecules ATM2 ATM(state~2) -Molecules ATM3 ATM(state~3) -Molecules ATM4 ATM(state~4) -Molecules ATM5 ATM(state~5) -Molecules ATM6 ATM(state~6) -Molecules ATM7 ATM(state~7) -Molecules ATM8 ATM(state~8) -Molecules ATM9 ATM(state~9) -Molecules ATM10 ATM(state~10) -Molecules ATM11 ATM(state~11) -Molecules ATM12 ATM(state~12) -Molecules ATM13 ATM(state~13) -Molecules ATM14 ATM(state~14) -Molecules ATM15 ATM(state~15) -Molecules ATM16 ATM(state~16) -Molecules ATM17 ATM(state~17) -Molecules ATM18 ATM(state~18) -Molecules ATM19 ATM(state~19) -Molecules ATM20 ATM(state~20) -Molecules ATM21 ATM(state~21) -Molecules ATM22 ATM(state~22) -Molecules ATM23 ATM(state~23) -Molecules ATM24 ATM(state~24) -Molecules ATM25 ATM(state~25) -Molecules ATM26 ATM(state~26) -Molecules ATM27 ATM(state~27) -Molecules ATM28 ATM(state~28) -Molecules ATM29 ATM(state~29) -Molecules ATM30 ATM(state~30) -Molecules ATM31 ATM(state~31) -Molecules ATM32 ATM(state~32) -Molecules ATM33 ATM(state~33) -Molecules ATM34 ATM(state~34) -Molecules ATM35 ATM(state~35) -Molecules ATM36 ATM(state~36) -Molecules ATM37 ATM(state~37) -Molecules ATM38 ATM(state~38) -Molecules ATM39 ATM(state~39) -Molecules ATM40 ATM(state~40) -Molecules ATM41 ATM(state~41) -Molecules ATM42 ATM(state~42) -Molecules ATM43 ATM(state~43) -Molecules ATM44 ATM(state~44) -Molecules ATM45 ATM(state~45) -Molecules ATM46 ATM(state~46) -Molecules ATM47 ATM(state~47) -Molecules ATM48 ATM(state~48) -Molecules ATM49 ATM(state~49) -Molecules ATM50 ATM(state~50) - - -Molecules Damage_Foci_1 DNA1(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_1 DNA1(h2ax!1~foc).ATM(state~1,h2ax!1) -Molecules Damage_Foci_2 DNA2(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_2 DNA2(h2ax!1~foc).ATM(state~2,h2ax!1) -Molecules Damage_Foci_3 DNA3(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_3 DNA3(h2ax!1~foc).ATM(state~3,h2ax!1) -Molecules Damage_Foci_4 DNA4(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_4 DNA4(h2ax!1~foc).ATM(state~4,h2ax!1) -Molecules Damage_Foci_5 DNA5(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_5 DNA5(h2ax!1~foc).ATM(state~5,h2ax!1) -Molecules Damage_Foci_6 DNA6(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_6 DNA6(h2ax!1~foc).ATM(state~6,h2ax!1) -Molecules Damage_Foci_7 DNA7(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_7 DNA7(h2ax!1~foc).ATM(state~7,h2ax!1) -Molecules Damage_Foci_8 DNA8(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_8 DNA8(h2ax!1~foc).ATM(state~8,h2ax!1) -Molecules Damage_Foci_9 DNA9(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_9 DNA9(h2ax!1~foc).ATM(state~9,h2ax!1) -Molecules Damage_Foci_10 DNA10(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_10 DNA10(h2ax!1~foc).ATM(state~10,h2ax!1) -Molecules Damage_Foci_11 DNA11(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_11 DNA11(h2ax!1~foc).ATM(state~11,h2ax!1) -Molecules Damage_Foci_12 DNA12(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_12 DNA12(h2ax!1~foc).ATM(state~12,h2ax!1) -Molecules Damage_Foci_13 DNA13(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_13 DNA13(h2ax!1~foc).ATM(state~13,h2ax!1) -Molecules Damage_Foci_14 DNA14(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_14 DNA14(h2ax!1~foc).ATM(state~14,h2ax!1) -Molecules Damage_Foci_15 DNA15(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_15 DNA15(h2ax!1~foc).ATM(state~15,h2ax!1) -Molecules Damage_Foci_16 DNA16(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_16 DNA16(h2ax!1~foc).ATM(state~16,h2ax!1) -Molecules Damage_Foci_17 DNA17(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_17 DNA17(h2ax!1~foc).ATM(state~17,h2ax!1) -Molecules Damage_Foci_18 DNA18(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_18 DNA18(h2ax!1~foc).ATM(state~18,h2ax!1) -Molecules Damage_Foci_19 DNA19(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_19 DNA19(h2ax!1~foc).ATM(state~19,h2ax!1) -Molecules Damage_Foci_20 DNA20(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_20 DNA20(h2ax!1~foc).ATM(state~20,h2ax!1) -Molecules Damage_Foci_21 DNA21(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_21 DNA21(h2ax!1~foc).ATM(state~21,h2ax!1) -Molecules Damage_Foci_22 DNA22(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_22 DNA22(h2ax!1~foc).ATM(state~22,h2ax!1) -Molecules Damage_Foci_23 DNA23(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_23 DNA23(h2ax!1~foc).ATM(state~23,h2ax!1) -Molecules Damage_Foci_24 DNA24(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_24 DNA24(h2ax!1~foc).ATM(state~24,h2ax!1) -Molecules Damage_Foci_25 DNA25(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_25 DNA25(h2ax!1~foc).ATM(state~25,h2ax!1) -Molecules Damage_Foci_26 DNA26(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_26 DNA26(h2ax!1~foc).ATM(state~26,h2ax!1) -Molecules Damage_Foci_27 DNA27(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_27 DNA27(h2ax!1~foc).ATM(state~27,h2ax!1) -Molecules Damage_Foci_28 DNA28(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_28 DNA28(h2ax!1~foc).ATM(state~28,h2ax!1) -Molecules Damage_Foci_29 DNA29(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_29 DNA29(h2ax!1~foc).ATM(state~29,h2ax!1) -Molecules Damage_Foci_30 DNA30(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_30 DNA30(h2ax!1~foc).ATM(state~30,h2ax!1) -Molecules Damage_Foci_31 DNA31(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_31 DNA31(h2ax!1~foc).ATM(state~31,h2ax!1) -Molecules Damage_Foci_32 DNA32(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_32 DNA32(h2ax!1~foc).ATM(state~32,h2ax!1) -Molecules Damage_Foci_33 DNA33(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_33 DNA33(h2ax!1~foc).ATM(state~33,h2ax!1) -Molecules Damage_Foci_34 DNA34(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_34 DNA34(h2ax!1~foc).ATM(state~34,h2ax!1) -Molecules Damage_Foci_35 DNA35(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_35 DNA35(h2ax!1~foc).ATM(state~35,h2ax!1) -Molecules Damage_Foci_36 DNA36(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_36 DNA36(h2ax!1~foc).ATM(state~36,h2ax!1) -Molecules Damage_Foci_37 DNA37(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_37 DNA37(h2ax!1~foc).ATM(state~37,h2ax!1) -Molecules Damage_Foci_38 DNA38(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_38 DNA38(h2ax!1~foc).ATM(state~38,h2ax!1) -Molecules Damage_Foci_39 DNA39(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_39 DNA39(h2ax!1~foc).ATM(state~39,h2ax!1) -Molecules Damage_Foci_40 DNA40(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_40 DNA40(h2ax!1~foc).ATM(state~40,h2ax!1) -Molecules Damage_Foci_41 DNA41(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_41 DNA41(h2ax!1~foc).ATM(state~41,h2ax!1) -Molecules Damage_Foci_42 DNA42(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_42 DNA42(h2ax!1~foc).ATM(state~42,h2ax!1) -Molecules Damage_Foci_43 DNA43(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_43 DNA43(h2ax!1~foc).ATM(state~43,h2ax!1) -Molecules Damage_Foci_44 DNA44(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_44 DNA44(h2ax!1~foc).ATM(state~44,h2ax!1) -Molecules Damage_Foci_45 DNA45(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_45 DNA45(h2ax!1~foc).ATM(state~45,h2ax!1) -Molecules Damage_Foci_46 DNA46(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_46 DNA46(h2ax!1~foc).ATM(state~46,h2ax!1) -Molecules Damage_Foci_47 DNA47(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_47 DNA47(h2ax!1~foc).ATM(state~47,h2ax!1) -Molecules Damage_Foci_48 DNA48(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_48 DNA48(h2ax!1~foc).ATM(state~48,h2ax!1) -Molecules Damage_Foci_49 DNA49(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_49 DNA49(h2ax!1~foc).ATM(state~49,h2ax!1) -Molecules Damage_Foci_50 DNA50(site!?~?,h2ax~foc) -Molecules Complete_Damage_Foci_50 DNA50(h2ax!1~foc).ATM(state~50,h2ax!1) - -Molecules Ku Ku(dna,cs,cys~?) -Molecules PARP PARP(dna,liIII) -Molecules Ku_Red Ku(dna,cs,cys~red) -Molecules Ku_Ox Ku(dna,cs,cys~ox) -Molecules DNA_PKcs DNAPKcs(ku,liIV,psite~u) -Molecules LiIII LiIII(PARP) -Molecules LiIV LiIV(cs) - -Molecules Senescent_Counter Sen(int~?,State~sen) -Molecules Sen_Min Sen(int~1,State~?) -Molecules Sink Sink() - - -end observables - -# functions -begin functions - -kku1() = if(Senescent_Counter>0,0.000000034,0.00034) -kku2() = if(Senescent_Counter>0,0.000000021,0.00021) -kplus() = if(p21>15,0.04,0) -kminus() = if(p21<=15&&Sen_Min<1,0.5,0) -kKuDown() = if(Senescent_Counter==1,0.01,0) -kKustop() = if(Ku<=250,0,1) -kParpDown() = if(Senescent_Counter==1,0.01,0) -kParpstop() = if(PARP<=5,0,1) -#Irrad()= if(Time<180&&Time>174,2000,0) -#IRoff()= if(Time>=180,1000,0) -#Timeoff()= if(Time>=200,0,1) -kDelete()= if(Sink<=5,0,10000) - - -end functions - -# reaction rules -begin reaction rules - -# Time -#T()-> T() + Time() Timeoff() - -# Irradiation Event -#E() -> E() + IR() Irrad() - -# Irradiation Off -#IR() -> Sink() IRoff() - -#Empty the Sink -D() + Sink() -> D() kDelete() DeleteMolecules - -# p53 mRNA Synthesis -P() -> p53_mRNA() + P() kp53mRNAsyn - -# p53 mRNA degredation -p53_mRNA() -> Sink() kp53mRNAdeg - -# p53 Synthesis -p53_mRNA() -> p53_mRNA() + p53(Site1~u) kp53syn - -# p53 Degradation -p53(Site1~u) -> Sink() kp53deg -p53(Site1~p) -> Sink() kp53deg -p53(Site1!1~u).MDM2(Site1!1~u) -> MDM2(Site1~u) kp53degMDM2dep DeleteMolecules - -# p53 Phosporylation -p53(Site1~u) + ATM(state~1,h2ax!?) -> p53(Site1~p) + ATM(state~1,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~2,h2ax!?) -> p53(Site1~p) + ATM(state~2,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~3,h2ax!?) -> p53(Site1~p) + ATM(state~3,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~4,h2ax!?) -> p53(Site1~p) + ATM(state~4,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~5,h2ax!?) -> p53(Site1~p) + ATM(state~5,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~6,h2ax!?) -> p53(Site1~p) + ATM(state~6,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~7,h2ax!?) -> p53(Site1~p) + ATM(state~7,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~8,h2ax!?) -> p53(Site1~p) + ATM(state~8,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~9,h2ax!?) -> p53(Site1~p) + ATM(state~9,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~10,h2ax!?) -> p53(Site1~p) + ATM(state~10,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~11,h2ax!?) -> p53(Site1~p) + ATM(state~11,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~12,h2ax!?) -> p53(Site1~p) + ATM(state~12,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~13,h2ax!?) -> p53(Site1~p) + ATM(state~13,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~14,h2ax!?) -> p53(Site1~p) + ATM(state~14,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~15,h2ax!?) -> p53(Site1~p) + ATM(state~15,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~16,h2ax!?) -> p53(Site1~p) + ATM(state~16,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~17,h2ax!?) -> p53(Site1~p) + ATM(state~17,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~18,h2ax!?) -> p53(Site1~p) + ATM(state~18,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~19,h2ax!?) -> p53(Site1~p) + ATM(state~19,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~20,h2ax!?) -> p53(Site1~p) + ATM(state~20,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~21,h2ax!?) -> p53(Site1~p) + ATM(state~21,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~22,h2ax!?) -> p53(Site1~p) + ATM(state~22,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~23,h2ax!?) -> p53(Site1~p) + ATM(state~23,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~24,h2ax!?) -> p53(Site1~p) + ATM(state~24,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~25,h2ax!?) -> p53(Site1~p) + ATM(state~25,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~26,h2ax!?) -> p53(Site1~p) + ATM(state~26,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~27,h2ax!?) -> p53(Site1~p) + ATM(state~27,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~28,h2ax!?) -> p53(Site1~p) + ATM(state~28,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~29,h2ax!?) -> p53(Site1~p) + ATM(state~29,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~30,h2ax!?) -> p53(Site1~p) + ATM(state~30,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~31,h2ax!?) -> p53(Site1~p) + ATM(state~31,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~32,h2ax!?) -> p53(Site1~p) + ATM(state~32,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~33,h2ax!?) -> p53(Site1~p) + ATM(state~33,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~34,h2ax!?) -> p53(Site1~p) + ATM(state~34,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~35,h2ax!?) -> p53(Site1~p) + ATM(state~35,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~36,h2ax!?) -> p53(Site1~p) + ATM(state~36,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~37,h2ax!?) -> p53(Site1~p) + ATM(state~37,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~38,h2ax!?) -> p53(Site1~p) + ATM(state~38,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~39,h2ax!?) -> p53(Site1~p) + ATM(state~39,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~40,h2ax!?) -> p53(Site1~p) + ATM(state~40,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~41,h2ax!?) -> p53(Site1~p) + ATM(state~41,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~42,h2ax!?) -> p53(Site1~p) + ATM(state~42,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~43,h2ax!?) -> p53(Site1~p) + ATM(state~43,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~44,h2ax!?) -> p53(Site1~p) + ATM(state~44,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~45,h2ax!?) -> p53(Site1~p) + ATM(state~45,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~46,h2ax!?) -> p53(Site1~p) + ATM(state~46,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~47,h2ax!?) -> p53(Site1~p) + ATM(state~47,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~48,h2ax!?) -> p53(Site1~p) + ATM(state~48,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~49,h2ax!?) -> p53(Site1~p) + ATM(state~49,h2ax!?) kp53phos -p53(Site1~u) + ATM(state~50,h2ax!?) -> p53(Site1~p) + ATM(state~50,h2ax!?) kp53phos - -# p53 Dehosporylation -p53(Site1~p) -> p53(Site1~u) kp53dphos - -# MDM2 mRNA Synthesis - -p53(Site1~u) -> MDM2_mRNA() + p53(Site1~u) kMDM2mRNAsyn -p53(Site1~p) -> MDM2_mRNA() + p53(Site1~p) kMDM2mRNAsyn - -# MDM2 mRNA degredation -MDM2_mRNA() -> Sink() kMDM2mRNAdeg - -# MDM2 Synthesis -MDM2_mRNA() -> MDM2_mRNA() + MDM2(Site1~u) kMDM2syn - -# MDM2 Degradation -MDM2(Site1~u) -> Sink() kMDM2deg -MDM2(Site1~p) -> Sink() kMDM2pdeg - -# MDM2 Phosporylation -MDM2(Site1~u) + ATM(state~1,h2ax!?) -> MDM2(Site1~p) + ATM(state~1,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~2,h2ax!?) -> MDM2(Site1~p) + ATM(state~2,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~3,h2ax!?) -> MDM2(Site1~p) + ATM(state~3,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~4,h2ax!?) -> MDM2(Site1~p) + ATM(state~4,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~5,h2ax!?) -> MDM2(Site1~p) + ATM(state~5,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~6,h2ax!?) -> MDM2(Site1~p) + ATM(state~6,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~7,h2ax!?) -> MDM2(Site1~p) + ATM(state~7,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~8,h2ax!?) -> MDM2(Site1~p) + ATM(state~8,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~9,h2ax!?) -> MDM2(Site1~p) + ATM(state~9,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~10,h2ax!?) -> MDM2(Site1~p) + ATM(state~10,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~11,h2ax!?) -> MDM2(Site1~p) + ATM(state~11,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~12,h2ax!?) -> MDM2(Site1~p) + ATM(state~12,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~13,h2ax!?) -> MDM2(Site1~p) + ATM(state~13,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~14,h2ax!?) -> MDM2(Site1~p) + ATM(state~14,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~15,h2ax!?) -> MDM2(Site1~p) + ATM(state~15,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~16,h2ax!?) -> MDM2(Site1~p) + ATM(state~16,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~17,h2ax!?) -> MDM2(Site1~p) + ATM(state~17,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~18,h2ax!?) -> MDM2(Site1~p) + ATM(state~18,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~19,h2ax!?) -> MDM2(Site1~p) + ATM(state~19,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~20,h2ax!?) -> MDM2(Site1~p) + ATM(state~20,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~21,h2ax!?) -> MDM2(Site1~p) + ATM(state~21,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~22,h2ax!?) -> MDM2(Site1~p) + ATM(state~22,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~23,h2ax!?) -> MDM2(Site1~p) + ATM(state~23,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~24,h2ax!?) -> MDM2(Site1~p) + ATM(state~24,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~25,h2ax!?) -> MDM2(Site1~p) + ATM(state~25,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~26,h2ax!?) -> MDM2(Site1~p) + ATM(state~26,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~27,h2ax!?) -> MDM2(Site1~p) + ATM(state~27,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~28,h2ax!?) -> MDM2(Site1~p) + ATM(state~28,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~29,h2ax!?) -> MDM2(Site1~p) + ATM(state~29,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~30,h2ax!?) -> MDM2(Site1~p) + ATM(state~30,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~31,h2ax!?) -> MDM2(Site1~p) + ATM(state~31,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~32,h2ax!?) -> MDM2(Site1~p) + ATM(state~32,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~33,h2ax!?) -> MDM2(Site1~p) + ATM(state~33,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~34,h2ax!?) -> MDM2(Site1~p) + ATM(state~34,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~35,h2ax!?) -> MDM2(Site1~p) + ATM(state~35,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~36,h2ax!?) -> MDM2(Site1~p) + ATM(state~36,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~37,h2ax!?) -> MDM2(Site1~p) + ATM(state~37,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~38,h2ax!?) -> MDM2(Site1~p) + ATM(state~38,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~39,h2ax!?) -> MDM2(Site1~p) + ATM(state~39,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~40,h2ax!?) -> MDM2(Site1~p) + ATM(state~40,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~41,h2ax!?) -> MDM2(Site1~p) + ATM(state~41,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~42,h2ax!?) -> MDM2(Site1~p) + ATM(state~42,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~43,h2ax!?) -> MDM2(Site1~p) + ATM(state~43,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~44,h2ax!?) -> MDM2(Site1~p) + ATM(state~44,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~45,h2ax!?) -> MDM2(Site1~p) + ATM(state~45,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~46,h2ax!?) -> MDM2(Site1~p) + ATM(state~46,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~47,h2ax!?) -> MDM2(Site1~p) + ATM(state~47,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~48,h2ax!?) -> MDM2(Site1~p) + ATM(state~48,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~49,h2ax!?) -> MDM2(Site1~p) + ATM(state~49,h2ax!?) kMDM2phos -MDM2(Site1~u) + ATM(state~50,h2ax!?) -> MDM2(Site1~p) + ATM(state~50,h2ax!?) kMDM2phos - -# MDM2 Dehosporylation -MDM2(Site1~p) -> MDM2(Site1~u) kMDM2dphos - -# p53-MDM2 Binding and Disociation -p53(Site1~u) + MDM2(Site1~u) -> p53(Site1!1~u).MDM2(Site1!1~u) kp53MDM2bind -p53(Site1!1~u).MDM2(Site1!1~u) -> p53(Site1~u) + MDM2(Site1~u) kp53MDM2dis - -# p21 mRNA Synthesis - -p53(Site1~u) -> p21_mRNA() + p53(Site1~u) kp21mRNAsyn -p53(Site1~p) -> p21_mRNA() + p53(Site1~p) kp21mRNAsynp - -# p21 mRNA degredation -p21_mRNA() -> Sink() kp21mRNAdeg - -# p21 Synthesis -p21_mRNA() -> p21(step~1) + p21_mRNA() kp21synstep1 -p21(step~1) -> p21(step~2) kp21synstep2 -p21(step~2) -> p21(step~3) kp21synstep3 - -# p21 Degradation -p21(step~3) -> Sink() kp21deg - -# GADD45 Activation -p21(step~3) -> p21(step~3) + GADD45() kGADD45act - -# GADD45 Degradation -GADD45() -> Sink() kGADD45deg - -# p38 Phosphorylation -p38(Site1~u) + GADD45() -> p38(Site1~p) + GADD45() kp38phos - -# p38 Dephosphorylation -p38(Site1~p) -> p38(Site1~u) kp38dphos - -# p38 ROS Generation -p38(Site1~p) -> ROS() + p38(Site1~p) kROSgen #*kpROSp38 - -# NHEJ Strts here - -# Ku binding -# simple -DNA1(site~sdsb) + Ku(dna,cs) -> DNA1(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA2(site~sdsb) + Ku(dna,cs) -> DNA2(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA3(site~sdsb) + Ku(dna,cs) -> DNA3(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA4(site~sdsb) + Ku(dna,cs) -> DNA4(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA5(site~sdsb) + Ku(dna,cs) -> DNA5(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA6(site~sdsb) + Ku(dna,cs) -> DNA6(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA7(site~sdsb) + Ku(dna,cs) -> DNA7(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA8(site~sdsb) + Ku(dna,cs) -> DNA8(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA9(site~sdsb) + Ku(dna,cs) -> DNA9(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA10(site~sdsb) + Ku(dna,cs) -> DNA10(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA11(site~sdsb) + Ku(dna,cs) -> DNA11(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA12(site~sdsb) + Ku(dna,cs) -> DNA12(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA13(site~sdsb) + Ku(dna,cs) -> DNA13(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA14(site~sdsb) + Ku(dna,cs) -> DNA14(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA15(site~sdsb) + Ku(dna,cs) -> DNA15(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA16(site~sdsb) + Ku(dna,cs) -> DNA16(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA17(site~sdsb) + Ku(dna,cs) -> DNA17(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA18(site~sdsb) + Ku(dna,cs) -> DNA18(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA19(site~sdsb) + Ku(dna,cs) -> DNA19(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA20(site~sdsb) + Ku(dna,cs) -> DNA20(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA21(site~sdsb) + Ku(dna,cs) -> DNA21(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA22(site~sdsb) + Ku(dna,cs) -> DNA22(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA23(site~sdsb) + Ku(dna,cs) -> DNA23(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA24(site~sdsb) + Ku(dna,cs) -> DNA24(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA25(site~sdsb) + Ku(dna,cs) -> DNA25(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA26(site~sdsb) + Ku(dna,cs) -> DNA26(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA27(site~sdsb) + Ku(dna,cs) -> DNA27(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA28(site~sdsb) + Ku(dna,cs) -> DNA28(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA29(site~sdsb) + Ku(dna,cs) -> DNA29(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA30(site~sdsb) + Ku(dna,cs) -> DNA30(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA31(site~sdsb) + Ku(dna,cs) -> DNA31(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA32(site~sdsb) + Ku(dna,cs) -> DNA32(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA33(site~sdsb) + Ku(dna,cs) -> DNA33(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA34(site~sdsb) + Ku(dna,cs) -> DNA34(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA35(site~sdsb) + Ku(dna,cs) -> DNA35(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA36(site~sdsb) + Ku(dna,cs) -> DNA36(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA37(site~sdsb) + Ku(dna,cs) -> DNA37(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA38(site~sdsb) + Ku(dna,cs) -> DNA38(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA39(site~sdsb) + Ku(dna,cs) -> DNA39(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA40(site~sdsb) + Ku(dna,cs) -> DNA40(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA41(site~sdsb) + Ku(dna,cs) -> DNA41(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA42(site~sdsb) + Ku(dna,cs) -> DNA42(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA43(site~sdsb) + Ku(dna,cs) -> DNA43(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA44(site~sdsb) + Ku(dna,cs) -> DNA44(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA45(site~sdsb) + Ku(dna,cs) -> DNA45(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA46(site~sdsb) + Ku(dna,cs) -> DNA46(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA47(site~sdsb) + Ku(dna,cs) -> DNA47(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA48(site~sdsb) + Ku(dna,cs) -> DNA48(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA49(site~sdsb) + Ku(dna,cs) -> DNA49(site!1~sdsb).Ku(dna!1,cs) kku1() -DNA50(site~sdsb) + Ku(dna,cs) -> DNA50(site!1~sdsb).Ku(dna!1,cs) kku1() -# complex -DNA1(site~cdsb) + Ku(dna,cs) -> DNA1(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA2(site~cdsb) + Ku(dna,cs) -> DNA2(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA3(site~cdsb) + Ku(dna,cs) -> DNA3(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA4(site~cdsb) + Ku(dna,cs) -> DNA4(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA5(site~cdsb) + Ku(dna,cs) -> DNA5(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA6(site~cdsb) + Ku(dna,cs) -> DNA6(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA7(site~cdsb) + Ku(dna,cs) -> DNA7(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA8(site~cdsb) + Ku(dna,cs) -> DNA8(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA9(site~cdsb) + Ku(dna,cs) -> DNA9(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA10(site~cdsb) + Ku(dna,cs) -> DNA10(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA11(site~cdsb) + Ku(dna,cs) -> DNA11(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA12(site~cdsb) + Ku(dna,cs) -> DNA12(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA13(site~cdsb) + Ku(dna,cs) -> DNA13(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA14(site~cdsb) + Ku(dna,cs) -> DNA14(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA15(site~cdsb) + Ku(dna,cs) -> DNA15(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA16(site~cdsb) + Ku(dna,cs) -> DNA16(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA17(site~cdsb) + Ku(dna,cs) -> DNA17(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA18(site~cdsb) + Ku(dna,cs) -> DNA18(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA19(site~cdsb) + Ku(dna,cs) -> DNA19(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA20(site~cdsb) + Ku(dna,cs) -> DNA20(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA21(site~cdsb) + Ku(dna,cs) -> DNA21(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA22(site~cdsb) + Ku(dna,cs) -> DNA22(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA23(site~cdsb) + Ku(dna,cs) -> DNA23(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA24(site~cdsb) + Ku(dna,cs) -> DNA24(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA25(site~cdsb) + Ku(dna,cs) -> DNA25(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA26(site~cdsb) + Ku(dna,cs) -> DNA26(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA27(site~cdsb) + Ku(dna,cs) -> DNA27(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA28(site~cdsb) + Ku(dna,cs) -> DNA28(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA29(site~cdsb) + Ku(dna,cs) -> DNA29(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA30(site~cdsb) + Ku(dna,cs) -> DNA30(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA31(site~cdsb) + Ku(dna,cs) -> DNA31(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA32(site~cdsb) + Ku(dna,cs) -> DNA32(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA33(site~cdsb) + Ku(dna,cs) -> DNA33(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA34(site~cdsb) + Ku(dna,cs) -> DNA34(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA35(site~cdsb) + Ku(dna,cs) -> DNA35(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA36(site~cdsb) + Ku(dna,cs) -> DNA36(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA37(site~cdsb) + Ku(dna,cs) -> DNA37(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA38(site~cdsb) + Ku(dna,cs) -> DNA38(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA39(site~cdsb) + Ku(dna,cs) -> DNA39(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA40(site~cdsb) + Ku(dna,cs) -> DNA40(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA41(site~cdsb) + Ku(dna,cs) -> DNA41(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA42(site~cdsb) + Ku(dna,cs) -> DNA42(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA43(site~cdsb) + Ku(dna,cs) -> DNA43(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA44(site~cdsb) + Ku(dna,cs) -> DNA44(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA45(site~cdsb) + Ku(dna,cs) -> DNA45(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA46(site~cdsb) + Ku(dna,cs) -> DNA46(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA47(site~cdsb) + Ku(dna,cs) -> DNA47(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA48(site~cdsb) + Ku(dna,cs) -> DNA48(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA49(site~cdsb) + Ku(dna,cs) -> DNA49(site!1~cdsb).Ku(dna!1,cs) kku2() -DNA50(site~cdsb) + Ku(dna,cs) -> DNA50(site!1~cdsb).Ku(dna!1,cs) kku2() - -# Ku dissociating -# simple -DNA1(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA1(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA2(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA2(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA3(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA3(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA4(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA4(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA5(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA5(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA6(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA6(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA7(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA7(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA8(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA8(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA9(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA9(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA10(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA10(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA11(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA11(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA12(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA12(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA13(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA13(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA14(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA14(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA15(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA15(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA16(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA16(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA17(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA17(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA18(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA18(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA19(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA19(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA20(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA20(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA21(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA21(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA22(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA22(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA23(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA23(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA24(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA24(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA25(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA25(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA26(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA26(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA27(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA27(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA28(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA28(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA29(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA29(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA30(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA30(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA31(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA31(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA32(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA32(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA33(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA33(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA34(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA34(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA35(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA35(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA36(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA36(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA37(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA37(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA38(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA38(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA39(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA39(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA40(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA40(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA41(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA41(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA42(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA42(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA43(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA43(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA44(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA44(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA45(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA45(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA46(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA46(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA47(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA47(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA48(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA48(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA49(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA49(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -DNA50(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA50(site~sdsb) + Ku(dna,cs,cys~red) kdku1 -# complex -DNA1(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA1(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA2(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA2(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA3(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA3(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA4(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA4(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA5(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA5(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA6(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA6(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA7(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA7(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA8(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA8(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA9(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA9(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA10(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA10(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA11(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA11(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA12(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA12(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA13(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA13(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA14(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA14(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA15(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA15(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA16(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA16(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA17(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA17(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA18(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA18(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA19(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA19(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA20(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA20(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA21(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA21(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA22(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA22(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA23(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA23(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA24(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA24(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA25(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA25(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA26(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA26(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA27(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA27(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA28(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA28(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA29(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA29(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA30(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA30(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA31(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA31(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA32(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA32(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA33(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA33(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA34(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA34(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA35(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA35(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA36(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA36(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA37(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA37(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA38(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA38(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA39(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA39(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA40(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA40(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA41(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA41(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA42(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA42(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA43(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA43(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA44(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA44(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA45(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA45(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA46(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA46(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA47(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA47(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA48(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA48(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA49(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA49(site~cdsb) + Ku(dna,cs,cys~red) kdku2 -DNA50(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA50(site~cdsb) + Ku(dna,cs,cys~red) kdku2 - -# DNAPKcs complex -# simple -DNA1(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA2(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA3(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA4(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA5(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA6(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA7(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA8(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA9(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA10(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA11(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA12(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA13(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA14(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA15(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA16(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA17(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA18(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA19(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA20(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA21(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA22(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA23(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA24(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA25(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA26(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA27(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA28(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA29(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA30(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA31(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA32(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA33(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA34(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA35(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA36(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA37(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA38(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA39(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA40(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA41(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA42(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA43(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA44(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA45(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA46(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA47(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA48(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA49(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -DNA50(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk1 -# complex -DNA1(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA2(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA3(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA4(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA5(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA6(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA7(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA8(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA9(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA10(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA11(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA12(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA13(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA14(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA15(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA16(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA17(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA18(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA19(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA20(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA21(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA22(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA23(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA24(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA25(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA26(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA27(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA28(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA29(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA30(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA31(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA32(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA33(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA34(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA35(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA36(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA37(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA38(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA39(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA40(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA41(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA42(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA43(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA44(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA45(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA46(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA47(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA48(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA49(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 -DNA50(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) kdnapk2 - -# dissociation -#simple -DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA1(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA2(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA3(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA4(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA5(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA6(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA7(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA8(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA9(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA10(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA11(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA12(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA13(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA14(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA15(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA16(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA17(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA18(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA19(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA20(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA21(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA22(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA23(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA24(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA25(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA26(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA27(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA28(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA29(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA30(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA31(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA32(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA33(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA34(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA35(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA36(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA37(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA38(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA39(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA40(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA41(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA42(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA43(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA44(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA45(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA46(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA47(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA48(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA49(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA50(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk1 -#complex -DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA1(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA2(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA3(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA4(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA5(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA6(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA7(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA8(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA9(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA10(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA11(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA12(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA13(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA14(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA15(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA16(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA17(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA18(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA19(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA20(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA21(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA22(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA23(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA24(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA25(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA26(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA27(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA28(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA29(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA30(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA31(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA32(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA33(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA34(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA35(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA36(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA37(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA38(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA39(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA40(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA41(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA42(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA43(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA44(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA45(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA46(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA47(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA48(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA49(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 -DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA50(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) kddnapk2 - -# DNAPKcs phosphorylation -# simple -DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos1 -# complex -DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 -DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kdnapkphos2 - -# Ligase IV complex formation -#simple -DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV1 -#complex -DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 -DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) kliIV2 - -# LiIV dissociation -#simple -DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV1 -#complex -DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 -DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) kdliIV2 - -# repair -#simple -DNA1(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA2(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA3(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA4(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA5(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA6(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA7(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA8(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA9(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA10(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA11(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA12(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA13(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA14(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA15(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA16(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA17(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA18(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA19(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA20(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA21(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA22(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA23(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA24(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA25(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA26(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA27(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA28(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA29(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA30(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA31(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA32(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA33(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA34(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA35(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA36(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA37(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA38(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA39(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA40(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA41(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA42(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA43(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA44(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA45(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA46(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA47(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA48(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA49(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -DNA50(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV1 -#complex -DNA1(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA2(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA3(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA4(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA5(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA6(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA7(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA8(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA9(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA10(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA11(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA12(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA13(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA14(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA15(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA16(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA17(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA18(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA19(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA20(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA21(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA22(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA23(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA24(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA25(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA26(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA27(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA28(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA29(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA30(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA31(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA32(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA33(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA34(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA35(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA36(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA37(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA38(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA39(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA40(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA41(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA42(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA43(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA44(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA45(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA46(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA47(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA48(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA49(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 -DNA50(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs) kfixIV2 - -# PARP binding -# simple -DNA1(site~sdsb) + PARP(dna,liIII) -> DNA1(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA2(site~sdsb) + PARP(dna,liIII) -> DNA2(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA3(site~sdsb) + PARP(dna,liIII) -> DNA3(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA4(site~sdsb) + PARP(dna,liIII) -> DNA4(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA5(site~sdsb) + PARP(dna,liIII) -> DNA5(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA6(site~sdsb) + PARP(dna,liIII) -> DNA6(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA7(site~sdsb) + PARP(dna,liIII) -> DNA7(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA8(site~sdsb) + PARP(dna,liIII) -> DNA8(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA9(site~sdsb) + PARP(dna,liIII) -> DNA9(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA10(site~sdsb) + PARP(dna,liIII) -> DNA10(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA11(site~sdsb) + PARP(dna,liIII) -> DNA11(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA12(site~sdsb) + PARP(dna,liIII) -> DNA12(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA13(site~sdsb) + PARP(dna,liIII) -> DNA13(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA14(site~sdsb) + PARP(dna,liIII) -> DNA14(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA15(site~sdsb) + PARP(dna,liIII) -> DNA15(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA16(site~sdsb) + PARP(dna,liIII) -> DNA16(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA17(site~sdsb) + PARP(dna,liIII) -> DNA17(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA18(site~sdsb) + PARP(dna,liIII) -> DNA18(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA19(site~sdsb) + PARP(dna,liIII) -> DNA19(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA20(site~sdsb) + PARP(dna,liIII) -> DNA20(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA21(site~sdsb) + PARP(dna,liIII) -> DNA21(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA22(site~sdsb) + PARP(dna,liIII) -> DNA22(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA23(site~sdsb) + PARP(dna,liIII) -> DNA23(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA24(site~sdsb) + PARP(dna,liIII) -> DNA24(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA25(site~sdsb) + PARP(dna,liIII) -> DNA25(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA26(site~sdsb) + PARP(dna,liIII) -> DNA26(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA27(site~sdsb) + PARP(dna,liIII) -> DNA27(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA28(site~sdsb) + PARP(dna,liIII) -> DNA28(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA29(site~sdsb) + PARP(dna,liIII) -> DNA29(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA30(site~sdsb) + PARP(dna,liIII) -> DNA30(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA31(site~sdsb) + PARP(dna,liIII) -> DNA31(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA32(site~sdsb) + PARP(dna,liIII) -> DNA32(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA33(site~sdsb) + PARP(dna,liIII) -> DNA33(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA34(site~sdsb) + PARP(dna,liIII) -> DNA34(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA35(site~sdsb) + PARP(dna,liIII) -> DNA35(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA36(site~sdsb) + PARP(dna,liIII) -> DNA36(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA37(site~sdsb) + PARP(dna,liIII) -> DNA37(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA38(site~sdsb) + PARP(dna,liIII) -> DNA38(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA39(site~sdsb) + PARP(dna,liIII) -> DNA39(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA40(site~sdsb) + PARP(dna,liIII) -> DNA40(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA41(site~sdsb) + PARP(dna,liIII) -> DNA41(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA42(site~sdsb) + PARP(dna,liIII) -> DNA42(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA43(site~sdsb) + PARP(dna,liIII) -> DNA43(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA44(site~sdsb) + PARP(dna,liIII) -> DNA44(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA45(site~sdsb) + PARP(dna,liIII) -> DNA45(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA46(site~sdsb) + PARP(dna,liIII) -> DNA46(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA47(site~sdsb) + PARP(dna,liIII) -> DNA47(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA48(site~sdsb) + PARP(dna,liIII) -> DNA48(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA49(site~sdsb) + PARP(dna,liIII) -> DNA49(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -DNA50(site~sdsb) + PARP(dna,liIII) -> DNA50(site!1~sdsb).PARP(dna!1,liIII) kPARP1 -# complex -DNA1(site~cdsb) + PARP(dna,liIII) -> DNA1(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA2(site~cdsb) + PARP(dna,liIII) -> DNA2(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA3(site~cdsb) + PARP(dna,liIII) -> DNA3(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA4(site~cdsb) + PARP(dna,liIII) -> DNA4(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA5(site~cdsb) + PARP(dna,liIII) -> DNA5(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA6(site~cdsb) + PARP(dna,liIII) -> DNA6(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA7(site~cdsb) + PARP(dna,liIII) -> DNA7(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA8(site~cdsb) + PARP(dna,liIII) -> DNA8(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA9(site~cdsb) + PARP(dna,liIII) -> DNA9(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA10(site~cdsb) + PARP(dna,liIII) -> DNA10(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA11(site~cdsb) + PARP(dna,liIII) -> DNA11(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA12(site~cdsb) + PARP(dna,liIII) -> DNA12(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA13(site~cdsb) + PARP(dna,liIII) -> DNA13(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA14(site~cdsb) + PARP(dna,liIII) -> DNA14(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA15(site~cdsb) + PARP(dna,liIII) -> DNA15(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA16(site~cdsb) + PARP(dna,liIII) -> DNA16(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA17(site~cdsb) + PARP(dna,liIII) -> DNA17(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA18(site~cdsb) + PARP(dna,liIII) -> DNA18(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA19(site~cdsb) + PARP(dna,liIII) -> DNA19(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA20(site~cdsb) + PARP(dna,liIII) -> DNA20(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA21(site~cdsb) + PARP(dna,liIII) -> DNA21(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA22(site~cdsb) + PARP(dna,liIII) -> DNA22(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA23(site~cdsb) + PARP(dna,liIII) -> DNA23(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA24(site~cdsb) + PARP(dna,liIII) -> DNA24(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA25(site~cdsb) + PARP(dna,liIII) -> DNA25(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA26(site~cdsb) + PARP(dna,liIII) -> DNA26(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA27(site~cdsb) + PARP(dna,liIII) -> DNA27(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA28(site~cdsb) + PARP(dna,liIII) -> DNA28(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA29(site~cdsb) + PARP(dna,liIII) -> DNA29(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA30(site~cdsb) + PARP(dna,liIII) -> DNA30(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA31(site~cdsb) + PARP(dna,liIII) -> DNA31(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA32(site~cdsb) + PARP(dna,liIII) -> DNA32(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA33(site~cdsb) + PARP(dna,liIII) -> DNA33(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA34(site~cdsb) + PARP(dna,liIII) -> DNA34(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA35(site~cdsb) + PARP(dna,liIII) -> DNA35(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA36(site~cdsb) + PARP(dna,liIII) -> DNA36(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA37(site~cdsb) + PARP(dna,liIII) -> DNA37(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA38(site~cdsb) + PARP(dna,liIII) -> DNA38(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA39(site~cdsb) + PARP(dna,liIII) -> DNA39(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA40(site~cdsb) + PARP(dna,liIII) -> DNA40(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA41(site~cdsb) + PARP(dna,liIII) -> DNA41(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA42(site~cdsb) + PARP(dna,liIII) -> DNA42(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA43(site~cdsb) + PARP(dna,liIII) -> DNA43(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA44(site~cdsb) + PARP(dna,liIII) -> DNA44(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA45(site~cdsb) + PARP(dna,liIII) -> DNA45(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA46(site~cdsb) + PARP(dna,liIII) -> DNA46(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA47(site~cdsb) + PARP(dna,liIII) -> DNA47(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA48(site~cdsb) + PARP(dna,liIII) -> DNA48(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA49(site~cdsb) + PARP(dna,liIII) -> DNA49(site!1~cdsb).PARP(dna!1,liIII) kPARP2 -DNA50(site~cdsb) + PARP(dna,liIII) -> DNA50(site!1~cdsb).PARP(dna!1,liIII) kPARP2 - -# PARP dissociating -# simple -DNA1(site!1~sdsb).PARP(dna!1,liIII) -> DNA1(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA2(site!1~sdsb).PARP(dna!1,liIII) -> DNA2(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA3(site!1~sdsb).PARP(dna!1,liIII) -> DNA3(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA4(site!1~sdsb).PARP(dna!1,liIII) -> DNA4(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA5(site!1~sdsb).PARP(dna!1,liIII) -> DNA5(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA6(site!1~sdsb).PARP(dna!1,liIII) -> DNA6(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA7(site!1~sdsb).PARP(dna!1,liIII) -> DNA7(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA8(site!1~sdsb).PARP(dna!1,liIII) -> DNA8(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA9(site!1~sdsb).PARP(dna!1,liIII) -> DNA9(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA10(site!1~sdsb).PARP(dna!1,liIII) -> DNA10(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA11(site!1~sdsb).PARP(dna!1,liIII) -> DNA11(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA12(site!1~sdsb).PARP(dna!1,liIII) -> DNA12(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA13(site!1~sdsb).PARP(dna!1,liIII) -> DNA13(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA14(site!1~sdsb).PARP(dna!1,liIII) -> DNA14(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA15(site!1~sdsb).PARP(dna!1,liIII) -> DNA15(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA16(site!1~sdsb).PARP(dna!1,liIII) -> DNA16(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA17(site!1~sdsb).PARP(dna!1,liIII) -> DNA17(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA18(site!1~sdsb).PARP(dna!1,liIII) -> DNA18(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA19(site!1~sdsb).PARP(dna!1,liIII) -> DNA19(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA20(site!1~sdsb).PARP(dna!1,liIII) -> DNA20(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA21(site!1~sdsb).PARP(dna!1,liIII) -> DNA21(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA22(site!1~sdsb).PARP(dna!1,liIII) -> DNA22(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA23(site!1~sdsb).PARP(dna!1,liIII) -> DNA23(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA24(site!1~sdsb).PARP(dna!1,liIII) -> DNA24(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA25(site!1~sdsb).PARP(dna!1,liIII) -> DNA25(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA26(site!1~sdsb).PARP(dna!1,liIII) -> DNA26(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA27(site!1~sdsb).PARP(dna!1,liIII) -> DNA27(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA28(site!1~sdsb).PARP(dna!1,liIII) -> DNA28(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA29(site!1~sdsb).PARP(dna!1,liIII) -> DNA29(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA30(site!1~sdsb).PARP(dna!1,liIII) -> DNA30(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA31(site!1~sdsb).PARP(dna!1,liIII) -> DNA31(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA32(site!1~sdsb).PARP(dna!1,liIII) -> DNA32(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA33(site!1~sdsb).PARP(dna!1,liIII) -> DNA33(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA34(site!1~sdsb).PARP(dna!1,liIII) -> DNA34(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA35(site!1~sdsb).PARP(dna!1,liIII) -> DNA35(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA36(site!1~sdsb).PARP(dna!1,liIII) -> DNA36(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA37(site!1~sdsb).PARP(dna!1,liIII) -> DNA37(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA38(site!1~sdsb).PARP(dna!1,liIII) -> DNA38(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA39(site!1~sdsb).PARP(dna!1,liIII) -> DNA39(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA40(site!1~sdsb).PARP(dna!1,liIII) -> DNA40(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA41(site!1~sdsb).PARP(dna!1,liIII) -> DNA41(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA42(site!1~sdsb).PARP(dna!1,liIII) -> DNA42(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA43(site!1~sdsb).PARP(dna!1,liIII) -> DNA43(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA44(site!1~sdsb).PARP(dna!1,liIII) -> DNA44(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA45(site!1~sdsb).PARP(dna!1,liIII) -> DNA45(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA46(site!1~sdsb).PARP(dna!1,liIII) -> DNA46(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA47(site!1~sdsb).PARP(dna!1,liIII) -> DNA47(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA48(site!1~sdsb).PARP(dna!1,liIII) -> DNA48(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA49(site!1~sdsb).PARP(dna!1,liIII) -> DNA49(site~sdsb) + PARP(dna,liIII) kdPARP1 -DNA50(site!1~sdsb).PARP(dna!1,liIII) -> DNA50(site~sdsb) + PARP(dna,liIII) kdPARP1 -# complex -DNA1(site!1~cdsb).PARP(dna!1,liIII) -> DNA1(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA2(site!1~cdsb).PARP(dna!1,liIII) -> DNA2(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA3(site!1~cdsb).PARP(dna!1,liIII) -> DNA3(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA4(site!1~cdsb).PARP(dna!1,liIII) -> DNA4(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA5(site!1~cdsb).PARP(dna!1,liIII) -> DNA5(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA6(site!1~cdsb).PARP(dna!1,liIII) -> DNA6(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA7(site!1~cdsb).PARP(dna!1,liIII) -> DNA7(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA8(site!1~cdsb).PARP(dna!1,liIII) -> DNA8(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA9(site!1~cdsb).PARP(dna!1,liIII) -> DNA9(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA10(site!1~cdsb).PARP(dna!1,liIII) -> DNA10(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA11(site!1~cdsb).PARP(dna!1,liIII) -> DNA11(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA12(site!1~cdsb).PARP(dna!1,liIII) -> DNA12(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA13(site!1~cdsb).PARP(dna!1,liIII) -> DNA13(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA14(site!1~cdsb).PARP(dna!1,liIII) -> DNA14(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA15(site!1~cdsb).PARP(dna!1,liIII) -> DNA15(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA16(site!1~cdsb).PARP(dna!1,liIII) -> DNA16(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA17(site!1~cdsb).PARP(dna!1,liIII) -> DNA17(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA18(site!1~cdsb).PARP(dna!1,liIII) -> DNA18(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA19(site!1~cdsb).PARP(dna!1,liIII) -> DNA19(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA20(site!1~cdsb).PARP(dna!1,liIII) -> DNA20(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA21(site!1~cdsb).PARP(dna!1,liIII) -> DNA21(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA22(site!1~cdsb).PARP(dna!1,liIII) -> DNA22(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA23(site!1~cdsb).PARP(dna!1,liIII) -> DNA23(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA24(site!1~cdsb).PARP(dna!1,liIII) -> DNA24(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA25(site!1~cdsb).PARP(dna!1,liIII) -> DNA25(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA26(site!1~cdsb).PARP(dna!1,liIII) -> DNA26(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA27(site!1~cdsb).PARP(dna!1,liIII) -> DNA27(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA28(site!1~cdsb).PARP(dna!1,liIII) -> DNA28(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA29(site!1~cdsb).PARP(dna!1,liIII) -> DNA29(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA30(site!1~cdsb).PARP(dna!1,liIII) -> DNA30(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA31(site!1~cdsb).PARP(dna!1,liIII) -> DNA31(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA32(site!1~cdsb).PARP(dna!1,liIII) -> DNA32(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA33(site!1~cdsb).PARP(dna!1,liIII) -> DNA33(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA34(site!1~cdsb).PARP(dna!1,liIII) -> DNA34(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA35(site!1~cdsb).PARP(dna!1,liIII) -> DNA35(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA36(site!1~cdsb).PARP(dna!1,liIII) -> DNA36(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA37(site!1~cdsb).PARP(dna!1,liIII) -> DNA37(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA38(site!1~cdsb).PARP(dna!1,liIII) -> DNA38(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA39(site!1~cdsb).PARP(dna!1,liIII) -> DNA39(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA40(site!1~cdsb).PARP(dna!1,liIII) -> DNA40(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA41(site!1~cdsb).PARP(dna!1,liIII) -> DNA41(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA42(site!1~cdsb).PARP(dna!1,liIII) -> DNA42(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA43(site!1~cdsb).PARP(dna!1,liIII) -> DNA43(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA44(site!1~cdsb).PARP(dna!1,liIII) -> DNA44(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA45(site!1~cdsb).PARP(dna!1,liIII) -> DNA45(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA46(site!1~cdsb).PARP(dna!1,liIII) -> DNA46(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA47(site!1~cdsb).PARP(dna!1,liIII) -> DNA47(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA48(site!1~cdsb).PARP(dna!1,liIII) -> DNA48(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA49(site!1~cdsb).PARP(dna!1,liIII) -> DNA49(site~cdsb) + PARP(dna,liIII) kdPARP2 -DNA50(site!1~cdsb).PARP(dna!1,liIII) -> DNA50(site~cdsb) + PARP(dna,liIII) kdPARP2 - -# Ligase III complex formation -# simple -DNA1(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA1(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA2(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA2(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA3(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA3(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA4(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA4(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA5(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA5(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA6(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA6(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA7(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA7(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA8(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA8(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA9(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA9(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA10(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA10(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA11(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA11(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA12(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA12(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA13(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA13(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA14(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA14(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA15(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA15(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA16(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA16(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA17(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA17(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA18(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA18(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA19(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA19(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA20(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA20(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA21(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA21(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA22(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA22(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA23(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA23(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA24(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA24(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA25(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA25(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA26(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA26(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA27(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA27(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA28(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA28(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA29(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA29(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA30(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA30(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA31(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA31(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA32(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA32(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA33(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA33(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA34(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA34(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA35(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA35(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA36(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA36(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA37(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA37(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA38(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA38(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA39(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA39(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA40(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA40(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA41(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA41(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA42(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA42(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA43(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA43(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA44(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA44(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA45(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA45(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA46(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA46(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA47(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA47(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA48(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA48(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA49(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA49(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -DNA50(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA50(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII1 -# complex -DNA1(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA1(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA2(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA2(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA3(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA3(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA4(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA4(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA5(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA5(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA6(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA6(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA7(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA7(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA8(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA8(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA9(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA9(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA10(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA10(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA11(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA11(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA12(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA12(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA13(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA13(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA14(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA14(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA15(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA15(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA16(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA16(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA17(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA17(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA18(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA18(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA19(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA19(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA20(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA20(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA21(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA21(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA22(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA22(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA23(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA23(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA24(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA24(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA25(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA25(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA26(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA26(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA27(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA27(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA28(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA28(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA29(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA29(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA30(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA30(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA31(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA31(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA32(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA32(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA33(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA33(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA34(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA34(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA35(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA35(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA36(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA36(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA37(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA37(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA38(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA38(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA39(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA39(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA40(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA40(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA41(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA41(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA42(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA42(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA43(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA43(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA44(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA44(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA45(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA45(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA46(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA46(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA47(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA47(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA48(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA48(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA49(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA49(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 -DNA50(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA50(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) kliIII2 - -# ligase dissociation -# simple -DNA1(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA1(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA2(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA2(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA3(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA3(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA4(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA4(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA5(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA5(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA6(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA6(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA7(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA7(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA8(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA8(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA9(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA9(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA10(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA10(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA11(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA11(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA12(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA12(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA13(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA13(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA14(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA14(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA15(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA15(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA16(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA16(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA17(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA17(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA18(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA18(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA19(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA19(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA20(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA20(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA21(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA21(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA22(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA22(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA23(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA23(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA24(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA24(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA25(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA25(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA26(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA26(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA27(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA27(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA28(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA28(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA29(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA29(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA30(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA30(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA31(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA31(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA32(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA32(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA33(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA33(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA34(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA34(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA35(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA35(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA36(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA36(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA37(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA37(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA38(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA38(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA39(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA39(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA40(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA40(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA41(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA41(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA42(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA42(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA43(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA43(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA44(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA44(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA45(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA45(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA46(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA46(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA47(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA47(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA48(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA48(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA49(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA49(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -DNA50(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA50(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII1 -# complex -DNA1(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA1(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA2(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA2(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA3(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA3(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA4(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA4(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA5(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA5(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA6(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA6(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA7(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA7(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA8(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA8(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA9(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA9(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA10(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA10(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA11(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA11(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA12(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA12(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA13(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA13(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA14(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA14(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA15(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA15(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA16(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA16(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA17(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA17(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA18(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA18(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA19(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA19(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA20(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA20(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA21(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA21(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA22(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA22(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA23(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA23(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA24(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA24(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA25(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA25(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA26(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA26(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA27(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA27(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA28(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA28(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA29(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA29(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA30(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA30(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA31(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA31(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA32(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA32(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA33(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA33(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA34(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA34(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA35(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA35(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA36(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA36(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA37(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA37(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA38(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA38(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA39(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA39(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA40(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA40(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA41(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA41(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA42(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA42(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA43(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA43(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA44(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA44(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA45(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA45(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA46(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA46(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA47(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA47(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA48(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA48(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA49(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA49(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 -DNA50(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA50(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) kdliIII2 - -# liIII repair -# accurate repair simple -DNA1(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA2(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA3(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA4(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA5(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA6(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA7(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA8(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA9(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA10(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA11(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA12(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA13(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA14(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA15(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA16(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA17(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA18(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA19(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA20(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA21(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA22(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA23(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA24(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA25(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA26(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA27(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA28(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA29(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA30(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA31(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA32(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA33(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA34(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA35(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA36(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA37(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA38(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA39(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA40(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA41(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA42(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA43(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA44(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA45(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA46(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA47(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA48(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA49(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -DNA50(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII1 -# accurate repair complex -DNA1(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA2(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA3(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA4(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA5(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA6(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA7(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA8(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA9(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA10(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA11(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA12(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA13(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA14(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA15(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA16(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA17(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA18(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA19(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA20(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA21(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA22(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA23(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA24(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA25(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA26(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA27(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA28(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA29(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA30(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA31(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA32(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA33(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA34(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA35(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA36(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA37(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA38(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA39(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA40(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA41(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA42(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA43(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA44(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA45(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA46(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA47(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA48(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA49(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 -DNA50(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII2 - -# inaccurate repairsimple -DNA1(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA2(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA3(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA4(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA5(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA6(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA7(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA8(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA9(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA10(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA11(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA12(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA13(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA14(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA15(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA16(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA17(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA18(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA19(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA20(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA21(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA22(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA23(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA24(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA25(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA26(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA27(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA28(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA29(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA30(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA31(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA32(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA33(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA34(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA35(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA36(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA37(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA38(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA39(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA40(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA41(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA42(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA43(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA44(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA45(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA46(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA47(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA48(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA49(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -DNA50(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII3 -# inaccurate repair complex -DNA1(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA2(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA3(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA4(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA5(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA6(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA7(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA8(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA9(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA10(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA11(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA12(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA13(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA14(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA15(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA16(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA17(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA18(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA19(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA20(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA21(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA22(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA23(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA24(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA25(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA26(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA27(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA28(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA29(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA30(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA31(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA32(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA33(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA34(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA35(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA36(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA37(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA38(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA39(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA40(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA41(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA42(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA43(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA44(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA45(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA46(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA47(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA48(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA49(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 -DNA50(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP) kfixIII4 - -# ATM Activation -DNA1(site!?~sdsb) + ATM(state~0,h2ax) -> DNA1(site!?~sdsb) + ATM(state~1,h2ax) kATMact -DNA2(site!?~sdsb) + ATM(state~0,h2ax) -> DNA2(site!?~sdsb) + ATM(state~2,h2ax) kATMact -DNA3(site!?~sdsb) + ATM(state~0,h2ax) -> DNA3(site!?~sdsb) + ATM(state~3,h2ax) kATMact -DNA4(site!?~sdsb) + ATM(state~0,h2ax) -> DNA4(site!?~sdsb) + ATM(state~4,h2ax) kATMact -DNA5(site!?~sdsb) + ATM(state~0,h2ax) -> DNA5(site!?~sdsb) + ATM(state~5,h2ax) kATMact -DNA6(site!?~sdsb) + ATM(state~0,h2ax) -> DNA6(site!?~sdsb) + ATM(state~6,h2ax) kATMact -DNA7(site!?~sdsb) + ATM(state~0,h2ax) -> DNA7(site!?~sdsb) + ATM(state~7,h2ax) kATMact -DNA8(site!?~sdsb) + ATM(state~0,h2ax) -> DNA8(site!?~sdsb) + ATM(state~8,h2ax) kATMact -DNA9(site!?~sdsb) + ATM(state~0,h2ax) -> DNA9(site!?~sdsb) + ATM(state~9,h2ax) kATMact -DNA10(site!?~sdsb) + ATM(state~0,h2ax) -> DNA10(site!?~sdsb) + ATM(state~10,h2ax) kATMact -DNA11(site!?~sdsb) + ATM(state~0,h2ax) -> DNA11(site!?~sdsb) + ATM(state~11,h2ax) kATMact -DNA12(site!?~sdsb) + ATM(state~0,h2ax) -> DNA12(site!?~sdsb) + ATM(state~12,h2ax) kATMact -DNA13(site!?~sdsb) + ATM(state~0,h2ax) -> DNA13(site!?~sdsb) + ATM(state~13,h2ax) kATMact -DNA14(site!?~sdsb) + ATM(state~0,h2ax) -> DNA14(site!?~sdsb) + ATM(state~14,h2ax) kATMact -DNA15(site!?~sdsb) + ATM(state~0,h2ax) -> DNA15(site!?~sdsb) + ATM(state~15,h2ax) kATMact -DNA16(site!?~sdsb) + ATM(state~0,h2ax) -> DNA16(site!?~sdsb) + ATM(state~16,h2ax) kATMact -DNA17(site!?~sdsb) + ATM(state~0,h2ax) -> DNA17(site!?~sdsb) + ATM(state~17,h2ax) kATMact -DNA18(site!?~sdsb) + ATM(state~0,h2ax) -> DNA18(site!?~sdsb) + ATM(state~18,h2ax) kATMact -DNA19(site!?~sdsb) + ATM(state~0,h2ax) -> DNA19(site!?~sdsb) + ATM(state~19,h2ax) kATMact -DNA20(site!?~sdsb) + ATM(state~0,h2ax) -> DNA20(site!?~sdsb) + ATM(state~20,h2ax) kATMact -DNA21(site!?~sdsb) + ATM(state~0,h2ax) -> DNA21(site!?~sdsb) + ATM(state~21,h2ax) kATMact -DNA22(site!?~sdsb) + ATM(state~0,h2ax) -> DNA22(site!?~sdsb) + ATM(state~22,h2ax) kATMact -DNA23(site!?~sdsb) + ATM(state~0,h2ax) -> DNA23(site!?~sdsb) + ATM(state~23,h2ax) kATMact -DNA24(site!?~sdsb) + ATM(state~0,h2ax) -> DNA24(site!?~sdsb) + ATM(state~24,h2ax) kATMact -DNA25(site!?~sdsb) + ATM(state~0,h2ax) -> DNA25(site!?~sdsb) + ATM(state~25,h2ax) kATMact -DNA26(site!?~sdsb) + ATM(state~0,h2ax) -> DNA26(site!?~sdsb) + ATM(state~26,h2ax) kATMact -DNA27(site!?~sdsb) + ATM(state~0,h2ax) -> DNA27(site!?~sdsb) + ATM(state~27,h2ax) kATMact -DNA28(site!?~sdsb) + ATM(state~0,h2ax) -> DNA28(site!?~sdsb) + ATM(state~28,h2ax) kATMact -DNA29(site!?~sdsb) + ATM(state~0,h2ax) -> DNA29(site!?~sdsb) + ATM(state~29,h2ax) kATMact -DNA30(site!?~sdsb) + ATM(state~0,h2ax) -> DNA30(site!?~sdsb) + ATM(state~30,h2ax) kATMact -DNA31(site!?~sdsb) + ATM(state~0,h2ax) -> DNA31(site!?~sdsb) + ATM(state~31,h2ax) kATMact -DNA32(site!?~sdsb) + ATM(state~0,h2ax) -> DNA32(site!?~sdsb) + ATM(state~32,h2ax) kATMact -DNA33(site!?~sdsb) + ATM(state~0,h2ax) -> DNA33(site!?~sdsb) + ATM(state~33,h2ax) kATMact -DNA34(site!?~sdsb) + ATM(state~0,h2ax) -> DNA34(site!?~sdsb) + ATM(state~34,h2ax) kATMact -DNA35(site!?~sdsb) + ATM(state~0,h2ax) -> DNA35(site!?~sdsb) + ATM(state~35,h2ax) kATMact -DNA36(site!?~sdsb) + ATM(state~0,h2ax) -> DNA36(site!?~sdsb) + ATM(state~36,h2ax) kATMact -DNA37(site!?~sdsb) + ATM(state~0,h2ax) -> DNA37(site!?~sdsb) + ATM(state~37,h2ax) kATMact -DNA38(site!?~sdsb) + ATM(state~0,h2ax) -> DNA38(site!?~sdsb) + ATM(state~38,h2ax) kATMact -DNA39(site!?~sdsb) + ATM(state~0,h2ax) -> DNA39(site!?~sdsb) + ATM(state~39,h2ax) kATMact -DNA40(site!?~sdsb) + ATM(state~0,h2ax) -> DNA40(site!?~sdsb) + ATM(state~40,h2ax) kATMact -DNA41(site!?~sdsb) + ATM(state~0,h2ax) -> DNA41(site!?~sdsb) + ATM(state~41,h2ax) kATMact -DNA42(site!?~sdsb) + ATM(state~0,h2ax) -> DNA42(site!?~sdsb) + ATM(state~42,h2ax) kATMact -DNA43(site!?~sdsb) + ATM(state~0,h2ax) -> DNA43(site!?~sdsb) + ATM(state~43,h2ax) kATMact -DNA44(site!?~sdsb) + ATM(state~0,h2ax) -> DNA44(site!?~sdsb) + ATM(state~44,h2ax) kATMact -DNA45(site!?~sdsb) + ATM(state~0,h2ax) -> DNA45(site!?~sdsb) + ATM(state~45,h2ax) kATMact -DNA46(site!?~sdsb) + ATM(state~0,h2ax) -> DNA46(site!?~sdsb) + ATM(state~46,h2ax) kATMact -DNA47(site!?~sdsb) + ATM(state~0,h2ax) -> DNA47(site!?~sdsb) + ATM(state~47,h2ax) kATMact -DNA48(site!?~sdsb) + ATM(state~0,h2ax) -> DNA48(site!?~sdsb) + ATM(state~48,h2ax) kATMact -DNA49(site!?~sdsb) + ATM(state~0,h2ax) -> DNA49(site!?~sdsb) + ATM(state~49,h2ax) kATMact -DNA50(site!?~sdsb) + ATM(state~0,h2ax) -> DNA50(site!?~sdsb) + ATM(state~50,h2ax) kATMact - -DNA1(site!?~cdsb) + ATM(state~0,h2ax) -> DNA1(site!?~cdsb) + ATM(state~1,h2ax) kATMact -DNA2(site!?~cdsb) + ATM(state~0,h2ax) -> DNA2(site!?~cdsb) + ATM(state~2,h2ax) kATMact -DNA3(site!?~cdsb) + ATM(state~0,h2ax) -> DNA3(site!?~cdsb) + ATM(state~3,h2ax) kATMact -DNA4(site!?~cdsb) + ATM(state~0,h2ax) -> DNA4(site!?~cdsb) + ATM(state~4,h2ax) kATMact -DNA5(site!?~cdsb) + ATM(state~0,h2ax) -> DNA5(site!?~cdsb) + ATM(state~5,h2ax) kATMact -DNA6(site!?~cdsb) + ATM(state~0,h2ax) -> DNA6(site!?~cdsb) + ATM(state~6,h2ax) kATMact -DNA7(site!?~cdsb) + ATM(state~0,h2ax) -> DNA7(site!?~cdsb) + ATM(state~7,h2ax) kATMact -DNA8(site!?~cdsb) + ATM(state~0,h2ax) -> DNA8(site!?~cdsb) + ATM(state~8,h2ax) kATMact -DNA9(site!?~cdsb) + ATM(state~0,h2ax) -> DNA9(site!?~cdsb) + ATM(state~9,h2ax) kATMact -DNA10(site!?~cdsb) + ATM(state~0,h2ax) -> DNA10(site!?~cdsb) + ATM(state~10,h2ax) kATMact -DNA11(site!?~cdsb) + ATM(state~0,h2ax) -> DNA11(site!?~cdsb) + ATM(state~12,h2ax) kATMact -DNA12(site!?~cdsb) + ATM(state~0,h2ax) -> DNA12(site!?~cdsb) + ATM(state~13,h2ax) kATMact -DNA13(site!?~cdsb) + ATM(state~0,h2ax) -> DNA13(site!?~cdsb) + ATM(state~13,h2ax) kATMact -DNA14(site!?~cdsb) + ATM(state~0,h2ax) -> DNA14(site!?~cdsb) + ATM(state~14,h2ax) kATMact -DNA15(site!?~cdsb) + ATM(state~0,h2ax) -> DNA15(site!?~cdsb) + ATM(state~15,h2ax) kATMact -DNA16(site!?~cdsb) + ATM(state~0,h2ax) -> DNA16(site!?~cdsb) + ATM(state~16,h2ax) kATMact -DNA17(site!?~cdsb) + ATM(state~0,h2ax) -> DNA17(site!?~cdsb) + ATM(state~17,h2ax) kATMact -DNA18(site!?~cdsb) + ATM(state~0,h2ax) -> DNA18(site!?~cdsb) + ATM(state~18,h2ax) kATMact -DNA19(site!?~cdsb) + ATM(state~0,h2ax) -> DNA19(site!?~cdsb) + ATM(state~19,h2ax) kATMact -DNA20(site!?~cdsb) + ATM(state~0,h2ax) -> DNA20(site!?~cdsb) + ATM(state~20,h2ax) kATMact -DNA21(site!?~cdsb) + ATM(state~0,h2ax) -> DNA21(site!?~cdsb) + ATM(state~21,h2ax) kATMact -DNA22(site!?~cdsb) + ATM(state~0,h2ax) -> DNA22(site!?~cdsb) + ATM(state~22,h2ax) kATMact -DNA23(site!?~cdsb) + ATM(state~0,h2ax) -> DNA23(site!?~cdsb) + ATM(state~23,h2ax) kATMact -DNA24(site!?~cdsb) + ATM(state~0,h2ax) -> DNA24(site!?~cdsb) + ATM(state~24,h2ax) kATMact -DNA25(site!?~cdsb) + ATM(state~0,h2ax) -> DNA25(site!?~cdsb) + ATM(state~25,h2ax) kATMact -DNA26(site!?~cdsb) + ATM(state~0,h2ax) -> DNA26(site!?~cdsb) + ATM(state~26,h2ax) kATMact -DNA27(site!?~cdsb) + ATM(state~0,h2ax) -> DNA27(site!?~cdsb) + ATM(state~27,h2ax) kATMact -DNA28(site!?~cdsb) + ATM(state~0,h2ax) -> DNA28(site!?~cdsb) + ATM(state~28,h2ax) kATMact -DNA29(site!?~cdsb) + ATM(state~0,h2ax) -> DNA29(site!?~cdsb) + ATM(state~29,h2ax) kATMact -DNA30(site!?~cdsb) + ATM(state~0,h2ax) -> DNA30(site!?~cdsb) + ATM(state~30,h2ax) kATMact -DNA31(site!?~cdsb) + ATM(state~0,h2ax) -> DNA31(site!?~cdsb) + ATM(state~31,h2ax) kATMact -DNA32(site!?~cdsb) + ATM(state~0,h2ax) -> DNA32(site!?~cdsb) + ATM(state~32,h2ax) kATMact -DNA33(site!?~cdsb) + ATM(state~0,h2ax) -> DNA33(site!?~cdsb) + ATM(state~33,h2ax) kATMact -DNA34(site!?~cdsb) + ATM(state~0,h2ax) -> DNA34(site!?~cdsb) + ATM(state~34,h2ax) kATMact -DNA35(site!?~cdsb) + ATM(state~0,h2ax) -> DNA35(site!?~cdsb) + ATM(state~35,h2ax) kATMact -DNA36(site!?~cdsb) + ATM(state~0,h2ax) -> DNA36(site!?~cdsb) + ATM(state~36,h2ax) kATMact -DNA37(site!?~cdsb) + ATM(state~0,h2ax) -> DNA37(site!?~cdsb) + ATM(state~37,h2ax) kATMact -DNA38(site!?~cdsb) + ATM(state~0,h2ax) -> DNA38(site!?~cdsb) + ATM(state~38,h2ax) kATMact -DNA39(site!?~cdsb) + ATM(state~0,h2ax) -> DNA39(site!?~cdsb) + ATM(state~39,h2ax) kATMact -DNA40(site!?~cdsb) + ATM(state~0,h2ax) -> DNA40(site!?~cdsb) + ATM(state~40,h2ax) kATMact -DNA41(site!?~cdsb) + ATM(state~0,h2ax) -> DNA41(site!?~cdsb) + ATM(state~41,h2ax) kATMact -DNA42(site!?~cdsb) + ATM(state~0,h2ax) -> DNA42(site!?~cdsb) + ATM(state~42,h2ax) kATMact -DNA43(site!?~cdsb) + ATM(state~0,h2ax) -> DNA43(site!?~cdsb) + ATM(state~43,h2ax) kATMact -DNA44(site!?~cdsb) + ATM(state~0,h2ax) -> DNA44(site!?~cdsb) + ATM(state~44,h2ax) kATMact -DNA45(site!?~cdsb) + ATM(state~0,h2ax) -> DNA45(site!?~cdsb) + ATM(state~45,h2ax) kATMact -DNA46(site!?~cdsb) + ATM(state~0,h2ax) -> DNA46(site!?~cdsb) + ATM(state~46,h2ax) kATMact -DNA47(site!?~cdsb) + ATM(state~0,h2ax) -> DNA47(site!?~cdsb) + ATM(state~47,h2ax) kATMact -DNA48(site!?~cdsb) + ATM(state~0,h2ax) -> DNA48(site!?~cdsb) + ATM(state~48,h2ax) kATMact -DNA49(site!?~cdsb) + ATM(state~0,h2ax) -> DNA49(site!?~cdsb) + ATM(state~49,h2ax) kATMact -DNA50(site!?~cdsb) + ATM(state~0,h2ax) -> DNA50(site!?~cdsb) + ATM(state~50,h2ax) kATMact - -# ATM Inactivation -ATM(state~1,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~2,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~3,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~4,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~5,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~6,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~7,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~8,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~9,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~10,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~11,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~12,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~13,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~14,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~15,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~16,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~17,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~18,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~19,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~20,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~21,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~22,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~23,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~24,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~25,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~26,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~27,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~28,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~29,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~30,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~31,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~32,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~33,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~34,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~35,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~36,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~37,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~38,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~39,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~40,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~41,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~42,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~43,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~44,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~45,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~46,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~47,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~48,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~49,h2ax) -> ATM(state~0,h2ax) kATMinact -ATM(state~50,h2ax) -> ATM(state~0,h2ax) kATMinact - - -# histone2ax -# histone phosphorylation -# simple -DNA1(site!?~sdsb,h2ax~u) + ATM(state~1,h2ax) -> DNA1(site!?~sdsb,h2ax~p) + ATM(state~1,h2ax) kh2axp1 -DNA2(site!?~sdsb,h2ax~u) + ATM(state~2,h2ax) -> DNA2(site!?~sdsb,h2ax~p) + ATM(state~2,h2ax) kh2axp1 -DNA3(site!?~sdsb,h2ax~u) + ATM(state~3,h2ax) -> DNA3(site!?~sdsb,h2ax~p) + ATM(state~3,h2ax) kh2axp1 -DNA4(site!?~sdsb,h2ax~u) + ATM(state~4,h2ax) -> DNA4(site!?~sdsb,h2ax~p) + ATM(state~4,h2ax) kh2axp1 -DNA5(site!?~sdsb,h2ax~u) + ATM(state~5,h2ax) -> DNA5(site!?~sdsb,h2ax~p) + ATM(state~5,h2ax) kh2axp1 -DNA6(site!?~sdsb,h2ax~u) + ATM(state~6,h2ax) -> DNA6(site!?~sdsb,h2ax~p) + ATM(state~6,h2ax) kh2axp1 -DNA7(site!?~sdsb,h2ax~u) + ATM(state~7,h2ax) -> DNA7(site!?~sdsb,h2ax~p) + ATM(state~7,h2ax) kh2axp1 -DNA8(site!?~sdsb,h2ax~u) + ATM(state~8,h2ax) -> DNA8(site!?~sdsb,h2ax~p) + ATM(state~8,h2ax) kh2axp1 -DNA9(site!?~sdsb,h2ax~u) + ATM(state~9,h2ax) -> DNA9(site!?~sdsb,h2ax~p) + ATM(state~9,h2ax) kh2axp1 -DNA10(site!?~sdsb,h2ax~u) + ATM(state~10,h2ax) -> DNA10(site!?~sdsb,h2ax~p) + ATM(state~10,h2ax) kh2axp1 -DNA11(site!?~sdsb,h2ax~u) + ATM(state~11,h2ax) -> DNA11(site!?~sdsb,h2ax~p) + ATM(state~11,h2ax) kh2axp1 -DNA12(site!?~sdsb,h2ax~u) + ATM(state~12,h2ax) -> DNA12(site!?~sdsb,h2ax~p) + ATM(state~12,h2ax) kh2axp1 -DNA13(site!?~sdsb,h2ax~u) + ATM(state~13,h2ax) -> DNA13(site!?~sdsb,h2ax~p) + ATM(state~13,h2ax) kh2axp1 -DNA14(site!?~sdsb,h2ax~u) + ATM(state~14,h2ax) -> DNA14(site!?~sdsb,h2ax~p) + ATM(state~14,h2ax) kh2axp1 -DNA15(site!?~sdsb,h2ax~u) + ATM(state~15,h2ax) -> DNA15(site!?~sdsb,h2ax~p) + ATM(state~15,h2ax) kh2axp1 -DNA16(site!?~sdsb,h2ax~u) + ATM(state~16,h2ax) -> DNA16(site!?~sdsb,h2ax~p) + ATM(state~16,h2ax) kh2axp1 -DNA17(site!?~sdsb,h2ax~u) + ATM(state~17,h2ax) -> DNA17(site!?~sdsb,h2ax~p) + ATM(state~17,h2ax) kh2axp1 -DNA18(site!?~sdsb,h2ax~u) + ATM(state~18,h2ax) -> DNA18(site!?~sdsb,h2ax~p) + ATM(state~18,h2ax) kh2axp1 -DNA19(site!?~sdsb,h2ax~u) + ATM(state~19,h2ax) -> DNA19(site!?~sdsb,h2ax~p) + ATM(state~19,h2ax) kh2axp1 -DNA20(site!?~sdsb,h2ax~u) + ATM(state~20,h2ax) -> DNA20(site!?~sdsb,h2ax~p) + ATM(state~20,h2ax) kh2axp1 -DNA21(site!?~sdsb,h2ax~u) + ATM(state~21,h2ax) -> DNA21(site!?~sdsb,h2ax~p) + ATM(state~21,h2ax) kh2axp1 -DNA22(site!?~sdsb,h2ax~u) + ATM(state~22,h2ax) -> DNA22(site!?~sdsb,h2ax~p) + ATM(state~22,h2ax) kh2axp1 -DNA23(site!?~sdsb,h2ax~u) + ATM(state~23,h2ax) -> DNA23(site!?~sdsb,h2ax~p) + ATM(state~23,h2ax) kh2axp1 -DNA24(site!?~sdsb,h2ax~u) + ATM(state~24,h2ax) -> DNA24(site!?~sdsb,h2ax~p) + ATM(state~24,h2ax) kh2axp1 -DNA25(site!?~sdsb,h2ax~u) + ATM(state~25,h2ax) -> DNA25(site!?~sdsb,h2ax~p) + ATM(state~25,h2ax) kh2axp1 -DNA26(site!?~sdsb,h2ax~u) + ATM(state~26,h2ax) -> DNA26(site!?~sdsb,h2ax~p) + ATM(state~26,h2ax) kh2axp1 -DNA27(site!?~sdsb,h2ax~u) + ATM(state~27,h2ax) -> DNA27(site!?~sdsb,h2ax~p) + ATM(state~27,h2ax) kh2axp1 -DNA28(site!?~sdsb,h2ax~u) + ATM(state~28,h2ax) -> DNA28(site!?~sdsb,h2ax~p) + ATM(state~28,h2ax) kh2axp1 -DNA29(site!?~sdsb,h2ax~u) + ATM(state~29,h2ax) -> DNA29(site!?~sdsb,h2ax~p) + ATM(state~29,h2ax) kh2axp1 -DNA30(site!?~sdsb,h2ax~u) + ATM(state~30,h2ax) -> DNA30(site!?~sdsb,h2ax~p) + ATM(state~30,h2ax) kh2axp1 -DNA31(site!?~sdsb,h2ax~u) + ATM(state~31,h2ax) -> DNA31(site!?~sdsb,h2ax~p) + ATM(state~31,h2ax) kh2axp1 -DNA32(site!?~sdsb,h2ax~u) + ATM(state~32,h2ax) -> DNA32(site!?~sdsb,h2ax~p) + ATM(state~32,h2ax) kh2axp1 -DNA33(site!?~sdsb,h2ax~u) + ATM(state~33,h2ax) -> DNA33(site!?~sdsb,h2ax~p) + ATM(state~33,h2ax) kh2axp1 -DNA34(site!?~sdsb,h2ax~u) + ATM(state~34,h2ax) -> DNA34(site!?~sdsb,h2ax~p) + ATM(state~34,h2ax) kh2axp1 -DNA35(site!?~sdsb,h2ax~u) + ATM(state~35,h2ax) -> DNA35(site!?~sdsb,h2ax~p) + ATM(state~35,h2ax) kh2axp1 -DNA36(site!?~sdsb,h2ax~u) + ATM(state~36,h2ax) -> DNA36(site!?~sdsb,h2ax~p) + ATM(state~36,h2ax) kh2axp1 -DNA37(site!?~sdsb,h2ax~u) + ATM(state~37,h2ax) -> DNA37(site!?~sdsb,h2ax~p) + ATM(state~37,h2ax) kh2axp1 -DNA38(site!?~sdsb,h2ax~u) + ATM(state~38,h2ax) -> DNA38(site!?~sdsb,h2ax~p) + ATM(state~38,h2ax) kh2axp1 -DNA39(site!?~sdsb,h2ax~u) + ATM(state~39,h2ax) -> DNA39(site!?~sdsb,h2ax~p) + ATM(state~39,h2ax) kh2axp1 -DNA40(site!?~sdsb,h2ax~u) + ATM(state~40,h2ax) -> DNA40(site!?~sdsb,h2ax~p) + ATM(state~40,h2ax) kh2axp1 -DNA41(site!?~sdsb,h2ax~u) + ATM(state~41,h2ax) -> DNA41(site!?~sdsb,h2ax~p) + ATM(state~41,h2ax) kh2axp1 -DNA42(site!?~sdsb,h2ax~u) + ATM(state~42,h2ax) -> DNA42(site!?~sdsb,h2ax~p) + ATM(state~42,h2ax) kh2axp1 -DNA43(site!?~sdsb,h2ax~u) + ATM(state~43,h2ax) -> DNA43(site!?~sdsb,h2ax~p) + ATM(state~43,h2ax) kh2axp1 -DNA44(site!?~sdsb,h2ax~u) + ATM(state~44,h2ax) -> DNA44(site!?~sdsb,h2ax~p) + ATM(state~44,h2ax) kh2axp1 -DNA45(site!?~sdsb,h2ax~u) + ATM(state~45,h2ax) -> DNA45(site!?~sdsb,h2ax~p) + ATM(state~45,h2ax) kh2axp1 -DNA46(site!?~sdsb,h2ax~u) + ATM(state~46,h2ax) -> DNA46(site!?~sdsb,h2ax~p) + ATM(state~46,h2ax) kh2axp1 -DNA47(site!?~sdsb,h2ax~u) + ATM(state~47,h2ax) -> DNA47(site!?~sdsb,h2ax~p) + ATM(state~47,h2ax) kh2axp1 -DNA48(site!?~sdsb,h2ax~u) + ATM(state~48,h2ax) -> DNA48(site!?~sdsb,h2ax~p) + ATM(state~48,h2ax) kh2axp1 -DNA49(site!?~sdsb,h2ax~u) + ATM(state~49,h2ax) -> DNA49(site!?~sdsb,h2ax~p) + ATM(state~49,h2ax) kh2axp1 -DNA50(site!?~sdsb,h2ax~u) + ATM(state~50,h2ax) -> DNA50(site!?~sdsb,h2ax~p) + ATM(state~50,h2ax) kh2axp1 -# complex -DNA1(site!?~cdsb,h2ax~u) + ATM(state~1,h2ax) -> DNA1(site!?~cdsb,h2ax~p) + ATM(state~1,h2ax) kh2axp1 -DNA2(site!?~cdsb,h2ax~u) + ATM(state~2,h2ax) -> DNA2(site!?~cdsb,h2ax~p) + ATM(state~2,h2ax) kh2axp1 -DNA3(site!?~cdsb,h2ax~u) + ATM(state~3,h2ax) -> DNA3(site!?~cdsb,h2ax~p) + ATM(state~3,h2ax) kh2axp1 -DNA4(site!?~cdsb,h2ax~u) + ATM(state~4,h2ax) -> DNA4(site!?~cdsb,h2ax~p) + ATM(state~4,h2ax) kh2axp1 -DNA5(site!?~cdsb,h2ax~u) + ATM(state~5,h2ax) -> DNA5(site!?~cdsb,h2ax~p) + ATM(state~5,h2ax) kh2axp1 -DNA6(site!?~cdsb,h2ax~u) + ATM(state~6,h2ax) -> DNA6(site!?~cdsb,h2ax~p) + ATM(state~6,h2ax) kh2axp1 -DNA7(site!?~cdsb,h2ax~u) + ATM(state~7,h2ax) -> DNA7(site!?~cdsb,h2ax~p) + ATM(state~7,h2ax) kh2axp1 -DNA8(site!?~cdsb,h2ax~u) + ATM(state~8,h2ax) -> DNA8(site!?~cdsb,h2ax~p) + ATM(state~8,h2ax) kh2axp1 -DNA9(site!?~cdsb,h2ax~u) + ATM(state~9,h2ax) -> DNA9(site!?~cdsb,h2ax~p) + ATM(state~9,h2ax) kh2axp1 -DNA10(site!?~cdsb,h2ax~u) + ATM(state~10,h2ax) -> DNA10(site!?~cdsb,h2ax~p) + ATM(state~10,h2ax) kh2axp1 -DNA11(site!?~cdsb,h2ax~u) + ATM(state~11,h2ax) -> DNA11(site!?~cdsb,h2ax~p) + ATM(state~11,h2ax) kh2axp1 -DNA12(site!?~cdsb,h2ax~u) + ATM(state~12,h2ax) -> DNA12(site!?~cdsb,h2ax~p) + ATM(state~12,h2ax) kh2axp1 -DNA13(site!?~cdsb,h2ax~u) + ATM(state~13,h2ax) -> DNA13(site!?~cdsb,h2ax~p) + ATM(state~13,h2ax) kh2axp1 -DNA14(site!?~cdsb,h2ax~u) + ATM(state~14,h2ax) -> DNA14(site!?~cdsb,h2ax~p) + ATM(state~14,h2ax) kh2axp1 -DNA15(site!?~cdsb,h2ax~u) + ATM(state~15,h2ax) -> DNA15(site!?~cdsb,h2ax~p) + ATM(state~15,h2ax) kh2axp1 -DNA16(site!?~cdsb,h2ax~u) + ATM(state~16,h2ax) -> DNA16(site!?~cdsb,h2ax~p) + ATM(state~16,h2ax) kh2axp1 -DNA17(site!?~cdsb,h2ax~u) + ATM(state~17,h2ax) -> DNA17(site!?~cdsb,h2ax~p) + ATM(state~17,h2ax) kh2axp1 -DNA18(site!?~cdsb,h2ax~u) + ATM(state~18,h2ax) -> DNA18(site!?~cdsb,h2ax~p) + ATM(state~18,h2ax) kh2axp1 -DNA19(site!?~cdsb,h2ax~u) + ATM(state~19,h2ax) -> DNA19(site!?~cdsb,h2ax~p) + ATM(state~19,h2ax) kh2axp1 -DNA20(site!?~cdsb,h2ax~u) + ATM(state~20,h2ax) -> DNA20(site!?~cdsb,h2ax~p) + ATM(state~20,h2ax) kh2axp1 -DNA21(site!?~cdsb,h2ax~u) + ATM(state~21,h2ax) -> DNA21(site!?~cdsb,h2ax~p) + ATM(state~21,h2ax) kh2axp1 -DNA22(site!?~cdsb,h2ax~u) + ATM(state~22,h2ax) -> DNA22(site!?~cdsb,h2ax~p) + ATM(state~22,h2ax) kh2axp1 -DNA23(site!?~cdsb,h2ax~u) + ATM(state~23,h2ax) -> DNA23(site!?~cdsb,h2ax~p) + ATM(state~23,h2ax) kh2axp1 -DNA24(site!?~cdsb,h2ax~u) + ATM(state~24,h2ax) -> DNA24(site!?~cdsb,h2ax~p) + ATM(state~24,h2ax) kh2axp1 -DNA25(site!?~cdsb,h2ax~u) + ATM(state~25,h2ax) -> DNA25(site!?~cdsb,h2ax~p) + ATM(state~25,h2ax) kh2axp1 -DNA26(site!?~cdsb,h2ax~u) + ATM(state~26,h2ax) -> DNA26(site!?~cdsb,h2ax~p) + ATM(state~26,h2ax) kh2axp1 -DNA27(site!?~cdsb,h2ax~u) + ATM(state~27,h2ax) -> DNA27(site!?~cdsb,h2ax~p) + ATM(state~27,h2ax) kh2axp1 -DNA28(site!?~cdsb,h2ax~u) + ATM(state~28,h2ax) -> DNA28(site!?~cdsb,h2ax~p) + ATM(state~28,h2ax) kh2axp1 -DNA29(site!?~cdsb,h2ax~u) + ATM(state~29,h2ax) -> DNA29(site!?~cdsb,h2ax~p) + ATM(state~29,h2ax) kh2axp1 -DNA30(site!?~cdsb,h2ax~u) + ATM(state~30,h2ax) -> DNA30(site!?~cdsb,h2ax~p) + ATM(state~30,h2ax) kh2axp1 -DNA31(site!?~cdsb,h2ax~u) + ATM(state~31,h2ax) -> DNA31(site!?~cdsb,h2ax~p) + ATM(state~31,h2ax) kh2axp1 -DNA32(site!?~cdsb,h2ax~u) + ATM(state~32,h2ax) -> DNA32(site!?~cdsb,h2ax~p) + ATM(state~32,h2ax) kh2axp1 -DNA33(site!?~cdsb,h2ax~u) + ATM(state~33,h2ax) -> DNA33(site!?~cdsb,h2ax~p) + ATM(state~33,h2ax) kh2axp1 -DNA34(site!?~cdsb,h2ax~u) + ATM(state~34,h2ax) -> DNA34(site!?~cdsb,h2ax~p) + ATM(state~34,h2ax) kh2axp1 -DNA35(site!?~cdsb,h2ax~u) + ATM(state~35,h2ax) -> DNA35(site!?~cdsb,h2ax~p) + ATM(state~35,h2ax) kh2axp1 -DNA36(site!?~cdsb,h2ax~u) + ATM(state~36,h2ax) -> DNA36(site!?~cdsb,h2ax~p) + ATM(state~36,h2ax) kh2axp1 -DNA37(site!?~cdsb,h2ax~u) + ATM(state~37,h2ax) -> DNA37(site!?~cdsb,h2ax~p) + ATM(state~37,h2ax) kh2axp1 -DNA38(site!?~cdsb,h2ax~u) + ATM(state~38,h2ax) -> DNA38(site!?~cdsb,h2ax~p) + ATM(state~38,h2ax) kh2axp1 -DNA39(site!?~cdsb,h2ax~u) + ATM(state~39,h2ax) -> DNA39(site!?~cdsb,h2ax~p) + ATM(state~39,h2ax) kh2axp1 -DNA40(site!?~cdsb,h2ax~u) + ATM(state~40,h2ax) -> DNA40(site!?~cdsb,h2ax~p) + ATM(state~40,h2ax) kh2axp1 -DNA41(site!?~cdsb,h2ax~u) + ATM(state~41,h2ax) -> DNA41(site!?~cdsb,h2ax~p) + ATM(state~41,h2ax) kh2axp1 -DNA42(site!?~cdsb,h2ax~u) + ATM(state~42,h2ax) -> DNA42(site!?~cdsb,h2ax~p) + ATM(state~42,h2ax) kh2axp1 -DNA43(site!?~cdsb,h2ax~u) + ATM(state~43,h2ax) -> DNA43(site!?~cdsb,h2ax~p) + ATM(state~43,h2ax) kh2axp1 -DNA44(site!?~cdsb,h2ax~u) + ATM(state~44,h2ax) -> DNA44(site!?~cdsb,h2ax~p) + ATM(state~44,h2ax) kh2axp1 -DNA45(site!?~cdsb,h2ax~u) + ATM(state~45,h2ax) -> DNA45(site!?~cdsb,h2ax~p) + ATM(state~45,h2ax) kh2axp1 -DNA46(site!?~cdsb,h2ax~u) + ATM(state~46,h2ax) -> DNA46(site!?~cdsb,h2ax~p) + ATM(state~46,h2ax) kh2axp1 -DNA47(site!?~cdsb,h2ax~u) + ATM(state~47,h2ax) -> DNA47(site!?~cdsb,h2ax~p) + ATM(state~47,h2ax) kh2axp1 -DNA48(site!?~cdsb,h2ax~u) + ATM(state~48,h2ax) -> DNA48(site!?~cdsb,h2ax~p) + ATM(state~48,h2ax) kh2axp1 -DNA49(site!?~cdsb,h2ax~u) + ATM(state~49,h2ax) -> DNA49(site!?~cdsb,h2ax~p) + ATM(state~49,h2ax) kh2axp1 -DNA50(site!?~cdsb,h2ax~u) + ATM(state~50,h2ax) -> DNA50(site!?~cdsb,h2ax~p) + ATM(state~50,h2ax) kh2axp1 - -#DNA-PKcs Phos -DNA1(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA1(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA2(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA2(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA3(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA3(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA4(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA4(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA5(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA5(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA6(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA6(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA7(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA7(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA8(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA8(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA9(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA9(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA10(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA10(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA11(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA11(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA12(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA12(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA13(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA13(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA14(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA14(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA15(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA15(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA16(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA16(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA17(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA17(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA18(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA18(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA19(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA19(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA20(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA20(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA21(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA21(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA22(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA22(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA23(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA23(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA24(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA24(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA25(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA25(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA26(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA26(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA27(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA27(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA28(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA28(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA29(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA29(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA30(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA30(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA31(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA31(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA32(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA32(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA33(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA33(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA34(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA34(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA35(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA35(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA36(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA36(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA37(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA37(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA38(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA38(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA39(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA39(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA40(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA40(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA41(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA41(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA42(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA42(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA43(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA43(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA44(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA44(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA45(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA45(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA46(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA46(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA47(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA47(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA48(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA48(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA49(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA49(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA50(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA50(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 - -DNA1(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA1(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA2(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA2(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA3(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA3(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA4(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA4(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA5(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA5(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA6(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA6(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA7(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA7(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA8(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA8(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA9(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA9(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA10(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA10(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA11(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA11(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA12(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA12(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA13(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA13(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA14(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA14(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA15(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA15(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA16(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA16(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA17(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA17(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA18(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA18(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA19(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA19(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA20(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA20(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA21(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA21(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA22(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA22(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA23(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA23(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA24(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA24(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA25(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA25(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA26(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA26(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA27(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA27(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA28(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA28(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA29(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA29(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA30(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA30(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA31(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA31(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA32(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA32(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA33(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA33(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA34(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA34(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA35(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA35(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA36(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA36(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA37(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA37(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA38(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA38(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA39(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA39(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA40(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA40(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA41(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA41(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA42(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA42(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA43(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA43(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA44(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA44(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA45(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA45(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA46(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA46(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA47(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA47(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA48(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA48(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA49(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA49(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 -DNA50(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA50(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) kh2axp2 - -#H2AX dephos -DNA1(h2ax~p) -> DNA1(h2ax~u) kh2axu -DNA2(h2ax~p) -> DNA2(h2ax~u) kh2axu -DNA3(h2ax~p) -> DNA3(h2ax~u) kh2axu -DNA4(h2ax~p) -> DNA4(h2ax~u) kh2axu -DNA5(h2ax~p) -> DNA5(h2ax~u) kh2axu -DNA6(h2ax~p) -> DNA6(h2ax~u) kh2axu -DNA7(h2ax~p) -> DNA7(h2ax~u) kh2axu -DNA8(h2ax~p) -> DNA8(h2ax~u) kh2axu -DNA9(h2ax~p) -> DNA9(h2ax~u) kh2axu -DNA10(h2ax~p) -> DNA10(h2ax~u) kh2axu -DNA11(h2ax~p) -> DNA11(h2ax~u) kh2axu -DNA12(h2ax~p) -> DNA12(h2ax~u) kh2axu -DNA13(h2ax~p) -> DNA13(h2ax~u) kh2axu -DNA14(h2ax~p) -> DNA14(h2ax~u) kh2axu -DNA15(h2ax~p) -> DNA15(h2ax~u) kh2axu -DNA16(h2ax~p) -> DNA16(h2ax~u) kh2axu -DNA17(h2ax~p) -> DNA17(h2ax~u) kh2axu -DNA18(h2ax~p) -> DNA18(h2ax~u) kh2axu -DNA19(h2ax~p) -> DNA19(h2ax~u) kh2axu -DNA20(h2ax~p) -> DNA20(h2ax~u) kh2axu -DNA21(h2ax~p) -> DNA21(h2ax~u) kh2axu -DNA22(h2ax~p) -> DNA22(h2ax~u) kh2axu -DNA23(h2ax~p) -> DNA23(h2ax~u) kh2axu -DNA24(h2ax~p) -> DNA24(h2ax~u) kh2axu -DNA25(h2ax~p) -> DNA25(h2ax~u) kh2axu -DNA26(h2ax~p) -> DNA26(h2ax~u) kh2axu -DNA27(h2ax~p) -> DNA27(h2ax~u) kh2axu -DNA28(h2ax~p) -> DNA28(h2ax~u) kh2axu -DNA29(h2ax~p) -> DNA29(h2ax~u) kh2axu -DNA30(h2ax~p) -> DNA30(h2ax~u) kh2axu -DNA31(h2ax~p) -> DNA31(h2ax~u) kh2axu -DNA32(h2ax~p) -> DNA32(h2ax~u) kh2axu -DNA33(h2ax~p) -> DNA33(h2ax~u) kh2axu -DNA34(h2ax~p) -> DNA34(h2ax~u) kh2axu -DNA35(h2ax~p) -> DNA35(h2ax~u) kh2axu -DNA36(h2ax~p) -> DNA36(h2ax~u) kh2axu -DNA37(h2ax~p) -> DNA37(h2ax~u) kh2axu -DNA38(h2ax~p) -> DNA38(h2ax~u) kh2axu -DNA39(h2ax~p) -> DNA39(h2ax~u) kh2axu -DNA40(h2ax~p) -> DNA40(h2ax~u) kh2axu -DNA41(h2ax~p) -> DNA41(h2ax~u) kh2axu -DNA42(h2ax~p) -> DNA42(h2ax~u) kh2axu -DNA43(h2ax~p) -> DNA43(h2ax~u) kh2axu -DNA44(h2ax~p) -> DNA44(h2ax~u) kh2axu -DNA45(h2ax~p) -> DNA45(h2ax~u) kh2axu -DNA46(h2ax~p) -> DNA46(h2ax~u) kh2axu -DNA47(h2ax~p) -> DNA47(h2ax~u) kh2axu -DNA48(h2ax~p) -> DNA48(h2ax~u) kh2axu -DNA49(h2ax~p) -> DNA49(h2ax~u) kh2axu -DNA50(h2ax~p) -> DNA50(h2ax~u) kh2axu - -#Foci Formation -DNA1(h2ax~p) -> DNA1(h2ax~foc) kh2axfoc -DNA2(h2ax~p) -> DNA2(h2ax~foc) kh2axfoc -DNA3(h2ax~p) -> DNA3(h2ax~foc) kh2axfoc -DNA4(h2ax~p) -> DNA4(h2ax~foc) kh2axfoc -DNA5(h2ax~p) -> DNA5(h2ax~foc) kh2axfoc -DNA6(h2ax~p) -> DNA6(h2ax~foc) kh2axfoc -DNA7(h2ax~p) -> DNA7(h2ax~foc) kh2axfoc -DNA8(h2ax~p) -> DNA8(h2ax~foc) kh2axfoc -DNA9(h2ax~p) -> DNA9(h2ax~foc) kh2axfoc -DNA10(h2ax~p) -> DNA10(h2ax~foc) kh2axfoc -DNA11(h2ax~p) -> DNA11(h2ax~foc) kh2axfoc -DNA12(h2ax~p) -> DNA12(h2ax~foc) kh2axfoc -DNA13(h2ax~p) -> DNA13(h2ax~foc) kh2axfoc -DNA14(h2ax~p) -> DNA14(h2ax~foc) kh2axfoc -DNA15(h2ax~p) -> DNA15(h2ax~foc) kh2axfoc -DNA16(h2ax~p) -> DNA16(h2ax~foc) kh2axfoc -DNA17(h2ax~p) -> DNA17(h2ax~foc) kh2axfoc -DNA18(h2ax~p) -> DNA18(h2ax~foc) kh2axfoc -DNA19(h2ax~p) -> DNA19(h2ax~foc) kh2axfoc -DNA20(h2ax~p) -> DNA20(h2ax~foc) kh2axfoc -DNA21(h2ax~p) -> DNA21(h2ax~foc) kh2axfoc -DNA22(h2ax~p) -> DNA22(h2ax~foc) kh2axfoc -DNA23(h2ax~p) -> DNA23(h2ax~foc) kh2axfoc -DNA24(h2ax~p) -> DNA24(h2ax~foc) kh2axfoc -DNA25(h2ax~p) -> DNA25(h2ax~foc) kh2axfoc -DNA26(h2ax~p) -> DNA26(h2ax~foc) kh2axfoc -DNA27(h2ax~p) -> DNA27(h2ax~foc) kh2axfoc -DNA28(h2ax~p) -> DNA28(h2ax~foc) kh2axfoc -DNA29(h2ax~p) -> DNA29(h2ax~foc) kh2axfoc -DNA30(h2ax~p) -> DNA30(h2ax~foc) kh2axfoc -DNA31(h2ax~p) -> DNA31(h2ax~foc) kh2axfoc -DNA32(h2ax~p) -> DNA32(h2ax~foc) kh2axfoc -DNA33(h2ax~p) -> DNA33(h2ax~foc) kh2axfoc -DNA34(h2ax~p) -> DNA34(h2ax~foc) kh2axfoc -DNA35(h2ax~p) -> DNA35(h2ax~foc) kh2axfoc -DNA36(h2ax~p) -> DNA36(h2ax~foc) kh2axfoc -DNA37(h2ax~p) -> DNA37(h2ax~foc) kh2axfoc -DNA38(h2ax~p) -> DNA38(h2ax~foc) kh2axfoc -DNA39(h2ax~p) -> DNA39(h2ax~foc) kh2axfoc -DNA40(h2ax~p) -> DNA40(h2ax~foc) kh2axfoc -DNA41(h2ax~p) -> DNA41(h2ax~foc) kh2axfoc -DNA42(h2ax~p) -> DNA42(h2ax~foc) kh2axfoc -DNA43(h2ax~p) -> DNA43(h2ax~foc) kh2axfoc -DNA44(h2ax~p) -> DNA44(h2ax~foc) kh2axfoc -DNA45(h2ax~p) -> DNA45(h2ax~foc) kh2axfoc -DNA46(h2ax~p) -> DNA46(h2ax~foc) kh2axfoc -DNA47(h2ax~p) -> DNA47(h2ax~foc) kh2axfoc -DNA48(h2ax~p) -> DNA48(h2ax~foc) kh2axfoc -DNA49(h2ax~p) -> DNA49(h2ax~foc) kh2axfoc -DNA50(h2ax~p) -> DNA50(h2ax~foc) kh2axfoc - -#Foci dephos -DNA1(h2ax~foc) -> DNA1(h2ax~u) kfocback -DNA2(h2ax~foc) -> DNA2(h2ax~u) kfocback -DNA3(h2ax~foc) -> DNA3(h2ax~u) kfocback -DNA4(h2ax~foc) -> DNA4(h2ax~u) kfocback -DNA5(h2ax~foc) -> DNA5(h2ax~u) kfocback -DNA6(h2ax~foc) -> DNA6(h2ax~u) kfocback -DNA7(h2ax~foc) -> DNA7(h2ax~u) kfocback -DNA8(h2ax~foc) -> DNA8(h2ax~u) kfocback -DNA9(h2ax~foc) -> DNA9(h2ax~u) kfocback -DNA10(h2ax~foc) -> DNA10(h2ax~u) kfocback -DNA11(h2ax~foc) -> DNA11(h2ax~u) kfocback -DNA12(h2ax~foc) -> DNA12(h2ax~u) kfocback -DNA13(h2ax~foc) -> DNA13(h2ax~u) kfocback -DNA14(h2ax~foc) -> DNA14(h2ax~u) kfocback -DNA15(h2ax~foc) -> DNA15(h2ax~u) kfocback -DNA16(h2ax~foc) -> DNA16(h2ax~u) kfocback -DNA17(h2ax~foc) -> DNA17(h2ax~u) kfocback -DNA18(h2ax~foc) -> DNA18(h2ax~u) kfocback -DNA19(h2ax~foc) -> DNA19(h2ax~u) kfocback -DNA20(h2ax~foc) -> DNA20(h2ax~u) kfocback -DNA21(h2ax~foc) -> DNA21(h2ax~u) kfocback -DNA22(h2ax~foc) -> DNA22(h2ax~u) kfocback -DNA23(h2ax~foc) -> DNA23(h2ax~u) kfocback -DNA24(h2ax~foc) -> DNA24(h2ax~u) kfocback -DNA25(h2ax~foc) -> DNA25(h2ax~u) kfocback -DNA26(h2ax~foc) -> DNA26(h2ax~u) kfocback -DNA27(h2ax~foc) -> DNA27(h2ax~u) kfocback -DNA28(h2ax~foc) -> DNA28(h2ax~u) kfocback -DNA29(h2ax~foc) -> DNA29(h2ax~u) kfocback -DNA30(h2ax~foc) -> DNA30(h2ax~u) kfocback -DNA31(h2ax~foc) -> DNA31(h2ax~u) kfocback -DNA32(h2ax~foc) -> DNA32(h2ax~u) kfocback -DNA33(h2ax~foc) -> DNA33(h2ax~u) kfocback -DNA34(h2ax~foc) -> DNA34(h2ax~u) kfocback -DNA35(h2ax~foc) -> DNA35(h2ax~u) kfocback -DNA36(h2ax~foc) -> DNA36(h2ax~u) kfocback -DNA37(h2ax~foc) -> DNA37(h2ax~u) kfocback -DNA38(h2ax~foc) -> DNA38(h2ax~u) kfocback -DNA39(h2ax~foc) -> DNA39(h2ax~u) kfocback -DNA40(h2ax~foc) -> DNA40(h2ax~u) kfocback -DNA41(h2ax~foc) -> DNA41(h2ax~u) kfocback -DNA42(h2ax~foc) -> DNA42(h2ax~u) kfocback -DNA43(h2ax~foc) -> DNA43(h2ax~u) kfocback -DNA44(h2ax~foc) -> DNA44(h2ax~u) kfocback -DNA45(h2ax~foc) -> DNA45(h2ax~u) kfocback -DNA46(h2ax~foc) -> DNA46(h2ax~u) kfocback -DNA47(h2ax~foc) -> DNA47(h2ax~u) kfocback -DNA48(h2ax~foc) -> DNA48(h2ax~u) kfocback -DNA49(h2ax~foc) -> DNA49(h2ax~u) kfocback -DNA50(h2ax~foc) -> DNA50(h2ax~u) kfocback - -#Complete Foci Formatiom - -DNA1(h2ax~foc) + ATM(state~1,h2ax) -> DNA1(h2ax!1~foc).ATM(state~1,h2ax!1) kh2axfull -DNA2(h2ax~foc) + ATM(state~2,h2ax) -> DNA2(h2ax!1~foc).ATM(state~2,h2ax!1) kh2axfull -DNA3(h2ax~foc) + ATM(state~3,h2ax) -> DNA3(h2ax!1~foc).ATM(state~3,h2ax!1) kh2axfull -DNA4(h2ax~foc) + ATM(state~4,h2ax) -> DNA4(h2ax!1~foc).ATM(state~4,h2ax!1) kh2axfull -DNA5(h2ax~foc) + ATM(state~5,h2ax) -> DNA5(h2ax!1~foc).ATM(state~5,h2ax!1) kh2axfull -DNA6(h2ax~foc) + ATM(state~6,h2ax) -> DNA6(h2ax!1~foc).ATM(state~6,h2ax!1) kh2axfull -DNA7(h2ax~foc) + ATM(state~7,h2ax) -> DNA7(h2ax!1~foc).ATM(state~7,h2ax!1) kh2axfull -DNA8(h2ax~foc) + ATM(state~8,h2ax) -> DNA8(h2ax!1~foc).ATM(state~8,h2ax!1) kh2axfull -DNA9(h2ax~foc) + ATM(state~9,h2ax) -> DNA9(h2ax!1~foc).ATM(state~9,h2ax!1) kh2axfull -DNA10(h2ax~foc) + ATM(state~10,h2ax) -> DNA10(h2ax!1~foc).ATM(state~10,h2ax!1) kh2axfull -DNA11(h2ax~foc) + ATM(state~11,h2ax) -> DNA11(h2ax!1~foc).ATM(state~11,h2ax!1) kh2axfull -DNA12(h2ax~foc) + ATM(state~12,h2ax) -> DNA12(h2ax!1~foc).ATM(state~12,h2ax!1) kh2axfull -DNA13(h2ax~foc) + ATM(state~13,h2ax) -> DNA13(h2ax!1~foc).ATM(state~13,h2ax!1) kh2axfull -DNA14(h2ax~foc) + ATM(state~14,h2ax) -> DNA14(h2ax!1~foc).ATM(state~14,h2ax!1) kh2axfull -DNA15(h2ax~foc) + ATM(state~15,h2ax) -> DNA15(h2ax!1~foc).ATM(state~15,h2ax!1) kh2axfull -DNA16(h2ax~foc) + ATM(state~16,h2ax) -> DNA16(h2ax!1~foc).ATM(state~16,h2ax!1) kh2axfull -DNA17(h2ax~foc) + ATM(state~17,h2ax) -> DNA17(h2ax!1~foc).ATM(state~17,h2ax!1) kh2axfull -DNA18(h2ax~foc) + ATM(state~18,h2ax) -> DNA18(h2ax!1~foc).ATM(state~18,h2ax!1) kh2axfull -DNA19(h2ax~foc) + ATM(state~19,h2ax) -> DNA19(h2ax!1~foc).ATM(state~19,h2ax!1) kh2axfull -DNA20(h2ax~foc) + ATM(state~20,h2ax) -> DNA20(h2ax!1~foc).ATM(state~20,h2ax!1) kh2axfull -DNA21(h2ax~foc) + ATM(state~21,h2ax) -> DNA21(h2ax!1~foc).ATM(state~21,h2ax!1) kh2axfull -DNA22(h2ax~foc) + ATM(state~22,h2ax) -> DNA22(h2ax!1~foc).ATM(state~22,h2ax!1) kh2axfull -DNA23(h2ax~foc) + ATM(state~23,h2ax) -> DNA23(h2ax!1~foc).ATM(state~23,h2ax!1) kh2axfull -DNA24(h2ax~foc) + ATM(state~24,h2ax) -> DNA24(h2ax!1~foc).ATM(state~24,h2ax!1) kh2axfull -DNA25(h2ax~foc) + ATM(state~25,h2ax) -> DNA25(h2ax!1~foc).ATM(state~25,h2ax!1) kh2axfull -DNA26(h2ax~foc) + ATM(state~26,h2ax) -> DNA26(h2ax!1~foc).ATM(state~26,h2ax!1) kh2axfull -DNA27(h2ax~foc) + ATM(state~27,h2ax) -> DNA27(h2ax!1~foc).ATM(state~27,h2ax!1) kh2axfull -DNA28(h2ax~foc) + ATM(state~28,h2ax) -> DNA28(h2ax!1~foc).ATM(state~28,h2ax!1) kh2axfull -DNA29(h2ax~foc) + ATM(state~29,h2ax) -> DNA29(h2ax!1~foc).ATM(state~29,h2ax!1) kh2axfull -DNA30(h2ax~foc) + ATM(state~30,h2ax) -> DNA30(h2ax!1~foc).ATM(state~30,h2ax!1) kh2axfull -DNA31(h2ax~foc) + ATM(state~31,h2ax) -> DNA31(h2ax!1~foc).ATM(state~31,h2ax!1) kh2axfull -DNA32(h2ax~foc) + ATM(state~32,h2ax) -> DNA32(h2ax!1~foc).ATM(state~32,h2ax!1) kh2axfull -DNA33(h2ax~foc) + ATM(state~33,h2ax) -> DNA33(h2ax!1~foc).ATM(state~33,h2ax!1) kh2axfull -DNA34(h2ax~foc) + ATM(state~34,h2ax) -> DNA34(h2ax!1~foc).ATM(state~34,h2ax!1) kh2axfull -DNA35(h2ax~foc) + ATM(state~35,h2ax) -> DNA35(h2ax!1~foc).ATM(state~35,h2ax!1) kh2axfull -DNA36(h2ax~foc) + ATM(state~36,h2ax) -> DNA36(h2ax!1~foc).ATM(state~36,h2ax!1) kh2axfull -DNA37(h2ax~foc) + ATM(state~37,h2ax) -> DNA37(h2ax!1~foc).ATM(state~37,h2ax!1) kh2axfull -DNA38(h2ax~foc) + ATM(state~38,h2ax) -> DNA38(h2ax!1~foc).ATM(state~38,h2ax!1) kh2axfull -DNA39(h2ax~foc) + ATM(state~39,h2ax) -> DNA39(h2ax!1~foc).ATM(state~39,h2ax!1) kh2axfull -DNA40(h2ax~foc) + ATM(state~40,h2ax) -> DNA40(h2ax!1~foc).ATM(state~40,h2ax!1) kh2axfull -DNA41(h2ax~foc) + ATM(state~41,h2ax) -> DNA41(h2ax!1~foc).ATM(state~41,h2ax!1) kh2axfull -DNA42(h2ax~foc) + ATM(state~42,h2ax) -> DNA42(h2ax!1~foc).ATM(state~42,h2ax!1) kh2axfull -DNA43(h2ax~foc) + ATM(state~43,h2ax) -> DNA43(h2ax!1~foc).ATM(state~43,h2ax!1) kh2axfull -DNA44(h2ax~foc) + ATM(state~44,h2ax) -> DNA44(h2ax!1~foc).ATM(state~44,h2ax!1) kh2axfull -DNA45(h2ax~foc) + ATM(state~45,h2ax) -> DNA45(h2ax!1~foc).ATM(state~45,h2ax!1) kh2axfull -DNA46(h2ax~foc) + ATM(state~46,h2ax) -> DNA46(h2ax!1~foc).ATM(state~46,h2ax!1) kh2axfull -DNA47(h2ax~foc) + ATM(state~47,h2ax) -> DNA47(h2ax!1~foc).ATM(state~47,h2ax!1) kh2axfull -DNA48(h2ax~foc) + ATM(state~48,h2ax) -> DNA48(h2ax!1~foc).ATM(state~48,h2ax!1) kh2axfull -DNA49(h2ax~foc) + ATM(state~49,h2ax) -> DNA49(h2ax!1~foc).ATM(state~49,h2ax!1) kh2axfull -DNA50(h2ax~foc) + ATM(state~50,h2ax) -> DNA50(h2ax!1~foc).ATM(state~50,h2ax!1) kh2axfull - -#Foci Resolution - -DNA1(h2ax!1~foc).ATM(state~1,h2ax!1) -> DNA1(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA2(h2ax!1~foc).ATM(state~2,h2ax!1) -> DNA2(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA3(h2ax!1~foc).ATM(state~3,h2ax!1) -> DNA3(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA4(h2ax!1~foc).ATM(state~4,h2ax!1) -> DNA4(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA5(h2ax!1~foc).ATM(state~5,h2ax!1) -> DNA5(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA6(h2ax!1~foc).ATM(state~6,h2ax!1) -> DNA6(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA7(h2ax!1~foc).ATM(state~7,h2ax!1) -> DNA7(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA8(h2ax!1~foc).ATM(state~8,h2ax!1) -> DNA8(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA9(h2ax!1~foc).ATM(state~9,h2ax!1) -> DNA9(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA10(h2ax!1~foc).ATM(state~10,h2ax!1) -> DNA10(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA11(h2ax!1~foc).ATM(state~11,h2ax!1) -> DNA11(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA12(h2ax!1~foc).ATM(state~12,h2ax!1) -> DNA12(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA13(h2ax!1~foc).ATM(state~13,h2ax!1) -> DNA13(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA14(h2ax!1~foc).ATM(state~14,h2ax!1) -> DNA14(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA15(h2ax!1~foc).ATM(state~15,h2ax!1) -> DNA15(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA16(h2ax!1~foc).ATM(state~16,h2ax!1) -> DNA16(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA17(h2ax!1~foc).ATM(state~17,h2ax!1) -> DNA17(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA18(h2ax!1~foc).ATM(state~18,h2ax!1) -> DNA18(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA19(h2ax!1~foc).ATM(state~19,h2ax!1) -> DNA19(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA20(h2ax!1~foc).ATM(state~20,h2ax!1) -> DNA20(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA21(h2ax!1~foc).ATM(state~21,h2ax!1) -> DNA21(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA22(h2ax!1~foc).ATM(state~22,h2ax!1) -> DNA22(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA23(h2ax!1~foc).ATM(state~23,h2ax!1) -> DNA23(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA24(h2ax!1~foc).ATM(state~24,h2ax!1) -> DNA24(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA25(h2ax!1~foc).ATM(state~25,h2ax!1) -> DNA25(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA26(h2ax!1~foc).ATM(state~26,h2ax!1) -> DNA26(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA27(h2ax!1~foc).ATM(state~27,h2ax!1) -> DNA27(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA28(h2ax!1~foc).ATM(state~28,h2ax!1) -> DNA28(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA29(h2ax!1~foc).ATM(state~29,h2ax!1) -> DNA29(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA30(h2ax!1~foc).ATM(state~30,h2ax!1) -> DNA30(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA31(h2ax!1~foc).ATM(state~31,h2ax!1) -> DNA31(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA32(h2ax!1~foc).ATM(state~32,h2ax!1) -> DNA32(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA33(h2ax!1~foc).ATM(state~33,h2ax!1) -> DNA33(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA34(h2ax!1~foc).ATM(state~34,h2ax!1) -> DNA34(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA35(h2ax!1~foc).ATM(state~35,h2ax!1) -> DNA35(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA36(h2ax!1~foc).ATM(state~36,h2ax!1) -> DNA36(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA37(h2ax!1~foc).ATM(state~37,h2ax!1) -> DNA37(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA38(h2ax!1~foc).ATM(state~38,h2ax!1) -> DNA38(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA39(h2ax!1~foc).ATM(state~39,h2ax!1) -> DNA39(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA40(h2ax!1~foc).ATM(state~40,h2ax!1) -> DNA40(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA41(h2ax!1~foc).ATM(state~41,h2ax!1) -> DNA41(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA42(h2ax!1~foc).ATM(state~42,h2ax!1) -> DNA42(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA43(h2ax!1~foc).ATM(state~43,h2ax!1) -> DNA43(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA44(h2ax!1~foc).ATM(state~44,h2ax!1) -> DNA44(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA45(h2ax!1~foc).ATM(state~45,h2ax!1) -> DNA45(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA46(h2ax!1~foc).ATM(state~46,h2ax!1) -> DNA46(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA47(h2ax!1~foc).ATM(state~47,h2ax!1) -> DNA47(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA48(h2ax!1~foc).ATM(state~48,h2ax!1) -> DNA48(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA49(h2ax!1~foc).ATM(state~49,h2ax!1) -> DNA49(h2ax~u) + ATM(state~0,h2ax) kfocfin -DNA50(h2ax!1~foc).ATM(state~50,h2ax!1) -> DNA50(h2ax~u) + ATM(state~0,h2ax) kfocfin - -# ROS production -I() -> I() + ROS() kROS -ROS() -> Sink() kdROS -IR() -> IR() + ROS() kIR - -#DNA Damage -#simple -DNA1(site~ok) + ROS() -> DNA1(site~sdsb) kdam1 -DNA2(site~ok) + ROS() -> DNA2(site~sdsb) kdam1 -DNA3(site~ok) + ROS() -> DNA3(site~sdsb) kdam1 -DNA4(site~ok) + ROS() -> DNA4(site~sdsb) kdam1 -DNA5(site~ok) + ROS() -> DNA5(site~sdsb) kdam1 -DNA6(site~ok) + ROS() -> DNA6(site~sdsb) kdam1 -DNA7(site~ok) + ROS() -> DNA7(site~sdsb) kdam1 -DNA8(site~ok) + ROS() -> DNA8(site~sdsb) kdam1 -DNA9(site~ok) + ROS() -> DNA9(site~sdsb) kdam1 -DNA10(site~ok) + ROS() -> DNA10(site~sdsb) kdam1 -DNA11(site~ok) + ROS() -> DNA11(site~sdsb) kdam1 -DNA12(site~ok) + ROS() -> DNA12(site~sdsb) kdam1 -DNA13(site~ok) + ROS() -> DNA13(site~sdsb) kdam1 -DNA14(site~ok) + ROS() -> DNA14(site~sdsb) kdam1 -DNA15(site~ok) + ROS() -> DNA15(site~sdsb) kdam1 -DNA16(site~ok) + ROS() -> DNA16(site~sdsb) kdam1 -DNA17(site~ok) + ROS() -> DNA17(site~sdsb) kdam1 -DNA18(site~ok) + ROS() -> DNA18(site~sdsb) kdam1 -DNA19(site~ok) + ROS() -> DNA19(site~sdsb) kdam1 -DNA20(site~ok) + ROS() -> DNA20(site~sdsb) kdam1 -DNA21(site~ok) + ROS() -> DNA21(site~sdsb) kdam1 -DNA22(site~ok) + ROS() -> DNA22(site~sdsb) kdam1 -DNA23(site~ok) + ROS() -> DNA23(site~sdsb) kdam1 -DNA24(site~ok) + ROS() -> DNA24(site~sdsb) kdam1 -DNA25(site~ok) + ROS() -> DNA25(site~sdsb) kdam1 -DNA26(site~ok) + ROS() -> DNA26(site~sdsb) kdam1 -DNA27(site~ok) + ROS() -> DNA27(site~sdsb) kdam1 -DNA28(site~ok) + ROS() -> DNA28(site~sdsb) kdam1 -DNA29(site~ok) + ROS() -> DNA29(site~sdsb) kdam1 -DNA30(site~ok) + ROS() -> DNA30(site~sdsb) kdam1 -DNA31(site~ok) + ROS() -> DNA31(site~sdsb) kdam1 -DNA32(site~ok) + ROS() -> DNA32(site~sdsb) kdam1 -DNA33(site~ok) + ROS() -> DNA33(site~sdsb) kdam1 -DNA34(site~ok) + ROS() -> DNA34(site~sdsb) kdam1 -DNA35(site~ok) + ROS() -> DNA35(site~sdsb) kdam1 -DNA36(site~ok) + ROS() -> DNA36(site~sdsb) kdam1 -DNA37(site~ok) + ROS() -> DNA37(site~sdsb) kdam1 -DNA38(site~ok) + ROS() -> DNA38(site~sdsb) kdam1 -DNA39(site~ok) + ROS() -> DNA39(site~sdsb) kdam1 -DNA40(site~ok) + ROS() -> DNA40(site~sdsb) kdam1 -DNA41(site~ok) + ROS() -> DNA41(site~sdsb) kdam1 -DNA42(site~ok) + ROS() -> DNA42(site~sdsb) kdam1 -DNA43(site~ok) + ROS() -> DNA43(site~sdsb) kdam1 -DNA44(site~ok) + ROS() -> DNA44(site~sdsb) kdam1 -DNA45(site~ok) + ROS() -> DNA45(site~sdsb) kdam1 -DNA46(site~ok) + ROS() -> DNA46(site~sdsb) kdam1 -DNA47(site~ok) + ROS() -> DNA47(site~sdsb) kdam1 -DNA48(site~ok) + ROS() -> DNA48(site~sdsb) kdam1 -DNA49(site~ok) + ROS() -> DNA49(site~sdsb) kdam1 -DNA50(site~ok) + ROS() -> DNA50(site~sdsb) kdam1 -# complex -DNA1(site~ok) + ROS() -> DNA1(site~cdsb) kdam2 -DNA2(site~ok) + ROS() -> DNA2(site~cdsb) kdam2 -DNA3(site~ok) + ROS() -> DNA3(site~cdsb) kdam2 -DNA4(site~ok) + ROS() -> DNA4(site~cdsb) kdam2 -DNA5(site~ok) + ROS() -> DNA5(site~cdsb) kdam2 -DNA6(site~ok) + ROS() -> DNA6(site~cdsb) kdam2 -DNA7(site~ok) + ROS() -> DNA7(site~cdsb) kdam2 -DNA8(site~ok) + ROS() -> DNA8(site~cdsb) kdam2 -DNA9(site~ok) + ROS() -> DNA9(site~cdsb) kdam2 -DNA10(site~ok) + ROS() -> DNA10(site~cdsb) kdam2 -DNA11(site~ok) + ROS() -> DNA11(site~cdsb) kdam2 -DNA12(site~ok) + ROS() -> DNA12(site~cdsb) kdam2 -DNA13(site~ok) + ROS() -> DNA13(site~cdsb) kdam2 -DNA14(site~ok) + ROS() -> DNA14(site~cdsb) kdam2 -DNA15(site~ok) + ROS() -> DNA15(site~cdsb) kdam2 -DNA16(site~ok) + ROS() -> DNA16(site~cdsb) kdam2 -DNA17(site~ok) + ROS() -> DNA17(site~cdsb) kdam2 -DNA18(site~ok) + ROS() -> DNA18(site~cdsb) kdam2 -DNA19(site~ok) + ROS() -> DNA19(site~cdsb) kdam2 -DNA20(site~ok) + ROS() -> DNA20(site~cdsb) kdam2 -DNA21(site~ok) + ROS() -> DNA21(site~cdsb) kdam2 -DNA22(site~ok) + ROS() -> DNA22(site~cdsb) kdam2 -DNA23(site~ok) + ROS() -> DNA23(site~cdsb) kdam2 -DNA24(site~ok) + ROS() -> DNA24(site~cdsb) kdam2 -DNA25(site~ok) + ROS() -> DNA25(site~cdsb) kdam2 -DNA26(site~ok) + ROS() -> DNA26(site~cdsb) kdam2 -DNA27(site~ok) + ROS() -> DNA27(site~cdsb) kdam2 -DNA28(site~ok) + ROS() -> DNA28(site~cdsb) kdam2 -DNA29(site~ok) + ROS() -> DNA29(site~cdsb) kdam2 -DNA30(site~ok) + ROS() -> DNA30(site~cdsb) kdam2 -DNA31(site~ok) + ROS() -> DNA31(site~cdsb) kdam2 -DNA32(site~ok) + ROS() -> DNA32(site~cdsb) kdam2 -DNA33(site~ok) + ROS() -> DNA33(site~cdsb) kdam2 -DNA34(site~ok) + ROS() -> DNA34(site~cdsb) kdam2 -DNA35(site~ok) + ROS() -> DNA35(site~cdsb) kdam2 -DNA36(site~ok) + ROS() -> DNA36(site~cdsb) kdam2 -DNA37(site~ok) + ROS() -> DNA37(site~cdsb) kdam2 -DNA38(site~ok) + ROS() -> DNA38(site~cdsb) kdam2 -DNA39(site~ok) + ROS() -> DNA39(site~cdsb) kdam2 -DNA40(site~ok) + ROS() -> DNA40(site~cdsb) kdam2 -DNA41(site~ok) + ROS() -> DNA41(site~cdsb) kdam2 -DNA42(site~ok) + ROS() -> DNA42(site~cdsb) kdam2 -DNA43(site~ok) + ROS() -> DNA43(site~cdsb) kdam2 -DNA44(site~ok) + ROS() -> DNA44(site~cdsb) kdam2 -DNA45(site~ok) + ROS() -> DNA45(site~cdsb) kdam2 -DNA46(site~ok) + ROS() -> DNA46(site~cdsb) kdam2 -DNA47(site~ok) + ROS() -> DNA47(site~cdsb) kdam2 -DNA48(site~ok) + ROS() -> DNA48(site~cdsb) kdam2 -DNA49(site~ok) + ROS() -> DNA49(site~cdsb) kdam2 -DNA50(site~ok) + ROS() -> DNA50(site~cdsb) kdam2 - -#Senesent Feedback - -#Ku Redox - -Ku(dna,cs,cys~red) + ROS() -> Ku(dna,cs,cys~ox) + ROS() kox -Ku(dna,cs,cys~ox) -> Ku(dna,cs,cys~red) kred - -# Ku dissociating (Oxidised) -# simple -DNA1(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA1(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA2(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA2(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA3(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA3(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA4(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA4(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA5(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA5(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA6(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA6(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA7(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA7(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA8(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA8(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA9(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA9(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA10(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA10(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA11(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA11(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA12(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA12(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA13(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA13(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA14(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA14(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA15(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA15(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA16(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA16(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA17(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA17(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA18(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA18(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA19(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA19(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA20(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA20(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA21(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA21(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA22(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA22(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA23(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA23(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA24(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA24(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA25(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA25(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA26(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA26(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA27(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA27(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA28(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA28(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA29(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA29(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA30(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA30(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA31(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA31(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA32(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA32(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA33(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA33(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA34(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA34(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA35(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA35(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA36(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA36(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA37(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA37(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA38(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA38(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA39(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA39(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA40(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA40(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA41(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA41(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA42(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA42(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA43(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA43(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA44(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA44(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA45(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA45(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA46(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA46(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA47(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA47(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA48(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA48(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA49(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA49(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -DNA50(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA50(site~sdsb) + Ku(dna,cs,cys~ox) kdku3 -# complex -DNA1(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA1(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA2(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA2(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA3(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA3(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA4(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA4(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA5(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA5(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA6(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA6(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA7(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA7(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA8(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA8(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA9(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA9(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA10(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA10(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA11(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA11(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA12(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA12(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA13(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA13(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA14(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA14(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA15(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA15(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA16(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA16(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA17(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA17(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA18(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA18(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA19(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA19(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA20(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA20(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA21(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA21(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA22(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA22(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA23(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA23(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA24(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA24(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA25(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA25(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA26(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA26(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA27(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA27(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA28(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA28(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA29(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA29(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA30(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA30(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA31(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA31(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA32(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA32(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA33(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA33(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA34(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA34(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA35(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA35(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA36(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA36(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA37(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA37(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA38(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA38(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA39(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA39(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA40(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA40(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA41(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA41(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA42(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA42(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA43(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA43(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA44(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA44(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA45(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA45(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA46(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA46(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA47(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA47(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA48(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA48(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA49(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA49(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 -DNA50(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA50(site~cdsb) + Ku(dna,cs,cys~ox) kdku4 - -#Senescent Shift Rules - -Sen(int~?,State~normal) -> Sen(int~PLUS,State~normal) kplus() -Sen(int~?,State~normal) -> Sen(int~MINUS,State~normal) kminus() -Sen(int~10,State~normal) -> Sen(int~10,State~sen) ksen - -Ku(dna,cs,cys~?) -> Sink() kKuDown() * kKustop() -PARP(dna,liIII) -> Sink() kParpDown() * kParpstop() - -end reaction rules - - -# actions -# generate_network({overwrite=>1}); -# simulate_ode({t_end=>5460,n_steps=>10,sparse=>1}); - - -simulate_nf({suffix=>"nf_run1",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run2",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run3",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run4",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run5",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run6",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run7",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run8",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run9",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run10",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run11",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run12",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run13",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run14",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run15",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run16",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run17",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run18",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run19",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run20",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run21",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run22",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run23",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run24",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run25",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run26",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run27",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run28",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run29",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run30",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run31",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run32",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run33",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run34",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run35",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run36",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run37",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run38",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run39",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run40",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run41",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run42",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run43",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run44",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run45",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run46",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run47",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run48",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run49",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); -simulate_nf({suffix=>"nf_run50",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"}); \ No newline at end of file diff --git a/Published/Dolan2015/Dolan_2015_metadata.yaml b/Published/Dolan2015/Dolan_2015_metadata.yaml new file mode 100644 index 00000000..2f58d3a6 --- /dev/null +++ b/Published/Dolan2015/Dolan_2015_metadata.yaml @@ -0,0 +1,40 @@ +id: "Dolan_2015" +name: "Dolan 2015" +description: "Insulin signaling" + +citaiton: + year: "2015" + pmid: "26020242" + reference: "Dolan et al., 2015" + +tags: ["published", "literature", "signaling", "dolan", "2015", "time", "t", "p", "e", "ir", "d", "p53_mrna", "p53"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + nfsim_compatible: false + uses_cbngl_compartments: false + uses_vcell_compartments: false + uses_energy: false + uses_functions: true + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: true + uses_exclude_include_reactants: false + uses_generate_network: false + default_sim_command: simulate_nf +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/literature/Dolan_2015.bngl" +playground: + visible: false + gallery_categories: ["metabolism"] + featured: false + difficulty: "advanced" diff --git a/Published/Dolan2015/metadata.yaml b/Published/Dolan2015/metadata.yaml index ed930271..e5405d48 100644 --- a/Published/Dolan2015/metadata.yaml +++ b/Published/Dolan2015/metadata.yaml @@ -4,6 +4,7 @@ description: "Insulin signaling" tags: ["published", "literature", "signaling", "dolan", "2015", "time", "t", "p", "e", "ir", "d", "p53_mrna", "p53"] category: "other" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008_metadata.yaml b/Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008_metadata.yaml new file mode 100644 index 00000000..a33c4ff9 --- /dev/null +++ b/Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008_metadata.yaml @@ -0,0 +1,23 @@ +id: "Dreisigmeyer_2008" +name: "Dreisigmeyer 2008" +description: "Lac operon" +tags: ["published", "gene-expression", "dreisigmeyer", "2008"] +category: "gene-expression" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "gene-expression" + featured: false + difficulty: "intermediate" diff --git a/Published/Dreisigmeyer2008/metadata.yaml b/Published/Dreisigmeyer2008/metadata.yaml index 6b27da34..1d54d3a9 100644 --- a/Published/Dreisigmeyer2008/metadata.yaml +++ b/Published/Dreisigmeyer2008/metadata.yaml @@ -4,6 +4,7 @@ description: "Lac operon" tags: ["published", "gene-expression", "dreisigmeyer", "2008"] category: "gene-expression" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Dushek2011/Dushek_2011_metadata.yaml b/Published/Dushek2011/Dushek_2011_metadata.yaml new file mode 100644 index 00000000..ff86c6fc --- /dev/null +++ b/Published/Dushek2011/Dushek_2011_metadata.yaml @@ -0,0 +1,24 @@ +id: "Dushek_2011" +name: "Dushek 2011" +description: "TCR signaling" +tags: ["published", "dushek", "2011", "s"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Dushek_2011.bngl" +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" diff --git a/Published/Dushek2011/metadata.yaml b/Published/Dushek2011/metadata.yaml index f54c7019..8192a5b2 100644 --- a/Published/Dushek2011/metadata.yaml +++ b/Published/Dushek2011/metadata.yaml @@ -4,6 +4,7 @@ description: "TCR signaling" tags: ["published", "dushek", "2011", "s"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Dushek2014/Dushek2014_aigenerated.md b/Published/Dushek2014/Dushek2014_aigenerated.md new file mode 100644 index 00000000..28477e30 --- /dev/null +++ b/Published/Dushek2014/Dushek2014_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Dushek 2014 + +## One-sentence summary + +A kinase–phosphatase cycle controls biosensor modification, folding, oligomerization, and sequestration across multiple complex sizes. + +## What the model shows + +This abstract biosensor model asks how enzymatic modification is translated into structural readouts. A kinase E and phosphatase F act on biosensor B, while B can make internal or intermolecular contacts and grow into oligomers as large as 15 units. + +## Biological story + +The kinase drives B into a phosphorylated form and the phosphatase reverses it. Modification changes which contacts B can make: a biosensor may close internally, associate with another B, or sequester the kinase. These competing states determine whether the signal appears as a compact sensor, a larger assembly, or unavailable enzyme. + +## Main biological players + +Biosensor B, kinase E, phosphatase F, unphosphorylated and phosphorylated B, internally bound B, B oligomers, and sequestered kinase. + +## Mechanism in plain English + +E transiently binds B and phosphorylates its tyrosine-like state; F binds the modified sensor and removes that mark. B can form an intramolecular contact or an intermolecular bond through its binding component. Repeated intermolecular association creates oligomers of different sizes. When E is captured in a complex, the free kinase pool falls and further modification can become limited. + +## Key modeled events + +- Kinase E phosphorylates B, while phosphatase F reverses the modification. +- B can switch between open and internally bound configurations. +- Intermolecular B contacts generate dimers and progressively larger oligomers. +- Binding to B sequesters E and reduces freely available kinase. + +## What the model measures + +The W and U readouts distinguish broad free/folded biosensor pattern classes, V2 through V15 report exact oligomer sizes, and the E readout tracks kinase captured in a bond. Together they separate modification from assembly and sequestration. + +## Expected behavior in plots + +Phosphorylated or binding-competent B should appear before large oligomers. Small V2/V3 complexes should rise earlier than high-order V states, while strong sequestration should increase bound E and limit additional biosensor conversion. Changing network truncation would most visibly affect the largest V curves. + +## Caveats + +E, F, and B are abstract and should not be assigned to a specific pathway. Oligomer generation is explicitly capped, so behavior near size 15 can reflect truncation rather than a physical maximum. diff --git a/Published/Dushek2014/Dushek2014_aigenerated_detailed.md b/Published/Dushek2014/Dushek2014_aigenerated_detailed.md new file mode 100644 index 00000000..ad639c4c --- /dev/null +++ b/Published/Dushek2014/Dushek2014_aigenerated_detailed.md @@ -0,0 +1,67 @@ +# Detailed Model Explanation: Dushek 2014 phosphorylation-coupled biosensor oligomerization model + +## 1. Model overview + +This abstract model couples a kinase–phosphatase cycle to the assembly state of a biosensor. Phosphorylation creates a site that can close against the sensor's own binding site or crosslink another sensor, while enzyme engagement temporarily marks the sensor as unavailable for those assembly reactions. + +## 2. BNGL block inventory + +The file contains 10 parameters, 3 molecule types, 3 seed species, 6 rules, 17 observables, and 3 actions. It has no enclosing model block, compartments, anchors, or functions. + +## 3. Parameters, functions, and rate laws + +The rate namespace is divided into enzyme binding/catalysis and biosensor closure. All rates are direct mass-action constants; no function or concentration-dependent expression modifies them. + +| Parameter group or names | Function in this model | +| --- | --- | +| `Ekf`, `Ekb`, `Ekc` | Kinase capture, release, and catalytic phosphorylation. Binding is reversible; catalysis releases the kinase and leaves the sensor phosphorylated. | +| `Fkf`, `Fkb`, `Fkc` | Matching phosphatase capture, release, and catalytic dephosphorylation. | +| `kon1`, `koff1` | Intramolecular closure/opening of one phosphorylated biosensor. The forward value (1000) is much larger than the intermolecular association rate. | +| `kon2`, `koff2` | Intermolecular association/dissociation between a phosphorylated sensor site and another sensor's binding site. | + +There are no active functions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `E` | 1 | `b` | None | None | Abstract kinase whose sole site binds the sensor's `Y` site during phosphorylation. | +| `F` | 1 | `b` | None | None | Abstract phosphatase that binds the same `Y` site after phosphorylation. | +| `B` | 3 | `e`, `b`, `Y` | `e: 0, 1`; `Y: U, P` | None | Biosensor: `e` records enzyme engagement, `Y` carries phosphorylation and accepts a bond, and `b` supports self-closure or sensor–sensor crosslinking. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial and begins with one free kinase, one free phosphatase, and 100 biosensors in the enzyme-free, unphosphorylated state. No closed or oligomerized sensors are seeded, so assembly requires kinase-driven production of `Y~P` first. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–2 form the kinase catalytic cycle, rules 3–4 mirror it for the phosphatase, and rules 5–6 compete for phosphorylated sensors through intra- versus intermolecular bonding. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | Reversible | Kinase `E.b`; sensor `B.Y~U` with `e~0` | `E.b` binds `B.Y`, and sensor engagement changes `e: 0 ↔ 1`; `Ekf`/`Ekb`. | Captures an unphosphorylated sensor in the kinase-bound intermediate required for rule 2. | +| 2 | One-way | Kinase-bound sensor with `Y~U` and `e~1` | Releases the E–B bond, changes `Y: U → P` and `e: 1 → 0`, and uses `Ekc`. | Completes phosphorylation while recycling kinase and exposing the phosphotyrosine-like assembly site. | +| 3 | Reversible | Phosphatase `F.b`; sensor `B.Y~P` with `e~0` | `F.b` binds `B.Y`, with `e: 0 ↔ 1`; `Fkf`/`Fkb`. | Selects phosphorylated sensors for reversal of the kinase output. | +| 4 | One-way | Phosphatase-bound sensor with `Y~P` and `e~1` | Releases F, changes `Y: P → U` and `e: 1 → 0`, and uses `Fkc`. | Dephosphorylates the sensor and removes its ability to close or crosslink. | +| 5 | Reversible | One enzyme-free sensor; its own `Y~P` and `b` sites | Creates/releases an intramolecular `Y–b` bond at `kon1`/`koff1`; phosphorylation is retained. | Sequesters the phosphorylated site in a closed monomer, competing with oligomer growth. | +| 6 | Reversible | Two enzyme-free sensors; one `Y~P`, the other free `b` | Creates/releases an intermolecular `Y–b` bond at `kon2`/`koff2`. | Builds chains or larger sensor assemblies whose size distribution is reported by `V2`–`V15`. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `W` | Molecule count | Open sensors plus enzyme-engaged sensors, across the listed phosphorylation/engagement alternatives | Composite “state 1” pool; because it sums alternatives, it should not be interpreted as phosphorylation alone. | +| `U` | Molecule count | Sensors closed through their own `b–Y~P` bond | Intramolecularly closed “state 2” sensors. | +| `V2`–`V15` | Species count | Complete species containing exactly 2 through 15 B molecules, respectively | Oligomer-size distribution; each observable isolates one aggregate stoichiometry. | +| `E` | Molecule count | Kinase whose `b` site is occupied | Sequestered enzyme in the phosphorylation intermediate. | + +## 8. Actions and simulation workflow + +The file generates a network with a maximum aggregate of 15, then overwrites it with a second network capped at aggregate size 2, and finally writes a MATLAB model file. No simulation is run, so an external caller must decide which generated network is intended and execute it. + +## 9. Technical caveats and ambiguities + +- `E`, `F`, and `B` are deliberately abstract; metadata associates the model with T-cell receptor signaling but does not map these symbols to named proteins. +- The two consecutive overwrite operations use conflicting aggregate limits, making the final exported network dependent on action semantics. +- `B==N` species-count syntax and spaced action names/keys may be parser-sensitive. +- Molecule-count observables can count pattern matches, whereas `V2`–`V15` count complete species by stoichiometry. diff --git a/Published/Dushek2014/Dushek_2014_metadata.yaml b/Published/Dushek2014/Dushek_2014_metadata.yaml new file mode 100644 index 00000000..21a22165 --- /dev/null +++ b/Published/Dushek2014/Dushek_2014_metadata.yaml @@ -0,0 +1,65 @@ +id: "Dushek_2014" +name: "Dushek 2014" +description: "TCR signaling dynamics" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2014" + pmid: "25099816" + reference: "Dushek et al., 2014" + +tags: ["published", "dushek", "2014", "e", "f", "b"] +date: + last_tested: 2026-07-16 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered == at line 51" + simulation_methods: ["ode", "ssa","nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim runs if remove begin and end actions and also lowering numbers of molecules MCP There was an issue parsing BNGL file NoneAction argument atol not recognized Check to make sure action is correctly formatted" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Dushek_2014.bngl" + +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" + + + diff --git a/Published/Dushek2014/metadata.yaml b/Published/Dushek2014/metadata.yaml index 43ea73da..b3866c18 100644 --- a/Published/Dushek2014/metadata.yaml +++ b/Published/Dushek2014/metadata.yaml @@ -4,6 +4,7 @@ description: "TCR signaling dynamics" tags: ["published", "dushek", "2014", "e", "f", "b"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Erdem2021/Erdem2021_aigenerated.md b/Published/Erdem2021/Erdem2021_aigenerated.md new file mode 100644 index 00000000..c1f5aa08 --- /dev/null +++ b/Published/Erdem2021/Erdem2021_aigenerated.md @@ -0,0 +1,45 @@ +# Model Explanation: Erdem 2021 + +## One-sentence summary + +IGF1–IGF1R and insulin–InsR signaling split into Ras–Raf–MEK–ERK and IRS–PI3K–PDK1–Akt–mTOR–RPS6K branches that inhibit one another through multiple feedback routes. + +## What the model shows + +This model represents early insulin receptor (InsR) and insulin-like growth factor 1 receptor (IGF1R) signaling in an MCF7-cell context. It compares how the two ligand–receptor pairs activate shared MAPK and Akt/mTOR pathways and how ERK, Akt, and RPS6K feedback suppresses intermediates, generating adaptation and cross-pathway control. + +## Biological story + +IGF1 binds IGF1R and insulin binds InsR; each occupied receptor becomes phosphorylated and can then activate IRS and SOS. SOS drives Ras, Raf, MEK, and ERK, whereas IRS drives PI3K, PDK1, Akt, TSC2, mTOR, and RPS6K. The branches are not independent: active ERK inhibits SOS, MEK, IRS, and Akt; active Akt inhibits Raf and IRS; and active RPS6K inhibits IRS. Inhibited intermediates can recover, and activated receptors are internalized and recycled to an unphosphorylated surface-ready state. + +## Main biological players + +- **IGF1, insulin, IGF1R, and InsR:** two specific ligand–receptor inputs that feed shared intracellular pathways. +- **IRS and SOS:** receptor-proximal intermediates that launch the Akt/mTOR and MAPK branches. +- **Ras, Raf, MEK, and ERK:** the mitogen-activated protein kinase cascade. +- **PI3K, PDK1, Akt, TSC2, mTOR, and RPS6K:** the growth and protein-synthesis signaling branch. +- **Feedback and recycling states:** reversible inhibition of pathway intermediates and return of internalized receptors. + +## Mechanism in plain English + +Each ligand binds only its matching receptor. Ligand-bound IGF1R or InsR becomes phosphorylated and catalytically activates IRS and SOS. Active SOS loads Ras with GTP, allowing Ras to activate Raf, Raf to phosphorylate MEK, and MEK to phosphorylate ERK. Active IRS separately activates PI3K and then PDK1 and Akt; Akt phosphorylates TSC2, enabling mTOR and RPS6K activation. Constitutive reversal reactions remove activation marks, while active ERK, Akt, and RPS6K add inhibitory states to selected upstream or parallel components. These inhibited proteins later recover, and receptor internalization followed by ligand loss returns unphosphorylated receptor to the responsive pool. + +## Key modeled events + +- IGF1 activates IGF1R and insulin activates InsR, with no cross-binding between the two ligand–receptor pairs. +- Phosphorylated receptors activate both IRS and SOS, splitting the signal toward Akt/mTOR and Ras/ERK. +- The IRS–PI3K–PDK1–Akt branch relieves TSC2 restraint and activates mTOR and RPS6K. +- ERK, Akt, and RPS6K inhibit multiple upstream intermediates, producing feedback within and between the two branches. +- Activated receptors internalize and recycle after ligand removal, restoring unphosphorylated receptor availability. + +## What the model measures + +The four principal readouts are total phosphorylated surface IGF1R and InsR, phosphorylated Akt, phosphorylated RPS6K, and phosphorylated ERK. They report proximal receptor activation, activity in the PI3K/Akt arm, output from the mTOR branch, and output from the MAPK branch, respectively. + +## Expected behavior in plots + +IGF1 or insulin stimulation should first increase phosphorylated surface receptor, followed by Akt, ERK, and RPS6K activation through their respective cascades. Akt and ERK need not follow identical time courses because they arise from different receptor-proximal intermediates and inhibit different targets. RPS6K should lag behind Akt because it lies downstream of TSC2 and mTOR. As ERK-, Akt-, and RPS6K-mediated feedback accumulates and receptors internalize, pathway outputs may peak and adapt even while ligand remains present; recovery and receptor recycling can restore later responsiveness. + +## Caveats + +The model includes one activation site per receptor and omits basal receptor phosphorylation, making receptor activation deliberately coarse. It captures signaling behavior fitted to MCF7-cell RPPA measurements but does not represent all receptor substrates, phosphosites, trafficking compartments, or transcriptional consequences. IGF1R and InsR share downstream mechanisms here, so receptor-specific biology beyond their ligand binding and fitted rates is limited. diff --git a/Published/Erdem2021/Erdem2021_aigenerated_detailed.md b/Published/Erdem2021/Erdem2021_aigenerated_detailed.md new file mode 100644 index 00000000..d5cb4e76 --- /dev/null +++ b/Published/Erdem2021/Erdem2021_aigenerated_detailed.md @@ -0,0 +1,91 @@ +# Detailed Model Explanation: Erdem 2021 InsR/IGF1R signaling model + +## 1. Model overview + +This model represents shared signaling from insulin and IGF1 receptors into Ras–RAF–MEK–ERK and IRS–PI3K–PDK1–AKT–TSC2–mTOR–RPS6K cascades. It emphasizes cross-pathway negative feedback, recovery from inhibited states, and ligand-driven receptor internalization and recycling rather than explicit multiprotein complex assembly. + +## 2. BNGL block inventory + +The model contains 66 parameters, 16 molecule types, 16 seed species, 48 reaction rules, four species-count observables, and three actions: network generation, ODE simulation, and LaTeX export. It has no functions, compartments, or anchors. + +## 3. Parameters, functions, and rate laws + +Sixteen `_0` parameters specify initial molecular populations. The remaining `kf` values are base-10 logarithms: every reaction rate is evaluated as `10^kf...`, so differences of one parameter unit represent tenfold kinetic changes rather than additive changes. + +| Parameter group or names | Function in this model | +| --- | --- | +| `IGF1_0`, `INS_0`; `IGF1R_0`, `INSR_0` | Set ligand and receptor pools. IGF1 is present initially at 100,000 molecules, whereas insulin starts at zero, making the encoded run an IGF1-only stimulation unless parameters are changed. | +| `IRS_0`, `SOS_0`, `RAS_0`, `RAF_0`, `MEK_0`, `ERK_0` | Initialize the adaptor and MAPK branch in inactive, uninhibited states. | +| `PI3K_0`, `PDK1_0`, `AKT_0`, `TSC2_0`, `MTOR_0`, `RPS6K_0` | Initialize the PI3K/AKT/mTOR branch; TSC2 begins unphosphorylated and mTOR inactive. | +| `kf1`, `kf1b`, `kf1c`, `kf1d` | Control IGF1–IGF1R association/dissociation, receptor phosphorylation, and ligand-loss/receptor-reset. | +| `kf2`, `kf2b`, `kf2c`, `kf2d` | Provide the analogous four rates for insulin and InsR. | +| `kf3`–`kf6` | Set receptor-specific catalytic activation of IRS and SOS by phosphorylated IGF1R or InsR. | +| `kf7`–`kf11` | Propagate the MAPK arm from IRS-to-SOS and SOS-to-Ras, then through Raf, MEK, and ERK. | +| `kf12`–`kf17` | Propagate the metabolic arm from IRS through PI3K, PDK1, Akt, inhibitory phosphorylation of TSC2, mTOR, and RPS6K. | +| `kf101`–`kf112` | Reset activated pathway nodes. The sequence covers IRS, SOS, Ras, Raf, MEK, PI3K, PDK1, TSC2, mTOR, Akt, RPS6K, and ERK, but not receptor states. | +| `kf201`–`kf204`, `kf206`–`kf208` | Set seven feedback processes: ERK inhibits SOS, MEK, IRS, and Akt; RPS6K and Akt inhibit IRS; Akt also inhibits Raf. | +| `kf301`–`kf304` | Restore IRS, SOS, Raf, and MEK from inhibited to responsive states. | +| `kf401`–`kf404` | Control internalization and recycling of ligand-bound phosphorylated IGF1R and InsR. | + +There are no active functions; exponentiation is written directly in every rule's rate expression. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `IGF1`, `Ins` | 1 each | `rec` | None | None | Alternative extracellular inputs that bind their cognate receptors; only IGF1 is initially present. | +| `IGF1R`, `InsR` | 3 each | `lig`, `phos`, `int` | `phos`: `U`, `P`; `int`: surface/not internalized `N`, internalized `Y` | None | Cognate receptors with explicit ligand binding, phosphorylation, and internalization state. | +| `IRS` | 2 | `phos`, `inh` | `phos`: `U`, `P`; `inh`: `N`, `Y` | None | Shared receptor substrate that activates both SOS and PI3K and receives three feedback inputs. | +| `SOS` | 2 | `act`, `inh` | Both: `N`, `Y` | None | Ras exchange-factor abstraction activated by receptors or IRS and inhibited by ERK. | +| `Ras` | 1 | `gtp` | `N`, `Y` | None | Binary Ras switch activated by SOS and reset by intrinsic/background turnover. | +| `Raf`, `MEK` | 2 each | `phos`, `inh` | `phos`: `U`, `P`; `inh`: `N`, `Y` | None | Sequential MAPK kinases whose activation is phosphorylation-like and whose inhibition is tracked separately. | +| `ERK` | 1 | `phos` | `U`, `P` | None | Terminal MAPK output and feedback regulator of SOS, MEK, IRS, and Akt. | +| `PI3K`, `PDK1`, `mTOR` | 1 each | `act` | `N`, `Y` | None | Binary active/inactive intermediates transmitting IRS input toward Akt and mTOR output. | +| `Akt`, `TSC2`, `RPS6K` | 1 each | `phos` | `U`, `P` | None | Akt transmits PDK1 input, phosphorylated TSC2 permits mTOR activation, and phosphorylated RPS6K is the branch output and an IRS feedback regulator. | + +## 5. Compartments, anchors, initial species, and setup + +The model is spatially implicit and starts every protein free, inactive or unphosphorylated, uninhibited, and—where applicable—not internalized. IGF1 begins at 100,000 molecules and insulin at zero, while both receptor types begin at 25,000; therefore, the embedded simulation probes IGF1R signaling with an unstimulated insulin receptor pool. Downstream abundances vary substantially, with MEK exceeding one million molecules and PI3K being one of the smaller pools, so depletion and relative pool size can shape the trajectories even though catalysts are carried through rules. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–21 transmit ligand input through the two receptor and downstream kinase branches. Rules 22–33 reset active states, rules 34–40 impose cross-pathway negative feedback, rules 41–44 restore responsiveness, and rules 45–48 internalize and recycle receptors. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–3 | Mixed | IGF1 `rec`; surface IGF1R `lig`, `phos`, `int` | Rule 1 reversibly forms the ligand–receptor bond at `10^kf1`/`10^kf1b`; rule 2 phosphorylates bound receptor at `10^kf1c`; rule 3 removes ligand while resetting receptor phosphorylation at `10^kf1d`. | Converts IGF1 exposure into a transient phosphorylated IGF1R population. | +| 4–6 | Mixed | Ins `rec`; surface InsR `lig`, `phos`, `int` | Repeats binding, bound-receptor phosphorylation, and ligand-loss/reset for insulin using `kf2`, `kf2b`, `kf2c`, and `kf2d`. | Provides a parallel insulin input, dormant under the default zero-insulin setup. | +| 7–8 | One-way | Phosphorylated surface IGF1R or InsR; responsive IRS `phos~U,inh~N` | Catalytically changes IRS phosphorylation from `U` to `P`; IGF1R uses `10^kf3`, InsR `10^kf4`. | Merges both receptor inputs into the IRS branch. | +| 9–10 | One-way | Phosphorylated surface receptor; responsive inactive SOS | Catalytically changes SOS `act` from `N` to `Y`; IGF1R uses `10^kf5`, InsR the much faster `10^kf6`. | Supplies a receptor-direct route into Ras/MAPK signaling. | +| 11–15 | One-way | IRS pY; SOS; Ras; Raf; MEK; ERK | Rule 11 activates SOS through IRS, then rules 12–15 change Ras GTP, Raf phosphorylation, MEK phosphorylation, and ERK phosphorylation to their active states using `kf7`–`kf11`, respectively. | Implements the forward MAPK cascade with catalytic carry-through at every step. | +| 16–21 | One-way | IRS pY; PI3K; PDK1; Akt; TSC2; mTOR; RPS6K | Rules 16–18 activate PI3K, PDK1, and Akt; rule 19 phosphorylates TSC2, rule 20 activates mTOR only from that TSC2 state, and rule 21 phosphorylates RPS6K. Rates use `kf12`–`kf17` in order. | Implements the PI3K/AKT/mTOR branch and produces the pRPS6K output. | +| 22–33 | One-way | IRS, SOS, Ras, Raf, MEK, PI3K, PDK1, TSC2, mTOR, Akt, RPS6K, ERK active sites | Each rule independently returns one active/phosphorylated state to inactive/unphosphorylated using `10^kf101` through `10^kf112` in the listed order. | Provides basal signal termination for every downstream forward-pathway node. | +| 34 | One-way | ERK pY; inactive, responsive SOS | Changes SOS inhibition from `N` to `Y` while leaving its activity `N`. | ERK suppresses renewed Ras activation upstream of itself. | +| 35 | One-way | ERK pY; unphosphorylated responsive MEK | Changes MEK inhibition from `N` to `Y`. | Adds direct terminal-to-intermediate feedback within the MAPK cascade. | +| 36, 38, 40 | One-way | Responsive unphosphorylated IRS; RPS6K pY (36), ERK pY (38), or Akt pY (40) | Each active kinase changes IRS inhibition from `N` to `Y` at its own `kf20...` rate. | Makes IRS a convergence point for negative feedback from both downstream branches. | +| 37 | One-way | Akt pY; unphosphorylated responsive Raf | Changes Raf inhibition from `N` to `Y`. | Allows the PI3K/Akt branch to suppress MAPK transmission. | +| 39 | One-way | ERK pY; Akt pY | Changes Akt from phosphorylated to unphosphorylated at `10^kf207`, with ERK unchanged. | Lets MAPK output directly reduce Akt activity. | +| 41–44 | One-way | Inhibited IRS, SOS, Raf, or MEK | Changes each `inh` state from `Y` back to `N` using `kf301`–`kf304`, respectively, without changing activation/phosphorylation. | Restores pathway responsiveness after feedback inhibition. | +| 45–46 | One-way | Ligand-bound phosphorylated IGF1R `int`; IGF1 | Rule 45 changes receptor internalization from `N` to `Y`; rule 46 removes the internalized ligand–receptor complex and creates a free, surface, unphosphorylated receptor, with no free IGF1 product. | Terminates IGF1 signaling and recycles IGF1R while consuming bound ligand. | +| 47–48 | One-way | Ligand-bound phosphorylated InsR `int`; insulin | Repeats internalization and ligand-consuming receptor reset for InsR using `kf403` and `kf404`. | Applies the same trafficking logic to the insulin input. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `pRecTot_free` | Species count | Sum of noninternalized phosphorylated IGF1R and InsR species, with ligand occupancy unconstrained. | Pools the two receptors into one surface activation readout; as a species observable, it counts matching chemical species rather than molecule embeddings. | +| `pAkt308_free` | Species count | Species containing phosphorylated Akt. | Represents the model's single Akt phosphorylation state; the name suggests T308, but the molecule type does not encode a residue number. | +| `pRPS6K_free` | Species count | Species containing phosphorylated RPS6K. | Terminal readout of the modeled mTOR branch. | +| `pERK_free` | Species count | Species containing phosphorylated ERK. | Terminal MAPK readout and the controller of several negative-feedback rules. | + +## 8. Actions and simulation workflow + +The model first generates the full reaction network, then integrates it deterministically with ODEs from time 0 to 1800 using 20,000 requested steps. After simulation it writes a LaTeX representation of the generated model; there is no equilibration, dose change, or parameter scan in the embedded workflow. + +## 9. Technical caveats and ambiguities + +- Every kinetic parameter is a base-10 exponent. Reading the stored negative numbers as direct rates would reverse their intended scale by many orders of magnitude. +- The default experiment contains IGF1 but no insulin, even though both receptor branches are fully encoded; comparing ligands requires changing `INS_0` and likely `IGF1_0` externally. +- The model uses abstract binary state changes and catalytic carry-through rather than explicit recruitment complexes for downstream signaling, so it should not be read as a stoichiometric interaction map. +- Receptor recycling consumes bound ligand because the ligand is omitted from the products of rules 46 and 48. This is a modeled degradation/removal event, not dissociation back to the free ligand pool. +- Metadata marks the model as not BNG2- or NFsim-compatible despite its embedded network-generation and ODE actions; the intended parser/runtime version should be verified before execution. diff --git a/Published/Erdem2021/Erdem_2021_metadata.yaml b/Published/Erdem2021/Erdem_2021_metadata.yaml new file mode 100644 index 00000000..27a351cd --- /dev/null +++ b/Published/Erdem2021/Erdem_2021_metadata.yaml @@ -0,0 +1,40 @@ +id: "Erdem_2021" +name: "Erdem 2021" +description: "InsR/IGF1R signaling" + +citation: + year: "2021" + pmid: "34191793" + reference: "Erdem et al., 2021" + +tags: ["published", "erdem", "2021", "igf1", "ins", "igf1r", "insr", "irs", "sos", "ras", "raf"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + nfsim_compatible: false + uses_cbngl_compartments: false + uses_vcell_compartments: false + uses_energy: false + uses_functions: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_generate_network: true + default_sim_command: simulate +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Erdem_2021.bngl" +playground: + visible: false + gallery_categories: ["metabolism"] + featured: false + difficulty: "advanced" diff --git a/Published/Erdem2021/metadata.yaml b/Published/Erdem2021/metadata.yaml index 0d70fdb1..c39ecdf1 100644 --- a/Published/Erdem2021/metadata.yaml +++ b/Published/Erdem2021/metadata.yaml @@ -4,6 +4,7 @@ description: "InsR/IGF1R signaling" tags: ["published", "erdem", "2021", "igf1", "ins", "igf1r", "insr", "irs", "sos", "ras", "raf"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Faeder2003/Faeder2003_aigenerated.md b/Published/Faeder2003/Faeder2003_aigenerated.md new file mode 100644 index 00000000..ce8b54dc --- /dev/null +++ b/Published/Faeder2003/Faeder2003_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Faeder 2003 + +## One-sentence summary + +Ligand-crosslinked high-affinity immunoglobulin E receptors recruit Lyn and Syk to initiate a phosphorylation cascade. + +## What the model shows + +This model captures proximal FcεRI signaling, where FcεRI means the high-affinity receptor for immunoglobulin E. It connects receptor aggregation to β- and γ-chain phosphorylation, Syk recruitment, and kinase activation. + +## Biological story + +A bivalent ligand brings receptors together. Constitutively associated Lyn starts receptor phosphorylation, newly phosphorylated sites recruit more Lyn and Syk, and kinases in the aggregate reinforce activation until phosphatases reverse it. + +## Main biological players + +Bivalent ligand, FcεRI, Lyn tyrosine kinase, Syk tyrosine kinase, receptor β and γ chains, and kinase activation-loop states. + +## Mechanism in plain English + +Ligand first binds and crosslinks receptors. Lyn associated with one receptor phosphorylates a neighboring receptor, creating Src homology 2 (SH2) docking sites. Lyn binds phosphorylated β chains, while tandem-SH2 Syk binds phosphorylated γ chains. Clustered kinases then phosphorylate Syk and additional receptor sites; dephosphorylation limits the signal. + +## Key modeled events + +- Ligand binds FcεRI and crosslinks receptors. +- Lyn phosphorylates receptor β and γ chains within aggregates. +- Phosphorylated γ chains recruit Syk, which becomes activated by transphosphorylation. +- Phosphatase activity returns receptor and Syk sites toward their basal state. + +## What the model measures + +Readouts distinguish free Lyn, receptor monomers and dimers, phosphorylated β and γ chains, receptor-bound Syk, and activated receptor-bound Syk. + +## Expected behavior in plots + +Receptor dimers should rise before receptor phosphorylation. Phosphorylated γ chains should then recruit Syk, with activated Syk appearing after the bound-Syk curve; strong dephosphorylation should cap or reverse these increases. + +## Caveats + +The model stops at early FcεRI kinase events and does not include LAT adaptors, calcium release, degranulation, or gene expression. diff --git a/Published/Faeder2003/Faeder_2003_metadata.yaml b/Published/Faeder2003/Faeder_2003_metadata.yaml new file mode 100644 index 00000000..11981f81 --- /dev/null +++ b/Published/Faeder2003/Faeder_2003_metadata.yaml @@ -0,0 +1,65 @@ +id: "Faeder_2003" +name: "Faeder 2003" +description: "FceRI signaling" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2003" + pmid: "12646643" + reference: "Faeder et al., 2003" + +tags: ["published", "immunology", "faeder", "2003", "lig", "lyn", "syk", "rec"] +date: + last_tested: 2026-07-16 + +category: "immunology" +biol_categories: ["immunology"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered . at line 108" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim runs after lowering number of molecules and changing molecules to molecule types MCP There was an issue with BNGL model: Faeder_2003.bngl XML file couldn't be generated" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/Faeder_2003.bngl" + +playground: + visible: true + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" + + + diff --git a/Published/Faeder2003/metadata.yaml b/Published/Faeder2003/metadata.yaml index 1d7353d5..0faa3bb0 100644 --- a/Published/Faeder2003/metadata.yaml +++ b/Published/Faeder2003/metadata.yaml @@ -4,6 +4,7 @@ description: "FceRI signaling" tags: ["published", "immunology", "faeder", "2003", "lig", "lyn", "syk", "rec"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Gardner2000/genetic_switch_gardner2000_metadata.yaml b/Published/Gardner2000/genetic_switch_gardner2000_metadata.yaml new file mode 100644 index 00000000..f69f7d7f --- /dev/null +++ b/Published/Gardner2000/genetic_switch_gardner2000_metadata.yaml @@ -0,0 +1,23 @@ +id: "Gardner_2000" +name: "Gardner 2000" +description: "Genetic toggle switch" +tags: ["published", "synthetic-biology", "gardner", "2000"] +category: "synthetic-biology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "synthetic-biology" + featured: false + difficulty: "intermediate" diff --git a/Published/Gardner2000/metadata.yaml b/Published/Gardner2000/metadata.yaml index b3ce5125..85a42a85 100644 --- a/Published/Gardner2000/metadata.yaml +++ b/Published/Gardner2000/metadata.yaml @@ -4,6 +4,7 @@ description: "Genetic toggle switch" tags: ["published", "synthetic-biology", "gardner", "2000"] category: "synthetic-biology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Goldstein1980/blbr_heterogeneity_goldstein1980_metadata.yaml b/Published/Goldstein1980/blbr_heterogeneity_goldstein1980_metadata.yaml new file mode 100644 index 00000000..fbc01b47 --- /dev/null +++ b/Published/Goldstein1980/blbr_heterogeneity_goldstein1980_metadata.yaml @@ -0,0 +1,23 @@ +id: "Goldstein_1980" +name: "Goldstein 1980" +description: "BLBR heterogeneity" +tags: ["published", "physics", "goldstein", "1980"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "physics" + featured: false + difficulty: "intermediate" diff --git a/Published/Goldstein1980/metadata.yaml b/Published/Goldstein1980/metadata.yaml index 36562150..947de9e2 100644 --- a/Published/Goldstein1980/metadata.yaml +++ b/Published/Goldstein1980/metadata.yaml @@ -4,6 +4,7 @@ description: "BLBR heterogeneity" tags: ["published", "physics", "goldstein", "1980"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Harmon2017/Harmon2017_aigenerated.md b/Published/Harmon2017/Harmon2017_aigenerated.md new file mode 100644 index 00000000..6aa35790 --- /dev/null +++ b/Published/Harmon2017/Harmon2017_aigenerated.md @@ -0,0 +1,44 @@ +# Model Explanation: Harmon 2017 + +## One-sentence summary + +Repeated antigen pulses activate an FcεRI–Syk–PIP3 degranulation pathway whose second response is restrained by the inducible SHIP1 cofactor X. + +## What the model shows + +This model shows how the interval between two antigen challenges can change FcεRI responsiveness. It focuses on a compact positive arm in which receptor-bound Syk produces PIP3 and a delayed negative arm in which receptor signaling activates X, allowing SHIP1 to clear PIP3 before a later challenge. + +## Biological story + +Antigen binds FcεRI and promotes phosphorylation of the receptor's β and γ signaling chains. The γ chain recruits Syk, which builds the PIP3 signal that drives degranulation, while the β chain recruits SHIP1. Receptor activity also turns X into an active cofactor; once X joins SHIP1, the complex removes PIP3. X can switch off or be degraded, allowing sensitivity to recover during sufficiently long antigen-free intervals. + +## Main biological players + +- **Antigen and FcεRI:** the stimulus and its receptor, with β- and γ-chain phosphorylation represented together. +- **Syk:** the receptor-recruited kinase that produces the positive PIP3 signal. +- **SHIP1 and X:** a two-input inhibitory module; SHIP1 must be receptor-associated and X-bound to provide induced PIP3 clearance. +- **PIP3:** the central signaling intermediate balancing Syk-dependent production and phosphatase-dependent removal. +- **Degranulation reporter:** a finite intracellular pool converted to an output state by PIP3. + +## Mechanism in plain English + +Antigen occupancy phosphorylates FcεRI and opens separate docking sites for Syk and SHIP1. Recruited Syk continuously produces PIP3, and PIP3 converts the degranulation reporter into its released-output state. In parallel, phosphorylated receptor activates X; active X binds receptor-associated SHIP1 and enables it to consume PIP3. Basal PIP3 degradation, X deactivation, and X degradation determine how rapidly the circuit loses memory of the first pulse and how strongly it responds when antigen returns. + +## Key modeled events + +- Antigen binds FcεRI, and the occupied receptor becomes phosphorylated on its β and γ signaling chains. +- Syk binds the phosphorylated γ chain and produces PIP3, which drives accumulation of the degranulation output. +- SHIP1 binds the phosphorylated β chain, while receptor signaling independently converts X into its active form. +- Active X joins receptor-bound SHIP1, creating an induced PIP3-clearing complex that can suppress a later antigen response. + +## What the model measures + +The readouts distinguish total and free antigen, bound and free receptor, phosphorylated and unphosphorylated receptor, recruited Syk, fully assembled SHIP1–X complexes, and the total PIP3 pool. Additional measurements separate total X, free active X, SHIP1-bound X, and accumulated degranulation, making it possible to relate recovery of the inhibitory cofactor to the response to a second pulse. + +## Expected behavior in plots + +During the first five-minute antigen pulse, receptor occupancy and phosphorylation should increase, followed by recruited Syk, PIP3, and degranulation. Active X and SHIP1–X complexes provide a delayed opposing response, so PIP3 need not simply track receptor occupancy. After antigen withdrawal, receptor signaling and PIP3 should subside while X deactivates or is degraded. A short wash interval should retain more inhibitory memory and produce a more restrained second degranulation response than a long wash interval, whereas the 120- and 240-minute conditions allow more recovery before rechallenge. + +## Caveats + +Antigen is treated as a fixed bath concentration rather than a depletable molecular pool. FcεRI β and γ phosphorylation switch together, Syk activity is represented by receptor recruitment, and X is an abstract fitted cofactor rather than an identified molecule. Degranulation is represented by conversion of a finite reporter pool and is reset before each second-pulse comparison. diff --git a/Published/Harmon2017/Harmon2017_aigenerated_detailed.md b/Published/Harmon2017/Harmon2017_aigenerated_detailed.md new file mode 100644 index 00000000..acf1d6e4 --- /dev/null +++ b/Published/Harmon2017/Harmon2017_aigenerated_detailed.md @@ -0,0 +1,90 @@ +# Detailed Model Explanation: Harmon 2017 antigen-pulse FcεRI model + +## 1. Model overview + +This model represents repeated antigen stimulation of a reduced FcεRI signaling circuit in which receptor phosphorylation recruits Syk and SHIP1, produces PIP3, and drives degranulation. An inducible cofactor `X` enables recruited SHIP1 to clear PIP3, so the model can compare how different antigen-free recovery intervals reshape the response to a second pulse. + +## 2. BNGL block inventory + +The model contains 48 parameters, seven molecule types, seven seed species, 14 reaction rules, 15 molecule-count observables, and a multi-stage ODE action workflow. It has no compartments, anchors, or active functions. + +## 3. Parameters, functions, and rate laws + +The first 17 `__FREE__` parameters are fitted constants in seconds, molar units, or dimensionless form. The remaining parameters convert them to molecule-based rates per minute using a single-cell extracellular volume, a cytoplasmic volume, Avogadro's number, and the scale factor `f`. + +| Parameter group or names | Function in this model | +| --- | --- | +| `f`, `NA`, `T`, `Vchannel`, `Nchannel`, `Vecf`, `Vcyt` | Convert fitted concentration-based rates and channel dimensions to molecule-number kinetics for one cell; `T = 60` converts seconds to minutes. | +| `Ag_tot_0`, `Ag_conc1`, `Ag_tot_1` | Define the off-pulse antigen level, the 10 nM on-pulse concentration, and its molecule count in the per-cell extracellular volume. | +| `R_tot`, `Syk_tot`, `Ship1_tot`, `X_tot__FREE__`, `X_tot`, `H_tot` | Set receptor, kinase, phosphatase, cofactor, and degranulation-reporter pools. `X_tot` is a fitted multiple of the SHIP1 pool. | +| `kon`, `koff` | Govern effective one-step antigen binding to and dissociation from FcεRI; `kon` is converted with `Vecf`, whereas `koff` is first order. | +| `kase`, `pase` | Control antigen-dependent simultaneous phosphorylation and pseudo-first-order dephosphorylation of the receptor β- and γ-chain variables. | +| `kp_Syk`, `km_Syk`; `kp_Ship1`, `km_Ship1` | Set recruitment and release of Syk at receptor γ pY and SHIP1 at receptor β pY. Association rates are scaled by cytoplasmic volume. | +| `k_Xon`, `k_Xoff` | Control receptor-dependent activation of cofactor X and its spontaneous return to the off state. Despite the name, `k_Xon` is a bimolecular catalytic rate involving receptor and X. | +| `kp_x`, `km_x` | Govern binding of activated X to SHIP1's `x` site and release of the complex. | +| `ksynth1`, `kdeg1`, `kpten` | Control PIP3 creation by receptor-bound Syk, clearance by receptor-bound SHIP1–X, and basal first-order PIP3 degradation. | +| `kdegX` | Removes activated X whether free or SHIP1-bound, while preserving SHIP1 in the latter case. | +| `kdegran` | Converts the intracellular reporter H to its output state in a PIP3-catalyzed reaction. | + +There are no active functions; the parameter block performs all unit conversion and algebra before the mass-action rules are evaluated. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `Ag` | 1 | `DNP` | None | None | Effective monovalent antigen stimulus whose concentration is switched between pulse-on and pulse-off values. | +| `R` | 3 | `IgE`, `Yb`, `Yg` | `Yb`, `Yg`: `0`, `P` | None | Lumped FcεRI receptor with antigen binding and β/γ phosphotyrosines that separately recruit SHIP1 and Syk. | +| `Syk` | 1 | `tSH2` | None | None | Kinase recruited to receptor γ pY; occupancy is treated as the active Syk state that synthesizes PIP3. | +| `Ship1` | 2 | `SH2`, `x` | None | None | Phosphatase recruited to receptor β pY and activated for PIP3 clearance only when it also binds active X. | +| `X` | 1 | `s` | `off`, `on` | None | Inducible, degradable cofactor that converts receptor history into SHIP1 activity. | +| `PIP3` | 0 | None | None | None | Explicit signaling product generated by bound Syk and removed by SHIP1–X or basal degradation. | +| `H` | 1 | `loc` | `in`, `out` | None | Conserved reporter whose conversion to `out` accumulates the modeled degranulation response. | + +## 5. Compartments, anchors, initial species, and setup + +The model is spatially implicit; extracellular and cytoplasmic volumes affect rate conversion but are not BNGL compartments. Antigen is seeded with a `$` prefix at the on-pulse amount, making it a fixed species whose level is controlled by actions rather than depleted through binding. Receptor, Syk, SHIP1, inactive X, and intracellular H begin at their specified totals, while PIP3 and extracellular/output-state H begin at zero. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–5 create the antigen-bound phosphorylated receptor and recruit its two effectors. Rules 6–13 generate the X-dependent negative-regulatory arm and balance PIP3 synthesis against clearance; rule 14 converts the resulting PIP3 signal into cumulative degranulation. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | Reversible | Antigen `DNP`; receptor `IgE` | Creates or releases the antigen–receptor bond at `kon` and `koff`. | Turns the externally imposed antigen concentration into receptor occupancy. | +| 2 | One-way | Antigen-bound receptor; receptor Yb and Yg | Simultaneously changes both receptor sites from `0` to `P` at `kase`; neither site can be singly phosphorylated by this rule. | Opens the SHIP1 and Syk docking sites together after antigen engagement. | +| 3 | One-way | Receptor with both Yb and Yg phosphorylated | Simultaneously returns both sites to `0` at `pase`, regardless of antigen occupancy. | Terminates both receptor effector branches in one reset event. | +| 4 | Reversible | Receptor Yg pY; Syk `tSH2` | Creates or releases the receptor–Syk bond at `kp_Syk` and `km_Syk`. | Defines receptor-bound Syk as the PIP3-producing kinase state. | +| 5 | Reversible | Receptor Yb pY; SHIP1 `SH2` | Creates or releases the receptor–SHIP1 bond at `kp_Ship1` and `km_Ship1`. | Positions the negative regulator at phosphorylated receptor. | +| 6 | One-way | Receptor Yb pY; X `s~off` | Catalytically changes X from `off` to `on` at the bimolecular `k_Xon` rate; receptor phosphorylation is preserved and its binding state is unconstrained. | Produces a receptor-history-dependent cofactor needed to complete SHIP1 activation. | +| 7 | One-way | Free X `s~on` | Changes X back to `off` at `k_Xoff`; SHIP1-bound X is not matched. | Removes free activated cofactor between or during pulses. | +| 8 | One-way creation | Receptor-bound Syk | Creates one PIP3 molecule at `ksynth1` without consuming or changing Syk. | Supplies the positive signal downstream of FcεRI. | +| 9 | Reversible | Active X; SHIP1 `x` | Creates or releases the X–SHIP1 bond at `kp_x` and `km_x`. | Completes the two-input SHIP1 complex when SHIP1 is receptor-bound. | +| 10 | One-way removal | Receptor-bound SHIP1 also bound to X; PIP3 | Consumes PIP3 at `kdeg1` while carrying the SHIP1–X complex through unchanged. | Implements induced PIP3 clearance and pulse-history-dependent inhibition. | +| 11 | One-way degradation | PIP3 | Removes PIP3 to sink `0` at `kpten`. | Represents basal PTEN-like lipid turnover independent of receptor complexes. | +| 12 | One-way degradation | Free active X | Removes the X molecule at `kdegX` rather than returning it to the off pool. | Slowly depletes the inducible regulator after activation. | +| 13 | One-way degradation | SHIP1-bound active X | Deletes X at `kdegX` and releases SHIP1 with a free `x` site. | Allows cofactor turnover without degrading the phosphatase. | +| 14 | One-way | PIP3; H `loc~in` | Catalytically changes H from `in` to `out` at `kdegran`, preserving PIP3. | Integrates PIP3 exposure into the accumulating degranulation output. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `Ag_total`, `Ag_free` | Molecule count | All antigen and antigen whose DNP site is unbound. | Because antigen is fixed, `Ag_total` follows the imposed pulse level rather than mass conservation; `Ag_free` reports the unbound fraction at that level. | +| `R_bound`, `R_free` | Molecule count | Receptors with occupied or free IgE sites. | Complementary occupancy measures for the conserved receptor pool. | +| `RP`, `R0` | Molecule count | Receptor γ site in state `P` or `0`, with RP allowing any bond occupancy. | Report the jointly phosphorylated and reset receptor populations through the γ variable. | +| `actSyk` | Molecule count | Syk with its tSH2 site bound. | Recruitment-based activity proxy; no separate Syk phosphorylation state exists. | +| `actShip1` | Molecule count | SHIP1 simultaneously bound through SH2 and its X-binding site. | Counts the assembled PIP3-clearing complex, not merely receptor-bound SHIP1. | +| `Ship1_total`, `PIP3_total`, `Xall` | Molecule count | Total SHIP1, PIP3, and X populations. | SHIP1 is conserved, PIP3 is dynamically created/deleted, and X can decrease through degradation. | +| `X_on_free`, `X_on_free_or_bound`, `XShip1` | Molecule count | Free active X; all active X regardless of bond; and the specific active-X–SHIP1 complex. | Separates available cofactor from total active cofactor and the fraction committed to SHIP1. | +| `degranulation` | Molecule count | H in the `out` state. | Cumulative response within each simulation segment; actions explicitly reset this output before each second pulse. | + +## 8. Actions and simulation workflow + +The workflow generates a 23-species, 86-reaction network and runs deterministic ODE pulse–wash–repulse experiments. Each first pulse lasts 5 minutes; antigen is then set to zero for 5, 30, 60, 120, or 240 minutes, after which antigen is restored and degranulation is reset for a 5-minute second-pulse measurement. Saved or reset concentrations ensure each interval comparison starts from the intended common post-first-pulse or baseline state. + +## 9. Technical caveats and ambiguities + +- `$Ag` is a fixed species, so antigen binding does not deplete the imposed bath concentration; action-driven changes represent the pulse boundaries. +- Receptor β and γ sites are phosphorylated and dephosphorylated only as a pair, despite being represented as separate sites for effector recruitment. +- Syk and SHIP1 activity are inferred from bonds rather than catalytic internal states, and `X` is an abstract fitted cofactor whose biochemical identity is not established locally. +- Degranulation is a state conversion of a finite reporter pool, not explicit granule release, and is manually reset between challenge phases. diff --git a/Published/Harmon2017/antigen_pulses_harmon2017_metadata.yaml b/Published/Harmon2017/antigen_pulses_harmon2017_metadata.yaml new file mode 100644 index 00000000..d5acf121 --- /dev/null +++ b/Published/Harmon2017/antigen_pulses_harmon2017_metadata.yaml @@ -0,0 +1,23 @@ +id: "Harmon_2017" +name: "Harmon 2017" +description: "Antigen pulses" +tags: ["published", "immunology", "harmon", "2017"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "immunology" + featured: false + difficulty: "intermediate" diff --git a/Published/Harmon2017/metadata.yaml b/Published/Harmon2017/metadata.yaml index 7d5b75c6..974c40a3 100644 --- a/Published/Harmon2017/metadata.yaml +++ b/Published/Harmon2017/metadata.yaml @@ -4,6 +4,7 @@ description: "Antigen pulses" tags: ["published", "immunology", "harmon", "2017"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Hat2016/Hat2016_aigenerated.md b/Published/Hat2016/Hat2016_aigenerated.md new file mode 100644 index 00000000..64ba7dfe --- /dev/null +++ b/Published/Hat2016/Hat2016_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Hat 2016 + +## One-sentence summary + +DNA damage engages a feedback-rich p53 network that can favor repair-associated arrest or Bax–caspase-mediated death. + +## What the model shows + +This model connects DNA double-strand breaks to ataxia-telangiectasia mutated kinase (ATM), p53 stabilization, Mdm2 feedback, phosphatase control, cell-cycle arrest, and apoptosis. It is designed to show how feedback strength and damage duration can move the same network among recovery, oscillatory, arrest, and death-associated regimes. + +## Biological story + +Irradiation creates DNA damage and activates ATM. ATM modifies p53 and its regulator Mdm2, while p53 induces Mdm2 and Wip1 as negative feedback. In parallel, p53 induces PTEN and p21 to oppose growth and cell-cycle progression, or Bax to engage the mitochondrial death module when the damage response becomes sufficiently strong. + +## Main biological players + +DNA double-strand breaks, ATM, p53, Mdm2, Wip1, SIAH1, HIPK2, PTEN, PI3K–AKT signaling, p21, cyclin E, Rb–E2F1, Bax, BclXL, Bad, 14-3-3, and caspase. + +## Mechanism in plain English + +Damage activates ATM, which stabilizes and phosphorylates p53. p53-dependent transcription produces Mdm2 and Wip1, which suppress p53 and ATM, forming delayed negative feedback. p53 also raises PTEN and p21, restraining AKT and cyclin E and reinforcing arrest. A stronger p53 modification state induces Bax; free Bax promotes caspase activation unless it is sequestered by BclXL, with Bad phosphorylation controlling that protection. + +## Key modeled events + +- DNA damage activates ATM and raises modified p53. +- p53 induces Mdm2 and Wip1, which feed back on p53 and ATM. +- The PTEN–AKT and p21–cyclin E branches support growth restraint and cell-cycle arrest. +- HIPK2-associated p53 modification favors Bax expression and caspase activation. +- BclXL, Bad, and 14-3-3 tune whether Bax remains available to promote death. + +## What the model measures + +Readouts span damage and ATM, distinct p53 modification states, Mdm2/Wip1 feedback, PTEN–AKT signaling, the p21–cyclin E–Rb–E2F1 arrest module, and Bax/BclXL/Bad/caspase death states. + +## Expected behavior in plots + +After irradiation, ATM and arrest-associated p53 should rise before the induced Mdm2 and Wip1 brakes. Repairable damage can yield p53 pulses and recovery; sustained damage should maintain the high p53 “kill” state, increase Bax and active caspase, and separate the death trajectory from the p21-dominated arrest trajectory. + +## Caveats + +The network is broad but still coarse-grains repair, transcription, and cell fate into selected modules. Its fate boundaries depend strongly on irradiation settings and parameters and should not be interpreted as universal thresholds. diff --git a/Published/Hat2016/Hat2016_aigenerated_detailed.md b/Published/Hat2016/Hat2016_aigenerated_detailed.md new file mode 100644 index 00000000..b109d18e --- /dev/null +++ b/Published/Hat2016/Hat2016_aigenerated_detailed.md @@ -0,0 +1,109 @@ +# Detailed Model Explanation: Hat 2016 DNA-Damage Response and Cell-Fate Control + +## 1. Model overview + +This model connects DNA double-strand breaks to ATM-dependent p53 modification and then separates p53 activity into arrest-associated and apoptosis-associated programs. Feedback through Wip1, Mdm2, PTEN–PI3K–AKT, Rb–E2F1, and Bax–BclXL–Bad determines whether damage is repaired, the cell-cycle arm is restrained, or caspase activation reinforces damage. + +## 2. BNGL block inventory + +The model contains 125 parameters, 30 molecule types, 15 seed species, 5 functions, 58 reaction rules, 58 molecule-count observables, and 2 actions. It has no compartments or anchors; nuclear/cytoplasmic status is carried only by the `Mdm2.loc` state. + +## 3. Parameters, functions, and rate laws + +The namespace groups irradiation and repair controls, conserved starting pools, p53-responsive gene expression, phosphorylation cycles, complex association, transport, and turnover. Rules combine mass action with observable-dependent Hill, saturation, feedback, and source/sink expressions; the `STOCHASTIC_GENES` switch selects between function-driven continuous transcription and explicit two-state gene switching. + +| Parameter group or names | Function in this model | +| --- | --- | +| `IR_duration`, `IR_Gy`, `DNA_DSB_per_1Gy`, `DNA_DSB_due_to_IR`, `is_IR_switched_on`, `h1` | Define the irradiation window and convert dose into DNA-break production; the supplied switch is initially off. | +| `has_DNA_DSB_repair`, `rep`, `DNA_DSB_Repair_Cplx_total`, `DNA_DSB_max`; `can_Caspase_make_DNA_DSB`, `h2` | Control saturable break repair, the damage ceiling, and caspase-driven reinforcement of damage. | +| `_total`; `SIAH1_total`, `ATM_total`, `AKT_total`, `PIP_total`, `Rb_total`, `E2F1_total`, `BclXL_total`, `Bad_total`, `Fourteen_3_3_total` | Establish the principal signaling, cell-cycle, and apoptotic pools; several are scaled from a common reference abundance. | +| `STOCHASTIC_GENES`, `q0_*`, `q1_*`, `q2`, `n_*_alleles`, `h` | Set basal and p53-induced switching for Wip1, Mdm2, p21, PTEN, and Bax genes. Arrest-form p53 drives Wip1/Mdm2/p21; S46-phosphorylated killer-form p53 drives PTEN/Bax. | +| `s1`–`s5`, `t1`–`t5`, `g1`–`g5` | Control transcript production, protein translation, and mRNA turnover for the five p53-responsive genes. | +| `s6`–`s10`, `g6`–`g20`, `g101` | Set constitutive synthesis and state-specific degradation of p53, HIPK2, cyclin E, caspases, PTEN, Wip1, Bax, p21, Mdm2, and related complexes. | +| `p1`–`p6`, `d1`–`d6`, `p11`, `d10`, `d11`, `M1` | Govern the ATM–SIAH1–p53–Mdm2 phosphorylation/dephosphorylation cycles, including Wip1-dependent reversal and HIPK2-dependent p53 S46 modification. | +| `p8`, `d7`, `p12`, `d8` | Implement PI3K/PTEN control of PIP2–PIP3 and PIP3-dependent AKT activation. | +| `p9`, `p10`, `d12`, `M2`, `M3`; `b4`, `u5`, `b5`, `u6` | Control cyclin-E/Rb/E2F1 cell-cycle feedback and p21 sequestration of cyclin E. | +| `p7`, `d9`; `b1`–`b3`, `u1`–`u3`; `a1`, `a2` | Govern Bad phosphorylation, Bax/BclXL/Bad/14-3-3 binding, and Bax- plus caspase-dependent procaspase activation. | +| `i1` | Imports doubly phosphorylated cytoplasmic Mdm2 into its nuclear state. | + +| Function | Inputs/dependencies | Meaning and use in this model | +| --- | --- | --- | +| `gene_Wip1_activity`, `gene_Mdm2_activity`, `gene_p21_activity` | Arrest-form p53 observable `p53_arr`, shared Hill exponent `h`, gene-specific `q0/q1`, and `q2` | Return bounded transcriptional activities for the repair/arrest program; rules 12, 23, and 37 use them when deterministic gene expression is selected. | +| `gene_PTEN_activity`, `gene_Bax_activity` | Killer-form p53 observable `p53_kill` and the analogous gene parameters | Compute the apoptosis-associated transcriptional response used by rules 32 and 46. | + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `DNA_DSB`, `ATM`, `SIAH1`, `HIPK2`, `Wip1` | 0; 1; 1; 0; 0 | ATM: `S1981`; SIAH1: `S19` | ATM/SIAH1: `0`, `P` | None | Damage marker and the kinase/phosphatase feedback core that establishes p53 signaling duration. | +| `p53` | 2 | `S15_S20`, `S46` | `S15_S20`: `0/PP`; `S46`: `0/P` | None | Encodes basal, arrest-associated, and apoptosis-associated p53 forms. | +| `Mdm2` | 3 | `S166_S186`, `S395`, `loc` | paired sites `0/PP`; S395 `0/P`; location `Nuc/Cyt` | None | p53-induced negative regulator whose phosphorylation controls nuclear entry and whose nuclear forms accelerate p53 loss. | +| `gene_Wip1`, `gene_Mdm2`, `gene_p21`, `gene_PTEN`, `gene_Bax` | 1 each | `tf` | off (`0`), on (`1`) | None | Optional discrete gene-state representation of the five p53 outputs. | +| `mRNA_Wip1`, `mRNA_Mdm2`, `mRNA_p21`, `mRNA_PTEN`, `mRNA_Bax` | 0 each | None | None | None | Transcript pools connecting gene activity to feedback, arrest, and apoptotic proteins. | +| `PTEN`, `PI3K` | 0 each | None | None | None | Opposing regulators of phosphoinositide state and therefore AKT activity. | +| `PtdIns`, `AKT` | 1 each | `s`; `T308` | PtdIns `PP/PPP`; AKT `0/P` | None | PIP2/PIP3 and inactive/active AKT states linking p53-induced PTEN to Mdm2 and Bad control. | +| `p21`, `Cyclin_E` | 1 each | `b` | None | None | Inhibitory cell-cycle protein and its cyclin target. | +| `Rb` | 2 | `S567`, `b` | `S567`: `0/P` | None | Sequesters E2F1 when unphosphorylated and releases it after cyclin-E-dependent phosphorylation. | +| `E2F1` | 1 | `b` | None | None | Drives cyclin E synthesis when free, completing the cell-cycle feedback loop. | +| `Bax`, `BclXL` | 1 each | `b` | None | None | Pro- and anti-apoptotic binding partners whose free Bax level controls caspase activation. | +| `Bad` | 2 | `S75_S99`, `b` | `0/PP` | None | AKT-regulated competitor that binds BclXL when unphosphorylated or 14-3-3 when phosphorylated. | +| `Fourteen_3_3` | 1 | `b` | None | None | Sequesters phosphorylated Bad away from BclXL. | +| `Caspase` | 1 | `csp` | proenzyme (`Pro`), active (`Act`) | None | Terminal switch activated by free Bax and positive caspase feedback. | + +## 5. Compartments, anchors, initial species, and setup + +No compartments or anchors are declared. The model begins with unphosphorylated ATM, SIAH1, AKT, Rb, and Bad; PIP2 is the initial phosphoinositide; E2F1, BclXL, Bad, and 14-3-3 are supplied as free pools. Two initially off copies of each regulated gene are seeded, whereas p53, Mdm2, transcripts, Bax, p21, cyclin E, HIPK2, and caspases are produced dynamically. DNA damage is also generated dynamically and irradiation begins disabled unless the control parameter is changed. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–14 establish gene control and the ATM/Wip1 damage-response loop; 15–31 generate and modify p53 and Mdm2; 32–45 implement PTEN/AKT and p21/Rb arrest control; 46–58 implement Bax/Bad/BclXL competition and the caspase decision. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–5 | Reversible | Five gene `tf` states; arrest-form or killer-form p53 observables | Switch each gene `0↔1`. Wip1/Mdm2/p21 use basal plus `p53_arr^h`; PTEN/Bax use basal plus `p53_kill^h`; all switch off at `q2`. | Supplies the stochastic-gene alternative to the continuous activity functions. | +| 6–8 | One-way | Source/sink `0`, `DNA_DSB`, active caspase | Radiation and active caspase create breaks in proportion to unused damage capacity; repair removes breaks with a load-dependent rate. | Combines external damage, repair saturation, and apoptotic positive feedback. | +| 9–10 | Reversible | `ATM.S1981`, `SIAH1.S19`; damage, Wip1, active ATM | Damage phosphorylates ATM and Wip1 reverses it; active ATM phosphorylates SIAH1, which dephosphorylates spontaneously. | Converts break abundance into the upstream p53-regulatory state. | +| 11 | Reversible source/sink | `HIPK2`; nuclear Mdm2 and unphosphorylated SIAH1 observables | Synthesizes HIPK2 and removes it at a rate proportional to both negative-regulator signals. | Makes the kinase that creates killer-form p53 sensitive to the Mdm2/SIAH1 context. | +| 12–14 | Reversible source/sink | Wip1 gene/function, `mRNA_Wip1`, `Wip1` | Rule 12 provides deterministic function-driven mRNA birth/death; rule 13 provides the `STOCHASTIC_GENES`-weighted allele route; rule 14 translates and degrades Wip1. | Implements alternative transcription modes for the phosphatase feedback loop. | +| 15–20 | One-way | Source `0`; the four p53 modification combinations; nuclear Mdm2 | Creates basal p53 (15), then removes basal/non-killer or modified forms through spontaneous or quadratic Mdm2-dependent rates (16–20). | Sets distinct lifetimes for basal, arrest, and killer p53 populations. | +| 21–22 | Reversible | `p53.S15_S20`, `p53.S46`; active ATM, HIPK2, Wip1 | ATM changes paired sites `0→PP`; HIPK2 changes S46 `0→P`; spontaneous or Wip1-dependent reverse rates restore zero states. | Separates the arrest transcriptional program from the stronger apoptosis-associated p53 form. | +| 23–25 | Reversible source/sink then one-way | Mdm2 gene/function, mRNA, and cytoplasmic unmodified Mdm2 | Rules 23–24 are deterministic/stochastic transcription alternatives; rule 25 creates Mdm2 from mRNA. | Produces the principal p53-induced negative regulator. | +| 26–28 | One-way | Mdm2 phosphorylation/location states | Removes unphosphorylated cytoplasmic, doubly phosphorylated, or S395-phosphorylated nuclear Mdm2 at state-specific rates. | Controls how long each regulatory Mdm2 form persists. | +| 29–31 | Reversible, one-way, reversible | `Mdm2.S166_S186`, `loc`, `S395`; active AKT, ATM, Wip1 | AKT sets paired sites `0→PP`; that cytoplasmic form imports to nucleus; ATM adds S395 phosphorylation and Wip1 removes it. | Connects PI3K–AKT signaling and DNA damage to nuclear Mdm2 activity. | +| 32–34 | Reversible source/sink | PTEN gene/function, mRNA, and PTEN protein | Deterministic or allele-state transcription creates PTEN mRNA, followed by mRNA-dependent translation and protein degradation. | Translates killer-form p53 into inhibition of the survival kinase pathway. | +| 35–36 | Reversible | `PtdIns.s`, `AKT.T308`; PI3K, PTEN, PIP3 | PI3K changes PIP2 `PP→PPP` and PTEN reverses it; PIP3 activates AKT `0→P`, followed by spontaneous deactivation. | Creates the survival signal controlling Mdm2 and Bad. | +| 37–39 | Reversible source/sink | p21 gene/function, mRNA, and p21 | Alternative transcription routes produce mRNA; p21 is translated and degraded. | Converts arrest-form p53 into inhibition of cyclin E. | +| 40 | Reversible source/sink | `Cyclin_E`; free E2F1 | Creates cyclin E through basal and E2F1-dependent synthesis and removes it at `g20`. | Supplies the positive cell-cycle arm restrained by p21 and Rb. | +| 41–42 | Reversible then one-way | `p21.b`, `Cyclin_E.b` | Forms a reversible p21–cyclin E bond; the complex can then be removed together at the cyclin degradation rate. | Sequesters and clears cyclin E. | +| 43 | Reversible | `Rb.S567`; free cyclin E and free phosphorylated Rb observables | Cyclin E phosphorylates Rb `0→P`; a saturating reverse expression restores the unphosphorylated state. | Controls whether Rb can bind and inhibit E2F1. | +| 44–45 | Reversible then one-way | `Rb.b/S567`, `E2F1.b`; free cyclin E | Unphosphorylated Rb binds E2F1; cyclin-E-dependent Rb phosphorylation breaks the bond and releases E2F1. | Couples cyclin activity to E2F1-driven cyclin synthesis. | +| 46–48 | Reversible source/sink | Bax gene/function, mRNA, and `Bax.b` | Deterministic or stochastic transcription creates Bax mRNA; translation creates Bax and degradation removes it. | Converts killer-form p53 into the pro-apoptotic effector pool. | +| 49–50 | Reversible then one-way | `Bax.b`, `BclXL.b` | Bax binds BclXL; bound Bax can be degraded while BclXL is released. | Buffers free Bax and delays caspase activation. | +| 51–52 | Reversible then one-way | Unphosphorylated `Bad.b`, `BclXL.b`; active AKT | Bad competes for BclXL; AKT-dependent Bad phosphorylation breaks that complex. | Allows survival signaling to restore BclXL-mediated Bax sequestration. | +| 53–55 | Reversible plus one-way | `Bad.S75_S99/b`, `Fourteen_3_3.b`; active AKT | AKT and phosphatase activity interconvert Bad `0↔PP`; phosphorylated Bad binds 14-3-3, and dephosphorylation releases it. | Partitions Bad between BclXL-binding and protected 14-3-3-bound forms. | +| 56–58 | One-way | Source/sink `0`, `Caspase.csp`, free Bax and active-caspase observables | Produces procaspase, degrades either caspase state, and changes `Pro→Act` at `a1*Bax_free + a2*Caspase_act^2`. | Implements the terminal apoptotic switch with Bax initiation and autocatalytic reinforcement. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `DNA_DSB_tot`, `ATM_tot`, `ATM_p`, `SIAH1_tot/u/p`, `HIPK2_tot`, `Wip1_tot` | Molecule count | Damage and state-resolved upstream regulators. | Resolve damage accumulation and the ATM/Wip1 feedback timing. | +| `p53_tot`, `p53_0p`, `p53_arr`, `p53_kill` | Molecule count | Total p53 and its basal, paired-site-phosphorylated, and S46-phosphorylated forms. | Distinguish the two p53 transcriptional programs used by the gene functions. | +| Five `gene_*_on` and five `mRNA_*` observables | Molecule count | Active gene copies and corresponding transcripts. | Permit comparison of discrete gene switching with downstream transcript production. | +| `Mdm2_tot`, `Mdm2_cyt_0p`, `Mdm2_cyt_2p`, `Mdm2_nuc_2p`, `Mdm2_nuc_3p` | Molecule count | Mdm2 phosphorylation and encoded location states. | Track progression toward the nuclear p53-degrading forms. | +| `PI3K_tot`, `PTEN_tot`, `PIP2`, `PIP3`, `AKT_p` | Molecule count | Survival-pathway pools and active AKT. | Report the p53/PTEN opposition to PI3K signaling. | +| p21/Cyclin-E/Rb/E2F1 observables | Molecule count | Total/free proteins, p21–cyclin E and Rb–E2F1 complexes, and free phosphorylated Rb. | Resolve sequestration and release events in the arrest module. | +| Bax/BclXL/Bad/14-3-3 observables | Molecule count | Total/free apoptotic regulators plus the three principal complexes and Bad phosphorylation states. | Show how survival signaling changes free Bax availability indirectly through binding competition. | +| `Caspase_tot`, `Caspase_pro`, `Caspase_act` | Molecule count | Total, proenzyme, and active caspase. | Measure entry into the terminal positive-feedback state. | + +## 8. Actions and simulation workflow + +The file generates the reaction network and exports it as SBML, but it does not launch an ODE or stochastic simulation. The deterministic-versus-stochastic gene choice and irradiation switch therefore must be set before network generation, and downstream software is expected to simulate the exported network. + +## 9. Technical caveats and ambiguities + +- The metadata advertises ODE and SSA methods, but the active actions only generate and export a network. +- `STOCHASTIC_GENES` is zero in the supplied parameters, so the explicit gene-switching route is kinetically disabled while the function-driven route remains active. +- Spatial labels occur only on Mdm2; there are no physical compartments or nuclear/cytoplasmic volume factors. +- Broad molecule-count patterns may count molecules in complexes and should not be interpreted as unique complex counts. +- Several source comments use shorthand such as “arrester” and “killer”; these refer to modeled p53 phosphorylation classes, not independently declared molecules. diff --git a/Published/Hat2016/Hat_2016_metadata.yaml b/Published/Hat2016/Hat_2016_metadata.yaml new file mode 100644 index 00000000..2c316bf9 --- /dev/null +++ b/Published/Hat2016/Hat_2016_metadata.yaml @@ -0,0 +1,66 @@ +id: "Hat_2016" +name: "Hat 2016" +description: "Nuclear transport" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2016" + pmid: "26928575" + reference: "Hat et al., 2016" + +tags: ["published", "hat", "2016", "dna_dsb", "atm", "siah1", "hipk2", "wip1", "gene_wip1", "mrna_wip1", "p53"] +date: + last_tested: 2026-07-16 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered ( at line 532" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim runs after lowering numbers of molecules MCP list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/Hat_2016.bngl" + +playground: + visible: true + gallery_categories: ["cell-cycle","multistage"] + featured: false + difficulty: "intermediate" + + + + diff --git a/Published/Hat2016/metadata.yaml b/Published/Hat2016/metadata.yaml index 8e37c765..514552a4 100644 --- a/Published/Hat2016/metadata.yaml +++ b/Published/Hat2016/metadata.yaml @@ -4,6 +4,7 @@ description: "Nuclear transport" tags: ["published", "hat", "2016", "dna_dsb", "atm", "siah1", "hipk2", "wip1", "gene_wip1", "mrna_wip1", "p53"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Published/Hlavacek1999/Hlavacek1999_aigenerated.md b/Published/Hlavacek1999/Hlavacek1999_aigenerated.md new file mode 100644 index 00000000..c96f216e --- /dev/null +++ b/Published/Hlavacek1999/Hlavacek1999_aigenerated.md @@ -0,0 +1,44 @@ +# Model Explanation: Hlavacek 1999 + +## One-sentence summary + +Steric crowding progressively reduces the ability of a 20-valent ligand to recruit additional cell-surface receptors as its occupancy increases. + +## What the model shows + +This model isolates how receptor footprint and ligand geometry can limit multivalent binding even when many nominal sites remain unoccupied. It follows the distribution of ligands carrying one through twenty receptor contacts and compares low-valence aggregates with highly occupied structures. + +## Biological story + +A ligand arrives from solution and forms its first receptor contact at the cell surface. Additional receptors can then join, but each bound receptor covers part of the ligand and obstructs nearby positions. As crowding increases, the number of geometrically accessible sites falls faster than the simple count of unused sites. Receptors can also detach one at a time, so the occupancy distribution reflects a balance among ligand supply, free-receptor depletion, steric exclusion, and contact loss. + +## Main biological players + +- **Multivalent ligand:** an abstract particle with a maximum of twenty receptor contacts. +- **Cell-surface receptors:** an implicit conserved pool depleted as ligand occupancy grows. +- **Free ligand:** an implicit solution pool depleted when ligands acquire their first surface contact. +- **Steric insertion factors:** occupancy-specific accessibility terms determined by the receptor footprint on the ligand surface. +- **Ligand occupancy classes:** twenty populations representing ligands with one through twenty attached receptors. + +## Mechanism in plain English + +The first receptor–ligand contact transfers ligand from the implicit free pool into the singly bound surface population. Each later binding event increases the ligand's occupancy by one and requires both an available free receptor and a geometrically accessible position. The accessibility penalty becomes stronger as the ligand fills, so high-occupancy states are harder to reach than they would be if all unused sites remained equivalent. Any existing receptor contact may dissociate, making highly occupied ligands lose contacts more frequently because they have more bonds that can break. + +## Key modeled events + +- Free ligand and free receptor combine to create the first surface-bound ligand population. +- Additional receptors bind sequentially, moving ligands through occupancy classes from one contact toward twenty. +- Steric exclusion reduces the effective number of available positions at each successive occupancy level. +- Receptor contacts dissociate individually, returning ligands to the next-lower occupancy class or, from the singly bound state, to the implicit free pool. + +## What the model measures + +The primary readouts are the normalized populations of ligands with exactly one through twenty attached receptors and the total amount of surface-bound ligand. Weighted combinations of those populations determine the remaining free-receptor fraction. Two aggregate measurements summarize the fraction of receptors in complexes with at least two contacts and the fraction in complexes with at least ten contacts. + +## Expected behavior in plots + +The singly bound population should appear first and feed progressively higher occupancy classes. Low- and intermediate-valence classes should accumulate more readily than near-saturated classes because receptor depletion and steric exclusion both oppose continued binding. The fraction of receptors in complexes with at least two contacts should rise earlier and to a larger value than the fraction in complexes with at least ten contacts. The high-valence measure is therefore the more sensitive indicator of the receptor-footprint penalty. + +## Caveats + +The model uses normalized, dimensionless densities rather than literal molecular counts. Receptors and physical ligand sites are not represented individually; ligands with the same occupancy are treated as equivalent regardless of the spatial arrangement of their contacts. The steric penalty is based on a particular circular-footprint approximation, so it captures excluded-area effects without resolving an explicit three-dimensional ligand geometry. diff --git a/Published/Hlavacek1999/Hlavacek1999_aigenerated_detailed.md b/Published/Hlavacek1999/Hlavacek1999_aigenerated_detailed.md new file mode 100644 index 00000000..1b687efd --- /dev/null +++ b/Published/Hlavacek1999/Hlavacek1999_aigenerated_detailed.md @@ -0,0 +1,75 @@ +# Detailed Model Explanation: Hlavacek 1999 steric-effects model + +## 1. Model overview + +This dimensionless model describes binding of monovalent cell-surface receptors to a ligand with up to 20 receptor contacts. Rather than representing individual sites and receptors explicitly, it tracks ligand occupancy as a 20-state counter and reduces each next-binding rate according to receptor depletion and an occupancy-dependent steric-exclusion factor. + +## 2. BNGL block inventory + +The model contains 25 parameters, one molecule type, one zero-valued seed species, 40 reaction rules, 21 molecule-count observables, ten active functions, and actions for network generation and ODE simulation. It has no compartments or anchors and is intentionally a dimensionless deterministic construction. + +## 3. Parameters, functions, and rate laws + +All quantities are dimensionless: ligand state populations represent surface-bound ligand normalized by total receptor density, and time is scaled by the reverse crosslinking rate. Rule rates combine constant factors with observable-dependent functions enforcing receptor and ligand conservation. + +| Parameter group or names | Function in this model | +| --- | --- | +| `n` | Sets the maximum ligand occupancy to 20 receptor contacts and supplies the unoccupied-site factor in the forward rates. | +| `vKLT` | Scaled ligand concentration used in the solution-to-surface first-binding flux. | +| `KxRT` | Scaled crosslinking affinity multiplying every additional receptor-binding transition. | +| `CRT_LT` | Converts total surface-bound ligand into depletion of the normalized free-ligand pool. | +| `kr_kmx` | Ratio of the first-bond and crosslink reverse rates; controls creation of singly bound ligand and its loss back to solution. | +| `aA` | Receptor footprint-to-ligand-area ratio, fixed at 0.01, used to reduce accessible binding area as occupancy grows. | +| `nu_1`–`nu_19` | Occupancy-specific numbers of sterically available sites. Each combines the remaining-site count `n-i` with excluded-area and insertion-probability factors that shrink nonlinearly with occupancy. | + +| Function | Inputs/dependencies | Meaning and use in this model | +| --- | --- | --- | +| `r_b_lo()`, `r_b_md()`, `r_b_hi()`, `r_b_vh()`, `r_b_xx()` | `Obs_L1`–`Obs_L20` in ranges 1–5, 6–10, 11–14, 15–18, and 19–20 | Compute grouped weighted sums `i × x_i`, partitioned only to keep the long receptor-occupancy expression manageable. | +| `r_free()` | All five weighted-sum functions | Computes the normalized free-receptor fraction as one minus receptors committed across every ligand occupancy state. It controls initial binding and every forward crosslinking rule. | +| `l_free()` | `CRT_LT`, `Obs_L_tot` | Computes normalized free ligand as one minus the converted total surface-bound ligand. | +| `fn_bind()` | `kr_kmx`, `vKLT`, `r_free()`, `l_free()` | Computes the source flux that creates singly receptor-bound ligand from implicit free receptor and free ligand pools. | +| `alpha_2()` | `r_free()`, `Obs_L1` | Reports the receptor fraction in ligand aggregates of at least two contacts by excluding free receptors and singly bound ligand. | +| `alpha_10()` | `Obs_L10`, `r_b_hi()`, `r_b_vh()`, `r_b_xx()` | Reports the receptor fraction in aggregates of at least ten contacts, including ten receptors from state 10 and all weighted occupancy above it. | + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `Lig` | 1 | `b` | Occupancy states `1` through `20` | None | Coarse-grained surface-bound ligand whose internal state records the number of attached receptors; neither receptors nor 20 physical binding components are explicitly represented. | + +## 5. Compartments, anchors, initial species, and setup + +There are no compartments or anchors. The only explicit seed, singly bound ligand `Lig(b~1)`, starts at zero; free ligand and receptor are implicit conservation pools initialized through `l_free() = 1` and `r_free() = 1`. The source rule then creates the first surface-bound ligand, after which occupancy can grow or shrink along the state chain. Because the species values are normalized densities, their numerical values are not molecule counts despite BNGL's `Molecules` observable keyword. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–2 exchange ligand between the implicit solution pool and the singly bound surface state. Rules 3–21 add receptors with sterically reduced, occupancy-dependent rates, and rules 22–40 remove receptors with rates proportional to current occupancy. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | One-way creation | Implicit free ligand and receptor pools; new ligand state `b~1` | Creates singly bound ligand from source `0` at `fn_bind() = kr_kmx × vKLT × r_free × l_free`. | Couples first binding to depletion of both conserved free pools without explicitly representing their species. | +| 2 | One-way removal | Ligand state `b~1` | Deletes singly bound ligand to sink `0` at `kr_kmx`; mass returns implicitly through the observable-based conservation functions. | Represents complete detachment from the surface. | +| 3–21 | One-way | Ligand occupancy states 1→2 through 19→20; implicit free receptors | Rule `i+2` changes occupancy `i` to `i+1` at `nu_i × KxRT × r_free()`. The `nu_1`–`nu_19` factors map respectively to starting states 1–19 and encode fewer geometrically accessible sites as coverage rises. | Builds multivalent receptor aggregates while combining receptor depletion with steric hindrance. | +| 22–40 | One-way | Ligand occupancy states 2→1 through 20→19 | Rule numbers 22–40 remove one contact from starting occupancies 2–20, respectively; the numeric rates 2–20 make total loss proportional to the number of existing receptor contacts. | Provides the reverse crosslinking flux and lets highly occupied ligands lose contacts more frequently. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_L1`–`Obs_L5` | Molecule count keyword; dimensionless density | Explicit ligand populations with 1–5 attached receptors. | Feed `r_b_lo()` and resolve low-valence aggregates; values represent `x_i = L_i/R_T`, not literal molecules. | +| `Obs_L6`–`Obs_L10` | Molecule count keyword; dimensionless density | Ligand populations with 6–10 attached receptors. | Feed `r_b_md()`; `Obs_L10` also contributes directly to the ≥10-contact receptor fraction. | +| `Obs_L11`–`Obs_L14` | Molecule count keyword; dimensionless density | Ligand populations with 11–14 contacts. | Feed `r_b_hi()` and therefore both free-receptor depletion and `alpha_10()`. | +| `Obs_L15`–`Obs_L18` | Molecule count keyword; dimensionless density | Ligand populations with 15–18 contacts. | Feed the very-high-occupancy weighted sum `r_b_vh()`. | +| `Obs_L19`, `Obs_L20` | Molecule count keyword; dimensionless density | Ligand populations with 19 or 20 contacts. | Feed `r_b_xx()` and report near-saturated or fully saturated ligands. | +| `Obs_L_tot` | Molecule count keyword; dimensionless density | Sum of every explicit surface-bound ligand state. | Drives free-ligand conservation after multiplication by `CRT_LT`; it is not receptor-weighted. | + +## 8. Actions and simulation workflow + +The model generates a 20-species, 40-reaction network and integrates it with deterministic ODEs from dimensionless time 0 to 2.5 using 500 steps. There is no stochastic run, equilibration phase, parameter scan, or explicit export beyond the standard generated outputs. + +## 9. Technical caveats and ambiguities + +- `Lig.b` is an occupancy counter, not one physical binding site, and no receptor molecule type exists. The model therefore cannot report receptor-level topology or distinguish arrangements having the same occupancy. +- Source and sink rules exchange mass with implicit free pools whose values are reconstructed from observables; this is a deterministic conservation-law device rather than molecular creation or degradation. +- Although observables use the `Molecules` keyword, all populations and time are dimensionless. Stochastic or molecule-count interpretations are inappropriate. +- The `nu_i` factors are a particular insertion-probability approximation for circular receptor footprints; changing `aA` changes both excluded area and the nonlinear occupancy penalty. diff --git a/Published/Hlavacek1999/metadata.yaml b/Published/Hlavacek1999/metadata.yaml index 5ebe402c..a5658a64 100644 --- a/Published/Hlavacek1999/metadata.yaml +++ b/Published/Hlavacek1999/metadata.yaml @@ -4,6 +4,7 @@ description: "Steric effects" tags: ["published", "physics", "hlavacek", "1999"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Hlavacek1999/steric_effects_hlavacek1999_metadata.yaml b/Published/Hlavacek1999/steric_effects_hlavacek1999_metadata.yaml new file mode 100644 index 00000000..4f662513 --- /dev/null +++ b/Published/Hlavacek1999/steric_effects_hlavacek1999_metadata.yaml @@ -0,0 +1,23 @@ +id: "Hlavacek_1999" +name: "Hlavacek 1999" +description: "Steric effects" +tags: ["published", "physics", "hlavacek", "1999"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "physics" + featured: false + difficulty: "intermediate" diff --git a/Published/Hlavacek2001/Hlavacek2001_aigenerated.md b/Published/Hlavacek2001/Hlavacek2001_aigenerated.md new file mode 100644 index 00000000..bbece160 --- /dev/null +++ b/Published/Hlavacek2001/Hlavacek2001_aigenerated.md @@ -0,0 +1,44 @@ +# Model Explanation: Hlavacek 2001 + +## One-sentence summary + +A bivalent ligand must keep two receptors crosslinked long enough to complete five sequential proofreading steps, making terminal signaling strongly dependent on complex lifetime. + +## What the model shows + +This model demonstrates kinetic proofreading in receptor aggregation. Two ligands that form similar numbers of receptor dimers can produce very different terminal signals if their dissociation rates differ, because every dimer must survive five consecutive modification steps before reaching the fully activated state. + +## Biological story + +A symmetric ligand first captures one monovalent receptor and then recruits a second receptor to form a dimer. The intact dimer progresses through five abstract modifications that can represent phosphorylation, kinase recruitment, adaptor assembly, or related maturation events. If either receptor separates before completion, all accumulated progress is lost and the remaining ligand complex returns to the unmodified state. + +## Main biological players + +- **Bivalent ligand:** carries two equivalent receptor-binding arms and the shared proofreading-stage counter. +- **Monovalent receptor:** binds one ligand arm and participates in singly bound or dimeric complexes. +- **Partially modified dimers:** intact complexes at stages zero through four of the proofreading sequence. +- **Terminal dimers:** complexes that retain both receptors through all five modifications. +- **Dissociation rate:** the scanned ligand-quality variable that competes with proofreading progression. + +## Mechanism in plain English + +Free ligand captures one receptor and then crosslinks a second. Once both arms are occupied, the complex advances one stage at a time at a common modification rate. At every stage, either ligand–receptor bond can break; that event releases a receptor and resets the ligand's modification history to zero. Consequently, slow-dissociating complexes are disproportionately likely to reach stage five, while rapidly dissociating complexes repeatedly restart before producing the terminal signal. + +## Key modeled events + +- A free bivalent ligand captures one receptor, creating the intermediate required for surface crosslinking. +- The second ligand arm captures another receptor and creates the dimer that can enter the proofreading sequence. +- Intact dimers advance irreversibly through five modification stages without changing receptor occupancy. +- Dissociation of either receptor at any stage erases all modifications and returns the ligand complex to the basal state. + +## What the model measures + +The measurements include free ligand, free receptor, singly occupied ligand, total receptor dimers, and the abundance of dimers at each modification stage from zero through five. Derived readouts report the fraction of receptors in dimers, the fraction of dimers reaching the terminal stage, the fraction of all receptors in terminal dimers, and the proofreading competition between modification and two possible bond-breaking events. + +## Expected behavior in plots + +After mixing, free ligand and receptor should be redistributed into singly bound complexes and dimers. The stage-zero dimer population appears before later stages, and stages one through five should show progressively delayed occupancy. In the dissociation-rate scan, low dissociation rates should preserve dimers long enough to enrich the terminal stage, whereas increasing dissociation should reduce the terminal fraction much more sharply than it reduces early or total dimer formation. The terminal yield therefore provides the clearest ligand-lifetime discrimination. + +## Caveats + +The five modification stages are deliberately abstract and are not assigned to particular residues or signaling proteins. All stages share one progression rate, and any bond loss causes complete rather than partial reset. The model captures the logic of proofreading but not downstream messenger production, receptor trafficking, or a detailed biochemical pathway. The model is labeled 2001, while its scientific description also draws on a 2002 mathematical treatment. diff --git a/Published/Hlavacek2001/Hlavacek2001_aigenerated_detailed.md b/Published/Hlavacek2001/Hlavacek2001_aigenerated_detailed.md new file mode 100644 index 00000000..efb51e07 --- /dev/null +++ b/Published/Hlavacek2001/Hlavacek2001_aigenerated_detailed.md @@ -0,0 +1,71 @@ +# Detailed Model Explanation: Hlavacek 2001 kinetic-proofreading model + +## 1. Model overview + +This model implements kinetic proofreading for a symmetric bivalent ligand that sequentially captures two monovalent receptors. Only ligand-crosslinked receptor dimers advance through five irreversible modification stages, while dissociation of either receptor resets the ligand counter, favoring long-lived complexes over rapidly dissociating ones. + +## 2. BNGL block inventory + +The model contains eight parameters, two molecule types, two seed species, 13 reaction rules, ten species-count observables, four active functions, and actions for network generation, ODE simulation, and a logarithmic dissociation-rate scan. It uses no compartments or anchors. + +## 3. Parameters, functions, and rate laws + +All reaction rules use mass-action kinetics in molecule counts and seconds. The bimolecular ligand-capture constant is converted using a reference extracellular volume, whereas receptor crosslinking is parameterized as a population-based surface encounter. + +| Parameter group or names | Function in this model | +| --- | --- | +| `NA`, `V_ref` | Convert concentration-based ligand capture into a per-molecule-pair rate for an extracellular volume of `10^-9` L per cell. | +| `NR`, `NL` | Set the initial pools to 300,000 receptors and 602 ligand molecules, corresponding locally to a 1 nM ligand condition. | +| `kon1` | Controls capture of the first receptor by either of the ligand's equivalent sites; BioNetGen's site symmetry supplies the multiplicity of two. | +| `kon2` | Controls binding of a second free receptor to singly occupied ligand, thereby forming the signaling dimer. | +| `koff` | Applies independently to either ligand–receptor bond and resets the modification counter after dissociation. | +| `kp` | Advances a fully crosslinked ligand through each of the five proofreading stages at the same first-order rate. | + +| Function | Inputs/dependencies | Meaning and use in this model | +| --- | --- | --- | +| `alpha()` | `kp`, `koff` | Computes the probability-like factor `kp/(kp + 2*koff)` that a dimer modifies before either of its two bonds breaks; terminal completion scales as its fifth power under the stated proofreading interpretation. | +| `frac_dimers()` | `Obs_Tot_Dimers`, `NR` | Reports the fraction of the receptor pool residing in ligand-centered dimers, counting two receptors per dimer. | +| `frac_term()` | `Obs_D5`, `Obs_Tot_Dimers` | Reports the terminally modified fraction of existing dimers; the tiny denominator offset prevents division by zero. | +| `frac_R_term()` | `Obs_D5`, `NR` | Reports the fraction of all receptors that are members of terminal dimers. | + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `L` | 3 | two repeated `r` sites; `mod` | `mod`: `0`, `1`, `2`, `3`, `4`, `5` | None | Symmetric bivalent ligand that centers the receptor dimer and stores its shared proofreading-stage counter. | +| `R` | 1 | `l` | None | None | Monovalent receptor captured by either ligand site; receptor state is represented entirely by its ligand complex and the ligand's modification counter. | + +## 5. Compartments, anchors, initial species, and setup + +The model is spatially implicit and has no anchors. It starts with 602 free ligands in modification state 0 and 300,000 free receptors, creating a receptor-rich regime in which first binding and surface crosslinking have distinct rate constants. No complexes or modified dimers are seeded, so every proofreading trajectory begins with ligand capture. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–2 assemble the singly and doubly receptor-bound ligand. Rules 3–8 implement bond loss with complete modification reset, and rules 9–13 advance intact dimers through the five proofreading stages. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | One-way | Free ligand `r` sites in `mod~0`; receptor `l` | Creates one ligand–receptor bond at `kon1`. Either equivalent ligand site can match, giving the appropriate symmetry factor. | Produces the singly occupied intermediate from solution. | +| 2 | One-way | Singly occupied ligand's free `r`; free receptor `l` | Creates the second ligand–receptor bond at `kon2` while keeping `mod~0`. | Forms the receptor dimer required for proofreading progression. | +| 3–8 | One-way | One ligand `r`–receptor `l` bond; ligand `mod` state 0–5, respectively | Breaks a matched bond at `koff`, releases one receptor, and changes the ligand counter to `0` for every starting stage. In a dimer, either of two bonds can match, producing the `2*koff` competition represented in `alpha()`. | Makes any premature dissociation erase accumulated proofreading progress rather than preserve a partially activated complex. | +| 9–13 | One-way | Ligand with both `r` sites bound; `mod` states 0→1→2→3→4→5 | Each rule increments the counter by one at `kp` without altering either receptor bond; rules 9–13 implement the five consecutive transitions. | Creates the delay that discriminates complexes by lifetime and defines state 5 as terminal activation. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Free_L`, `Obs_Free_R` | Species count | Completely free state-0 ligand and free receptor species. | Track depletion of the two starting pools as complexes form. | +| `Obs_Singly_Bound` | Species count | State-0 ligand with one occupied and one free receptor-binding site. | Counts the crosslinking intermediate; repeated equivalent sites may introduce symmetry/embedding considerations in generated species accounting. | +| `Obs_Tot_Dimers` | Species count | Ligand with both receptor-binding sites occupied, regardless of modification stage. | Denominator for terminal yield and basis for the receptor-in-dimers function. | +| `Obs_D0`, `Obs_D1`, `Obs_D2`, `Obs_D3`, `Obs_D4`, `Obs_D5` | Species count | Intact receptor dimers at each successive ligand modification state. | Resolves progression through the proofreading chain; `Obs_D5` is the terminal signaling-competent population. | + +## 8. Actions and simulation workflow + +The workflow generates a nine-species, 14-reaction network, saves and resets the initial concentrations, and runs a deterministic ODE trajectory for 600 seconds with 300 steps. It then resets again and scans `koff` logarithmically from 0.001 to 1.0 across 30 points, integrating each condition to 1000 seconds to expose how complex lifetime controls dimer completion. + +## 9. Technical caveats and ambiguities + +- The folder and file use “2001,” while comments also cite a 2002 mathematical treatment; the summary retains the repository's model name rather than choosing between publication labels. +- Modification states 1–5 are abstract proofreading events that may stand for phosphorylation, recruitment, or other steps; they are not assigned to specific molecules or residues. +- Association is encoded as one-way rules and dissociation as separate reset rules, so the reverse of crosslinking is not a simple topology-only reversal. +- Observables are species counts, whereas functions translate those species into receptor fractions; these should not be interpreted as direct unique-molecule observables without the stated factors of two. diff --git a/Published/Hlavacek2001/kinetic_proofreading_hlavacek2001_metadata.yaml b/Published/Hlavacek2001/kinetic_proofreading_hlavacek2001_metadata.yaml new file mode 100644 index 00000000..c9a1f8cc --- /dev/null +++ b/Published/Hlavacek2001/kinetic_proofreading_hlavacek2001_metadata.yaml @@ -0,0 +1,23 @@ +id: "Hlavacek_2001" +name: "Hlavacek 2001" +description: "Kinetic proofreading" +tags: ["published", "physics", "hlavacek", "2001"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "physics" + featured: false + difficulty: "intermediate" diff --git a/Published/Hlavacek2001/metadata.yaml b/Published/Hlavacek2001/metadata.yaml index 9792cdcf..cd007a67 100644 --- a/Published/Hlavacek2001/metadata.yaml +++ b/Published/Hlavacek2001/metadata.yaml @@ -4,6 +4,7 @@ description: "Kinetic proofreading" tags: ["published", "physics", "hlavacek", "2001"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Hlavacek2018Egg/egg_metadata.yaml b/Published/Hlavacek2018Egg/egg_metadata.yaml new file mode 100644 index 00000000..fc4ff393 --- /dev/null +++ b/Published/Hlavacek2018Egg/egg_metadata.yaml @@ -0,0 +1,21 @@ +id: Hlavacek2018Egg_egg +name: Hlavacek2018Egg +description: End of permute change log +tags: ["a0__free", "a1__free", "a2__free", "b1__free", "b2__free", "c0__free", "c1__free", "c2__free", "d1__free", "d2__free", "a0", "a1", "a2", "b1", "b2", "c0", "c1", "c2", "d1", "d2", "period", "t", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Hlavacek2018Egg/metadata.yaml b/Published/Hlavacek2018Egg/metadata.yaml index 98808fdd..329e153d 100644 --- a/Published/Hlavacek2018Egg/metadata.yaml +++ b/Published/Hlavacek2018Egg/metadata.yaml @@ -4,6 +4,7 @@ description: End of permute change log tags: ["a0__free", "a1__free", "a2__free", "b1__free", "b2__free", "c0__free", "c1__free", "c2__free", "d1__free", "d2__free", "a0", "a1", "a2", "b1", "b2", "c0", "c1", "c2", "d1", "d2", "period", "t", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Hlavacek2018Elephant/Hlavacek2018Elephant_aigenerated.md b/Published/Hlavacek2018Elephant/Hlavacek2018Elephant_aigenerated.md new file mode 100644 index 00000000..2eeb9b92 --- /dev/null +++ b/Published/Hlavacek2018Elephant/Hlavacek2018Elephant_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Hlavacek 2018 Elephant + +## One-sentence summary + +Two fitted periodic signals are reconstructed as smooth harmonic time courses over one 464-unit cycle. + +## What the model shows + +This mathematical benchmark represents a measured two-dimensional periodic trajectory using Fourier harmonics rather than a biochemical pathway. It is useful for evaluating parameter fitting of oscillatory data. + +## Biological story + +A clock-like variable advances uniformly. Two fitted functions, X and Y, combine a baseline with 20 sine and cosine harmonics, allowing a complex closed trajectory to be reproduced over one period. + +## Main biological players + +A time counter, periodic outputs X and Y, a 464-unit period, and fitted harmonic coefficients. + +## Mechanism in plain English + +Time increases at a constant rate. Each output sums oscillations at the fundamental frequency and its first 20 harmonics. Different amplitudes and phases shape X and Y, so plotting one against the other reconstructs the fitted “elephant” contour while plotting against time reveals the component waveforms. + +## Key modeled events + +- A counter advances uniformly through one complete period. +- Twenty harmonics contribute to the X coordinate. +- A separate set of 20 harmonics shapes the Y coordinate. +- The paired outputs trace a closed periodic curve. + +## What the model measures + +The reported counter gives time, while the two calculated outputs provide the fitted X and Y coordinates. + +## Expected behavior in plots + +X and Y should each repeat after 464 time units. A phase plot of Y against X should close on itself and reproduce the intended elephant-like outline; a time plot should show structured, non-sinusoidal periodic waveforms. + +## Caveats + +This is an abstract curve-fitting benchmark, not a biological mechanism. The coordinates and time unit have no assigned molecular interpretation. diff --git a/Published/Hlavacek2018Elephant/metadata.yaml b/Published/Hlavacek2018Elephant/metadata.yaml index 0c16dcec..d736c05a 100644 --- a/Published/Hlavacek2018Elephant/metadata.yaml +++ b/Published/Hlavacek2018Elephant/metadata.yaml @@ -4,6 +4,8 @@ description: BNGL model: elephant_EFA tags: ["a0", "a1", "a2", "a3", "a4", "a5", "a6", "a7", "a8", "a9", "a10", "a11", "a12", "a13", "a14", "a15", "a16", "a17", "a18", "a19", "a20", "b0", "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "c0", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "c8", "c9", "c10", "c11", "c12", "c13", "c14", "c15", "c16", "c17", "c18", "c19", "c20", "d0", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8", "d9", "d10", "d11", "d12", "d13", "d14", "d15", "d16", "d17", "d18", "d19", "d20", "period", "t", "species"] category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Hlavacek2018Restructuration/Hlavacek2018Restructuration_aigenerated.md b/Published/Hlavacek2018Restructuration/Hlavacek2018Restructuration_aigenerated.md new file mode 100644 index 00000000..1661a107 --- /dev/null +++ b/Published/Hlavacek2018Restructuration/Hlavacek2018Restructuration_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Hlavacek 2018 Restructuration + +## One-sentence summary + +Three independent two-state populations demonstrate how a joint-state quantity can be computed after model decoupling. + +## What the model shows + +This compact benchmark examines restructuring of a model whose three components switch independently between inactive and active states. A derived quantity estimates the population simultaneously active in all three dimensions. + +## Biological story + +X, Y, and Z each reversibly switch on and off. Their active fractions are multiplied to reconstruct the expected triple-active population without explicitly coupling the three switches. + +## Main biological players + +Abstract components X, Y, and Z; inactive and active states; and the derived triple-active quantity R111. + +## Mechanism in plain English + +Each population independently transitions between state 0 and state 1 with matched forward and reverse rates. The model measures each active population directly, then multiplies their normalized active fractions and rescales by total abundance to estimate joint activation. This illustrates probabilistic decoupling rather than biochemical causation. + +## Key modeled events + +- X independently switches between inactive and active states. +- Y and Z undergo the same reversible switching. +- Active fractions approach their individual equilibria. +- The product of the three fractions yields the estimated triple-active population. + +## What the model measures + +Readouts include active X, active Y, active Z, and the calculated R111 quantity representing simultaneous activation under independence. + +## Expected behavior in plots + +The three active populations should overlap and approach half of their totals with equal rates. R111 should rise more slowly and settle near one eighth of the total because it requires all three independent active fractions. + +## Caveats + +X, Y, and Z are abstract variables. The independence assumption is built in, so the derived joint state cannot represent correlations or direct interactions. diff --git a/Published/Hlavacek2018Restructuration/Hlavacek2018Restructuration_aigenerated_detailed.md b/Published/Hlavacek2018Restructuration/Hlavacek2018Restructuration_aigenerated_detailed.md new file mode 100644 index 00000000..a95a54eb --- /dev/null +++ b/Published/Hlavacek2018Restructuration/Hlavacek2018Restructuration_aigenerated_detailed.md @@ -0,0 +1,73 @@ +# Coder Model Explanation: Hlavacek2018Restructuration after decoupling + +## 1. Model identity and scope + +- **Selected pair:** `Published/Hlavacek2018Restructuration/after_decoupling.bngl` with the same-directory `metadata.yaml`. +- **Metadata id/title:** `Hlavacek2018Restructuration_after_bunching` / Hlavacek2018Restructuration. +- **Scope:** three independent binary-state populations and a function that reconstructs their expected joint-active abundance under factorization. + +The metadata names `after_bunching`, not the selected `after_decoupling.bngl`; that mismatch is recorded rather than silently treated as model identity. + +## 2. BNGL block inventory + +| Construct | Count | Contribution | +| --- | ---: | --- | +| Parameters | 7 | Six transition rates plus common total `RTOT`. | +| Molecule types | 3 | Binary-state `X`, `Y`, and `Z`. | +| Initial species | 3 | One inactive pool per type. | +| Observables | 3 | Active-state species counts `X1`, `Y1`, `Z1`. | +| Functions | 1 | Factorized joint-active estimate `R111()`. | +| Reaction rules | 3 | One reversible switch per molecule. | +| Actions | 2 | Network generation and ODE simulation. | +| Compartments / anchors | 0 / 0 | Nonspatial. | + +## 3. Parameters, functions, and rate laws + +| Name | Value | Use | +| --- | ---: | --- | +| `kpX`, `kmX` | 1, 1 | X `0→1` and `1→0` rates. | +| `kpY`, `kmY` | 1, 1 | Y forward and reverse rates. | +| `kpZ`, `kmZ` | 1, 1 | Z forward and reverse rates. | +| `RTOT` | 100 | Initial amount of each type and normalization in `R111`. | + +`R111()=(X1/RTOT)*(Y1/RTOT)*(Z1/RTOT)*RTOT`. It multiplies the three active fractions and rescales by `RTOT`; it is a derived independence estimate, not an explicitly represented X–Y–Z complex. It is printed during simulation and is not used as a reaction rate. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `X` | 1 | `S` | `S~0~1` | None | Abstract binary switch. | No bonds. | +| `Y` | 1 | `S` | `S~0~1` | None | Independent binary switch. | No bonds. | +| `Z` | 1 | `S` | `S~0~1` | None | Independent binary switch. | No bonds. | + +## 5. Compartments, anchors, initial species, and setup + +There are no compartments, anchors, or binding sites. `X(S~0)`, `Y(S~0)`, and `Z(S~0)` each start at `RTOT=100`; active states start at zero. The three pools are conserved independently because every rule only flips `S` and neither creates nor destroys a molecule. + +## 6. Complete reaction-rule inventory + +| # | Direction and participants | Exact modeled change | Rates | Technical meaning | +| ---: | --- | --- | --- | --- | +| 1 | Reversible; `X` only | `X.S 0↔1`; no bond edit. | `kpX`, `kmX` | Independent X activation/deactivation. | +| 2 | Reversible; `Y` only | `Y.S 0↔1`; no bond edit. | `kpY`, `kmY` | Independent Y activation/deactivation. | +| 3 | Reversible; `Z` only | `Z.S 0↔1`; no bond edit. | `kpZ`, `kmZ` | Independent Z activation/deactivation. | + +No rule couples X, Y, or Z. Their only joint quantity is computed by `R111()`. + +## 7. Observables and technical readouts + +| Name | Type | Counted target | Interpretation | +| --- | --- | --- | --- | +| `X1` | `Species` | Exact `X(S~1)` species | Active X abundance. | +| `Y1` | `Species` | Exact `Y(S~1)` species | Active Y abundance. | +| `Z1` | `Species` | Exact `Z(S~1)` species | Active Z abundance. | + +The additional printed function `R111` reports `X1*Y1*Z1/RTOT^2`, the expected triple-active count if the three switches are statistically independent. + +## 8. Actions and simulation workflow + +`generate_network({overwrite=>1})` regenerates the finite network. `simulate({method=>"ode",t_end=>10,n_steps=>100,print_functions=>1})` performs deterministic ODE integration from 0 to 10 with 100 output intervals and includes `R111` with the three observables. + +## 9. Technical caveats and ambiguities + +X, Y, Z, and state `S` are intentionally abstract. The metadata points to a different variant (`after_bunching`) and incorrectly reports `uses_functions: false` despite active `R111()`. Because `R111` assumes factorization, it would stop representing a true joint population if later rules introduced coupling or correlations. diff --git a/Published/Hlavacek2018Restructuration/metadata.yaml b/Published/Hlavacek2018Restructuration/metadata.yaml index 00f6fdf0..58b8b940 100644 --- a/Published/Hlavacek2018Restructuration/metadata.yaml +++ b/Published/Hlavacek2018Restructuration/metadata.yaml @@ -4,6 +4,8 @@ description: BNGL model: after_bunching tags: ["na", "vecf", "egftot", "egfrtot", "kd", "kr", "kpx", "kmx", "kp", "kdp", "molecules"] category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023_metadata.yaml b/Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023_metadata.yaml new file mode 100644 index 00000000..4986d490 --- /dev/null +++ b/Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023_metadata.yaml @@ -0,0 +1,65 @@ +id: "Jaruszewicz-Blonska_2023" +name: "Jaruszewicz 2023" +description: "T-cell discrimination" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2023" + pmid: "37267242" + reference: "Jaruszewicz-Blonska et al., 2023" + +tags: ["published", "immunology", "jaruszewicz", "blonska", "2023", "ikk", "ikba", "ikba_mrna", "a20", "nfkb"] +date: + last_tested: 2026-07-18 + +category: "immunology" +biol_categories: ["immunology"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered a_3 at line 95" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: false + comments: "nf false in original but runs with nf MCP There was an issue parsing BNGL file NoneAction argument atol not recognized! Check to make sure action is correctly formatted" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/Jaruszewicz-Blonska_2023.bngl" + +playground: + visible: true + gallery_categories: ["immunology"] + featured: false + difficulty: "intermediate" + + + + diff --git a/Published/JaruszewiczBlonska2023/JaruszewiczBlonska2023_aigenerated.md b/Published/JaruszewiczBlonska2023/JaruszewiczBlonska2023_aigenerated.md new file mode 100644 index 00000000..612986fd --- /dev/null +++ b/Published/JaruszewiczBlonska2023/JaruszewiczBlonska2023_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Jaruszewicz-Blonska 2023 + +## One-sentence summary + +Canonical nuclear factor κB signaling balances IKK activation with IκBα and A20 negative feedback. + +## What the model shows + +This identifiable pathway model focuses on the core canonical NF-κB module. NF-κB means nuclear factor kappa B, IKK is the IκB kinase complex, IκBα is its inhibitory binding protein, and A20 is a feedback inhibitor. + +## Biological story + +Active IKK promotes removal of IκBα, freeing NF-κB to accumulate in the nucleus. Nuclear NF-κB induces new IκBα and A20; IκBα recaptures NF-κB, while A20 restrains upstream IKK activity. + +## Main biological players + +IKK, IκBα protein and messenger RNA, nuclear NF-κB, and A20. + +## Mechanism in plain English + +IKK shifts into an active form and accelerates IκBα loss. Released NF-κB enters the nuclear pool and stimulates transcription of IκBα and A20. Newly synthesized IκBα suppresses NF-κB directly, whereas A20 weakens the activating arm. Their different production and decay times create delayed negative feedback. + +## Key modeled events + +- IKK becomes active and removes the IκBα brake. +- NF-κB accumulates in the nucleus after inhibitor loss. +- Nuclear NF-κB induces IκBα and A20 expression. +- IκBα and A20 shut down the response through complementary feedback routes. + +## What the model measures + +Readouts follow active and neutral IKK, nuclear NF-κB, IκBα protein and transcript, and A20 abundance. + +## Expected behavior in plots + +Active IKK should rise before nuclear NF-κB. IκBα transcript and A20 should lag behind NF-κB, then help drive NF-κB and IKK downward; depending on feedback timing, the response may pulse or show damped oscillatory structure. + +## Caveats + +This reduced model emphasizes identifiable core feedback and omits receptor-specific inputs, cell-to-cell spatial detail, and many NF-κB target genes. diff --git a/Published/JaruszewiczBlonska2023/JaruszewiczBlonska2023_aigenerated_detailed.md b/Published/JaruszewiczBlonska2023/JaruszewiczBlonska2023_aigenerated_detailed.md new file mode 100644 index 00000000..7f32610e --- /dev/null +++ b/Published/JaruszewiczBlonska2023/JaruszewiczBlonska2023_aigenerated_detailed.md @@ -0,0 +1,81 @@ +# Detailed Model Explanation: Jaruszewicz-Blonska 2023 canonical NF-κB feedback model + +## 1. Model overview + +This reduced canonical NF-κB model converts a binary TNF-receptor input into IKK activation, nuclear NF-κB production, and induction of the inhibitors IκBα and A20. A20 suppresses active IKK, while IκBα removes nuclear NF-κB and is itself degraded by active IKK, creating coupled negative-feedback loops. + +## 2. BNGL block inventory + +The file contains 14 active parameters, 5 molecule types, 6 seed declarations, 6 species-count observables, 3 functions, 14 one-way rules, and 4 active actions. It has no compartments or anchors; extensive stimulation protocols are present only as disabled comments. + +## 3. Parameters, functions, and rate laws + +The model uses lumped first-order production/removal constants plus three observable-dependent functions. `TR` is a binary stimulus switch, and the nonlinear transport functions make NF-κB/IκBα turnover depend on their current observable levels. + +| Parameter group or names | Function in this model | +| --- | --- | +| `TR`, `k_1`, `k_3`, `k_deg` | TNF input and IKK lifecycle: stimulus-dependent activation, extra loss of active IKK, and basal creation/removal. | +| `k_2` | A20-mediated removal of active IKK, gated by `TR` in the rule rate. | +| `c_deg` | Shared A20 production and degradation rate, making NF-κB-driven synthesis and turnover symmetric in this reduced representation. | +| `c_3a`, `c_4a`, `c_5a` | IκBα mRNA production/decay, translation, and protein decay. The same `c_3a` controls transcript birth and death. | +| `a_3`, `delta`, `epsilon`, `a_2`, `i_1a` | Shape the three nonlinear NF-κB import/export and IκBα-removal functions, including saturation offsets and basal IκBα transport. | + +| Function | Inputs/dependencies | Meaning and use in this model | +| --- | --- | --- | +| `k_NFkBimport` | Nuclear NF-κB `NFkB_n`, cytoplasmic IκBα `IkBa`, plus `a_3` and `delta` | Decreases as nuclear NF-κB approaches its normalized ceiling and as IκBα rises; used by active IKK to produce nuclear NF-κB in rule 12. | +| `k_NFkBexport` | `NFkB_n`, `i_1a`, `epsilon` | Per-pair removal rate for NF-κB plus IκBα; the denominator slows the rate as nuclear NF-κB increases. Used in rule 13. | +| `k_IkBatransport` | `NFkB_n`, `IkBa`, `a_2`, `a_3`, `delta` | Combines basal and NF-κB-dependent removal of IκBα by active IKK. Used in rule 14. | + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `IKK` | 1 | `st` | `n, a` | None | Kinase pool switching between neutral and active states; active IKK releases NF-κB and removes IκBα. | +| `IkBa` | 0 | None | None | None | Lumped cytoplasmic IκBα inhibitor; binding is not explicit, so its action appears through joint-removal rules and rate functions. | +| `IkBa_mRNA` | 0 | None | None | None | Transcript induced by NF-κB and translated into IκBα. | +| `A20` | 0 | None | None | None | NF-κB-induced negative regulator that catalytically removes active IKK. | +| `NFkB` | 0 | None | None | None | Lumped nuclear NF-κB output; localization is encoded by molecule identity/observable, not a compartment or internal state. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial and starts with one neutral IKK molecule; active IKK, NF-κB, IκBα, its transcript, and A20 all start at zero. `TR` is initialized to 0, so the active workflow first seeks the unstimulated steady state. The source normalizes several feedback expressions around unit-scale NF-κB rather than representing explicit molecular binding or transport compartments. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–4 maintain the IKK pool and couple it to TNF input. Rules 5–10 implement NF-κB-dependent A20 and IκBα expression, while rules 11–14 close the feedback loops by removing active IKK, producing NF-κB, and clearing NF-κB/IκBα. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | One-way | Neutral `IKK.st~n` | Changes `IKK.st: n → a` at `k_1*TR`. | Converts the binary TNF input into kinase activation; no activation occurs when `TR=0`. | +| 2 | One-way | Source `0` | Creates neutral IKK at `k_deg`. | Replenishes the IKK pool lost through rules 3, 4, and 11. | +| 3 | One-way | Active `IKK.st~a` | Removes active IKK to sink `0` at `k_deg+k_3`. | Gives active IKK both basal and activation-specific turnover. | +| 4 | One-way | Neutral `IKK.st~n` | Removes neutral IKK at `k_deg`. | Balances constitutive neutral-IKK production in the absence of signaling. | +| 5–6 | One-way | Nuclear NF-κB in rule 5; A20 in rule 6 | NF-κB catalytically creates A20, while A20 is independently removed; both rates are `c_deg`. | Establishes an NF-κB-induced A20 pool with matched production and decay scales. | +| 7–8 | One-way | Nuclear NF-κB in rule 7; IκBα mRNA in rule 8 | NF-κB catalytically creates `IkBa_mRNA`, and the transcript decays; both use `c_3a`. | Creates the transcript stage of delayed IκBα feedback. | +| 9–10 | One-way | IκBα mRNA in rule 9; IκBα protein in rule 10 | The transcript is retained while producing IκBα at `c_4a`; IκBα decays at `c_5a`. | Converts transcription into a transient inhibitor pool whose lifetime is independent of its mRNA. | +| 11 | One-way | A20 and active IKK | Removes active IKK while retaining A20, at `k_2*TR`. | Implements catalytic A20 feedback on the stimulus-driven IKK branch. | +| 12 | One-way | Active IKK | Retains active IKK and creates NF-κB at `k_NFkBimport()`. | Represents IKK-dependent release/import of NF-κB with feedback from current NF-κB and IκBα levels. | +| 13 | One-way | NF-κB and IκBα | Removes one of each at `k_NFkBexport()`. | Lumped resequestration/export: newly made IκBα terminates nuclear NF-κB while being consumed in the event. | +| 14 | One-way | Active IKK and IκBα | Removes IκBα while retaining active IKK, at `k_IkBatransport()`. | Represents IKK-driven inhibitor clearance, opposing IκBα feedback and permitting renewed NF-κB production. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `IKK_a`, `IKK_n` | Species count | Active and neutral IKK species | Partition of the kinase pool used to track stimulus response and recovery. | +| `tIkBa` | Species count | IκBα mRNA | Transcriptional-feedback intermediate upstream of IκBα protein. | +| `IkBa` | Species count | IκBα protein | Inhibitor level used directly by all three nonlinear functions. | +| `A20` | Species count | A20 protein | Strength of the IKK-targeting feedback arm. | +| `NFkB_n` | Species count | Nuclear NF-κB | Primary signaling output and input to A20/IκBα production and transport functions. | + +## 8. Actions and simulation workflow + +The active workflow generates the network, forces `TR=0`, and performs a 30-day sparse ODE steady-state run with 200 output steps before saving concentrations. All continuous-stimulation, pulse, and A20-knockout protocols below that point are commented or auto-disabled, so they describe intended experiments but are not executed by the checked-in file. + +## 9. Technical caveats and ambiguities + +- Metadata labels the model “T-cell discrimination,” whereas the BNGL header and mechanism describe a reduced canonical NF-κB pathway. +- Localization is conceptual: there are no compartments, and `NFkB` specifically represents the nuclear pool while `IkBa` represents cytoplasmic inhibitor. +- Rules 13 and 14 consume IκBα rather than representing explicit shuttling, binding, phosphorylation, and degradation intermediates. +- `TR` also gates A20-mediated IKK removal, so A20 cannot clear active IKK through rule 11 when stimulus is off. +- The active steady-state action repeats the `sparse` argument and uses extremely tight tolerances, which may be solver- or parser-sensitive. diff --git a/Published/JaruszewiczBlonska2023/metadata.yaml b/Published/JaruszewiczBlonska2023/metadata.yaml index b469a530..01bdba50 100644 --- a/Published/JaruszewiczBlonska2023/metadata.yaml +++ b/Published/JaruszewiczBlonska2023/metadata.yaml @@ -4,6 +4,7 @@ description: "T-cell discrimination" tags: ["published", "immunology", "jaruszewicz", "blonska", "2023", "ikk", "ikba", "ikba_mrna", "a20", "nfkb"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Jung2017/Jung2017_aigenerated.md b/Published/Jung2017/Jung2017_aigenerated.md new file mode 100644 index 00000000..7a3862dc --- /dev/null +++ b/Published/Jung2017/Jung2017_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Jung 2017 + +## One-sentence summary + +Agonist-driven M1 receptor phosphorylation organizes arrestin-dependent ERK activation and phosphatase-mediated signal reversal. + +## What the model shows + +This model follows oxotremorine engagement of the M1 muscarinic receptor at the plasma membrane, receptor phosphorylation, arrestin recruitment, and assembly of a MEK–ERK signaling complex. It also represents receptor and ERK dephosphorylation, making it useful for examining how a transient agonist exposure can create and then terminate an ERK response. + +## Biological story + +An extracellular agonist is converted into receptor-binding Oxo and activates membrane M1R. GRK or CK2 phosphorylates the occupied receptor, arrestin binds the modified receptor, and arrestin recruits MEK and ERK. PP1 acts on the receptor, whereas PP2A acts through arrestin to oppose ERK phosphorylation. + +## Main biological players + +M1 muscarinic receptor, oxotremorine/Oxo, arrestin, GRK, CK2, PP1, PP2A, MEK, ERK, phosphorylated ERK, and a phosphorylation probe. + +## Mechanism in plain English + +Oxo binds M1R and allows receptor-directed kinases to modify two regulatory serines. Phosphorylated receptor captures arrestin, which serves as a platform for MEK and ERK; ERK on this platform is converted to phosphorylated ERK and can dissociate. PP1 removes receptor phosphorylation, while arrestin-bound PP2A converts phosphorylated ERK back to ERK. A timed agonist function limits receptor stimulation to a defined exposure window. + +## Key modeled events + +- Oxo binds membrane M1R and promotes receptor phosphorylation by GRK or CK2. +- Arrestin recognizes occupied receptor states and recruits MEK and ERK into a membrane-associated signaling assembly. +- MEK promotes ERK phosphorylation, whereas PP2A reverses that modification. +- PP1 dephosphorylates M1R, weakening the phosphorylated receptor–arrestin state. + +## What the model measures + +Readouts distinguish total receptor and agonist, phosphorylated receptor complexes, arrestin-containing assemblies, free and phosphorylated ERK, PP2A recruitment, and conversion of a phosphorylation probe. + +## Expected behavior in plots + +During agonist exposure, phosphorylated M1R and arrestin–MEK–ERK complexes should accumulate before phosphorylated ERK and the phosphorylated probe increase. When stimulation ends, receptor dephosphorylation and PP2A activity should reduce those complexes and shift the ERK readout back toward its unphosphorylated form. + +## Caveats + +The pathway is a focused receptor–arrestin–ERK module. It does not represent the broader G-protein and second-messenger branches normally associated with M1 receptors. diff --git a/Published/Jung2017/Jung_2017_metadata.yaml b/Published/Jung2017/Jung_2017_metadata.yaml new file mode 100644 index 00000000..1332bf42 --- /dev/null +++ b/Published/Jung2017/Jung_2017_metadata.yaml @@ -0,0 +1,24 @@ +id: "Jung_2017" +name: "Jung 2017" +description: "M1 receptor signaling" +tags: ["published", "jung", "2017", "m1r", "oxo", "arrestin", "mek", "erk", "perk", "oxo_ec", "pp2a"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Jung_2017.bngl" +playground: + visible: false + gallery_categories: ["neuroscience"] + featured: false + difficulty: "advanced" diff --git a/Published/Jung2017/metadata.yaml b/Published/Jung2017/metadata.yaml index bba84b04..01eb4e1b 100644 --- a/Published/Jung2017/metadata.yaml +++ b/Published/Jung2017/metadata.yaml @@ -4,6 +4,7 @@ description: "M1 receptor signaling" tags: ["published", "jung", "2017", "m1r", "oxo", "arrestin", "mek", "erk", "perk", "oxo_ec", "pp2a"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: true diff --git a/Published/Kesseler2013/Kesseler2013_aigenerated.md b/Published/Kesseler2013/Kesseler2013_aigenerated.md new file mode 100644 index 00000000..f2d199d8 --- /dev/null +++ b/Published/Kesseler2013/Kesseler2013_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Kesseler 2013 + +## One-sentence summary + +Interlocking kinase, phosphatase, and transport controls govern commitment from the G2 checkpoint into mitosis. + +## What the model shows + +This detailed cell-cycle model follows activation of maturation-promoting factor (MPF), the cyclin B–CDK1 complex, together with CDC25 phosphatases, WEE1/MYT1 kinases, polo-like kinase 1 (PLK1), and checkpoint kinases. + +## Biological story + +Before mitosis, WEE1 and MYT1 keep MPF inhibited. CDC25 removes inhibitory phosphates, active MPF reinforces CDC25 and suppresses WEE1, and PLK1 supports the switch. CHK1 and CHK2 preserve checkpoint arrest when damage signaling is present. + +## Main biological players + +MPF, CDC25A/B/C, WEE1, MYT1, PLK1, CHK1, CHK2, PP2A phosphatase, PIN1, import/export factors, and histone H3. + +## Mechanism in plain English + +Competing enzymes write and erase inhibitory marks on MPF. Once CDC25 activity gains an advantage, MPF activation feeds back positively on its activators and negatively on its inhibitors, producing switch-like entry into mitosis. Nuclear transport changes access to regulators, while checkpoint kinases and PP2A oppose commitment. PLK1 and histone H3 phosphorylation mark progression. + +## Key modeled events + +- WEE1 and MYT1 impose inhibitory phosphorylation on MPF. +- CDC25 phosphatases remove inhibition and activate MPF. +- Active MPF and PLK1 reinforce CDC25 while weakening WEE1. +- CHK1/CHK2 and PP2A stabilize checkpoint restraint. +- Histone H3 phosphorylation reports mitotic entry. + +## What the model measures + +The extensive readouts distinguish active and localized CDC25 isoforms, WEE1 and PLK1 states, MPF-related regulators, and phosphorylated histone H3. + +## Expected behavior in plots + +A successful transition should show a sharp rise in active CDC25, MPF-associated positive feedback, active PLK1, and histone H3 phosphorylation, accompanied by loss of active WEE1. Checkpoint engagement should delay or suppress that coordinated switch. + +## Caveats + +The model is large and mechanistically annotated but not a complete cell cycle. Its many fitted or assumed rates make qualitative state ordering more secure than exact timing without reproducing the original conditions. diff --git a/Published/Kesseler2013/Kesseler_2013_metadata.yaml b/Published/Kesseler2013/Kesseler_2013_metadata.yaml new file mode 100644 index 00000000..e4b53132 --- /dev/null +++ b/Published/Kesseler2013/Kesseler_2013_metadata.yaml @@ -0,0 +1,24 @@ +id: "Kesseler_2013" +name: "Kesseler 2013" +description: "G2/Mitosis transition" +tags: ["published", "kesseler", "2013", "mpf", "cdc25", "wee1", "myt1", "pin1", "pp2a", "prox", "e33"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Kesseler_2013.bngl" +playground: + visible: false + gallery_categories: ["cell-cycle"] + featured: false + difficulty: "advanced" diff --git a/Published/Kesseler2013/metadata.yaml b/Published/Kesseler2013/metadata.yaml index 86b76e09..76fd2c85 100644 --- a/Published/Kesseler2013/metadata.yaml +++ b/Published/Kesseler2013/metadata.yaml @@ -4,6 +4,7 @@ description: "G2/Mitosis transition" tags: ["published", "kesseler", "2013", "mpf", "cdc25", "wee1", "myt1", "pin1", "pp2a", "prox", "e33"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Kocieniewski2012/Kocieniewski2012_aigenerated.md b/Published/Kocieniewski2012/Kocieniewski2012_aigenerated.md new file mode 100644 index 00000000..9c6c7ff3 --- /dev/null +++ b/Published/Kocieniewski2012/Kocieniewski2012_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Kocieniewski 2012 + +## One-sentence summary + +A three-tier MAP kinase cascade uses a shared scaffold to coordinate sequential MAP3K, MAP2K, and MAPK activation. + +## What the model shows + +This compact scaffold model asks how colocalizing three kinase tiers changes productive signaling. MAP3K, MAP2K, and MAPK can each occupy a dedicated position on the scaffold, and phosphorylation proceeds when the required upstream and downstream kinases share that platform. + +## Biological story + +An activating input switches MAP3K on. Active MAP3K phosphorylates scaffold-bound MAP2K, and doubly phosphorylated MAP2K then phosphorylates scaffold-bound MAPK. Constitutive dephosphorylation competes with this relay, while completed MAPK can leave the scaffold. + +## Main biological players + +MAP3K, MAP2K, MAPK, and a three-position scaffold. + +## Mechanism in plain English + +The scaffold independently captures each kinase tier. Once active MAP3K and MAP2K are neighbors, MAP3K modifies both MAP2K regulatory residues. Fully modified MAP2K similarly modifies the two MAPK residues. Each kinase can lose phosphate groups away from productive complexes, so output depends on the balance between scaffold-assisted phosphorylation, dissociation, and dephosphorylation. + +## Key modeled events + +- MAP3K switches from inactive to active in response to a constant input. +- The scaffold recruits MAP3K, MAP2K, and MAPK through separate docking positions. +- Active scaffold-bound MAP3K phosphorylates MAP2K at two residues. +- Fully phosphorylated MAP2K phosphorylates scaffold-bound MAPK, which can then be released. + +## What the model measures + +The two readouts count productive scaffold chains containing activated MAP2K together with either phosphorylated MAPK or active MAP3K. They report assembly of the middle-to-output and input-to-middle portions of the cascade. + +## Expected behavior in plots + +The active-MAP3K/MAP2K chain should appear as the cascade is engaged, followed by the MAP2K/MAPK chain as phosphorylation propagates downstream. Strong dephosphorylation or rapid scaffold release should limit the persistence of both complexes. + +## Caveats + +Despite its metadata description, the represented mechanism is a generic scaffolded MAPK cascade rather than an explicit actin network. The kinase names are tier labels, not a complete named cellular pathway. diff --git a/Published/Kocieniewski2012/Kocieniewski2012_aigenerated_detailed.md b/Published/Kocieniewski2012/Kocieniewski2012_aigenerated_detailed.md new file mode 100644 index 00000000..c823d0e2 --- /dev/null +++ b/Published/Kocieniewski2012/Kocieniewski2012_aigenerated_detailed.md @@ -0,0 +1,69 @@ +# Detailed Model Explanation: Kocieniewski 2012 scaffolded MAPK cascade + +## 1. Model overview + +This model represents a three-layer MAP3K–MAP2K–MAPK cascade organized by a scaffold with one docking site for each kinase layer. Activation is passed only between kinases co-bound to the same scaffold, while constitutive deactivation and dephosphorylation act regardless of scaffold occupancy. + +## 2. BNGL block inventory + +The model contains 10 parameters, 4 molecule types, 4 free seed species, 2 molecule-count observables, and 20 rules. It has no compartments, anchors, functions, or actions. + +## 3. Parameters, functions, and rate laws + +The model uses one common docking pair, one fast state-dependent release rate, one scaffold-local phosphorylation rate, and one global reversal rate. All kinetics are direct mass action; there are no algebraic or observable-dependent functions. + +| Parameter group or names | Function in this model | +| --- | --- | +| `Atot`, `Btot`, `Ctot`, `Stot` | Initial totals for MAP3K, MAP2K, MAPK, and scaffold. MAPK starts fivefold more abundant than each other pool. | +| `a`, `d1` | Shared association and dissociation rates for ordinary kinase docking to the matching scaffold site. | +| `d2` | Fast one-way release of inactive MAP3K or doubly phosphorylated MAPK from scaffold, enforcing state-dependent unloading. | +| `S` | Basal conversion rate from inactive to active MAP3K. | +| `pscaff` | Phosphorylation rate for MAP2K or MAPK when the required upstream/downstream pair is co-docked. | +| `u` | Shared MAP3K deactivation and MAP2K/MAPK site-dephosphorylation rate. | + +There are no functions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `MAP3K` | 2 | `s`, `S` | `S: I, A` | None | Upstream kinase; `s` docks to the scaffold and active `S~A` phosphorylates co-docked MAP2K. | +| `MAP2K` | 3 | `s`, `R1`, `R2` | `R1: Y, Yp`; `R2: Y, Yp` | None | Middle kinase; both regulatory sites must be phosphorylated before it can modify co-docked MAPK. | +| `MAPK` | 3 | `s`, `R1`, `R2` | `R1: Y, Yp`; `R2: Y, Yp` | None | Output kinase whose two phosphorylation sites are modified on scaffold and reversed globally. | +| `Scaff` | 3 | `map3k`, `map2k`, `mapk` | None | None | Typed docking platform that can hold one kinase from each cascade layer simultaneously. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial and starts with empty scaffold plus free inactive MAP3K and fully unphosphorylated MAP2K/MAPK. Initial totals are 100,000 for MAP3K, MAP2K, and scaffold and 500,000 for MAPK; no active or scaffold-bound complexes are seeded. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rule 1 supplies basal upstream activation. Rules 2–11 load and unload kinases according to modification state, rules 12–15 pass phosphorylation down co-occupied scaffold slots, and rules 16–20 erase kinase activation or phosphorylation without requiring scaffold release. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | One-way | Free MAP3K `S~I` | Changes `S: I → A` at rate `S`; the docking site remains free. | Creates the active upstream kinase that can enter the scaffolded cascade. | +| 2–3 | Reversible in rule 2; one-way in rule 3 | MAP3K `s` and scaffold `map3k`; rule 2 requires `S~A`, rule 3 requires scaffold-bound `S~I` | Rule 2 docks/releases active MAP3K at `a`/`d1`; rule 3 releases inactive MAP3K at fast rate `d2`. | Retains active MAP3K through ordinary affinity but rapidly clears it after global deactivation. | +| 4–7 | Reversible | MAP2K `s` and scaffold `map2k`; rules 4–7 cover `R1/R2` states `Y/Y`, `Yp/Y`, `Y/Yp`, and `Yp/Yp` | Every phosphorylation state docks with the same `a`/`d1`; no regulatory state changes during binding. | Lets MAP2K remain scaffold-accessible throughout its two-step phosphorylation cycle. | +| 8–11 | Reversible in rules 8–10; one-way in rule 11 | MAPK `s` and scaffold `mapk`; rules 8–10 cover unmodified and singly phosphorylated forms, rule 11 the doubly phosphorylated form | The first three states dock at `a`/`d1`; doubly phosphorylated MAPK is released at `d2`. | Loads substrate MAPK for modification, then rapidly ejects the completed two-site product. | +| 12–13 | One-way | Active scaffold-bound MAP3K and scaffold-bound MAP2K; MAP2K `R1~Y` or `R2~Y` | Changes MAP2K `R1` in rule 12 or `R2` in rule 13 from `Y → Yp` at `pscaff`, preserving both scaffold bonds. | Allows either order of the two MAP2K phosphorylation steps but only under scaffold colocalization. | +| 14–15 | One-way | Doubly phosphorylated scaffold-bound MAP2K and scaffold-bound MAPK; MAPK `R1~Y` or `R2~Y` | Changes MAPK `R1` in rule 14 or `R2` in rule 15 from `Y → Yp` at `pscaff`, retaining the complex. | Passes activity to the output layer; completion of both sites then triggers rule 11 unloading. | +| 16–20 | One-way | Active MAP3K, phospho-MAP2K `R1`/`R2`, or phospho-MAPK `R1`/`R2`, respectively | Rule 16 changes MAP3K `A → I`; rules 17–20 change the named site `Yp → Y`, all at `u` and with no binding constraint. | Provides uniform signal reversal for free and scaffold-bound kinases, allowing shutdown at every layer. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `MAPKchainone` | Molecule count | Scaffold carrying doubly phosphorylated MAP2K and MAPK phosphorylated at `R1` | Captures the lower-cascade complex after one MAPK modification; MAPK `R2` is unconstrained. | +| `MAPKchaintwo` | Molecule count | Scaffold carrying active MAP3K and doubly phosphorylated MAP2K | Captures an upper-cascade signaling complex competent to have completed MAP2K activation. | + +## 8. Actions and simulation workflow + +The file defines model logic only and includes no network-generation or simulation action. An external workflow must choose the simulator, duration, and output schedule. + +## 9. Technical caveats and ambiguities + +- Metadata describes “Actin dynamics,” but the BNGL is a scaffolded MAPK cascade. +- Rules 16–20 use partial patterns, so reversal can occur while a kinase remains scaffold-bound. +- The two observables report selected scaffold configurations rather than total active MAP2K or MAPK. +- MAP2K and MAPK sites are abstract `R1`/`R2` states; local files do not identify physical residues. diff --git a/Published/Kocieniewski2012/Kocieniewski_2012_metadata.yaml b/Published/Kocieniewski2012/Kocieniewski_2012_metadata.yaml new file mode 100644 index 00000000..577048b0 --- /dev/null +++ b/Published/Kocieniewski2012/Kocieniewski_2012_metadata.yaml @@ -0,0 +1,66 @@ +id: "Kocieniewski_2012" +name: "Kocieniewski 2012" +description: "Actin dynamics" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2012" + pmid: "22123371" + reference: "Kocieniewski et al., 2012" + +tags: ["published", "kocieniewski", "2012", "map3k", "map2k", "mapk", "scaff"] +date: + last_tested: 2026-07-16 + +category: "regulation" +biol_categories: ["regulation"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa","nf"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim runs after lowering numbers of molecules MCP cannot access local variable stdout_str where it is not associated with a value" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/Kocieniewski_2012.bngl" + +playground: + visible: false + gallery_category: "regulation" + featured: false + difficulty: "advanced" + + + + diff --git a/Published/Kocieniewski2012/metadata.yaml b/Published/Kocieniewski2012/metadata.yaml index d08a90c6..7600112c 100644 --- a/Published/Kocieniewski2012/metadata.yaml +++ b/Published/Kocieniewski2012/metadata.yaml @@ -4,6 +4,7 @@ description: "Actin dynamics" tags: ["published", "kocieniewski", "2012", "map3k", "map2k", "mapk", "scaff"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Korwek2023/Korwek2023_aigenerated.md b/Published/Korwek2023/Korwek2023_aigenerated.md new file mode 100644 index 00000000..582f2ec8 --- /dev/null +++ b/Published/Korwek2023/Korwek2023_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Korwek 2023 + +## One-sentence summary + +Double-stranded non-self RNA coordinates antiviral translation arrest, RNA decay, NF-κB signaling, and interferon-β feedback. + +## What the model shows + +This innate-immune model links polyinosinic:polycytidylic acid, abbreviated poly(I:C), to several antiviral sensors. It integrates RIG-I–MAVS, PKR–eIF2α, OAS3–RNase L, NF-κB, and interferon regulatory factor signaling. + +## Biological story + +Cytoplasmic non-self RNA activates retinoic acid-inducible gene I (RIG-I), protein kinase R (PKR), and oligoadenylate synthetase 3 (OAS3). These branches inhibit translation, degrade RNA, and induce cytokines and antiviral genes, which feed back through interferon signaling. + +## Main biological players + +poly(I:C), RIG-I, MAVS, PKR, eIF2α, OAS3, RNase L, TAK1, IKK, NF-κB, TBK1, IRF3, interferon-β, and JAK–STAT feedback. + +## Mechanism in plain English + +RIG-I binds RNA and signals through mitochondrial antiviral-signaling protein (MAVS). PKR phosphorylates eukaryotic initiation factor 2α (eIF2α) to suppress translation. OAS3 activates RNase L to remove RNA. Parallel kinase routes activate nuclear factor κB (NF-κB) and interferon regulatory factor 3 (IRF3), inducing cytokines and antiviral sensor expression. + +## Key modeled events + +- Non-self RNA activates RIG-I, PKR, and OAS3. +- PKR phosphorylates eIF2α and reduces protein synthesis. +- OAS3 activates RNase L to accelerate RNA degradation. +- NF-κB and IRF3 induce inflammatory and interferon outputs. +- Interferon feedback raises antiviral sensor abundance. + +## What the model measures + +Readouts span sensor proteins and transcripts, active RNase L, phosphorylated eIF2α, nuclear NF-κB, kinase states, cytokines, and interferon-pathway outputs. + +## Expected behavior in plots + +Sensor activation should precede eIF2α phosphorylation and RNase L activity. Nuclear NF-κB and IRF3-dependent outputs should then rise, followed by slower interferon-driven increases in RIG-I, PKR, OAS3, and RNase L expression. + +## Caveats + +The model integrates many antiviral branches but still compresses RNA species, translation, and cytokine communication into population-level processes. diff --git a/Published/Korwek2023/Korwek2023_aigenerated_detailed.md b/Published/Korwek2023/Korwek2023_aigenerated_detailed.md new file mode 100644 index 00000000..7cd59db3 --- /dev/null +++ b/Published/Korwek2023/Korwek2023_aigenerated_detailed.md @@ -0,0 +1,100 @@ +# Detailed Model Explanation: Korwek 2023 Antiviral Innate-Immune Signaling + +## 1. Model overview + +This model follows cytosolic poly(I:C) recognition through RIG-I/MAVS and couples it to PKR–eIF2α translational inhibition, OAS3–RNase L RNA decay, NF-κB and IRF3 activation, interferon-β production, and IFNAR–STAT1/STAT2 feedback. The resulting network contains both antiviral amplification—through interferon-stimulated gene expression—and self-limitation through A20, IκBα, transcript degradation, and protein turnover. + +## 2. BNGL block inventory + +The model contains 93 parameters, 29 molecule types, 30 seed species, 83 logical reaction rules, 42 declared observables (53 physical lines because several patterns continue), and 7 actions. There are no functions, compartments, or anchors; extracellular, cytoplasmic, and nuclear locations are encoded as molecule states. + +## 3. Parameters, functions, and rate laws + +Parameter prefixes form a deliberate namespace: `a/d` activate or deactivate, `b/u` bind or unbind, `i/e` import or export, `p/q` phosphorylate or dephosphorylate, `t/s/g` control transcription, translation, or degradation, and `m` denotes saturation constants. Rules combine mass action with observable-dependent rational expressions; RNase L accelerates transcript loss, phosphorylated eIF2α suppresses translation, and STAT1/2 dimers, NF-κB, and IRF3 provide saturating transcriptional inputs. + +| Parameter group or names | Function in this model | +| --- | --- | +| Cell and pool parameters (`n_*`, volume/scaling terms) | Establish initial antiviral proteins, NF-κB components, interferon machinery, and extracellular/cytoplasmic stimulus pools. | +| `n_IFNb_stimulation`, `n_polyIC_stimulation` | Define the two sequential experimental perturbations applied by actions after equilibration. | +| Poly(I:C)/RIG-I/MAVS rates (`i_Polyic`, `b_Rigi_Polyic`, `b_RigiPolyic_Mavs`, `sg_Rigi`) | Import poly(I:C), assemble the sensing complex, and turn over RIG-I while releasing ligand and MAVS. | +| `a_Pkr_by_Polyic`, `d_Pkr`, `a_Oas3_by_Polyic`, `d_Oas3`, `a_Rnasel_by_Oas3`, `d_Rnasel` | Activate and reset the PKR and OAS3/RNase L antiviral effector branches. | +| `p_Eif2a_by_Pkr`, `p_Eif2a_basal`, `q_Eif2a`, `m_Eif2a` | Set eIF2α phosphorylation and its inhibitory effect on translation rates. | +| ISG transcription/turnover terms (`tg_Isg_mrna`, `ma_*_gene_basal`, `a_gene_by_Stat12dim`, `m_Rnasel`, `h_*`) | Produce RIG-I, PKR, OAS3, and RNase L transcripts from basal and STAT-dimer inputs, apply knockout switches, and accelerate their decay through active RNase L. | +| TAK1/IKK terms (`a_Tak1_by_*`, `d_Tak1`, `a_Ikk`, `d_Ikk_1`–`d_Ikk_3`) | Connect RIG-I/MAVS or TNFα to nonlinear IKK activation and an A20-sensitive refractory cycle. | +| NF-κB/IκBα/A20 terms (`b_Nfkb_Ikba_*`, `p_Ikba_by_Ikk`, `g_Ikba_*`, `i_Nfkb`, `e_Nfkb_with_Ikba`, `i/e_Ikba`, `tg_*_mrna`, `a/d_*_gene`, `s_Ikba`, `sg_A20`) | Control sequestration, IκBα phosphorylation/removal, transport, feedback-gene expression, and A20 turnover. | +| TBK1/IRF3 terms (`p_Tbk1_by_RigiMavs`, `q_Tbk1`, `q_Tbk1_by_A20`, `p_Irf3_by_Tbk1`, `q_Irf3`) | Drive and restrain the second transcription-factor arm downstream of RIG-I/MAVS. | +| IFNβ/IFNAR terms (`b_Ifnar_Ifnb_*`, `tg_Ifnar_mrna`, `s/g_Ifnar*`, `tg_Ifnb_mrna`, `sg_Ifnb`, `m_Ifnb_mrna_NfkbIrf3`) | Implement receptor binding, receptor synthesis/turnover, cooperative NF-κB–IRF3 interferon transcription, and interferon production/removal. | +| STAT terms (`p_Stat`, `q_Stat`, `m_Ifnar_a`, `b/qu_Stat1_Stat2`, `tg_Stat_mrna`, `sg_Stat`, `ma_Stat*_gene_basal`) | Phosphorylate STAT1/2 in response to occupied IFNAR, form and reset the heterodimer, and induce STAT expression. | + +There are no active functions; all nonlinear regulation is written directly in reaction-rate expressions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `PolyIC`, `RIGI`, `MAVS` | 2; 2; 1 | PolyIC: `Rigi`, `loc`; RIGI: `Polyic`, `Mavs`; MAVS: `Rigi` | PolyIC location `ext/cyt` | None | Synthetic RNA input and the two-component recognition scaffold that initiates TAK1 and TBK1 signaling. | +| `PKR`, `OAS3`, `RNaseL`, `eIF2a` | 1 each | `st`; `st`; `st`; `st` | first three `i/a`; eIF2α `0/p` | None | Antiviral effector switches controlling translation and RNase-L-dependent RNA loss. | +| `RIGI_mRNA`, `PKR_mRNA`, `OAS3_mRNA`, `RNaseL_mRNA` | 0 each | None | None | None | Interferon-stimulated transcripts that replenish the four antiviral proteins. | +| `TNFa`, `A20` | 0 each | None | None | None | TNFα provides an alternate TAK1 input; A20 suppresses IKK and TBK1 signaling. | +| `TAK1`, `IKK` | 1 each | `st` | TAK1 `i/a`; IKK `n/a/i/ii` | None | Sequential NF-κB-pathway kinase switches with an explicit IKK refractory cycle. | +| `IkBa`, `NFkB` | 3; 2 | IκBα: `Nfkb`, `loc`, `Ser32_Ser36`; NF-κB: `Ikba`, `loc` | locations `nuc/cyt`; IκBα sites `0/pp` | None | Inhibitor/transcription-factor pair whose binding, phosphorylation, degradation, and shuttling determine nuclear NF-κB. | +| `IkBa_mRNA`, `A20_mRNA` | 0 each | None | None | None | NF-κB feedback transcripts subject to RNase-L-enhanced decay and eIF2α-dependent translation. | +| `TBK1`, `IRF3` | 1 each | `Ser172`; `Ser396` | `0/p` | None | Kinase and transcription factor forming the interferon-induction branch. | +| `IFNAR`, `IFNb` | 1; 2 | IFNAR: `Ifnb`; IFNβ: `Ifnar`, `loc` | IFNβ location `ext/cyt` | None | Receptor/ligand pair coupling secreted or added interferon to STAT phosphorylation. | +| `IFNAR_mRNA`, `IFNb_mRNA` | 0 each | None | None | None | Transcripts for receptor replenishment and induced interferon production. | +| `STAT1`, `STAT2` | 2 each | reciprocal dimer site; Tyr701 or Tyr690 | phosphosite `0/p` | None | IFNAR-responsive factors that form the heterodimer driving antiviral-gene transcription. | +| `STAT1_mRNA`, `STAT2_mRNA` | 0 each | None | None | None | Positively regulated transcripts that reinforce the STAT pool. | + +## 5. Compartments, anchors, initial species, and setup + +No BNGL compartments or anchors are used. Location states place the initial poly(I:C) and IFNβ stimuli outside the cell and distinguish nuclear from cytoplasmic NF-κB/IκBα; the seeded signaling proteins otherwise begin in inactive, unphosphorylated, or unbound forms. Basal mRNA and protein pools permit equilibration before either stimulus is added, while the staged actions later impose IFNβ first and poly(I:C) second. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–30 implement sensing and antiviral effectors; 31–55 form the NF-κB feedback module; 56–60 activate IRF3; 61–70 produce and sense IFNβ; and 71–83 close the STAT-driven interferon-stimulated-gene loop. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–5 | One-way | `PolyIC.loc/Rigi`, `RIGI.Polyic/Mavs`, `MAVS.Rigi` | Imports ligand `ext→cyt`, binds RIG-I, degrades ligand-bound RIG-I while releasing poly(I:C), recruits MAVS, and then removes RIG-I from the ternary complex while releasing both partners. | Creates a renewable ligand-driven RIG-I/MAVS signaling platform. | +| 6–14 | One-way | Cytoplasmic PolyIC; PKR/OAS3/RNaseL/eIF2α states | Poly(I:C) catalytically changes PKR and OAS3 `i→a`; PKR changes eIF2α `0→p`; OAS3 changes RNase L `i→a`; dedicated rules reset all states and add basal eIF2α phosphorylation. | Activates translational arrest and RNA degradation as parallel antiviral outputs. | +| 15–18 | One-way source | Four ISG mRNAs; `STAT12_dimer` | Creates each transcript with a bounded basal-plus-STAT-dimer expression; PKR and RNase L include gene-presence multipliers. | Converts interferon signaling into increased sensor/effector capacity. | +| 19–22 | One-way sink | Four ISG mRNAs; `RNaseL_a` | Removes every transcript at a common base rate multiplied by `(m_Rnasel+RNaseL_a)/m_Rnasel`. | Makes RNase L globally shorten antiviral-transcript lifetime. | +| 23–30 | One-way | Four mRNAs and proteins | Rules 23–26 retain each mRNA while creating inactive protein; 27–30 remove the corresponding protein at the same `sg_*` scale. | Balances replenishment and turnover of the sensing module. | +| 31–33 | One-way | RIG-I/MAVS complex or TNFα; `TAK1.st` | Either upstream signal changes TAK1 `i→a`; rule 33 returns it to inactive. | Merges RNA sensing and inflammatory input upstream of NF-κB. | +| 34–37 | One-way | `IKK.st`; `TAK1_a`, A20 | Neutral IKK activates with a quadratic TAK1-dependent rate, enters `i` with an A20-increased rate, and traverses `i→ii→n`. | Produces a pulse with an explicit refractory recovery cycle. | +| 38–39 | One-way | Unphosphorylated IκBα and NF-κB binding sites at matched location | Forms cytoplasmic or nuclear IκBα–NF-κB complexes with location-specific association rates. | Sequesters NF-κB and permits inhibitor-mediated nuclear export. | +| 40–45 | One-way | Active IKK; free or NF-κB-bound cytoplasmic IκBα | IKK changes IκBα `0→pp`; phosphorylated IκBα is removed, releasing NF-κB if bound; slower rules remove unphosphorylated free or bound inhibitor. | Liberates NF-κB while defining basal and signal-driven inhibitor turnover. | +| 46–48 | One-way or reversible | NF-κB/IκBα location states | Free NF-κB imports to nucleus; bound complex exports to cytoplasm; free unphosphorylated IκBα shuttles both directions. | Couples feedback-protein abundance to nuclear NF-κB residence. | +| 49–55 | One-way | Nuclear free NF-κB, nuclear free IκBα, feedback mRNAs, eIF2α-p, RNaseL-a | NF-κB and IκBα compete in bounded transcription rates for IκBα/A20; RNase L accelerates mRNA loss; eIF2α-p suppresses translation; A20 is also degraded. | Implements inducible negative feedback under antiviral translation/RNA-decay constraints. | +| 56–60 | One-way | RIG-I/MAVS, TBK1 Ser172, IRF3 Ser396, A20 | Sensor complex phosphorylates TBK1; basal and A20-dependent rules dephosphorylate it; active TBK1 phosphorylates IRF3, which is then reset. | Generates the IRF3 input required jointly with NF-κB for interferon transcription. | +| 61–62 | One-way | IFNAR and cytoplasmic or extracellular IFNβ binding sites | Both ligand pools create an occupied receptor, representing autocrine secretion or external stimulation. | Converts endogenous or experimental interferon into the same receptor signal. | +| 63–66 | Reversible source/sink or one-way | IFNAR mRNA and receptor | Creates/degrades mRNA with RNase-L sensitivity, translates receptor with eIF2α inhibition, and removes free or ligand-bound receptor at distinct rates. | Maintains receptor availability while permitting signal-dependent turnover. | +| 67–70 | One-way | `NFkB_nuc_free`, `IRF3_p`, IFNβ mRNA/protein | Joint NF-κB×IRF3 activity saturably creates IFNβ mRNA; transcript produces cytoplasmic IFNβ; separate rules remove both. | Forms the central interferon output requiring both transcription-factor branches. | +| 71–74 | Reversible or one-way | IFNAR occupancy; STAT1 Tyr701, STAT2 Tyr690, dimer sites | Occupied receptor drives saturable phosphorylation; phospho-STAT1/2 bind; the dimer is reset directly to free unphosphorylated monomers. | Creates the transcriptionally active STAT heterodimer and terminates it in one step. | +| 75–78 | One-way source/sink | STAT1/2 mRNAs; `STAT12_dimer`, RNaseL-a | Bounded basal-plus-dimer rates create transcripts, and RNase L accelerates their loss. | Adds positive feedback to the interferon-response capacity. | +| 79–83 | One-way | STAT mRNAs, monomers, and heterodimer | Each mRNA produces unphosphorylated protein; monomers and the dimer are removed at the common `sg_Stat` rate. | Balances STAT amplification with turnover of every binding state. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `RIG_I_total`, `PKR_total`, `OAS3_total`, `RNaseL_total`, `RNaseL_a`, `eIF2a_total`, `eIF2a_p` | Species or molecule count | Sensor/effector abundance plus active RNase L and phospho-eIF2α. | `RNaseL_a` and `eIF2a_p` are regulatory inputs to multiple rate expressions. | +| `RIGI_mRNA`, `PKR_mRNA`, `OAS3_mRNA`, `RNaseL_mRNA` | Species count | Four antiviral transcripts. | Resolve STAT-driven induction against RNase-L-accelerated loss. | +| `TAK1_a`, `IKK_a`, `NFkB_nuc_free`, `NFkB_nuc_total`, `NFkB_total` | Species count | Kinase activity and free/total nuclear or global NF-κB. | `NFkB_nuc_free` is the transcription-driving pool, not all nuclear NF-κB. | +| `IkBa_total`, `IkBa_nuc_total`, `IkBa_cyt_total`, `IkBa_cyt_free`, `IkBa_p_cyt`, `IkBa_nuc_free` | Species count | Explicit sums over inhibitor location, binding, and phosphorylation states. | These multi-pattern sums intentionally combine distinct molecular contexts; `IkBa_nuc_free` enters gene rates. | +| `A20`, `IkBa_mRNA`, `A20_mRNA` | Species count | Feedback protein and transcripts. | Report the two negative-feedback arms downstream of NF-κB. | +| `IRF3_total`, `IRF3_p` | Species count | Total and Ser396-phosphorylated IRF3. | Separate branch capacity from the active interferon-transcription input. | +| `IFNAR_total`, `IFNAR_a`, `IFNb_ext`, `IFNb_cyt`, `IFNAR_mRNA`, `IFNb_mRNA` | Species count | Receptor, occupied receptor, interferon pools, and their transcripts. | Distinguish experimental/extracellular interferon from newly synthesized cytoplasmic ligand. | +| `STAT1_total`, `STAT2_total`, `STAT1_p`, `STAT2_p`, `STAT1_u`, `STAT2_u`, `STAT12_dimer`, `STAT1_mRNA`, `STAT2_mRNA` | Species or molecule count | STAT abundance, phosphorylation, unbound substrate pools, heterodimer, and transcripts. | The mixed observable types should not be treated as interchangeable counts when complexes are present. | + +## 8. Actions and simulation workflow + +The file contains two active workflows: a direct 30-day ODE simulation, followed by a staged protocol that first equilibrates to time 100,000 minus 24 hours, adds extracellular IFNβ for 24 hours, then adds extracellular poly(I:C) and continues for 10 hours. Each perturbation uses continuation, so the second stimulus acts on the interferon-preconditioned state rather than restarting the model. + +## 9. Technical caveats and ambiguities + +- Localization is encoded by states rather than physical compartments, so no volume conversion accompanies nuclear/cytoplasmic or extracellular/cytoplasmic changes unless included explicitly in a rate. +- Several observables use `Species` while others use `Molecules`; complexes therefore affect their numerical interpretation differently. +- Global RNase-L-dependent transcript decay and eIF2α-dependent translation inhibition are broad abstractions applied across multiple gene products. +- The metadata describes this as a validation/test-case model and its description is incomplete; biological scope here is derived from the BNGL comments and constructs. +- Two simulation sequences are active in one file; running all actions produces both the long unperturbed output and the staged stimulation outputs. diff --git a/Published/Korwek2023/Korwek_2023_metadata.yaml b/Published/Korwek2023/Korwek_2023_metadata.yaml new file mode 100644 index 00000000..03f7f35e --- /dev/null +++ b/Published/Korwek2023/Korwek_2023_metadata.yaml @@ -0,0 +1,68 @@ +id: "Korwek_2023" +name: "Korwek_2023" +description: "This BioNetGen file features the article:" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2021" + pmid: "33495441" + reference: "McMillan et al., 2021" + +tags: ["validation", "korwek", "2023", "polyic", "rigi", "mavs", "pkr", "oas3", "rnasel", "eif2a", "rigi_mrna"] +date: + last_tested: 2026-07-19 + +category: "validation" +biol_categories: ["validation"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: false + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 1 at line 45" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: false + comments: "MCP XML file couldn't be generated nfsim Invalid component name in '1,2,3)' (must begin with a letter or underscore) at line 45" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: true + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/Korwek_2023.bngl" + +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" + + + + + + + diff --git a/Published/Korwek2023/metadata.yaml b/Published/Korwek2023/metadata.yaml index d836cd9b..f67bcb39 100644 --- a/Published/Korwek2023/metadata.yaml +++ b/Published/Korwek2023/metadata.yaml @@ -4,6 +4,7 @@ description: "This BioNetGen file features the article:" tags: ["validation", "korwek", "2023", "polyic", "rigi", "mavs", "pkr", "oas3", "rnasel", "eif2a", "rigi_mrna"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Kozer2013/Kozer2013_aigenerated.md b/Published/Kozer2013/Kozer2013_aigenerated.md new file mode 100644 index 00000000..02a13136 --- /dev/null +++ b/Published/Kozer2013/Kozer2013_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Kozer 2013 + +## One-sentence summary + +EGF binding drives higher-order EGFR oligomerization, kinase-tail association, and receptor phosphorylation. + +## What the model shows + +This model connects ligand occupancy to EGFR cluster size and phosphorylation. It distinguishes EGF binding to receptors in different oligomeric contexts, extracellular receptor crosslinking, cytosolic-tail activation, tail-to-tail association, and phosphorylation, allowing receptor clustering and signaling output to be compared directly. + +## Biological story + +EGFR can bind EGF as a monomer or within a crosslinked assembly. Ligand occupancy favors an open cytosolic conformation; open tails associate and phosphorylate receptor tyrosines. Receptor contacts can close within pre-existing assemblies, producing rings and oligomers beyond dimers. + +## Main biological players + +EGF, EGFR ectodomains, EGFR cytosolic kinase/juxtamembrane contacts, and phosphorylated EGFR tyrosines. + +## Mechanism in plain English + +EGF first occupies receptor ectodomains with affinities that depend on neighboring receptor occupancy. Ectodomain contacts join receptors, including closure reactions within larger assemblies. Ligand-bound receptors switch their cytosolic tails into an active conformation, active tails associate, and one tail phosphorylates another. Deactivation and dephosphorylation counter these processes. + +## Key modeled events + +- EGF binds free and crosslinked EGFR with context-dependent affinity. +- EGFR ectodomains form dimers and higher-order closed assemblies. +- Ligand occupancy promotes an active cytosolic-tail conformation and tail association. +- Associated active tails phosphorylate EGFR, while dephosphorylation removes the signal. + +## What the model measures + +Measurements include free EGF, free EGFR, total receptor-cluster density, monomers, dimers, trimers, larger oligomers, and phosphorylated EGFR. + +## Expected behavior in plots + +Increasing EGF should reduce free receptor and redistribute EGFR from monomers toward dimers and larger clusters. Phosphorylated EGFR should track the ligand-supported active-tail population, while cluster-size curves can reveal whether higher-order oligomers become prominent at the chosen dose. + +## Caveats + +The model concentrates on receptor assembly and phosphorylation. It does not follow downstream adaptor pathways, trafficking, degradation, or transcriptional responses. diff --git a/Published/Kozer2013/Kozer_2013_metadata.yaml b/Published/Kozer2013/Kozer_2013_metadata.yaml new file mode 100644 index 00000000..f6f838bc --- /dev/null +++ b/Published/Kozer2013/Kozer_2013_metadata.yaml @@ -0,0 +1,24 @@ +id: "Kozer_2013" +name: "Kozer 2013" +description: "EGFR oligomerization" +tags: ["published", "kozer", "2013", "egf", "egfr"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Kozer_2013.bngl" +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" diff --git a/Published/Kozer2013/metadata.yaml b/Published/Kozer2013/metadata.yaml index b9044604..06746711 100644 --- a/Published/Kozer2013/metadata.yaml +++ b/Published/Kozer2013/metadata.yaml @@ -4,6 +4,7 @@ description: "EGFR oligomerization" tags: ["published", "kozer", "2013", "egf", "egfr"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Kozer2014/Kozer2014_aigenerated.md b/Published/Kozer2014/Kozer2014_aigenerated.md new file mode 100644 index 00000000..043048b5 --- /dev/null +++ b/Published/Kozer2014/Kozer2014_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Kozer 2014 + +## One-sentence summary + +EGFR oligomerization and phosphorylation create cluster-dependent docking opportunities for the adaptor Grb2. + +## What the model shows + +This extension of an EGFR oligomerization model links receptor cluster architecture to Grb2 recruitment. It retains ligand-sensitive ectodomain and cytosolic-tail interactions, then adds reversible binding of Grb2 to phosphorylated EGFR so adaptor occupancy can be compared across monomers, distinct dimers, and larger receptor assemblies. + +## Biological story + +EGF promotes receptor crosslinking and active tail associations, which generate phosphorylated EGFR. Grb2 recognizes those phosphorylated receptors, and the number and arrangement of modified receptors determine whether a cluster recruits one or several adaptor molecules. + +## Main biological players + +EGF, EGFR, phosphorylated EGFR tails, and the SH2 adaptor Grb2. + +## Mechanism in plain English + +Ligand occupancy changes EGFR assembly and tail conformation. Active paired tails phosphorylate receptor tyrosines, creating binding sites for Grb2. Grb2 associates reversibly with those sites without itself driving phosphorylation. Because receptors can form several oligomeric arrangements, the model resolves adaptor recruitment to different dimer states as well as the overall clustered population. + +## Key modeled events + +- EGF binding and ectodomain contacts build EGFR dimers and higher-order oligomers. +- Active cytosolic tails associate and phosphorylate receptor tyrosines. +- Grb2 binds phosphorylated EGFR and dissociates reversibly. +- Distinct readouts separate Grb2 recruitment to monomeric and differently configured dimeric receptors. + +## What the model measures + +The model tracks free ligand and receptor, receptor cluster sizes, phosphorylated EGFR, free Grb2, total Grb2-bound receptor, and several Grb2–EGFR dimer configurations. + +## Expected behavior in plots + +As EGF increases, receptor clustering and phosphorylation should create more Grb2 docking sites, lowering free Grb2 while increasing Grb2-bound EGFR. Individual dimer readouts may differ because ligand occupancy and tail associations make some receptor arrangements more phosphorylation-competent than others. + +## Caveats + +The model ends at adaptor recruitment: it does not include SOS, Ras, ERK, receptor internalization, or Grb2-driven downstream signaling. diff --git a/Published/Kozer2014/Kozer2014_aigenerated_detailed.md b/Published/Kozer2014/Kozer2014_aigenerated_detailed.md new file mode 100644 index 00000000..2f2ecb46 --- /dev/null +++ b/Published/Kozer2014/Kozer2014_aigenerated_detailed.md @@ -0,0 +1,76 @@ +# Detailed Model Explanation: Kozer 2014 EGFR tetramer and Grb2 recruitment model + +## 1. Model overview + +This model links EGF occupancy to EGFR ectodomain crosslinking, opening and association of cytosolic tails, receptor phosphorylation, and Grb2 recruitment. It explicitly represents alternative ligand states and ring-closing steps within four-receptor assemblies so tetramer topology changes the effective association rate. + +## 2. BNGL block inventory + +The file contains 36 parameters, 3 molecule types, 3 free seed species, 16 rules, 15 observables, and 2 actions. It has no enclosing model block, compartments, anchors, or functions; network generation caps EGF and EGFR stoichiometry at four. + +## 3. Parameters, functions, and rate laws + +Concentration and cell-volume parameters convert experimental pool sizes and bimolecular rates into molecular units. Binding rates are separated by ligand/oligomer context, while `chi_r` boosts only ring-closing events whose partners are already held in one assembly. + +| Parameter group or names | Function in this model | +| --- | --- | +| `NA`, `f`, `V`, `cellDen`, `Vo`; `LT`, `RT`, `GT` | Unit/volume conversion and initial EGF, EGFR, and Grb2 pools. | +| `K11`, `k11f`, `k11r` | EGF binding to EGFR not ectodomain-crosslinked to another receptor. | +| `K21`, `k21f`, `k21r`; `K22`, `k22f`, `k22r` | First and second EGF-binding events on an ectodomain-linked receptor pair; the second ligand has a distinct, weaker context. | +| `L20`, `l20f`, `l20r`; `L21`, `l21f`, `l21r`; `L22`, `l22f`, `l22r` | Ectodomain crosslinking for zero, one, or two EGF-occupied receptors, respectively. | +| `k_o`, `k_c` | Ligand-dependent cytosolic-tail opening and ligand-independent closing. | +| `kaf`, `kar` | Association/dissociation of two open EGFR cytosolic tails. | +| `chi_r` | Effective-concentration multiplier for closing an ectodomain or tail edge inside a preassembled four-receptor topology. | +| `kp`, `kdp` | EGFR phosphorylation across a tail pair and global dephosphorylation. | +| `KDg`, `kmg`; derived `kpg` | Grb2–phospho-EGFR affinity, dissociation, and volume-scaled association. | + +There are no functions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `EGF` | 1 | `rec` | None | None | Ligand whose receptor-facing site occupies EGFR `lig`. | +| `EGFR` | 4 | `back`, `lig`, `cd`, `Y` | `cd: c, o`; `Y: u, p` | None | Receptor combining ectodomain crosslinking (`back`), ligand binding, tail conformation/association (`cd`), and a phosphorylatable Grb2 docking site (`Y`). | +| `Grb2` | 1 | `SH2` | None | None | Adaptor recruited specifically to phosphorylated EGFR `Y~p`. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial and starts with free EGF, closed unphosphorylated EGFR, and free Grb2. Pool expressions correspond to the modeled fraction of a cell and its surrounding fluid; no receptor dimers, tetramers, phospho-EGFR, or Grb2 complexes are seeded. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–9 couple EGF occupancy to ectodomain edges, including closure inside tetramers. Rules 10–13 open and connect cytosolic tails, and rules 14–16 turn tail association into phosphorylation and Grb2 loading. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–3 | Reversible | EGF `rec` and EGFR `lig`; rule 1 uses non-crosslinked EGFR, rule 2 the first ligand on an unliganded `back` dimer, rule 3 the second ligand | Creates/releases `rec–lig` using `k11f/k11r`, `k21f/k21r`, or `k22f/k22r`, respectively. | Makes ligand affinity depend on ectodomain assembly and prior occupancy rather than treating all sites identically. | +| 4–6 | Reversible | Two EGFR `back` sites with zero, one, or two bound EGF molecules, respectively | Creates/releases the ectodomain `back–back` edge using the matching `l20`, `l21`, or `l22` forward/reverse pair. | Produces the three ligand-defined ectodomain dimer classes from freely encountering receptors. | +| 7–9 | Reversible | Two still-free `back` sites inside a four-EGFR assembly already tethered by tail and ectodomain edges; zero, one, or two target receptors are liganded | Closes/opens the remaining ectodomain edge with `chi_r*l20f`, `chi_r*l21f`, or `chi_r*l22f`; reverse rates are unchanged. | Converts open four-receptor chains into rings and represents their high intracomplex encounter probability. | +| 10–11 | One-way | EGFR `cd`; rule 10 additionally requires bound ligand | Rule 10 changes `cd: c → o` at `k_o`; rule 11 changes any `o → c` at `k_c`. | Couples ligand to tail exposure while allowing spontaneous closure to oppose activation. | +| 12–13 | Reversible | Two open EGFR `cd` sites; rule 13 places the free pair inside a four-receptor assembly | Creates/releases a `cd–cd` tail edge at `kaf/kar`; intratetramer closure multiplies only the forward rate by `chi_r`. | Builds tail dimers in free encounters or closes the second tail edge within a tetramer. | +| 14 | One-way | Two EGFR molecules joined through open tails; one receptor has `Y~u` | Changes that receptor `Y: u → p` at `kp`, preserving the tail bond. | Implements transphosphorylation only in the associated-tail context. | +| 15 | One-way | Any EGFR `Y~p` | Changes `Y: p → u` at `kdp`, without requiring oligomer dissociation. | Erases the adaptor docking state throughout the receptor population. | +| 16 | Reversible | EGFR `Y~p` and Grb2 `SH2` | Creates/releases the phosphotyrosine–SH2 bond at `kpg/kmg`. | Converts receptor phosphorylation into measurable Grb2 recruitment. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `EGFfree`, `EGFRfree`, `Grb2Free` | Molecule count | Free ligand site, free receptor ligand site, or free Grb2 SH2 site | Unoccupied pools; `EGFRfree` concerns ligand occupancy, not whether the receptor is oligomerized. | +| `Clusters`; `monomer`, `dimer`, `trimer`, `tetramer` | Species count | EGFR-containing species grouped by receptor count | Assembly-size distribution. `Clusters` combines sizes 1–4, while `tetramer` uses a greater-than-three cardinality condition. | +| `pEGFR` | Molecule count | EGFR with phosphorylated `Y`, whether free or Grb2-bound | Total receptor phosphorylation output. | +| `Grb2_pEGFR` | Molecule count | Explicit phospho-EGFR–Grb2 bond | Total recruited adaptor, independent of receptor oligomer size. | +| `Grb2EGFRMonomer` | Species count | Grb2-bound phospho-EGFR with free `back` and `cd` | Recruited adaptor on a receptor not crosslinked through either receptor–receptor interface. | +| `Grb2EGFRDimer1`–`4` | Species count | Back-linked or tail-linked EGFR dimers carrying one or two Grb2 molecules | Resolves adaptor occupancy and whether the dimer is joined through ectodomain (`1`, `3`) or open tails (`2`, `4`). | + +## 8. Actions and simulation workflow + +The file generates a network capped at four EGF and four EGFR molecules per species, preventing assemblies larger than the modeled tetramer. It then runs an ODE simulation to time 120 with 100 output steps. + +## 9. Technical caveats and ambiguities + +- Ring-closure rules match a specific four-receptor topology; `chi_r` is not a general multiplier for all oligomerization. +- `Clusters` lists several cardinality patterns compactly, and `EGFR>3` support may depend on parser version. +- Species-pattern observables may count embeddings rather than unique physical assemblies. +- The model has no explicit membrane or cytosolic compartments despite describing ectodomain and tail processes. diff --git a/Published/Kozer2014/Kozer_2014_metadata.yaml b/Published/Kozer2014/Kozer_2014_metadata.yaml new file mode 100644 index 00000000..e15f3d81 --- /dev/null +++ b/Published/Kozer2014/Kozer_2014_metadata.yaml @@ -0,0 +1,66 @@ +id: "Kozer_2014" +name: "Kozer 2014" +description: "Grb2-EGFR recruitment" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2014" + pmid: "24697349" + reference: "Kozer et al., 2014" + +tags: ["published", "kozer", "2014", "egf", "egfr", "grb2"] +date: + last_tested: 2026-07-16 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered = at line 17" + simulation_methods: + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim runs on bng2 but not bngp MCP could not convert string to float: '(3.0*NA)*Vo (after removing generate network)" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Kozer_2014.bngl" + +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" + + + + diff --git a/Published/Kozer2014/metadata.yaml b/Published/Kozer2014/metadata.yaml index aaca3fe5..8b61e07b 100644 --- a/Published/Kozer2014/metadata.yaml +++ b/Published/Kozer2014/metadata.yaml @@ -4,6 +4,7 @@ description: "Grb2-EGFR recruitment" tags: ["published", "kozer", "2014", "egf", "egfr", "grb2"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Lang2024/Lang2024_aigenerated.md b/Published/Lang2024/Lang2024_aigenerated.md new file mode 100644 index 00000000..85d3da02 --- /dev/null +++ b/Published/Lang2024/Lang2024_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Lang 2024 + +## One-sentence summary + +An E2F–RB1 transcriptional switch coordinates cyclin accumulation, mitotic regulators, and cell-cycle progression. + +## What the model shows + +This model connects the retinoblastoma protein RB1 and E2F transcription factors to cyclins, anaphase-promoting complex regulation, and mitotic entry. Abbreviations are expanded as they appear: APC/C is the anaphase-promoting complex/cyclosome, and PP2A is protein phosphatase 2A. + +## Biological story + +Cyclin D activity releases E2F from RB1 restraint. E2F induces cyclins E and A plus later regulators, while cyclin-dependent kinase inhibitor p21 restrains cyclin activity. Greatwall kinase and ENSA/ARPP19 inhibit PP2A, helping mitotic phosphorylation persist. + +## Main biological players + +E2F, RB1, cyclins D/E/A/B, p21, FOXM1, APC/C, CDC20, FZR1, FBXO5, WEE1, Greatwall/MASTL, ENSA/ARPP19, and PP2A-B55. + +## Mechanism in plain English + +RB1 binding suppresses E2F. Cyclin-dependent phosphorylation weakens RB1, allowing E2F-driven transcription to amplify cyclins and mitotic regulators. FOXM1 supports cyclin B and CDC20 expression. FBXO5 and FZR1 tune APC/C activity, while Greatwall-mediated inhibition of PP2A-B55 protects mitotic phosphates. Negative regulators prevent premature progression. + +## Key modeled events + +- Cyclin activity phosphorylates RB1 and releases E2F. +- E2F induces cyclins E/A and regulators needed later in the cycle. +- FOXM1 promotes cyclin B and CDC20 expression. +- Greatwall–ENSA/ARPP19 inhibits PP2A-B55 to sustain mitotic phosphorylation. +- APC/C regulators control exit-associated protein turnover. + +## What the model measures + +Primary readouts are total cyclins E, A, and B and the inhibitor p21, with internal quantities representing E2F, APC/C, phosphatase, and kinase states. + +## Expected behavior in plots + +Cyclin E should rise near E2F activation, followed by cyclin A and then cyclin B as the program advances. p21 can delay or flatten those waves. A successful mitotic transition should coincide with high cyclin B and suppressed PP2A-B55 activity. + +## Caveats + +The model is a regulatory synthesis of cell-cycle modules rather than a spatially resolved cell. Exact phase durations depend on its parameterization and starting state. diff --git a/Published/Lang2024/Lang_2024_metadata.yaml b/Published/Lang2024/Lang_2024_metadata.yaml new file mode 100644 index 00000000..aa33e7c0 --- /dev/null +++ b/Published/Lang2024/Lang_2024_metadata.yaml @@ -0,0 +1,24 @@ +id: "Lang_2024" +name: "Lang 2024" +description: "Cell cycle regulation" +tags: ["published", "lang", "2024", "e2f", "rb1", "ppp2r2b", "ccnb_promoter", "ccna", "ccna_promoter", "foxm1_promoter", "ensa_arpp19"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/growth-factor-signaling/Lang_2024.bngl" +playground: + visible: true + gallery_categories: ["cell-cycle"] + featured: false + difficulty: "intermediate" diff --git a/Published/Lang2024/metadata.yaml b/Published/Lang2024/metadata.yaml index fde4a072..7650f9c1 100644 --- a/Published/Lang2024/metadata.yaml +++ b/Published/Lang2024/metadata.yaml @@ -4,6 +4,7 @@ description: "Cell cycle regulation" tags: ["published", "lang", "2024", "e2f", "rb1", "ppp2r2b", "ccnb_promoter", "ccna", "ccna_promoter", "foxm1_promoter", "ensa_arpp19"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Published/Ligon2014/Ligon2014_aigenerated.md b/Published/Ligon2014/Ligon2014_aigenerated.md new file mode 100644 index 00000000..e6e1b4d7 --- /dev/null +++ b/Published/Ligon2014/Ligon2014_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Ligon 2014 + +## One-sentence summary + +Clathrin-pit loading and endosomal escape connect extracellular lipoplex uptake to mRNA release and GFP expression. + +## What the model shows + +This delivery model follows lipoplexes from an extracellular pool through progressive loading of a clathrin-coated pit, conversion to an endosomal state, release of internal cargo, mRNA production, and GFP expression. It is designed to connect uptake bottlenecks with a delayed reporter output. + +## Biological story + +External lipoplexes can be washed away or attach sequentially to a pit with finite capacity. A loaded pit becomes an endosome, internal lipoplex cargo escapes, and successful delivery yields mRNA that produces GFP before both cargo and products are cleared. + +## Main biological players + +External and internal lipoplex, clathrin-coated pit/endosome, delivered mRNA, GFP, a degradation sink, and a timer/input variable. + +## Mechanism in plain English + +Lipoplexes accumulate one by one on a pit until uptake converts that assembly into an endosome. Internalized particles are released from the carrier and can generate mRNA; mRNA then drives GFP production. Washing and degradation compete with delivery, while finite pit capacity makes the number of attached particles an explicit uptake constraint. + +## Key modeled events + +- Extracellular lipoplex is removed by washing or captured by a clathrin-coated pit. +- Successive particles load a pit up to a finite capacity before endosomal conversion. +- Internal lipoplex escapes from the endosome and produces an mRNA population. +- mRNA is translated into GFP, while delivery intermediates and products are cleared. + +## What the model measures + +Readouts follow extracellular lipoplex, pits, endosomes, internal lipoplex, mRNA, GFP, and elapsed timer counts. + +## Expected behavior in plots + +Pit occupancy should rise before endosomes and internal cargo appear. mRNA should lag behind uptake, and GFP should lag behind mRNA and persist according to its production and loss rates. Strong washing should suppress the early extracellular pool and reduce all later delivery readouts. + +## Caveats + +The delivery stages are deliberately coarse population steps. Membrane fusion, endosomal maturation, individual nucleic-acid molecules, and cell-to-cell variability are not mechanistically resolved. diff --git a/Published/Ligon2014/Ligon2014_aigenerated_detailed.md b/Published/Ligon2014/Ligon2014_aigenerated_detailed.md new file mode 100644 index 00000000..268057d7 --- /dev/null +++ b/Published/Ligon2014/Ligon2014_aigenerated_detailed.md @@ -0,0 +1,82 @@ +# Detailed Model Explanation: Ligon 2014 Lipoplex Delivery + +## 1. Model overview + +This model follows extracellular lipoplexes as they load sequentially into pits, enter an endosomal state, release internal cargo, and produce green fluorescent protein (GFP). It combines a distribution of lipoplex cargo sizes with an explicit uptake-capacity mechanism, but implements only a deliberately limited subset of the possible multi-particle release and unpacking reactions. + +## 2. BNGL block inventory + +The model contains 11 parameters, 8 molecule types (including four population types), 16 seed species, 1 function, 33 active reaction rules, 7 molecule-count observables, and 1 network-free simulation action. It has no compartments or anchors; extracellular, pit, endosomal, and internal status are represented by molecule identity or internal state. + +## 3. Parameters, functions, and rate laws + +Rates are named by process and are converted from per-second source values to per-hour values where the factor `3600` appears. Rules otherwise use mass-action rates, except for the time-dependent wash function. + +| Parameter group or names | Function in this model | +| --- | --- | +| `kA`, `kE` | Control successive lipoplex capture by a pit and conversion of a loaded pit to an endosome, respectively. | +| `kL`, `kU` | Set endosomal lysis/cargo release and conversion of selected internal lipoplexes into messenger RNA (mRNA). | +| `kTL` | Controls catalytic GFP production by mRNA; the mRNA is retained during translation. | +| `dE`, `dL` | Remove empty endosomes and internal lipoplexes. | +| `dM`, `dG` | Set turnover of the mRNA and fluorescent reporter pools. | +| `kFast`, `dW` | Declared but unused by active rules; washing is instead governed by `wash`. | + +| Function | Inputs/dependencies | Meaning and use in this model | +| --- | --- | --- | +| `wash` | `TimerCount` | Returns zero until the timer exceeds 3,600 counts, then returns an extremely large removal rate. Rule 1 uses this as an abrupt delayed wash of extracellular lipoplex. | + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `Lext` | 2 | `p`, `n` | `n`: 345–355 | None | An extracellular lipoplex; `p` binds a pit slot and `n` records its cargo-size class. | +| `Pit` | 11 | `s`; `l1`–`l10` | `s`: pit (`p`) or endosome (`e`) | None | A ten-slot uptake carrier whose state distinguishes surface capture from internalized cargo. | +| `Lint` | 1 | `n` | `n`: 345–355 | None | Released intracellular lipoplex, retaining the cargo-size class of its extracellular precursor. | +| `mRNA`, `GFP` | 0 each | None | Population types | None | Coarse-grained cargo transcript and translated fluorescent output. | +| `I`, `Timer` | 0 each | None | Population types | None | `I` is a persistent clock catalyst; `Timer` accumulates one unit at a time and triggers washing. | +| `Trash` | 0 | None | None | None | Sink receiving washed or degraded material. | + +## 5. Compartments, anchors, initial species, and setup + +There are no explicit compartments or anchors. The extracellular input is distributed over cargo classes 345–355 with a peaked abundance centered near 350, while one empty pit starts in the surface-pit state. The internal lipoplex, mRNA, GFP, and timer pools start at zero; a single `I` population particle drives timer accumulation. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–8 govern exposure and pit loading, rules 9–14 internalize or clear pits, rules 15–27 release and remove internal cargo, and rules 28–33 turn a small implemented subset of that cargo into the fluorescent readout. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | One-way | `Lext`; timer-dependent `wash` | Sends any extracellular lipoplex to `Trash` at the conditional wash rate. | Terminates further uptake after the modeled exposure period. | +| 2–8 | One-way | `Lext.p`; `Pit.l1`–`l7` in state `s=p` | Adds one lipoplex to the next free pit slot at `kA`; rules 2–8 fill `l1` through `l7`, respectively. Rule 2 also produces an additional empty pit. | Builds pit occupancy stepwise while preserving the cargo class of every captured lipoplex. | +| 9–13 | One-way | Loaded `Pit` with `l1` through `l1`–`l5` occupied | Changes `Pit.s` from `p` to `e` at `kE` for occupancy levels one through five; `DeleteMolecules` applies to unmatched context. | Internalizes explicitly represented low-occupancy pits as endosomes. | +| 14 | One-way | Empty `Pit` with `s=e` | Removes an unoccupied endosome to `Trash` at `dE`. | Clears endosomal carriers that contain no lipoplex. | +| 15–25 | One-way | One `Lext` bound at `Pit.l1`; cargo state 345–355 | Consumes the one-particle endosome and creates the matching `Lint.n` class at `kL`; rules 15–25 map states 345–355, respectively. | Represents endosomal escape while retaining cargo-size identity. | +| 26 | One-way | Two `Lext` particles of class 345 at `Pit.l1,l2` | Consumes the two-particle endosome and releases two class-345 internal lipoplexes at `kL`. | Supplies the sole implemented example of multi-particle endosomal lysis. | +| 27 | One-way | `Lint` | Sends any internal lipoplex class to `Trash` at `dL`. | Competes with productive unpacking and limits intracellular cargo persistence. | +| 28–29 | One-way | `Lint.n=345` or `346` | Consumes one selected internal lipoplex and creates five mRNA population units at `kU`. | Implements productive unpacking only for two cargo classes, with a five-transcript yield rather than the numeric state value. | +| 30 | One-way | `mRNA` | Removes mRNA to `Trash` at `dM`. | Limits the duration of reporter production. | +| 31 | One-way | `mRNA`, `GFP` | Retains mRNA while adding one GFP unit at `kTL`. | Converts delivered cargo into the measured fluorescent signal. | +| 32 | One-way | `GFP` | Removes GFP to `Trash` at `dG`. | Gives the reporter a finite lifetime. | +| 33 | One-way | `I`, `Timer` | Retains `I` and creates Timer at unit rate. | Provides the internal clock used by the delayed wash function. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `Lext` | Molecule count | Extracellular lipoplex molecules across cargo classes and binding states. | Reports material remaining outside or associated with pits before internal conversion. | +| `Pit`, `Endo` | Molecule count | `Pit` molecules in surface (`p`) and endosomal (`e`) states. | Separates capture carriers from internalized carriers, independent of their occupancy. | +| `Lint` | Molecule count | All released internal lipoplex classes. | Measures cargo that escaped an endosome but has not unpacked or degraded. | +| `mRNA`, `GFP` | Molecule count | Population units of transcript and fluorescent protein. | These are the productive-delivery intermediate and final reporter, not explicit molecular complexes. | +| `TimerCount` | Molecule count | Accumulated Timer population. | Directly controls when `wash` switches on. | + +## 8. Actions and simulation workflow + +The model runs a 30-hour network-free simulation with 300 output intervals. Network-free simulation avoids enumerating the pit-loading combinatorics, while the timer generated during the same run switches on extracellular clearance after 3,600 timer units. + +## 9. Technical caveats and ambiguities + +- Pit loading is active only through seven of ten slots, and endocytosis is active only for one-to-five-particle pits; the higher-occupancy variants are absent or commented out. +- Complete lysis would require cargo-class combinations for every occupancy. Only all one-particle classes and one two-particle class are active. +- Productive unpacking exists only for cargo states 345 and 346, and both yield five mRNA units; the declared numeric cargo state should therefore not be read as the implemented transcript yield. +- Rule 2 creates a second empty pit as well as the loaded pit, so the pit pool can expand during first capture. +- The metadata and README disagree about BNG2 compatibility; the active workflow is explicitly network-free. diff --git a/Published/Ligon2014/Ligon_2014_metadata.yaml b/Published/Ligon2014/Ligon_2014_metadata.yaml new file mode 100644 index 00000000..6b2dd38e --- /dev/null +++ b/Published/Ligon2014/Ligon_2014_metadata.yaml @@ -0,0 +1,66 @@ +id: "Ligon_2014" +name: "Ligon 2014" +description: "Lipoplex delivery" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2014" + pmid: "25237886" + reference: "Ligon et al., 2014" + +tags: ["published", "nfsim", "ligon", "2014", "lext", "pit", "lint"] +date: + last_tested: 2026-07-16 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered population at line 22" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: true + comments: "Bareword nf not allowed while strict subs in use at (eval 60) line 1 at line 133 MCP There was an issue parsing BNGL file Ligon_2014.bnglFailed to parse action simulate_nf({suffix=>nf,t_end=>30*3600,n_steps=>300});" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/growth-factor-signaling/Ligon_2014.bngl" + +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" + + + + diff --git a/Published/Ligon2014/metadata.yaml b/Published/Ligon2014/metadata.yaml index 198fe7aa..b01858f5 100644 --- a/Published/Ligon2014/metadata.yaml +++ b/Published/Ligon2014/metadata.yaml @@ -4,6 +4,7 @@ description: "Lipoplex delivery" tags: ["published", "nfsim", "ligon", "2014", "lext", "pit", "lint"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/Lin2019/Lin2019_aigenerated.md b/Published/Lin2019/Lin2019_aigenerated.md new file mode 100644 index 00000000..d80bbc33 --- /dev/null +++ b/Published/Lin2019/Lin2019_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Lin 2019 ERK model + +## One-sentence summary + +EGF receptor activation propagates through SOS, RAS, RAF, MEK, and ERK with feedback-sensitive signaling dynamics. + +## What the model shows + +This model follows the epidermal growth factor (EGF) receptor to extracellular signal-regulated kinase (ERK) and was used to compare stochastic scaling methods. SOS is Son of Sevenless, a RAS nucleotide-exchange factor. + +## Biological story + +Activated EGFR recruits SOS, which converts RAS from GDP- to GTP-bound form. RAS activates RAF, RAF activates MEK, and MEK activates ERK. GAP proteins and phosphatases reset the cascade, while feedback changes SOS activity. + +## Main biological players + +EGF, EGFR, SOS, RAS, RAS-GAP, RAF, MEK, ERK, and pathway phosphatases. + +## Mechanism in plain English + +Ligand activates EGFR and creates an SOS docking platform. SOS promotes guanosine triphosphate (GTP) loading of RAS; RAS-GTP recruits the RAF kinase, which passes activity through MEK to ERK. GTPase-activating protein (GAP) accelerates RAS shutoff, and phosphatases reverse kinase phosphorylation. + +## Key modeled events + +- EGF activates EGFR and recruits SOS. +- SOS loads RAS with GTP, while RAS-GAP promotes inactivation. +- RAS activates RAF, followed by MEK and ERK phosphorylation. +- Phosphatases and feedback restrain cascade duration. + +## What the model measures + +Representative readouts include inactive ERK, RAS-GTP bound to RAS-GAP, EGFR–SOS complexes, and EGFR–SOS complexes carrying active RAS. + +## Expected behavior in plots + +Receptor–SOS complexes should form before RAS-GTP and downstream ERK activation. GAP-bound RAS should follow RAS activation, while phosphatases should eventually restore inactive ERK; feedback can make the response transient rather than sustained. + +## Caveats + +This summary describes the mechanistic ERK variant selected from a three-model collection. The model was also designed for simulation-scaling studies, not solely biological calibration. diff --git a/Published/Lin2019/metadata.yaml b/Published/Lin2019/metadata.yaml index 7e47ccfc..e84ad35e 100644 --- a/Published/Lin2019/metadata.yaml +++ b/Published/Lin2019/metadata.yaml @@ -4,6 +4,8 @@ description: filename: ERK_model.bngl tags: ["egf", "erkpp_sos1_fb", "erkpp_mek_fb", "erkpp_raf1_fb", "lambda", "egfr_tot", "ras_tot", "sos_tot", "rasgap_tot", "raf_tot", "mek_tot", "erk_tot", "ekar3_tot", "erktr_tot", "a1", "d1", "b1", "u1a", "u1b", "b2a", "u2a", "b2b", "u2b", "k2a", "k2b", "b3", "u3", "k3", "a2", "d2", "p1", "q1", "p2", "q2", "p3", "q3", "p4", "q4", "q5", "p6", "q6", "a0_ekar3", "d0_ekar3", "a0_erktr", "d0_erktr", "species"] category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode", "ssa"] diff --git a/Published/LinERK2019/Lin_ERK_2019_metadata.yaml b/Published/LinERK2019/Lin_ERK_2019_metadata.yaml new file mode 100644 index 00000000..929041b1 --- /dev/null +++ b/Published/LinERK2019/Lin_ERK_2019_metadata.yaml @@ -0,0 +1,24 @@ +id: "Lin_ERK_2019" +name: "Lin 2019" +description: "ERK signaling" +tags: ["published", "literature", "signaling", "lin", "erk", "2019", "egfr", "sos", "ras", "rasgap", "raf", "mek", "ekar3"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/literature/Lin_ERK_2019.bngl" +playground: + visible: true + gallery_categories: ["developmental"] + featured: false + difficulty: "intermediate" diff --git a/Published/LinERK2019/metadata.yaml b/Published/LinERK2019/metadata.yaml index 8c2ee395..c41588af 100644 --- a/Published/LinERK2019/metadata.yaml +++ b/Published/LinERK2019/metadata.yaml @@ -4,6 +4,7 @@ description: "ERK signaling" tags: ["published", "literature", "signaling", "lin", "erk", "2019", "egfr", "sos", "ras", "rasgap", "raf", "mek", "ekar3"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Published/LinPrion2019/LinPrion2019_aigenerated.md b/Published/LinPrion2019/LinPrion2019_aigenerated.md new file mode 100644 index 00000000..67313c4c --- /dev/null +++ b/Published/LinPrion2019/LinPrion2019_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Lin Prion 2019 + +## One-sentence summary + +Prion replication emerges from conversion-dependent polymer growth, fragmentation, synthesis, and clearance of PrP conformers. + +## What the model shows + +This nucleated-polymerization model follows normal cellular PrP and misfolded PrPSc polymers over days. It captures how chain elongation and breakage can amplify replication-competent ends while synthesis, degradation, clearance, and conformational reversion oppose accumulation. + +## Biological story + +Normal PrP is continually supplied and removed. Misfolded chains recruit normal protein at their ends, converting it into the PrPSc state; chains also break, increasing the number of growth-capable fragments. Slow clearance removes entire PrPSc-containing chains, and short misfolded units can revert to the normal conformation. + +## Main biological players + +Cellular PrP, misfolded PrPSc, polymer ends, short and long PrPSc chains, and synthesis/clearance processes. + +## Mechanism in plain English + +New PrP enters the normal pool. A normal molecule attaches to a misfolded chain and adopts the misfolded conformation, extending the polymer. Fragmentation splits chains and creates more ends, accelerating subsequent recruitment. Whole-chain clearance and normal-protein degradation remove material, while conformational reversion provides an additional loss route for short misfolded assemblies. + +## Key modeled events + +- Normal PrP is synthesized and degraded continuously. +- PrPSc chains recruit normal PrP and convert it during elongation. +- Polymer breakage generates additional fragments and growth-capable ends. +- Slow chain clearance and conformational reversion oppose PrPSc accumulation. + +## What the model measures + +Readouts distinguish free normal PrP and representative PrPSc polymers containing 3, 15, or 30 molecules, providing snapshots of the chain-length distribution. + +## Expected behavior in plots + +Normal PrP may initially approach a supply–loss balance while small PrPSc chains seed growth. If elongation and fragmentation dominate clearance, short-chain abundance should rise first and longer 15- and 30-unit chains should appear later; stronger clearance should blunt or delay that progression. + +## Caveats + +Polymer lengths are truncated for tractability, and only selected chain sizes are reported. The model addresses replication kinetics rather than neuronal toxicity, tissue spread, or detailed prion structure. diff --git a/Published/LinPrion2019/Lin_Prion_2019_metadata.yaml b/Published/LinPrion2019/Lin_Prion_2019_metadata.yaml new file mode 100644 index 00000000..07052ac2 --- /dev/null +++ b/Published/LinPrion2019/Lin_Prion_2019_metadata.yaml @@ -0,0 +1,24 @@ +id: "Lin_Prion_2019" +name: "Lin 2019" +description: "Prion replication" +tags: ["published", "literature", "prion", "lin", "2019", "prp", "scaledupspecies1", "scaledupspecies2", "scaledupspecies15", "scaledupspecies30"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/literature/Lin_Prion_2019.bngl" +playground: + visible: false + gallery_categories: ["neuroscience"] + featured: false + difficulty: "advanced" diff --git a/Published/LinPrion2019/metadata.yaml b/Published/LinPrion2019/metadata.yaml index ad5b740c..351f6c3a 100644 --- a/Published/LinPrion2019/metadata.yaml +++ b/Published/LinPrion2019/metadata.yaml @@ -4,6 +4,7 @@ description: "Prion replication" tags: ["published", "literature", "prion", "lin", "2019", "prp", "scaledupspecies1", "scaledupspecies2", "scaledupspecies15", "scaledupspecies30"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Published/LinTCR2019/LinTCR2019_aigenerated.md b/Published/LinTCR2019/LinTCR2019_aigenerated.md new file mode 100644 index 00000000..8f992fc5 --- /dev/null +++ b/Published/LinTCR2019/LinTCR2019_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Lin TCR 2019 + +## One-sentence summary + +pMHC-triggered T-cell receptor signaling balances Lck/ZAP activation, a MEK–ERK cascade, and inhibitory SHP feedback. + +## What the model shows + +This model links ligand binding at the T-cell receptor to kinase recruitment, receptor phosphorylation, ZAP activation, and downstream MEK–ERK signaling. An SHP-dependent inhibitory branch competes with productive signaling, allowing transient activation and negative regulation to emerge from the same receptor complex. + +## Biological story + +pMHC engages TCR and recruits Lck. Lck phosphorylates the receptor and ZAP, ZAP activates MEK, and MEK activates ERK. Lck can also activate SHP, which returns to receptor complexes and disrupts productive phosphorylation; ligand dissociation resets receptor-associated states. + +## Main biological players + +pMHC, TCR, Lck, ZAP, MEK, ERK, SHP, and phosphorylated receptor complexes. + +## Mechanism in plain English + +Ligand-bound TCR captures Lck and becomes phosphorylated. ZAP associates with and is activated near the receptor, then transfers the signal to MEK and ERK. In parallel, SHP becomes phosphorylated and can bind receptor complexes, where it promotes inhibitory resetting. Dephosphorylation and pMHC dissociation remove kinase activity and separate the complex. + +## Key modeled events + +- pMHC binds TCR and enables recruitment of Lck. +- Lck phosphorylates TCR and ZAP to launch the kinase cascade. +- Activated ZAP phosphorylates MEK, which in turn phosphorylates ERK. +- Activated SHP returns to receptor complexes and opposes productive signaling. + +## What the model measures + +The reported quantities emphasize unphosphorylated and phosphorylated MEK, with additional model functions summarizing scaled populations used to compare simulation strategies. + +## Expected behavior in plots + +After receptor engagement, phosphorylated MEK should rise only after Lck and ZAP activation. SHP feedback and ligand dissociation should limit that rise, producing either a peak or a restrained plateau rather than unchecked activation; unphosphorylated MEK should change in the opposite direction. + +## Caveats + +This is a compact signaling-and-feedback model used partly to study stochastic scaling. It does not represent the full T-cell activation program, calcium signaling, transcription, or cell fate. diff --git a/Published/LinTCR2019/Lin_TCR_2019_metadata.yaml b/Published/LinTCR2019/Lin_TCR_2019_metadata.yaml new file mode 100644 index 00000000..8373112d --- /dev/null +++ b/Published/LinTCR2019/Lin_TCR_2019_metadata.yaml @@ -0,0 +1,24 @@ +id: "Lin_TCR_2019" +name: "Lin 2019" +description: "TCR signaling" +tags: ["published", "literature", "immune", "lin", "tcr", "2019", "pmhc", "lck", "shp", "zap", "mek", "erk"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/literature/Lin_TCR_2019.bngl" +playground: + visible: true + gallery_categories: ["immunology"] + featured: false + difficulty: "intermediate" diff --git a/Published/LinTCR2019/metadata.yaml b/Published/LinTCR2019/metadata.yaml index 9b72e6b3..63418220 100644 --- a/Published/LinTCR2019/metadata.yaml +++ b/Published/LinTCR2019/metadata.yaml @@ -4,6 +4,7 @@ description: "TCR signaling" tags: ["published", "literature", "immune", "lin", "tcr", "2019", "pmhc", "lck", "shp", "zap", "mek", "erk"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Published/Macken1982/Macken1982_aigenerated.md b/Published/Macken1982/Macken1982_aigenerated.md new file mode 100644 index 00000000..1af41429 --- /dev/null +++ b/Published/Macken1982/Macken1982_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Macken 1982 + +## One-sentence summary + +Trivalent ligands crosslink bivalent receptors into finite branched aggregates below a sol–gel transition. + +## What the model shows + +This model tests classical multivalent aggregation theory by following ligand capture, receptor crosslinking, and bond dissociation. Its default regime remains below gelation, making small aggregate abundances and equilibrium free-site fractions directly comparable with branching-process predictions. + +## Biological story + +A three-armed ligand first captures a receptor, then its remaining arms recruit receptors belonging to other complexes. Receptors provide two ligand-binding positions, so repeated crosslinking builds branched structures. Bonds can break, and intracomplex ring closure is excluded, preserving tree-like aggregates. + +## Main biological players + +Trivalent ligand, bivalent receptor, ligand–receptor bonds, free binding sites, and finite branched aggregates. + +## Mechanism in plain English + +Free ligand arms bind free receptor sites. Once a ligand is receptor-bound, another available arm can capture a receptor from a different complex and expand the aggregate. Every bond dissociates with the same loss process. Ligand saturation and crosslinking propensity together determine whether most material remains small or approaches a macroscopic connected cluster. + +## Key modeled events + +- Free trivalent ligand captures an available site on a bivalent receptor. +- Additional ligand arms crosslink receptors from separate complexes, creating branches. +- Ligand–receptor bonds dissociate and release binding sites. +- Ring closure is excluded so aggregate statistics follow branching theory. + +## What the model measures + +Measurements include free ligand and receptor, total bonds, free sites on each partner, and selected small aggregates such as one-ligand/one-receptor pairs, trimers, and three-receptor stars. + +## Expected behavior in plots + +At the default subcritical setting, bonds and small aggregates should rise from the all-free state and settle within a few hundred seconds. Free-site readouts should fall toward equilibrium, while the selected small complexes remain appreciable rather than disappearing into a system-spanning aggregate. + +## Caveats + +The theory-oriented model assumes identical sites and excludes rings. It does not represent receptor signaling, membrane geometry, or molecular differences within an aggregate. diff --git a/Published/Macken1982/metadata.yaml b/Published/Macken1982/metadata.yaml index 15149819..a15caf59 100644 --- a/Published/Macken1982/metadata.yaml +++ b/Published/Macken1982/metadata.yaml @@ -4,6 +4,7 @@ description: "TLBR solution macken 1982" tags: ["published", "physics", "macken", "1982"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Macken1982/tlbr_solution_macken1982_metadata.yaml b/Published/Macken1982/tlbr_solution_macken1982_metadata.yaml new file mode 100644 index 00000000..027073a4 --- /dev/null +++ b/Published/Macken1982/tlbr_solution_macken1982_metadata.yaml @@ -0,0 +1,23 @@ +id: "Macken_1982" +name: "Macken 1982" +description: "TLBR solution macken 1982" +tags: ["published", "physics", "macken", "1982"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "physics" + featured: false + difficulty: "intermediate" diff --git a/Published/Mallela2021/Mallela2021_aigenerated.md b/Published/Mallela2021/Mallela2021_aigenerated.md new file mode 100644 index 00000000..4b7a64ad --- /dev/null +++ b/Published/Mallela2021/Mallela2021_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Mallela 2021 — New Jersey + +## One-sentence summary + +A staged COVID-19 transmission model links social distancing, case detection, hospitalization, recovery, and death in New Jersey. + +## What the model shows + +This regional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) model divides infection into multiple exposed stages before asymptomatic or symptomatic disease. The selected state member uses New Jersey population and fitted intervention timing. + +## Biological story + +In New Jersey, susceptible people move between mixing and protected behavior. Infection progresses through five exposed stages, then branches into asymptomatic or symptomatic outcomes; detected cases can enter quarantine, and severe cases enter hospital before recovery or death. + +## Main biological players + +Susceptible people in New Jersey, five exposed stages, asymptomatic infection, symptomatic infection, hospitalized, recovered, deceased, quarantined counterparts, and a dynamic social-distancing variable. + +## Mechanism in plain English + +Infectious people transmit within the New Jersey mixing susceptible population, with lower exposure among protected people. A chain of exposed stages approximates a distributed incubation period. Symptomatic detection redirects cases toward isolation, while hospitalization and outcome processes account for severe disease. Social-distancing setpoints change over time and feed back on contact. + +## Key modeled events + +- Behavioral transitions redistribute the New Jersey population between mixing and protected susceptible groups. +- New infections pass through five exposed stages. +- Cases branch into asymptomatic and symptomatic infectious populations. +- Detection and quarantine remove infectious people from ordinary mixing. +- Hospitalization resolves into recovery or death. + +## What the model measures + +Readouts report susceptible behavior, each exposed stage, asymptomatic and symptomatic infection, quarantine, hospitalization, recovery, death, and cumulative detected cases for New Jersey. + +## Expected behavior in plots + +After introduction, exposed stages should rise in sequence before symptomatic cases and hospitalizations. Stronger distancing should lower and delay the infectious peak; deaths and cumulative detected cases should lag behind incidence. The selected state member uses New Jersey population and fitted intervention timing. + +## Caveats + +This is the fitted New Jersey member of a larger collection. It represents population averages and does not resolve age, household structure, individual contact networks, or viral evolution. diff --git a/Published/Mallela2021/metadata.yaml b/Published/Mallela2021/metadata.yaml index 9c5459d6..371f5171 100644 --- a/Published/Mallela2021/metadata.yaml +++ b/Published/Mallela2021/metadata.yaml @@ -4,6 +4,8 @@ description: "Parameter-fit COVID-19 epidemiological models for all 50 US states tags: ["covid-19", "epidemiology", "parameter-estimation", "pybionetgen"] category: "epidemiology" compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Mallela2021_Cities/Mallela2021_Cities_aigenerated.md b/Published/Mallela2021_Cities/Mallela2021_Cities_aigenerated.md new file mode 100644 index 00000000..46f4cc9a --- /dev/null +++ b/Published/Mallela2021_Cities/Mallela2021_Cities_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Mallela 2021 — Philadelphia metropolitan area + +## One-sentence summary + +A staged COVID-19 transmission model links social distancing, case detection, hospitalization, recovery, and death in the Philadelphia metropolitan area. + +## What the model shows + +This regional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) model divides infection into multiple exposed stages before asymptomatic or symptomatic disease. The selected “Brotherly Love” member represents the Philadelphia metropolitan statistical area (MSA). + +## Biological story + +In the Philadelphia metropolitan area, susceptible people move between mixing and protected behavior. Infection progresses through five exposed stages, then branches into asymptomatic or symptomatic outcomes; detected cases can enter quarantine, and severe cases enter hospital before recovery or death. + +## Main biological players + +Susceptible people in the Philadelphia metropolitan area, five exposed stages, asymptomatic infection, symptomatic infection, hospitalized, recovered, deceased, quarantined counterparts, and a dynamic social-distancing variable. + +## Mechanism in plain English + +Infectious people transmit within the the Philadelphia metropolitan area mixing susceptible population, with lower exposure among protected people. A chain of exposed stages approximates a distributed incubation period. Symptomatic detection redirects cases toward isolation, while hospitalization and outcome processes account for severe disease. Social-distancing setpoints change over time and feed back on contact. + +## Key modeled events + +- Behavioral transitions redistribute the the Philadelphia metropolitan area population between mixing and protected susceptible groups. +- New infections pass through five exposed stages. +- Cases branch into asymptomatic and symptomatic infectious populations. +- Detection and quarantine remove infectious people from ordinary mixing. +- Hospitalization resolves into recovery or death. + +## What the model measures + +Readouts report susceptible behavior, each exposed stage, asymptomatic and symptomatic infection, quarantine, hospitalization, recovery, death, and cumulative detected cases for the Philadelphia metropolitan area. + +## Expected behavior in plots + +After introduction, exposed stages should rise in sequence before symptomatic cases and hospitalizations. Stronger distancing should lower and delay the infectious peak; deaths and cumulative detected cases should lag behind incidence. The selected “Brotherly Love” member represents the Philadelphia metropolitan statistical area (MSA). + +## Caveats + +This is the fitted the Philadelphia metropolitan area member of a larger collection. It represents population averages and does not resolve age, household structure, individual contact networks, or viral evolution. diff --git a/Published/Mallela2021_Cities/metadata.yaml b/Published/Mallela2021_Cities/metadata.yaml index ecd80da1..fa1602d3 100644 --- a/Published/Mallela2021_Cities/metadata.yaml +++ b/Published/Mallela2021_Cities/metadata.yaml @@ -4,6 +4,8 @@ description: "Parameter-fit COVID-19 epidemiological models for major US cities. tags: ["covid-19", "epidemiology", "parameter-estimation", "pybionetgen"] category: "epidemiology" compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Mallela2022/Alabama/Alabama_aigenerated.md b/Published/Mallela2022/Alabama/Alabama_aigenerated.md new file mode 100644 index 00000000..768c0258 --- /dev/null +++ b/Published/Mallela2022/Alabama/Alabama_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Mallela 2022 — Alabama + +## One-sentence summary + +A staged COVID-19 transmission model links social distancing, case detection, hospitalization, recovery, and death in Alabama. + +## What the model shows + +This regional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) model divides infection into multiple exposed stages before asymptomatic or symptomatic disease. The selected state member uses Alabama-specific population and distancing parameters. + +## Biological story + +In Alabama, susceptible people move between mixing and protected behavior. Infection progresses through five exposed stages, then branches into asymptomatic or symptomatic outcomes; detected cases can enter quarantine, and severe cases enter hospital before recovery or death. + +## Main biological players + +Susceptible people in Alabama, five exposed stages, asymptomatic infection, symptomatic infection, hospitalized, recovered, deceased, quarantined counterparts, and a dynamic social-distancing variable. + +## Mechanism in plain English + +Infectious people transmit within the Alabama mixing susceptible population, with lower exposure among protected people. A chain of exposed stages approximates a distributed incubation period. Symptomatic detection redirects cases toward isolation, while hospitalization and outcome processes account for severe disease. Social-distancing setpoints change over time and feed back on contact. + +## Key modeled events + +- Behavioral transitions redistribute the Alabama population between mixing and protected susceptible groups. +- New infections pass through five exposed stages. +- Cases branch into asymptomatic and symptomatic infectious populations. +- Detection and quarantine remove infectious people from ordinary mixing. +- Hospitalization resolves into recovery or death. + +## What the model measures + +Readouts report susceptible behavior, each exposed stage, asymptomatic and symptomatic infection, quarantine, hospitalization, recovery, death, and cumulative detected cases for Alabama. + +## Expected behavior in plots + +After introduction, exposed stages should rise in sequence before symptomatic cases and hospitalizations. Stronger distancing should lower and delay the infectious peak; deaths and cumulative detected cases should lag behind incidence. The selected state member uses Alabama-specific population and distancing parameters. + +## Caveats + +This is the fitted Alabama member of a larger collection. It represents population averages and does not resolve age, household structure, individual contact networks, or viral evolution. diff --git a/Published/Mallela2022/Alabama/Alabama_metadata.yaml b/Published/Mallela2022/Alabama/Alabama_metadata.yaml new file mode 100644 index 00000000..844118d1 --- /dev/null +++ b/Published/Mallela2022/Alabama/Alabama_metadata.yaml @@ -0,0 +1,24 @@ +id: "Alabama" +name: "Alabama" +description: "reporting period (1 d)" +tags: ["alabama", "fdcs", "counter", "s", "e1", "e2", "e3", "e4", "e5"] +category: "epidemiology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/Mallela_2022/Alabama.bngl" +playground: + visible: false + gallery_category: "epidemiology" + featured: false + difficulty: "advanced" diff --git a/Published/Mallela2022/Alabama/metadata.yaml b/Published/Mallela2022/Alabama/metadata.yaml index bb85e394..43c42cad 100644 --- a/Published/Mallela2022/Alabama/metadata.yaml +++ b/Published/Mallela2022/Alabama/metadata.yaml @@ -4,6 +4,7 @@ description: "reporting period (1 d)" tags: ["alabama", "fdcs", "counter", "s", "e1", "e2", "e3", "e4", "e5"] category: "epidemiology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Mallela2022_MSAs/Mallela2022_MSAs_aigenerated.md b/Published/Mallela2022_MSAs/Mallela2022_MSAs_aigenerated.md new file mode 100644 index 00000000..26aba090 --- /dev/null +++ b/Published/Mallela2022_MSAs/Mallela2022_MSAs_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Mallela 2022 — Scranton–Wilkes-Barre + +## One-sentence summary + +A staged COVID-19 transmission model links social distancing, case detection, hospitalization, recovery, and death in the Scranton–Wilkes-Barre metropolitan area. + +## What the model shows + +This regional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) model divides infection into multiple exposed stages before asymptomatic or symptomatic disease. The metropolitan statistical area (MSA) member is fitted to Scranton–Wilkes-Barre, Pennsylvania. + +## Biological story + +In the Scranton–Wilkes-Barre metropolitan area, susceptible people move between mixing and protected behavior. Infection progresses through five exposed stages, then branches into asymptomatic or symptomatic outcomes; detected cases can enter quarantine, and severe cases enter hospital before recovery or death. + +## Main biological players + +Susceptible people in the Scranton–Wilkes-Barre metropolitan area, five exposed stages, asymptomatic infection, symptomatic infection, hospitalized, recovered, deceased, quarantined counterparts, and a dynamic social-distancing variable. + +## Mechanism in plain English + +Infectious people transmit within the the Scranton–Wilkes-Barre metropolitan area mixing susceptible population, with lower exposure among protected people. A chain of exposed stages approximates a distributed incubation period. Symptomatic detection redirects cases toward isolation, while hospitalization and outcome processes account for severe disease. Social-distancing setpoints change over time and feed back on contact. + +## Key modeled events + +- Behavioral transitions redistribute the the Scranton–Wilkes-Barre metropolitan area population between mixing and protected susceptible groups. +- New infections pass through five exposed stages. +- Cases branch into asymptomatic and symptomatic infectious populations. +- Detection and quarantine remove infectious people from ordinary mixing. +- Hospitalization resolves into recovery or death. + +## What the model measures + +Readouts report susceptible behavior, each exposed stage, asymptomatic and symptomatic infection, quarantine, hospitalization, recovery, death, and cumulative detected cases for the Scranton–Wilkes-Barre metropolitan area. + +## Expected behavior in plots + +After introduction, exposed stages should rise in sequence before symptomatic cases and hospitalizations. Stronger distancing should lower and delay the infectious peak; deaths and cumulative detected cases should lag behind incidence. The metropolitan statistical area (MSA) member is fitted to Scranton–Wilkes-Barre, Pennsylvania. + +## Caveats + +This is the fitted the Scranton–Wilkes-Barre metropolitan area member of a larger collection. It represents population averages and does not resolve age, household structure, individual contact networks, or viral evolution. diff --git a/Published/Mallela2022_MSAs/metadata.yaml b/Published/Mallela2022_MSAs/metadata.yaml index 529c1c0b..eb324197 100644 --- a/Published/Mallela2022_MSAs/metadata.yaml +++ b/Published/Mallela2022_MSAs/metadata.yaml @@ -4,6 +4,8 @@ description: "Parameter-fit COVID-19 epidemiological models for US metropolitan tags: ["covid-19", "epidemiology", "parameter-estimation", "pybionetgen"] category: "epidemiology" compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Massole2023/Massole2023_aigenerated.md b/Published/Massole2023/Massole2023_aigenerated.md new file mode 100644 index 00000000..7c24756b --- /dev/null +++ b/Published/Massole2023/Massole2023_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Massole 2023 + +## One-sentence summary + +Multivalent erythroid-associated components form crosslinked pairs through shared EPO and hydroxyl-like interaction sites. + +## What the model shows + +This highly abstract model examines assembly among four particle classes with different numbers and states of interaction sites. Erythroid progenitor-like and erythrocyte-like components can each engage two EPO-associated particle types, and particles of the same class can also pair after site activation. + +## Biological story + +Two multivalent partners, EG and PERYT, present several phosphorylated interaction positions. EO and PO begin with inactive hydroxyl-like positions and an EPO-associated site; contact with EG or PERYT activates those positions while forming a complex. Activated EO or PO can then pair with another member of the same class. + +## Main biological players + +Abstract EG and PERYT multivalent partners, EO and PO EPO-associated particles, and inactive versus activated interaction positions. + +## Mechanism in plain English + +EG or PERYT binds EO or PO and simultaneously converts the contacted position from inactive to active. That activated particle can subsequently bind another activated member of its own class, creating a second layer of association. Different valences—two positions on EG and four on PERYT—allow the model to explore how interaction capacity affects assembly. + +## Key modeled events + +- EG binds EO or PO and activates the contacted interaction position. +- PERYT binds the same partners through any of four equivalent positions. +- Activated EO particles pair with one another. +- Activated PO particles pair with one another. + +## What the model measures + +No explicit plotted readouts are defined. The biologically interpretable quantities would therefore be free EO and PO, EG- or PERYT-bound complexes, activated positions, and EO–EO or PO–PO pairs. + +## Expected behavior in plots + +Starting from the specified mixture, EG/PERYT-bound complexes and activated EO or PO should accumulate first. Same-class EO and PO pairs can appear only after activation, so those associations should lag behind the initial cross-class contacts. + +## Caveats + +The molecule labels are abstract and the model supplies no explanatory comments or explicit measurements. The summary therefore does not assign more specific erythropoietin biology than the names and binding logic support. diff --git a/Published/Massole2023/Massole2023_aigenerated_detailed.md b/Published/Massole2023/Massole2023_aigenerated_detailed.md new file mode 100644 index 00000000..9d063a76 --- /dev/null +++ b/Published/Massole2023/Massole2023_aigenerated_detailed.md @@ -0,0 +1,55 @@ +# Detailed Model Explanation: Massole 2023 Epo-associated assembly model + +## 1. Model overview + +This compact model represents irreversible assembly among four abstract species associated by the metadata with erythropoietin (Epo) receptor signaling. Two initially unmodified receptor-like pools acquire an `oh~1` state as they bind either multivalent phosphorylated partners or another modified receptor-like molecule. + +## 2. BNGL block inventory + +The model contains 4 molecule types, 4 seed species, and 6 one-way reaction rules inside a model block. It has no parameters, functions, observables, compartments, anchors, or execution actions. + +## 3. Parameters, functions, and rate laws + +The model has no parameter namespace or functions: all six rules use the same literal rate `1.0`. Consequently, differences in flux arise from molecular abundance and available-site multiplicity rather than rule-specific kinetic constants. + +| Parameter group or names | Function in this model | +| --- | --- | +| Literal rate `1.0` | Applies uniformly to all partner-capture and receptor-pairing events; no forward-rate hierarchy or reverse process is encoded. | + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `_EO_`, `_PO_` | 2 each | `epo`, `oh` | `oh: 0, 1` | None | Two receptor-like pools with the same interface design: `epo` captures a partner, while `oh` records the transition from the initial (`0`) to modified/binding-competent (`1`) form. | +| `_EG_` | 2 | `oh`, `oh` | both repeated sites: `p` only | None | A bivalent phosphorylated partner; either indistinguishable `oh~p` site can capture an `_EO_` or `_PO_` molecule. | +| `_PERYT_` | 4 | `oh`, `oh`, `oh`, `oh` | all repeated sites: `p` only | None | A tetravalent phosphorylated partner that can recruit multiple receptor-like molecules and therefore supports larger assemblies than `_EG_`. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial. It starts with 580 `_EO_` and 70,907 `_PO_` molecules in the unmodified `oh~0` state, alongside 27,373 bivalent `_EG_` and 1,140 tetravalent `_PERYT_` molecules. The large excess of `_PO_` over `_EO_`, together with the repeated phosphorylated sites on `_EG_` and `_PERYT_`, sets the main stoichiometric bias; no complexes are initially present. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–4 load `_EO_` or `_PO_` onto the repeated phosphorylated sites of `_EG_` and `_PERYT_`. Rules 5–6 then let a still-unmodified receptor-like molecule bind the `oh~1` site of a modified molecule of its own type, extending homogeneous `_EO_` or `_PO_` assemblies. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–2 | One-way | One phosphorylated `oh` site on `_EG_`; `_EO_.epo` in rule 1 or `_PO_.epo` in rule 2; receptor-like `oh~0` | The selected `_EG_.oh~p` site bonds to the receptor-like `epo` site, and the recruited molecule changes `oh: 0 → 1`. Both variants use rate `1.0`. | Loads either receptor-like pool onto the bivalent `_EG_` scaffold and simultaneously marks the recruited molecule as modified. | +| 3–4 | One-way | One of four `_PERYT_.oh~p` sites; `_EO_.epo` in rule 3 or `_PO_.epo` in rule 4; receptor-like `oh~0` | The chosen `_PERYT_` site bonds to `epo`, with the recruited `_EO_` or `_PO_` changing `oh: 0 → 1`; rate `1.0`. | Performs the same capture on a tetravalent scaffold, allowing higher occupancy and potentially larger assemblies. | +| 5 | One-way | Unmodified `_EO_.epo`; a second `_EO_` with `oh~1` | The first molecule changes `oh: 0 → 1` while its `epo` site bonds to the second molecule's modified `oh~1` site; rate `1.0`. | Extends the `_EO_` population through a receptor-to-receptor contact after an `oh~1` form has been generated by rules 1 or 3. | +| 6 | One-way | Unmodified `_PO_.epo`; a second `_PO_` with `oh~1` | The first molecule changes `oh: 0 → 1` and bonds through `epo` to the partner's `oh~1`; rate `1.0`. | Mirrors rule 5 for the much more abundant `_PO_` pool, making `_PO_` self-association the quantitatively favored extension route. | + +## 7. Observables and technical readouts + +No observables are declared. A user must add readouts for free pools, `oh~1` abundance, scaffold occupancy, or aggregate size before the model can directly report assembly behavior. + +## 8. Actions and simulation workflow + +The file defines the model but contains no network-generation or simulation command. Metadata advertises ODE use, so execution requires an external caller to generate the network, choose a simulation duration, and define outputs. + +## 9. Technical caveats and ambiguities + +- The local files do not expand `_EO_`, `_PO_`, `_EG_`, or `_PERYT_`; their biological identities beyond the Epo-signaling metadata label are therefore uncertain. +- All rules are irreversible and share a literal rate, so the model describes progressive capture rather than binding equilibrium. +- Repeated `oh` sites on `_EG_` and `_PERYT_` are indistinguishable; match multiplicity can create statistical factors in generated reaction rates. +- With no observables or actions, the source is not a self-contained simulation workflow. diff --git a/Published/Massole2023/Massole_2023_metadata.yaml b/Published/Massole2023/Massole_2023_metadata.yaml new file mode 100644 index 00000000..d3a95bf8 --- /dev/null +++ b/Published/Massole2023/Massole_2023_metadata.yaml @@ -0,0 +1,67 @@ +id: "Massole_2023" +name: "Massole 2023" +description: "Epo receptor signaling" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2023" + pmid: "no id" + reference: "Massole et al., 2023" + +tags: ["published", "massole", "2023"] +date: + last_tested: 2026-07-18 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: false + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Site oh already exists in Molecule _EG_! Multiple identical Sites not supported witin a Molecule. " + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: true + mpd_compatible: false + comments: "nf does not run with bngp Model incompatible with nfsim but runs with MCP and bng2" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: true + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Massole_2023.bngl" + +playground: + visible: false + gallery_categories: ["developmental"] + featured: false + difficulty: "advanced" + + + + + + diff --git a/Published/Massole2023/metadata.yaml b/Published/Massole2023/metadata.yaml index 7827faf2..58e0d088 100644 --- a/Published/Massole2023/metadata.yaml +++ b/Published/Massole2023/metadata.yaml @@ -4,6 +4,7 @@ description: "Epo receptor signaling" tags: ["published", "massole", "2023"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/McMillan2021/McMillan2021_aigenerated.md b/Published/McMillan2021/McMillan2021_aigenerated.md new file mode 100644 index 00000000..f13c8eff --- /dev/null +++ b/Published/McMillan2021/McMillan2021_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: McMillan 2021 + +## One-sentence summary + +Trimeric TNF recruits one, two, or three receptors with affinity that changes at each occupancy step. + +## What the model shows + +This model isolates sequential binding of a three-position TNF ligand to receptors. By assigning distinct affinities to the first, second, and third recruitment events, it tests how occupancy-dependent binding shapes receptor loading without adding downstream TNF signaling. + +## Biological story + +Free TNF first captures one receptor. The partially occupied ligand can then recruit a second and finally a third receptor, while every contact can dissociate. Receptor self-association routes are documented but inactive, so TNF occupancy—not ligand-independent receptor dimerization—drives complex formation. + +## Main biological players + +Trimeric TNF, a receptor with parallel and antiparallel interaction faces, and TNF complexes carrying one, two, or three receptors. + +## Mechanism in plain English + +Each equivalent face of TNF can bind a receptor. The first event has the strongest affinity, while the second and third use progressively weaker association constants. Dissociation returns receptors to the free pool. Because spontaneous receptor dimerization is disabled, the model cleanly attributes higher receptor occupancy to multivalent TNF. + +## Key modeled events + +- Free TNF binds the first receptor through any of its three equivalent positions. +- Singly occupied TNF recruits a second receptor with a different affinity. +- Doubly occupied TNF recruits a third receptor through the remaining position. +- Each TNF–receptor contact can dissociate, reversing occupancy. + +## What the model measures + +Readouts separate free TNF, monomeric receptor, and TNF carrying exactly one, two, or three bound receptors. + +## Expected behavior in plots + +Free TNF should decline as singly occupied complexes appear. Doubly and triply occupied TNF should develop later and may remain less abundant because successive binding steps are weaker; at equilibrium, the four TNF occupancy curves reveal how receptor availability competes with declining affinity. + +## Caveats + +The model describes ligand–receptor stoichiometry only. It omits receptor activation, membrane organization, internalization, and all downstream inflammatory or apoptotic signaling. diff --git a/Published/McMillan2021/McMillan2021_aigenerated_detailed.md b/Published/McMillan2021/McMillan2021_aigenerated_detailed.md new file mode 100644 index 00000000..d66b1984 --- /dev/null +++ b/Published/McMillan2021/McMillan2021_aigenerated_detailed.md @@ -0,0 +1,68 @@ +# Detailed Model Explanation: McMillan 2021 trivalent TNF–receptor occupancy model + +## 1. Model overview + +This model isolates sequential binding of three receptors to the three sites of a trivalent TNF molecule. The first, second, and third receptor additions use progressively weaker equilibrium constants, allowing the model to resolve ligand occupancy without including downstream TNF signaling. + +## 2. BNGL block inventory + +The file contains 17 parameters, 2 molecule types, 2 seed species, 5 active observables, 12 active reversible rules, and 2 active actions. It has no compartments, anchors, or functions; two receptor-dimerization rules and several aggregate observables are commented out. + +## 3. Parameters, functions, and rate laws + +Concentrations and macroscopic equilibrium constants are converted to molecule counts and microscopic association rates for a one-femtoliter volume. Every binding step shares `koff = 0.01`, while the association rate decreases with occupancy because `K1 < K2 < K3`. + +| Parameter group or names | Function in this model | +| --- | --- | +| `Na`, `Vol` | Avogadro conversion and the modeled volume used to translate nanomolar inputs into molecule counts and microscopic association rates. | +| `R0_conc`, `T0_conc`; derived `R0_tot`, `T0_tot` | Initial receptor and TNF concentrations and their converted molecule totals. | +| `K1`, `K2`, `K3` | Macroscopic constants for the first, second, and third receptor-binding events. Values 10, 100, and 1000 encode decreasing affinity as TNF occupancy rises. | +| `k1`, `k2`, `k3` | Corresponding microscopic on-rates derived as `koff/(K*Na*Vol)` with unit conversion; therefore `k1 > k2 > k3`. | +| `Kp`, `Ka`; derived `kp`, `ka` | Parallel/antiparallel receptor-dimerization constants and on-rates. Their rules are commented out, so these parameters do not affect the active model. | +| `koff` | Shared reverse rate for every active TNF–receptor bond. | + +There are no functions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `R` | 2 | `p`, `a` | None | None | Receptor with potential parallel (`p`) and antiparallel (`a`) interfaces; only `a` binds TNF in active rules because receptor-dimerization rules are disabled. | +| `T` | 3 | `1`, `2`, `3` | None | None | Trivalent TNF ligand with three equivalent-in-form binding sites whose occupancy is tracked explicitly. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial. Free receptor and free TNF are initialized from 20,000 nM and 6,250 nM, respectively, after conversion to molecule counts in a one-femtoliter volume. No complexes are seeded, and the active system contains no receptor dimers independent of TNF. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 3–5 add the first receptor to any TNF site, rules 6–11 add a second receptor to either remaining site for each singly occupied ligand, and rules 12–14 complete occupancy of each doubly bound topology. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 3–5 | Reversible | Free receptor `R.a`; unoccupied TNF site `1`, `2`, or `3`, respectively | Creates/releases one `T.site–R.a` bond using first-binding on-rate `k1` and shared `koff`. | Generates all three singly occupied TNF topologies without privileging a ligand site. | +| 6–7 | Reversible | TNF with site 1 occupied; free receptor `a`; TNF site 2 or 3 | Adds/removes the second receptor at site 2 (rule 6) or site 3 (rule 7) using `k2`/`koff`. | Extends the site-1-bound ligand to either possible doubly occupied form. | +| 8–9 | Reversible | TNF with site 2 occupied; free receptor `a`; TNF site 1 or 3 | Adds/removes the second receptor at site 1 (rule 8) or site 3 (rule 9), again with `k2`/`koff`. | Covers the two extensions of the site-2-bound ligand. | +| 10–11 | Reversible | TNF with site 3 occupied; free receptor `a`; TNF site 1 or 2 | Adds/removes the second receptor at site 1 (rule 10) or site 2 (rule 11), using `k2`/`koff`. | Completes the six ordered routes into the three doubly occupied TNF topologies. | +| 12–14 | Reversible | Doubly occupied TNF missing site 3, 2, or 1, respectively; free receptor `a` | Fills/releases the final open site using the weakest on-rate `k3` and shared `koff`. | Produces fully occupied TNF and makes the third recruitment step less favorable than the first two. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `MonomerReceptor` | Molecule count | Receptors with both `p` and `a` free | Truly unbound receptor, since active rules use `a` and no active rule uses `p`. | +| `freeTNF` | Molecule count | TNF with sites 1–3 all free | Unoccupied ligand pool. | +| `TNF1R` | Molecule count | Sum of the three singly occupied TNF site patterns | Total ligand carrying exactly one receptor, independent of which site is occupied. | +| `TNF2R` | Molecule count | Sum of the three doubly occupied TNF patterns | Total ligand carrying exactly two receptors. | +| `TNF3R` | Molecule count | TNF with all three sites occupied | Fully saturated ligand and endpoint of rules 12–14. | + +## 8. Actions and simulation workflow + +The active workflow generates the complete network and runs a five-output-step ODE simulation to time 10,000. A truncated-network action and an NFsim command remain commented out, so despite NFsim-oriented metadata the checked-in workflow executes ODEs. + +## 9. Technical caveats and ambiguities + +- The metadata calls this “TNF signaling,” but the BNGL stops at receptor occupancy and contains no downstream signaling species. +- `K1`, `K2`, and `K3` are described as constants in nM, while their ordering is implemented through derived on-rates with a common off-rate; interpretation as dissociation constants should follow the source's conversion formula. +- Parallel and antiparallel receptor dimerization parameters are inactive because both corresponding rules are commented out. +- Active observables report ligand occupancy, not the size of receptor aggregates beyond one trivalent TNF. diff --git a/Published/McMillan2021/McMillan_2021_metadata.yaml b/Published/McMillan2021/McMillan_2021_metadata.yaml new file mode 100644 index 00000000..0d9443d4 --- /dev/null +++ b/Published/McMillan2021/McMillan_2021_metadata.yaml @@ -0,0 +1,68 @@ +id: "McMillan_2021" +name: "McMillan 2021" +description: "TNF signaling" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2021" + pmid: "33495441" + reference: "McMillan et al., 2021" + +tags: ["published", "nfsim", "mcmillan", "2021", "r0_tot", "t0_tot", "r", "t", "generate_network", "simulate_ode"] +date: + last_tested: 2026-07-19 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: false + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered 1 at line 45" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: false + comments: "MCP XML file couldn't be generated nfsim Invalid component name in '1,2,3)' (must begin with a letter or underscore) at line 45" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: true + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/McMillan_2021.bngl" + +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" + + + + + + + diff --git a/Published/McMillan2021/metadata.yaml b/Published/McMillan2021/metadata.yaml index 5f911a83..37ca5491 100644 --- a/Published/McMillan2021/metadata.yaml +++ b/Published/McMillan2021/metadata.yaml @@ -4,6 +4,7 @@ description: "TNF signaling" tags: ["published", "nfsim", "mcmillan", "2021", "r0_tot", "t0_tot", "r", "t", "generate_network", "simulate_ode"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/Mertins2023/Mertins2023_aigenerated.md b/Published/Mertins2023/Mertins2023_aigenerated.md new file mode 100644 index 00000000..bcad4945 --- /dev/null +++ b/Published/Mertins2023/Mertins2023_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Mertins 2023 + +## One-sentence summary + +DNA damage couples PARP-dependent repair chemistry to p53-driven Bax expression and caspase activation. + +## What the model shows + +This model joins two DNA-damage responses: PARP recruitment and substrate PARylation at breaks, and a p53–Bax apoptotic module. It also represents competitive PARP inhibition, allowing repair-associated occupancy to be related to Bax availability and caspase activation. + +## Biological story + +DNA double-strand breaks recruit both p53 and PARP. Active PARP consumes NAD to modify XRCC1, while PARG reverses that modification; an inhibitor competes at the PARP NAD pocket and releases PARP from DNA. Bound p53 promotes Bax expression, and Bax can overcome BclXL restraint to activate caspases. + +## Main biological players + +DNA double-strand breaks, p53, PARP, NAD, XRCC1, PARG, PARP inhibitor, Bax, BclXL, Bad, AKT, 14-3-3, and caspase. + +## Mechanism in plain English + +p53 and PARP compete for damage-associated binding. PARP uses NAD to PARylate XRCC1, and PARG removes the modification; inhibitor binding blocks the NAD pocket. Damage-bound p53 increases Bax mRNA, which produces Bax protein. BclXL sequesters Bax, while Bad competes for BclXL and AKT-controlled Bad phosphorylation shifts that competition. Free Bax activates procaspase, and active caspase reinforces activation. + +## Key modeled events + +- DNA breaks recruit p53 and activate PARP. +- PARP uses NAD to modify XRCC1, while PARG reverses the modification. +- A PARP inhibitor occupies the substrate pocket and displaces PARP from damage. +- p53 induces Bax, and free Bax promotes caspase activation against BclXL restraint. + +## What the model measures + +Readouts follow Bax mRNA, free Bax, active caspase, DNA-bound p53, and inhibitor-bound PARP. + +## Expected behavior in plots + +PARP–inhibitor complexes should increase with inhibitor exposure as productive PARP engagement falls. DNA-bound p53 should drive a delayed Bax-mRNA rise, followed by free Bax and then active caspase; strong BclXL sequestration can separate Bax production from caspase activation. + +## Caveats + +The model combines repair and apoptosis modules at a coarse level and contains inconsistent initial-quantity names that require curation before quantitative interpretation. diff --git a/Published/Mertins2023/Mertins2023_aigenerated_detailed.md b/Published/Mertins2023/Mertins2023_aigenerated_detailed.md new file mode 100644 index 00000000..991bae82 --- /dev/null +++ b/Published/Mertins2023/Mertins2023_aigenerated_detailed.md @@ -0,0 +1,95 @@ +# Detailed Model Explanation: Mertins 2023 DNA-Damage, PARP Inhibition, and Apoptosis + +## 1. Model overview + +This model is intended to couple competition between p53 and PARP at DNA double-strand breaks to Bax production and caspase activation. A PARP inhibitor competes with NAD at activated, DNA-bound PARP and releases PARP from damage, while the Bax–BclXL–Bad module determines how much free Bax can drive apoptosis. + +## 2. BNGL block inventory + +The text contains 38 intended parameter declarations, 13 molecule types, 10 seed species, 5 molecule-count observables, and 19 intended reactions, with no functions, compartments, anchors, or actions. However, missing/mismatched block terminators prevent these from forming valid active BNGL blocks as written; the counts describe the clearly delimited intended content rather than successfully parsed model blocks. + +## 3. Parameters, functions, and rate laws + +The namespace separates synthesis/degradation (`s*`, `d*`), reversible binding (`b*`, `u*`, `kf*`, `kr*`), phosphorylation (`p1`, `q1`), caspase activation (`a1`, `a2`), PAR turnover (`kcat1`, `kcat2`), and initial totals. Reactions mix mass action with an observable-dependent Hill transcription term and an additive caspase activation rate; these expressions are interpretable but not executable until the block syntax and undefined seed symbols are repaired. + +| Parameter group or names | Function in this model | +| --- | --- | +| `s1`, `s2`, `d1`, `M` | Control basal Bax-mRNA production, p53/DNA-bound inducible production, transcript loss, and the half-saturation scale of the squared p53 response. | +| `s4`, `d2` | Translate Bax in proportion to mRNA and remove free or BclXL-bound Bax. | +| `s3`, `d3`, `a1`, `a2` | Produce procaspase, turn over either caspase state, and activate procaspase through free Bax plus quadratic active-caspase feedback. | +| `b1/u1`, `b2/u2`, `b3/u3` | Reversibly bind Bax–BclXL, unphosphorylated Bad–BclXL, and phosphorylated Bad–14-3-3. | +| `p1`, `q1`, `AKTtot` | Set AKT-dependent Bad phosphorylation and reverse dephosphorylation; `AKTtot=0` disables the forward reaction in the supplied setup. | +| `b4`, `u4` | Give p53 and PARP a shared association/dissociation scale for competing at the DNA-break site. | +| `kf1/kr1`, `kcat1` | Control NAD binding to DNA-activated PARP and PARP-catalyzed PARylation of XRCC1. | +| `kcat2` | Controls PARG-catalyzed removal of PAR from XRCC1. | +| `IC50`, `kf2`, `kr2` | Define inhibitor competition at the PARP NAD pocket; `kr2` is derived from `IC50` and the NAD dissociation scale. | +| `DNADSBtot`, `p53tot`, `BADtot`, `BCLXLtot`, `SCAFtot`, `PARPtot`, `NADtot`, `XRCC1tot`, `PARGtot`, `Inhtot` | Intended initial amounts for damage, p53, apoptotic regulators, PAR metabolism, repair scaffold, and inhibitor. | + +There are no declared functions. The p53-dependent transcription and caspase feedback calculations are written directly as rule-rate expressions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `DNADSB`, `p53` | 1 each | `br`; `dna` | None | None | Competing damage site and p53 DNA-binding participant used to drive Bax transcription. | +| `mRNA_Bax` | 0 | None | None | None | Transcript produced basally or through damage-bound p53. | +| `Bax`, `BclXL` | 1 each | `b` | None | None | Pro-apoptotic Bax is buffered by binding the anti-apoptotic BclXL pool. | +| `Bad` | 2 | `S75_S99`, `b` | `0/PP` | None | Competes with Bax for BclXL when unphosphorylated and switches to 14-3-3 binding after phosphorylation. | +| `Fourteen_3_3` | 1 | `b` | None | None | Sequesters phosphorylated Bad. | +| `Caspase` | 1 | `csp` | `Pro/Act` | None | Terminal protease switch activated by free Bax and by active-caspase feedback. | +| `PARP` | 3 | `DNA`, `CD`, `NAD` | catalytic domain `inact/act` | None | Binds damage, becomes catalytically active, and uses its NAD pocket for substrate or inhibitor binding. | +| `NAD` | 1 | `sub` | None | None | PARP substrate that is bound before XRCC1 PARylation. | +| `XRCC1` | 1 | `Glu` | unmodified (`uPAR`) or PARylated (`PAR`) | None | Representative repair scaffold modified by PARP and reversed by PARG. | +| `PARG` | 1 | `CD` | None | None | Catalytically removes PAR from XRCC1. | +| `Inh` | 1 | `isub` | None | None | Competitive PARP inhibitor occupying the NAD site. | + +## 5. Compartments, anchors, initial species, and setup + +No spatial structure is intended. Damage, p53, BclXL, unphosphorylated Bad, 14-3-3, inactive PARP, NAD, unmodified XRCC1, PARG, and inhibitor are seeded; Bax mRNA, Bax, and caspase arise dynamically. Two seed expressions refer to undefined names—`BCLXtot` instead of `BCLXLtot` and `NADPtot` instead of `NADtot`—so even after block repair those initial pools require correction. Active AKT is initialized to zero, making Bad phosphorylation and the associated release reactions silent unless that parameter is changed. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Intended reactions 1–6 describe competition and catalysis at DNA damage, 7–11 produce and buffer Bax, 12–16 control Bad's choice of binding partner, and 17–19 implement caspase production, turnover, and activation. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | Reversible | `p53.dna`, `DNADSB.br` | Creates or releases the p53–break bond at `b4/u4`. | Generates the `p53_DNAbound` signal used by inducible Bax transcription. | +| 2 | Reversible | Inactive `PARP.DNA/CD`, free `DNADSB.br` | PARP binds the break and changes its catalytic domain `inact→act`; dissociation restores free inactive PARP. | Makes PARP compete with p53 for the same damage pool and licenses catalysis. | +| 3 | Reversible | DNA-bound active PARP `NAD`, `NAD.sub` | Creates the PARP–NAD bond at `kf1` and releases it at `kr1`. | Loads activated PARP with substrate. | +| 4 | One-way | NAD-loaded DNA-bound PARP, `XRCC1.Glu=uPAR` | Releases NAD, retains PARP on DNA, and changes XRCC1 `uPAR→PAR` at `kcat1`. | Represents one repair-scaffold PARylation cycle. | +| 5 | One-way | `PARG`, `XRCC1.Glu=PAR` | Retains PARG and changes XRCC1 `PAR→uPAR` at `kcat2`. | Reverses the PARP modification. | +| 6 | Reversible | `Inh.isub`; active DNA-bound PARP `NAD`; damage site | Inhibitor binding occupies the NAD pocket and simultaneously releases PARP from DNA; reverse binding restores the DNA complex and frees inhibitor. | Encodes inhibitor competition as both catalytic blockade and PARP displacement. | +| 7 | Reversible source/sink | `mRNA_Bax` | Creates transcript basally at `s1` and removes it at `d1`. | Establishes basal Bax expression. | +| 8 | One-way source | Observable `p53_DNAbound` | Creates mRNA at `s2*p53_DNAbound²/(M²+p53_DNAbound²)`. | Converts p53 occupancy of damage into a saturating transcriptional response. | +| 9 | Reversible source/sink | Observable `mRNA_Bax`, free `Bax.b` | Creates Bax at `s4*mRNA_Bax` and removes it at `d2`. | Links transcription to the pro-apoptotic protein pool. | +| 10 | Reversible | `Bax.b`, `BclXL.b` | Creates or releases the inhibitory Bax–BclXL bond at `b1/u1`. | Buffers free Bax away from caspase activation. | +| 11 | One-way | Bax–BclXL complex | Removes bound Bax at `d2` and releases BclXL. | Recycles the anti-apoptotic binding capacity. | +| 12 | Reversible | Unphosphorylated `Bad.b`, `BclXL.b` | Creates or releases the Bad–BclXL bond at `b2/u2`. | Lets Bad displace the Bax-buffering role of BclXL. | +| 13 | Reversible | Free `Bad.S75_S99` | Changes Bad `0↔PP` at `p1*AKTtot` and `q1`. | Couples the binding competition to survival-kinase activity. | +| 14 | Reversible | Phosphorylated `Bad.b`, `Fourteen_3_3.b` | Creates or releases the Bad–14-3-3 bond at `b3/u3`. | Sequesters phosphorylated Bad away from BclXL. | +| 15 | One-way | BclXL-bound unphosphorylated Bad | AKT-dependent phosphorylation changes Bad `0→PP` and releases both partners. | Restores free BclXL when survival signaling is active. | +| 16 | One-way | 14-3-3-bound phosphorylated Bad | Dephosphorylation changes Bad `PP→0` and releases 14-3-3. | Returns Bad to the BclXL-competitive pool. | +| 17 | One-way source | `Caspase.csp=Pro` | Creates procaspase at `s3`. | Supplies substrate for the terminal activation switch. | +| 18 | One-way sink | Either caspase state | Removes caspase at `d3`. | Limits both proenzyme and active enzyme abundance. | +| 19 | One-way | `Caspase.csp=Pro`; `Bax_free`, `Caspase_act` observables | Changes procaspase `Pro→Act` at `a1*Bax_free + a2*Caspase_act²`. | Combines Bax initiation with autocatalytic amplification of apoptosis. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `mRNA_Bax`, `Bax_free` | Molecule count | Bax transcript and unbound Bax. | These drive protein synthesis and the linear component of caspase activation, respectively. | +| `Caspase_act` | Molecule count | Active caspase. | Serves as both apoptotic output and the squared positive-feedback term in reaction 19. | +| `p53_DNAbound` | Molecule count | p53 engaged through its DNA site. | Drives the Hill transcription term; because the pattern only requires a bond, its partner is inferred from the available reaction topology. | +| `PARP_Inhbound` | Molecule count | Catalytically active PARP with inhibitor in its NAD pocket and no DNA bond required by the pattern. | Reports inhibited PARP produced by the displacement reaction, not total inhibitor or all PARP-bound complexes. | + +## 8. Actions and simulation workflow + +There is no active simulation workflow. The intended reactions imply an ODE-compatible concentration model, but the malformed block structure, undefined seed symbols, and absence of network-generation or simulation actions must be resolved before it can be executed. + +## 9. Technical caveats and ambiguities + +- The `parameters` block is never closed; reactions begin with `begin reactions` but end with both `end reaction rules` and `end reactions`. Standard BNGL expects a consistently named reaction-rule block. +- `BCLXtot` and `NADPtot` are undefined; the likely declared candidates are `BCLXLtot` and `NADtot`, but this summary does not silently substitute them. +- Metadata claims ODE and NFsim properties despite there being no active action and no currently parseable reaction-rule block. +- The same `b4/u4` rates are reused for p53 and PARP binding to damage, which is a modeling simplification rather than evidence of identical molecular affinities. +- With `AKTtot=0`, reactions 13 forward and 15 are inactive, biasing Bad toward its unphosphorylated BclXL-binding form. diff --git a/Published/Mertins2023/Mertins_2023_metadata.yaml b/Published/Mertins2023/Mertins_2023_metadata.yaml new file mode 100644 index 00000000..73448c1b --- /dev/null +++ b/Published/Mertins2023/Mertins_2023_metadata.yaml @@ -0,0 +1,67 @@ +id: "Mertins_2023" +name: "Mertins 2023" +description: "DNA damage response" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2023" + pmid: "no id" + reference: "Mertins et al., 2023" + +tags: ["published", "mertins", "2023", "dnadsb", "p53", "mrna_bax", "bax", "bclxl", "bad", "fourteen_3_3", "caspase"] +date: + last_tested: 2026-07-19 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered begin at line 41" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: false + comments: "MCP There was an issue with BNGL model Mertins_2023.bngl XML file couldn't be generated nfsim begin block before end of previous block parameters at line 41" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: true + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/growth-factor-signaling/Mertins_2023.bngl" + +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" + + + + + + diff --git a/Published/Mertins2023/metadata.yaml b/Published/Mertins2023/metadata.yaml index 3f0ac837..ff7e97e5 100644 --- a/Published/Mertins2023/metadata.yaml +++ b/Published/Mertins2023/metadata.yaml @@ -4,6 +4,7 @@ description: "DNA damage response" tags: ["published", "mertins", "2023", "dnadsb", "p53", "mrna_bax", "bax", "bclxl", "bad", "fourteen_3_3", "caspase"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Miller2022_NavajoNation/Miller2022_NavajoNation_aigenerated.md b/Published/Miller2022_NavajoNation/Miller2022_NavajoNation_aigenerated.md new file mode 100644 index 00000000..f6c961a9 --- /dev/null +++ b/Published/Miller2022_NavajoNation/Miller2022_NavajoNation_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Miller 2022 — Navajo Nation + +## One-sentence summary + +A staged COVID-19 transmission model links social distancing, case detection, hospitalization, recovery, and death in the Navajo Nation. + +## What the model shows + +This regional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) model divides infection into multiple exposed stages before asymptomatic or symptomatic disease. This member is fitted to Navajo Nation regional data rather than a state aggregate. + +## Biological story + +In the Navajo Nation, susceptible people move between mixing and protected behavior. Infection progresses through five exposed stages, then branches into asymptomatic or symptomatic outcomes; detected cases can enter quarantine, and severe cases enter hospital before recovery or death. + +## Main biological players + +Susceptible people in the Navajo Nation, five exposed stages, asymptomatic infection, symptomatic infection, hospitalized, recovered, deceased, quarantined counterparts, and a dynamic social-distancing variable. + +## Mechanism in plain English + +Infectious people transmit within the the Navajo Nation mixing susceptible population, with lower exposure among protected people. A chain of exposed stages approximates a distributed incubation period. Symptomatic detection redirects cases toward isolation, while hospitalization and outcome processes account for severe disease. Social-distancing setpoints change over time and feed back on contact. + +## Key modeled events + +- Behavioral transitions redistribute the the Navajo Nation population between mixing and protected susceptible groups. +- New infections pass through five exposed stages. +- Cases branch into asymptomatic and symptomatic infectious populations. +- Detection and quarantine remove infectious people from ordinary mixing. +- Hospitalization resolves into recovery or death. + +## What the model measures + +Readouts report susceptible behavior, each exposed stage, asymptomatic and symptomatic infection, quarantine, hospitalization, recovery, death, and cumulative detected cases for the Navajo Nation. + +## Expected behavior in plots + +After introduction, exposed stages should rise in sequence before symptomatic cases and hospitalizations. Stronger distancing should lower and delay the infectious peak; deaths and cumulative detected cases should lag behind incidence. This member is fitted to Navajo Nation regional data rather than a state aggregate. + +## Caveats + +This is the fitted the Navajo Nation member of a larger collection. It represents population averages and does not resolve age, household structure, individual contact networks, or viral evolution. diff --git a/Published/Miller2022_NavajoNation/metadata.yaml b/Published/Miller2022_NavajoNation/metadata.yaml index 1e421f8e..ae7e9396 100644 --- a/Published/Miller2022_NavajoNation/metadata.yaml +++ b/Published/Miller2022_NavajoNation/metadata.yaml @@ -4,6 +4,8 @@ description: "COVID-19 epidemiological models fit to Navajo Nation regional data tags: ["covid-19", "epidemiology", "pybionetgen"] category: "epidemiology" compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Miller2025_MEK/Miller2025_MEK_aigenerated.md b/Published/Miller2025_MEK/Miller2025_MEK_aigenerated.md new file mode 100644 index 00000000..2a1fba9c --- /dev/null +++ b/Published/Miller2025_MEK/Miller2025_MEK_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Miller 2025 MEK1 N78G + +## One-sentence summary + +The MEK1 N78G variant reshapes ERK amplitude and duration through MEK1–MEK2 heterodimerization and negative feedback. + +## What the model shows + +This selected variant follows the epidermal growth factor receptor (EGFR)–RAS–RAF–MEK–ERK cascade. MEK denotes mitogen-activated protein kinase kinase, and ERK denotes extracellular signal-regulated kinase. + +## Biological story + +EGFR activates RAS and RAF, which phosphorylate MEK1 and MEK2. MEK heterodimers transmit signal to ERK, while active ERK feeds back to receptor-proximal components and MEK1. The N78G substitution is represented in the MEK1 branch. + +## Main biological players + +EGFR, SOS1, RAS, RAF, MEK1 N78G, MEK2, ERK, phosphatase, source and sink pools. + +## Mechanism in plain English + +Ligand-activated EGFR recruits SOS1 to activate RAS. RAS activates RAF, which modifies MEK isoforms; MEK then activates ERK. MEK1 and MEK2 associate, allowing isoform state to influence output. ERK feedback phosphorylates upstream components and helps limit signal duration. + +## Key modeled events + +- EGFR–SOS1 activates RAS and RAF. +- RAF phosphorylates MEK1 N78G and MEK2. +- MEK isoforms heterodimerize and activate ERK. +- Active ERK feeds back on SOS1, EGFR, and MEK1. + +## What the model measures + +Readouts include phosphorylated SOS1 and EGFR, doubly phosphorylated ERK, activated MEK1 and MEK2, and their combined active pool. + +## Expected behavior in plots + +EGFR and SOS1 modification should precede MEK and ERK activation. The N78G-dependent MEK1 trajectory can be compared with MEK2 to see whether heterodimerization changes ERK peak height or persistence; feedback should eventually reduce upstream drive. + +## Caveats + +This is one optimized perturbation from a multi-variant collection. Interpretation of the N78G effect requires comparison with wild type and other fitted variants. diff --git a/Published/Miller2025_MEK/metadata.yaml b/Published/Miller2025_MEK/metadata.yaml index e2e7fb59..97321765 100644 --- a/Published/Miller2025_MEK/metadata.yaml +++ b/Published/Miller2025_MEK/metadata.yaml @@ -4,6 +4,8 @@ description: "MEK isoform variant models curated for PyBioNetGen." tags: ["mek", "isoforms", "signaling", "pybionetgen"] category: "signaling" compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Mitra2019/02-egfr/bnf1/InputFiles/egfr_metadata.yaml b/Published/Mitra2019/02-egfr/bnf1/InputFiles/egfr_metadata.yaml new file mode 100644 index 00000000..a3901807 --- /dev/null +++ b/Published/Mitra2019/02-egfr/bnf1/InputFiles/egfr_metadata.yaml @@ -0,0 +1,21 @@ +id: Mitra2019_02_egfr_bnf1_InputFiles_egfr +name: InputFiles +description: EGFR model +tags: ["signaling"] +category: signaling +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml b/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml index 5e810194..0cd4725f 100644 --- a/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml +++ b/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml @@ -4,6 +4,7 @@ description: EGFR model tags: ["signaling"] category: signaling compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/02-egfr/metadata.yaml b/Published/Mitra2019/02-egfr/metadata.yaml index 8d4eaebe..17b166fd 100644 --- a/Published/Mitra2019/02-egfr/metadata.yaml +++ b/Published/Mitra2019/02-egfr/metadata.yaml @@ -4,6 +4,8 @@ description: EGFR model tags: ["signaling"] category: signaling compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/03-fcerig/fceri_gamma2_metadata.yaml b/Published/Mitra2019/03-fcerig/fceri_gamma2_metadata.yaml new file mode 100644 index 00000000..6637af43 --- /dev/null +++ b/Published/Mitra2019/03-fcerig/fceri_gamma2_metadata.yaml @@ -0,0 +1,21 @@ +id: 03_fcerig_fceri_gamma2 +name: 03-fcerig +description: Added molecule type definition block so that the +tags: ["immunology"] +category: immunology +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/03-fcerig/metadata.yaml b/Published/Mitra2019/03-fcerig/metadata.yaml index cb9e95d5..0962ac36 100644 --- a/Published/Mitra2019/03-fcerig/metadata.yaml +++ b/Published/Mitra2019/03-fcerig/metadata.yaml @@ -4,6 +4,7 @@ description: Added molecule type definition block so that the tags: ["immunology"] category: immunology compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/04-egfrnf/egfr_nf_metadata.yaml b/Published/Mitra2019/04-egfrnf/egfr_nf_metadata.yaml new file mode 100644 index 00000000..c03961a6 --- /dev/null +++ b/Published/Mitra2019/04-egfrnf/egfr_nf_metadata.yaml @@ -0,0 +1,21 @@ +id: 04_egfrnf_egfr_nf +name: example2_starting_point.bngl +description: Filename: example2_starting_point.bngl +tags: ["f", "lt_nm", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "molecules"] +category: signaling +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/04-egfrnf/metadata.yaml b/Published/Mitra2019/04-egfrnf/metadata.yaml index 2e2f6699..91700b09 100644 --- a/Published/Mitra2019/04-egfrnf/metadata.yaml +++ b/Published/Mitra2019/04-egfrnf/metadata.yaml @@ -4,6 +4,7 @@ description: Filename: example2_starting_point.bngl tags: ["f", "lt_nm", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "molecules"] category: signaling compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["nf"] diff --git a/Published/Mitra2019/05-threestep/05-threestep_aigenerated.md b/Published/Mitra2019/05-threestep/05-threestep_aigenerated.md new file mode 100644 index 00000000..abc98e93 --- /dev/null +++ b/Published/Mitra2019/05-threestep/05-threestep_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Mitra 2019 three-step cascade + +## One-sentence summary + +A four-state irreversible cascade exposes how three sequential rates shape signal delay and output accumulation. + +## What the model shows + +This toy model provides a transparent parameter-fitting example rather than a named biochemical pathway. A starting population passes through intermediates B and C before reaching terminal state D. + +## Biological story + +All material begins as A. It is converted to B, then C, then D, with a separate rate governing each step and no reverse flow. + +## Main biological players + +Abstract states A, B, C, and D and three transition rates. + +## Mechanism in plain English + +The first process consumes A and produces B. B then feeds C, and C feeds the terminal D pool. Because each intermediate must be populated before the next step can proceed, the model turns rate differences into measurable delays and transient intermediate peaks. + +## Key modeled events + +- A is converted irreversibly to B. +- B is converted irreversibly to C. +- C is converted irreversibly to terminal state D. + +## What the model measures + +Readouts report the abundance of A, B, C, and D throughout the time course. + +## Expected behavior in plots + +A should decay monotonically and D should rise monotonically. B should peak first and C later; the slowest of the three transitions should create the largest upstream buildup and dominate the delay before D accumulates. + +## Caveats + +The states are intentionally abstract and do not correspond to named molecules. The model omits synthesis, degradation, feedback, and reversibility. diff --git a/Published/Mitra2019/05-threestep/05-threestep_aigenerated_detailed.md b/Published/Mitra2019/05-threestep/05-threestep_aigenerated_detailed.md new file mode 100644 index 00000000..7ad155d3 --- /dev/null +++ b/Published/Mitra2019/05-threestep/05-threestep_aigenerated_detailed.md @@ -0,0 +1,58 @@ +# Coder Model Explanation: Three-step signaling cascade + +## 1. Model identity and scope + +- **Metadata id:** `05_threestep_m1`. +- **Purpose:** toy irreversible three-step cascade for fitting or workflow demonstrations. +- **Paths:** `Published/Mitra2019/05-threestep/m1.bngl` and same-directory `metadata.yaml`. + +The implementation transfers a conserved population from A through B and C to D. The letters have no locally documented biological expansion. + +## 2. BNGL block inventory + +| Construct | Count | Contribution | +| --- | ---: | --- | +| Parameters | 4 | Three externally substituted rates and `Ainit`. | +| Molecule types | 4 | Site-free `A`, `B`, `C`, `D`. | +| Initial species | 1 | A-only starting pool. | +| Observables | 4 | Total count of each type. | +| Reaction rules | 3 | Irreversible A→B→C→D transfers. | +| Actions | 2 | Network generation and ODE integration. | +| Compartments / anchors / functions | 0 / 0 / 0 | No spatial or derived logic. | + +## 3. Parameters, functions, and rate laws + +`k1`, `k2`, and `k3` receive placeholder tokens `k1__FREE`, `k2__FREE`, and `k3__FREE`. They must be replaced or supplied by the fitting workflow before ordinary execution. Each is used as a first-order mass-action rate for its corresponding transfer. `Ainit=100` initializes A. There are no algebraic functions. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `A` | 0 | None | None | None | Source stage for rule 1. | Abstract. | +| `B` | 0 | None | None | None | Product of rule 1 and source for rule 2. | Abstract intermediate. | +| `C` | 0 | None | None | None | Product of rule 2 and source for rule 3. | Abstract intermediate. | +| `D` | 0 | None | None | None | Terminal product. | No outgoing rule. | + +## 5. Compartments, anchors, initial species, and setup + +The model is nonspatial and has no anchors. `A()` starts at 100; B, C, and D are absent initially and appear only through conversion. Total A+B+C+D is conserved because each rule consumes one upstream molecule and creates one downstream molecule. + +## 6. Complete reaction-rule inventory + +| # | Direction and participants | Exact modeled change | Rate | Technical meaning | +| ---: | --- | --- | --- | --- | +| 1 | One-way; A and B | Removes one site-free `A()` and creates one site-free `B()`; no state or bond edit exists. | `k1` | First-stage population transfer. | +| 2 | One-way; B and C | Removes `B()` and creates `C()`. | `k2` | Second-stage transfer and B turnover. | +| 3 | One-way; C and D | Removes `C()` and creates terminal `D()`. | `k3` | Final-stage transfer and D accumulation. | + +## 7. Observables and technical readouts + +All four are `Molecules` observables: `A` counts `A()`, `B` counts `B()`, `C` counts `C()`, and `D` counts `D()`. With no sites or complexes, each readout is also the complete population of that type. Their sum should remain 100 subject to numerical tolerance. + +## 8. Actions and simulation workflow + +`generate_network({overwrite=>1})` replaces any prior network. `simulate({method=>"ode",t_start=>0,t_end=>200,n_steps=>40,suffix=>"d1"})` runs deterministic ODE integration over 200 time units and requests 40 intervals; the suffix distinguishes its output files. + +## 9. Technical caveats and ambiguities + +The metadata title is grammatically incomplete, and A–D have no biological definitions. The `__FREE` tokens are fitting placeholders rather than numeric BNGL values, so standalone execution requires substitution. Because all transitions are irreversible and there are no source/sink terms, D necessarily becomes the terminal reservoir whenever all three rates are positive. diff --git a/Published/Mitra2019/05-threestep/metadata.yaml b/Published/Mitra2019/05-threestep/metadata.yaml index 11faf009..39d516bf 100644 --- a/Published/Mitra2019/05-threestep/metadata.yaml +++ b/Published/Mitra2019/05-threestep/metadata.yaml @@ -4,6 +4,8 @@ description: Toy model of a 3-step signaling cascade tags: ["k1", "k2", "k3", "ainit", "molecules"] category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/06-degranulation/metadata.yaml b/Published/Mitra2019/06-degranulation/metadata.yaml index 19633eb2..93f62ffc 100644 --- a/Published/Mitra2019/06-degranulation/metadata.yaml +++ b/Published/Mitra2019/06-degranulation/metadata.yaml @@ -4,6 +4,7 @@ description: A model of IgE receptor signaling tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/06-degranulation/model_tofit_metadata.yaml b/Published/Mitra2019/06-degranulation/model_tofit_metadata.yaml new file mode 100644 index 00000000..d7cd41ce --- /dev/null +++ b/Published/Mitra2019/06-degranulation/model_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: 06_degranulation_model_tofit +name: of IgE receptor signaling +description: A model of IgE receptor signaling +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/07-egg/egg_metadata.yaml b/Published/Mitra2019/07-egg/egg_metadata.yaml new file mode 100644 index 00000000..4436c9c0 --- /dev/null +++ b/Published/Mitra2019/07-egg/egg_metadata.yaml @@ -0,0 +1,21 @@ +id: 07_egg_egg +name: 07-egg +description: BNGL model: egg +tags: ["a0", "a1", "a2", "b1", "b2", "c0", "c1", "c2", "d1", "d2", "period", "t", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/07-egg/metadata.yaml b/Published/Mitra2019/07-egg/metadata.yaml index 8d900bd2..f83f9957 100644 --- a/Published/Mitra2019/07-egg/metadata.yaml +++ b/Published/Mitra2019/07-egg/metadata.yaml @@ -4,6 +4,7 @@ description: BNGL model: egg tags: ["a0", "a1", "a2", "b1", "b2", "c0", "c1", "c2", "d1", "d2", "period", "t", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/10-egfr/egfr_ode_metadata.yaml b/Published/Mitra2019/10-egfr/egfr_ode_metadata.yaml new file mode 100644 index 00000000..c226256e --- /dev/null +++ b/Published/Mitra2019/10-egfr/egfr_ode_metadata.yaml @@ -0,0 +1,21 @@ +id: 10_egfr_egfr_ode +name: example1.bngl +description: Filename: example1.bngl +tags: ["lt", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "alpha1", "alpha2", "alpha3", "alpha4", "molecules", "species"] +category: signaling +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/10-egfr/metadata.yaml b/Published/Mitra2019/10-egfr/metadata.yaml index 80c23865..ae6001a7 100644 --- a/Published/Mitra2019/10-egfr/metadata.yaml +++ b/Published/Mitra2019/10-egfr/metadata.yaml @@ -4,6 +4,7 @@ description: Filename: example1.bngl tags: ["lt", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "alpha1", "alpha2", "alpha3", "alpha4", "molecules", "species"] category: signaling compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/11-TLBR/metadata.yaml b/Published/Mitra2019/11-TLBR/metadata.yaml index 74cad65e..3d0a9883 100644 --- a/Published/Mitra2019/11-TLBR/metadata.yaml +++ b/Published/Mitra2019/11-TLBR/metadata.yaml @@ -4,6 +4,7 @@ description: BNGL model: tlbr tags: ["alpha", "molecules", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["nf"] diff --git a/Published/Mitra2019/11-TLBR/tlbr_metadata.yaml b/Published/Mitra2019/11-TLBR/tlbr_metadata.yaml new file mode 100644 index 00000000..55f890ca --- /dev/null +++ b/Published/Mitra2019/11-TLBR/tlbr_metadata.yaml @@ -0,0 +1,21 @@ +id: 11_TLBR_tlbr +name: 11-TLBR +description: BNGL model: tlbr +tags: ["alpha", "molecules", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/12-TCR/metadata.yaml b/Published/Mitra2019/12-TCR/metadata.yaml index f012f6e8..3c51dc42 100644 --- a/Published/Mitra2019/12-TCR/metadata.yaml +++ b/Published/Mitra2019/12-TCR/metadata.yaml @@ -4,6 +4,7 @@ description: A model of T cell receptor signaling tags: ["immunology"] category: immunology compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["nf"] diff --git a/Published/Mitra2019/12-TCR/tcr_metadata.yaml b/Published/Mitra2019/12-TCR/tcr_metadata.yaml new file mode 100644 index 00000000..d499ff39 --- /dev/null +++ b/Published/Mitra2019/12-TCR/tcr_metadata.yaml @@ -0,0 +1,21 @@ +id: 12_TCR_tcr +name: of T cell receptor signaling +description: A model of T cell receptor signaling +tags: ["immunology"] +category: immunology +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/13-receptor/metadata.yaml b/Published/Mitra2019/13-receptor/metadata.yaml index 7876568c..346953ed 100644 --- a/Published/Mitra2019/13-receptor/metadata.yaml +++ b/Published/Mitra2019/13-receptor/metadata.yaml @@ -4,6 +4,8 @@ description: A simple model tags: ["ligand_ispresent", "molecules", "species"] category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/14-receptor-nf/metadata.yaml b/Published/Mitra2019/14-receptor-nf/metadata.yaml index 453cb286..e30502b0 100644 --- a/Published/Mitra2019/14-receptor-nf/metadata.yaml +++ b/Published/Mitra2019/14-receptor-nf/metadata.yaml @@ -4,6 +4,7 @@ description: A simple model of ligand/receptor binding and receptor phosphorylat tags: ["molecules", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["nf"] diff --git a/Published/Mitra2019/14-receptor-nf/receptor_nf_metadata.yaml b/Published/Mitra2019/14-receptor-nf/receptor_nf_metadata.yaml new file mode 100644 index 00000000..415a6b3e --- /dev/null +++ b/Published/Mitra2019/14-receptor-nf/receptor_nf_metadata.yaml @@ -0,0 +1,21 @@ +id: 14_receptor_nf_receptor_nf +name: of ligand/receptor binding and receptor phosphorylation. +description: A simple model of ligand/receptor binding and receptor phosphorylation. +tags: ["molecules", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/15-igf1r/IGF1R_fit_all_metadata.yaml b/Published/Mitra2019/15-igf1r/IGF1R_fit_all_metadata.yaml new file mode 100644 index 00000000..e0fdd6ba --- /dev/null +++ b/Published/Mitra2019/15-igf1r/IGF1R_fit_all_metadata.yaml @@ -0,0 +1,21 @@ +id: 15_igf1r_IGF1R_fit_all +name: 15-igf1r +description: Author: William S. Hlavacek +tags: ["dilution", "a1_permpers", "a2_permpers", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/15-igf1r/metadata.yaml b/Published/Mitra2019/15-igf1r/metadata.yaml index eaa977d6..a4633530 100644 --- a/Published/Mitra2019/15-igf1r/metadata.yaml +++ b/Published/Mitra2019/15-igf1r/metadata.yaml @@ -4,6 +4,7 @@ description: Author: William S. Hlavacek tags: ["dilution", "a1_permpers", "a2_permpers", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/17-egfr-ssa/metadata.yaml b/Published/Mitra2019/17-egfr-ssa/metadata.yaml index ea3c02a2..fe70110d 100644 --- a/Published/Mitra2019/17-egfr-ssa/metadata.yaml +++ b/Published/Mitra2019/17-egfr-ssa/metadata.yaml @@ -4,6 +4,8 @@ description: EGFR model tags: ["signaling"] category: signaling compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/18-mapk/metadata.yaml b/Published/Mitra2019/18-mapk/metadata.yaml index c0360c88..42ab3507 100644 --- a/Published/Mitra2019/18-mapk/metadata.yaml +++ b/Published/Mitra2019/18-mapk/metadata.yaml @@ -4,6 +4,8 @@ description: For "ground truth" model, use median values such that hierarchy H1 tags: ["signaling"] category: signaling compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/19-raf-constraint/RAFi_metadata.yaml b/Published/Mitra2019/19-raf-constraint/RAFi_metadata.yaml new file mode 100644 index 00000000..b94bed53 --- /dev/null +++ b/Published/Mitra2019/19-raf-constraint/RAFi_metadata.yaml @@ -0,0 +1,21 @@ +id: 19_raf_constraint_RAFi +name: 19-raf-constraint +description: BNGL model: RAFi +tags: ["k1", "k2", "k3", "k5", "kf1", "kf2", "kf3", "kf4", "kf5", "kf6", "rtot", "ifree", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/19-raf-constraint/metadata.yaml b/Published/Mitra2019/19-raf-constraint/metadata.yaml index 6899a68b..97f32325 100644 --- a/Published/Mitra2019/19-raf-constraint/metadata.yaml +++ b/Published/Mitra2019/19-raf-constraint/metadata.yaml @@ -4,6 +4,7 @@ description: BNGL model: RAFi tags: ["k1", "k2", "k3", "k5", "kf1", "kf2", "kf3", "kf4", "kf5", "kf6", "rtot", "ifree", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/20-raf-constraint4/RAFi_metadata.yaml b/Published/Mitra2019/20-raf-constraint4/RAFi_metadata.yaml new file mode 100644 index 00000000..8b7b2248 --- /dev/null +++ b/Published/Mitra2019/20-raf-constraint4/RAFi_metadata.yaml @@ -0,0 +1,21 @@ +id: 20_raf_constraint4_RAFi +name: 20-raf-constraint4 +description: BNGL model: RAFi +tags: ["k1", "k2", "k3", "k5", "kf1", "kf2", "kf3", "kf4", "kf5", "kf6", "rtot", "ifree", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/20-raf-constraint4/metadata.yaml b/Published/Mitra2019/20-raf-constraint4/metadata.yaml index 27072fe1..ce203d4c 100644 --- a/Published/Mitra2019/20-raf-constraint4/metadata.yaml +++ b/Published/Mitra2019/20-raf-constraint4/metadata.yaml @@ -4,6 +4,7 @@ description: BNGL model: RAFi tags: ["k1", "k2", "k3", "k5", "kf1", "kf2", "kf3", "kf4", "kf5", "kf6", "rtot", "ifree", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/24-jnk/JNKmodel_180724_bnf_metadata.yaml b/Published/Mitra2019/24-jnk/JNKmodel_180724_bnf_metadata.yaml new file mode 100644 index 00000000..9461f4ad --- /dev/null +++ b/Published/Mitra2019/24-jnk/JNKmodel_180724_bnf_metadata.yaml @@ -0,0 +1,21 @@ +id: 24_jnk_JNKmodel_180724_bnf +name: 24-jnk +description: BNGL model: JNKmodel_180724_bnf +tags: ["scale_t", "ani", "k3_zakbyu1", "k1_u1tozak", "d3_zak", "d1_zak", "k3_mkk4byzak", "k1_zaktomkk4", "d3_mkk4", "d1_mkk4", "k3_mkk7byzak", "k1_zaktomkk7", "f3_mkk7byzak", "d3_mkk7", "d1_mkk7", "k3_jnkbymkk4", "k1_mkk4tojnk", "k3_jnkbymkk7", "k1_mkk7tojnk", "f3_jnkbymkk7", "d3_jnk", "d1_jnk", "k3_mkk7byjnk", "k1_jnktomkk7", "inh_jnk", "d3_mkk7byjnkpt", "d1_jnkpttomkk7", "f1_zaktomkk7p", "k1_zaktojnk", "k3_mkk4byakt", "k1_akttomkk4", "k3_mkk7byakt", "k1_akttomkk7", "d3_mkk4byaktpt", "d1_aktpttomkk4", "d3_mkk7byaktpt", "d1_aktpttomkk7", "scale_ppmkk4", "scale_ppmkk7", "scale_ppjnk", "pakt", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/24-jnk/metadata.yaml b/Published/Mitra2019/24-jnk/metadata.yaml index f2c51fc1..d284cb12 100644 --- a/Published/Mitra2019/24-jnk/metadata.yaml +++ b/Published/Mitra2019/24-jnk/metadata.yaml @@ -4,6 +4,7 @@ description: BNGL model: JNKmodel_180724_bnf tags: ["scale_t", "ani", "k3_zakbyu1", "k1_u1tozak", "d3_zak", "d1_zak", "k3_mkk4byzak", "k1_zaktomkk4", "d3_mkk4", "d1_mkk4", "k3_mkk7byzak", "k1_zaktomkk7", "f3_mkk7byzak", "d3_mkk7", "d1_mkk7", "k3_jnkbymkk4", "k1_mkk4tojnk", "k3_jnkbymkk7", "k1_mkk7tojnk", "f3_jnkbymkk7", "d3_jnk", "d1_jnk", "k3_mkk7byjnk", "k1_jnktomkk7", "inh_jnk", "d3_mkk7byjnkpt", "d1_jnkpttomkk7", "f1_zaktomkk7p", "k1_zaktojnk", "k3_mkk4byakt", "k1_akttomkk4", "k3_mkk7byakt", "k1_akttomkk7", "d3_mkk4byaktpt", "d1_aktpttomkk4", "d3_mkk7byaktpt", "d1_aktpttomkk7", "scale_ppmkk4", "scale_ppmkk7", "scale_ppjnk", "pakt", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019/26-tcr-sens/metadata.yaml b/Published/Mitra2019/26-tcr-sens/metadata.yaml index f3c37ff2..d843cb9b 100644 --- a/Published/Mitra2019/26-tcr-sens/metadata.yaml +++ b/Published/Mitra2019/26-tcr-sens/metadata.yaml @@ -4,6 +4,7 @@ description: Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves tags: ["immunology"] category: immunology compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["ode"] diff --git a/Published/Mitra2019/26-tcr-sens/tcr_sens_tofit_metadata.yaml b/Published/Mitra2019/26-tcr-sens/tcr_sens_tofit_metadata.yaml new file mode 100644 index 00000000..b267f3eb --- /dev/null +++ b/Published/Mitra2019/26-tcr-sens/tcr_sens_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: 26_tcr_sens_tcr_sens_tofit +name: for the Manz/Groves 2011 data +description: Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data +tags: ["immunology"] +category: immunology +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/28-mapk/metadata.yaml b/Published/Mitra2019/28-mapk/metadata.yaml index 51c8c28f..68c1e349 100644 --- a/Published/Mitra2019/28-mapk/metadata.yaml +++ b/Published/Mitra2019/28-mapk/metadata.yaml @@ -4,6 +4,8 @@ description: Ensemble model translated into BNGL tags: ["signaling"] category: signaling compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["ode"] diff --git a/Published/Mitra2019/30-jobs/metadata.yaml b/Published/Mitra2019/30-jobs/metadata.yaml index c923871c..e857c382 100644 --- a/Published/Mitra2019/30-jobs/metadata.yaml +++ b/Published/Mitra2019/30-jobs/metadata.yaml @@ -4,6 +4,8 @@ description: NFsim simulation of the job market tags: ["other"] category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["ode"] diff --git a/Published/Mitra2019/31-elephant/elephant_metadata.yaml b/Published/Mitra2019/31-elephant/elephant_metadata.yaml new file mode 100644 index 00000000..cd110ed1 --- /dev/null +++ b/Published/Mitra2019/31-elephant/elephant_metadata.yaml @@ -0,0 +1,21 @@ +id: 31_elephant_elephant +name: 31-elephant +description: BNGL model: elephant +tags: ["a0", "a1", "a2", "a3", "a4", "a5", "a6", "a7", "a8", "a9", "a10", "a11", "a12", "a13", "a14", "a15", "a16", "a17", "a18", "a19", "a20", "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "c0", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "c8", "c9", "c10", "c11", "c12", "c13", "c14", "c15", "c16", "c17", "c18", "c19", "c20", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8", "d9", "d10", "d11", "d12", "d13", "d14", "d15", "d16", "d17", "d18", "d19", "d20", "tmax", "t", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/31-elephant/metadata.yaml b/Published/Mitra2019/31-elephant/metadata.yaml index 69006b17..b3a090d1 100644 --- a/Published/Mitra2019/31-elephant/metadata.yaml +++ b/Published/Mitra2019/31-elephant/metadata.yaml @@ -4,6 +4,7 @@ description: BNGL model: elephant tags: ["a0", "a1", "a2", "a3", "a4", "a5", "a6", "a7", "a8", "a9", "a10", "a11", "a12", "a13", "a14", "a15", "a16", "a17", "a18", "a19", "a20", "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "c0", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "c8", "c9", "c10", "c11", "c12", "c13", "c14", "c15", "c16", "c17", "c18", "c19", "c20", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8", "d9", "d10", "d11", "d12", "d13", "d14", "d15", "d16", "d17", "d18", "d19", "d20", "tmax", "t", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/Mitra2019Likelihood_aigenerated.md b/Published/Mitra2019Likelihood/Mitra2019Likelihood_aigenerated.md new file mode 100644 index 00000000..c62a9f0d --- /dev/null +++ b/Published/Mitra2019Likelihood/Mitra2019Likelihood_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Mitra 2019 degranulation ground truth + +## One-sentence summary + +Antigen-driven FcεRI signaling produces PIP3 and SHIP1-dependent control of mast-cell degranulation. + +## What the model shows + +This ground-truth model connects immunoglobulin E receptor signaling to secretion. FcεRI is the high-affinity immunoglobulin E receptor, PIP3 is phosphatidylinositol-3,4,5-trisphosphate, and SHIP1 is an inositol phosphatase. + +## Biological story + +Multivalent antigen crosslinks IgE-bound receptor, recruits and activates Syk, and creates docking sites for SHIP1. Lipid signaling shifts a regulatory switch that controls release of a β-hexosaminidase-like secretion marker. + +## Main biological players + +DNP antigen, IgE–FcεRI receptor, Syk, SHIP1, PIP3, a regulatory switch, and a secreted degranulation marker. + +## Mechanism in plain English + +Antigen clusters receptors and enables receptor phosphorylation. Syk binds and becomes active in these complexes. SHIP1 is recruited through phosphotyrosine contacts and modulates PIP3-associated signaling. The balance of kinase and phosphatase activity controls a downstream switch, which transfers reporter material from an intracellular to secreted state. + +## Key modeled events + +- Antigen crosslinks IgE-bound FcεRI. +- Clustered receptors recruit and activate Syk. +- SHIP1 engagement modulates PIP3-dependent signaling. +- The downstream switch controls secretion of the degranulation reporter. + +## What the model measures + +The principal readout is secreted β-hexosaminidase, a proxy for degranulation; internal states also capture receptor, kinase, phosphatase, lipid, and switch activation. + +## Expected behavior in plots + +Receptor/Syk activation should precede PIP3-dependent switch activation. Secreted reporter should rise after that signaling delay and accumulate, while stronger SHIP1 restraint should reduce or postpone release. + +## Caveats + +The parameters were designated as fitting ground truth. The secretion marker is a proxy, and granule fusion and calcium dynamics are not represented explicitly. diff --git a/Published/Mitra2019Likelihood/metadata.yaml b/Published/Mitra2019Likelihood/metadata.yaml index f36e1832..77c3e12e 100644 --- a/Published/Mitra2019Likelihood/metadata.yaml +++ b/Published/Mitra2019Likelihood/metadata.yaml @@ -50,6 +50,7 @@ tags: - molecules category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: diff --git a/Published/Mitra2019Likelihood/model_ground_metadata.yaml b/Published/Mitra2019Likelihood/model_ground_metadata.yaml new file mode 100644 index 00000000..4708ca4a --- /dev/null +++ b/Published/Mitra2019Likelihood/model_ground_metadata.yaml @@ -0,0 +1,69 @@ +id: model_ground +name: model_ground.bngl +description: filename: model_ground.bngl +tags: + - x_tot__free + - k_xoff__free + - k_xon__free + - kase__free + - kdegx__free + - kdegran__free + - km_ship1__free + - km_syk__free + - km_x__free + - koff__free + - kp_ship1__free + - kp_syk__free + - kp_x__free + - kpten__free + - ksynth1__free + - pase__free + - f + - na + - t + - vchannel + - nchannel + - vcyt + - ag_tot_0 + - ag_conc1 + - r_tot + - syk_tot + - ship1_tot + - kon + - koff + - kase + - pase + - kp_syk + - km_syk + - kp_ship1 + - km_ship1 + - ksynth1 + - kdeg1 + - kpten + - h_tot + - kdegran + - kdegx + - k_xon + - k_xoff + - kp_x + - km_x + - molecules +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: + - ode + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: + [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem16/metadata.yaml b/Published/Mitra2019Likelihood/problem16/metadata.yaml index e65d938d..6eef811b 100644 --- a/Published/Mitra2019Likelihood/problem16/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem16/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem16/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem16/model0_tofit_metadata.yaml new file mode 100644 index 00000000..89d8574c --- /dev/null +++ b/Published/Mitra2019Likelihood/problem16/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem16_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml index 0b33b205..481ce4ae 100644 --- a/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem16_3cat/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem16_3cat/model0_tofit_metadata.yaml new file mode 100644 index 00000000..5e29d63e --- /dev/null +++ b/Published/Mitra2019Likelihood/problem16_3cat/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem16_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem32/metadata.yaml b/Published/Mitra2019Likelihood/problem32/metadata.yaml index 1014c664..256b9a23 100644 --- a/Published/Mitra2019Likelihood/problem32/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem32/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem32/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem32/model0_tofit_metadata.yaml new file mode 100644 index 00000000..d280dc7e --- /dev/null +++ b/Published/Mitra2019Likelihood/problem32/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem32_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml index a4aab663..599c6084 100644 --- a/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem32_3cat/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem32_3cat/model0_tofit_metadata.yaml new file mode 100644 index 00000000..2fc920e1 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem32_3cat/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem32_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem4/metadata.yaml b/Published/Mitra2019Likelihood/problem4/metadata.yaml index ed346e45..9f52ceda 100644 --- a/Published/Mitra2019Likelihood/problem4/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem4/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem4/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem4/model0_tofit_metadata.yaml new file mode 100644 index 00000000..90849598 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem4/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem4_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml index 87229b8b..60c8c069 100644 --- a/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem4_3cat/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem4_3cat/model0_tofit_metadata.yaml new file mode 100644 index 00000000..a530af8a --- /dev/null +++ b/Published/Mitra2019Likelihood/problem4_3cat/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem4_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem64/metadata.yaml b/Published/Mitra2019Likelihood/problem64/metadata.yaml index ecab0a22..dd864880 100644 --- a/Published/Mitra2019Likelihood/problem64/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem64/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem64/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem64/model0_tofit_metadata.yaml new file mode 100644 index 00000000..a631869c --- /dev/null +++ b/Published/Mitra2019Likelihood/problem64/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem64_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml index 4a277525..33a45c94 100644 --- a/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem64_3cat/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem64_3cat/model0_tofit_metadata.yaml new file mode 100644 index 00000000..1c451417 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem64_3cat/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem64_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem8/metadata.yaml b/Published/Mitra2019Likelihood/problem8/metadata.yaml index 49757c27..5e309c39 100644 --- a/Published/Mitra2019Likelihood/problem8/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem8/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem8/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem8/model0_tofit_metadata.yaml new file mode 100644 index 00000000..cefeb7bd --- /dev/null +++ b/Published/Mitra2019Likelihood/problem8/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem8_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml index 93ac8bbf..fd8ac607 100644 --- a/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem8_3cat/model0_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem8_3cat/model0_tofit_metadata.yaml new file mode 100644 index 00000000..730b5566 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem8_3cat/model0_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem8_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Likelihood/problem_quant/metadata.yaml b/Published/Mitra2019Likelihood/problem_quant/metadata.yaml index 3d21f85e..02e9e443 100644 --- a/Published/Mitra2019Likelihood/problem_quant/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem_quant/metadata.yaml @@ -4,6 +4,7 @@ description: filename: model.bngl tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Mitra2019Likelihood/problem_quant/model_tofit_metadata.yaml b/Published/Mitra2019Likelihood/problem_quant/model_tofit_metadata.yaml new file mode 100644 index 00000000..c027a1a3 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem_quant/model_tofit_metadata.yaml @@ -0,0 +1,21 @@ +id: problem_quant_model_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019Rab/Mitra2019Rab_aigenerated.md b/Published/Mitra2019Rab/Mitra2019Rab_aigenerated.md new file mode 100644 index 00000000..04cafabe --- /dev/null +++ b/Published/Mitra2019Rab/Mitra2019Rab_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Mitra 2019 Rab conversion + +## One-sentence summary + +EGFR trafficking drives a Rab5-to-Rab7 endosomal identity switch through coordinated GEF and GAP recruitment. + +## What the model shows + +This model connects epidermal growth factor receptor (EGFR) endocytosis to Rab-family GTPase control. GEF means guanine nucleotide exchange factor, and GAP means GTPase-activating protein. + +## Biological story + +Activated, ubiquitinated EGFR enters endosomes and recruits Rab5 activators. Rab5-GTP establishes early-endosome identity, then recruits the MON1–CCZ1 complex that activates Rab7. Rab7 and GAP activity displace Rab5 as the compartment matures toward degradation. + +## Main biological players + +EGFR, Rab5, Rab7, Rabex5/RABGEF1, RIN1, Rabaptin/RABEP1, SGSM3, MON1, CCZ1, and a digestion endpoint. + +## Mechanism in plain English + +Receptor activation and ubiquitination recruit exchange factors that load Rab5 with GTP. Rab5-GTP recruits effectors and the MON1–CCZ1 Rab7 GEF. Rab7 activation rises as SGSM3 accelerates Rab5 GTP hydrolysis, producing an ordered identity transition. Mature endosomes deliver EGFR to digestion. + +## Key modeled events + +- Activated EGFR is internalized and ubiquitinated. +- Rab5 GEFs create Rab5-GTP on the early endosome. +- Rab5 recruits MON1–CCZ1, which activates Rab7. +- SGSM3 inactivates Rab5 as Rab7 identity increases. +- Mature endosomes deliver EGFR toward digestion. + +## What the model measures + +Readouts track total, phosphorylated, and ubiquitinated EGFR; free and bound Rab5 states; catalytic GEF complexes; free and endosomal Rab7-GTP; and recruited SGSM3 GAP. + +## Expected behavior in plots + +Rab5-GTP and its effector complexes should rise early after EGFR entry. MON1–CCZ1 recruitment should precede Rab7-GTP, while SGSM3 should accompany decline of Rab5 activity. EGFR digestion should be the latest event. + +## Caveats + +The selected wild-type member belongs to a perturbation collection. Organelle geometry and many additional Rab effectors are omitted. diff --git a/Published/Mitra2019Rab/metadata.yaml b/Published/Mitra2019Rab/metadata.yaml index f9a4af30..d8e27bee 100644 --- a/Published/Mitra2019Rab/metadata.yaml +++ b/Published/Mitra2019Rab/metadata.yaml @@ -55,6 +55,8 @@ tags: - 0 category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: diff --git a/Published/Mitra2019Rab/pybnf_files/metadata.yaml b/Published/Mitra2019Rab/pybnf_files/metadata.yaml index 036cae43..3398c7c8 100644 --- a/Published/Mitra2019Rab/pybnf_files/metadata.yaml +++ b/Published/Mitra2019Rab/pybnf_files/metadata.yaml @@ -4,6 +4,8 @@ description: filename:rab_mon1ccz1_ox.bngl tags: ["rab5_expr", "rab7_expr", "mon1_expr", "ccz1_expr", "kf_mon1_ccz1", "kr_mon1_ccz1", "egf_conc_ngml", "ub_hill_coef", "ub_half_coef", "ub_basal_coef", "ub_scale_coef", "py_hill_coef", "py_half_coef", "py_basal_coef", "py_scale_coef", "gtp_to_gdp_ratio", "kcatgtp_rab5", "k_gdp_gef_eff", "kcatgtp_rab7", "molecules", "0"] category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/ModelZAP/ModelZAP_aigenerated.md b/Published/ModelZAP/ModelZAP_aigenerated.md new file mode 100644 index 00000000..48ecd575 --- /dev/null +++ b/Published/ModelZAP/ModelZAP_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Model ZAP + +## One-sentence summary + +Ligand-bound CD16 uses a six-ITAM ζ chain to compare ZAP-70 and Syk recruitment, activation, inhibition, and turnover. + +## What the model shows + +This model examines how two related tyrosine kinases compete for phosphorylated immunoreceptor tyrosine-based activation motifs (ITAMs). ZAP-70 is ζ-chain-associated protein kinase 70, Syk is spleen tyrosine kinase, and SHP is an inhibitory phosphatase. + +## Biological story + +Ligand activates CD16 and its associated ζ chain. Lck phosphorylates six ITAMs, permitting ZAP-70 or Syk binding and activation. SHP can occupy kinase states, while CBL promotes removal of activated signaling components. + +## Main biological players + +CD16, ligand, six-ITAM ζ chain, Lck, ZAP-70, Syk, SHP phosphatase, CBL ubiquitin ligase, and an inactive/dead pool. + +## Mechanism in plain English + +Ligand engagement assembles receptor and ζ chain. Lck creates doubly phosphorylated ITAMs, which bind inactive ZAP-70 or Syk and support their activation. Activated kinases can remain receptor-bound or dissociate. SHP suppresses kinase states, and CBL binding directs activated components toward loss. + +## Key modeled events + +- Ligand engages CD16 and associates the receptor with ζ chain. +- Lck phosphorylates six ζ-chain ITAMs. +- ZAP-70 and Syk bind phosphorylated motifs and become activated. +- SHP inhibits signaling kinase states. +- CBL promotes turnover of activated complexes. + +## What the model measures + +Readouts separate free and bound phosphorylated ZAP-70 and Syk, total kinase recruitment, phosphorylated and open ζ-chain motifs, SHP occupancy, ligand–receptor complexes, and receptor abundance. + +## Expected behavior in plots + +Ligand–receptor complexes and phosphorylated ζ motifs should rise first. Bound ZAP-70/Syk should follow, then activated free kinase pools. SHP and CBL engagement should limit the duration and abundance of those active states. + +## Caveats + +The receptor system is stylized and uses a six-motif ζ chain. Downstream calcium, MAPK, cytotoxicity, and transcriptional responses are not included. diff --git a/Published/ModelZAP/Model_ZAP_metadata.yaml b/Published/ModelZAP/Model_ZAP_metadata.yaml new file mode 100644 index 00000000..11ba4b11 --- /dev/null +++ b/Published/ModelZAP/Model_ZAP_metadata.yaml @@ -0,0 +1,24 @@ +id: "Model_ZAP" +name: "Model ZAP" +description: "ZAP-70 recruitment" +tags: ["published", "immunology", "nfsim", "model", "zap", "kon", "a", "cbl", "cd16", "lck", "ligand", "zeta", "dead"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/Model_ZAP.bngl" +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" diff --git a/Published/ModelZAP/metadata.yaml b/Published/ModelZAP/metadata.yaml index 4b45d424..eb3af050 100644 --- a/Published/ModelZAP/metadata.yaml +++ b/Published/ModelZAP/metadata.yaml @@ -4,6 +4,7 @@ description: "ZAP-70 recruitment" tags: ["published", "immunology", "nfsim", "model", "zap", "kon", "a", "cbl", "cd16", "lck", "ligand", "zeta", "dead"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/Mukhopadhyay2013/Mukhopadhyay2013_aigenerated.md b/Published/Mukhopadhyay2013/Mukhopadhyay2013_aigenerated.md new file mode 100644 index 00000000..a8d7b9aa --- /dev/null +++ b/Published/Mukhopadhyay2013/Mukhopadhyay2013_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Mukhopadhyay 2013 + +## One-sentence summary + +Ordered phosphorylation of three TCR ζ-chain ITAMs controls progressive recruitment and retention of ZAP-70. + +## What the model shows + +This model isolates enzymatic modification of a substrate representing the TCR ζ chain. A kinase and phosphatase move three ITAMs through unphosphorylated, singly phosphorylated, and doubly phosphorylated states in sequence, while ZAP-70 binds fully modified ITAMs with position-dependent stability. + +## Biological story + +A kinase begins at the first ITAM and adds two phosphates before modification proceeds to the second and third. A phosphatase can reverse each step. Fully phosphorylated motifs become docking sites for ZAP-70, and later ITAMs retain ZAP-70 more strongly in the parameterization. + +## Main biological players + +TCR ζ-chain substrate with three ITAMs, a kinase, a phosphatase, and ZAP-70. + +## Mechanism in plain English + +The kinase transiently binds an available ITAM and adds phosphates one at a time. Modification is ordered: downstream ITAMs become substrates only after earlier motifs are fully modified. The phosphatase removes those phosphates through corresponding intermediate states. ZAP-70 recognizes any doubly phosphorylated ITAM, but its dissociation rate depends on which motif is occupied. + +## Key modeled events + +- The kinase adds two phosphates sequentially to ITAM 1. +- After ITAM 1 is complete, phosphorylation advances through ITAM 2 and then ITAM 3. +- A phosphatase reverses every phosphorylation step. +- ZAP-70 binds doubly phosphorylated ITAMs with motif-specific residence times. + +## What the model measures + +Readouts count bound ZAP-70 and seven successive ζ-chain phosphorylation classes, from no phosphorylation through complete double phosphorylation of all three ITAMs. + +## Expected behavior in plots + +The phosphorylation classes should progress in order, with early states appearing before the fully modified state. Bound ZAP-70 should rise as doubly phosphorylated ITAMs accumulate and may persist preferentially on the motif with the slowest dissociation. + +## Caveats + +The kinase and phosphatase are generic, and receptor ligation, Lck regulation, membrane localization, and downstream ZAP-70 signaling are outside this focused ITAM-processing model. diff --git a/Published/Mukhopadhyay2013/Mukhopadhyay_2013_metadata.yaml b/Published/Mukhopadhyay2013/Mukhopadhyay_2013_metadata.yaml new file mode 100644 index 00000000..35c590a9 --- /dev/null +++ b/Published/Mukhopadhyay2013/Mukhopadhyay_2013_metadata.yaml @@ -0,0 +1,24 @@ +id: "Mukhopadhyay_2013" +name: "Mukhopadhyay 2013" +description: "FceRI signaling" +tags: ["published", "immunology", "mukhopadhyay", "2013", "s", "e", "f", "z"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/Mukhopadhyay_2013.bngl" +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" diff --git a/Published/Mukhopadhyay2013/metadata.yaml b/Published/Mukhopadhyay2013/metadata.yaml index b2fbb7f6..0190491c 100644 --- a/Published/Mukhopadhyay2013/metadata.yaml +++ b/Published/Mukhopadhyay2013/metadata.yaml @@ -4,6 +4,7 @@ description: "FceRI signaling" tags: ["published", "immunology", "mukhopadhyay", "2013", "s", "e", "f", "z"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/MyrtleBeachConwayNorthMyrtleBeachSCNC_aigenerated.md b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/MyrtleBeachConwayNorthMyrtleBeachSCNC_aigenerated.md new file mode 100644 index 00000000..54b5a6e8 --- /dev/null +++ b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/MyrtleBeachConwayNorthMyrtleBeachSCNC_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Myrtle Beach–Conway–North Myrtle Beach COVID-19 model + +## One-sentence summary + +A staged COVID-19 transmission model links social distancing, case detection, hospitalization, recovery, and death in the Myrtle Beach–Conway–North Myrtle Beach region. + +## What the model shows + +This regional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) model divides infection into multiple exposed stages before asymptomatic or symptomatic disease. The selected runtime model includes two successive social-distancing phases fitted for this South Carolina–North Carolina metropolitan region. + +## Biological story + +In the Myrtle Beach–Conway–North Myrtle Beach region, susceptible people move between mixing and protected behavior. Infection progresses through five exposed stages, then branches into asymptomatic or symptomatic outcomes; detected cases can enter quarantine, and severe cases enter hospital before recovery or death. + +## Main biological players + +Susceptible people in the Myrtle Beach–Conway–North Myrtle Beach region, five exposed stages, asymptomatic infection, symptomatic infection, hospitalized, recovered, deceased, quarantined counterparts, and a dynamic social-distancing variable. + +## Mechanism in plain English + +Infectious people transmit within the the Myrtle Beach–Conway–North Myrtle Beach region mixing susceptible population, with lower exposure among protected people. A chain of exposed stages approximates a distributed incubation period. Symptomatic detection redirects cases toward isolation, while hospitalization and outcome processes account for severe disease. Social-distancing setpoints change over time and feed back on contact. + +## Key modeled events + +- Behavioral transitions redistribute the the Myrtle Beach–Conway–North Myrtle Beach region population between mixing and protected susceptible groups. +- New infections pass through five exposed stages. +- Cases branch into asymptomatic and symptomatic infectious populations. +- Detection and quarantine remove infectious people from ordinary mixing. +- Hospitalization resolves into recovery or death. + +## What the model measures + +Readouts report susceptible behavior, each exposed stage, asymptomatic and symptomatic infection, quarantine, hospitalization, recovery, death, and cumulative detected cases for the Myrtle Beach–Conway–North Myrtle Beach region. + +## Expected behavior in plots + +After introduction, exposed stages should rise in sequence before symptomatic cases and hospitalizations. Stronger distancing should lower and delay the infectious peak; deaths and cumulative detected cases should lag behind incidence. The selected runtime model includes two successive social-distancing phases fitted for this South Carolina–North Carolina metropolitan region. + +## Caveats + +This is the fitted the Myrtle Beach–Conway–North Myrtle Beach region member of a larger collection. It represents population averages and does not resolve age, household structure, individual contact networks, or viral evolution. diff --git a/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC_metadata.yaml b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC_metadata.yaml new file mode 100644 index 00000000..dc01cca3 --- /dev/null +++ b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC_metadata.yaml @@ -0,0 +1,24 @@ +id: "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC" +name: "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC" +description: "Runtime-only BNGL model migrated from public/models: Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC" +tags: ["myrtle", "beach", "conway", "north", "sc", "nc"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "contributed" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "public/models/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml index cb0d6e8b..7a5afd6a 100644 --- a/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml +++ b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml @@ -4,6 +4,7 @@ description: "Runtime-only BNGL model migrated from public/models: Myrtle_Beach- tags: ["myrtle", "beach", "conway", "north", "sc", "nc"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Nag2009/Nag2009_aigenerated.md b/Published/Nag2009/Nag2009_aigenerated.md new file mode 100644 index 00000000..15c56187 --- /dev/null +++ b/Published/Nag2009/Nag2009_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Nag 2009 + +## One-sentence summary + +FcεRI activation phosphorylates LAT and drives multivalent LAT–Grb2–SOS1 crosslinking. + +## What the model shows + +This model connects early FcεRI/Syk signaling to assembly of a LAT-centered adaptor network. Ligand aggregates receptors, receptor-associated Syk becomes phosphorylated, active Syk modifies LAT, and phosphorylated LAT recruits Grb2 and bivalent SOS1 to build larger signaling complexes. + +## Biological story + +Multivalent ligand brings FcεRI receptors together and enables Syk recruitment and activation. Active Syk phosphorylates LAT, creating docking sites for Grb2. Grb2 then links LAT to SOS1, whose two Grb2-binding positions allow LAT-containing assemblies to crosslink. + +## Main biological players + +Multivalent ligand, FcεRI receptor, Syk, LAT, Grb2, and SOS1. + +## Mechanism in plain English + +Ligand first aggregates receptors. Receptor phosphorylation creates Syk-binding sites, and neighboring kinases promote Syk activation. Active Syk modifies LAT. Grb2 binds phosphorylated LAT through its SH2 domain and binds SOS1 through its SH3 domain; because SOS1 can engage two Grb2 molecules, repeated recruitment creates crosslinked LAT assemblies. Dephosphorylation and reversible binding oppose assembly. + +## Key modeled events + +- Ligand crosslinks FcεRI and creates receptor-associated Syk complexes. +- Syk is activated within receptor aggregates and phosphorylates LAT. +- Grb2 docks on phosphorylated LAT and recruits SOS1. +- Bivalent SOS1 links Grb2-bound LAT molecules into larger assemblies. + +## What the model measures + +Readouts distinguish several receptor–Syk activation states together with free, bound, and phosphorylated LAT, free Grb2, and free SOS1. + +## Expected behavior in plots + +Receptor–Syk complexes should rise first after ligand aggregation. Phosphorylated LAT should follow, accompanied by loss of free Grb2 and SOS1 as LAT-centered assemblies form. The timing between receptor activation and LAT occupancy exposes the handoff from FcεRI to the adaptor layer. + +## Caveats + +The model emphasizes LAT crosslinking and omits many parallel FcεRI outputs. Several possible aggregate measurements are not explicitly reported, so network size is inferred through component depletion and LAT states. diff --git a/Published/Nag2009/Nag_2009_metadata.yaml b/Published/Nag2009/Nag_2009_metadata.yaml new file mode 100644 index 00000000..445878bd --- /dev/null +++ b/Published/Nag2009/Nag_2009_metadata.yaml @@ -0,0 +1,24 @@ +id: "Nag_2009" +name: "Nag 2009" +description: "LAT-Grb2-SOS1 signaling" +tags: ["published", "nag", "2009", "lig", "lyn", "syk", "rec", "lat", "grb", "sos"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Nag_2009.bngl" +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" diff --git a/Published/Nag2009/metadata.yaml b/Published/Nag2009/metadata.yaml index 3c347840..4361dae8 100644 --- a/Published/Nag2009/metadata.yaml +++ b/Published/Nag2009/metadata.yaml @@ -4,6 +4,7 @@ description: "LAT-Grb2-SOS1 signaling" tags: ["published", "nag", "2009", "lig", "lyn", "syk", "rec", "lat", "grb", "sos"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Nosbisch2022/Nosbisch2022_aigenerated.md b/Published/Nosbisch2022/Nosbisch2022_aigenerated.md new file mode 100644 index 00000000..961883e7 --- /dev/null +++ b/Published/Nosbisch2022/Nosbisch2022_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Nosbisch 2022 + +## One-sentence summary + +RTK binding, Tyr783 phosphorylation, and intramolecular SH2 engagement govern PLCγ1 activation and shutoff. + +## What the model shows + +This compact model separates receptor recruitment of PLCγ1 from its internal activation switch. It tracks how an RTK captures inactive or active PLCγ1, promotes Tyr783 phosphorylation, and enables an intramolecular interaction that relieves autoinhibition, followed by dephosphorylation and return to the inactive state. + +## Biological story + +PLCγ1 begins largely inactive in the cytosol. A phosphorylated RTK recruits it through the N-terminal SH2 domain. Tyr783 becomes phosphorylated, can engage the C-terminal SH2 domain internally, and helps shift the catalytic core toward activity. Reversal steps disengage the internal contact and reset PLCγ1. + +## Main biological players + +Phosphorylated RTK, PLCγ1 N- and C-terminal SH2 domains, Tyr783, and the inactive/active PLCγ1 core. + +## Mechanism in plain English + +RTK captures PLCγ1 and holds it near the receptor. Bound PLCγ1 is phosphorylated at Tyr783. The phosphorylated tyrosine associates internally with the C-terminal SH2 domain, competing with an autoinhibitory core contact and favoring the active conformation. PLCγ1 can detach, lose Tyr783 phosphorylation, close its inhibitory contact, and return to inactivity. + +## Key modeled events + +- Phosphorylated RTK recruits PLCγ1 through its N-terminal SH2 domain. +- Receptor-bound PLCγ1 becomes phosphorylated at Tyr783. +- Tyr783 engages the C-terminal SH2 domain and favors catalytic-core activation. +- Dephosphorylation and inhibitory reclosure return PLCγ1 to the inactive pool. + +## What the model measures + +Readouts separate total PLCγ1, active and inactive forms, Tyr783 phosphorylation, RTK-bound PLCγ1, inactive receptor complexes, and cytosolic inactive PLCγ1. + +## Expected behavior in plots + +RTK-bound inactive PLCγ1 should rise early, followed by Tyr783 phosphorylation and active PLCγ1. As dissociation, dephosphorylation, and reclosure proceed, receptor-bound and active curves should fall while inactive cytosolic PLCγ1 recovers. + +## Caveats + +The model focuses on the PLCγ1 conformational switch. It does not include phospholipid hydrolysis, calcium release, PKC activation, or broader RTK signaling. diff --git a/Published/Nosbisch2022/Nosbisch2022_aigenerated_detailed.md b/Published/Nosbisch2022/Nosbisch2022_aigenerated_detailed.md new file mode 100644 index 00000000..ce7b0142 --- /dev/null +++ b/Published/Nosbisch2022/Nosbisch2022_aigenerated_detailed.md @@ -0,0 +1,75 @@ +# Detailed Model Explanation: Nosbisch 2022 RTK–PLCγ1 activation model + +## 1. Model overview + +This model follows phospholipase C gamma 1 (PLCγ1) recruitment to a phosphorylated receptor tyrosine kinase (RTK), phosphorylation of PLCγ1 Tyr783, and rearrangement of its inhibitory intramolecular contacts. Receptor binding and a time-gated background pathway activate the PLCγ1 core, while dephosphorylation, contact re-formation, and core inactivation return it toward the resting state. + +## 2. BNGL block inventory + +The model has 1 three-dimensional compartment, an empty parameters block, 2 molecule types, 2 seed species, 9 observables, an empty functions block, 12 labeled rules, and 1 network-generation action. It has no anchors and no simulation action. + +## 3. Parameters, functions, and rate laws + +Most rules use literal first-order or association rates. Two rules use time-dependent Boolean expressions intended to turn off at `t = 5000`, and one of them multiplies that gate by `kact_p`, which is not declared locally. + +| Parameter group or names | Function in this model | +| --- | --- | +| Literal association rates `1000.0` and `100.0` | Drive fast active-PLCγ1 recruitment to RTK and rapid formation of inhibitory or Tyr783–cSH2 intramolecular contacts. | +| Literal transition rates `10.0`, `1.0`, and `0.1` | Control receptor-bound core activation, most bond/state reversals, and slow spontaneous core inactivation, respectively. | +| Time gate `(t < 5000)` | Limits inactive PLCγ1 recruitment in `r01` and background activation in `r11` to the early phase, assuming the parser evaluates the comparison numerically. | +| `kact_p` | Scales the gated background activation rule `r11`, but no value is declared in the BNGL file. | + +There are no active functions despite the empty functions block. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `RTK` | 1 | `pY` | None | `cell` | A receptor represented only by a phosphotyrosine docking site for PLCγ1 `nSH2`; receptor phosphorylation itself is not modeled as a state transition. | +| `PLCgamma1` | 4 | `nSH2`, `Tyr783`, `cSH2`, `core` | `Tyr783: u, p`; `core: inactive, active` | `cell` | The signaling protein: `nSH2` docks to RTK, Tyr783 is phosphorylated/dephosphorylated, `cSH2` forms alternative intramolecular contacts, and `core` records catalytic activation. | + +## 5. Compartments, anchors, initial species, and setup + +All species occupy one unit-volume, three-dimensional `cell` compartment; there are no anchors or transport rules. RTK begins free at 0.05, while PLCγ1 begins at 0.02 in an inactive, Tyr783-unphosphorylated conformation whose `cSH2` and `core` sites are internally bonded. Thus the initial PLCγ1 pool must first open or be activated before it can explore all modeled contacts. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules `r01`–`r05` cover receptor docking and Tyr783 modification. Rules `r06`–`r09` exchange the resting cSH2–core contact for a phospho-Tyr783–cSH2 contact. Rules `r10`–`r12` govern activation and deactivation of the PLCγ1 core. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| `r02` | One-way | RTK `pY`; active PLCγ1 `nSH2` | Creates the RTK-pY–PLCγ1-nSH2 bond at `1000.0`; no PLCγ1 state changes. | Rapidly captures already-active PLCγ1 at the receptor. | +| `r01` | One-way | RTK `pY`; inactive PLCγ1 `nSH2`; any existing bond on `core` is allowed | Creates the same receptor–nSH2 bond only while `(t < 5000)` evaluates true. | Restricts recruitment of inactive PLCγ1 to the intended early stimulation window. | +| `r03` | One-way | RTK-bound PLCγ1 through `pY–nSH2` | Releases the receptor–nSH2 bond at `1.0`. | Returns both proteins to their free docking states and opposes `r01`/`r02`. | +| `r04` | One-way | RTK-bound PLCγ1 with `Tyr783~u`, regardless of a Tyr783 bond | Changes `Tyr783: u → p` at `1.0` while retaining receptor binding. | Couples receptor residence to phosphorylation of the PLCγ1 regulatory tyrosine. | +| `r05` | One-way | Any PLCγ1 with unbound `Tyr783~p` | Changes `Tyr783: p → u` at `1.0`. | Removes the phosphotyrosine signal, but cannot act while Tyr783 is engaged with cSH2. | +| `r06` | One-way | Inactive PLCγ1 with an internal `cSH2–core` bond | Breaks the cSH2–core bond at `1.0`; the core remains inactive. | Opens the resting autoinhibitory contact without directly activating the core. | +| `r07` | One-way | Inactive PLCγ1 with free `cSH2` and `core` | Re-forms the internal cSH2–core bond at `100.0`. | Strongly favors restoration of the closed resting conformation. | +| `r08` | One-way | PLCγ1 with phosphorylated, free Tyr783 and free cSH2 | Creates an intramolecular Tyr783-p–cSH2 bond at `100.0`. | Lets phosphorylated Tyr783 sequester cSH2 away from the inhibitory core contact. | +| `r09` | One-way | PLCγ1 containing the Tyr783-p–cSH2 bond | Releases that intramolecular bond at `1.0` without dephosphorylating Tyr783. | Reopens both sites so cSH2 can rebind the core or Tyr783 can be dephosphorylated. | +| `r10` | One-way | RTK-bound PLCγ1 with inactive core | Changes `core: inactive → active` at `10.0`; receptor binding remains intact. | Makes receptor recruitment a direct activation route. | +| `r11` | One-way | Cytosolic PLCγ1 with free nSH2 and inactive core | Changes `core: inactive → active` at `(t < 5000) * kact_p`. | Provides a receptor-independent, early-phase activation route whose strength depends on the missing `kact_p`. | +| `r12` | One-way | Any PLCγ1 with active core | Changes `core: active → inactive` at `0.1`. | Supplies basal signal termination regardless of receptor or intramolecular-contact state. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `O0_RTK_tot`, `O0_PLCgamma1_tot` | Molecule count | All RTK or all PLCγ1 molecules in `cell` | Conservation checks for the two molecular pools. | +| `O0_PLCgamma1_active`, `O0_PLCgamma1_inactive` | Molecule count | PLCγ1 grouped by core state, independent of whether the core site is bonded | The principal activation-state readouts; together they partition the PLCγ1 pool by core activity. | +| `O0_PLCgamma1_pTyr783`, `O0_PLCgamma1_dpTyr783` | Molecule count | Phosphorylated or unphosphorylated Tyr783, with either bond status | Reports the regulatory-tyrosine cycle separately from core activation. | +| `O0_PLCgamma1_RTK_bound_inactive` | Molecule count | Inactive PLCγ1 joined from nSH2 to RTK pY | Isolates the recruited-but-not-yet-activated intermediate consumed by `r10`. | +| `O0_PLCgamma1_RTK_bound` | Molecule count | Any PLCγ1 joined to RTK through nSH2 | Total receptor recruitment, irrespective of Tyr783 or core state. | +| `O0_PLCgamma1_cytosol` | Molecule count | Inactive PLCγ1 with free nSH2 | Operational “cytosolic” pool; because there is only one compartment, this means receptor-unbound rather than a distinct spatial location. | + +## 8. Actions and simulation workflow + +The file generates a bounded reaction network with at most seven iterations, aggregate size 10, and up to 100 copies each of RTK and PLCγ1. It does not run a simulation; an external workflow must supply `kact_p`, select a simulator, and integrate across the `t = 5000` gate if that syntax is supported. + +## 9. Technical caveats and ambiguities + +- `kact_p` is referenced but undeclared, so `r11` cannot be assigned a numerical rate from this file alone. +- The comparison expression in `r01` is itself placed in the rate position; support for Boolean-valued time expressions is parser-dependent. +- Metadata claims ODE support even though the file contains only network generation and the compatibility record marks BNG2 as false. +- “Cytosol” is an observable name, not a separate compartment. +- The initial cSH2–core bond is intramolecular; summaries or visualizers that treat it as an intermolecular complex would misread the setup. diff --git a/Published/Nosbisch2022/Nosbisch_2022_metadata.yaml b/Published/Nosbisch2022/Nosbisch_2022_metadata.yaml new file mode 100644 index 00000000..caf4a201 --- /dev/null +++ b/Published/Nosbisch2022/Nosbisch_2022_metadata.yaml @@ -0,0 +1,67 @@ +id: "Nosbisch_2022" +name: "Nosbisch 2022" +description: "RTK-PLCgamma1 signaling" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2023" + pmid: "35367415" + reference: "Nosbisch et al., 2022" + +tags: ["published", "nosbisch", "2022", "rtk", "plcgamma1", "generate_network"] +date: + last_tested: 2026-07-19 + +category: "signaling" +biol_categories: ["signaling"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: false + comments: "nfsim Parameter t is referenced but not defined at line 52MCP There was an issue with BNGL model: Nosbisch_2022.bngl XML file couldn't be generated after removing generate network and 0.05 nfsim begin block before end of previous block parameters at line 41" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: true + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Nosbisch_2022.bngl" + +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" + + + + + + diff --git a/Published/Nosbisch2022/metadata.yaml b/Published/Nosbisch2022/metadata.yaml index 0c755c1c..762c06b7 100644 --- a/Published/Nosbisch2022/metadata.yaml +++ b/Published/Nosbisch2022/metadata.yaml @@ -4,6 +4,7 @@ description: "RTK-PLCgamma1 signaling" tags: ["published", "nosbisch", "2022", "rtk", "plcgamma1", "generate_network"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: true diff --git a/Published/Ordyan2020/CaMKIIholo/CaMKII_holo_metadata.yaml b/Published/Ordyan2020/CaMKIIholo/CaMKII_holo_metadata.yaml new file mode 100644 index 00000000..6def41f9 --- /dev/null +++ b/Published/Ordyan2020/CaMKIIholo/CaMKII_holo_metadata.yaml @@ -0,0 +1,24 @@ +id: "CaMKII_holo" +name: "Ordyan 2020: CaMKII holo" +description: "CaMKII holo" +tags: ["published", "neuroscience", "camkii", "holo", "ca", "cam", "ng", "pp1", "time_counter"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/Ordyan_2020/CaMKII_holo.bngl" +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: "advanced" diff --git a/Published/Ordyan2020/CaMKIIholo/CaMKIIholo_aigenerated.md b/Published/Ordyan2020/CaMKIIholo/CaMKIIholo_aigenerated.md new file mode 100644 index 00000000..b154f9c1 --- /dev/null +++ b/Published/Ordyan2020/CaMKIIholo/CaMKIIholo_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Ordyan 2020 CaMKII holoenzyme + +## One-sentence summary + +Calcium-loaded calmodulin activates a multimeric CaMKII holoenzyme whose autophosphorylation stores and erases signaling history. + +## What the model shows + +This model follows calcium/calmodulin-dependent protein kinase II (CaMKII) as a holoenzyme rather than isolated subunits. Calmodulin (CaM), neurogranin, and protein phosphatase 1 (PP1) control activation and memory-like phosphorylation. + +## Biological story + +Calcium binds the N- and C-terminal lobes of CaM. Loaded CaM leaves neurogranin, binds CaMKII subunits, and exposes kinase activity. Neighboring active subunits phosphorylate Thr286, supporting persistent activity, while Ser306 phosphorylation and PP1 promote shutoff. + +## Main biological players + +Calcium, CaM, neurogranin, CaMKII holoenzyme subunits, Thr286, Ser306, and PP1. + +## Mechanism in plain English + +Calcium loads CaM in multiple steps and changes its affinity for neurogranin and CaMKII. Bound CaM activates subunits within the ring-like holoenzyme. Adjacent active subunits autophosphorylate Thr286, allowing activity to outlast the calcium pulse; competing Ser306 modification and PP1 dephosphorylation reset the complex. + +## Key modeled events + +- Calcium loads both lobes of calmodulin. +- Calcium-loaded CaM disengages from neurogranin and binds CaMKII. +- Neighboring active CaMKII subunits phosphorylate Thr286. +- Ser306 phosphorylation restricts CaM rebinding. +- PP1 removes activating phosphorylation. + +## What the model measures + +Readouts distinguish CaM calcium-loading states, CaM-bound CaMKII forms, phosphorylation states, and holoenzyme activation across the simulated pulse protocol. + +## Expected behavior in plots + +Calcium-loaded CaM should rise immediately with a calcium pulse, followed by CaM-bound kinase and Thr286 phosphorylation. Thr286 activity may persist after free calcium falls, whereas PP1 should drive slower recovery; neurogranin-bound CaM should change oppositely to available CaM. + +## Caveats + +The model resolves many biochemical states but represents one idealized holoenzyme population. Synaptic geometry, diffusion, and other CaMKII substrates are not included. diff --git a/Published/Ordyan2020/CaMKIIholo/metadata.yaml b/Published/Ordyan2020/CaMKIIholo/metadata.yaml index dfcbd0d8..fcd21bb7 100644 --- a/Published/Ordyan2020/CaMKIIholo/metadata.yaml +++ b/Published/Ordyan2020/CaMKIIholo/metadata.yaml @@ -4,6 +4,7 @@ description: "CaMKII holo" tags: ["published", "neuroscience", "camkii", "holo", "ca", "cam", "ng", "pp1", "time_counter"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/Ordyan2020/extraCaMKIIHolo/extra_CaMKII_Holo_metadata.yaml b/Published/Ordyan2020/extraCaMKIIHolo/extra_CaMKII_Holo_metadata.yaml new file mode 100644 index 00000000..8661b1e4 --- /dev/null +++ b/Published/Ordyan2020/extraCaMKIIHolo/extra_CaMKII_Holo_metadata.yaml @@ -0,0 +1,24 @@ +id: "extra_CaMKII_Holo" +name: "Ordyan 2020: extra CaMKII holo" +description: "Extra CaMKII holo (supplement)" +tags: ["published", "neuroscience", "extra", "camkii", "holo", "t1", "t2", "t3", "t4", "t5", "t6", "t7", "t8"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/Ordyan_2020/extra_CaMKII_Holo.bngl" +playground: + visible: false + gallery_category: "signaling" + featured: false + difficulty: "advanced" diff --git a/Published/Ordyan2020/extraCaMKIIHolo/metadata.yaml b/Published/Ordyan2020/extraCaMKIIHolo/metadata.yaml index 0cbd1c9d..62e14f0a 100644 --- a/Published/Ordyan2020/extraCaMKIIHolo/metadata.yaml +++ b/Published/Ordyan2020/extraCaMKIIHolo/metadata.yaml @@ -4,6 +4,7 @@ description: "Extra CaMKII holo (supplement)" tags: ["published", "neuroscience", "extra", "camkii", "holo", "t1", "t2", "t3", "t4", "t5", "t6", "t7", "t8"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Ordyan2020/mCaMKIICaSpike/mCaMKII_Ca_Spike_metadata.yaml b/Published/Ordyan2020/mCaMKIICaSpike/mCaMKII_Ca_Spike_metadata.yaml new file mode 100644 index 00000000..edf6dc58 --- /dev/null +++ b/Published/Ordyan2020/mCaMKIICaSpike/mCaMKII_Ca_Spike_metadata.yaml @@ -0,0 +1,24 @@ +id: "mCaMKII_Ca_Spike" +name: "Ordyan 2020: mCaMKII Ca Spike" +description: "mCaMKII Ca Spike model" +tags: ["published", "neuroscience", "mcamkii", "ca", "spike", "cam", "ng", "camkii", "pp1", "time_counter"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/Ordyan_2020/mCaMKII_Ca_Spike.bngl" +playground: + visible: true + gallery_category: "signaling" + featured: false + difficulty: "intermediate" diff --git a/Published/Ordyan2020/mCaMKIICaSpike/metadata.yaml b/Published/Ordyan2020/mCaMKIICaSpike/metadata.yaml index 3b80909f..fcda264b 100644 --- a/Published/Ordyan2020/mCaMKIICaSpike/metadata.yaml +++ b/Published/Ordyan2020/mCaMKIICaSpike/metadata.yaml @@ -4,6 +4,7 @@ description: "mCaMKII Ca Spike model" tags: ["published", "neuroscience", "mcamkii", "ca", "spike", "cam", "ng", "camkii", "pp1", "time_counter"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Pekalski2013/Pekalski2013_aigenerated.md b/Published/Pekalski2013/Pekalski2013_aigenerated.md new file mode 100644 index 00000000..bbe7c162 --- /dev/null +++ b/Published/Pekalski2013/Pekalski2013_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Pekalski 2013 + +## One-sentence summary + +Autocrine TNF–NF-κB signaling generates spontaneous inflammatory pulses restrained by IκBα and A20 feedback. + +## What the model shows + +This model couples tumor necrosis factor (TNF) secretion to its own receptor pathway. NF-κB means nuclear factor kappa B, IKK is IκB kinase, and IκBα is the inhibitor that retains NF-κB outside the nucleus. + +## Biological story + +Basal fluctuations activate TNF receptor 1, which drives an IKK kinase cascade. IKK removes IκBα and releases NF-κB. Nuclear NF-κB induces TNF, IκBα, and A20; secreted TNF reinforces receptor signaling, while IκBα and A20 terminate it. + +## Main biological players + +TNF and TNFR1, IKKK, IKK, NF-κB, IκBα, A20, their transcripts, and stochastic gene switches. + +## Mechanism in plain English + +Receptor activation propagates through IKKK to IKK. IKK phosphorylates IκBα, causing inhibitor loss and nuclear NF-κB entry. NF-κB switches target genes on, producing new TNF plus two inhibitors. Extracellular TNF closes a positive autocrine loop; newly synthesized IκBα and A20 impose delayed negative feedback. + +## Key modeled events + +- TNFR1 activates the IKKK–IKK cascade. +- IKK removes IκBα and releases NF-κB. +- NF-κB induces TNF, IκBα, and A20 genes. +- Secreted TNF reinforces receptor activation. +- IκBα and A20 terminate each inflammatory episode. + +## What the model measures + +Readouts include receptor and kinase states, nuclear and cytoplasmic NF-κB, NF-κB–IκBα complexes, extracellular and intracellular TNF, and A20/IκBα transcripts and proteins. + +## Expected behavior in plots + +A spontaneous receptor event can generate an IKK pulse followed by nuclear NF-κB. TNF feedback may amplify that episode, while delayed IκBα and A20 should drive recovery and create separated pulses rather than sustained maximal activity. + +## Caveats + +The pulse mechanism is a reduced single-cell regulatory system. Tissue cytokine transport, immune-cell diversity, and many TNF targets are omitted. diff --git a/Published/Pekalski2013/Pekalski2013_aigenerated_detailed.md b/Published/Pekalski2013/Pekalski2013_aigenerated_detailed.md new file mode 100644 index 00000000..0934b5ed --- /dev/null +++ b/Published/Pekalski2013/Pekalski2013_aigenerated_detailed.md @@ -0,0 +1,94 @@ +# Detailed Model Explanation: Pekalski 2013 Spontaneous TNF–NF-κB Signaling + +## 1. Model overview + +This model couples tumor necrosis factor (TNF) receptor activation to an IKKK–IKK kinase relay and nuclear factor κB (NF-κB) control of TNF, A20, and IκBα gene expression. Its feedback architecture combines self-amplifying TNF production with A20-mediated signal restraint and IκBα-mediated sequestration and export of NF-κB. + +## 2. BNGL block inventory + +The file contains 42 parameters, 14 molecule types, 29 seed species, 4 functions, 40 reaction rules, 29 observables, and 4 actions. There are no explicit compartments or anchors; localization is encoded by internal `loc` states. + +## 3. Parameters, functions, and rate laws + +The namespace separates receptor/kinase activation, binary gene switching, expression and turnover, binding/phosphorylation, and nucleocytoplasmic transport. Most rules are one-way mass-action transitions; four observable-dependent functions make receptor and kinase activation state dependent, and two derived rates combine base parameters algebraically. + +| Parameter group or names | Function in this model | +| --- | --- | +| `R`, `K_N`, `K_NN`, `NFkB_tot`, `k_v` | Define initial receptor, kinase, and NF-κB pools plus the nuclear/cytoplasmic volume scaling used in nuclear NF-κB–IκBα association. | +| `c_deg`, `k_b`, `c_sec`, `c_b`, `k_f` | Control extracellular TNF removal, external or internal TNF-driven receptor activation, and receptor return to the inactive state. | +| `k_a`, `k_A20`, `k_i`, `k_1`–`k_4` | Drive the IKKK–IKK relay and its recovery cycle; A20 enters the calculated IKKK and IKK transition rates. | +| `q_1`, `q_2`, `q_1t`, `q_2t`, `q_2tt` | Switch A20, IκBα, and TNF gene copies on or off in response to nuclear NF-κB or IκBα, including autonomous TNF-gene shutoff. | +| `lambda`, `c_1`, `c_3`, `c_3t`, `c_4`, `c_4t` | Set transcription, transcript decay, and translation for the three feedback products. | +| `a_1`, `a_2`, `a_3`, `k_NFkBIkB`, `t_p`, `c_6a` | Govern NF-κB–IκBα association, IKK-catalyzed IκBα phosphorylation, and loss of free or NF-κB-bound IκBα. | +| `c_5`, `c_5a`, `c_5t`, `k_TNFdeg` | Set turnover of A20, unphosphorylated IκBα, and internal TNF; `k_TNFdeg` combines secretion and intracellular loss. | +| `i_1`, `i_1a`, `e_1a`, `e_2a` | Control nuclear import of free NF-κB and IκBα, export of free IκBα, and export of the nuclear NF-κB–IκBα complex. | + +| Function | Inputs/dependencies | Meaning and use in this model | +| --- | --- | --- | +| `k_Ractivation` | Inactive-receptor observable `TNFR_i`; `c_sec`, `c_b` | Makes internal-TNF receptor activation inversely dependent on the current inactive receptor pool. | +| `k_IKKKactivation` | Active receptor `TNFR_a`, A20; `k_a`, `k_A20` | Converts receptor activity into IKKK activation while applying an A20-dependent saturating factor. | +| `k_IKKactivation` | Active IKKK `IKKK_a`; `k_1` | Uses the square of active IKKK, making IKK activation strongly nonlinear. | +| `k_IKKintermetiation` | A20; `k_2`, `k_3` | Sets active IKK entry into its inactive intermediate and increases that transition with A20 abundance. | + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `TNFR` | 1 | `st` | active (`a`), inactive (`i`) | None | Lumped TNF receptor whose activity feeds the kinase cascade. | +| `IKKK` | 1 | `st` | neutral (`n`), active (`a`) | None | Upstream kinase activated from the receptor/A20-dependent function. | +| `IKK` | 1 | `st` | neutral (`n`), active (`a`), inactive (`i`), inactive intermediate (`ii`) | None | Kinase that phosphorylates IκBα and then traverses a two-step refractory cycle. | +| `NFkB` | 2 | `loc`, `bin` | `loc`: nuclear (`n`) or cytoplasmic (`c`) | None | Transcriptional regulator whose free nuclear form switches feedback genes on. | +| `IkBa` | 3 | `loc`, `pho`, `bin` | `loc`: `n`/`c`; `pho`: unphosphorylated (`0`) or phosphorylated (`p`) | None | NF-κB inhibitor; binding, phosphorylation, and transport determine NF-κB availability. | +| `TNF` | 1 | `loc` | extracellular (`e`), intracellular (`i`) | None | Secreted stimulus and transcriptional feedback product. | +| `GA20`, `GIkBa`, `GTNF` | 1 each | `st` | off (`0`), on (`1`) | None | Two-state gene copies that gate production of their respective transcripts. | +| `A20_mRNA`, `IkBa_mRNA`, `TNF_mRNA` | 0 each | None | None | None | Transcript pools connecting gene state to protein production. | +| `A20` | 0 | None | None | None | Negative-feedback regulator of the receptor-to-IKK relay. | +| `Trash` | 0 | None | None | None | Sink for extracellular ligand, transcripts, and degraded proteins. | + +## 5. Compartments, anchors, initial species, and setup + +No geometrical compartments are declared. Nuclear and cytoplasmic location is carried by NF-κB and IκBα states, whereas TNF distinguishes intracellular from extracellular pools. The initial condition places the receptor and kinases predominantly in inactive/neutral states, seeds cytoplasmic NF-κB bound to unphosphorylated IκBα, supplies basal A20 and transcript pools, and initializes two off copies of each regulated gene. Extracellular TNF initially vanishes; it is introduced later by an action. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–10 transmit TNF input through the receptor and kinase relay, 11–26 implement gene-state feedback and expression, 27–36 control NF-κB–IκBα chemistry and protein turnover, and 37–40 move free or inhibited regulators between nuclear and cytoplasmic states. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1 | One-way | Extracellular `TNF.loc=e` | Removes TNF to `Trash` at `c_deg`. | Limits the duration of extracellular stimulation. | +| 2–4 | One-way | `TNFR.st`; external or internal `TNF.loc` | Rules 2 and 3 change inactive receptor to active without consuming TNF, using `k_b` and `k_Ractivation`; rule 4 resets active receptor at `k_f`. | Converts either TNF pool into transient receptor activity. | +| 5–6 | One-way | `IKKK.st` | Neutral IKKK becomes active at receptor/A20-dependent `k_IKKKactivation`, then returns at `k_i`. | Creates the first reversible-in-effect stage of the kinase pulse. | +| 7–10 | One-way | `IKK.st` | Neutral IKK activates at quadratic `k_IKKactivation`; active IKK enters `i` through the A20-sensitive function, then passes `i→ii→n` at `k_4`. | Produces active IKK while enforcing a refractory recovery path. | +| 11–16 | One-way | Free nuclear `NFkB` or IκBα; gene `st` | NF-κB switches A20/IκBα/TNF genes `0→1` (11,12,15); nuclear IκBα switches them `1→0` (13,14,16). Regulators are catalytic and retained. | Opposes NF-κB-driven transcription with an inhibitor-dependent gene shutoff mechanism. | +| 17 | One-way | `GTNF.st=1` | Turns the active TNF gene off at `q_2tt` without requiring IκBα. | Adds an intrinsic limit to the TNF transcriptional episode. | +| 18–20 | One-way | Active TNF, A20, or IκBα gene | Retains the on-state gene and creates its transcript at `lambda` (TNF) or `c_1` (A20/IκBα). | Converts discrete gene activation into continuous transcript production. | +| 21–26 | One-way | Three mRNAs and their protein products | A20 and IκBα transcripts decay at `c_3` and translate at `c_4`; TNF mRNA decays at `c_3t` and creates internal TNF at `c_4t`. | Implements expression kinetics for positive and negative feedback arms. | +| 27–28 | One-way | `NFkB.bin`, unphosphorylated `IkBa.bin`; matched location | Creates the inhibitor bond in cytoplasm at `a_1` or nucleus at volume-scaled `k_NFkBIkB`. | Sequesters free NF-κB in either location. | +| 29–30 | One-way | Active `IKK`; free or NF-κB-bound cytoplasmic `IkBa.pho` | Changes IκBα phosphorylation `0→p` at `a_2` (free) or `a_3` (bound), retaining IKK and any NF-κB bond. | Marks the inhibitor for removal while preserving catalytic IKK. | +| 31–36 | One-way | A20, free/bound IκBα, internal TNF | Removes A20 (31), phosphorylated free IκBα (32), bound phosphorylated IκBα while releasing NF-κB (33), unphosphorylated IκBα (34), internal TNF (35), or bound unphosphorylated IκBα while releasing NF-κB (36), each at its named turnover rate. | Sets feedback lifetimes and regenerates free NF-κB when its inhibitor is lost. | +| 37–39 | One-way | Free `NFkB.loc` or unphosphorylated free `IkBa.loc` | NF-κB imports `c→n` at `i_1`; IκBα imports at `i_1a` and exports at `e_1a`. | Supplies nuclear NF-κB for gene activation and nuclear IκBα for shutoff. | +| 40 | One-way | Nuclear NF-κB–IκBα complex | Changes both partners from nuclear to cytoplasmic while retaining their bond, at `e_2a`. | Removes inhibited NF-κB from the nucleus as a complex. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `TNFR_a`, `TNFR_i`; `IKKK_a`; `IKK_a`, `IKK_n`, `IKK_i` | Species count | Receptor and kinase state-specific species. | Resolve signal propagation and IKK recovery; `IKK_i` does not include the separate `ii` state. | +| `NFkB_nuc`, `NFkB_cyt` | Species count | Free NF-κB in each encoded location. | Measure transcriptionally available versus cytoplasmic NF-κB rather than total NF-κB. | +| `NFkB_IkBa_p_cyt`, `NFkB_IkBa_u_cyt`, `NFkB_IkBa_u_nuc` | Species count | Location- and phosphorylation-specific NF-κB–IκBα complexes. | Distinguish inhibited complexes from the phosphorylated complex poised for IκBα loss. | +| `IkBa_p_cyt`, `IkBa_u_cyt`, `IkBa_u_nuc` | Species count | Free IκBα states and locations. | Track inhibitor availability outside complexes. | +| `TNF_ext`, `TNF_int`, `A20` | Species count | The two TNF pools and A20 protein. | Report the positive feedback signal and its receptor-pathway antagonist. | +| `tA20`, `tIkB`, `tTNF` | Species count | Each feedback transcript. | Separate transcriptional responses from downstream protein abundance. | +| `gA20_a/i`, `gIkBa_a/i`, `gTNF_a/i` | Species count | On and off gene-copy states. | Expose the binary switching layer directly. | +| `IKK_tot_`, `IKKK_tot_`, `NFkB_tot_` | Molecule count | Each molecule across internal states, locations, and binding contexts. | Conservation checks that can be compared with the corresponding state-resolved observables. | + +## 8. Actions and simulation workflow + +The model first generates a reaction network and integrates its ordinary differential equations for 300 hours to establish an unstimulated trajectory. It then sets extracellular TNF to one unit and continues the same system for 10 hours, producing separate pre-stimulus and post-stimulus output suffixes. + +## 9. Technical caveats and ambiguities + +- “Spontaneous signaling” is represented by state-dependent activation functions and basal initialized pools; no stochastic simulation is used. +- Localization states substitute for physical compartments, so nuclear/cytoplasmic volume effects enter only where explicitly encoded, notably `k_NFkBIkB`. +- Several observables use `Species`, whereas the three totals use `Molecules`; their numerical meanings differ when complexes are present. +- The two inactive IKK states (`i` and `ii`) form a sequence, but only `i` has a dedicated observable. diff --git a/Published/Pekalski2013/Pekalski_2013_metadata.yaml b/Published/Pekalski2013/Pekalski_2013_metadata.yaml new file mode 100644 index 00000000..545a445b --- /dev/null +++ b/Published/Pekalski2013/Pekalski_2013_metadata.yaml @@ -0,0 +1,65 @@ +id: "Pekalski_2013" +name: "Pekalski 2013" +description: "Spontaneous signaling" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2013" + pmid: "24324544" + reference: "Pekalski et al., 2013" + +tags: ["published", "pekalski", "2013", "tnfr", "ikk", "ikkk", "ikba", "ikba_mrna", "a20", "a20_mrna", "nfkb"] +date: + last_tested: 2026-07-16 + +category: "regulation" +biol_categories: ["regulation"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered c_sec at line 187" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: true + uses_compartments: false + nfsim_compatible: true + molclustpy_compatible: false + mpd_compatible: true + comments: "nfsim false in original but runs with bng2 MCP list index out of range" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: true + uses_compartments: false + uses_energy: false + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/Pekalski_2013.bngl" + +playground: + visible: true + gallery_category: "regulation" + featured: false + difficulty: "intermediate" + + + + diff --git a/Published/Pekalski2013/metadata.yaml b/Published/Pekalski2013/metadata.yaml index a4f6c9ac..62446033 100644 --- a/Published/Pekalski2013/metadata.yaml +++ b/Published/Pekalski2013/metadata.yaml @@ -4,6 +4,7 @@ description: "Spontaneous signaling" tags: ["published", "pekalski", "2013", "tnfr", "ikk", "ikkk", "ikba", "ikba_mrna", "a20", "a20_mrna", "nfkb"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Posner1995/Posner1995_aigenerated.md b/Published/Posner1995/Posner1995_aigenerated.md new file mode 100644 index 00000000..f865c744 --- /dev/null +++ b/Published/Posner1995/Posner1995_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Posner 1995 + +## One-sentence summary + +Bivalent ligand and receptor form chains that can reversibly close into cyclic dimers, producing a prozone-sensitive aggregate response. + +## What the model shows + +This aggregation model adds a specific ring-closure route to otherwise linear bivalent ligand–receptor chains. It can distinguish chain bonds from ring bonds and therefore asks when a four-member cyclic dimer dominates over open aggregates across ligand doses. + +## Biological story + +Ligand captures receptor and uses its second arm to crosslink another receptor. Repetition extends alternating chains. A particular two-ligand/two-receptor chain can close into a ring, and that ring can reopen; excess ligand eventually saturates receptor sites and suppresses crosslinking. + +## Main biological players + +Bivalent ligand, bivalent receptor, chain bonds, ring bonds, open chains, and a cyclic two-ligand/two-receptor complex. + +## Mechanism in plain English + +Free ligand binds receptor, then tethered ligand recruits receptor from a separate complex to extend a chain. Bond dissociation shortens or separates chains. When the ends of the specified four-member chain meet, they form a cyclic dimer; an explicit opening process restores the chain. Distinct bond states ensure ring opening is treated separately from ordinary chain breakup. + +## Key modeled events + +- Ligand capture creates the first ligand–receptor bond. +- A free ligand arm crosslinks an additional receptor to grow an open chain. +- A two-ligand/two-receptor chain closes reversibly into a cyclic dimer. +- High ligand occupancy can block crosslinking and create a bell-shaped dose response. + +## What the model measures + +Measurements include free ligand and receptor, total bonds, free sites, and the cyclic dimer population. + +## Expected behavior in plots + +At intermediate ligand dose, bond formation and cyclic dimers should be favored. Very low ligand gives little capture, whereas high ligand saturates receptors independently and suppresses bridging, so the cyclic-dimer or crosslinking response should show a prozone-like maximum. + +## Caveats + +Only one ring size is allowed, and larger cyclic structures are excluded. The model addresses aggregation physics rather than receptor signaling or cellular secretion. diff --git a/Published/Posner1995/blbr_rings_posner1995_metadata.yaml b/Published/Posner1995/blbr_rings_posner1995_metadata.yaml new file mode 100644 index 00000000..5ee40353 --- /dev/null +++ b/Published/Posner1995/blbr_rings_posner1995_metadata.yaml @@ -0,0 +1,23 @@ +id: "Posner_1995" +name: "Posner 1995" +description: "BLBR rings" +tags: ["published", "physics", "posner", "1995"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "physics" + featured: false + difficulty: "intermediate" diff --git a/Published/Posner1995/metadata.yaml b/Published/Posner1995/metadata.yaml index 049820c7..c1670e82 100644 --- a/Published/Posner1995/metadata.yaml +++ b/Published/Posner1995/metadata.yaml @@ -4,6 +4,7 @@ description: "BLBR rings" tags: ["published", "physics", "posner", "1995"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Posner2004/Posner2004_aigenerated.md b/Published/Posner2004/Posner2004_aigenerated.md new file mode 100644 index 00000000..8dc23cde --- /dev/null +++ b/Published/Posner2004/Posner2004_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Posner 2004 + +## One-sentence summary + +Negatively cooperative anti-IgE binding drives occupancy and linear crosslinking of bivalent IgE–FcεRI receptors. + +## What the model shows + +This model represents the monoclonal anti-IgE antibody 23G3 binding to two epitopes on receptor-bound IgE. It distinguishes first-site binding from reduced-affinity second-site binding and permits unbounded linear crosslinking, supporting equilibrium dose-response analysis under negative cooperativity. + +## Biological story + +Each bivalent 23G3 ligand can bind an epitope on an IgE–FcεRI receptor and use its second arm to recruit another receptor. Once one receptor epitope is occupied, the second epitope binds less favorably. Reversible binding redistributes receptors among free, singly occupied, and crosslinked states. + +## Main biological players + +Bivalent 23G3 anti-IgE antibody, bivalent IgE–FcεRI receptor units, free epitopes, and linear receptor–ligand chains. + +## Mechanism in plain English + +A free antibody arm captures a receptor epitope. Its remaining arm can crosslink another receptor, extending an alternating chain. Receptor occupancy reduces affinity at the other receptor epitope, representing negative cooperativity. Every contact can dissociate, allowing equilibrium occupancy to respond continuously to antibody concentration. + +## Key modeled events + +- 23G3 binds any available IgE epitope on a receptor unit. +- The second antibody arm recruits another receptor and extends a linear chain. +- Occupancy of one receptor epitope reduces binding at the other. +- Reversible dissociation returns ligand and receptor sites to the free pools. + +## What the model measures + +Readouts follow total antibody, occupancy of each receptor epitope, and fully free receptor. Together they define the fraction of available IgE sites engaged over an antibody concentration scan. + +## Expected behavior in plots + +Bound-epitope fractions should rise with 23G3 concentration and approach saturation, while free receptor falls. Negative cooperativity should broaden or flatten the transition compared with independent sites, and the two symmetric receptor-site curves should overlap. + +## Caveats + +Ring formation and secretory signaling are not represented. The model treats receptor–IgE units and antibody arms symmetrically and focuses on equilibrium binding rather than cell activation. diff --git a/Published/Posner2004/blbr_cooperativity_posner2004_metadata.yaml b/Published/Posner2004/blbr_cooperativity_posner2004_metadata.yaml new file mode 100644 index 00000000..21c1b36e --- /dev/null +++ b/Published/Posner2004/blbr_cooperativity_posner2004_metadata.yaml @@ -0,0 +1,23 @@ +id: "Posner_2004" +name: "Posner 2004" +description: "BLBR cooperativity" +tags: ["published", "physics", "posner", "2004"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "physics" + featured: false + difficulty: "intermediate" diff --git a/Published/Posner2004/metadata.yaml b/Published/Posner2004/metadata.yaml index 572cd50d..761f747a 100644 --- a/Published/Posner2004/metadata.yaml +++ b/Published/Posner2004/metadata.yaml @@ -4,6 +4,7 @@ description: "BLBR cooperativity" tags: ["published", "physics", "posner", "2004"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml index 45302f87..2fba8427 100644 --- a/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml +++ b/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml @@ -4,6 +4,7 @@ description: "c = 0.20 /d t_1/2 = 3.5 d (inferred)" tags: ["pt303", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/HIVdynamics/pt303/pt303_metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt303/pt303_metadata.yaml new file mode 100644 index 00000000..28fc0250 --- /dev/null +++ b/Published/PyBioNetGen/HIVdynamics/pt303/pt303_metadata.yaml @@ -0,0 +1,24 @@ +id: "pt303" +name: "pt303" +description: "c = 0.20 /d t_1/2 = 3.5 d (inferred)" +tags: ["pt303", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/HIVdynamics_aMCMC/pt303/pt303.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml index 9ea6825e..0a2c69aa 100644 --- a/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml +++ b/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml @@ -4,6 +4,7 @@ description: "c = 0.23 /d t_1/2 = 3.0 d (inferred)" tags: ["pt403", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/HIVdynamics/pt403/pt403_metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt403/pt403_metadata.yaml new file mode 100644 index 00000000..0fd84655 --- /dev/null +++ b/Published/PyBioNetGen/HIVdynamics/pt403/pt403_metadata.yaml @@ -0,0 +1,24 @@ +id: "pt403" +name: "pt403" +description: "c = 0.23 /d t_1/2 = 3.0 d (inferred)" +tags: ["pt403", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/HIVdynamics_aMCMC/pt403/pt403.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml index ef7cde20..43c5eab4 100644 --- a/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml +++ b/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml @@ -4,6 +4,7 @@ description: "c = 0.39 /d t_1/2 = 1.8 d (inferred)" tags: ["pt409", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/HIVdynamics/pt409/pt409_metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt409/pt409_metadata.yaml new file mode 100644 index 00000000..cf401b0f --- /dev/null +++ b/Published/PyBioNetGen/HIVdynamics/pt409/pt409_metadata.yaml @@ -0,0 +1,24 @@ +id: "pt409" +name: "pt409" +description: "c = 0.39 /d t_1/2 = 1.8 d (inferred)" +tags: ["pt409", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/HIVdynamics_aMCMC/pt409/pt409.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf_metadata.yaml b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf_metadata.yaml new file mode 100644 index 00000000..b6e5e632 --- /dev/null +++ b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf_metadata.yaml @@ -0,0 +1,24 @@ +id: "IGF1R_Model_receptor_activation_bnf" +name: "IGF1R Model receptor activation bnf" +description: "Author: William S. Hlavacek" +tags: ["igf1r", "model", "receptor", "activation", "bnf", "igf1"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/igf1r/IGF1R_Model_receptor_activation_bnf.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml index e4a09811..1122c5d4 100644 --- a/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml +++ b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml @@ -4,6 +4,7 @@ description: "Author: William S. Hlavacek" tags: ["igf1r", "model", "receptor", "activation", "bnf", "igf1"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/RAFi/RAFi_metadata.yaml b/Published/PyBioNetGen/core/RAFi/RAFi_metadata.yaml new file mode 100644 index 00000000..2dea0741 --- /dev/null +++ b/Published/PyBioNetGen/core/RAFi/RAFi_metadata.yaml @@ -0,0 +1,24 @@ +id: "RAFi" +name: "RAFi" +description: "BioNetGen model: RAFi" +tags: ["rafi", "r", "i", "ybar", "activity"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/constraint_raf/RAFi.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/RAFi/metadata.yaml b/Published/PyBioNetGen/core/RAFi/metadata.yaml index 0593a0f4..3e66c491 100644 --- a/Published/PyBioNetGen/core/RAFi/metadata.yaml +++ b/Published/PyBioNetGen/core/RAFi/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: RAFi" tags: ["rafi", "r", "i", "ybar", "activity"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/RAFiground/RAFi_ground_metadata.yaml b/Published/PyBioNetGen/core/RAFiground/RAFi_ground_metadata.yaml new file mode 100644 index 00000000..acb24376 --- /dev/null +++ b/Published/PyBioNetGen/core/RAFiground/RAFi_ground_metadata.yaml @@ -0,0 +1,24 @@ +id: "RAFi_ground" +name: "RAFi ground" +description: "BioNetGen model: RAFi ground" +tags: ["rafi", "ground", "r", "i", "ybar", "activity"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/constraint_raf/RAFi_ground.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/RAFiground/metadata.yaml b/Published/PyBioNetGen/core/RAFiground/metadata.yaml index d852548a..86506f95 100644 --- a/Published/PyBioNetGen/core/RAFiground/metadata.yaml +++ b/Published/PyBioNetGen/core/RAFiground/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: RAFi ground" tags: ["rafi", "ground", "r", "i", "ybar", "activity"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/degranulationmodel/degranulation_model_metadata.yaml b/Published/PyBioNetGen/core/degranulationmodel/degranulation_model_metadata.yaml new file mode 100644 index 00000000..44faae7c --- /dev/null +++ b/Published/PyBioNetGen/core/degranulationmodel/degranulation_model_metadata.yaml @@ -0,0 +1,24 @@ +id: "degranulation_model" +name: "PyBNG: Degranulation model" +description: "Degranulation model" +tags: ["published", "pybng", "degranulation", "model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/degranulation_model.bngl" +playground: + visible: true + gallery_categories: ["immunology"] + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml b/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml index 6b5f68d9..081965c7 100644 --- a/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml +++ b/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml @@ -4,6 +4,7 @@ description: "Degranulation model" tags: ["published", "pybng", "degranulation", "model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/egfr/egfr_metadata.yaml b/Published/PyBioNetGen/core/egfr/egfr_metadata.yaml new file mode 100644 index 00000000..8d657af8 --- /dev/null +++ b/Published/PyBioNetGen/core/egfr/egfr_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr" +name: "egfr" +description: "Blinov et al. 2006. Biosystems, 83:136" +tags: ["egfr", "egf", "grb2", "shc", "sos"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/egfr_benchmark/egfr.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/egfr/metadata.yaml b/Published/PyBioNetGen/core/egfr/metadata.yaml index 75bdf5f9..7c47106b 100644 --- a/Published/PyBioNetGen/core/egfr/metadata.yaml +++ b/Published/PyBioNetGen/core/egfr/metadata.yaml @@ -4,6 +4,7 @@ description: "Blinov et al. 2006. Biosystems, 83:136" tags: ["egfr", "egf", "grb2", "shc", "sos"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/egfrground/egfr_ground_metadata.yaml b/Published/PyBioNetGen/core/egfrground/egfr_ground_metadata.yaml new file mode 100644 index 00000000..6eaceae4 --- /dev/null +++ b/Published/PyBioNetGen/core/egfrground/egfr_ground_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr_ground" +name: "egfr ground" +description: "Blinov et al. 2006. Biosystems, 83:136" +tags: ["egfr", "ground", "egf", "grb2", "shc", "sos"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/egfr_benchmark/egfr_ground.bngl" +playground: + visible: true + gallery_category: "other" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/core/egfrground/metadata.yaml b/Published/PyBioNetGen/core/egfrground/metadata.yaml index 5982fdb6..f4df81e9 100644 --- a/Published/PyBioNetGen/core/egfrground/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrground/metadata.yaml @@ -4,6 +4,7 @@ description: "Blinov et al. 2006. Biosystems, 83:136" tags: ["egfr", "ground", "egf", "grb2", "shc", "sos"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/egfrnf/egfr_nf_metadata.yaml b/Published/PyBioNetGen/core/egfrnf/egfr_nf_metadata.yaml new file mode 100644 index 00000000..5aa45673 --- /dev/null +++ b/Published/PyBioNetGen/core/egfrnf/egfr_nf_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr_nf" +name: "egfr nf" +description: "Filename: example2_starting_point.bngl" +tags: ["egfr", "nf", "egf", "clusters", "pre1_dose", "pre2_time"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/egfr_nf/egfr_nf.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/egfrnf/metadata.yaml b/Published/PyBioNetGen/core/egfrnf/metadata.yaml index 01155ea1..6d5345f1 100644 --- a/Published/PyBioNetGen/core/egfrnf/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrnf/metadata.yaml @@ -4,6 +4,7 @@ description: "Filename: example2_starting_point.bngl" tags: ["egfr", "nf", "egf", "clusters", "pre1_dose", "pre2_time"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/egfrode/egfr_ode_metadata.yaml b/Published/PyBioNetGen/core/egfrode/egfr_ode_metadata.yaml new file mode 100644 index 00000000..620db17c --- /dev/null +++ b/Published/PyBioNetGen/core/egfrode/egfr_ode_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr_ode" +name: "egfr ode" +description: "Filename: example1.bngl" +tags: ["egfr", "ode", "egf", "pre1_dose", "pre2_time", "pre3_dose"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/egfr_ode/egfr_ode.bngl" +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/egfrode/metadata.yaml b/Published/PyBioNetGen/core/egfrode/metadata.yaml index f2096c0a..2e1d6ecf 100644 --- a/Published/PyBioNetGen/core/egfrode/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrode/metadata.yaml @@ -4,6 +4,7 @@ description: "Filename: example1.bngl" tags: ["egfr", "ode", "egf", "pre1_dose", "pre2_time", "pre3_dose"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode_metadata.yaml b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode_metadata.yaml new file mode 100644 index 00000000..e50b7e82 --- /dev/null +++ b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr_ode" +name: "PyBNG: EGFR ODE" +description: "EGFR ODE" +tags: ["published", "pybng", "egfr", "ode", "egf", "pre1_dose", "pre2_time", "pre3_dose"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/egfr_ode.bngl" +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml index f8c53c9f..1ffa7791 100644 --- a/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml @@ -4,6 +4,7 @@ description: "EGFR ODE" tags: ["published", "pybng", "egfr", "ode", "egf", "pre1_dose", "pre2_time", "pre3_dose"] category: "other" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/example1/example1_aigenerated.md b/Published/PyBioNetGen/core/example1/example1_aigenerated.md new file mode 100644 index 00000000..514f0ff0 --- /dev/null +++ b/Published/PyBioNetGen/core/example1/example1_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: PyBioNetGen EGFR example + +## One-sentence summary + +EGF-dependent EGFR oligomerization links receptor cluster size to cytosolic-tail activation and phosphorylation. + +## What the model shows + +This PyBioNetGen reference example follows epidermal growth factor (EGF) binding to its receptor (EGFR), higher-order receptor assembly, kinase-tail association, and receptor phosphorylation. + +## Biological story + +EGF binds receptors with context-dependent affinity. Occupied receptors form extracellular contacts, their cytosolic tails open and associate, and associated tails phosphorylate one another. Ring closure permits receptor assemblies larger than dimers. + +## Main biological players + +EGF, EGFR extracellular contacts, EGFR cytosolic tails, receptor oligomers, and phosphorylated receptor tyrosines. + +## Mechanism in plain English + +Ligand capture changes receptor crosslinking and favors an open tail conformation. Receptor ectodomains and tails make reversible contacts, including closure within existing assemblies. Tail association enables phosphorylation, while deactivation and dephosphorylation oppose the signal. + +## Key modeled events + +- EGF binds monomeric and clustered EGFR. +- Receptor ectodomains form dimers and higher-order assemblies. +- Ligand occupancy opens cytosolic tails and permits tail association. +- Associated tails phosphorylate EGFR tyrosines. + +## What the model measures + +Readouts include free EGF and EGFR, receptor monomers, dimers, trimers and tetramers, overall cluster density, and phosphorylated EGFR. + +## Expected behavior in plots + +Ligand addition should reduce free receptor and increase dimers before larger oligomers accumulate. Phosphorylated EGFR should follow formation of active tail pairs, while cluster-size curves reveal how material partitions among oligomers. + +## Caveats + +This is one reference example selected from a broad software-support collection. It ends at receptor phosphorylation and omits trafficking and downstream Ras–ERK signaling. diff --git a/Published/PyBioNetGen/core/example1/example1_metadata.yaml b/Published/PyBioNetGen/core/example1/example1_metadata.yaml new file mode 100644 index 00000000..2a8a98bf --- /dev/null +++ b/Published/PyBioNetGen/core/example1/example1_metadata.yaml @@ -0,0 +1,24 @@ +id: "example1" +name: "example1" +description: "Filename: example1.bngl" +tags: ["example1", "egf", "egfr", "pre1_dose", "pre2_time", "pre3_dose"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/egfr_ode/example1.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/example1/metadata.yaml b/Published/PyBioNetGen/core/example1/metadata.yaml index ead4ad06..9644954e 100644 --- a/Published/PyBioNetGen/core/example1/metadata.yaml +++ b/Published/PyBioNetGen/core/example1/metadata.yaml @@ -4,6 +4,7 @@ description: "Filename: example1.bngl" tags: ["example1", "egf", "egfr", "pre1_dose", "pre2_time", "pre3_dose"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/example2startingpoint/example2_starting_point_metadata.yaml b/Published/PyBioNetGen/core/example2startingpoint/example2_starting_point_metadata.yaml new file mode 100644 index 00000000..aae9b285 --- /dev/null +++ b/Published/PyBioNetGen/core/example2startingpoint/example2_starting_point_metadata.yaml @@ -0,0 +1,24 @@ +id: "example2_starting_point" +name: "example2 starting point" +description: "Filename: example2_starting_point.bngl" +tags: ["example2", "starting", "point", "egf", "egfr", "clusters", "pre1_dose", "pre2_time"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/egfr_nf/example2_starting_point.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml b/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml index d94f6e2b..080e7984 100644 --- a/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml +++ b/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml @@ -4,6 +4,7 @@ description: "Filename: example2_starting_point.bngl" tags: ["example2", "starting", "point", "egf", "egfr", "clusters", "pre1_dose", "pre2_time"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2_metadata.yaml b/Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2_metadata.yaml new file mode 100644 index 00000000..703d932f --- /dev/null +++ b/Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2_metadata.yaml @@ -0,0 +1,24 @@ +id: "fceri_gamma2" +name: "fceri gamma2" +description: "BioNetGen model: fceri gamma2" +tags: ["fceri", "gamma2", "lig", "lyn", "syk", "rec"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/fceri_gamma/fceri_gamma2.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml b/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml index b53c12d8..d4ed45dc 100644 --- a/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml +++ b/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: fceri gamma2" tags: ["fceri", "gamma2", "lig", "lyn", "syk", "rec"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth_metadata.yaml b/Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth_metadata.yaml new file mode 100644 index 00000000..0124c0c1 --- /dev/null +++ b/Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth_metadata.yaml @@ -0,0 +1,24 @@ +id: "fceri_gamma2_ground_truth" +name: "fceri gamma2 ground truth" +description: "BioNetGen model: fceri gamma2 ground truth" +tags: ["fceri", "gamma2", "ground", "truth", "lig", "lyn", "syk", "rec"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/fceri_gamma/fceri_gamma2_ground_truth.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml b/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml index 058ed46b..d790e2dd 100644 --- a/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml +++ b/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: fceri gamma2 ground truth" tags: ["fceri", "gamma2", "ground", "truth", "lig", "lyn", "syk", "rec"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/model/metadata.yaml b/Published/PyBioNetGen/core/model/metadata.yaml index 24f9b09c..bf8e21ea 100644 --- a/Published/PyBioNetGen/core/model/metadata.yaml +++ b/Published/PyBioNetGen/core/model/metadata.yaml @@ -4,6 +4,7 @@ description: "filename: model.bngl" tags: ["model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/model/model_metadata.yaml b/Published/PyBioNetGen/core/model/model_metadata.yaml new file mode 100644 index 00000000..3f17e8ba --- /dev/null +++ b/Published/PyBioNetGen/core/model/model_metadata.yaml @@ -0,0 +1,24 @@ +id: "model" +name: "model" +description: "filename: model.bngl" +tags: ["model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/degranulation/model.bngl" +playground: + visible: true + gallery_category: "other" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml index b3237498..e90d7259 100644 --- a/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml +++ b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml @@ -4,6 +4,7 @@ description: "A model of IgE receptor signaling" tags: ["model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/model_Degranulation_aMCMC/model_metadata.yaml b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/model_metadata.yaml new file mode 100644 index 00000000..2bf1ed6a --- /dev/null +++ b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/model_metadata.yaml @@ -0,0 +1,24 @@ +id: "model" +name: "model" +description: "A model of IgE receptor signaling" +tags: ["model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/Degranulation_aMCMC/model.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/modeltofit/metadata.yaml b/Published/PyBioNetGen/core/modeltofit/metadata.yaml index 91294c38..c0e457d6 100644 --- a/Published/PyBioNetGen/core/modeltofit/metadata.yaml +++ b/Published/PyBioNetGen/core/modeltofit/metadata.yaml @@ -4,6 +4,7 @@ description: "A model of IgE receptor signaling" tags: ["model", "tofit", "ag", "r", "syk", "ship1", "x", "pip3", "h"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/modeltofit/model_tofit_metadata.yaml b/Published/PyBioNetGen/core/modeltofit/model_tofit_metadata.yaml new file mode 100644 index 00000000..d7f647af --- /dev/null +++ b/Published/PyBioNetGen/core/modeltofit/model_tofit_metadata.yaml @@ -0,0 +1,24 @@ +id: "model_tofit" +name: "model tofit" +description: "A model of IgE receptor signaling" +tags: ["model", "tofit", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/degranulation/model_tofit.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/parabola/metadata.yaml b/Published/PyBioNetGen/core/parabola/metadata.yaml index 748c2c2c..25cd5c03 100644 --- a/Published/PyBioNetGen/core/parabola/metadata.yaml +++ b/Published/PyBioNetGen/core/parabola/metadata.yaml @@ -4,6 +4,7 @@ description: "Implementation of the parabola from the Mitra constrained optimiza tags: ["parabola", "counter", "par", "line", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/parabola/parabola_metadata.yaml b/Published/PyBioNetGen/core/parabola/parabola_metadata.yaml new file mode 100644 index 00000000..1ac2a51c --- /dev/null +++ b/Published/PyBioNetGen/core/parabola/parabola_metadata.yaml @@ -0,0 +1,24 @@ +id: "parabola" +name: "parabola" +description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" +tags: ["parabola", "counter", "par", "line", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/constraint_demo/parabola.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/parabola_demo/metadata.yaml b/Published/PyBioNetGen/core/parabola_demo/metadata.yaml index 6141d622..bec6844d 100644 --- a/Published/PyBioNetGen/core/parabola_demo/metadata.yaml +++ b/Published/PyBioNetGen/core/parabola_demo/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["parabola", "counter", "y", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/parabola_demo/parabola_metadata.yaml b/Published/PyBioNetGen/core/parabola_demo/parabola_metadata.yaml new file mode 100644 index 00000000..3ea90846 --- /dev/null +++ b/Published/PyBioNetGen/core/parabola_demo/parabola_metadata.yaml @@ -0,0 +1,24 @@ +id: "parabola" +name: "parabola" +description: "Original values used to generate parabola.exp" +tags: ["parabola", "counter", "y", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/demo/parabola.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/parabolaground/metadata.yaml b/Published/PyBioNetGen/core/parabolaground/metadata.yaml index 2190cb9c..941557c5 100644 --- a/Published/PyBioNetGen/core/parabolaground/metadata.yaml +++ b/Published/PyBioNetGen/core/parabolaground/metadata.yaml @@ -4,6 +4,7 @@ description: "Implementation of the parabola from the Mitra constrained optimiza tags: ["parabola", "ground", "counter", "par", "line", "generate_network", "simulate"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/parabolaground/parabola_ground_metadata.yaml b/Published/PyBioNetGen/core/parabolaground/parabola_ground_metadata.yaml new file mode 100644 index 00000000..1d45bee8 --- /dev/null +++ b/Published/PyBioNetGen/core/parabolaground/parabola_ground_metadata.yaml @@ -0,0 +1,24 @@ +id: "parabola_ground" +name: "parabola ground" +description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" +tags: ["parabola", "ground", "counter", "par", "line", "generate_network", "simulate"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/constraint_demo/parabola_ground.bngl" +playground: + visible: true + gallery_category: "other" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/core/polynomial/metadata.yaml b/Published/PyBioNetGen/core/polynomial/metadata.yaml index 7cf26109..095db82a 100644 --- a/Published/PyBioNetGen/core/polynomial/metadata.yaml +++ b/Published/PyBioNetGen/core/polynomial/metadata.yaml @@ -4,6 +4,7 @@ description: "Implementation of the parabola from the Mitra constrained optimiza tags: ["polynomial", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/polynomial/polynomial_metadata.yaml b/Published/PyBioNetGen/core/polynomial/polynomial_metadata.yaml new file mode 100644 index 00000000..10d52901 --- /dev/null +++ b/Published/PyBioNetGen/core/polynomial/polynomial_metadata.yaml @@ -0,0 +1,24 @@ +id: "polynomial" +name: "polynomial" +description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" +tags: ["polynomial", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/constraint_advanced/polynomial.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/polynomialground/metadata.yaml b/Published/PyBioNetGen/core/polynomialground/metadata.yaml index 7d905e0c..2d9c98f9 100644 --- a/Published/PyBioNetGen/core/polynomialground/metadata.yaml +++ b/Published/PyBioNetGen/core/polynomialground/metadata.yaml @@ -4,6 +4,7 @@ description: "Implementation of the parabola from the Mitra constrained optimiza tags: ["polynomial", "ground", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/polynomialground/polynomial_ground_metadata.yaml b/Published/PyBioNetGen/core/polynomialground/polynomial_ground_metadata.yaml new file mode 100644 index 00000000..0796a0ce --- /dev/null +++ b/Published/PyBioNetGen/core/polynomialground/polynomial_ground_metadata.yaml @@ -0,0 +1,24 @@ +id: "polynomial_ground" +name: "polynomial ground" +description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" +tags: ["polynomial", "ground", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/constraint_advanced/polynomial_ground.bngl" +playground: + visible: true + gallery_category: "other" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/core/receptor/metadata.yaml b/Published/PyBioNetGen/core/receptor/metadata.yaml index 70a58972..63db7f4c 100644 --- a/Published/PyBioNetGen/core/receptor/metadata.yaml +++ b/Published/PyBioNetGen/core/receptor/metadata.yaml @@ -4,6 +4,7 @@ description: "A simple model of ligand/receptor binding and receptor phosphoryla tags: ["receptor", "l", "r", "func"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/receptor/receptor_metadata.yaml b/Published/PyBioNetGen/core/receptor/receptor_metadata.yaml new file mode 100644 index 00000000..3044e15b --- /dev/null +++ b/Published/PyBioNetGen/core/receptor/receptor_metadata.yaml @@ -0,0 +1,24 @@ +id: "receptor" +name: "receptor" +description: "A simple model of ligand/receptor binding and receptor phosphorylation." +tags: ["receptor", "l", "r", "func"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/receptor/receptor.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/receptornf/metadata.yaml b/Published/PyBioNetGen/core/receptornf/metadata.yaml index 3d8963dd..e943961e 100644 --- a/Published/PyBioNetGen/core/receptornf/metadata.yaml +++ b/Published/PyBioNetGen/core/receptornf/metadata.yaml @@ -4,6 +4,7 @@ description: "A simple model of ligand/receptor binding and receptor phosphoryla tags: ["receptor", "nf", "l", "r"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/receptornf/receptor_nf_metadata.yaml b/Published/PyBioNetGen/core/receptornf/receptor_nf_metadata.yaml new file mode 100644 index 00000000..ab45ca75 --- /dev/null +++ b/Published/PyBioNetGen/core/receptornf/receptor_nf_metadata.yaml @@ -0,0 +1,24 @@ +id: "receptor_nf" +name: "receptor nf" +description: "A simple model of ligand/receptor binding and receptor phosphorylation." +tags: ["receptor", "nf", "l", "r"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/receptor_nf/receptor_nf.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/tcr/metadata.yaml b/Published/PyBioNetGen/core/tcr/metadata.yaml index d55d0fe7..e99dbf2f 100644 --- a/Published/PyBioNetGen/core/tcr/metadata.yaml +++ b/Published/PyBioNetGen/core/tcr/metadata.yaml @@ -4,6 +4,7 @@ description: "A model of T cell receptor signaling" tags: ["tcr", "lig1", "lig2", "lig3", "cd28", "lck", "itk", "zap70"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/tcr/tcr_metadata.yaml b/Published/PyBioNetGen/core/tcr/tcr_metadata.yaml new file mode 100644 index 00000000..7aa3265b --- /dev/null +++ b/Published/PyBioNetGen/core/tcr/tcr_metadata.yaml @@ -0,0 +1,24 @@ +id: "tcr" +name: "tcr" +description: "A model of T cell receptor signaling" +tags: ["tcr", "lig1", "lig2", "lig3", "cd28", "lck", "itk", "zap70"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tcr/tcr.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/core/tlbr/metadata.yaml b/Published/PyBioNetGen/core/tlbr/metadata.yaml index 64f5111f..f7aafa32 100644 --- a/Published/PyBioNetGen/core/tlbr/metadata.yaml +++ b/Published/PyBioNetGen/core/tlbr/metadata.yaml @@ -4,6 +4,7 @@ description: "A model of trivalent ligand, bivalent receptor" tags: ["tlbr", "l", "r", "lambda", "fl"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/core/tlbr/tlbr_metadata.yaml b/Published/PyBioNetGen/core/tlbr/tlbr_metadata.yaml new file mode 100644 index 00000000..12ed38a1 --- /dev/null +++ b/Published/PyBioNetGen/core/tlbr/tlbr_metadata.yaml @@ -0,0 +1,24 @@ +id: "tlbr" +name: "tlbr" +description: "A model of trivalent ligand, bivalent receptor" +tags: ["tlbr", "l", "r", "lambda", "fl"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tlbr/tlbr.bngl" +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees_metadata.yaml b/Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees_metadata.yaml new file mode 100644 index 00000000..3b54f889 --- /dev/null +++ b/Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees_metadata.yaml @@ -0,0 +1,24 @@ +id: "ErrNoFrees" +name: "ErrNoFrees" +description: "An example from a real application" +tags: ["errnofrees", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/ErrNoFrees.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml b/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml index 8e8ba78e..f865cb1d 100644 --- a/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml +++ b/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["errnofrees", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/LilyIgE/LilyIgE_metadata.yaml b/Published/PyBioNetGen/tests/LilyIgE/LilyIgE_metadata.yaml new file mode 100644 index 00000000..6e15069f --- /dev/null +++ b/Published/PyBioNetGen/tests/LilyIgE/LilyIgE_metadata.yaml @@ -0,0 +1,24 @@ +id: "LilyIgE" +name: "LilyIgE" +description: "An example from a real application" +tags: ["lilyige", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/LilyIgE.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml b/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml index d4f94854..f90ef883 100644 --- a/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml +++ b/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["lilyige", "ag", "r", "syk", "ship1", "x", "pip3", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/NFmodel/NFmodel_metadata.yaml b/Published/PyBioNetGen/tests/NFmodel/NFmodel_metadata.yaml new file mode 100644 index 00000000..4130d0c3 --- /dev/null +++ b/Published/PyBioNetGen/tests/NFmodel/NFmodel_metadata.yaml @@ -0,0 +1,24 @@ +id: "NFmodel" +name: "NFmodel" +description: "BioNetGen model: NFmodel" +tags: ["nfmodel", "ag", "ab", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/NFmodel.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/NFmodel/metadata.yaml b/Published/PyBioNetGen/tests/NFmodel/metadata.yaml index b949d741..bb8fd1a0 100644 --- a/Published/PyBioNetGen/tests/NFmodel/metadata.yaml +++ b/Published/PyBioNetGen/tests/NFmodel/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: NFmodel" tags: ["nfmodel", "ag", "ab", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere_metadata.yaml b/Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere_metadata.yaml new file mode 100644 index 00000000..9dccff88 --- /dev/null +++ b/Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere_metadata.yaml @@ -0,0 +1,24 @@ +id: "ParamsEverywhere" +name: "ParamsEverywhere" +description: "An example from a real application" +tags: ["paramseverywhere", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/ParamsEverywhere.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml b/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml index b6ba3843..7288d249 100644 --- a/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml +++ b/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["paramseverywhere", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/Simple/Simple_metadata.yaml b/Published/PyBioNetGen/tests/Simple/Simple_metadata.yaml new file mode 100644 index 00000000..84a1f603 --- /dev/null +++ b/Published/PyBioNetGen/tests/Simple/Simple_metadata.yaml @@ -0,0 +1,24 @@ +id: "Simple" +name: "Simple" +description: "An example from a real application" +tags: ["simple", "setoption", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/Simple.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/Simple/metadata.yaml b/Published/PyBioNetGen/tests/Simple/metadata.yaml index 4d4a9a11..b6e1818f 100644 --- a/Published/PyBioNetGen/tests/Simple/metadata.yaml +++ b/Published/PyBioNetGen/tests/Simple/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["simple", "setoption", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions_metadata.yaml b/Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions_metadata.yaml new file mode 100644 index 00000000..cca27975 --- /dev/null +++ b/Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions_metadata.yaml @@ -0,0 +1,24 @@ +id: "Simple_AddActions" +name: "Simple AddActions" +description: "An example from a real application" +tags: ["simple", "addactions", "setoption", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/Simple_AddActions.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml b/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml index 3dd89218..dc51ca57 100644 --- a/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml +++ b/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["simple", "addactions", "setoption", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer_metadata.yaml b/Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer_metadata.yaml new file mode 100644 index 00000000..1fd7ec22 --- /dev/null +++ b/Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer_metadata.yaml @@ -0,0 +1,24 @@ +id: "Simple_Answer" +name: "Simple Answer" +description: "An example from a real application" +tags: ["simple", "answer", "setoption", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/Simple_Answer.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml b/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml index 1412c103..2d6dfa5f 100644 --- a/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml +++ b/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["simple", "answer", "setoption", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly_metadata.yaml b/Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly_metadata.yaml new file mode 100644 index 00000000..f2afbc88 --- /dev/null +++ b/Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly_metadata.yaml @@ -0,0 +1,24 @@ +id: "Simple_GenOnly" +name: "Simple GenOnly" +description: "An example from a real application" +tags: ["simple", "genonly", "setoption", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/Simple_GenOnly.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml b/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml index a02cc1f6..d82f2ad5 100644 --- a/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml +++ b/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["simple", "genonly", "setoption", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/Simplenogen/Simple_nogen_metadata.yaml b/Published/PyBioNetGen/tests/Simplenogen/Simple_nogen_metadata.yaml new file mode 100644 index 00000000..a189bac6 --- /dev/null +++ b/Published/PyBioNetGen/tests/Simplenogen/Simple_nogen_metadata.yaml @@ -0,0 +1,24 @@ +id: "Simple_nogen" +name: "Simple nogen" +description: "An example from a real application" +tags: ["simple", "nogen", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/Simple_nogen.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml b/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml index 3e480dd2..e07e12d6 100644 --- a/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml +++ b/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["simple", "nogen", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/Tricky/Tricky_metadata.yaml b/Published/PyBioNetGen/tests/Tricky/Tricky_metadata.yaml new file mode 100644 index 00000000..b09c86bc --- /dev/null +++ b/Published/PyBioNetGen/tests/Tricky/Tricky_metadata.yaml @@ -0,0 +1,24 @@ +id: "Tricky" +name: "Tricky" +description: "An example from a real application" +tags: ["tricky", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/Tricky.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/Tricky/metadata.yaml b/Published/PyBioNetGen/tests/Tricky/metadata.yaml index 0b2271ca..49db670f 100644 --- a/Published/PyBioNetGen/tests/Tricky/metadata.yaml +++ b/Published/PyBioNetGen/tests/Tricky/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["tricky", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/TrickyUS/TrickyUS_metadata.yaml b/Published/PyBioNetGen/tests/TrickyUS/TrickyUS_metadata.yaml new file mode 100644 index 00000000..90511b95 --- /dev/null +++ b/Published/PyBioNetGen/tests/TrickyUS/TrickyUS_metadata.yaml @@ -0,0 +1,24 @@ +id: "TrickyUS" +name: "TrickyUS" +description: "An example from a real application" +tags: ["trickyus", "ag", "r", "h"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/TrickyUS.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml b/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml index 968aef11..7f33bb48 100644 --- a/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml +++ b/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml @@ -4,6 +4,7 @@ description: "An example from a real application" tags: ["trickyus", "ag", "r", "h"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/actionssyntax/actions_syntax_metadata.yaml b/Published/PyBioNetGen/tests/actionssyntax/actions_syntax_metadata.yaml new file mode 100644 index 00000000..9fa52652 --- /dev/null +++ b/Published/PyBioNetGen/tests/actionssyntax/actions_syntax_metadata.yaml @@ -0,0 +1,24 @@ +id: "actions_syntax" +name: "actions syntax" +description: "Original values used to generate parabola.exp" +tags: ["actions", "syntax", "counter", "y", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/errors/actions_syntax.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml b/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml index 83bf6fad..6d159863 100644 --- a/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml +++ b/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["actions", "syntax", "counter", "y", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/bngerror/bng_error_metadata.yaml b/Published/PyBioNetGen/tests/bngerror/bng_error_metadata.yaml new file mode 100644 index 00000000..358eaa21 --- /dev/null +++ b/Published/PyBioNetGen/tests/bngerror/bng_error_metadata.yaml @@ -0,0 +1,24 @@ +id: "bng_error" +name: "bng error" +description: "Original values used to generate parabola.exp" +tags: ["bng", "error", "counter", "y", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/errors/bng_error.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/bngerror/metadata.yaml b/Published/PyBioNetGen/tests/bngerror/metadata.yaml index bb875170..f1d97b87 100644 --- a/Published/PyBioNetGen/tests/bngerror/metadata.yaml +++ b/Published/PyBioNetGen/tests/bngerror/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["bng", "error", "counter", "y", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/egg/egg_metadata.yaml b/Published/PyBioNetGen/tests/egg/egg_metadata.yaml new file mode 100644 index 00000000..cda8b610 --- /dev/null +++ b/Published/PyBioNetGen/tests/egg/egg_metadata.yaml @@ -0,0 +1,24 @@ +id: "egg" +name: "egg" +description: "BioNetGen model: egg" +tags: ["egg", "x", "y", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/full_tests/T3-de-egg/egg.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/egg/metadata.yaml b/Published/PyBioNetGen/tests/egg/metadata.yaml index 828bf245..2377474b 100644 --- a/Published/PyBioNetGen/tests/egg/metadata.yaml +++ b/Published/PyBioNetGen/tests/egg/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: egg" tags: ["egg", "x", "y", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/freemissing/free_missing_metadata.yaml b/Published/PyBioNetGen/tests/freemissing/free_missing_metadata.yaml new file mode 100644 index 00000000..4943cf24 --- /dev/null +++ b/Published/PyBioNetGen/tests/freemissing/free_missing_metadata.yaml @@ -0,0 +1,24 @@ +id: "free_missing" +name: "free missing" +description: "Original values used to generate parabola.exp" +tags: ["free", "missing", "counter", "y", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/errors/free_missing.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/freemissing/metadata.yaml b/Published/PyBioNetGen/tests/freemissing/metadata.yaml index beebbe0c..9b713c48 100644 --- a/Published/PyBioNetGen/tests/freemissing/metadata.yaml +++ b/Published/PyBioNetGen/tests/freemissing/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["free", "missing", "counter", "y", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/nofrees/metadata.yaml b/Published/PyBioNetGen/tests/nofrees/metadata.yaml index 9fdad126..00b58cf5 100644 --- a/Published/PyBioNetGen/tests/nofrees/metadata.yaml +++ b/Published/PyBioNetGen/tests/nofrees/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["no", "frees", "counter", "y", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/nofrees/no_frees_metadata.yaml b/Published/PyBioNetGen/tests/nofrees/no_frees_metadata.yaml new file mode 100644 index 00000000..5dbec256 --- /dev/null +++ b/Published/PyBioNetGen/tests/nofrees/no_frees_metadata.yaml @@ -0,0 +1,24 @@ +id: "no_frees" +name: "no frees" +description: "Original values used to generate parabola.exp" +tags: ["no", "frees", "counter", "y", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/errors/no_frees.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml b/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml index 27072098..387c5c95 100644 --- a/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml +++ b/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["no", "generate", "network", "counter", "y", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network_metadata.yaml b/Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network_metadata.yaml new file mode 100644 index 00000000..b06f6277 --- /dev/null +++ b/Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network_metadata.yaml @@ -0,0 +1,24 @@ +id: "no_generate_network" +name: "no generate network" +description: "Original values used to generate parabola.exp" +tags: ["no", "generate", "network", "counter", "y", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/errors/no_generate_network.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/nosuffix/metadata.yaml b/Published/PyBioNetGen/tests/nosuffix/metadata.yaml index 2975ea14..490f5c41 100644 --- a/Published/PyBioNetGen/tests/nosuffix/metadata.yaml +++ b/Published/PyBioNetGen/tests/nosuffix/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["no", "suffix", "counter", "y", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/nosuffix/no_suffix_metadata.yaml b/Published/PyBioNetGen/tests/nosuffix/no_suffix_metadata.yaml new file mode 100644 index 00000000..95dde1e7 --- /dev/null +++ b/Published/PyBioNetGen/tests/nosuffix/no_suffix_metadata.yaml @@ -0,0 +1,24 @@ +id: "no_suffix" +name: "no suffix" +description: "Original values used to generate parabola.exp" +tags: ["no", "suffix", "counter", "y", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/errors/no_suffix.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/parabola/metadata.yaml b/Published/PyBioNetGen/tests/parabola/metadata.yaml index 180c2637..2920407b 100644 --- a/Published/PyBioNetGen/tests/parabola/metadata.yaml +++ b/Published/PyBioNetGen/tests/parabola/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["parabola", "counter", "y", "generate_network", "simulate", "resetconcentrations"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/parabola/parabola_metadata.yaml b/Published/PyBioNetGen/tests/parabola/parabola_metadata.yaml new file mode 100644 index 00000000..4c9493c9 --- /dev/null +++ b/Published/PyBioNetGen/tests/parabola/parabola_metadata.yaml @@ -0,0 +1,24 @@ +id: "parabola" +name: "parabola" +description: "Original values used to generate parabola.exp" +tags: ["parabola", "counter", "y", "generate_network", "simulate", "resetconcentrations"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/errors/constraint_domain/parabola.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/parabola2/metadata.yaml b/Published/PyBioNetGen/tests/parabola2/metadata.yaml index cf90f9f8..53e85967 100644 --- a/Published/PyBioNetGen/tests/parabola2/metadata.yaml +++ b/Published/PyBioNetGen/tests/parabola2/metadata.yaml @@ -4,6 +4,7 @@ description: "A file for testing behavior with duplicate file names" tags: ["parabola2", "counter", "y", "generate_network", "simulate", "resetconcentrations"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/parabola2/parabola2_metadata.yaml b/Published/PyBioNetGen/tests/parabola2/parabola2_metadata.yaml new file mode 100644 index 00000000..0ffe3d28 --- /dev/null +++ b/Published/PyBioNetGen/tests/parabola2/parabola2_metadata.yaml @@ -0,0 +1,24 @@ +id: "parabola2" +name: "parabola2" +description: "A file for testing behavior with duplicate file names" +tags: ["parabola2", "counter", "y", "generate_network", "simulate", "resetconcentrations"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/special_cases/duplicate_names/parabola2.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml b/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml index fb487fb5..e09b140a 100644 --- a/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml +++ b/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["parabola", "counter", "y", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/parabola_bngl_files/parabola_metadata.yaml b/Published/PyBioNetGen/tests/parabola_bngl_files/parabola_metadata.yaml new file mode 100644 index 00000000..081d60ec --- /dev/null +++ b/Published/PyBioNetGen/tests/parabola_bngl_files/parabola_metadata.yaml @@ -0,0 +1,24 @@ +id: "parabola" +name: "parabola" +description: "Original values used to generate parabola.exp" +tags: ["parabola", "counter", "y", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/parabola.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/metadata.yaml b/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/metadata.yaml index 5bcdaa14..99b5784f 100644 --- a/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/metadata.yaml +++ b/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/metadata.yaml @@ -4,6 +4,7 @@ description: "Original values used to generate parabola.exp" tags: ["parabola", "counter", "y", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola_metadata.yaml b/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola_metadata.yaml new file mode 100644 index 00000000..054c2805 --- /dev/null +++ b/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola_metadata.yaml @@ -0,0 +1,24 @@ +id: "parabola" +name: "parabola" +description: "Original values used to generate parabola.exp" +tags: ["parabola", "counter", "y", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/special_cases/model_check/parabola.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/tests/polynomial/metadata.yaml b/Published/PyBioNetGen/tests/polynomial/metadata.yaml index 6f197bb6..25eea72d 100644 --- a/Published/PyBioNetGen/tests/polynomial/metadata.yaml +++ b/Published/PyBioNetGen/tests/polynomial/metadata.yaml @@ -4,6 +4,7 @@ description: "Implementation of the parabola from the Mitra constrained optimiza tags: ["polynomial", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/polynomial/polynomial_metadata.yaml b/Published/PyBioNetGen/tests/polynomial/polynomial_metadata.yaml new file mode 100644 index 00000000..c659d67d --- /dev/null +++ b/Published/PyBioNetGen/tests/polynomial/polynomial_metadata.yaml @@ -0,0 +1,24 @@ +id: "polynomial" +name: "polynomial" +description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" +tags: ["polynomial", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/full_tests/T1-ssprop/polynomial.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml b/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml index 248fddc2..cac535eb 100644 --- a/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml +++ b/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml @@ -4,6 +4,7 @@ description: "Implementation of the parabola from the Mitra constrained optimiza tags: ["polynomial", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial_metadata.yaml b/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial_metadata.yaml new file mode 100644 index 00000000..2359377b --- /dev/null +++ b/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial_metadata.yaml @@ -0,0 +1,24 @@ +id: "polynomial" +name: "polynomial" +description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" +tags: ["polynomial", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/full_tests/T6-check/polynomial.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Published/PyBioNetGen/tests/receptornf/metadata.yaml b/Published/PyBioNetGen/tests/receptornf/metadata.yaml index 257afe50..43fea5b5 100644 --- a/Published/PyBioNetGen/tests/receptornf/metadata.yaml +++ b/Published/PyBioNetGen/tests/receptornf/metadata.yaml @@ -4,6 +4,7 @@ description: "A simple model of ligand/receptor binding and receptor phosphoryla tags: ["receptor", "nf", "l", "r"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/receptornf/receptor_nf_metadata.yaml b/Published/PyBioNetGen/tests/receptornf/receptor_nf_metadata.yaml new file mode 100644 index 00000000..f50aa860 --- /dev/null +++ b/Published/PyBioNetGen/tests/receptornf/receptor_nf_metadata.yaml @@ -0,0 +1,24 @@ +id: "receptor_nf" +name: "receptor nf" +description: "A simple model of ligand/receptor binding and receptor phosphorylation." +tags: ["receptor", "nf", "l", "r"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/full_tests/T4-pso-nf/receptor_nf.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml b/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml index 4ec7b9b0..33cf67c9 100644 --- a/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml +++ b/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: simple nf seed" tags: ["simple", "nf", "seed", "a", "b", "function1", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed_metadata.yaml b/Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed_metadata.yaml new file mode 100644 index 00000000..6b072171 --- /dev/null +++ b/Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed_metadata.yaml @@ -0,0 +1,24 @@ +id: "simple_nf_seed" +name: "simple nf seed" +description: "BioNetGen model: simple nf seed" +tags: ["simple", "nf", "seed", "a", "b", "function1", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/bngl_files/errors/simple_nf_seed.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/PyBioNetGen/tests/trivial/metadata.yaml b/Published/PyBioNetGen/tests/trivial/metadata.yaml index e533f071..17003b32 100644 --- a/Published/PyBioNetGen/tests/trivial/metadata.yaml +++ b/Published/PyBioNetGen/tests/trivial/metadata.yaml @@ -4,6 +4,7 @@ description: "A trivial model file for testing MCMC distributions." tags: ["trivial", "q", "r", "output", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/PyBioNetGen/tests/trivial/trivial_metadata.yaml b/Published/PyBioNetGen/tests/trivial/trivial_metadata.yaml new file mode 100644 index 00000000..6748bb0a --- /dev/null +++ b/Published/PyBioNetGen/tests/trivial/trivial_metadata.yaml @@ -0,0 +1,24 @@ +id: "trivial" +name: "trivial" +description: "A trivial model file for testing MCMC distributions." +tags: ["trivial", "q", "r", "output", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/tests/full_tests/T5-pt-trivial/trivial.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Published/RulebasedRantransport/Rule_based_Ran_transport_metadata.yaml b/Published/RulebasedRantransport/Rule_based_Ran_transport_metadata.yaml new file mode 100644 index 00000000..fb55a9ff --- /dev/null +++ b/Published/RulebasedRantransport/Rule_based_Ran_transport_metadata.yaml @@ -0,0 +1,24 @@ +id: "Rule_based_Ran_transport" +name: "Rule based Ran transport" +description: "Nuclear Ran transport" +tags: ["published", "rule", "based", "ran", "transport", "c", "rcc1", "generate_network"] +category: "regulation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/Rule_based_Ran_transport.bngl" +playground: + visible: false + gallery_category: "regulation" + featured: false + difficulty: "advanced" diff --git a/Published/RulebasedRantransport/RulebasedRantransport_aigenerated.md b/Published/RulebasedRantransport/RulebasedRantransport_aigenerated.md new file mode 100644 index 00000000..87de8e42 --- /dev/null +++ b/Published/RulebasedRantransport/RulebasedRantransport_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Rule based Ran transport + +## One-sentence summary + +Ran-mediated nuclear export couples cargo phosphorylation state to RCC1-dependent release and cytoplasmic accumulation. + +## What the model shows + +This compact transport model follows Ran and an abstract cargo between nucleus and cytoplasm. Cargo carries three reversible phosphorylation sites, and nuclear RCC1 competes for Ran so that cargo–Ran complexes can be disassembled after transport. + +## Biological story + +Ran–cargo complexes move from nucleus to cytoplasm. Cargo phosphorylation is controlled in the cytoplasm, while nuclear RCC1 binds Ran and favors cargo release. The model therefore links transport direction, binding competition, and cargo modification without naming a specific cargo protein. + +## Main biological players + +Ran, an abstract three-site cargo, nuclear RCC1, nuclear and cytoplasmic compartments, and phosphorylated cargo states. + +## Mechanism in plain English + +Ran binds cargo in either compartment, but the transport step carries bound Ran toward the cytoplasm. In the nucleus, RCC1 captures Ran and competes with cargo, promoting separation. Cargo can gain or lose phosphate independently at three positions, so phosphorylation state can be compared with localization and Ran occupancy. + +## Key modeled events + +- Ran binds the abstract cargo and the complex is exported to the cytoplasm. +- Nuclear RCC1 binds Ran and competes with cargo for the same partner. +- Cargo is reversibly phosphorylated at three independent positions. +- Binding, release, and transport redistribute free cargo and Ran-bound cargo between compartments. + +## What the model measures + +Readouts track cytoplasmic Ran, nuclear and cytoplasmic cargo, phosphorylated cargo, nuclear RCC1, and cytoplasmic Ran–cargo complexes. + +## Expected behavior in plots + +Ran-bound cargo should transfer toward the cytoplasm, raising cytoplasmic complex and cargo readouts. Nuclear RCC1 should favor free nuclear cargo by drawing Ran away, while the phosphorylated-cargo curves reflect how modification equilibrates relative to transport. + +## Caveats + +The cargo is deliberately abstract, and canonical RanGTP/RanGDP nucleotide cycling is not represented explicitly. Directionality is imposed through the transport and competition scheme. diff --git a/Published/RulebasedRantransport/metadata.yaml b/Published/RulebasedRantransport/metadata.yaml index 153da82c..410fd49f 100644 --- a/Published/RulebasedRantransport/metadata.yaml +++ b/Published/RulebasedRantransport/metadata.yaml @@ -4,6 +4,7 @@ description: "Nuclear Ran transport" tags: ["published", "rule", "based", "ran", "transport", "c", "rcc1", "generate_network"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: true diff --git a/Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft_metadata.yaml b/Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft_metadata.yaml new file mode 100644 index 00000000..4b98e605 --- /dev/null +++ b/Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft_metadata.yaml @@ -0,0 +1,24 @@ +id: "Rule_based_Ran_transport_draft" +name: "Rule based Ran transport draft" +description: "Ran transport (draft)" +tags: ["published", "rule", "based", "ran", "transport", "draft", "c", "rcc1", "generate_network"] +category: "regulation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/Rule_based_Ran_transport_draft.bngl" +playground: + visible: false + gallery_category: "regulation" + featured: false + difficulty: "advanced" diff --git a/Published/RulebasedRantransportdraft/metadata.yaml b/Published/RulebasedRantransportdraft/metadata.yaml index 2a5d9cb3..01bcd50b 100644 --- a/Published/RulebasedRantransportdraft/metadata.yaml +++ b/Published/RulebasedRantransportdraft/metadata.yaml @@ -4,6 +4,7 @@ description: "Ran transport (draft)" tags: ["published", "rule", "based", "ran", "transport", "draft", "c", "rcc1", "generate_network"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: true diff --git a/Published/Rulebasedegfrcompart/Rule_based_egfr_compart_metadata.yaml b/Published/Rulebasedegfrcompart/Rule_based_egfr_compart_metadata.yaml new file mode 100644 index 00000000..b376f4e0 --- /dev/null +++ b/Published/Rulebasedegfrcompart/Rule_based_egfr_compart_metadata.yaml @@ -0,0 +1,24 @@ +id: "Rule_based_egfr_compart" +name: "Rule based egfr compart" +description: "Compartmental EGFR model" +tags: ["published", "rule", "based", "egfr", "compart", "egf", "grb2", "shc", "generate_network"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/growth-factor-signaling/Rule_based_egfr_compart.bngl" +playground: + visible: false + gallery_category: "signaling" + featured: false + difficulty: "advanced" diff --git a/Published/Rulebasedegfrcompart/Rulebasedegfrcompart_aigenerated.md b/Published/Rulebasedegfrcompart/Rulebasedegfrcompart_aigenerated.md new file mode 100644 index 00000000..9569cbeb --- /dev/null +++ b/Published/Rulebasedegfrcompart/Rulebasedegfrcompart_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Rule based EGFR compartments + +## One-sentence summary + +Compartment-resolved EGF–EGFR signaling links membrane dimerization to receptor and Shc phosphorylation. + +## What the model shows + +This model separates extracellular ligand, membrane receptor, and cytoplasmic adaptor pools while following the early EGFR activation sequence. EGF-bound receptors dimerize, phosphorylate two tyrosines, and recruit Shc, which itself becomes phosphorylated. + +## Biological story + +Extracellular EGF engages membrane EGFR. Ligand-occupied receptors pair through their transmembrane region and phosphorylate Y1068 and Y1173. Cytoplasmic Shc binds phosphorylated Y1173 and is modified while receptor and Shc phosphatases continually reverse activation. + +## Main biological players + +EGF, EGFR, receptor tyrosines Y1068 and Y1173, cytoplasmic Shc, and Grb2 as a declared but unused adaptor. + +## Mechanism in plain English + +EGF binding creates dimerization-competent EGFR. Receptor dimers phosphorylate both tyrosines, while constitutive dephosphorylation removes those marks. Shc recognizes phosphorylated Y1173, becomes phosphorylated while receptor-bound, and can dissociate into the cytoplasm before being dephosphorylated. + +## Key modeled events + +- Extracellular EGF binds membrane EGFR. +- Ligand-bound EGFR forms reversible membrane dimers. +- Dimerization enables phosphorylation of Y1068 and Y1173. +- Shc binds Y1173, becomes phosphorylated, and returns to the cytoplasmic pool. + +## What the model measures + +Readouts follow total receptor and extracellular ligand, EGFR dimers, phosphorylation at each receptor tyrosine, total receptor phosphorylation, cytoplasmic Shc, and phosphorylated cytoplasmic Shc. + +## Expected behavior in plots + +Dimers should rise soon after EGF binding, followed by Y1068 and Y1173 phosphorylation. Phosphorylated Shc should lag behind Y1173 because it requires receptor docking and modification; dephosphorylation should limit all three phosphotyrosine signals. + +## Caveats + +Only the first receptor/adaptor layer is active. Grb2 is declared but not used, and Ras–ERK signaling, receptor trafficking, and degradation are omitted. diff --git a/Published/Rulebasedegfrcompart/metadata.yaml b/Published/Rulebasedegfrcompart/metadata.yaml index 35a3fbe2..3d531eb3 100644 --- a/Published/Rulebasedegfrcompart/metadata.yaml +++ b/Published/Rulebasedegfrcompart/metadata.yaml @@ -4,6 +4,7 @@ description: "Compartmental EGFR model" tags: ["published", "rule", "based", "egfr", "compart", "egf", "grb2", "shc", "generate_network"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: true diff --git a/Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial_metadata.yaml b/Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial_metadata.yaml new file mode 100644 index 00000000..ce505c37 --- /dev/null +++ b/Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial_metadata.yaml @@ -0,0 +1,24 @@ +id: "Rule_based_egfr_tutorial" +name: "Faeder 2009" +description: "EGFR signaling" +tags: ["published", "rule", "based", "egfr", "tutorial", "egf", "grb2", "shc", "generate_network"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/growth-factor-signaling/Rule_based_egfr_tutorial.bngl" +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" diff --git a/Published/Rulebasedegfrtutorial/Rulebasedegfrtutorial_aigenerated.md b/Published/Rulebasedegfrtutorial/Rulebasedegfrtutorial_aigenerated.md new file mode 100644 index 00000000..e8f4c3e1 --- /dev/null +++ b/Published/Rulebasedegfrtutorial/Rulebasedegfrtutorial_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Faeder 2009 EGFR tutorial + +## One-sentence summary + +EGF-induced EGFR dimerization creates two phosphotyrosine docking routes for Grb2 and Shc. + +## What the model shows + +This tutorial-scale model presents the core early EGFR mechanism: ligand binding, receptor dimerization, phosphorylation of two receptor tyrosines, direct Grb2 recruitment, and Shc recruitment and phosphorylation. It is useful for comparing receptor assembly with site-specific signaling output. + +## Biological story + +EGF engages EGFR and brings receptors together. Dimerization enables phosphorylation at Y1 and Y2. Grb2 binds the first modified site, whereas Shc binds the second and is phosphorylated, creating two distinct adaptor branches from the same receptor dimer. + +## Main biological players + +EGF, EGFR, receptor sites Y1 and Y2, Grb2, and Shc. + +## Mechanism in plain English + +Ligand binds receptor reversibly and occupied receptors dimerize. Within dimers, both regulatory tyrosines gain phosphate and lose it through constitutive reversal. Grb2 directly docks on phosphorylated Y1. Shc docks on phosphorylated Y2, becomes phosphorylated, and can remain associated or dissociate according to its state. + +## Key modeled events + +- EGF binds EGFR and promotes reversible receptor dimerization. +- Dimerized receptors phosphorylate Y1 and Y2. +- Grb2 docks directly on phosphorylated Y1. +- Shc binds phosphorylated Y2 and becomes phosphorylated. + +## What the model measures + +Measurements include total ligand, receptor, Grb2, and Shc; receptor dimers; and phosphorylation of Y1, Y2, and both sites combined. + +## Expected behavior in plots + +Receptor dimers should rise first after ligand engagement. Y1 and Y2 phosphorylation should follow together because both require dimers, while adaptor occupancy would be inferred from depletion or complex populations rather than a dedicated plotted signal. Dephosphorylation should establish a finite plateau. + +## Caveats + +The site names are generic teaching labels, and the model stops before SOS, Ras, or ERK. It illustrates early receptor logic rather than a complete EGFR pathway. diff --git a/Published/Rulebasedegfrtutorial/metadata.yaml b/Published/Rulebasedegfrtutorial/metadata.yaml index 3671927e..29e1ed41 100644 --- a/Published/Rulebasedegfrtutorial/metadata.yaml +++ b/Published/Rulebasedegfrtutorial/metadata.yaml @@ -4,6 +4,7 @@ description: "EGFR signaling" tags: ["published", "rule", "based", "egfr", "tutorial", "egf", "grb2", "shc", "generate_network"] category: "signaling" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/190127_CHO_EGFR_forBNF_metadata.yaml b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/190127_CHO_EGFR_forBNF_metadata.yaml new file mode 100644 index 00000000..79db4c96 --- /dev/null +++ b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/190127_CHO_EGFR_forBNF_metadata.yaml @@ -0,0 +1,21 @@ +id: PyBNF_fitting_setup_190127_CHO_EGFR_forBNF +name: PyBNF-fitting-setup +description: BNGL model: 190127_CHO_EGFR_forBNF +tags: ["kdephosy1068_f", "kdephosy1173_f", "kphos_f", "grb2_f", "ratio_kdephosy1173", "ratio_kphosy1173", "offrate_f", "onrate_f", "kdephosy1068_pre", "kdephosy1173_pre", "kdephosyn_pre", "kphosy1068_pre", "kphosy1173_pre", "kphosyn_pre", "kdephosy1068", "kdephosy1173", "kdephosyn", "kphosy1068", "kphosy1173", "kphosyn", "ratio_kphos_receiver", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml index 085bf494..20922132 100644 --- a/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml +++ b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml @@ -4,6 +4,7 @@ description: BNGL model: 190127_CHO_EGFR_forBNF tags: ["kdephosy1068_f", "kdephosy1173_f", "kphos_f", "grb2_f", "ratio_kdephosy1173", "ratio_kphosy1173", "offrate_f", "onrate_f", "kdephosy1068_pre", "kdephosy1173_pre", "kdephosyn_pre", "kphosy1068_pre", "kphosy1173_pre", "kphosyn_pre", "kdephosy1068", "kdephosy1173", "kdephosyn", "kphosy1068", "kphosy1173", "kphosyn", "ratio_kphos_receiver", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Salazar-Cavazos2019/Salazar-Cavazos2019_aigenerated.md b/Published/Salazar-Cavazos2019/Salazar-Cavazos2019_aigenerated.md new file mode 100644 index 00000000..c8c331bd --- /dev/null +++ b/Published/Salazar-Cavazos2019/Salazar-Cavazos2019_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Salazar-Cavazos 2019 MCF10A EGFR + +## One-sentence summary + +EGF-stabilized EGFR dimers move through active and receiver conformations that determine site-specific phosphorylation and adaptor recruitment. + +## What the model shows + +This selected MCF10A-cell model represents epidermal growth factor receptor (EGFR) activation with several dimer and kinase states. GRB2 is growth factor receptor-bound protein 2, and SHC1 is an adaptor protein with a phosphotyrosine-binding domain. + +## Biological story + +EGF binds EGFR and stabilizes dimers. Receptors occupy asymmetric kinase roles, phosphorylate Y1068, Y1173, and additional tail sites, then recruit GRB2 or SHC1. Ligand-dependent dimer lifetimes shape the duration of phosphorylation. + +## Main biological players + +EGF, EGFR monomers and dimers, active and receiver kinase states, phosphotyrosines Y1068/Y1173, GRB2, and SHC1. + +## Mechanism in plain English + +Ligand-bound receptors dimerize and adopt catalytic or receiver roles. Active dimers phosphorylate multiple tail sites. GRB2 recognizes phosphorylated Y1068, while SHC1 binds its preferred phosphorylated site. Rapid phosphate turnover and dimer dissociation compete with adaptor binding, connecting receptor lifetime to downstream recruitment. + +## Key modeled events + +- EGF binds EGFR and stabilizes receptor dimers. +- Dimers adopt active and receiver kinase conformations. +- EGFR tails become phosphorylated at Y1068, Y1173, and other sites. +- GRB2 and SHC1 bind their corresponding phosphotyrosines. + +## What the model measures + +Readouts separate ligand-bound receptor, monomeric and dimeric EGFR, active/receiver dimers, individual phosphotyrosines, unphosphorylated receptor, and GRB2/SHC1-bound receptor. + +## Expected behavior in plots + +Ligand-bound dimers should rise before phosphotyrosines and adaptor complexes. Active/receiver dimer populations should predict the phosphorylation pulse, while GRB2 and SHC1 recruitment may differ because their docking sites turn over differently. + +## Caveats + +This is one cell-line member of a larger calibrated collection. It does not extend adaptor recruitment through Ras, ERK, or transcription. diff --git a/Published/Salazar-Cavazos2019/metadata.yaml b/Published/Salazar-Cavazos2019/metadata.yaml index f32e34b3..ee3238d9 100644 --- a/Published/Salazar-Cavazos2019/metadata.yaml +++ b/Published/Salazar-Cavazos2019/metadata.yaml @@ -1,9 +1,11 @@ -id: Salazar_Cavazos2019_190127_CHO_EGFR_best_fit -name: Salazar-Cavazos2019 -description: BNGL model: 190127_CHO_EGFR_best-fit +id: "Salazar_Cavazos2019_190127_CHO_EGFR_best_fit" +name: "Salazar-Cavazos2019" +description: "BNGL model: 190127_CHO_EGFR_best-fit" tags: ["grb2_total__free", "shc1_total__free", "kdephosy1068__free", "kdephosyn__free", "ratio_kpkd_y1068__free", "ratio_kpkd_yn__free", "kdephosy1068_f", "kdephosy1173_f", "kphos_f", "grb2_f", "ratio_kdephosy1173", "ratio_kphosy1173", "offrate_f", "onrate_f", "kdephosy1068_pre", "kdephosy1173_pre", "kdephosyn_pre", "kphosy1068_pre", "kphosy1173_pre", "kphosyn_pre", "kdephosy1068", "kdephosy1173", "kdephosyn", "kphosy1068", "kphosy1173", "kphosyn", "ratio_kphos_receiver", "molecules"] -category: other +category: "other" compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Thomas2016/Thomas2016_aigenerated.md b/Published/Thomas2016/Thomas2016_aigenerated.md new file mode 100644 index 00000000..96b4ca1a --- /dev/null +++ b/Published/Thomas2016/Thomas2016_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Thomas 2016 trivalent-ligand fitting example + +## One-sentence summary + +A trivalent ligand crosslinks bivalent receptors, producing a dose-dependent bound fraction used for parameter estimation. + +## What the model shows + +This fitting example represents multivalent ligand–receptor aggregation. ECF means extracellular fluid, and the model rescales molecule numbers to a sampled fraction of a cell. + +## Biological story + +A free three-site ligand captures a receptor, then another ligand arm recruits a receptor from a different complex. Bonds dissociate, so ligand concentration and the two association strengths determine equilibrium receptor occupancy. + +## Main biological players + +Trivalent ligand, bivalent receptor, free ligand, ligand–receptor bonds, and extracellular volume scaling. + +## Mechanism in plain English + +The first association step captures receptor with free ligand. A tethered ligand uses a remaining site for crosslinking, while a common dissociation process reverses either contact. A ligand-dose scan converts bound ligand into a normalized fractional response for fitting. + +## Key modeled events + +- Free ligand binds the first receptor site. +- A bound ligand arm crosslinks an additional receptor. +- Ligand–receptor bonds dissociate reversibly. +- A concentration scan samples equilibrium binding across ligand doses. + +## What the model measures + +Readouts report total receptor, total ligand, free ligand, the bound fraction, and a scaled fluorescence-like response. + +## Expected behavior in plots + +At low ligand, the bound fraction should rise with dose. Intermediate concentrations favor crosslinking, while high dose can shift occupancy toward independently bound receptors. The fitted response scale changes magnitude without changing binding chemistry. + +## Caveats + +The partners are abstract and ring formation is excluded. The example is designed for parameter fitting rather than downstream receptor biology. diff --git a/Published/Thomas2016/example1_BNFfiles/example1_metadata.yaml b/Published/Thomas2016/example1_BNFfiles/example1_metadata.yaml new file mode 100644 index 00000000..61f412e3 --- /dev/null +++ b/Published/Thomas2016/example1_BNFfiles/example1_metadata.yaml @@ -0,0 +1,21 @@ +id: example1_BNFfiles_example1 +name: example1_starting_point.bngl +description: Filename: example1_starting_point.bngl +tags: ["lt", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "alpha1", "alpha2", "alpha3", "alpha4", "molecules", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example1_BNFfiles/metadata.yaml b/Published/Thomas2016/example1_BNFfiles/metadata.yaml index f3148710..e7af47c3 100644 --- a/Published/Thomas2016/example1_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example1_BNFfiles/metadata.yaml @@ -4,6 +4,7 @@ description: Filename: example1_starting_point.bngl tags: ["lt", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "alpha1", "alpha2", "alpha3", "alpha4", "molecules", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Thomas2016/example2_BNFfiles/example2_metadata.yaml b/Published/Thomas2016/example2_BNFfiles/example2_metadata.yaml new file mode 100644 index 00000000..14e14831 --- /dev/null +++ b/Published/Thomas2016/example2_BNFfiles/example2_metadata.yaml @@ -0,0 +1,21 @@ +id: example2_BNFfiles_example2 +name: example2_starting_point.bngl +description: Filename: example2_starting_point.bngl +tags: ["f", "lt_nm", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "molecules"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example2_BNFfiles/metadata.yaml b/Published/Thomas2016/example2_BNFfiles/metadata.yaml index 8572deea..11b4f2fa 100644 --- a/Published/Thomas2016/example2_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example2_BNFfiles/metadata.yaml @@ -4,6 +4,7 @@ description: Filename: example2_starting_point.bngl tags: ["f", "lt_nm", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "molecules"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["nf"] diff --git a/Published/Thomas2016/example3_BNFfiles/example3_metadata.yaml b/Published/Thomas2016/example3_BNFfiles/example3_metadata.yaml new file mode 100644 index 00000000..65332027 --- /dev/null +++ b/Published/Thomas2016/example3_BNFfiles/example3_metadata.yaml @@ -0,0 +1,21 @@ +id: example3_BNFfiles_example3 +name: example3 BNFfiles +description: BNGL model: example3 +tags: ["alpha", "molecules", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example3_BNFfiles/metadata.yaml b/Published/Thomas2016/example3_BNFfiles/metadata.yaml index 1e96950a..7243b843 100644 --- a/Published/Thomas2016/example3_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example3_BNFfiles/metadata.yaml @@ -4,6 +4,7 @@ description: BNGL model: example3 tags: ["alpha", "molecules", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["nf"] diff --git a/Published/Thomas2016/example4_BNFfiles/example4_metadata.yaml b/Published/Thomas2016/example4_BNFfiles/example4_metadata.yaml new file mode 100644 index 00000000..23f82a71 --- /dev/null +++ b/Published/Thomas2016/example4_BNFfiles/example4_metadata.yaml @@ -0,0 +1,21 @@ +id: example4_BNFfiles_example4 +name: in BNGL. For a description of BNGL, see: +description: Supplementary File A in File S1 +tags: ["other"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example4_BNFfiles/metadata.yaml b/Published/Thomas2016/example4_BNFfiles/metadata.yaml index 0fb8c643..f54e52cd 100644 --- a/Published/Thomas2016/example4_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example4_BNFfiles/metadata.yaml @@ -4,6 +4,7 @@ description: Supplementary File A in File S1 tags: ["other"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["nf"] diff --git a/Published/Thomas2016/example5_BNFfiles/example5_metadata.yaml b/Published/Thomas2016/example5_BNFfiles/example5_metadata.yaml new file mode 100644 index 00000000..61b0ef00 --- /dev/null +++ b/Published/Thomas2016/example5_BNFfiles/example5_metadata.yaml @@ -0,0 +1,21 @@ +id: example5_BNFfiles_example5 +name: example5 BNFfiles +description: A simple model +tags: ["ligand_ispresent", "molecules", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example5_BNFfiles/metadata.yaml b/Published/Thomas2016/example5_BNFfiles/metadata.yaml index e7175e04..be1030cd 100644 --- a/Published/Thomas2016/example5_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example5_BNFfiles/metadata.yaml @@ -4,6 +4,7 @@ description: A simple model tags: ["ligand_ispresent", "molecules", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/Thomas2016/example6_BNFfiles/example6_metadata.yaml b/Published/Thomas2016/example6_BNFfiles/example6_metadata.yaml new file mode 100644 index 00000000..76de8db3 --- /dev/null +++ b/Published/Thomas2016/example6_BNFfiles/example6_metadata.yaml @@ -0,0 +1,21 @@ +id: example6_BNFfiles_example6 +name: example6 BNFfiles +description: A simple model +tags: ["molecules", "species"] +category: other +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example6_BNFfiles/metadata.yaml b/Published/Thomas2016/example6_BNFfiles/metadata.yaml index 4130d68b..437a0348 100644 --- a/Published/Thomas2016/example6_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example6_BNFfiles/metadata.yaml @@ -4,6 +4,7 @@ description: A simple model tags: ["molecules", "species"] category: other compatibility: + database_visible: true bng2_compatible: true nfsim_compatible: true simulation_methods: ["ode"] diff --git a/Published/Thomas2016/metadata.yaml b/Published/Thomas2016/metadata.yaml index 7e11e6ab..d11b20eb 100644 --- a/Published/Thomas2016/metadata.yaml +++ b/Published/Thomas2016/metadata.yaml @@ -4,6 +4,8 @@ description: Filename: example1_starting_point.bngl tags: ["chi_r__free__", "k_c__free__", "k_o__free__", "kaf__free__", "kar__free__", "alpha1_pre__free__", "alpha2_pre__free__", "alpha3_pre__free__", "alpha4_pre__free__", "lt", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "alpha1", "alpha2", "alpha3", "alpha4", "molecules", "species"] category: other compatibility: + database_visible: true + bngp_compatible: true bng2_compatible: true nfsim_compatible: false simulation_methods: ["ode"] diff --git a/Published/VaxAndVariants/Dallas/Dallas_metadata.yaml b/Published/VaxAndVariants/Dallas/Dallas_metadata.yaml new file mode 100644 index 00000000..d46eff4b --- /dev/null +++ b/Published/VaxAndVariants/Dallas/Dallas_metadata.yaml @@ -0,0 +1,24 @@ +id: "Dallas" +name: "Dallas" +description: "- This model is intended to be consistent with the compartmental model" +tags: ["dallas", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] +category: "epidemiology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/Vax_and_Variants/Dallas/Dallas.bngl" +playground: + visible: false + gallery_category: "epidemiology" + featured: false + difficulty: "advanced" diff --git a/Published/VaxAndVariants/Dallas/metadata.yaml b/Published/VaxAndVariants/Dallas/metadata.yaml index 072485cd..3b27163f 100644 --- a/Published/VaxAndVariants/Dallas/metadata.yaml +++ b/Published/VaxAndVariants/Dallas/metadata.yaml @@ -4,6 +4,7 @@ description: "- This model is intended to be consistent with the compartmental m tags: ["dallas", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] category: "epidemiology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/VaxAndVariants/Houston/Houston_metadata.yaml b/Published/VaxAndVariants/Houston/Houston_metadata.yaml new file mode 100644 index 00000000..3039e33b --- /dev/null +++ b/Published/VaxAndVariants/Houston/Houston_metadata.yaml @@ -0,0 +1,24 @@ +id: "Houston" +name: "Houston" +description: "- This model is intended to be consistent with the compartmental model" +tags: ["houston", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] +category: "epidemiology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/Vax_and_Variants/Houston/Houston.bngl" +playground: + visible: false + gallery_category: "epidemiology" + featured: false + difficulty: "advanced" diff --git a/Published/VaxAndVariants/Houston/metadata.yaml b/Published/VaxAndVariants/Houston/metadata.yaml index b2acaba6..8c9d4f45 100644 --- a/Published/VaxAndVariants/Houston/metadata.yaml +++ b/Published/VaxAndVariants/Houston/metadata.yaml @@ -4,6 +4,7 @@ description: "- This model is intended to be consistent with the compartmental m tags: ["houston", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] category: "epidemiology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/VaxAndVariants/NYC/NYC_aigenerated.md b/Published/VaxAndVariants/NYC/NYC_aigenerated.md new file mode 100644 index 00000000..30ba5ebb --- /dev/null +++ b/Published/VaxAndVariants/NYC/NYC_aigenerated.md @@ -0,0 +1,41 @@ +# Model Explanation: Vax and Variants — New York City + +## One-sentence summary + +Vaccination and four viral strains reshape staged COVID-19 transmission, hospitalization, recovery, and death in New York City. + +## What the model shows + +This New York City model extends a staged coronavirus disease 2019 (COVID-19) framework with vaccination and strain-specific susceptibility. SARS-CoV-2 denotes severe acute respiratory syndrome coronavirus 2. + +## Biological story + +Susceptible people vary in distancing behavior, receive vaccine through a multi-stage process, and may acquire infections from four strains. Infection progresses through exposed stages to asymptomatic or symptomatic disease, with vaccination modifying susceptibility and outcomes. + +## Main biological players + +Mixing and protected susceptible groups, vaccinated susceptible groups, four viral strains, five exposed stages, asymptomatic and symptomatic infection, hospitalization, recovery, and death. + +## Mechanism in plain English + +Contacts move susceptible people into strain-labeled infection chains. Vaccination progresses through delayed stages before protection develops, and breakthrough infections retain vaccination status. Distancing alters exposure, while detection, hospitalization, recovery, and death shape each epidemic wave. + +## Key modeled events + +- Vaccination moves people through delayed stages toward protection. +- Four strains compete for susceptible and vaccinated hosts. +- Each infection progresses through five exposed stages. +- Cases branch into asymptomatic, symptomatic, hospitalized, recovered, or deceased populations. +- Social distancing changes effective contact over time. + +## What the model measures + +Readouts separate susceptible behavior, vaccine stages, strain-specific susceptibility, exposed stages, infectious classes, hospitalization, recovery, deaths, and cumulative detected cases. + +## Expected behavior in plots + +Vaccination should progressively reduce the fully susceptible pool before lowering severe outcomes. A more transmissible or immune-evasive strain can generate a later wave despite vaccination; exposed stages should lead symptomatic cases, and hospitalizations and deaths should lag. + +## Caveats + +This summary covers the New York City member of a four-city collection. The model uses population averages and does not resolve individual immunity, age, or contact networks. diff --git a/Published/VaxAndVariants/NYC/NYC_metadata.yaml b/Published/VaxAndVariants/NYC/NYC_metadata.yaml new file mode 100644 index 00000000..b4f20103 --- /dev/null +++ b/Published/VaxAndVariants/NYC/NYC_metadata.yaml @@ -0,0 +1,24 @@ +id: "NYC" +name: "NYC" +description: "- This model is intended to be consistent with the compartmental model" +tags: ["nyc", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] +category: "epidemiology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/Vax_and_Variants/NYC/NYC.bngl" +playground: + visible: false + gallery_category: "epidemiology" + featured: false + difficulty: "advanced" diff --git a/Published/VaxAndVariants/NYC/metadata.yaml b/Published/VaxAndVariants/NYC/metadata.yaml index 00643421..b9d4f2f2 100644 --- a/Published/VaxAndVariants/NYC/metadata.yaml +++ b/Published/VaxAndVariants/NYC/metadata.yaml @@ -4,6 +4,7 @@ description: "- This model is intended to be consistent with the compartmental m tags: ["nyc", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] category: "epidemiology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/VaxAndVariants/Phoenix/Phoenix_metadata.yaml b/Published/VaxAndVariants/Phoenix/Phoenix_metadata.yaml new file mode 100644 index 00000000..02ee4e69 --- /dev/null +++ b/Published/VaxAndVariants/Phoenix/Phoenix_metadata.yaml @@ -0,0 +1,24 @@ +id: "Phoenix" +name: "Phoenix" +description: "- This model is intended to be consistent with the compartmental model" +tags: ["phoenix", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] +category: "epidemiology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/PyBNG/Vax_and_Variants/Phoenix/Phoenix.bngl" +playground: + visible: false + gallery_category: "epidemiology" + featured: false + difficulty: "advanced" diff --git a/Published/VaxAndVariants/Phoenix/metadata.yaml b/Published/VaxAndVariants/Phoenix/metadata.yaml index 8b25a650..bf36a17d 100644 --- a/Published/VaxAndVariants/Phoenix/metadata.yaml +++ b/Published/VaxAndVariants/Phoenix/metadata.yaml @@ -4,6 +4,7 @@ description: "- This model is intended to be consistent with the compartmental m tags: ["phoenix", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] category: "epidemiology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Yang2008/Yang2008_aigenerated.md b/Published/Yang2008/Yang2008_aigenerated.md new file mode 100644 index 00000000..456687e7 --- /dev/null +++ b/Published/Yang2008/Yang2008_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Yang 2008 + +## One-sentence summary + +Trivalent ligand crosslinks bivalent receptors into reversible aggregates whose size is controlled by saturation and crosslinking propensity. + +## What the model shows + +This network-free aggregation model studies how multivalent binding produces a sol–gel transition. With its default subcritical parameters, it provides a clean comparison between stochastic aggregate formation and mean-field predictions for bond counts and free-site fractions. + +## Biological story + +A three-site ligand captures a two-site receptor, then uses another arm to recruit a receptor from a different complex. Repeated capture builds branched aggregates, while bond dissociation breaks them apart. Changing ligand saturation or crosslinking propensity can move the system from small clusters toward a macroscopic aggregate. + +## Main biological players + +Trivalent ligand, bivalent receptor, ligand–receptor bonds, free ligand sites, free receptor sites, and branched aggregates. + +## Mechanism in plain English + +The first bond captures a receptor with free ligand. A receptor-bound ligand then crosslinks a receptor belonging to another complex, avoiding rings. Any bond can dissociate. The competition among available sites, crosslinking, and dissociation determines equilibrium connectivity and proximity to the percolation threshold. + +## Key modeled events + +- Free ligand captures an available receptor site. +- A bound ligand uses a remaining arm to crosslink a separate receptor complex. +- Repeated crosslinking builds branched receptor aggregates without rings. +- Bond dissociation releases sites and limits aggregate growth. + +## What the model measures + +Readouts measure free ligand and receptor, total ligand–receptor bonds, and free sites on both partners. These quantities summarize aggregate formation without enumerating every cluster topology. + +## Expected behavior in plots + +From the all-free state, bond counts should rise rapidly while free ligand and receptor sites fall toward equilibrium. At the default below-threshold setting, these curves should stabilize without wholesale depletion into a gel; increasing crosslinking propensity would deepen site depletion and enlarge aggregates. + +## Caveats + +The partners are abstract and all sites are equivalent. The model excludes rings, membrane geometry, downstream receptor signaling, and biochemical heterogeneity. diff --git a/Published/Yang2008/metadata.yaml b/Published/Yang2008/metadata.yaml index 5a382f8b..b09d512e 100644 --- a/Published/Yang2008/metadata.yaml +++ b/Published/Yang2008/metadata.yaml @@ -4,6 +4,7 @@ description: "TLBR yang 2008" tags: ["published", "physics", "yang", "2008"] category: "physics" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Yang2008/tlbr_yang2008_metadata.yaml b/Published/Yang2008/tlbr_yang2008_metadata.yaml new file mode 100644 index 00000000..c0ec2442 --- /dev/null +++ b/Published/Yang2008/tlbr_yang2008_metadata.yaml @@ -0,0 +1,23 @@ +id: "Yang_2008" +name: "Yang 2008" +description: "TLBR yang 2008" +tags: ["published", "physics", "yang", "2008"] +category: "physics" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen/BNGL-Models" +playground: + visible: true + gallery_category: "physics" + featured: false + difficulty: "intermediate" diff --git a/Published/Zhang2021/Zhang_2021_metadata.yaml b/Published/Zhang2021/Zhang_2021_metadata.yaml new file mode 100644 index 00000000..78ee5a94 --- /dev/null +++ b/Published/Zhang2021/Zhang_2021_metadata.yaml @@ -0,0 +1,24 @@ +id: "Zhang_2021" +name: "Zhang 2021" +description: "CAR-T signaling" +tags: ["published", "zhang", "2021", "tie2", "tie1", "ang1_4", "ang2_2", "ang2_3", "ang2_4", "veptp", "pten"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Zhang_2021.bngl" +playground: + visible: false + gallery_categories: ["developmental"] + featured: false + difficulty: "advanced" diff --git a/Published/Zhang2021/metadata.yaml b/Published/Zhang2021/metadata.yaml index ce5c9450..8dc14725 100644 --- a/Published/Zhang2021/metadata.yaml +++ b/Published/Zhang2021/metadata.yaml @@ -4,6 +4,7 @@ description: "CAR-T signaling" tags: ["published", "zhang", "2021", "tie2", "tie1", "ang1_4", "ang2_2", "ang2_3", "ang2_4", "veptp", "pten"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/Zhang2023/Zhang2023_aigenerated.md b/Published/Zhang2023/Zhang2023_aigenerated.md new file mode 100644 index 00000000..5222fb49 --- /dev/null +++ b/Published/Zhang2023/Zhang2023_aigenerated.md @@ -0,0 +1,45 @@ +# Model Explanation: Zhang 2023 + +## One-sentence summary + +VEGF165a signaling through VEGFR1, VEGFR2, and neuropilin-1 couples receptor trafficking to calcium, AKT–eNOS, sphingosine-1-phosphate, and MAPK responses that are reshaped by CD47 and thrombospondin-1. + +## What the model shows + +The model shows how the composition and location of vascular endothelial growth factor (VEGF) receptor complexes can influence several downstream signaling branches at once. It distinguishes VEGFR2 signaling from VEGFR1 competition, includes neuropilin-1 (NRP1) as a co-receptor that alters complex assembly and routing, and lets CD47/SIRPα and thrombospondin-1 (TSP1) change receptor dephosphorylation, recycling, and degradation. + +## Biological story + +VEGF165a can engage VEGFR1, VEGFR2, and NRP1 in several orders, producing receptor monomers, homodimers, heterodimers, and co-receptor-containing complexes at the cell surface. Ligand-crosslinked VEGFR2 becomes phosphorylated and can continue signaling as complexes move through early internal, later internal, and recycling states. Some complexes return to the surface, whereas others are degraded; association with NRP1, CD47/SIRPα, or TSP1 changes this balance. The surviving phospho-VEGFR2 signal is distributed among second-messenger, survival, nitric-oxide, and MAPK pathways. + +## Main biological players + +- **VEGF165a, VEGFR1, and VEGFR2:** ligand and receptors that compete, crosslink, dimerize, signal, and traffic. +- **NRP1, CD47/SIRPα, and TSP1:** extracellular and membrane regulators that alter receptor-complex composition and fate. +- **PLCγ, PIP2, IP3, DAG, calcium, calmodulin, and PKC:** the second-messenger branch connecting phospho-VEGFR2 to calcium release and PKC activity. +- **TSAD/Src, Axl, PI3K, PTEN, PDK1, mTOR, AKT, eNOS, and caveolin-1:** the survival and nitric-oxide branch. +- **CIB1, sphingosine kinase, sphingosine-1-phosphate, Ras, Raf, MEK, and ERK:** the lipid-to-MAPK branch that also feeds back to sphingosine kinase. + +## Mechanism in plain English + +VEGF165a first binds one or two receptor molecules and may also recruit NRP1, while receptors can associate before or after ligand engagement. Ligand-linked VEGFR2 is phosphorylated at its signaling tyrosine and activates PLCγ from the surface or internal states. PLCγ converts PIP2 into IP3 and DAG: IP3 promotes calcium release from the endoplasmic-reticulum pool, and calcium plus DAG assembles active PKC. In parallel, phospho-VEGFR2 activates TSAD/Src and Axl, which activates PI3K; PIP3 then recruits PDK1 and AKT so AKT can acquire both activating phosphorylations and stimulate eNOS. Calcium-loaded CIB1 moves sphingosine kinase toward the membrane, where phosphorylated sphingosine kinase produces sphingosine-1-phosphate and supports Ras–Raf–MEK–ERK signaling. Throughout this process, receptor internalization, recycling, dephosphorylation, and degradation determine how long each branch remains supplied with active VEGFR2. + +## Key modeled events + +- VEGF165a assembles VEGFR1, VEGFR2, and NRP1 into alternative monomeric, homodimeric, and heterodimeric complexes rather than following one fixed binding order. +- VEGFR2 phosphorylation persists across surface and internal trafficking states, while complex-specific dephosphorylation, recycling, and degradation compete to terminate or restore signaling. +- PLCγ produces IP3 and DAG, linking active VEGFR2 to endoplasmic-reticulum calcium release, calcium buffering and pumping, and calcium/DAG-dependent PKC assembly. +- Src and Axl activate the PI3K–PIP3–AKT pathway, allowing doubly phosphorylated AKT and calcium-bound calmodulin to promote eNOS activation. +- Calcium/CIB1 and ERK activate sphingosine kinase, whose sphingosine-1-phosphate output promotes Ras–Raf–MEK–ERK signaling and connects the calcium and MAPK branches. + +## What the model measures + +The receptor-level readouts distinguish free VEGF, free and bound NRP1, VEGFR1- and VEGFR2-containing complexes, receptor dimers, surface versus internal receptor pools, and phosphorylated VEGFR2 in several complex contexts. Downstream measurements include active PLCγ, PIP2 and PIP3, IP3 and DAG, cytosolic and endoplasmic-reticulum calcium, active PKC, phosphorylated Src and Axl, singly and doubly phosphorylated AKT, phosphorylated eNOS, membrane-associated or phosphorylated sphingosine kinase, sphingosine-1-phosphate, RasGTP, Raf phosphoforms, and phosphorylated MEK and ERK. + +## Expected behavior in plots + +After VEGF engagement, ligand-bound receptor complexes and VEGFR2 phosphorylation should rise before or alongside the redistribution of receptor material from the surface into early and later internal pools. Recycling can restore surface VEGFR2 and NRP1, whereas TSP1-associated CD47/SIRPα complexes are expected to favor faster signal loss through enhanced dephosphorylation or degradation. Active PLCγ should precede increases in IP3, DAG, and cytosolic calcium; calcium and DAG together should support active PKC. PIP3 should accompany phosphorylation of AKT at S473 and T308, with doubly phosphorylated AKT preceding phosphorylated eNOS. Sphingosine-1-phosphate and RasGTP should feed the later Raf–MEK–ERK response, so phospho-MEK and phospho-ERK may lag behind proximal receptor and calcium readouts. + +## Caveats + +The model represents surface, internal, and recycling locations as discrete molecular labels rather than spatially resolved cellular regions. Its receptor section deliberately enumerates many overlapping complex topologies, so similarly named receptor measurements are not mutually exclusive populations. Calcium transport and several ligand or metabolite pools are represented by calculated net fluxes, and the generated network is exported for downstream simulation rather than being simulated directly here. The pathway integrates VEGFR trafficking, calcium, eNOS, sphingolipid, and MAPK mechanisms at substantial breadth, but it does not establish that every parameterized interaction has equal experimental support. diff --git a/Published/Zhang2023/Zhang2023_aigenerated_detailed.md b/Published/Zhang2023/Zhang2023_aigenerated_detailed.md new file mode 100644 index 00000000..edfb6312 --- /dev/null +++ b/Published/Zhang2023/Zhang2023_aigenerated_detailed.md @@ -0,0 +1,133 @@ +# Detailed Model Explanation: Zhang 2023 VEGF Receptor Trafficking and Multibranch Signaling + +## 1. Model overview + +This model follows VEGF165a binding to VEGFR1, VEGFR2, and neuropilin-1 (NRP1), the formation and trafficking of receptor complexes, and regulation by CD47/SIRPα and thrombospondin-1 (TSP1). Phosphorylated VEGFR2 feeds PLCγ–calcium–PKC, Src–Axl–PI3K–AKT–eNOS, and CIB1–sphingosine kinase–S1P–Ras–Raf–MEK–ERK branches, linking receptor routing to calcium, survival, nitric-oxide, and MAPK outputs. + +## 2. BNGL block inventory + +The model contains 180 parameters, 38 molecule types, 34 seed species, 232 logical reaction rules (318 active physical lines because many rules continue), 129 observables, and 2 actions. It has no BNGL compartments or anchors; surface, two internal stages, recycling, cytosolic, and membrane locations are represented by internal states. + +## 3. Parameters, functions, and rate laws + +The namespace is organized by biochemical module rather than a single rate convention. Receptor binding and trafficking mostly use mass action, whereas ligand bookkeeping, calcium fluxes, lipid conversion, and kinase cascades use observable-dependent balance, Hill, or Michaelis–Menten-like expressions; `I` is retained as a source catalyst for several continuous pool-flux approximations. + +| Parameter group or names | Function in this model | +| --- | --- | +| `Volcyto`, `VolER`, `fextmolar`, `cellarea` | Convert between cytosolic, endoplasmic-reticulum, extracellular concentration, and surface-count scales in ligand and calcium flux expressions. | +| `VEGF165a_0`, `VEGFR2_0`, `VEGFR1_0`, `NRP1_0`, `TSP1_0` | Establish extracellular ligand and receptor/co-receptor pools. | +| `kvron/off`, `kvr1on/off`, `kcVR`, `kcRR`, `kdRR`, `kdeltaVR`, `kdeltaRR` | Control VEGF binding to VEGFR2/VEGFR1, ligand-independent receptor coupling, and ligand-assisted receptor dimerization. | +| `kVEGFNRP1*`, `kNRP1VEGFR1*`, `kNRP1VEGFR2*`, `kVEGFR1NRP1*`, `kVEGFR2NRP1*` | Build NRP1–VEGF and NRP1-associated VEGFR1/2 complexes in multiple assembly orders. | +| `kpr2`, `kdps`, `kdpi`, `kdpr` | Phosphorylate VEGFR2 Y1175 in ligand-crosslinked complexes and dephosphorylate it at surface, internal, or recycling states. | +| `kr2si`, `kr2ii2`, `kr2i2i`, `kr2rs`; corresponding `kr2NRP1*` | Move receptor complexes from surface to early internal, late internal, recycling, and back to surface, with NRP1-specific routing where declared. | +| `kdegi*`, `kdegr2NRP1*`, `f_TSP1deg`, `ksingleR2syn/deg/si/is` | Control phosphostate-, NRP1-, TSP1-, and location-dependent degradation plus synthesis/trafficking of single VEGFR2. | +| `kcd47free_on`, `kr2CD47off`, `kDCD47TSP1`, `koffCD47TSP1`, `CD47free_0`, `fTSP1dp`, `fTSP1i2r` | Couple CD47/SIRPα and TSP1 to VEGFR2 binding, dephosphorylation, degradation, and recycling biases. | +| `PLCgamma_0`, `kp/kdpPLCgamma`, `PIP2_0`, `kPIP2gen`, `kmPIP2PLCgamma`, `nDAG`, `kcatPLCgammaDAG`, `kdeg_ip3`, `kdeg_DAG` | Activate PLCγ from phospho-VEGFR2 and generate/clear IP3 and DAG from PIP2. | +| `Calcium_0`, `CaER_0`, `CaF_0`, `CaFbound_0`, `CaM_0`; IP3R/PMCA/SERCA/leak and buffer parameters | Set cytosolic/ER calcium pools, IP3-dependent release, plasma-membrane removal, ER uptake/leak, buffering, and calmodulin binding. | +| `ICracamp`, `Kcrac`, `Istim0`, `tau_stim`, `ncrac`, `CSQN_total`, `KCSQN` | Define store-operated calcium stimulation and ER calsequestrin buffering. | +| `Src_0`, `Axl_0`, `kp/kdpSrc`, `kpSrcAxl`, `kpAxlauto`, `kdpautoAxl`, `kdpSrcAxl` | Activate TSAD/Src from phospho-VEGFR2 and relay it through two Axl phosphorylation sites. | +| `PI3K_0`, `PTEN_0`, `PIP2_0`, `AKT_0`, `PDK1_0`, `mTOR_0`; PI3K/PTEN/PIP3/AKT kinetic terms | Convert PIP2/PIP3, recruit PDK1 and AKT, and phosphorylate AKT at S473 and T308. | +| `eNOS_0`, `kon/offCaMeNOS`, `koncaveNOS`, `koffeNOScav1`, `kcateNOSAKT`, `kdpeNOS` | Control calmodulin/caveolin binding and doubly phosphorylated AKT activation of eNOS S1177. | +| `PKC_0`, `kon/offCaPKC`, `kon/offDAGPKC`, `kcatPKC`, `kmPKCRaf` | Assemble calcium/DAG-bound PKC and phosphorylate Raf at its PKC-regulated serine. | +| `CIB1_0`, `SphK_0`, `Sph_0`, `S1P_0`; CIB1/SphK binding, transport, phosphorylation, and S1P terms | Couple calcium-loaded CIB1 and ERK2 to membrane SphK activation and sphingosine-to-S1P conversion. | +| `RasGTP_0`, `RasGDP_0`, `Raf_0`, `MEK12_0`, `ERK12_0`; Ras/Raf/MEK/ERK kinetic terms | Generate RasGTP from S1P, activate Raf, phosphorylate both MEK sites and ERK1/2, and reset each kinase. | + +There are no active functions; all nonlinear calculations appear directly in rule-rate expressions. + +## 4. Molecule types, sites, and states + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | +| `vegf` | 4 | two repeated `r`, `nrp1bd`, `c` | `c`: `s/i/i2/r` | None | Bivalent VEGF165a ligand that can crosslink receptors, bind NRP1, and travel with complexes. | +| `vegfr2` | 5 | `l1`, `Y1175`, `CD47bd`, `dimer`, `c` | Y1175 `Y/pY`; `c`: `s/i/i2/r` | None | Principal signaling receptor with ligand, dimer, CD47, phosphosite, and routing information. | +| `vegfr1` | 4 | `l2`, `dimer`, `nrp1bd`, `c` | `c`: `s` | None | Competing VEGF receptor that forms homo/heterodimers and associates with NRP1. | +| `NRP1` | 2 | `vegfabd`, `c` | `c`: `s/i/i2/r` | None | Co-receptor that alters VEGFR complex assembly, degradation, and recycling. | +| `CD47SIRPa` | 4 | `VEGFR2bd`, `TSP1bd`, `Y1`, `c` | Y1 `Y/pY`; `c`: `s/i/i2/r` | None | Composite inhibitory/regulatory receptor that binds VEGFR2 and TSP1 during trafficking. | +| `TSP1` | 1 | `CD47bd` | None | None | Extracellular ligand that engages CD47/SIRPα and modifies receptor fate. | +| `PI`, `PLCgamma`, `DAG`, `IP3_cyto` | 1 each | `PIsite`; `Yplc`; `pkcbd`; `ip3rbd` | PI `3P/4P`; PLCγ `Y/pY` | None | PIP2/PIP3 and PLCγ-derived second-messenger machinery. | +| `Calcium_cyto`, `CaER`, `CaF`, `CSQNF` | 1 each | `bd`; `bd`; `cabd`; `cabd` | None | None | Cytosolic and ER calcium plus cytosolic and ER buffering species. | +| `CaM` | 5 | two repeated `NCaM`, two repeated `CCaM`, `CaMtargetbd` | None | None | Calmodulin with four explicit calcium-binding components and an effector-binding site. | +| `I`, `Istim`, `Trash` | 0 each | None | None | None | Persistent source catalyst, store-operated influx signal, and degradation sink. | +| `PTEN`, `PI3K` | 1 each | `PIP3docking`; `state` | PI3K `active/inactive` | None | Opposing PIP3 regulator and Axl-responsive lipid kinase. | +| `TSADSrc` | 1 | `Y1` | `Y/pY` | None | VEGFR2-responsive Src-like relay upstream of Axl. | +| `Axl` | 2 | `Ysrc`, `Yaxl` | each `Y/pY` | None | Two-stage receptor kinase relay that activates PI3K after Src and auto-phosphorylation. | +| `AKT` | 3 | `PHakt`, `T308`, `S473` | T308/S473 `S/pS` | None | PIP3-recruited kinase requiring two activating phosphorylations. | +| `PDK1`, `mTOR` | 2; 1 | PDK1: `PHpdk1`, `aktbd`; mTOR: `aktbd` | None | None | PIP3-recruited T308 kinase and implicit S473 kinase input. | +| `eNOS`, `caveolin1` | 3; 1 | eNOS: `CaMBD`, `S1177`, `cav1BD`; caveolin: `eNOSbd` | S1177 `S/pS` | None | Nitric-oxide synthase controlled positively by CaM/AKT and negatively by caveolin binding. | +| `PKC` | 2 | `CalciumBD`, `DAGBD` | None | None | Requires calcium and DAG contacts to phosphorylate Raf. | +| `CIB1` | 4 | `EF1`, `EF2`, `sk1bd`, `location` | `cytosol/membrane` | None | Calcium sensor that recruits SphK and transports it to the membrane. | +| `SphK`, `Sph`, `S1P` | 2; 1; 1 | SphK: `CIB1bd`, `Serk`; Sph: `skbd`; S1P: `bd` | SphK Ser `S/pS` | None | Sphingosine kinase branch generating S1P after ERK-dependent activation. | +| `RasGDP`, `RasGTP` | 1 each | `rafbd` | None | None | Inactive and active Ras pools; the model generates RasGTP directly from the S1P readout. | +| `Raf` | 4 | `mekbd`, `rasbd`, `Y1Y2`, `Spkc` | Y1Y2 `Y/pY`; Spkc `S/pS` | None | Integrates Ras-dependent tyrosine phosphorylation and PKC-dependent serine phosphorylation. | +| `MEK12` | 3 | `bd`, `S1`, `S2` | both sites `S/pS` | None | Dual-site MAPK kinase activated by multiple Raf phosphoforms. | +| `ERK1`, `ERK2` | 2 each | `MEK12bd`, `S1` or `S2` | `S/pS` | None | Terminal MAPKs; ERK2 additionally phosphorylates SphK. | + +## 5. Compartments, anchors, initial species, and setup + +No physical compartments or anchors are declared. Receptor and ligand state `s` represents the starting surface pool, while `i`, `i2`, and `r` encode sequential early-internal, late-internal, and recycling states; downstream proteins begin as unbound and generally unphosphorylated pools. PIP2, cytosolic and ER calcium, buffers, calmodulin, caveolin-bound basal eNOS, and inactive kinases establish the signaling substrate. Several source-catalyzed rules maintain ligand, receptor, lipid, calcium, and sphingosine pools through calculated fluxes rather than discrete synthesis reactions. + +## 6. Reaction-rule inventory + +**Rule-family orientation.** Rules 1–48 assemble VEGF/VEGFR/NRP1 complexes; 49–153 phosphorylate, route, recycle, degrade, and replenish receptors with CD47/TSP1 modulation; 154–174 generate PLCγ, IP3/DAG, and calcium/CaM signals; 175–198 form the Src–Axl–PI3K–AKT–eNOS branch; and 199–232 connect TSP1/CD47, PKC, CIB1/SphK/S1P, and Ras–MAPK signaling. + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | +| 1–6 | Reversible | Surface VEGFR1/2 `dimer`; VEGF-crosslinked receptor pairs | Form receptor homo- or heterodimers either without ligand (1–3) or within VEGF-crosslinked pairs (4–6), using basal versus ligand-assisted coupling rates. | Establishes receptor association before and after ligand crosslinking. | +| 7–16 | Reversible or source-balanced | VEGFR1, NRP1, VEGF `nrp1bd/r` | Binds VEGFR1 directly to NRP1, binds VEGF to NRP1, and adds VEGFR1/2 to NRP1-bound ligand in monomeric or dimerized receptor contexts. Source-catalyzed rule 8 balances free ligand against the measured NRP1 complex. | Permits multiple assembly orders for the co-receptor-containing signal complex. | +| 17–41 | Reversible or source-balanced | VEGF repeated `r`, VEGFR1 `l2`, VEGFR2 `l1`, NRP1 | Rules 17–35 bind one or two receptor molecules to VEGF across homo/heterodimer and NRP1 contexts; 36–41 add NRP1 to preassembled ligand–receptor complexes. | Enumerates the major surface stoichiometries without assuming a single binding sequence. | +| 42–48 | Reversible or source-balanced | VEGF and VEGFR1/2 | Balances VEGF–VEGFR1 binding and extends a singly ligated VEGFR1 into VEGFR1 homodimers or VEGFR1–VEGFR2 heterodimers, including pre-coupled receptors. | Adds VEGFR1 competition and mixed receptor complexes to the VEGFR2-focused network. | +| 49–52 | One-way | VEGF-crosslinked VEGFR2 Y1175 in `s/i/i2/r` | Changes Y1175 `Y→pY` at the same receptor phosphorylation rate in all four routing states. | Allows signaling competence to arise or persist during trafficking. | +| 53–62 | One-way | VEGFR2 Y1175; CD47/SIRPα-bound or free contexts | Dephosphorylates Y1175 at surface, internal, or recycling-specific rates; CD47/TSP1 contexts use the corresponding modifiers. | Makes receptor activity sensitive to both location and inhibitory complex composition. | +| 63–74 | Reversible | VEGF–VEGFR2 complexes with optional receptor dimer, NRP1, and one/two CD47/SIRPα partners | Moves complete complexes `s↔i`, preserving all ligand and regulatory bonds; NRP1- and TSP1-containing variants use adjusted rates. | Internalizes intact receptor assemblies rather than stripping them at the membrane. | +| 75–86 | Reversible | The same complex variants in `i/i2` | Moves early-internal complexes `i↔i2`, with separate NRP1 routing constants and retained CD47/TSP1 topology. | Creates a second sorting stage before recycling or degradation. | +| 87–96 | One-way | Late-internal NRP1/VEGFR2 complexes, optional CD47/TSP1 | Changes all complex members `i2→r`; TSP1-bound variants apply its recycling factor. | Selects late-internal complexes for the recycling route. | +| 97–104 | One-way | Free recycling VEGFR2, NRP1, CD47/SIRPα and assembled complexes | Returns free components `r→s`, releases VEGF and/or NRP1, breaks receptor dimers, and dissociates CD47 or TSP1 contacts. | Resets recycled material into surface-competent building blocks. | +| 105–128 | One-way sink | VEGF–VEGFR2 complexes in `i/i2`, with phospho/unphospho receptor, NRP1, and zero/one/two CD47 partners | Sends each enumerated topology to `Trash`; rates distinguish location, Y1175 state, and NRP1 content. | Competes degradation against receptor recycling across the combinatorial complex family. | +| 129–144 | One-way sink | The corresponding complexes with TSP1-bound CD47/SIRPα | Removes the same phosphostate/location/NRP1 variants with rates multiplied by `f_TSP1deg`. | Encodes TSP1-dependent bias toward complex degradation. | +| 145–153 | One-way or reversible | Single VEGFR2, CD47/SIRPα, receptor dimer, surface/internal states | Degrades single internal receptor with or without CD47/TSP1 (145–147), synthesizes surface receptor (148), and moves free/dimer/CD47-bound single receptor `s↔i` (149–153). | Maintains and routes receptor not incorporated into VEGF-crosslinked complexes. | +| 154–157 | One-way | PLCγ Yplc; phospho-VEGFR2 in `s/i/i2` | Catalytically changes PLCγ `Y→pY` from any signaling location, followed by dephosphorylation. | Couples receptor activity to the phosphoinositide/calcium branch. | +| 158–162 | One-way | Active PLCγ, PIP2, IP3, DAG, source catalyst | Active PLCγ consumes PIP2 to create IP3 or DAG with saturating PIP2 dependence; PIP2 is replenished and both messengers degrade. | Produces the two inputs required for calcium release and PKC activation. | +| 163–170 | Reversible binding or source-balanced flux | Cytosolic/ER calcium, CaF, `Istim`, IP3 and pump/buffer observables | Buffers cytosolic calcium and implements store-operated influx, IP3R release, PMCA export, SERCA uptake, ER leak, and calsequestrin correction through signed pool fluxes. | Approximates continuous calcium homeostasis without explicit channel molecules. | +| 171–174 | One-way association/dissociation | Repeated N- and C-lobe CaM sites; cytosolic calcium | Loads one calcium onto an available N- or C-lobe site while retaining a free calcium product, then unloads it at lobe-specific rates. | Builds calcium-bound CaM states used for eNOS and CIB1-linked signaling. | +| 175–178 | One-way | TSADSrc Y1; phospho-VEGFR2 in `s/i/i2` | Receptor catalytically changes Src `Y→pY` in three locations; Src then dephosphorylates. | Starts the Axl/PI3K branch from routed receptor. | +| 179–184 | One-way | Active Src, Axl Ysrc/Yaxl, PI3K state | Src phosphorylates Axl Ysrc, Axl auto-phosphorylates Yaxl, both sites reset independently, and Yaxl-p activates PI3K, which later inactivates. | Converts receptor/Src activity into a transient lipid-kinase signal. | +| 185–192 | One-way or reversible | PI3K/PTEN, PI `3P/4P`, PDK1/AKT PH sites, AKT S473/T308 | PI3K makes PIP3 and PTEN restores PIP2; PIP3 recruits PDK1/AKT; mTOR-dependent S473 and PDK1-dependent T308 phosphorylation produce doubly active AKT; phosphatases reset both sites. | Implements the survival/AKT arm with ordered membrane recruitment and dual phosphorylation. | +| 193–198 | Reversible or one-way | Calcium-loaded CaM, eNOS CaMBD/cav1BD/S1177, caveolin, doubly active AKT | CaM binds eNOS, CaM or S1177 phosphorylation releases caveolin, caveolin can rebind basal eNOS, AKT changes S1177 `S→pS`, and phosphatase resets it. | Integrates calcium and AKT signals at eNOS. | +| 199–204 | Source-balanced or reversible | TSP1–CD47/SIRPα, VEGFR2–CD47, PKC calcium/DAG sites | Balances TSP1 binding, binds CD47/SIRPα to VEGFR2, and independently loads PKC with calcium and DAG. | Connects extracellular inhibition to receptor fate and assembles active PKC. | +| 205–210 | Reversible or one-way | CIB1 EF1/EF2, calcium, CIB1–SphK bond/location, SphK Ser | Loads both CIB1 EF sites, binds phosphorylated SphK, and moves the complex cytosol↔membrane; calcium-free membrane CIB1 returns to cytosol. | Couples calcium to localization of the S1P-producing enzyme. | +| 208, 211–216 | One-way | Active ERK2 or PKC; SphK/Raf phosphosites; sphingosine/S1P | ERK2 phosphorylates SphK; active PKC phosphorylates Raf; both reset. Source maintains sphingosine, membrane phospho-SphK converts it to S1P, and S1P reverts to sphingosine. | Creates cross-talk from MAPK and PKC into the S1P relay. | +| 217–220 | Source-balanced or reversible/one-way | S1P, RasGTP, Raf `rasbd/Y1Y2` | S1P-dependent production and GAP loss control RasGTP; RasGTP binds Raf and enables Raf tyrosine phosphorylation, which later resets. | Converts the lipid messenger into active Raf. | +| 221–228 | One-way | Raf Y1Y2/Spkc combinations; MEK12 S1/S2 | Any signaling-competent Raf phosphoform catalyzes site-specific MEK phosphorylation with substrate saturation; separate rules dephosphorylate both MEK sites. | Integrates Ras- and PKC-derived Raf activation at the dual-site MEK node. | +| 229–232 | One-way | Doubly phosphorylated MEK12; ERK1 S1, ERK2 S2 | Active MEK phosphorylates ERK1 or ERK2 with saturating rates; each ERK resets independently. | Produces terminal MAPK outputs, including ERK2 input to SphK rule 208. | + +## 7. Observables and technical readouts + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | +| `vegffrees`, `VEGFR2total`, `VEGFR2tots`, `VEGFR2toti`, `vr2s`, `vr2i`, `R2singlei`, `vr1s`, `vegfr1tots`, `NRP1totals`, `NRP1totali`, `totalnrp1` | Molecule count | Free ligand and receptor/co-receptor totals by routing state, including unligated internal single VEGFR2. | Broad totals include bound contexts unless a free site is explicitly required. | +| `NRP1frees`, `NRP1freei`, `NRP1bounds`, `NRP1boundi`, `singleNRP1totals`, `singleNRP1totali`, `nrp1s`, `nrp1r1s` | Molecule count | Free, VEGF-bound, single, and VEGFR1-associated NRP1 at surface/internal states. | Resolve the co-receptor's alternative binding and routing roles. | +| `vegfnrp1s`, `vegfnrp1i`, `vegfr1s`, `vegfr2s`, `vegfr2i`, `vegfr2total`, `NRP1VEGFR2s`, `NRP1VEGFR2i`, `vr2dimers`, `vr2dimeri` | Molecule/species count | Ligand–receptor/co-receptor complexes and receptor dimers by location. | Species-count entries refer to complete matching complexes, unlike embedding-based molecule counts. | +| `bvegfr2`, `bnrp1`, `bvegfr1`, `bvegfr1dimer`, `bvegfr2_2`, `bvegfr1_2`, `vegfbound_1`, `vegfbound_2`, `vegfbound_3`, `vegfbound_4` | Mixed molecule/species count | Alternative VEGF binding topologies. | Provide overlapping views of ligand occupancy; they should not be summed as disjoint populations. | +| `vegfr2Y1175ps`, `vegfr2Y1175pi`, `pr2Y1175total`, `vr2Y1175s`, `vr2Y1175i`, `vr2r2py1175s`, `vr2r2py1175i`, `vr2py1175s`, `vr2py1175i`, `r2singlepy1175s`, `r2singlepy1175i`, `vr1r2pY1165s` | Mixed molecule/species count | Phospho-Y1175 VEGFR2 in total, single, ligand-bound, homo/heteroreceptor, surface, or internal contexts. | Distinguish receptor activity from receptor abundance and routing. | +| `tsp1frees`, `cd47tsp1s`, `cd47s`, `phosphoAxltotal`, `phosphoAxlpSrc`, `phosphoAxlpauto`, `activeSrc` | Molecule count | TSP1/CD47 availability and Src/Axl phosphostates. | Track the inhibitory extracellular arm and the proximal PI3K-activating relay. | +| `freeDAGs`, `activePLCgamma`, `pplcgamma`, `plcgammafree`, `yplcgamma`, `PIP2`, `PIP3`, `freepip2`, `freepip3`, `freeip3cyto` | Molecule count | PLCγ state, phosphoinositides, DAG, and IP3. | Several names overlap intentionally; “freeDAGs” allows either DAG bond state because its pattern uses a bond wildcard. | +| `Cac`, `Caer`, `CaBuf_fer`, `Iopenstim`, `activePKCs`, `activePKCtot`, `CIB1mem`, `freecib1`, `calciumcib1`, `sk1bcib1` | Molecule count | Calcium pools/buffering, influx proxy, PKC assembly, and calcium-loaded CIB1. | Translate signed calcium-flux rules into experimentally interpretable pool readouts. | +| `ps473akt`, `ps308akt`, `ppAkt`, `phosphoeNOS` | Molecule count | Singly/doubly phosphorylated AKT and active eNOS. | `ppAkt` is the kinase state used by the eNOS phosphorylation rule. | +| `SphKpkc`, `SphK1`, `SphK1mempS`, `SphK1cytosol`, `activeSphK1`, `freeSK1`, `freeSK1mem`, `freeSphK1`, `pSK1`, `freesphingosin`, `S1phosphate`, `frees1p` | Molecule count | SphK phosphorylation/binding/location plus sphingosine and S1P pools. | Resolve activation and membrane delivery of the S1P-producing branch; several “free” patterns differ in whether binding or phosphorylation is constrained. | +| `rasgdpfree`, `rasgtpfree`, `gtpfreeras`, `freeraf`, `activeRafbyrastot`, `activeRafPKC`, `activeRafPKCERK1`, `activeRafPKCERK2`, `activeRafPKCERK3`, `rafY1Y2pY`, `rafY1Y2pYpS`, `rafpS`, `py1y2rafs`, `rafpkc` | Molecule count | Ras nucleotide pools and Raf tyrosine/serine phosphoforms. | Separate Ras-bound activation from PKC phosphorylation and combined Raf states. | +| `phosphoMEK12tot`, `mek12s`, `mek12ps`, `mek12ps1`, `mek12ps2`, `phosphoMEKpS1`, `phosphoMEKpS2`, `mek12s1`, `mek12s2` | Molecule count | Total and site-specific MEK12 phosphorylation/substrate pools. | Rate-law substrate observables such as `mek12s1/2` are narrower than total unphosphorylated MEK. | +| `phosphoERK1tot`, `phosphoERK2tot`, `erk1s`, `pERK1s`, `pERK2s`, `erk1ps`, `erk2ps`, `phosphoERKpS1`, `phosphoERKpS2`, `erk12s1`, `erk12s2` | Molecule count | ERK1/2 unphosphorylated and phosphorylated pools under several pattern constraints. | Report terminal MAPK activation and provide substrate denominators for saturating rules. | +| `freepip3`, `freeSphK1`, `frees1p`, `gtpfreeras`, `Iopenstim` | Molecule count | Free metabolic/signaling pools reused directly in rate expressions. | These repeated regulatory readouts are highlighted because changing their pattern semantics changes multiple nonlinear fluxes. | + +## 8. Actions and simulation workflow + +The file generates the reaction network with aggregate size capped at 10 and then exports the resulting network as SBML. It does not run a trajectory itself; the many trafficking states, continuous source-flux expressions, and nonlinear calcium/kinase rates are intended for simulation by an SBML-capable downstream solver. + +## 9. Technical caveats and ambiguities + +- The model has 232 logical rules but 318 active physical lines because continued patterns span lines; grouped rule numbers here follow complete reactions. +- Surface/internal/recycling and cytosol/membrane labels are internal states, not BNGL compartments, so spatial volume effects occur only where explicitly included in rate expressions. +- Many observables overlap substantially and mix `Molecules` with `Species`; summing them can double-count embeddings or complexes. +- Several source-catalyzed rules use signed rates to approximate continuous pool fluxes. Their direction and positivity depend on the current observables rather than a simple irreversible chemical event. +- The receptor-trafficking inventory groups repetitive topology variants, but every rule range preserves distinctions in NRP1, CD47/SIRPα, TSP1, phosphostate, and routing state that determine the chosen rate. +- The `CaM` type repeats both N- and C-lobe components, so pattern matching can create symmetry/embedding multiplicities that should be checked in generated reactions. diff --git a/Published/Zhang2023/Zhang_2023_metadata.yaml b/Published/Zhang2023/Zhang_2023_metadata.yaml new file mode 100644 index 00000000..bc7954cb --- /dev/null +++ b/Published/Zhang2023/Zhang_2023_metadata.yaml @@ -0,0 +1,66 @@ +id: "Zhang_2023" +name: "Zhang 2023" +description: "VEGF signaling" +contributors: + - name: "Nabil Mardhy" + +citation: + year: "2023" + pmid: "no id" + reference: "Zhang et al., 2023" + +tags: ["published", "zhang", "2023", "vegf", "vegfr2", "vegfr1", "nrp1", "pi", "plcgamma", "dag", "ip3_cyto"] +date: + last_tested: 2026-07-18 + +category: "immunology" +biol_categories: ["immunology"] +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true + vcell_compatible: false + vcell_errors: "model won't open on VCell with no error message" + simulation_methods: ["ode", "ssa"] + uses_energy: false + uses_functions: false + uses_compartments: false + nfsim_compatible: false + molclustpy_compatible: false + mpd_compatible: false + comments: "nfsim dangling edge not allowed in species graph! at line 317 MCP There was an issue with BNGL model Zhang_2023.bngl XML file couldn't be generated" + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + uses_functions: false + uses_compartments: false + uses_energy: false + +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/Zhang_2023.bngl" + +playground: + visible: false + gallery_categories: ["developmental"] + featured: false + difficulty: "advanced" + + + + + diff --git a/Published/Zhang2023/metadata.yaml b/Published/Zhang2023/metadata.yaml index a2f4ec2e..d0f4eee4 100644 --- a/Published/Zhang2023/metadata.yaml +++ b/Published/Zhang2023/metadata.yaml @@ -4,6 +4,7 @@ description: "VEGF signaling" tags: ["published", "zhang", "2023", "vegf", "vegfr2", "vegfr1", "nrp1", "pi", "plcgamma", "dag", "ip3_cyto"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/fcerifyn/fceri_fyn_metadata.yaml b/Published/fcerifyn/fceri_fyn_metadata.yaml new file mode 100644 index 00000000..34f3a071 --- /dev/null +++ b/Published/fcerifyn/fceri_fyn_metadata.yaml @@ -0,0 +1,24 @@ +id: "fceri_fyn" +name: "FceRI Fyn" +description: "FceRI signaling" +tags: ["published", "immunology", "fceri", "fyn", "lig", "lyn", "syk", "rec"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/fceri_fyn.bngl" +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" diff --git a/Published/fcerifyn/fcerifyn_aigenerated.md b/Published/fcerifyn/fcerifyn_aigenerated.md new file mode 100644 index 00000000..d7576803 --- /dev/null +++ b/Published/fcerifyn/fcerifyn_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: FcεRI Fyn + +## One-sentence summary + +Ligand-crosslinked FcεRI recruits Lyn, Fyn, and Syk into a phosphorylation network controlled by receptor aggregation and phosphatases. + +## What the model shows + +This early FcεRI model contrasts constitutive Lyn with SH2-recruited Lyn and Fyn during receptor activation. Ligand-driven receptor aggregation enables phosphorylation of receptor β and γ chains, recruitment of Syk, and reciprocal kinase phosphorylation. + +## Biological story + +Bivalent ligand aggregates FcεRI. Constitutively associated Lyn initiates phosphorylation, creating SH2 docking sites for additional Lyn, Fyn, and Syk. Kinases in neighboring receptors then phosphorylate one another and the receptor, while dephosphorylation erases both membrane and cytosolic kinase activation. + +## Main biological players + +FcεRI receptor β and γ chains, bivalent ligand, Lyn, Fyn, Syk, SH2 domains, and kinase activation-loop phosphorylation. + +## Mechanism in plain English + +Ligand links receptors into dimers. Receptor-bound Lyn phosphorylates β and γ chains, which recruit Lyn or Fyn to β and Syk to γ. Proximity within aggregates enables transphosphorylation of receptor chains and kinase activation sites. Syk can further activate neighboring Syk. Constitutive dephosphorylation reverses receptor and kinase modifications, with distinct treatment of membrane-bound and cytosolic Syk. + +## Key modeled events + +- Ligand crosslinks FcεRI receptors into signaling-competent aggregates. +- Constitutive Lyn phosphorylates receptor β and γ chains. +- Phosphorylated β recruits Lyn or Fyn, while phosphorylated γ recruits Syk. +- Clustered Lyn, Fyn, and Syk undergo transphosphorylation, opposed by dephosphorylation. + +## What the model measures + +No explicit plotted readouts are defined. Useful biological measurements would include receptor aggregates, phosphorylated β and γ chains, receptor-bound Lyn/Fyn/Syk, and activated Syk. + +## Expected behavior in plots + +Receptor aggregates and receptor phosphorylation should precede accumulation of recruited kinases. Activated Syk should appear after γ-chain phosphorylation, whereas rapid dephosphorylation should keep activation transient and return released Syk toward its basal state. + +## Caveats + +The model covers proximal FcεRI phosphorylation only. It omits LAT, calcium, MAPK, degranulation, and explicit cell compartments, and it supplies no predefined plots. diff --git a/Published/fcerifyn/metadata.yaml b/Published/fcerifyn/metadata.yaml index 32dadeff..df33001c 100644 --- a/Published/fcerifyn/metadata.yaml +++ b/Published/fcerifyn/metadata.yaml @@ -4,6 +4,7 @@ description: "FceRI signaling" tags: ["published", "immunology", "fceri", "fyn", "lig", "lyn", "syk", "rec"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/innateimmunity/innate_immunity_metadata.yaml b/Published/innateimmunity/innate_immunity_metadata.yaml new file mode 100644 index 00000000..5d6f4463 --- /dev/null +++ b/Published/innateimmunity/innate_immunity_metadata.yaml @@ -0,0 +1,24 @@ +id: "innate_immunity" +name: "Korwek 2023" +description: "Immune response" +tags: ["published", "immunology", "innate", "immunity", "polyic", "rigi", "mavs", "pkr", "oas3", "rnasel", "eif2a", "rigi_mrna"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/innate_immunity.bngl" +playground: + visible: true + gallery_categories: ["immunology"] + featured: false + difficulty: "intermediate" diff --git a/Published/innateimmunity/metadata.yaml b/Published/innateimmunity/metadata.yaml index 4d96b539..8d516756 100644 --- a/Published/innateimmunity/metadata.yaml +++ b/Published/innateimmunity/metadata.yaml @@ -4,6 +4,7 @@ description: "Immune response" tags: ["published", "immunology", "innate", "immunity", "polyic", "rigi", "mavs", "pkr", "oas3", "rnasel", "eif2a", "rigi_mrna"] category: "immunology" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/mapkdimers/mapk-dimers_metadata.yaml b/Published/mapkdimers/mapk-dimers_metadata.yaml new file mode 100644 index 00000000..c7654765 --- /dev/null +++ b/Published/mapkdimers/mapk-dimers_metadata.yaml @@ -0,0 +1,24 @@ +id: "mapk-dimers" +name: "MAPK Dimers" +description: "MAPK dimerization" +tags: ["published", "mapk", "dimers", "ste5", "ste11", "ste7", "fus3"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/mapk-dimers.bngl" +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" diff --git a/Published/mapkdimers/mapkdimers_aigenerated.md b/Published/mapkdimers/mapkdimers_aigenerated.md new file mode 100644 index 00000000..16323f5f --- /dev/null +++ b/Published/mapkdimers/mapkdimers_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: MAPK Dimers + +## One-sentence summary + +Dimerization of Ste5 scaffolds changes how the Ste11–Ste7–Fus3 kinase cascade assembles and phosphorylates Fus3. + +## What the model shows + +This model examines a yeast MAPK cascade on a scaffold that can dimerize. Each Ste5 recruits Ste11, Ste7, and Fus3, while scaffold–scaffold association creates larger assemblies that can redistribute the spatial relationships among the kinase tiers. + +## Biological story + +Ste5 captures the three kinases and can pair with another Ste5. Scaffold-bound Ste11 becomes active, phosphorylates nearby Ste7, and activated Ste7 phosphorylates Fus3. Constitutive dephosphorylation competes with this scaffold-supported relay. + +## Main biological players + +Ste5 scaffold dimers, Ste11, Ste7, Fus3, and phosphorylated forms of all three kinases. + +## Mechanism in plain English + +Ste5 molecules reversibly dimerize and independently recruit each kinase. Ste11 is activated on a scaffold; active Ste11 modifies scaffold-associated Ste7, and modified Ste7 activates associated Fus3. Phosphate removal continually resets each tier. Fus3 can therefore be phosphorylated while free or while participating in different scaffold-containing assemblies. + +## Key modeled events + +- Ste5 scaffolds reversibly dimerize. +- Ste11, Ste7, and Fus3 bind dedicated positions on Ste5. +- Activated Ste11 phosphorylates Ste7, which then phosphorylates Fus3. +- Dephosphorylation opposes each kinase tier. + +## What the model measures + +Readouts separate total phosphorylated Fus3, free phosphorylated Fus3, scaffold-associated phosphorylated Fus3, and Fus3 associated with Ste5 or Ste7-containing assemblies. + +## Expected behavior in plots + +Phosphorylated Fus3 should rise as loaded Ste5 assemblies form. Scaffold-associated Fus3 should respond before or alongside the total signal, while free phosphorylated Fus3 reflects release; dimerization may retain more output in larger scaffold assemblies than the monomeric counterpart. + +## Caveats + +The model uses uniform rates and no upstream pheromone input. It is best interpreted as a scaffold-architecture comparison, not a calibrated reconstruction of the full yeast mating pathway. diff --git a/Published/mapkdimers/metadata.yaml b/Published/mapkdimers/metadata.yaml index 507ffc1f..504f70c6 100644 --- a/Published/mapkdimers/metadata.yaml +++ b/Published/mapkdimers/metadata.yaml @@ -4,6 +4,7 @@ description: "MAPK dimerization" tags: ["published", "mapk", "dimers", "ste5", "ste11", "ste7", "fus3"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/mapkmonomers/mapk-monomers_metadata.yaml b/Published/mapkmonomers/mapk-monomers_metadata.yaml new file mode 100644 index 00000000..b01ae108 --- /dev/null +++ b/Published/mapkmonomers/mapk-monomers_metadata.yaml @@ -0,0 +1,24 @@ +id: "mapk-monomers" +name: "MAPK Monomers" +description: "MAPK cascade" +tags: ["published", "mapk", "monomers", "ste5", "ste11", "ste7", "fus3"] +category: "signaling" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/complex-models/mapk-monomers.bngl" +playground: + visible: false + gallery_categories: ["cancer"] + featured: false + difficulty: "advanced" diff --git a/Published/mapkmonomers/mapkmonomers_aigenerated.md b/Published/mapkmonomers/mapkmonomers_aigenerated.md new file mode 100644 index 00000000..c560d625 --- /dev/null +++ b/Published/mapkmonomers/mapkmonomers_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: MAPK Monomers + +## One-sentence summary + +Monomeric Ste5 scaffolds organize sequential Ste11–Ste7–Fus3 phosphorylation without scaffold dimerization. + +## What the model shows + +This companion model provides the monomeric-scaffold baseline for a yeast MAPK cascade. A single Ste5 can recruit all three kinase tiers, allowing direct propagation from Ste11 through Ste7 to Fus3 while excluding scaffold–scaffold association. + +## Biological story + +Kinases load onto separate positions of Ste5. Scaffold-associated Ste11 is activated, passes phosphate to Ste7, and active Ste7 modifies Fus3. Each kinase can be dephosphorylated, so the output reflects productive scaffold occupancy versus resetting. + +## Main biological players + +Monomeric Ste5, Ste11, Ste7, Fus3, and their phosphorylated states. + +## Mechanism in plain English + +Ste5 independently binds Ste11, Ste7, and Fus3. Bound Ste11 becomes phosphorylated and can modify neighboring Ste7; fully active Ste7 then phosphorylates scaffold-associated Fus3. Dephosphorylation returns each kinase to its inactive form. Without Ste5 dimerization, every productive complex is organized around one scaffold molecule. + +## Key modeled events + +- Ste11, Ste7, and Fus3 reversibly load onto one Ste5 scaffold. +- Scaffold-bound Ste11 becomes active and phosphorylates Ste7. +- Activated Ste7 phosphorylates Fus3 on the same scaffold. +- Dephosphorylation resets Ste11, Ste7, and Fus3. + +## What the model measures + +Readouts distinguish total phosphorylated Fus3, free phosphorylated Fus3, scaffold-bound phosphorylated Fus3, and Fus3 in Ste5/Ste7-containing assemblies. + +## Expected behavior in plots + +Scaffold-associated phosphorylated Fus3 should rise as fully loaded Ste5 complexes form, with free phosphorylated Fus3 increasing as output leaves the platform. Compared with the dimeric version, no signal should be assigned to cross-scaffold organization. + +## Caveats + +The cascade is deliberately minimal and uses generic equal-rate phosphorylation and binding. It omits the upstream pheromone pathway and downstream transcriptional response. diff --git a/Published/mapkmonomers/mapkmonomers_aigenerated_detailed.md b/Published/mapkmonomers/mapkmonomers_aigenerated_detailed.md new file mode 100644 index 00000000..8999e487 --- /dev/null +++ b/Published/mapkmonomers/mapkmonomers_aigenerated_detailed.md @@ -0,0 +1,74 @@ +# Coder Model Explanation: MAPK Monomers + +## 1. Model identity and scope + +- **Metadata id/title:** `mapk-monomers` / MAPK Monomers. +- **Paths:** `Published/mapkmonomers/mapk-monomers.bngl` and `Published/mapkmonomers/metadata.yaml`. +- **Purpose:** minimal Ste5-scaffolded Ste11→Ste7→Fus3 mitogen-activated protein kinase (MAPK) cascade without Ste5 dimerization. + +## 2. BNGL block inventory + +This file uses legacy top-level `begin molecules` and `begin species` blocks rather than a `begin model` wrapper. + +| Construct | Count | Contribution | +| --- | ---: | --- | +| Parameters | 6 | Four initial totals and shared `kp`/`km`. | +| Molecule declarations | 4 | Ste5, Ste11, Ste7, Fus3. | +| Initial species | 4 | Free scaffold and inactive free kinases. | +| Reaction rules | 9 | Three docking, three phosphorylation, three dephosphorylation rules. | +| Observables | 5 | Total/free/scaffold-context phosphorylated Fus3. | +| Inline actions | 3 | Network, SBML export, ODE simulation. | +| Compartments / anchors / functions | 0 / 0 / 0 | Nonspatial, direct mass action. | + +## 3. Parameters, functions, and rate laws + +`S5_0`, `S11_0`, `S7_0`, and `F3_0` are all 100 and initialize Ste5, Ste11, Ste7, and Fus3. `kp=1` serves as every association rate and every phosphorylation rate. `km=1` serves as every dissociation and dephosphorylation rate. No function modifies these rates, so binding and catalytic processes share values despite representing different dimensions in conventional mass action. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Ste5` | 3 | `s1`, `s2`, `s3` | None | None | Docks Ste11 at `s1`, Ste7 at `s2`, Fus3 at `s3`. | Monomeric scaffold; no dimer site. | +| `Ste11` | 2 | `s1`, `Y` | `Y~U~P` | None | `s1` docks Ste5; `Y` is inactive/unphosphorylated (`U`) or phosphorylated (`P`). | Upstream tier. | +| `Ste7` | 2 | `s2`, `Y` | `Y~U~P` | None | `s2` docks Ste5; `Y` receives phosphorylation from Ste11. | Middle tier. | +| `Fus3` | 2 | `s3`, `Y` | `Y~U~P` | None | `s3` docks Ste5; `Y` receives phosphorylation from Ste7. | Output tier. | + +## 5. Compartments, anchors, initial species, and setup + +There are no spatial blocks. Free `Ste5(s1,s2,s3)`, inactive `Ste11(Y~U)`, inactive `Ste7(Y~U)`, and inactive `Fus3(Y~U)` each start at 100. Every docking site is initially free. No phosphorylated kinase or preassembled scaffold complex is initialized. + +## 6. Complete reaction-rule inventory + +### Rule-family orientation + +Rules 1–3 load one kinase per dedicated Ste5 site. Rules 4–6 implement ordered phosphorylation and require the relevant kinase pair to share one Ste5. Rules 7–9 remove phosphorylation regardless of scaffold occupancy because their patterns constrain only `Y~P`. + +| # | Direction and participants | Exact site/state/bond edit | Rate | Technical meaning | +| ---: | --- | --- | --- | --- | +| 1 | Reversible; Ste5, Ste11 | Forms/releases `Ste5.s1–Ste11.s1`. | `kp`, `km` | Ste11 docking. | +| 2 | Reversible; Ste5, Ste7 | Forms/releases `Ste5.s2–Ste7.s2`. | `kp`, `km` | Ste7 docking. | +| 3 | Reversible; Ste5, Fus3 | Forms/releases `Ste5.s3–Fus3.s3`. | `kp`, `km` | Fus3 docking. | +| 4 | One-way; Ste5-bound Ste11 | Preserves `Ste5.s1–Ste11.s1`; changes `Ste11.Y U→P`. | `kp` | Scaffold occupancy enables Ste11 activation without an explicit upstream catalyst. | +| 5 | One-way; Ste5, Ste11, Ste7 | Preserves `Ste5.s1–Ste11.s1` and `Ste5.s2–Ste7.s2`; requires `Ste11.Y~P`; changes `Ste7.Y U→P`. | `kp` | Active Ste11 phosphorylates colocalized Ste7. | +| 6 | One-way; Ste5, Ste7, Fus3 | Preserves `Ste5.s2–Ste7.s2` and `Ste5.s3–Fus3.s3`; requires `Ste7.Y~P`; changes `Fus3.Y U→P`. | `kp` | Active Ste7 phosphorylates colocalized Fus3. | +| 7 | One-way; Ste11 | Changes `Ste11.Y P→U`; binding state of `s1` is unconstrained. | `km` | Global Ste11 dephosphorylation. | +| 8 | One-way; Ste7 | Changes `Ste7.Y P→U`; `s2` is unconstrained. | `km` | Global Ste7 dephosphorylation. | +| 9 | One-way; Fus3 | Changes `Fus3.Y P→U`; `s3` is unconstrained. | `km` | Global Fus3 dephosphorylation. | + +## 7. Observables and technical readouts + +| Name | Type | Target | Interpretation | +| --- | --- | --- | --- | +| `Fus3_P_total` | Molecules | Any `Fus3(Y~P)` | Total phosphorylated Fus3. | +| `Fus3_P_cytosol` | Molecules | `Fus3(s3,Y~P)` | Phosphorylated Fus3 with free scaffold site; “cytosol” is a naming convention, not a compartment. | +| `Fus3_P_aggregate` | Molecules | `Fus3(s3!3,Y~P)` | Phosphorylated Fus3 bound through `s3`. | +| `Fus3_P_aggregate_Ste5` | Molecules | Ste5–Fus3 bond | Scaffold-bound phosphorylated Fus3. | +| `Fus3_P_aggregate_Ste7` | Molecules | Ste5-bound Ste7 connected to phosphorylated Fus3 through a bond between Ste7 `Y` and Fus3 `s3` | The pattern's bond topology does not match rule 6, which never forms a Ste7–Fus3 bond. This readout is likely zero or malformed relative to intent. | + +## 8. Actions and simulation workflow + +`generate_network()` constructs the finite network. `writeSBML()` exports Systems Biology Markup Language (SBML). `simulate_ode({t_end=>50,n_steps=>50})` runs deterministic integration to time 50 with 50 intervals. These are inline commands rather than a `begin actions` block. + +## 9. Technical caveats and ambiguities + +The legacy `molecules`/`species` syntax and absent model wrapper may affect modern parsers; metadata already marks BNG2 compatibility false. `kp` and `km` are reused across association, catalysis, dissociation, and dephosphorylation. “Cytosol” is not spatially encoded. Most importantly, `Fus3_P_aggregate_Ste7` requests a Ste7–Fus3 bond not created by any rule, so its intended topology should be curated. diff --git a/Published/mapkmonomers/metadata.yaml b/Published/mapkmonomers/metadata.yaml index 5cc66e29..b6db6d55 100644 --- a/Published/mapkmonomers/metadata.yaml +++ b/Published/mapkmonomers/metadata.yaml @@ -4,6 +4,7 @@ description: "MAPK cascade" tags: ["published", "mapk", "monomers", "ste5", "ste11", "ste7", "fus3"] category: "signaling" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/notch/metadata.yaml b/Published/notch/metadata.yaml index df047f78..d186fa2a 100644 --- a/Published/notch/metadata.yaml +++ b/Published/notch/metadata.yaml @@ -4,6 +4,7 @@ description: "Notch signaling" tags: ["published", "notch", "icn", "ofut1", "fringe", "furin", "dsl", "csl", "maml"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/notch/notch_aigenerated.md b/Published/notch/notch_aigenerated.md new file mode 100644 index 00000000..ed96390b --- /dev/null +++ b/Published/notch/notch_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Notch + +## One-sentence summary + +Notch maturation and DSL-triggered cleavage release ICN to assemble a nuclear ICN–CSL–MAML complex. + +## What the model shows + +This sketch follows the core spatial sequence of Notch signaling from receptor processing in the ER and Golgi to ligand engagement at the membrane and transcription-complex assembly in the nucleus. It emphasizes movement and complex formation rather than detailed enzymology. + +## Biological story + +Notch and its intracellular domain mature together through the secretory pathway with OFUT1, Fringe, and Furin represented as processing factors. Membrane DSL engagement triggers cleavage, freeing ICN to enter the nucleus and recruit CSL and MAML. + +## Main biological players + +Notch receptor, intracellular Notch domain (ICN), OFUT1, Fringe, Furin, DSL ligand, CSL, and MAML. + +## Mechanism in plain English + +OFUT1 accompanies receptor movement from ER to Golgi, and Fringe/Furin accompany maturation to the membrane. DSL binds mature Notch. Subsequent cleavage separates ICN from the membrane receptor and assigns ICN to the nucleus. Nuclear ICN binds CSL, then recruits MAML to form the three-component signaling complex associated with transcriptional activation. + +## Key modeled events + +- Notch and ICN mature from ER through Golgi to the membrane. +- DSL binds membrane Notch. +- Ligand-dependent cleavage releases ICN for nuclear entry. +- Nuclear ICN binds CSL and recruits MAML into a ternary complex. + +## What the model measures + +Two readouts report the Notch–ICN precursor complex and the nuclear ICN–CSL–MAML complex. They mark receptor maturation versus the final nuclear signaling assembly. + +## Expected behavior in plots + +The precursor complex should be consumed as processing and cleavage proceed, whereas the nuclear ternary complex should appear later after membrane ligand engagement and ICN release. Its delayed accumulation is the clearest signature of completed signaling. + +## Caveats + +Processing, cleavage, and transport are lumped into coarse steps, and spatial effects are not calculated. The model does not include target-gene transcription or pathway feedback. diff --git a/Published/notch/notch_aigenerated_detailed.md b/Published/notch/notch_aigenerated_detailed.md new file mode 100644 index 00000000..d57c0587 --- /dev/null +++ b/Published/notch/notch_aigenerated_detailed.md @@ -0,0 +1,76 @@ +# Coder Model Explanation: Notch + +## 1. Model identity and scope + +- **Metadata id/title:** `notch` / Notch. +- **Paths:** `Published/notch/notch.bngl` and `Published/notch/metadata.yaml`. +- **Purpose:** sketch of Notch maturation, ligand-triggered intracellular-domain release, nuclear import, and ICN–CSL–MAML complex assembly, based on Figure 2 of Grabner et al. + +ICN denotes intracellular Notch, DSL denotes the Delta/Serrate/LAG-2 ligand family, CSL denotes the DNA-binding transcription factor family, and MAML denotes Mastermind-like coactivator. + +## 2. BNGL block inventory + +The source uses legacy `begin molecules` and `begin species` syntax and has no outer model wrapper. + +| Construct | Count | Contribution | +| --- | ---: | --- | +| Parameters | 10 | Eight initial totals and shared `kp1`/`km1`. | +| Molecule declarations | 8 | Notch, ICN, OFUT1, Fringe, Furin, DSL, CSL, MAML. | +| Initial species | 8 | ER-localized receptor/ICN plus free processing and nuclear factors. | +| Reaction rules | 6 | Two maturation steps, ligand binding, cleavage/import, and two nuclear binding steps. | +| Observables | 2 | Precursor Notch–ICN and nuclear ternary complex. | +| Inline actions | 1 | Network generation only. | +| Compartments / anchors / functions | 0 / 0 / 0 | Localization is encoded as internal states, not spatial grammar. | + +## 3. Parameters, functions, and rate laws + +`ICN_tot`, `Notch_tot`, `Fringe_tot`, `Furin_tot`, `OFUT1_tot`, `DSL_tot`, `CSL_tot`, and `MAML_tot` are each 100. `kp1=0.1` drives all one-way maturation/cleavage events and every forward association. `km1=0.1` drives the three reverse binding directions (DSL, CSL, and MAML binding). No functions or time-dependent rate laws occur. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Notch` | 3 | `location`, `DSLbind`, `Ibind` | `location~ER~G~M` | None | `DSLbind` captures DSL; `Ibind` binds ICN; location state encodes ER/Golgi/membrane. | Localization is not a true compartment. | +| `ICN` | 4 | `location`, `Nbind`, `CSLbind`, `MAMLbind` | `location~ER~G~M~N` | None | `Nbind` binds Notch; `CSLbind` binds CSL; `MAMLbind` binds MAML; `N` means nucleus. | Separate molecule from Notch. | +| `OFUT1` | 0 | None | None | None | Catalyst in rule 1. | Carried through unchanged. | +| `Fringe` | 0 | None | None | None | Catalyst in rule 2. | No explicit glycan state. | +| `Furin` | 0 | None | None | None | Catalyst in rule 2. | No explicit cleavage state. | +| `DSL` | 1 | `Nbind` | None | None | Binds `Notch.DSLbind`. | Ligand family abstraction. | +| `CSL` | 2 | `Ibind`, `MAMLbind` | None | None | `Ibind` binds `ICN.CSLbind`; `MAMLbind` binds `MAML.Cbind`. | Nuclear location is only implied by ICN state. | +| `MAML` | 2 | `Cbind`, `Ibind` | None | None | `Cbind` binds `CSL.MAMLbind`; `Ibind` binds `ICN.MAMLbind`. | Makes two bonds in the ternary complex. | + +## 5. Compartments, anchors, initial species, and setup + +No compartment or anchor block exists. Instead, `location` states stand for endoplasmic reticulum (`ER`), Golgi (`G`), membrane (`M`), and nucleus (`N`). Notch and ICN each start as separate unbound pools at `location~ER`, both abundance 100. OFUT1, Fringe, Furin, DSL, CSL, and MAML each start free at 100. Thus the initial Notch and ICN are not pre-bound even though rule 1 creates their first bond. + +## 6. Complete reaction-rule inventory + +### Rule-family orientation + +The first two rules collapse processing and movement into state rewrites. Rule 3 is ordinary reversible ligand binding. Rule 4 removes the Notch–ICN bond while changing ICN location. Rules 5 and 6 assemble the nuclear complex; the source labels both as rule “5,” so table numbering below follows file order. + +| # | Source label | Direction and participants | Exact site/state/bond edit | Rate(s) | Technical meaning | +| ---: | --- | --- | --- | --- | --- | +| 1 | `1 Fucosylation...` | One-way; Notch, ICN, catalytic OFUT1 | Changes `Notch.location ER→G` and `ICN.location ER→G`; forms `Notch.Ibind–ICN.Nbind`; OFUT1 appears unchanged on both sides. | `kp1` | Lumps fucosylation, ER-to-Golgi movement, and precursor heterodimerization. | +| 2 | `2 Glycosylation...` | One-way; bound Notch–ICN plus catalytic Furin and Fringe | Changes both locations `G→M`; retains the existing Notch–ICN bond; Furin and Fringe are unchanged. | `kp1` | Lumps glycosylation, S1 cleavage, membrane movement, and mature heterodimer formation. | +| 3 | `3 DSL binding` | Reversible; Notch and DSL | Forms/releases `Notch.DSLbind–DSL.Nbind`; requires `Notch.location~M`. | `kp1`, `km1` | Reversible ligand occupancy of membrane-state Notch. | +| 4 | `4 S2, S3 cleavage...` | One-way; ligand-bound Notch–ICN complex | Releases `Notch.Ibind–ICN.Nbind`; preserves the unspecified existing DSL bond; changes `ICN.location M→N`; Notch remains `M`. | `kp1` | Lumps proteolysis, ICN dissociation, and nuclear entry. | +| 5 | first source `5` | Reversible; nuclear ICN and CSL | Forms/releases `ICN.CSLbind–CSL.Ibind`; requires `ICN.location~N`; leaves `ICN.MAMLbind` and `CSL.MAMLbind` free. | `kp1`, `km1` | Binary nuclear ICN–CSL assembly. | +| 6 | second source `5` | Reversible; ICN–CSL complex and MAML | Simultaneously forms `ICN.MAMLbind–MAML.Ibind` and `CSL.MAMLbind–MAML.Cbind`; preserves the ICN–CSL bond. Reverse direction releases both MAML bonds together. | `kp1`, `km1` | Cooperative-looking ternary-complex completion encoded as one two-bond event. | + +## 7. Observables and technical readouts + +The legacy declarations omit an explicit `Molecules` or `Species` keyword. + +| Name | Declared target | Technical interpretation | +| --- | --- | --- | +| `Notch_ICN_Complex` | Connected `Notch.ICN` pattern without site constraints | Counts matches containing a Notch–ICN bond, chiefly the Golgi/membrane precursor generated by rules 1–2. | +| `Nucleus_complex` | Connected `ICN.CSL.MAML` pattern | Counts ternary ICN–CSL–MAML assemblies; the location is not written in the readout but rule 6 derives from nuclear ICN. | + +## 8. Actions and simulation workflow + +`generate_network({overwrite=>1})` is the sole inline action. It regenerates the network but does not simulate it, export SBML, or specify output times. A caller must add an ODE/SSA action or use the generated network externally. + +## 9. Technical caveats and ambiguities + +The source comments explicitly describe the signaling steps as sketchy. Localization is encoded as molecule state, so there are no volumes, transport rates tied to compartment geometry, or anchor constraints. Rules 1–2 treat OFUT1, Furin, and Fringe as unchanged catalysts while lumping several biological events. Rule 6 forms or removes two MAML bonds in one elementary event. Duplicate source label `5`, untyped observables, legacy syntax, and the metadata's `bng2_compatible: false` all merit parser-specific testing. diff --git a/Published/notch/notch_metadata.yaml b/Published/notch/notch_metadata.yaml new file mode 100644 index 00000000..9e2025bb --- /dev/null +++ b/Published/notch/notch_metadata.yaml @@ -0,0 +1,24 @@ +id: "notch" +name: "Notch" +description: "Notch signaling" +tags: ["published", "notch", "icn", "ofut1", "fringe", "furin", "dsl", "csl", "maml"] +category: "regulation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/notch.bngl" +playground: + visible: false + gallery_category: "regulation" + featured: false + difficulty: "advanced" diff --git a/Published/tlbr/metadata.yaml b/Published/tlbr/metadata.yaml index cd87cbf9..a98bc604 100644 --- a/Published/tlbr/metadata.yaml +++ b/Published/tlbr/metadata.yaml @@ -4,6 +4,7 @@ description: "Ligand binding" tags: ["published", "immunology", "tlbr", "l", "r", "simulate_rm"] category: "immunology" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/tlbr/tlbr_metadata.yaml b/Published/tlbr/tlbr_metadata.yaml new file mode 100644 index 00000000..c01b87ce --- /dev/null +++ b/Published/tlbr/tlbr_metadata.yaml @@ -0,0 +1,24 @@ +id: "tlbr" +name: "TLBR Tutorial" +description: "Ligand binding" +tags: ["published", "immunology", "tlbr", "l", "r", "simulate_rm"] +category: "immunology" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/immune-signaling/tlbr.bngl" +playground: + visible: false + gallery_categories: ["immunology"] + featured: false + difficulty: "advanced" diff --git a/Published/vilar2002/metadata.yaml b/Published/vilar2002/metadata.yaml index ac90aab5..4907f843 100644 --- a/Published/vilar2002/metadata.yaml +++ b/Published/vilar2002/metadata.yaml @@ -4,6 +4,7 @@ description: "Genetic oscillator" tags: ["published", "vilar", "2002", "dna", "a", "r"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/vilar2002/vilar_2002_metadata.yaml b/Published/vilar2002/vilar_2002_metadata.yaml new file mode 100644 index 00000000..0ea68111 --- /dev/null +++ b/Published/vilar2002/vilar_2002_metadata.yaml @@ -0,0 +1,24 @@ +id: "vilar_2002" +name: "Vilar 2002" +description: "Genetic oscillator" +tags: ["published", "vilar", "2002", "dna", "a", "r"] +category: "regulation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/vilar_2002.bngl" +playground: + visible: false + gallery_categories: ["cell-cycle"] + featured: false + difficulty: "advanced" diff --git a/Published/vilar2002b/metadata.yaml b/Published/vilar2002b/metadata.yaml index 5e2bfb11..24c8a0ac 100644 --- a/Published/vilar2002b/metadata.yaml +++ b/Published/vilar2002b/metadata.yaml @@ -4,6 +4,7 @@ description: "Gene oscillator" tags: ["published", "vilar", "2002b", "dna", "a", "r"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/vilar2002b/vilar_2002b_metadata.yaml b/Published/vilar2002b/vilar_2002b_metadata.yaml new file mode 100644 index 00000000..616e1f4d --- /dev/null +++ b/Published/vilar2002b/vilar_2002b_metadata.yaml @@ -0,0 +1,24 @@ +id: "vilar_2002b" +name: "Vilar 2002b" +description: "Gene oscillator" +tags: ["published", "vilar", "2002b", "dna", "a", "r"] +category: "regulation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/vilar_2002b.bngl" +playground: + visible: true + gallery_categories: ["cell-cycle"] + featured: false + difficulty: "intermediate" diff --git a/Published/vilar2002c/metadata.yaml b/Published/vilar2002c/metadata.yaml index 5bc378b9..d19fd4d6 100644 --- a/Published/vilar2002c/metadata.yaml +++ b/Published/vilar2002c/metadata.yaml @@ -4,6 +4,7 @@ description: "Gene oscillator" tags: ["published", "vilar", "2002c", "dna", "a", "r"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/vilar2002c/vilar_2002c_metadata.yaml b/Published/vilar2002c/vilar_2002c_metadata.yaml new file mode 100644 index 00000000..72ef580c --- /dev/null +++ b/Published/vilar2002c/vilar_2002c_metadata.yaml @@ -0,0 +1,24 @@ +id: "vilar_2002c" +name: "Vilar 2002c" +description: "Gene oscillator" +tags: ["published", "vilar", "2002c", "dna", "a", "r"] +category: "regulation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/vilar_2002c.bngl" +playground: + visible: true + gallery_category: "regulation" + featured: false + difficulty: "intermediate" diff --git a/Published/wnt/metadata.yaml b/Published/wnt/metadata.yaml index f850063f..200bf356 100644 --- a/Published/wnt/metadata.yaml +++ b/Published/wnt/metadata.yaml @@ -4,6 +4,7 @@ description: "Wnt signaling" tags: ["published", "wnt", "dsh", "axc", "frz", "lrp5", "bcat"] category: "regulation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Published/wnt/wnt_aigenerated.md b/Published/wnt/wnt_aigenerated.md new file mode 100644 index 00000000..80a0c3ea --- /dev/null +++ b/Published/wnt/wnt_aigenerated.md @@ -0,0 +1,40 @@ +# Model Explanation: Wnt Signaling + +## One-sentence summary + +Wnt assembles a Frizzled–Dishevelled–Axin–LRP5 complex that releases β-catenin from Axin. + +## What the model shows + +This compact Wnt model focuses on receptor-complex assembly and liberation of β-catenin. It follows ordered recruitment of Dishevelled and an Axin-containing complex to Wnt-bound Frizzled, engagement of LRP5, and release of β-catenin from the assembled platform. + +## Biological story + +Wnt first binds Frizzled. Frizzled recruits Dishevelled, which captures Axin; that assembly then engages LRP5. β-catenin initially associated with Axin is released once the full receptor complex forms, increasing the free β-catenin pool. + +## Main biological players + +Wnt, Frizzled, Dishevelled (DSH), Axin complex (AxC), LRP5, and β-catenin. + +## Mechanism in plain English + +Ligand-bound Frizzled recruits DSH, and DSH recruits AxC. Frizzled and AxC then make coordinated contacts with LRP5 to create a higher-order receptor complex. When β-catenin is carried into that complex through AxC, it is released, leaving the receptor assembly intact and increasing free β-catenin. + +## Key modeled events + +- Wnt binds Frizzled reversibly. +- Activated Frizzled recruits DSH, which then recruits AxC. +- The Frizzled–DSH–AxC assembly engages LRP5. +- Completion of the receptor complex releases β-catenin from AxC. + +## What the model measures + +Readouts track free β-catenin and three successive complexes: DSH–AxC, Wnt–Frizzled–DSH–AxC, and the full LRP5-containing assembly with β-catenin. Total pools of the major components are also followed. + +## Expected behavior in plots + +The DSH–AxC complex should appear before the Frizzled-containing intermediate, with the full LRP5 complex forming later. Free β-catenin should rise only as the complete assembly turns over its bound β-catenin, giving a delayed output relative to receptor-complex formation. + +## Caveats + +The model represents β-catenin release but not its synthesis, destruction-complex phosphorylation, nuclear entry, or transcription. Several Wnt pathway components are compressed into AxC. diff --git a/Published/wnt/wnt_metadata.yaml b/Published/wnt/wnt_metadata.yaml new file mode 100644 index 00000000..cf287d30 --- /dev/null +++ b/Published/wnt/wnt_metadata.yaml @@ -0,0 +1,24 @@ +id: "wnt" +name: "Wnt Signaling" +description: "Wnt signaling" +tags: ["published", "wnt", "dsh", "axc", "frz", "lrp5", "bcat"] +category: "regulation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "published" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/cell-regulation/wnt.bngl" +playground: + visible: false + gallery_category: "regulation" + featured: false + difficulty: "advanced" diff --git a/Tutorials/CaOscillateFunc/CaOscillate_Func_metadata.yaml b/Tutorials/CaOscillateFunc/CaOscillate_Func_metadata.yaml new file mode 100644 index 00000000..089bffe3 --- /dev/null +++ b/Tutorials/CaOscillateFunc/CaOscillate_Func_metadata.yaml @@ -0,0 +1,24 @@ +id: "CaOscillate_Func" +name: "CaOscillate_Func" +description: "Calcium oscillations (func)" +tags: ["validation", "caoscillate", "func", "null", "ga", "plc", "ca"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/CaOscillate_Func.bngl" +playground: + visible: true + gallery_categories: [] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/CaOscillateFunc/metadata.yaml b/Tutorials/CaOscillateFunc/metadata.yaml index a35afa2e..6b568303 100644 --- a/Tutorials/CaOscillateFunc/metadata.yaml +++ b/Tutorials/CaOscillateFunc/metadata.yaml @@ -4,6 +4,7 @@ description: "Calcium oscillations (func)" tags: ["validation", "caoscillate", "func", "null", "ga", "plc", "ca"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Tutorials/CaOscillateSat/CaOscillate_Sat_metadata.yaml b/Tutorials/CaOscillateSat/CaOscillate_Sat_metadata.yaml new file mode 100644 index 00000000..c9cfcfad --- /dev/null +++ b/Tutorials/CaOscillateSat/CaOscillate_Sat_metadata.yaml @@ -0,0 +1,24 @@ +id: "CaOscillate_Sat" +name: "CaOscillate_Sat" +description: "Calcium oscillations (sat)" +tags: ["validation", "caoscillate", "sat", "null", "ga", "plc", "ca"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/CaOscillate_Sat.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/CaOscillateSat/metadata.yaml b/Tutorials/CaOscillateSat/metadata.yaml index fee41162..8e6a509e 100644 --- a/Tutorials/CaOscillateSat/metadata.yaml +++ b/Tutorials/CaOscillateSat/metadata.yaml @@ -4,6 +4,7 @@ description: "Calcium oscillations (sat)" tags: ["validation", "caoscillate", "sat", "null", "ga", "plc", "ca"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Tutorials/General/chemistry/chemistry_metadata.yaml b/Tutorials/General/chemistry/chemistry_metadata.yaml new file mode 100644 index 00000000..9d7eebdb --- /dev/null +++ b/Tutorials/General/chemistry/chemistry_metadata.yaml @@ -0,0 +1,54 @@ +id: "chemistry" +name: "chemistry" +description: "Basic chemical reactions" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["published", "tutorials", "chemistry", "a", "b", "c", "d", "e"] + +date: + last_tested: 2026-06-30 + +biol_categories: ["tutorial"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: false + vcell_compatible: false + vcell_errors: " encountered exclude_reactants" + simulation_methods: ["ode", "ssa",] + nfsim_compatible: false + molclustpy_compatible: false + +Features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: true + +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/tutorials/chemistry.bngl" + +playground: + visible: false + gallery_categories: ["tutorials"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Tutorials/General/chemistry/metadata.yaml b/Tutorials/General/chemistry/metadata.yaml index f3cec572..b6ad5ff2 100644 --- a/Tutorials/General/chemistry/metadata.yaml +++ b/Tutorials/General/chemistry/metadata.yaml @@ -4,6 +4,7 @@ description: "Basic chemical reactions" tags: ["published", "tutorials", "chemistry", "a", "b", "c", "d", "e"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/General/polymer/metadata.yaml b/Tutorials/General/polymer/metadata.yaml index 60e9885e..58877821 100644 --- a/Tutorials/General/polymer/metadata.yaml +++ b/Tutorials/General/polymer/metadata.yaml @@ -4,6 +4,7 @@ description: "Polymerization model" tags: ["published", "tutorials", "nfsim", "polymer", "a", "b", "c", "simulate_nf"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: true diff --git a/Tutorials/General/polymer/polymer_metadata.yaml b/Tutorials/General/polymer/polymer_metadata.yaml new file mode 100644 index 00000000..d2aa27f7 --- /dev/null +++ b/Tutorials/General/polymer/polymer_metadata.yaml @@ -0,0 +1,55 @@ +id: "polymer" +name: "polymer" +description: "Polymerization model" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["published", "tutorials", "nfsim", "polymer", "a", "b", "c", "simulate_nf"] + +date: + last_tested: 2026-06-30 + +biol_categories: ["tutorial"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + vcell_compatible: true + vcell_errors: + simulation_methods: ["ode", "ssa","nf"] + nfsim_compatible: true + molclustpy_compatible: false + comments: "bng2: true in original metadata.yaml, but when ran in bionetgen shows this error: WARNING: Species with more than 20 molecules will be labeled with the Quasi method.readNFspecies::Reading from file polymer.species cannot access local variable 'stdout_str' where it is not associated with a value" + +features: + uses_generate_network: false + default_sim_command: "nf" + uses_energy: false + uses_functions: true + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/tutorials/polymer.bngl" + +playground: + visible: false + gallery_categories: ["tutorials"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Tutorials/General/polymerdraft/metadata.yaml b/Tutorials/General/polymerdraft/metadata.yaml index ab4a1780..d9c7c59d 100644 --- a/Tutorials/General/polymerdraft/metadata.yaml +++ b/Tutorials/General/polymerdraft/metadata.yaml @@ -4,6 +4,7 @@ description: "Polymerization (draft)" tags: ["published", "tutorials", "nfsim", "polymer", "draft", "a", "b", "c", "simulate_nf"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: true diff --git a/Tutorials/General/polymerdraft/polymer_draft_metadata.yaml b/Tutorials/General/polymerdraft/polymer_draft_metadata.yaml new file mode 100644 index 00000000..5179ea65 --- /dev/null +++ b/Tutorials/General/polymerdraft/polymer_draft_metadata.yaml @@ -0,0 +1,24 @@ +id: "polymer_draft" +name: "polymer draft" +description: "Polymerization (draft)" +tags: ["published", "tutorials", "nfsim", "polymer", "draft", "a", "b", "c", "simulate_nf"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/tutorials/polymer_draft.bngl" +playground: + visible: false + gallery_categories: ["tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/General/quasiequilibrium/metadata.yaml b/Tutorials/General/quasiequilibrium/metadata.yaml index ce39e334..bed23a5e 100644 --- a/Tutorials/General/quasiequilibrium/metadata.yaml +++ b/Tutorials/General/quasiequilibrium/metadata.yaml @@ -4,6 +4,7 @@ description: "Quasi-equilibrium approximation" tags: ["published", "toy models", "quasi", "equilibrium", "a", "b", "c"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/General/quasiequilibrium/quasi_equilibrium_metadata.yaml b/Tutorials/General/quasiequilibrium/quasi_equilibrium_metadata.yaml new file mode 100644 index 00000000..7d7e725b --- /dev/null +++ b/Tutorials/General/quasiequilibrium/quasi_equilibrium_metadata.yaml @@ -0,0 +1,24 @@ +id: "quasi_equilibrium" +name: "quasi equilibrium" +description: "Quasi-equilibrium approximation" +tags: ["published", "toy models", "quasi", "equilibrium", "a", "b", "c"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/toy-models/quasi_equilibrium.bngl" +playground: + visible: false + gallery_categories: ["tutorials","native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/General/simple/metadata.yaml b/Tutorials/General/simple/metadata.yaml index 1b28cf6a..2ad0f954 100644 --- a/Tutorials/General/simple/metadata.yaml +++ b/Tutorials/General/simple/metadata.yaml @@ -4,6 +4,7 @@ description: "Simple binding model" tags: ["published", "tutorials", "simple", "s", "t", "dnat", "trash"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/General/simple/simple_metadata.yaml b/Tutorials/General/simple/simple_metadata.yaml new file mode 100644 index 00000000..3fc0dd8e --- /dev/null +++ b/Tutorials/General/simple/simple_metadata.yaml @@ -0,0 +1,24 @@ +id: "simple" +name: "simple" +description: "Simple binding model" +tags: ["published", "tutorials", "simple", "s", "t", "dnat", "trash"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/tutorials/simple.bngl" +playground: + visible: false + gallery_categories: ["tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/General/toy1/metadata.yaml b/Tutorials/General/toy1/metadata.yaml index 78534b1d..50c9be52 100644 --- a/Tutorials/General/toy1/metadata.yaml +++ b/Tutorials/General/toy1/metadata.yaml @@ -4,6 +4,7 @@ description: "Basic signaling toy" tags: ["published", "tutorials", "toy1", "l", "r", "a", "generate_network", "writesbml", "simulate_ode"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/General/toy1/toy1_metadata.yaml b/Tutorials/General/toy1/toy1_metadata.yaml new file mode 100644 index 00000000..e5637202 --- /dev/null +++ b/Tutorials/General/toy1/toy1_metadata.yaml @@ -0,0 +1,54 @@ +id: "toy1" +name: "toy1" +description: "Basic signaling toy" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["published", "tutorials", "toy1", "l", "r", "a", "generate_network", "writesbml", "simulate_ode"] + +date: + last_tested: 2026-06-30 + +biol_categories: ["tutorial"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + bngp_compatible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true #False in original metadata.yaml, have to change "molecules" to "molecule types" in toy1.bngl to make it compatible with bng2 + vcell_compatible: false + vcell_errors: " Encountered ! - at line 76, column 21 " + simulation_methods: ["ode", "ssa",] + nfsim_compatible: false + molclustpy_compatible: false + +Features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/tutorials/toy1.bngl" + +playground: + visible: false + gallery_categories: ["tutorials"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Tutorials/General/toy2/metadata.yaml b/Tutorials/General/toy2/metadata.yaml index 54c70820..e3b8934e 100644 --- a/Tutorials/General/toy2/metadata.yaml +++ b/Tutorials/General/toy2/metadata.yaml @@ -4,6 +4,7 @@ description: "Enzymatic reaction toy" tags: ["published", "tutorials", "toy2", "l", "r", "a", "k"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/General/toy2/toy2_metadata.yaml b/Tutorials/General/toy2/toy2_metadata.yaml new file mode 100644 index 00000000..7d8dccf2 --- /dev/null +++ b/Tutorials/General/toy2/toy2_metadata.yaml @@ -0,0 +1,54 @@ +id: "toy2" +name: "toy2" +description: "Enzymatic reaction toy" + +contributors: + - name: "Achyudhan" + - name: "Nabil Mardhy" + +tags: ["published", "tutorials", "toy2", "l", "r", "a", "k"] + +date: + last_tested: 2026-06-30 + +biol_categories: ["tutorial"] + +comp_categories: ["other"] + +compatibility: + database_visible: true + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: false + bngp_compatible: true + vcell_compatible: false + vcell_errors: "Encountered kmL at line 65" + simulation_methods: ["ode", "ssa",] + nfsim_compatible: false # + molclustpy_compatible: false + +features: + uses_generate_network: true + default_sim_command: "ode" + uses_energy: false + uses_functions: false + uses_totalrate: false + uses_moveconnected: false + uses_trash_molecules: false + uses_anchors: false + uses_multiple_identical_sites: false + uses_deletes_molecules: false + uses_exclude_include_reactants: false + +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/tutorials/toy2.bngl" + +playground: + visible: false + gallery_categories: ["tutorials"] + featured: false + difficulty: "advanced" + \ No newline at end of file diff --git a/Tutorials/Haugh2b/Haugh2b_metadata.yaml b/Tutorials/Haugh2b/Haugh2b_metadata.yaml new file mode 100644 index 00000000..3843f638 --- /dev/null +++ b/Tutorials/Haugh2b/Haugh2b_metadata.yaml @@ -0,0 +1,24 @@ +id: "Haugh2b" +name: "Haugh2b" +description: "R(KD,Y1~U,Y2~U) 1.00" +tags: ["validation", "haugh2b", "r", "s1", "s2", "exclude_reactants", "include_reactants"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/Haugh2b.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/Haugh2b/metadata.yaml b/Tutorials/Haugh2b/metadata.yaml index 904e50e1..b44e4663 100644 --- a/Tutorials/Haugh2b/metadata.yaml +++ b/Tutorials/Haugh2b/metadata.yaml @@ -4,6 +4,7 @@ description: "R(KD,Y1~U,Y2~U) 1.00" tags: ["validation", "haugh2b", "r", "s1", "s2", "exclude_reactants", "include_reactants"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/Kiefhaberemodel/Kiefhaber_emodel_metadata.yaml b/Tutorials/Kiefhaberemodel/Kiefhaber_emodel_metadata.yaml new file mode 100644 index 00000000..f9219d25 --- /dev/null +++ b/Tutorials/Kiefhaberemodel/Kiefhaber_emodel_metadata.yaml @@ -0,0 +1,24 @@ +id: "Kiefhaber_emodel" +name: "Kiefhaber_emodel" +description: "Allow molar units to be used for bimolecular rate constants" +tags: ["validation", "kiefhaber", "emodel", "setoption", "l", "p", "s", "a"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/Kiefhaber_emodel.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Tutorials/Kiefhaberemodel/metadata.yaml b/Tutorials/Kiefhaberemodel/metadata.yaml index b4e91b6c..08ea2104 100644 --- a/Tutorials/Kiefhaberemodel/metadata.yaml +++ b/Tutorials/Kiefhaberemodel/metadata.yaml @@ -4,6 +4,7 @@ description: "Allow molar units to be used for bimolecular rate constants" tags: ["validation", "kiefhaber", "emodel", "setoption", "l", "p", "s", "a"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/Motivatingexample/Motivating_example_metadata.yaml b/Tutorials/Motivatingexample/Motivating_example_metadata.yaml new file mode 100644 index 00000000..494fd65d --- /dev/null +++ b/Tutorials/Motivatingexample/Motivating_example_metadata.yaml @@ -0,0 +1,24 @@ +id: "Motivating_example" +name: "Motivating_example" +description: "Signal Transduction with receptor internalization" +tags: ["validation", "motivating", "example", "l", "r", "tf", "dna", "mrna1", "mrna2", "p1", "p2"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/Motivating_example.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/Motivatingexample/metadata.yaml b/Tutorials/Motivatingexample/metadata.yaml index 9dfc9870..5c8b0d37 100644 --- a/Tutorials/Motivatingexample/metadata.yaml +++ b/Tutorials/Motivatingexample/metadata.yaml @@ -4,6 +4,7 @@ description: "Signal Transduction with receptor internalization" tags: ["validation", "motivating", "example", "l", "r", "tf", "dna", "mrna1", "mrna2", "p1", "p2"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/MotivatingexamplecBNGL/Motivating_example_cBNGL_metadata.yaml b/Tutorials/MotivatingexamplecBNGL/Motivating_example_cBNGL_metadata.yaml new file mode 100644 index 00000000..0b6bb78c --- /dev/null +++ b/Tutorials/MotivatingexamplecBNGL/Motivating_example_cBNGL_metadata.yaml @@ -0,0 +1,24 @@ +id: "Motivating_example_cBNGL" +name: "Motivating_example_cBNGL" +description: "Signal transduction with receptor internalization" +tags: ["validation", "motivating", "example", "cbngl", "l", "r", "tf", "dna", "mrna1", "mrna2", "p1", "p2"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/Motivating_example_cBNGL.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/MotivatingexamplecBNGL/metadata.yaml b/Tutorials/MotivatingexamplecBNGL/metadata.yaml index 19dc7a0a..a4a4b8b2 100644 --- a/Tutorials/MotivatingexamplecBNGL/metadata.yaml +++ b/Tutorials/MotivatingexamplecBNGL/metadata.yaml @@ -4,6 +4,7 @@ description: "Signal transduction with receptor internalization" tags: ["validation", "motivating", "example", "cbngl", "l", "r", "tf", "dna", "mrna1", "mrna2", "p1", "p2"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/NativeTutorials/AB/AB_metadata.yaml b/Tutorials/NativeTutorials/AB/AB_metadata.yaml new file mode 100644 index 00000000..4cd61f5e --- /dev/null +++ b/Tutorials/NativeTutorials/AB/AB_metadata.yaml @@ -0,0 +1,24 @@ +id: "AB" +name: "AB" +description: "BioNetGen model: AB" +tags: ["ab", "a", "b", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/AB/AB.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/AB/metadata.yaml b/Tutorials/NativeTutorials/AB/metadata.yaml index b0648ffb..727be896 100644 --- a/Tutorials/NativeTutorials/AB/metadata.yaml +++ b/Tutorials/NativeTutorials/AB/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: AB" tags: ["ab", "a", "b", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/ABC/ABC_metadata.yaml b/Tutorials/NativeTutorials/ABC/ABC_metadata.yaml new file mode 100644 index 00000000..f89aa5c0 --- /dev/null +++ b/Tutorials/NativeTutorials/ABC/ABC_metadata.yaml @@ -0,0 +1,24 @@ +id: "ABC" +name: "ABC" +description: "BioNetGen model: ABC" +tags: ["abc", "a", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABC/ABC.bngl" +playground: + visible: true + gallery_categories: ["metabolism","native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/ABC/metadata.yaml b/Tutorials/NativeTutorials/ABC/metadata.yaml index 1e0c6e08..ec12d883 100644 --- a/Tutorials/NativeTutorials/ABC/metadata.yaml +++ b/Tutorials/NativeTutorials/ABC/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: ABC" tags: ["abc", "a", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/ABCscan/ABC_scan_metadata.yaml b/Tutorials/NativeTutorials/ABCscan/ABC_scan_metadata.yaml new file mode 100644 index 00000000..6fbf77a1 --- /dev/null +++ b/Tutorials/NativeTutorials/ABCscan/ABC_scan_metadata.yaml @@ -0,0 +1,24 @@ +id: "ABC_scan" +name: "ABC scan" +description: "BioNetGen model: ABC scan" +tags: ["abc", "scan", "a", "generate_network", "parameter_scan"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABC/ABC_scan.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/ABCscan/metadata.yaml b/Tutorials/NativeTutorials/ABCscan/metadata.yaml index bf69d4b3..e41e946b 100644 --- a/Tutorials/NativeTutorials/ABCscan/metadata.yaml +++ b/Tutorials/NativeTutorials/ABCscan/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: ABC scan" tags: ["abc", "scan", "a", "generate_network", "parameter_scan"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/ABCssa/ABC_ssa_metadata.yaml b/Tutorials/NativeTutorials/ABCssa/ABC_ssa_metadata.yaml new file mode 100644 index 00000000..4ba00d87 --- /dev/null +++ b/Tutorials/NativeTutorials/ABCssa/ABC_ssa_metadata.yaml @@ -0,0 +1,24 @@ +id: "ABC_ssa" +name: "ABC ssa" +description: "BioNetGen model: ABC ssa" +tags: ["abc", "ssa", "a", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABC/ABC_ssa.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/ABCssa/metadata.yaml b/Tutorials/NativeTutorials/ABCssa/metadata.yaml index 6538b9d5..c2057bb3 100644 --- a/Tutorials/NativeTutorials/ABCssa/metadata.yaml +++ b/Tutorials/NativeTutorials/ABCssa/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: ABC ssa" tags: ["abc", "ssa", "a", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ssa"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/ABp/ABp_metadata.yaml b/Tutorials/NativeTutorials/ABp/ABp_metadata.yaml new file mode 100644 index 00000000..e7e031a8 --- /dev/null +++ b/Tutorials/NativeTutorials/ABp/ABp_metadata.yaml @@ -0,0 +1,24 @@ +id: "ABp" +name: "ABp" +description: "title: ABp.bngl" +tags: ["abp", "a", "b", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABp/ABp.bngl" +playground: + visible: true + gallery_categories: ["metabolism","native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/ABp/metadata.yaml b/Tutorials/NativeTutorials/ABp/metadata.yaml index 3166f632..cb9a3bac 100644 --- a/Tutorials/NativeTutorials/ABp/metadata.yaml +++ b/Tutorials/NativeTutorials/ABp/metadata.yaml @@ -4,6 +4,7 @@ description: "title: ABp.bngl" tags: ["abp", "a", "b", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/ABpapprox/ABp_approx_metadata.yaml b/Tutorials/NativeTutorials/ABpapprox/ABp_approx_metadata.yaml new file mode 100644 index 00000000..0327e208 --- /dev/null +++ b/Tutorials/NativeTutorials/ABpapprox/ABp_approx_metadata.yaml @@ -0,0 +1,24 @@ +id: "ABp_approx" +name: "ABp approx" +description: "title: ABp.bngl" +tags: ["abp", "approx", "km", "a", "b", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABp/ABp_approx.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/ABpapprox/metadata.yaml b/Tutorials/NativeTutorials/ABpapprox/metadata.yaml index fa5eaffd..71ba7b79 100644 --- a/Tutorials/NativeTutorials/ABpapprox/metadata.yaml +++ b/Tutorials/NativeTutorials/ABpapprox/metadata.yaml @@ -4,6 +4,7 @@ description: "title: ABp.bngl" tags: ["abp", "approx", "km", "a", "b", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/BAB/BAB_metadata.yaml b/Tutorials/NativeTutorials/BAB/BAB_metadata.yaml new file mode 100644 index 00000000..570cfb91 --- /dev/null +++ b/Tutorials/NativeTutorials/BAB/BAB_metadata.yaml @@ -0,0 +1,24 @@ +id: "BAB" +name: "BAB" +description: "Simple binding model with a bivalent A molecule that has two identical sites" +tags: ["bab", "a", "b", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/BAB/BAB.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/BAB/metadata.yaml b/Tutorials/NativeTutorials/BAB/metadata.yaml index 33124b3e..e91e66d3 100644 --- a/Tutorials/NativeTutorials/BAB/metadata.yaml +++ b/Tutorials/NativeTutorials/BAB/metadata.yaml @@ -4,6 +4,7 @@ description: "Simple binding model with a bivalent A molecule that has two ident tags: ["bab", "a", "b", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/BABcoop/BAB_coop_metadata.yaml b/Tutorials/NativeTutorials/BABcoop/BAB_coop_metadata.yaml new file mode 100644 index 00000000..cf816e3e --- /dev/null +++ b/Tutorials/NativeTutorials/BABcoop/BAB_coop_metadata.yaml @@ -0,0 +1,24 @@ +id: "BAB_coop" +name: "BAB coop" +description: "Simple binding model with a bivalent A molecule that has two identical sites" +tags: ["bab", "coop", "a", "b", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/BAB/BAB_coop.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/BABcoop/metadata.yaml b/Tutorials/NativeTutorials/BABcoop/metadata.yaml index 9bd00b19..6366eaf7 100644 --- a/Tutorials/NativeTutorials/BABcoop/metadata.yaml +++ b/Tutorials/NativeTutorials/BABcoop/metadata.yaml @@ -4,6 +4,7 @@ description: "Simple binding model with a bivalent A molecule that has two ident tags: ["bab", "coop", "a", "b", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/BABscan/BAB_scan_metadata.yaml b/Tutorials/NativeTutorials/BABscan/BAB_scan_metadata.yaml new file mode 100644 index 00000000..4bbf28c3 --- /dev/null +++ b/Tutorials/NativeTutorials/BABscan/BAB_scan_metadata.yaml @@ -0,0 +1,24 @@ +id: "BAB_scan" +name: "BAB scan" +description: "Simple binding model with a bivalent A molecule that has two identical sites" +tags: ["bab", "scan", "a", "b", "generate_network", "parameter_scan"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/BAB/BAB_scan.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/BABscan/metadata.yaml b/Tutorials/NativeTutorials/BABscan/metadata.yaml index 4cb50c19..03869636 100644 --- a/Tutorials/NativeTutorials/BABscan/metadata.yaml +++ b/Tutorials/NativeTutorials/BABscan/metadata.yaml @@ -4,6 +4,7 @@ description: "Simple binding model with a bivalent A molecule that has two ident tags: ["bab", "scan", "a", "b", "generate_network", "parameter_scan"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/BLBR/BLBR_metadata.yaml b/Tutorials/NativeTutorials/BLBR/BLBR_metadata.yaml new file mode 100644 index 00000000..a9bd857c --- /dev/null +++ b/Tutorials/NativeTutorials/BLBR/BLBR_metadata.yaml @@ -0,0 +1,24 @@ +id: "BLBR" +name: "BLBR" +description: "title: BLBR.bngl" +tags: ["blbr", "setoption", "r", "l", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "nf"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/BLBR.bngl" +playground: + visible: false + gallery_category: "tutorial" + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/BLBR/metadata.yaml b/Tutorials/NativeTutorials/BLBR/metadata.yaml index d56a714e..1c2c3b50 100644 --- a/Tutorials/NativeTutorials/BLBR/metadata.yaml +++ b/Tutorials/NativeTutorials/BLBR/metadata.yaml @@ -4,6 +4,7 @@ description: "title: BLBR.bngl" tags: ["blbr", "setoption", "r", "l", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "nf"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/Chyleklibrary/Chylek_library_metadata.yaml b/Tutorials/NativeTutorials/Chyleklibrary/Chylek_library_metadata.yaml new file mode 100644 index 00000000..713ff8c5 --- /dev/null +++ b/Tutorials/NativeTutorials/Chyleklibrary/Chylek_library_metadata.yaml @@ -0,0 +1,24 @@ +id: "Chylek_library" +name: "Chylek library" +description: "Created by BioNetGen 2.2.6" +tags: ["chylek", "library", "kflatplcg", "kfgrb2gab2", "kflcp2plcg1", "kd1", "kd2", "sink", "pre", "pag1"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/LargerModels/Chylek_library.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml b/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml index d3759316..856cb68d 100644 --- a/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml +++ b/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml @@ -4,6 +4,7 @@ description: "Created by BioNetGen 2.2.6" tags: ["chylek", "library", "kflatplcg", "kfgrb2gab2", "kflcp2plcg1", "kd1", "kd2", "sink", "pre", "pag1"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/CircadianOscillator/CircadianOscillator_metadata.yaml b/Tutorials/NativeTutorials/CircadianOscillator/CircadianOscillator_metadata.yaml new file mode 100644 index 00000000..84a9e58a --- /dev/null +++ b/Tutorials/NativeTutorials/CircadianOscillator/CircadianOscillator_metadata.yaml @@ -0,0 +1,24 @@ +id: "CircadianOscillator" +name: "CircadianOscillator" +description: "Circadian rhythm" +tags: ["published", "tutorial", "native", "circadianoscillator", "a", "r", "pa", "pr", "mrna_a", "mrna_r"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/SynDeg/CircadianOscillator.bngl" +playground: + visible: false + gallery_categories: ["cell-cycle","native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml b/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml index 2d1bb8db..b0b47595 100644 --- a/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml +++ b/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml @@ -4,6 +4,7 @@ description: "Circadian rhythm" tags: ["published", "tutorial", "native", "circadianoscillator", "a", "r", "pa", "pr", "mrna_a", "mrna_r"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ssa"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/ComplexDegradation/ComplexDegradation_metadata.yaml b/Tutorials/NativeTutorials/ComplexDegradation/ComplexDegradation_metadata.yaml new file mode 100644 index 00000000..b9758bd3 --- /dev/null +++ b/Tutorials/NativeTutorials/ComplexDegradation/ComplexDegradation_metadata.yaml @@ -0,0 +1,24 @@ +id: "ComplexDegradation" +name: "ComplexDegradation" +description: "Degradation model" +tags: ["published", "tutorial", "native", "complexdegradation", "a", "b", "c", "generate_network"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/SynDeg/ComplexDegradation.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml b/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml index 04ebf11d..d6e53109 100644 --- a/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml +++ b/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml @@ -4,6 +4,7 @@ description: "Degradation model" tags: ["published", "tutorial", "native", "complexdegradation", "a", "b", "c", "generate_network"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/Creamer2012/Creamer_2012_metadata.yaml b/Tutorials/NativeTutorials/Creamer2012/Creamer_2012_metadata.yaml new file mode 100644 index 00000000..234d75dd --- /dev/null +++ b/Tutorials/NativeTutorials/Creamer2012/Creamer_2012_metadata.yaml @@ -0,0 +1,24 @@ +id: "Creamer_2012" +name: "Creamer 2012" +description: "Initial values" +tags: ["creamer", "2012", "egf", "hrg", "egfr", "erbb2", "erbb3", "erbb4", "p52shc1", "grb2"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/LargerModels/Creamer_2012.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/Creamer2012/metadata.yaml b/Tutorials/NativeTutorials/Creamer2012/metadata.yaml index fd58eccd..e987da9a 100644 --- a/Tutorials/NativeTutorials/Creamer2012/metadata.yaml +++ b/Tutorials/NativeTutorials/Creamer2012/metadata.yaml @@ -4,6 +4,7 @@ description: "Initial values" tags: ["creamer", "2012", "egf", "hrg", "egfr", "erbb2", "erbb3", "erbb4", "p52shc1", "grb2"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/FceRIji/FceRI_ji_metadata.yaml b/Tutorials/NativeTutorials/FceRIji/FceRI_ji_metadata.yaml new file mode 100644 index 00000000..57d129d1 --- /dev/null +++ b/Tutorials/NativeTutorials/FceRIji/FceRI_ji_metadata.yaml @@ -0,0 +1,24 @@ +id: "FceRI_ji" +name: "FceRI ji" +description: "title: FceRI_ji.bngl" +tags: ["fceri", "ji", "lig", "lyn", "syk", "rec"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/LargerModels/FceRI_ji.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/FceRIji/metadata.yaml b/Tutorials/NativeTutorials/FceRIji/metadata.yaml index 2addfe00..642ae512 100644 --- a/Tutorials/NativeTutorials/FceRIji/metadata.yaml +++ b/Tutorials/NativeTutorials/FceRIji/metadata.yaml @@ -4,6 +4,7 @@ description: "title: FceRI_ji.bngl" tags: ["fceri", "ji", "lig", "lyn", "syk", "rec"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/FceRIviz/FceRI_viz_metadata.yaml b/Tutorials/NativeTutorials/FceRIviz/FceRI_viz_metadata.yaml new file mode 100644 index 00000000..55a34d25 --- /dev/null +++ b/Tutorials/NativeTutorials/FceRIviz/FceRI_viz_metadata.yaml @@ -0,0 +1,24 @@ +id: "FceRI_viz" +name: "FceRI Viz" +description: "FcεRI (viz)" +tags: ["published", "tutorial", "native", "fceri", "viz", "fcr", "ige", "lat", "lyn", "syk", "pb", "pg", "sykp"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/Viz/FceRI_viz.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/FceRIviz/metadata.yaml b/Tutorials/NativeTutorials/FceRIviz/metadata.yaml index 2eb2af1c..0a78ecb9 100644 --- a/Tutorials/NativeTutorials/FceRIviz/metadata.yaml +++ b/Tutorials/NativeTutorials/FceRIviz/metadata.yaml @@ -4,6 +4,7 @@ description: "FcεRI (viz)" tags: ["published", "tutorial", "native", "fceri", "viz", "fcr", "ige", "lat", "lyn", "syk", "pb", "pg", "sykp"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/GK/GK_metadata.yaml b/Tutorials/NativeTutorials/GK/GK_metadata.yaml new file mode 100644 index 00000000..8f542136 --- /dev/null +++ b/Tutorials/NativeTutorials/GK/GK_metadata.yaml @@ -0,0 +1,24 @@ +id: "GK" +name: "GK" +description: "title: GK.bngl" +tags: ["gk", "b", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABp/GK.bngl" +playground: + visible: true + gallery_categories: ["metabolism","native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/GK/metadata.yaml b/Tutorials/NativeTutorials/GK/metadata.yaml index a5a674c5..47effc19 100644 --- a/Tutorials/NativeTutorials/GK/metadata.yaml +++ b/Tutorials/NativeTutorials/GK/metadata.yaml @@ -4,6 +4,7 @@ description: "title: GK.bngl" tags: ["gk", "b", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/LR/LR_metadata.yaml b/Tutorials/NativeTutorials/LR/LR_metadata.yaml new file mode 100644 index 00000000..b692ee9f --- /dev/null +++ b/Tutorials/NativeTutorials/LR/LR_metadata.yaml @@ -0,0 +1,24 @@ +id: "LR" +name: "LR" +description: "title: LR.bngl" +tags: ["lr", "l", "r", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/LR.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LR/metadata.yaml b/Tutorials/NativeTutorials/LR/metadata.yaml index 670e47fa..d462af06 100644 --- a/Tutorials/NativeTutorials/LR/metadata.yaml +++ b/Tutorials/NativeTutorials/LR/metadata.yaml @@ -4,6 +4,7 @@ description: "title: LR.bngl" tags: ["lr", "l", "r", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/LRR/LRR_metadata.yaml b/Tutorials/NativeTutorials/LRR/LRR_metadata.yaml new file mode 100644 index 00000000..51f544a7 --- /dev/null +++ b/Tutorials/NativeTutorials/LRR/LRR_metadata.yaml @@ -0,0 +1,24 @@ +id: "LRR" +name: "LRR" +description: "title: LRR.bngl" +tags: ["lrr", "l", "r"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/LRR.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/LRR/metadata.yaml b/Tutorials/NativeTutorials/LRR/metadata.yaml index 3a9da1f1..c8ed5546 100644 --- a/Tutorials/NativeTutorials/LRR/metadata.yaml +++ b/Tutorials/NativeTutorials/LRR/metadata.yaml @@ -4,6 +4,7 @@ description: "title: LRR.bngl" tags: ["lrr", "l", "r"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/LRRcomp/LRR_comp_metadata.yaml b/Tutorials/NativeTutorials/LRRcomp/LRR_comp_metadata.yaml new file mode 100644 index 00000000..e728f266 --- /dev/null +++ b/Tutorials/NativeTutorials/LRRcomp/LRR_comp_metadata.yaml @@ -0,0 +1,24 @@ +id: "LRR_comp" +name: "LRR comp" +description: "title: LRR_comp.bngl" +tags: ["lrr", "comp", "l", "r", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/LRR_comp.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LRRcomp/metadata.yaml b/Tutorials/NativeTutorials/LRRcomp/metadata.yaml index ceea2712..84ae7ad8 100644 --- a/Tutorials/NativeTutorials/LRRcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LRRcomp/metadata.yaml @@ -4,6 +4,7 @@ description: "title: LRR_comp.bngl" tags: ["lrr", "comp", "l", "r", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/NativeTutorials/LRcomp/LR_comp_metadata.yaml b/Tutorials/NativeTutorials/LRcomp/LR_comp_metadata.yaml new file mode 100644 index 00000000..7a00b0a8 --- /dev/null +++ b/Tutorials/NativeTutorials/LRcomp/LR_comp_metadata.yaml @@ -0,0 +1,24 @@ +id: "LR_comp" +name: "LR comp" +description: "title: LR_comp.bngl" +tags: ["lr", "comp", "l", "r", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/LR_comp.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LRcomp/metadata.yaml b/Tutorials/NativeTutorials/LRcomp/metadata.yaml index 47204c62..6d26475e 100644 --- a/Tutorials/NativeTutorials/LRcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LRcomp/metadata.yaml @@ -4,6 +4,7 @@ description: "title: LR_comp.bngl" tags: ["lr", "comp", "l", "r", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/NativeTutorials/LV/LV_metadata.yaml b/Tutorials/NativeTutorials/LV/LV_metadata.yaml new file mode 100644 index 00000000..edd94cc6 --- /dev/null +++ b/Tutorials/NativeTutorials/LV/LV_metadata.yaml @@ -0,0 +1,24 @@ +id: "LV" +name: "LV" +description: "title: LV.bgl" +tags: ["lv", "s", "w", "generate_network", "writesbml", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABC/LV.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LV/metadata.yaml b/Tutorials/NativeTutorials/LV/metadata.yaml index 7fda6798..7b48c8f2 100644 --- a/Tutorials/NativeTutorials/LV/metadata.yaml +++ b/Tutorials/NativeTutorials/LV/metadata.yaml @@ -4,6 +4,7 @@ description: "title: LV.bgl" tags: ["lv", "s", "w", "generate_network", "writesbml", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/LVcomp/LV_comp_metadata.yaml b/Tutorials/NativeTutorials/LVcomp/LV_comp_metadata.yaml new file mode 100644 index 00000000..987114e0 --- /dev/null +++ b/Tutorials/NativeTutorials/LVcomp/LV_comp_metadata.yaml @@ -0,0 +1,24 @@ +id: "LV_comp" +name: "LV comp" +description: "title: LV_comp.bgl" +tags: ["lv", "comp", "k2", "s", "w"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/LV_comp.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/LVcomp/metadata.yaml b/Tutorials/NativeTutorials/LVcomp/metadata.yaml index ab19072b..8a139dc1 100644 --- a/Tutorials/NativeTutorials/LVcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LVcomp/metadata.yaml @@ -4,6 +4,7 @@ description: "title: LV_comp.bgl" tags: ["lv", "comp", "k2", "s", "w"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: true diff --git a/Tutorials/NativeTutorials/Lisman/Lisman_metadata.yaml b/Tutorials/NativeTutorials/Lisman/Lisman_metadata.yaml new file mode 100644 index 00000000..a29cd2fa --- /dev/null +++ b/Tutorials/NativeTutorials/Lisman/Lisman_metadata.yaml @@ -0,0 +1,24 @@ +id: "Lisman" +name: "Lisman" +description: "title: auto.bngl" +tags: ["lisman", "k1", "p", "input", "visualize", "setparameter", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABp/Lisman.bngl" +playground: + visible: true + gallery_categories: ["neuroscience","native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/Lisman/metadata.yaml b/Tutorials/NativeTutorials/Lisman/metadata.yaml index 09a1be55..4e02fae5 100644 --- a/Tutorials/NativeTutorials/Lisman/metadata.yaml +++ b/Tutorials/NativeTutorials/Lisman/metadata.yaml @@ -4,6 +4,7 @@ description: "title: auto.bngl" tags: ["lisman", "k1", "p", "input", "visualize", "setparameter", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/Lismanbifurcate/Lisman_bifurcate_metadata.yaml b/Tutorials/NativeTutorials/Lismanbifurcate/Lisman_bifurcate_metadata.yaml new file mode 100644 index 00000000..1576b770 --- /dev/null +++ b/Tutorials/NativeTutorials/Lismanbifurcate/Lisman_bifurcate_metadata.yaml @@ -0,0 +1,24 @@ +id: "Lisman_bifurcate" +name: "Lisman bifurcate" +description: "title: Lisman_bifurcate.bngl" +tags: ["lisman", "bifurcate", "k1", "p"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABp/Lisman_bifurcate.bngl" +playground: + visible: false + gallery_categories: ["neuroscience","native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml b/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml index 5e5a68df..ba45e34d 100644 --- a/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml +++ b/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml @@ -4,6 +4,7 @@ description: "title: Lisman_bifurcate.bngl" tags: ["lisman", "bifurcate", "k1", "p"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/Repressilator/Repressilator_metadata.yaml b/Tutorials/NativeTutorials/Repressilator/Repressilator_metadata.yaml new file mode 100644 index 00000000..5a180e6e --- /dev/null +++ b/Tutorials/NativeTutorials/Repressilator/Repressilator_metadata.yaml @@ -0,0 +1,24 @@ +id: "Repressilator" +name: "Repressilator" +description: "Repressilator circuit" +tags: ["published", "tutorial", "native", "repressilator", "gtetr", "gci", "glaci", "mtetr", "mci", "mlaci", "ptetr", "pci"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/SynDeg/Repressilator.bngl" +playground: + visible: true + gallery_categories: ["cell-cycle","synbio","native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/Repressilator/metadata.yaml b/Tutorials/NativeTutorials/Repressilator/metadata.yaml index 10ea1210..befad7d1 100644 --- a/Tutorials/NativeTutorials/Repressilator/metadata.yaml +++ b/Tutorials/NativeTutorials/Repressilator/metadata.yaml @@ -4,6 +4,7 @@ description: "Repressilator circuit" tags: ["published", "tutorial", "native", "repressilator", "gtetr", "gci", "glaci", "mtetr", "mci", "mlaci", "ptetr", "pci"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/SIR/SIR_metadata.yaml b/Tutorials/NativeTutorials/SIR/SIR_metadata.yaml new file mode 100644 index 00000000..18645aed --- /dev/null +++ b/Tutorials/NativeTutorials/SIR/SIR_metadata.yaml @@ -0,0 +1,24 @@ +id: "SIR" +name: "SIR" +description: "BioNetGen model: SIR" +tags: ["sir", "saveconcentrations", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/ABC/SIR.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/SIR/metadata.yaml b/Tutorials/NativeTutorials/SIR/metadata.yaml index 555c05c7..9a6e3d12 100644 --- a/Tutorials/NativeTutorials/SIR/metadata.yaml +++ b/Tutorials/NativeTutorials/SIR/metadata.yaml @@ -4,6 +4,7 @@ description: "BioNetGen model: SIR" tags: ["sir", "saveconcentrations", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/Suderman2013/Suderman_2013_metadata.yaml b/Tutorials/NativeTutorials/Suderman2013/Suderman_2013_metadata.yaml new file mode 100644 index 00000000..9ad6584b --- /dev/null +++ b/Tutorials/NativeTutorials/Suderman2013/Suderman_2013_metadata.yaml @@ -0,0 +1,24 @@ +id: "Suderman_2013" +name: "Suderman 2013" +description: "Ensemble model translated into BNGL" +tags: ["suderman", "2013", "i", "trash", "pheromone", "ste2", "gpa1", "ste4", "sst2", "ste20"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/LargerModels/Suderman_2013.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/Suderman2013/metadata.yaml b/Tutorials/NativeTutorials/Suderman2013/metadata.yaml index 8d8122ab..435d8fdd 100644 --- a/Tutorials/NativeTutorials/Suderman2013/metadata.yaml +++ b/Tutorials/NativeTutorials/Suderman2013/metadata.yaml @@ -4,6 +4,7 @@ description: "Ensemble model translated into BNGL" tags: ["suderman", "2013", "i", "trash", "pheromone", "ste2", "gpa1", "ste4", "sst2", "ste20"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/birthdeath/birth-death_metadata.yaml b/Tutorials/NativeTutorials/birthdeath/birth-death_metadata.yaml new file mode 100644 index 00000000..e0112510 --- /dev/null +++ b/Tutorials/NativeTutorials/birthdeath/birth-death_metadata.yaml @@ -0,0 +1,24 @@ +id: "birth-death" +name: "Birth-Death" +description: "Stochastic process" +tags: ["published", "tutorial", "native", "birth", "death", "a", "generate_network", "saveconcentrations", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/SynDeg/birth-death.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/birthdeath/metadata.yaml b/Tutorials/NativeTutorials/birthdeath/metadata.yaml index 039e683c..2e5771d6 100644 --- a/Tutorials/NativeTutorials/birthdeath/metadata.yaml +++ b/Tutorials/NativeTutorials/birthdeath/metadata.yaml @@ -4,6 +4,7 @@ description: "Stochastic process" tags: ["published", "tutorial", "native", "birth", "death", "a", "generate_network", "saveconcentrations", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode", "ssa"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/cBNGLsimple/cBNGL_simple_metadata.yaml b/Tutorials/NativeTutorials/cBNGLsimple/cBNGL_simple_metadata.yaml new file mode 100644 index 00000000..6e494d6e --- /dev/null +++ b/Tutorials/NativeTutorials/cBNGLsimple/cBNGL_simple_metadata.yaml @@ -0,0 +1,24 @@ +id: "cBNGL_simple" +name: "cBNGL simple" +description: "A simplified signal transduction model including the following processes:" +tags: ["cbngl", "simple", "l", "r", "tf", "dna", "mrna", "p"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/cBNGL_simple.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml b/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml index b78f498a..eb3eacca 100644 --- a/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml +++ b/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml @@ -4,6 +4,7 @@ description: "A simplified signal transduction model including the following pro tags: ["cbngl", "simple", "l", "r", "tf", "dna", "mrna", "p"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/NativeTutorials/egfrsimple/egfr_simple_metadata.yaml b/Tutorials/NativeTutorials/egfrsimple/egfr_simple_metadata.yaml new file mode 100644 index 00000000..42ae4826 --- /dev/null +++ b/Tutorials/NativeTutorials/egfrsimple/egfr_simple_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr_simple" +name: "egfr simple" +description: "This is a demo model of EGFR signaling." +tags: ["egfr", "simple", "egf", "grb2", "sos1"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/LargerModels/egfr_simple.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/egfrsimple/metadata.yaml b/Tutorials/NativeTutorials/egfrsimple/metadata.yaml index f2963470..0b44cea6 100644 --- a/Tutorials/NativeTutorials/egfrsimple/metadata.yaml +++ b/Tutorials/NativeTutorials/egfrsimple/metadata.yaml @@ -4,6 +4,7 @@ description: "This is a demo model of EGFR signaling." tags: ["egfr", "simple", "egf", "grb2", "sos1"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/organelletransport/metadata.yaml b/Tutorials/NativeTutorials/organelletransport/metadata.yaml index c8bd4316..71c080df 100644 --- a/Tutorials/NativeTutorials/organelletransport/metadata.yaml +++ b/Tutorials/NativeTutorials/organelletransport/metadata.yaml @@ -4,6 +4,7 @@ description: "title: organelle_transport.bngl" tags: ["organelle", "transport", "a", "b", "c", "d", "t1", "at1", "ct1", "t2"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/NativeTutorials/organelletransport/organelle_transport_metadata.yaml b/Tutorials/NativeTutorials/organelletransport/organelle_transport_metadata.yaml new file mode 100644 index 00000000..3a6a607f --- /dev/null +++ b/Tutorials/NativeTutorials/organelletransport/organelle_transport_metadata.yaml @@ -0,0 +1,24 @@ +id: "organelle_transport" +name: "organelle transport" +description: "title: organelle_transport.bngl" +tags: ["organelle", "transport", "a", "b", "c", "d", "t1", "at1", "ct1", "t2"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/organelle_transport.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml b/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml index 7fbda96d..71f3c642 100644 --- a/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml +++ b/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml @@ -4,6 +4,7 @@ description: "title: organelle_transport_abcd.bngl" tags: ["organelle", "transport", "struct", "a", "b", "t1", "t2"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/NativeTutorials/organelletransportstruct/organelle_transport_struct_metadata.yaml b/Tutorials/NativeTutorials/organelletransportstruct/organelle_transport_struct_metadata.yaml new file mode 100644 index 00000000..0be328c2 --- /dev/null +++ b/Tutorials/NativeTutorials/organelletransportstruct/organelle_transport_struct_metadata.yaml @@ -0,0 +1,24 @@ +id: "organelle_transport_struct" +name: "organelle transport struct" +description: "title: organelle_transport_abcd.bngl" +tags: ["organelle", "transport", "struct", "a", "b", "t1", "t2"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/CBNGL/organelle_transport_struct.bngl" +playground: + visible: true + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/toggle/metadata.yaml b/Tutorials/NativeTutorials/toggle/metadata.yaml index 68257b09..2a63a801 100644 --- a/Tutorials/NativeTutorials/toggle/metadata.yaml +++ b/Tutorials/NativeTutorials/toggle/metadata.yaml @@ -4,6 +4,7 @@ description: "Toggle switch" tags: ["published", "tutorial", "native", "toggle", "x", "y", "generate_network", "writemfile", "setconcentration"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ssa"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/toggle/toggle_metadata.yaml b/Tutorials/NativeTutorials/toggle/toggle_metadata.yaml new file mode 100644 index 00000000..da785c1f --- /dev/null +++ b/Tutorials/NativeTutorials/toggle/toggle_metadata.yaml @@ -0,0 +1,24 @@ +id: "toggle" +name: "Toggle" +description: "Toggle switch" +tags: ["published", "tutorial", "native", "toggle", "x", "y", "generate_network", "writemfile", "setconcentration"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ssa"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/SynDeg/toggle.bngl" +playground: + visible: false + gallery_categories: ["synbio","native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/translateSBML/metadata.yaml b/Tutorials/NativeTutorials/translateSBML/metadata.yaml index 97d233d9..fea9159f 100644 --- a/Tutorials/NativeTutorials/translateSBML/metadata.yaml +++ b/Tutorials/NativeTutorials/translateSBML/metadata.yaml @@ -4,6 +4,7 @@ description: "title: translateSBML.bngl" tags: ["translatesbml", "generate_network", "simulate"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/translateSBML/translateSBML_metadata.yaml b/Tutorials/NativeTutorials/translateSBML/translateSBML_metadata.yaml new file mode 100644 index 00000000..8fafe930 --- /dev/null +++ b/Tutorials/NativeTutorials/translateSBML/translateSBML_metadata.yaml @@ -0,0 +1,24 @@ +id: "translateSBML" +name: "translateSBML" +description: "title: translateSBML.bngl" +tags: ["translatesbml", "generate_network", "simulate"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/SBML/translateSBML.bngl" +playground: + visible: false + gallery_category: "tutorial" + featured: false + difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/visualize/metadata.yaml b/Tutorials/NativeTutorials/visualize/metadata.yaml index 3af25815..538aa269 100644 --- a/Tutorials/NativeTutorials/visualize/metadata.yaml +++ b/Tutorials/NativeTutorials/visualize/metadata.yaml @@ -4,6 +4,7 @@ description: "Visualization toy" tags: ["published", "tutorial", "native", "visualize", "x", "a1", "a2", "b"] category: "tutorial" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/NativeTutorials/visualize/visualize_metadata.yaml b/Tutorials/NativeTutorials/visualize/visualize_metadata.yaml new file mode 100644 index 00000000..f2958d44 --- /dev/null +++ b/Tutorials/NativeTutorials/visualize/visualize_metadata.yaml @@ -0,0 +1,24 @@ +id: "visualize" +name: "Visualize" +description: "Visualization toy" +tags: ["published", "tutorial", "native", "visualize", "x", "a1", "a2", "b"] +category: "tutorial" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "tutorial" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/native-tutorials/Viz/visualize.bngl" +playground: + visible: false + gallery_categories: ["native-tutorials"] + featured: false + difficulty: "advanced" diff --git a/Tutorials/SHP2basemodel/SHP2_base_model_metadata.yaml b/Tutorials/SHP2basemodel/SHP2_base_model_metadata.yaml new file mode 100644 index 00000000..01d0dc37 --- /dev/null +++ b/Tutorials/SHP2basemodel/SHP2_base_model_metadata.yaml @@ -0,0 +1,24 @@ +id: "SHP2_base_model" +name: "SHP2_base_model" +description: "Base model of Shp2 regulation" +tags: ["validation", "shp2", "base", "model", "r", "s", "exclude_reactants"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/SHP2_base_model.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/SHP2basemodel/metadata.yaml b/Tutorials/SHP2basemodel/metadata.yaml index 2007ff75..49e2a361 100644 --- a/Tutorials/SHP2basemodel/metadata.yaml +++ b/Tutorials/SHP2basemodel/metadata.yaml @@ -4,6 +4,7 @@ description: "Base model of Shp2 regulation" tags: ["validation", "shp2", "base", "model", "r", "s", "exclude_reactants"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/catalysis/catalysis_metadata.yaml b/Tutorials/catalysis/catalysis_metadata.yaml new file mode 100644 index 00000000..87bcb472 --- /dev/null +++ b/Tutorials/catalysis/catalysis_metadata.yaml @@ -0,0 +1,24 @@ +id: "catalysis" +name: "catalysis" +description: "Catalysis in energy BNG" +tags: ["validation", "catalysis", "version", "setoption", "s", "kinase", "pptase", "atp", "adp"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/catalysis.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/catalysis/metadata.yaml b/Tutorials/catalysis/metadata.yaml index 3847ec03..f94f37b1 100644 --- a/Tutorials/catalysis/metadata.yaml +++ b/Tutorials/catalysis/metadata.yaml @@ -4,6 +4,7 @@ description: "Catalysis in energy BNG" tags: ["validation", "catalysis", "version", "setoption", "s", "kinase", "pptase", "atp", "adp"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/continue/continue_metadata.yaml b/Tutorials/continue/continue_metadata.yaml new file mode 100644 index 00000000..d44b87ae --- /dev/null +++ b/Tutorials/continue/continue_metadata.yaml @@ -0,0 +1,24 @@ +id: "continue" +name: "continue" +description: "Test trajectory continuation" +tags: ["validation", "continue", "a", "b", "c", "trash"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/continue.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/continue/metadata.yaml b/Tutorials/continue/metadata.yaml index 23badc1e..9e80b334 100644 --- a/Tutorials/continue/metadata.yaml +++ b/Tutorials/continue/metadata.yaml @@ -4,6 +4,7 @@ description: "Test trajectory continuation" tags: ["validation", "continue", "a", "b", "c", "trash"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/egfrnet/egfr_net_metadata.yaml b/Tutorials/egfrnet/egfr_net_metadata.yaml new file mode 100644 index 00000000..a247db61 --- /dev/null +++ b/Tutorials/egfrnet/egfr_net_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr_net" +name: "egfr_net" +description: "check detailed balanced" +tags: ["validation", "egfr", "net", "egf", "shc", "grb2", "sos"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/egfr_net.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/egfrnet/metadata.yaml b/Tutorials/egfrnet/metadata.yaml index d9756d78..04822c44 100644 --- a/Tutorials/egfrnet/metadata.yaml +++ b/Tutorials/egfrnet/metadata.yaml @@ -4,6 +4,7 @@ description: "check detailed balanced" tags: ["validation", "egfr", "net", "egf", "shc", "grb2", "sos"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/egfrnetred/egfr_net_red_metadata.yaml b/Tutorials/egfrnetred/egfr_net_red_metadata.yaml new file mode 100644 index 00000000..e2375c21 --- /dev/null +++ b/Tutorials/egfrnetred/egfr_net_red_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr_net_red" +name: "egfr_net_red" +description: "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics" +tags: ["validation", "egfr", "net", "red", "egf", "egfr_1", "egfr_2", "egfr_3", "grb2", "shc", "sos"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/egfr_net_red.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/egfrnetred/metadata.yaml b/Tutorials/egfrnetred/metadata.yaml index e203993f..92e130bf 100644 --- a/Tutorials/egfrnetred/metadata.yaml +++ b/Tutorials/egfrnetred/metadata.yaml @@ -4,6 +4,7 @@ description: "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE d tags: ["validation", "egfr", "net", "red", "egf", "egfr_1", "egfr_2", "egfr_3", "grb2", "shc", "sos"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/egfrpath/egfr_path_metadata.yaml b/Tutorials/egfrpath/egfr_path_metadata.yaml new file mode 100644 index 00000000..b726a7bb --- /dev/null +++ b/Tutorials/egfrpath/egfr_path_metadata.yaml @@ -0,0 +1,24 @@ +id: "egfr_path" +name: "egfr_path" +description: "The primary focus of the model developed by Kholodenko" +tags: ["validation", "egfr", "path", "generate_network", "setconcentration", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/egfr_path.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/egfrpath/metadata.yaml b/Tutorials/egfrpath/metadata.yaml index a7125010..d903cf02 100644 --- a/Tutorials/egfrpath/metadata.yaml +++ b/Tutorials/egfrpath/metadata.yaml @@ -4,6 +4,7 @@ description: "The primary focus of the model developed by Kholodenko" tags: ["validation", "egfr", "path", "generate_network", "setconcentration", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/energyexample1/energy_example1_metadata.yaml b/Tutorials/energyexample1/energy_example1_metadata.yaml new file mode 100644 index 00000000..722cc1dc --- /dev/null +++ b/Tutorials/energyexample1/energy_example1_metadata.yaml @@ -0,0 +1,24 @@ +id: "energy_example1" +name: "energy_example1" +description: "Illustration of energy modeling approach w/ a simple protein scaffold model" +tags: ["validation", "energy", "example1", "version", "setoption", "s", "a", "b", "c"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: true + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/energy_example1.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/energyexample1/metadata.yaml b/Tutorials/energyexample1/metadata.yaml index fc9a555d..d3dc1015 100644 --- a/Tutorials/energyexample1/metadata.yaml +++ b/Tutorials/energyexample1/metadata.yaml @@ -4,6 +4,7 @@ description: "Illustration of energy modeling approach w/ a simple protein scaff tags: ["validation", "energy", "example1", "version", "setoption", "s", "a", "b", "c"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/example1/example1_metadata.yaml b/Tutorials/example1/example1_metadata.yaml new file mode 100644 index 00000000..53064026 --- /dev/null +++ b/Tutorials/example1/example1_metadata.yaml @@ -0,0 +1,24 @@ +id: "example1" +name: "example1" +description: "Example file for BNG2 tutorial." +tags: ["validation", "example1", "version", "generate_network", "simulate_ode"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/example1.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/example1/metadata.yaml b/Tutorials/example1/metadata.yaml index 71bb8b5c..c1a45da3 100644 --- a/Tutorials/example1/metadata.yaml +++ b/Tutorials/example1/metadata.yaml @@ -4,6 +4,7 @@ description: "Example file for BNG2 tutorial." tags: ["validation", "example1", "version", "generate_network", "simulate_ode"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/fcerijicomp/fceri_ji_comp_metadata.yaml b/Tutorials/fcerijicomp/fceri_ji_comp_metadata.yaml new file mode 100644 index 00000000..ea9e83ac --- /dev/null +++ b/Tutorials/fcerijicomp/fceri_ji_comp_metadata.yaml @@ -0,0 +1,24 @@ +id: "fceri_ji_comp" +name: "fceri_ji_comp" +description: "Ligand-receptor binding" +tags: ["validation", "fceri", "ji", "comp", "lig", "lyn", "syk", "rec"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/fceri_ji_comp.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Tutorials/fcerijicomp/metadata.yaml b/Tutorials/fcerijicomp/metadata.yaml index 63d628b7..3529fde4 100644 --- a/Tutorials/fcerijicomp/metadata.yaml +++ b/Tutorials/fcerijicomp/metadata.yaml @@ -4,6 +4,7 @@ description: "Ligand-receptor binding" tags: ["validation", "fceri", "ji", "comp", "lig", "lyn", "syk", "rec"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/heise/heise_metadata.yaml b/Tutorials/heise/heise_metadata.yaml new file mode 100644 index 00000000..7c05e0ee --- /dev/null +++ b/Tutorials/heise/heise_metadata.yaml @@ -0,0 +1,24 @@ +id: "heise" +name: "heise" +description: "Validate state inheritance in a symmetric context" +tags: ["validation", "heise", "a", "b", "generate_network", "simulate_ode", "setparameter"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/heise.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/heise/metadata.yaml b/Tutorials/heise/metadata.yaml index a7c85bea..5185962e 100644 --- a/Tutorials/heise/metadata.yaml +++ b/Tutorials/heise/metadata.yaml @@ -4,6 +4,7 @@ description: "Validate state inheritance in a symmetric context" tags: ["validation", "heise", "a", "b", "generate_network", "simulate_ode", "setparameter"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/issue198short/issue_198_short_metadata.yaml b/Tutorials/issue198short/issue_198_short_metadata.yaml new file mode 100644 index 00000000..6d48c476 --- /dev/null +++ b/Tutorials/issue198short/issue_198_short_metadata.yaml @@ -0,0 +1,24 @@ +id: "issue_198_short" +name: "issue_198_short" +description: "No description available" +tags: ["validation", "issue", "198", "short", "a", "b", "c", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/issue_198_short.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/issue198short/metadata.yaml b/Tutorials/issue198short/metadata.yaml index 11f43c89..f96198d6 100644 --- a/Tutorials/issue198short/metadata.yaml +++ b/Tutorials/issue198short/metadata.yaml @@ -4,6 +4,7 @@ description: "No description available" tags: ["validation", "issue", "198", "short", "a", "b", "c", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/localfunc/localfunc_metadata.yaml b/Tutorials/localfunc/localfunc_metadata.yaml new file mode 100644 index 00000000..6db56c4a --- /dev/null +++ b/Tutorials/localfunc/localfunc_metadata.yaml @@ -0,0 +1,24 @@ +id: "localfunc" +name: "localfunc" +description: "Test local function expansion" +tags: ["validation", "localfunc", "a", "b", "c", "trash", "f_synth"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/localfunc.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/localfunc/metadata.yaml b/Tutorials/localfunc/metadata.yaml index a7398643..f003b13d 100644 --- a/Tutorials/localfunc/metadata.yaml +++ b/Tutorials/localfunc/metadata.yaml @@ -4,6 +4,7 @@ description: "Test local function expansion" tags: ["validation", "localfunc", "a", "b", "c", "trash", "f_synth"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/michment/metadata.yaml b/Tutorials/michment/metadata.yaml index f559cda8..a3b83f09 100644 --- a/Tutorials/michment/metadata.yaml +++ b/Tutorials/michment/metadata.yaml @@ -4,6 +4,7 @@ description: "Michaelis Menten" tags: ["validation", "michment", "e", "s", "generate_network"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/michment/michment_metadata.yaml b/Tutorials/michment/michment_metadata.yaml new file mode 100644 index 00000000..57809782 --- /dev/null +++ b/Tutorials/michment/michment_metadata.yaml @@ -0,0 +1,24 @@ +id: "michment" +name: "michment" +description: "Michaelis Menten" +tags: ["validation", "michment", "e", "s", "generate_network"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/michment.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/michmentcont/metadata.yaml b/Tutorials/michmentcont/metadata.yaml index a5a96387..26c2531d 100644 --- a/Tutorials/michmentcont/metadata.yaml +++ b/Tutorials/michmentcont/metadata.yaml @@ -4,6 +4,7 @@ description: "Michaelis Menten Continue" tags: ["validation", "michment", "cont", "readfile", "setconcentration", "simulate_ode", "addconcentration"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/michmentcont/michment_cont_metadata.yaml b/Tutorials/michmentcont/michment_cont_metadata.yaml new file mode 100644 index 00000000..eec8afb7 --- /dev/null +++ b/Tutorials/michmentcont/michment_cont_metadata.yaml @@ -0,0 +1,24 @@ +id: "michment_cont" +name: "michment_cont" +description: "Michaelis Menten Continue" +tags: ["validation", "michment", "cont", "readfile", "setconcentration", "simulate_ode", "addconcentration"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/michment_cont.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Tutorials/motor/metadata.yaml b/Tutorials/motor/metadata.yaml index 5be78627..7e8820b2 100644 --- a/Tutorials/motor/metadata.yaml +++ b/Tutorials/motor/metadata.yaml @@ -4,6 +4,7 @@ description: "Motor protein" tags: ["validation", "motor", "chey", "kplus", "kminus"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/motor/motor_metadata.yaml b/Tutorials/motor/motor_metadata.yaml new file mode 100644 index 00000000..a9b651fd --- /dev/null +++ b/Tutorials/motor/motor_metadata.yaml @@ -0,0 +1,24 @@ +id: "motor" +name: "motor" +description: "Motor protein" +tags: ["validation", "motor", "chey", "kplus", "kminus"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/motor.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/mwc/metadata.yaml b/Tutorials/mwc/metadata.yaml index 63a2624e..f99a6c92 100644 --- a/Tutorials/mwc/metadata.yaml +++ b/Tutorials/mwc/metadata.yaml @@ -4,6 +4,7 @@ description: "Monod-Wyman-Changeux model" tags: ["validation", "mwc", "setoption", "h", "ox", "b"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/mwc/mwc_metadata.yaml b/Tutorials/mwc/mwc_metadata.yaml new file mode 100644 index 00000000..0fcd6a73 --- /dev/null +++ b/Tutorials/mwc/mwc_metadata.yaml @@ -0,0 +1,24 @@ +id: "mwc" +name: "mwc" +description: "Monod-Wyman-Changeux model" +tags: ["validation", "mwc", "setoption", "h", "ox", "b"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: true + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/mwc.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/nfkb/metadata.yaml b/Tutorials/nfkb/metadata.yaml index a20ed85a..bb1e8176 100644 --- a/Tutorials/nfkb/metadata.yaml +++ b/Tutorials/nfkb/metadata.yaml @@ -4,6 +4,7 @@ description: "NF-kB signaling pathway" tags: ["validation", "nfkb", "tnfr", "ikkk", "tnf", "ikk", "ikba", "a20", "competitor"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/nfkb/nfkb_metadata.yaml b/Tutorials/nfkb/nfkb_metadata.yaml new file mode 100644 index 00000000..cdb4e3ee --- /dev/null +++ b/Tutorials/nfkb/nfkb_metadata.yaml @@ -0,0 +1,24 @@ +id: "nfkb" +name: "nfkb" +description: "NF-kB signaling pathway" +tags: ["validation", "nfkb", "tnfr", "ikkk", "tnf", "ikk", "ikba", "a20", "competitor"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/nfkb.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/nfkbillustratingprotocols/metadata.yaml b/Tutorials/nfkbillustratingprotocols/metadata.yaml index c9d42b3a..b1b6408b 100644 --- a/Tutorials/nfkbillustratingprotocols/metadata.yaml +++ b/Tutorials/nfkbillustratingprotocols/metadata.yaml @@ -4,6 +4,7 @@ description: "NF-kB signaling pathway" tags: ["validation", "nfkb", "illustrating", "protocols", "tnfr", "ikkk", "tnf", "ikk", "ikba", "a20", "competitor"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols_metadata.yaml b/Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols_metadata.yaml new file mode 100644 index 00000000..81f7bb99 --- /dev/null +++ b/Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols_metadata.yaml @@ -0,0 +1,24 @@ +id: "nfkb_illustrating_protocols" +name: "nfkb_illustrating_protocols" +description: "NF-kB signaling pathway" +tags: ["validation", "nfkb", "illustrating", "protocols", "tnfr", "ikkk", "tnf", "ikk", "ikba", "a20", "competitor"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/nfkb_illustrating_protocols.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Tutorials/polymerfixed/metadata.yaml b/Tutorials/polymerfixed/metadata.yaml index 100a7c63..617aecc5 100644 --- a/Tutorials/polymerfixed/metadata.yaml +++ b/Tutorials/polymerfixed/metadata.yaml @@ -4,6 +4,7 @@ description: "Runtime-only BNGL model migrated from public/models: polymer_fixed tags: ["polymer", "fixed"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/polymerfixed/polymer_fixed_metadata.yaml b/Tutorials/polymerfixed/polymer_fixed_metadata.yaml new file mode 100644 index 00000000..1dd5e347 --- /dev/null +++ b/Tutorials/polymerfixed/polymer_fixed_metadata.yaml @@ -0,0 +1,24 @@ +id: "polymer_fixed" +name: "polymer_fixed" +description: "Runtime-only BNGL model migrated from public/models: polymer_fixed" +tags: ["polymer", "fixed"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: true + nfsim_compatible: true +source: + origin: "contributed" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "public/models/polymer_fixed.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Tutorials/recdim/metadata.yaml b/Tutorials/recdim/metadata.yaml index 770914e6..ea13889b 100644 --- a/Tutorials/recdim/metadata.yaml +++ b/Tutorials/recdim/metadata.yaml @@ -4,6 +4,7 @@ description: "Ligand-receptor binding" tags: ["validation", "rec", "dim", "lig", "writemdl", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/recdim/rec_dim_metadata.yaml b/Tutorials/recdim/rec_dim_metadata.yaml new file mode 100644 index 00000000..90652dcb --- /dev/null +++ b/Tutorials/recdim/rec_dim_metadata.yaml @@ -0,0 +1,24 @@ +id: "rec_dim" +name: "rec_dim" +description: "Ligand-receptor binding" +tags: ["validation", "rec", "dim", "lig", "writemdl", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/rec_dim.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Tutorials/recdimcomp/metadata.yaml b/Tutorials/recdimcomp/metadata.yaml index 886ff55d..55c1def7 100644 --- a/Tutorials/recdimcomp/metadata.yaml +++ b/Tutorials/recdimcomp/metadata.yaml @@ -4,6 +4,7 @@ description: "name dimension volume contained_by" tags: ["validation", "rec", "dim", "comp", "kp1", "kp2", "lig", "writemdl", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/recdimcomp/rec_dim_comp_metadata.yaml b/Tutorials/recdimcomp/rec_dim_comp_metadata.yaml new file mode 100644 index 00000000..5b9ac405 --- /dev/null +++ b/Tutorials/recdimcomp/rec_dim_comp_metadata.yaml @@ -0,0 +1,24 @@ +id: "rec_dim_comp" +name: "rec_dim_comp" +description: "name dimension volume contained_by" +tags: ["validation", "rec", "dim", "comp", "kp1", "kp2", "lig", "writemdl", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/rec_dim_comp.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Tutorials/simplenfsimtest/metadata.yaml b/Tutorials/simplenfsimtest/metadata.yaml index 9dab484d..fee0f5dd 100644 --- a/Tutorials/simplenfsimtest/metadata.yaml +++ b/Tutorials/simplenfsimtest/metadata.yaml @@ -4,6 +4,7 @@ description: "Runtime-only BNGL model migrated from public/models: simple_nfsim_ tags: ["simple", "nfsim", "test"] category: "other" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["nf"] uses_compartments: true diff --git a/Tutorials/simplenfsimtest/simple_nfsim_test_metadata.yaml b/Tutorials/simplenfsimtest/simple_nfsim_test_metadata.yaml new file mode 100644 index 00000000..efcdd7d3 --- /dev/null +++ b/Tutorials/simplenfsimtest/simple_nfsim_test_metadata.yaml @@ -0,0 +1,24 @@ +id: "simple_nfsim_test" +name: "simple_nfsim_test" +description: "Runtime-only BNGL model migrated from public/models: simple_nfsim_test" +tags: ["simple", "nfsim", "test"] +category: "other" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["nf"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: true +source: + origin: "contributed" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "public/models/simple_nfsim_test.bngl" +playground: + visible: false + gallery_category: "other" + featured: false + difficulty: "advanced" diff --git a/Tutorials/simplesbmlimport/metadata.yaml b/Tutorials/simplesbmlimport/metadata.yaml index 962e4340..496b48a8 100644 --- a/Tutorials/simplesbmlimport/metadata.yaml +++ b/Tutorials/simplesbmlimport/metadata.yaml @@ -4,6 +4,7 @@ description: "SBML import test" tags: ["validation", "simple", "sbml", "import", "readfile", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/simplesbmlimport/simple_sbml_import_metadata.yaml b/Tutorials/simplesbmlimport/simple_sbml_import_metadata.yaml new file mode 100644 index 00000000..98f96084 --- /dev/null +++ b/Tutorials/simplesbmlimport/simple_sbml_import_metadata.yaml @@ -0,0 +1,24 @@ +id: "simple_sbml_import" +name: "simple_sbml_import" +description: "SBML import test" +tags: ["validation", "simple", "sbml", "import", "readfile", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/simple_sbml_import.bngl" +playground: + visible: false + gallery_category: "validation" + featured: false + difficulty: "advanced" diff --git a/Tutorials/simplesystem/metadata.yaml b/Tutorials/simplesystem/metadata.yaml index 2e3cd412..9778df06 100644 --- a/Tutorials/simplesystem/metadata.yaml +++ b/Tutorials/simplesystem/metadata.yaml @@ -4,6 +4,7 @@ description: "Simple binding system" tags: ["validation", "simple", "system", "x", "y"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/simplesystem/simple_system_metadata.yaml b/Tutorials/simplesystem/simple_system_metadata.yaml new file mode 100644 index 00000000..95b532bd --- /dev/null +++ b/Tutorials/simplesystem/simple_system_metadata.yaml @@ -0,0 +1,24 @@ +id: "simple_system" +name: "simple_system" +description: "Simple binding system" +tags: ["validation", "simple", "system", "x", "y"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/simple_system.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testANGsynthesissimple/metadata.yaml b/Tutorials/testANGsynthesissimple/metadata.yaml index 6b35b5de..b704ee7a 100644 --- a/Tutorials/testANGsynthesissimple/metadata.yaml +++ b/Tutorials/testANGsynthesissimple/metadata.yaml @@ -4,6 +4,7 @@ description: "Synthesis network test" tags: ["validation", "test", "ang", "synthesis", "simple", "a", "b", "c", "source", "source2", "generate_network"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple_metadata.yaml b/Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple_metadata.yaml new file mode 100644 index 00000000..da3a5bf3 --- /dev/null +++ b/Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_ANG_synthesis_simple" +name: "test_ANG_synthesis_simple" +description: "Synthesis network test" +tags: ["validation", "test", "ang", "synthesis", "simple", "a", "b", "c", "source", "source2", "generate_network"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_ANG_synthesis_simple.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testMM/metadata.yaml b/Tutorials/testMM/metadata.yaml index f3780771..fd8699e0 100644 --- a/Tutorials/testMM/metadata.yaml +++ b/Tutorials/testMM/metadata.yaml @@ -4,6 +4,7 @@ description: "Kinetic constants" tags: ["validation", "test", "mm", "e", "s", "p", "generate_network"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/testMM/test_MM_metadata.yaml b/Tutorials/testMM/test_MM_metadata.yaml new file mode 100644 index 00000000..ead2a6a1 --- /dev/null +++ b/Tutorials/testMM/test_MM_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_MM" +name: "test_MM" +description: "Kinetic constants" +tags: ["validation", "test", "mm", "e", "s", "p", "generate_network"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_MM.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testfixed/metadata.yaml b/Tutorials/testfixed/metadata.yaml index 21a8cf4e..b26761c6 100644 --- a/Tutorials/testfixed/metadata.yaml +++ b/Tutorials/testfixed/metadata.yaml @@ -4,6 +4,7 @@ description: "# actions ##" tags: ["validation", "test", "fixed", "a", "b", "generate_network", "simulate"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/testfixed/test_fixed_metadata.yaml b/Tutorials/testfixed/test_fixed_metadata.yaml new file mode 100644 index 00000000..8817ae3e --- /dev/null +++ b/Tutorials/testfixed/test_fixed_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_fixed" +name: "test_fixed" +description: "# actions ##" +tags: ["validation", "test", "fixed", "a", "b", "generate_network", "simulate"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_fixed.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testmratio/metadata.yaml b/Tutorials/testmratio/metadata.yaml index c6df3f00..a98824aa 100644 --- a/Tutorials/testmratio/metadata.yaml +++ b/Tutorials/testmratio/metadata.yaml @@ -4,6 +4,7 @@ description: "Reaction ratio test" tags: ["validation", "test", "mratio", "a", "b", "c_theory", "c_upper", "c_lower"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/testmratio/test_mratio_metadata.yaml b/Tutorials/testmratio/test_mratio_metadata.yaml new file mode 100644 index 00000000..ef55389c --- /dev/null +++ b/Tutorials/testmratio/test_mratio_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_mratio" +name: "test_mratio" +description: "Reaction ratio test" +tags: ["validation", "test", "mratio", "a", "b", "c_theory", "c_upper", "c_lower"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_mratio.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testnetworkgen/metadata.yaml b/Tutorials/testnetworkgen/metadata.yaml index 7c113221..8f2c351f 100644 --- a/Tutorials/testnetworkgen/metadata.yaml +++ b/Tutorials/testnetworkgen/metadata.yaml @@ -4,6 +4,7 @@ description: "fceri model with network generation" tags: ["validation", "test", "network", "gen", "lig", "lyn", "syk", "rec"] category: "validation" compatibility: + database_visible: true bng2_compatible: false simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/testnetworkgen/test_network_gen_metadata.yaml b/Tutorials/testnetworkgen/test_network_gen_metadata.yaml new file mode 100644 index 00000000..918d6ba9 --- /dev/null +++ b/Tutorials/testnetworkgen/test_network_gen_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_network_gen" +name: "test_network_gen" +description: "fceri model with network generation" +tags: ["validation", "test", "network", "gen", "lig", "lyn", "syk", "rec"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_network_gen.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testsat/metadata.yaml b/Tutorials/testsat/metadata.yaml index dfe97a4d..6c0615d4 100644 --- a/Tutorials/testsat/metadata.yaml +++ b/Tutorials/testsat/metadata.yaml @@ -4,6 +4,7 @@ description: "Kinetic constants" tags: ["validation", "test", "sat", "e", "s", "p", "generate_network"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/testsat/test_sat_metadata.yaml b/Tutorials/testsat/test_sat_metadata.yaml new file mode 100644 index 00000000..477c5f8f --- /dev/null +++ b/Tutorials/testsat/test_sat_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_sat" +name: "test_sat" +description: "Kinetic constants" +tags: ["validation", "test", "sat", "e", "s", "p", "generate_network"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_sat.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testsynthesiscBNGLsimple/metadata.yaml b/Tutorials/testsynthesiscBNGLsimple/metadata.yaml index c5b92ee1..dfb1f8d1 100644 --- a/Tutorials/testsynthesiscBNGLsimple/metadata.yaml +++ b/Tutorials/testsynthesiscBNGLsimple/metadata.yaml @@ -4,6 +4,7 @@ description: "Compartmental synthesis" tags: ["validation", "test", "synthesis", "cbngl", "simple", "a", "a2", "b", "c", "source", "source2"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple_metadata.yaml b/Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple_metadata.yaml new file mode 100644 index 00000000..1158801d --- /dev/null +++ b/Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_synthesis_cBNGL_simple" +name: "test_synthesis_cBNGL_simple" +description: "Compartmental synthesis" +tags: ["validation", "test", "synthesis", "cbngl", "simple", "a", "a2", "b", "c", "source", "source2"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_synthesis_cBNGL_simple.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testsynthesiscomplex/metadata.yaml b/Tutorials/testsynthesiscomplex/metadata.yaml index 6360ed18..c835a494 100644 --- a/Tutorials/testsynthesiscomplex/metadata.yaml +++ b/Tutorials/testsynthesiscomplex/metadata.yaml @@ -4,6 +4,7 @@ description: "Complex synthesis test" tags: ["validation", "test", "synthesis", "complex", "a", "b", "c", "receptor", "source", "source2"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/testsynthesiscomplex/test_synthesis_complex_metadata.yaml b/Tutorials/testsynthesiscomplex/test_synthesis_complex_metadata.yaml new file mode 100644 index 00000000..7b8ff397 --- /dev/null +++ b/Tutorials/testsynthesiscomplex/test_synthesis_complex_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_synthesis_complex" +name: "test_synthesis_complex" +description: "Complex synthesis test" +tags: ["validation", "test", "synthesis", "complex", "a", "b", "c", "receptor", "source", "source2"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_synthesis_complex.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml b/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml index eebdce3a..8a68b08a 100644 --- a/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml +++ b/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml @@ -4,6 +4,7 @@ description: "volume-surface" tags: ["validation", "test", "synthesis", "complex", "0", "cbngl", "volume_molecule1", "volume_molecule2", "surface_molecule1", "surface_molecule2", "volume_molecule3", "volume_molecule4", "volume_receptor", "surface_receptor"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL_metadata.yaml b/Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL_metadata.yaml new file mode 100644 index 00000000..2324bae1 --- /dev/null +++ b/Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_synthesis_complex_0_cBNGL" +name: "test_synthesis_complex_0_cBNGL" +description: "volume-surface" +tags: ["validation", "test", "synthesis", "complex", "0", "cbngl", "volume_molecule1", "volume_molecule2", "surface_molecule1", "surface_molecule2", "volume_molecule3", "volume_molecule4", "volume_receptor", "surface_receptor"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_synthesis_complex_0_cBNGL.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml b/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml index 6d0c5554..22d84ed9 100644 --- a/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml +++ b/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml @@ -4,6 +4,7 @@ description: "volume-surface" tags: ["validation", "test", "synthesis", "complex", "source", "cbngl", "volume_molecule1", "volume_molecule2", "surface_molecule1", "surface_molecule2", "volume_molecule3", "volume_molecule4", "volume_receptor", "surface_receptor"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL_metadata.yaml b/Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL_metadata.yaml new file mode 100644 index 00000000..33e761b9 --- /dev/null +++ b/Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_synthesis_complex_source_cBNGL" +name: "test_synthesis_complex_source_cBNGL" +description: "volume-surface" +tags: ["validation", "test", "synthesis", "complex", "source", "cbngl", "volume_molecule1", "volume_molecule2", "surface_molecule1", "surface_molecule2", "volume_molecule3", "volume_molecule4", "volume_receptor", "surface_receptor"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_synthesis_complex_source_cBNGL.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/testsynthesissimple/metadata.yaml b/Tutorials/testsynthesissimple/metadata.yaml index 75f920e6..71f75a00 100644 --- a/Tutorials/testsynthesissimple/metadata.yaml +++ b/Tutorials/testsynthesissimple/metadata.yaml @@ -4,6 +4,7 @@ description: "Simple synthesis test" tags: ["validation", "test", "synthesis", "simple", "a", "b", "c", "source", "source2", "generate_network"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/testsynthesissimple/test_synthesis_simple_metadata.yaml b/Tutorials/testsynthesissimple/test_synthesis_simple_metadata.yaml new file mode 100644 index 00000000..c84041e2 --- /dev/null +++ b/Tutorials/testsynthesissimple/test_synthesis_simple_metadata.yaml @@ -0,0 +1,24 @@ +id: "test_synthesis_simple" +name: "test_synthesis_simple" +description: "Simple synthesis test" +tags: ["validation", "test", "synthesis", "simple", "a", "b", "c", "source", "source2", "generate_network"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/test_synthesis_simple.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/tlmr/metadata.yaml b/Tutorials/tlmr/metadata.yaml index 469b93d0..d0aba5ff 100644 --- a/Tutorials/tlmr/metadata.yaml +++ b/Tutorials/tlmr/metadata.yaml @@ -4,6 +4,7 @@ description: "Trivalent ligand monovalent receptor" tags: ["validation", "tlmr", "l", "r", "generate_network", "simulate_ode"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/tlmr/tlmr_metadata.yaml b/Tutorials/tlmr/tlmr_metadata.yaml new file mode 100644 index 00000000..d03f3283 --- /dev/null +++ b/Tutorials/tlmr/tlmr_metadata.yaml @@ -0,0 +1,24 @@ +id: "tlmr" +name: "tlmr" +description: "Trivalent ligand monovalent receptor" +tags: ["validation", "tlmr", "l", "r", "generate_network", "simulate_ode"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/tlmr.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/toyjim/metadata.yaml b/Tutorials/toyjim/metadata.yaml index e9baaa4d..d0547353 100644 --- a/Tutorials/toyjim/metadata.yaml +++ b/Tutorials/toyjim/metadata.yaml @@ -4,6 +4,7 @@ description: "The model consists of a monovalent extracellular ligand," tags: ["validation", "toy", "jim", "l", "r", "a", "k", "null"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false diff --git a/Tutorials/toyjim/toy-jim_metadata.yaml b/Tutorials/toyjim/toy-jim_metadata.yaml new file mode 100644 index 00000000..f289057f --- /dev/null +++ b/Tutorials/toyjim/toy-jim_metadata.yaml @@ -0,0 +1,24 @@ +id: "toy-jim" +name: "toy-jim" +description: "The model consists of a monovalent extracellular ligand," +tags: ["validation", "toy", "jim", "l", "r", "a", "k", "null"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/toy-jim.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/Tutorials/univsynth/metadata.yaml b/Tutorials/univsynth/metadata.yaml index 8b87d740..7dd4def1 100644 --- a/Tutorials/univsynth/metadata.yaml +++ b/Tutorials/univsynth/metadata.yaml @@ -4,6 +4,7 @@ description: "example of universal synthesis" tags: ["validation", "univ", "synth", "a", "b", "c", "generate_network", "simulate_ode"] category: "validation" compatibility: + database_visible: true bng2_compatible: true simulation_methods: ["ode"] uses_compartments: true diff --git a/Tutorials/univsynth/univ_synth_metadata.yaml b/Tutorials/univsynth/univ_synth_metadata.yaml new file mode 100644 index 00000000..c3c8c9c4 --- /dev/null +++ b/Tutorials/univsynth/univ_synth_metadata.yaml @@ -0,0 +1,24 @@ +id: "univ_synth" +name: "univ_synth" +description: "example of universal synthesis" +tags: ["validation", "univ", "synth", "a", "b", "c", "generate_network", "simulate_ode"] +category: "validation" +compatibility: + database_visible: true + bngp_compatible: true + bng2_compatible: true + simulation_methods: ["ode"] + uses_compartments: true + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: "test-case" + original_format: "bngl" + original_repository: "bionetgen-web-simulator" + source_path: "published-models/validation/univ_synth.bngl" +playground: + visible: true + gallery_category: "validation" + featured: false + difficulty: "intermediate" diff --git a/data/ai_summaries.json b/data/ai_summaries.json new file mode 100644 index 00000000..a8fa1fa0 --- /dev/null +++ b/data/ai_summaries.json @@ -0,0 +1,689 @@ +[ + { + "model_id": "An_2009", + "title": "An 2009", + "bngl_path": "Published/An2009/An_2009.bngl", + "yaml_path": "Published/An2009/metadata.yaml", + "markdown_path": "data/summaries/An2009_aigenerated.md", + "summary": "Toll-like receptor 4 signaling from LPS recognition to NF-kB-driven inflammatory gene expression.", + "key_events": [ + "LPS is assembled with CD14 and MD2 before engaging TLR4, so receptor activation depends on coreceptor-mediated ligand presentation.", + "TLR4 complexes branch through TRAM/TRIF and MAL/MyD88 adaptor routes, allowing the same stimulus to feed multiple inflammatory signaling arms.", + "IKK-driven NF-kB activation is countered by A20 and IkB feedback, so the model can show both signal rise and signal shutoff." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Barua_2007", + "title": "Barua 2007", + "bngl_path": "Published/Barua2007/Barua_2007.bngl", + "yaml_path": "Published/Barua2007/metadata.yaml", + "markdown_path": "data/summaries/Barua2007_aigenerated.md", + "summary": "SHP2 regulation by phosphorylated receptor dimers and intracomplex SH2-domain engagement.", + "key_events": [ + "Phosphorylated receptor dimers recruit SHP2 through SH2-domain contacts, creating receptor-bound phosphatase complexes.", + "SHP2 can transition from a closed inhibited form toward an open form when receptor binding stabilizes active conformations.", + "Open SHP2 removes phosphate groups from receptor sites, creating a negative-feedback loop on the receptor scaffold itself." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Barua_2009", + "title": "Barua 2009", + "bngl_path": "Published/Barua2009/Barua_2009.bngl", + "yaml_path": "Published/Barua2009/metadata.yaml", + "markdown_path": "data/summaries/Barua2009_aigenerated.md", + "summary": "SH2B dimerization as a scaffold for JAK2 phosphorylation.", + "key_events": [ + "Phosphorylated JAK2 recruits SH2B, linking kinase activation to scaffold binding.", + "SH2B dimerization brings two JAK2 molecules into the same assembly, increasing opportunities for JAK2-to-JAK2 phosphorylation.", + "A partially activated JAK2-containing complex phosphorylates remaining inactive JAK2 more quickly, representing cooperative amplification." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Barua_2013", + "title": "Barua 2013", + "bngl_path": "Published/Barua2013/Barua_2013.bngl", + "yaml_path": "Published/Barua2013/metadata.yaml", + "markdown_path": "data/summaries/Barua2013_aigenerated.md", + "summary": "Beta-catenin control by the Axin/APC/GSK3/CK1 destruction complex.", + "key_events": [ + "Beta-catenin binds APC and Axin, placing it into the destruction-complex environment.", + "CK1 and GSK3 phosphorylate beta-catenin in sequence, converting it into a form that is removed more rapidly.", + "When beta-catenin is degraded, associated APC or Axin partners are released so the scaffold can participate in another cycle." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "BaruaBCR_2012", + "title": "Barua 2012", + "bngl_path": "Published/BaruaBCR2012/BaruaBCR_2012.bngl", + "yaml_path": "Published/BaruaBCR2012/metadata.yaml", + "markdown_path": "data/summaries/BaruaBCR2012_aigenerated.md", + "summary": "Early B-cell receptor signaling with Lyn, Fyn, Syk, Csk, PAG, CD22, and phosphatase feedback.", + "key_events": [ + "Antigen input strengthens B-cell receptor signaling by promoting receptor phosphorylation and receptor-proximal complex assembly.", + "Lyn and Fyn phosphorylate receptor ITAMs and themselves switch between activating and inhibitory phosphorylation states.", + "Syk recruitment and activation provide positive signaling, while Csk, PAG, CD22, SHP1, SHIP, Dok, and RasGAP restrain the response." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "BaruaFceRI_2012", + "title": "BaruaFceRI 2012", + "bngl_path": "Published/BaruaFceRI2012/BaruaFceRI_2012.bngl", + "yaml_path": "Published/BaruaFceRI2012/metadata.yaml", + "markdown_path": "data/summaries/BaruaFceRI2012_aigenerated.md", + "summary": "FcεRI signaling regulated by ligand crosslinking, Lyn/Syk activation, LAT signaling, and raft localization.", + "key_events": [ + "Ligand and hapten binding crosslink FcεRI, converting receptor occupancy into receptor clustering.", + "Lyn phosphorylates receptor chains, allowing Syk recruitment and activation at the membrane.", + "LAT phosphorylation and Grb2 recruitment transmit the receptor signal downstream, while raft localization changes the effective strength of phosphorylation and dephosphorylation." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Blinov_2006", + "title": "Blinov 2006", + "bngl_path": "Published/Blinov2006/Blinov_2006.bngl", + "yaml_path": "Published/Blinov2006/metadata.yaml", + "markdown_path": "data/summaries/Blinov2006_aigenerated.md", + "summary": "EGF receptor signaling through ligand binding, receptor aggregation, receptor phosphorylation, and Shc adaptor recruitment.", + "key_events": [ + "EGF binding creates ligand-bound EGFR complexes that can aggregate with other receptors.", + "Aggregated receptors phosphorylate one another on docking sites, creating binding platforms for adaptor proteins.", + "Shc recruitment, Shc phosphorylation, and Grb2/SOS assembly connect receptor phosphorylation to downstream signaling." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Blinov_egfr", + "title": "Blinov egfr", + "bngl_path": "Published/Blinovegfr/Blinov_egfr.bngl", + "yaml_path": "Published/Blinovegfr/metadata.yaml", + "markdown_path": "data/summaries/Blinovegfr_aigenerated.md", + "summary": "A compact EGFR example showing receptor-ligand binding and receptor complex formation.", + "key_events": [ + "Ligand binding shifts EGFR from free receptor toward ligand-associated receptor complexes.", + "Receptor interaction states are tracked as complexes rather than as a single active/inactive switch.", + "The model emphasizes the formation and loss of receptor-containing assemblies as the central EGFR behavior." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Blinov_ran", + "title": "Blinov ran", + "bngl_path": "Published/Blinovran/Blinov_ran.bngl", + "yaml_path": "Published/Blinovran/metadata.yaml", + "markdown_path": "data/summaries/Blinovran_aigenerated.md", + "summary": "A compact Ran-system example focused on nucleotide-state and compartment-related molecular cycling.", + "key_events": [ + "Ran-related species move through state changes that represent molecular cycling.", + "Binding partners recognize particular Ran states, making interaction dependent on the current molecular form.", + "Compartment-aware transitions shape where each Ran-related state accumulates." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Chattaraj_2021", + "title": "Chattaraj 2021", + "bngl_path": "Published/Chattaraj2021/Chattaraj_2021.bngl", + "yaml_path": "Published/Chattaraj2021/metadata.yaml", + "markdown_path": "data/summaries/Chattaraj2021_aigenerated.md", + "summary": "Multivalent Nephrin-Nck-NWASP clustering as a model of heterotypic biomolecular condensate formation.", + "key_events": [ + "Nephrin recruits Nck through repeated binding modules, creating multivalent receptor-proximal assemblies.", + "Nck links Nephrin to NWASP, and NWASP adds more interaction sites that enlarge clusters.", + "Binding affinity and the number of available sites determine whether molecules remain dispersed or form larger condensate-like clusters." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Cheemalavagu_JAK_STAT", + "title": "Cheemalavagu 2024", + "bngl_path": "Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT.bngl", + "yaml_path": "Published/CheemalavaguJAKSTAT/metadata.yaml", + "markdown_path": "data/summaries/CheemalavaguJAKSTAT_aigenerated.md", + "summary": "IL-6 and IL-10 JAK/STAT signaling with STAT activation and SOCS-mediated inhibition.", + "key_events": [ + "IL-6 and IL-10 first assemble receptor complexes that can recruit JAK kinases.", + "JAK-associated receptor complexes phosphorylate STAT1 or STAT3, producing the activated transcription-factor signal.", + "SOCS proteins bind pathway components and inhibit further signaling, creating cytokine-induced negative regulation." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "ChylekFceRI_2014", + "title": "Chylek 2014 (FceRI)", + "bngl_path": "Published/ChylekFceRI2014/ChylekFceRI_2014.bngl", + "yaml_path": "Published/ChylekFceRI2014/metadata.yaml", + "markdown_path": "data/summaries/ChylekFceRI2014_aigenerated.md", + "summary": "Detailed early FcεRI signaling from antigen crosslinking to Lyn, Fyn, Syk, PAG, Csk, and phosphatase regulation.", + "key_events": [ + "DNP-BSA crosslinks IgE-FcεRI through exposed hapten sites, initiating receptor aggregation.", + "Lyn and Fyn phosphorylate receptor ITAMs and regulate their own activity through activating and inhibitory phosphorylation.", + "Syk recruitment amplifies signaling, while PAG/Csk, SHP1, and SHIP1 create counteracting inhibitory control." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "ChylekTCR_2014", + "title": "Chylek 2014 (TCR)", + "bngl_path": "Published/ChylekTCR2014/ChylekTCR_2014.bngl", + "yaml_path": "Published/ChylekTCR2014/metadata.yaml", + "markdown_path": "data/summaries/ChylekTCR2014_aigenerated.md", + "summary": "Early T-cell receptor phosphorylation-site dynamics and adaptor assembly.", + "key_events": [ + "LCK phosphorylates TCR/CD3 sites, creating docking sites for ZAP70.", + "Activated ZAP70 phosphorylates adaptor proteins such as LAT and LCP2, enabling larger signaling assemblies.", + "Phosphatases and inhibitory kinases oppose activation, so the model can show how site-specific phosphorylation patterns are shaped by competing enzymes." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Dembo_1978", + "title": "Dembo 1978", + "bngl_path": "Published/Dembo1978/blbr_dembo1978.bngl", + "yaml_path": "Published/Dembo1978/metadata.yaml", + "markdown_path": "data/summaries/Dembo1978_aigenerated.md", + "summary": "Symmetric bivalent hapten-receptor crosslinking without ring formation.", + "key_events": [ + "A free bivalent hapten arm binds one receptor site, creating a singly bound intermediate.", + "The second hapten arm can bind a receptor on another complex, forming a linear crosslink between receptors.", + "At very high ligand abundance, receptors become occupied without being efficiently bridged, producing the prozone drop in crosslinking." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "lac_operon_dreisigmeyer2008", + "title": "Dreisigmeyer 2008", + "bngl_path": "Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl", + "yaml_path": "Published/Dreisigmeyer2008/metadata.yaml", + "markdown_path": "data/summaries/Dreisigmeyer2008_aigenerated.md", + "summary": "Lactose induction of the E. coli lac operon through transport, metabolism, allolactose, and beta-galactosidase expression.", + "key_events": [ + "Lactose import increases intracellular lactose, with transport asymmetry affecting how strongly extracellular lactose drives the system.", + "Lactose metabolism creates allolactose, which induces beta-galactosidase expression through cooperative regulation.", + "Beta-galactosidase both rises as an output and consumes lactose/allolactose, creating a coupled induction-and-metabolism loop." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Dushek_2011", + "title": "Dushek 2011", + "bngl_path": "Published/Dushek2011/Dushek_2011.bngl", + "yaml_path": "Published/Dushek2011/metadata.yaml", + "markdown_path": "data/summaries/Dushek2011_aigenerated.md", + "summary": "Encounter-complex control of a kinase/phosphatase modifying a substrate with many sites.", + "key_events": [ + "Kinase or phosphatase first enters an encounter complex with the multisite substrate before productive catalysis occurs.", + "A catalytic event changes the substrate modification count and temporarily inactivates the enzyme.", + "Repeated encounter, modification, release, and reactivation events shape the distribution of substrate molecules across phosphorylation levels." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Dushek_2014", + "title": "Dushek 2014", + "bngl_path": "Published/Dushek2014/Dushek_2014.bngl", + "yaml_path": "Published/Dushek2014/metadata.yaml", + "markdown_path": "data/summaries/Dushek2014_aigenerated.md", + "summary": "Kinase/phosphatase control of a biosensor with intra- and intermolecular signaling states.", + "key_events": [ + "Kinase activity pushes the biosensor toward a modified state, while phosphatase activity reverses that state.", + "The modified biosensor can adopt distinct intramolecular or intermolecular configurations, creating multiple sensor outputs.", + "Sequestration limits available signaling protein and changes how much biosensor can enter signaling-competent states." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Erdem_2021", + "title": "Erdem 2021", + "bngl_path": "Published/Erdem2021/Erdem_2021.bngl", + "yaml_path": "Published/Erdem2021/metadata.yaml", + "markdown_path": "data/summaries/Erdem2021_aigenerated.md", + "summary": "Early insulin and IGF1 receptor signaling in MCF7 cells fit to RPPA-style signaling data.", + "key_events": [ + "Insulin and IGF1 bind their matching receptors, producing receptor phosphorylation rather than a generic growth-factor signal.", + "Phosphorylated receptors drive downstream signaling outputs through adaptor-like steps calibrated to MCF7 signaling measurements.", + "Feedback, resensitization, and receptor recycling allow signaling to decline and receptor responsiveness to recover." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "genetic_switch_gardner2000", + "title": "Gardner 2000", + "bngl_path": "Published/Gardner2000/genetic_switch_gardner2000.bngl", + "yaml_path": "Published/Gardner2000/metadata.yaml", + "markdown_path": "data/summaries/Gardner2000_aigenerated.md", + "summary": "A bistable genetic toggle switch made from two mutually repressing gene products.", + "key_events": [ + "Each gene product represses production of the other, creating mutual antagonism.", + "Cooperative repression makes intermediate states unstable, so the system tends to commit to one dominant gene-expression state.", + "Protein degradation prevents unlimited accumulation and helps set the time scale for switching or maintenance." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "blbr_heterogeneity_goldstein1980", + "title": "Goldstein 1980", + "bngl_path": "Published/Goldstein1980/blbr_heterogeneity_goldstein1980.bngl", + "yaml_path": "Published/Goldstein1980/metadata.yaml", + "markdown_path": "data/summaries/Goldstein1980_aigenerated.md", + "summary": "Bivalent hapten crosslinking of a heterogeneous antibody-receptor population.", + "key_events": [ + "Bivalent hapten binds either high-affinity or low-affinity receptor populations.", + "A receptor-bound hapten can bridge to another receptor complex, producing polymers across a mixed receptor population.", + "Different receptor affinities distort the crosslinking dose-response compared with a homogeneous receptor system." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "antigen_pulses_harmon2017", + "title": "Harmon 2017", + "bngl_path": "Published/Harmon2017/antigen_pulses_harmon2017.bngl", + "yaml_path": "Published/Harmon2017/metadata.yaml", + "markdown_path": "data/summaries/Harmon2017_aigenerated.md", + "summary": "History-dependent FcεRI mast-cell responses to pulsed antigen stimulation.", + "key_events": [ + "Antigen pulses rapidly create a Syk-positive FcεRI activation signal.", + "A slower Ship1/X negative branch changes PIP3 signaling and stores information about recent stimulation.", + "Short pulse intervals can yield desensitization, while longer intervals can permit priming and stronger degranulation." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Hat_2016", + "title": "Hat 2016", + "bngl_path": "Published/Hat2016/Hat_2016.bngl", + "yaml_path": "Published/Hat2016/metadata.yaml", + "markdown_path": "data/summaries/Hat2016_aigenerated.md", + "summary": "p53 feedback, bifurcation, and cell-fate decision behavior after DNA damage.", + "key_events": [ + "DNA damage activates upstream signaling that stabilizes and elevates p53.", + "p53 induces regulators such as Mdm2 and other target genes, creating both negative feedback and fate-related outputs.", + "Feedback and threshold effects allow the same pathway to support low-p53, oscillatory, or high-p53 response regimes." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "steric_effects_hlavacek1999", + "title": "Hlavacek 1999", + "bngl_path": "Published/Hlavacek1999/steric_effects_hlavacek1999.bngl", + "yaml_path": "Published/Hlavacek1999/metadata.yaml", + "markdown_path": "data/summaries/Hlavacek1999_aigenerated.md", + "summary": "Steric hindrance in multivalent ligand binding to cell-surface receptors.", + "key_events": [ + "A multivalent ligand gains receptors one at a time as receptor sites bind to available ligand surface.", + "Each bound receptor covers physical space, reducing the chance that another nearby receptor can attach.", + "The model therefore predicts less high-occupancy binding than would be expected from independent identical sites." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "kinetic_proofreading_hlavacek2001", + "title": "Hlavacek 2001", + "bngl_path": "Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl", + "yaml_path": "Published/Hlavacek2001/metadata.yaml", + "markdown_path": "data/summaries/Hlavacek2001_aigenerated.md", + "summary": "Kinetic proofreading by receptor dimers that must survive sequential modification steps.", + "key_events": [ + "A bivalent ligand forms a receptor dimer that can begin a sequence of signaling modifications.", + "The dimer must remain intact through multiple steps to reach the terminal signaling state.", + "If either receptor bond breaks too early, accumulated progress is reset, allowing long-lived ligand complexes to signal disproportionately well." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Hlavacek2018Egg_egg", + "title": "Hlavacek2018Egg", + "bngl_path": "Published/Hlavacek2018Egg/egg.bngl", + "yaml_path": "Published/Hlavacek2018Egg/metadata.yaml", + "markdown_path": "data/summaries/Hlavacek2018Egg_aigenerated.md", + "summary": "A small parameterized example model used to demonstrate fitted or transformed rate expressions.", + "key_events": [ + "Abstract species change according to fitted or transformed numerical relationships.", + "The model demonstrates how a compact rule-based system can encode a sequence of parameter-dependent changes.", + "Because the species are not biologically named, the useful behavior is the example dynamics rather than a specific pathway claim." + ], + "summary_type": "simple", + "audience": "biologists" + }, + { + "model_id": "Hlavacek2018Egg_egg", + "title": "Hlavacek2018Egg", + "bngl_path": "Published/Hlavacek2018Egg/egg.bngl", + "yaml_path": "Published/Hlavacek2018Egg/metadata.yaml", + "markdown_path": "data/summaries_coders/Hlavacek2018Egg_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "Coder-facing explanation of a compact ODE model that advances an abstract species t and prints two fitted Fourier-like functions over one period.", + "molecule_type_count": 1, + "reaction_rule_count": 1, + "observable_count": 1, + "key_constructs": [ + "abstract zero-site species", + "printed functions", + "constant source rule", + "ODE action" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Barua_2009", + "title": "Barua 2009", + "bngl_path": "Published/Barua2009/Barua_2009.bngl", + "yaml_path": "Published/Barua2009/metadata.yaml", + "markdown_path": "data/summaries_coders/Barua2009_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "Coder-facing explanation of SH2B dimerization and SH2-mediated recruitment that scaffold two JAK2 molecules for slow then fast JAK2 phosphorylation.", + "molecule_type_count": 2, + "reaction_rule_count": 4, + "observable_count": 6, + "key_constructs": [ + "SH2-domain binding", + "SH2B dimerization", + "scaffolded JAK2 phosphorylation", + "ODE network generation" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Gardner_2000", + "title": "Gardner 2000", + "bngl_path": "Published/Gardner2000/genetic_switch_gardner2000.bngl", + "yaml_path": "Published/Gardner2000/metadata.yaml", + "markdown_path": "data/summaries_coders/Gardner2000_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "Coder-facing explanation of a dimensionless genetic toggle switch implemented with two zero-site repressors, Hill-repressed synthesis functions, degradation rules, and ODE/scan actions.", + "molecule_type_count": 2, + "reaction_rule_count": 4, + "observable_count": 2, + "key_constructs": [ + "Hill functions", + "mutual repression", + "dimensionless ODE model", + "parameter scan" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Dembo_1978", + "title": "Dembo 1978", + "bngl_path": "Published/Dembo1978/blbr_dembo1978.bngl", + "yaml_path": "Published/Dembo1978/metadata.yaml", + "markdown_path": "data/summaries_coders/Dembo1978_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "Coder-facing explanation of bivalent hapten and bivalent receptor cross-linking with capture, inter-complex chain extension, and bond dissociation under NFsim.", + "molecule_type_count": 2, + "reaction_rule_count": 3, + "observable_count": 5, + "key_constructs": [ + "repeated symmetric sites", + "bivalent cross-linking", + "NFsim same-complex binding block", + "unbounded chains" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Blinov_ran", + "title": "Blinov ran", + "bngl_path": "Published/Blinovran/Blinov_ran.bngl", + "yaml_path": "Published/Blinovran/metadata.yaml", + "markdown_path": "data/summaries_coders/Blinovran_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "Coder-facing explanation of a compartmental Ran-cargo-RCC1 transport model with nuclear export, cargo phosphorylation, Ran-cargo binding, and RCC1 binding rules.", + "molecule_type_count": 3, + "reaction_rule_count": 7, + "observable_count": 7, + "key_constructs": [ + "compartments", + "anchors", + "transport rule", + "cytoplasmic phosphorylation", + "NFsim action" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Dolan_2015", + "title": "Dolan 2015", + "bngl_path": "Published/Dolan2015/Dolan_2015.bngl", + "yaml_path": "Published/Dolan2015/metadata.yaml", + "markdown_path": "data/summaries_coders/Dolan2015_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A combined DNA-damage, p53/MDM2/p21 stress-response, oxidative damage, non-homologous end joining (NHEJ), PARP/Ligase repair, ATM/H2AX focus, and senescence-switching model.", + "molecule_type_count": 74, + "reaction_rule_count": 2339, + "observable_count": 176, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "functions", + "large explicit rule families", + "observables" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Zhang_2023", + "title": "Zhang 2023", + "bngl_path": "Published/Zhang2023/Zhang_2023.bngl", + "yaml_path": "Published/Zhang2023/metadata.yaml", + "markdown_path": "data/summaries_coders/Zhang2023_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A large VEGF signaling model centered on VEGF165a, VEGFR2, VEGFR1, NRP1, CD47/TSP1, PI3K/AKT, PLCγ/IP3/DAG/calcium, eNOS, PKC/CIB1/SphK/S1P, Ras/Raf/MEK/ERK, and Axl/Src cross-talk.", + "molecule_type_count": 38, + "reaction_rule_count": 232, + "observable_count": 129, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "large explicit rule families", + "observables" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Dreisigmeyer_2008", + "title": "Dreisigmeyer 2008", + "bngl_path": "Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl", + "yaml_path": "Published/Dreisigmeyer2008/metadata.yaml", + "markdown_path": "data/summaries_coders/Dreisigmeyer2008_lac_operon_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A concentration-based lac operon ODE model with three explicit dynamic species: intracellular lactose, allolactose, and beta-galactosidase.", + "molecule_type_count": 3, + "reaction_rule_count": 8, + "observable_count": 3, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "small published model", + "functions" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Hlavacek_2001", + "title": "Hlavacek 2001", + "bngl_path": "Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl", + "yaml_path": "Published/Hlavacek2001/metadata.yaml", + "markdown_path": "data/summaries_coders/Hlavacek2001_kinetic_proofreading_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A compact kinetic-proofreading receptor signaling model: bivalent ligand captures receptors, forms receptor dimers, advances through five ligand-centered modification states, and resets modification to zero when ligand-receptor bonds dissociate.", + "molecule_type_count": 2, + "reaction_rule_count": 13, + "observable_count": 10, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "small published model", + "functions" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "McMillan_2021", + "title": "McMillan 2021", + "bngl_path": "Published/McMillan2021/McMillan_2021.bngl", + "yaml_path": "Published/McMillan2021/metadata.yaml", + "markdown_path": "data/summaries_coders/McMillan2021_TNF_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A small TNF-receptor binding model in which trivalent TNF has three binding sites and recruits up to three receptor molecules through the receptor a site.", + "molecule_type_count": 2, + "reaction_rule_count": 12, + "observable_count": 5, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "small published model", + "direct rule rates" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Jaruszewicz-Blonska_2023", + "title": "Jaruszewicz 2023", + "bngl_path": "Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023.bngl", + "yaml_path": "Published/JaruszewiczBlonska2023/metadata.yaml", + "markdown_path": "data/summaries_coders/JaruszewiczBlonska2023_NFkB_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A canonical NF-kappaB signaling ODE model with active/neutral IKK, IkBa mRNA/protein, A20, and nuclear NFkB.", + "molecule_type_count": 5, + "reaction_rule_count": 14, + "observable_count": 6, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "small published model", + "functions" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Jung_2017", + "title": "Jung 2017", + "bngl_path": "Published/Jung2017/Jung_2017.bngl", + "yaml_path": "Published/Jung2017/metadata.yaml", + "markdown_path": "data/summaries_coders/Jung2017_M1R_signaling_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A compartmental M1 muscarinic receptor signaling model in which extracellular oxotremorine binds plasma-membrane M1R, receptor phosphorylation controls arrestin recruitment, arrestin scaffolds MEK/ERK/PP2A, and ERK phosphorylation is tracked through pERK and probe readouts.", + "molecule_type_count": 13, + "reaction_rule_count": 19, + "observable_count": 20, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "small published model", + "functions" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Kocieniewski_2012", + "title": "Kocieniewski 2012", + "bngl_path": "Published/Kocieniewski2012/Kocieniewski_2012.bngl", + "yaml_path": "Published/Kocieniewski2012/metadata.yaml", + "markdown_path": "data/summaries_coders/Kocieniewski2012_MAPK_scaffold_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A scaffolded MAPK cascade model where MAP3K activation, scaffold binding, scaffold-localized phosphorylation of MAP2K and MAPK, and global dephosphorylation determine how signaling complexes form on Scaff.", + "molecule_type_count": 4, + "reaction_rule_count": 20, + "observable_count": 2, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "small published model", + "direct rule rates" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Chattaraj_2021", + "title": "Chattaraj 2021", + "bngl_path": "Published/Chattaraj2021/Chattaraj_2021.bngl", + "yaml_path": "Published/Chattaraj2021/metadata.yaml", + "markdown_path": "data/summaries_coders/Chattaraj2021_condensate_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A multivalent binding/condensation model for Nephrin, Nck, and NWASP: three Nephrin phosphotyrosines bind Nck SH2, while three Nck SH3 sites bind six NWASP proline-rich motifs to generate heterotypic clusters.", + "molecule_type_count": 3, + "reaction_rule_count": 21, + "observable_count": 11, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "small published model", + "direct rule rates" + ], + "rule_inventory_in_markdown": true + }, + { + "model_id": "Ligon_2014", + "title": "Ligon 2014", + "bngl_path": "Published/Ligon2014/Ligon_2014.bngl", + "yaml_path": "Published/Ligon2014/metadata.yaml", + "markdown_path": "data/summaries_coders/Ligon2014_lipoplex_delivery_coder.md", + "summary_type": "advanced", + "audience": "coders", + "summary": "A lipoplex delivery model that tracks external lipoplex attachment to pits, conversion of pits to endosomes, lysis/unpacking into internal lipoplex cargo, mRNA production, GFP translation, washout, degradation, and a timer species for wash control.", + "molecule_type_count": 8, + "reaction_rule_count": 33, + "observable_count": 7, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": [ + "complete rule inventory", + "small published model", + "functions" + ], + "rule_inventory_in_markdown": true + } +] diff --git a/data/renaming_audit.md b/data/renaming_audit.md new file mode 100644 index 00000000..bee05542 --- /dev/null +++ b/data/renaming_audit.md @@ -0,0 +1,494 @@ +# Metadata Renaming Audit + +This audit records the recursive BNGL-based metadata copy pass over `Published/`, `Examples/`, and `Tutorials/`. +For an unambiguous directory containing `metadata.yaml` and exactly one same-directory `.bngl` file, the metadata was copied to `_metadata.yaml`. Metadata contents were not modified. + +## Summary + +- Created **313** BNGL-named metadata copies. +- Left **112** already-correct BNGL-named metadata copies unchanged. +- Skipped **20** directories with multiple same-directory BNGL files. +- Skipped **0** directories with `metadata.yaml` but no same-directory BNGL file. +- Removed **11** ID/directory-named copies from the earlier pass because their directories have ambiguous multi-BNGL pairings. + +## Created copies + +| Directory | BNGL file | Created metadata copy | +|---|---|---| +| `Published/CheemalavaguJAKSTAT` | `Cheemalavagu_JAK_STAT.bngl` | `Cheemalavagu_JAK_STAT_metadata.yaml` | +| `Published/Dembo1978` | `blbr_dembo1978.bngl` | `blbr_dembo1978_metadata.yaml` | +| `Published/Dreisigmeyer2008` | `lac_operon_dreisigmeyer2008.bngl` | `lac_operon_dreisigmeyer2008_metadata.yaml` | +| `Published/Gardner2000` | `genetic_switch_gardner2000.bngl` | `genetic_switch_gardner2000_metadata.yaml` | +| `Published/Goldstein1980` | `blbr_heterogeneity_goldstein1980.bngl` | `blbr_heterogeneity_goldstein1980_metadata.yaml` | +| `Published/Harmon2017` | `antigen_pulses_harmon2017.bngl` | `antigen_pulses_harmon2017_metadata.yaml` | +| `Published/Hlavacek1999` | `steric_effects_hlavacek1999.bngl` | `steric_effects_hlavacek1999_metadata.yaml` | +| `Published/Hlavacek2001` | `kinetic_proofreading_hlavacek2001.bngl` | `kinetic_proofreading_hlavacek2001_metadata.yaml` | +| `Published/Hlavacek2018Egg` | `egg.bngl` | `egg_metadata.yaml` | +| `Published/Macken1982` | `tlbr_solution_macken1982.bngl` | `tlbr_solution_macken1982_metadata.yaml` | +| `Published/Mallela2022/Alabama` | `Alabama.bngl` | `Alabama_metadata.yaml` | +| `Published/Mitra2019/02-egfr/bnf1/InputFiles` | `egfr.bngl` | `egfr_metadata.yaml` | +| `Published/Mitra2019/03-fcerig` | `fceri_gamma2.bngl` | `fceri_gamma2_metadata.yaml` | +| `Published/Mitra2019/04-egfrnf` | `egfr_nf.bngl` | `egfr_nf_metadata.yaml` | +| `Published/Mitra2019/06-degranulation` | `model_tofit.bngl` | `model_tofit_metadata.yaml` | +| `Published/Mitra2019/07-egg` | `egg.bngl` | `egg_metadata.yaml` | +| `Published/Mitra2019/10-egfr` | `egfr_ode.bngl` | `egfr_ode_metadata.yaml` | +| `Published/Mitra2019/11-TLBR` | `tlbr.bngl` | `tlbr_metadata.yaml` | +| `Published/Mitra2019/12-TCR` | `tcr.bngl` | `tcr_metadata.yaml` | +| `Published/Mitra2019/14-receptor-nf` | `receptor_nf.bngl` | `receptor_nf_metadata.yaml` | +| `Published/Mitra2019/15-igf1r` | `IGF1R_fit_all.bngl` | `IGF1R_fit_all_metadata.yaml` | +| `Published/Mitra2019/19-raf-constraint` | `RAFi.bngl` | `RAFi_metadata.yaml` | +| `Published/Mitra2019/20-raf-constraint4` | `RAFi.bngl` | `RAFi_metadata.yaml` | +| `Published/Mitra2019/24-jnk` | `JNKmodel_180724_bnf.bngl` | `JNKmodel_180724_bnf_metadata.yaml` | +| `Published/Mitra2019/26-tcr-sens` | `tcr_sens_tofit.bngl` | `tcr_sens_tofit_metadata.yaml` | +| `Published/Mitra2019/31-elephant` | `elephant.bngl` | `elephant_metadata.yaml` | +| `Published/Mitra2019Likelihood` | `model_ground.bngl` | `model_ground_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem16` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem16_3cat` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem32` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem32_3cat` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem4` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem4_3cat` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem64` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem64_3cat` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem8` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem8_3cat` | `model0_tofit.bngl` | `model0_tofit_metadata.yaml` | +| `Published/Mitra2019Likelihood/problem_quant` | `model_tofit.bngl` | `model_tofit_metadata.yaml` | +| `Published/Ordyan2020/CaMKIIholo` | `CaMKII_holo.bngl` | `CaMKII_holo_metadata.yaml` | +| `Published/Ordyan2020/extraCaMKIIHolo` | `extra_CaMKII_Holo.bngl` | `extra_CaMKII_Holo_metadata.yaml` | +| `Published/Ordyan2020/mCaMKIICaSpike` | `mCaMKII_Ca_Spike.bngl` | `mCaMKII_Ca_Spike_metadata.yaml` | +| `Published/Posner1995` | `blbr_rings_posner1995.bngl` | `blbr_rings_posner1995_metadata.yaml` | +| `Published/Posner2004` | `blbr_cooperativity_posner2004.bngl` | `blbr_cooperativity_posner2004_metadata.yaml` | +| `Published/PyBioNetGen/HIVdynamics/pt303` | `pt303.bngl` | `pt303_metadata.yaml` | +| `Published/PyBioNetGen/HIVdynamics/pt403` | `pt403.bngl` | `pt403_metadata.yaml` | +| `Published/PyBioNetGen/HIVdynamics/pt409` | `pt409.bngl` | `pt409_metadata.yaml` | +| `Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf` | `IGF1R_Model_receptor_activation_bnf.bngl` | `IGF1R_Model_receptor_activation_bnf_metadata.yaml` | +| `Published/PyBioNetGen/core/RAFi` | `RAFi.bngl` | `RAFi_metadata.yaml` | +| `Published/PyBioNetGen/core/RAFiground` | `RAFi_ground.bngl` | `RAFi_ground_metadata.yaml` | +| `Published/PyBioNetGen/core/degranulationmodel` | `degranulation_model.bngl` | `degranulation_model_metadata.yaml` | +| `Published/PyBioNetGen/core/egfr` | `egfr.bngl` | `egfr_metadata.yaml` | +| `Published/PyBioNetGen/core/egfrground` | `egfr_ground.bngl` | `egfr_ground_metadata.yaml` | +| `Published/PyBioNetGen/core/egfrnf` | `egfr_nf.bngl` | `egfr_nf_metadata.yaml` | +| `Published/PyBioNetGen/core/egfrode` | `egfr_ode.bngl` | `egfr_ode_metadata.yaml` | +| `Published/PyBioNetGen/core/egfrode_published-models_PyBNG` | `egfr_ode.bngl` | `egfr_ode_metadata.yaml` | +| `Published/PyBioNetGen/core/example1` | `example1.bngl` | `example1_metadata.yaml` | +| `Published/PyBioNetGen/core/example2startingpoint` | `example2_starting_point.bngl` | `example2_starting_point_metadata.yaml` | +| `Published/PyBioNetGen/core/fcerigamma2` | `fceri_gamma2.bngl` | `fceri_gamma2_metadata.yaml` | +| `Published/PyBioNetGen/core/fcerigamma2groundtruth` | `fceri_gamma2_ground_truth.bngl` | `fceri_gamma2_ground_truth_metadata.yaml` | +| `Published/PyBioNetGen/core/model` | `model.bngl` | `model_metadata.yaml` | +| `Published/PyBioNetGen/core/model_Degranulation_aMCMC` | `model.bngl` | `model_metadata.yaml` | +| `Published/PyBioNetGen/core/modeltofit` | `model_tofit.bngl` | `model_tofit_metadata.yaml` | +| `Published/PyBioNetGen/core/parabola` | `parabola.bngl` | `parabola_metadata.yaml` | +| `Published/PyBioNetGen/core/parabola_demo` | `parabola.bngl` | `parabola_metadata.yaml` | +| `Published/PyBioNetGen/core/parabolaground` | `parabola_ground.bngl` | `parabola_ground_metadata.yaml` | +| `Published/PyBioNetGen/core/polynomial` | `polynomial.bngl` | `polynomial_metadata.yaml` | +| `Published/PyBioNetGen/core/polynomialground` | `polynomial_ground.bngl` | `polynomial_ground_metadata.yaml` | +| `Published/PyBioNetGen/core/receptor` | `receptor.bngl` | `receptor_metadata.yaml` | +| `Published/PyBioNetGen/core/receptornf` | `receptor_nf.bngl` | `receptor_nf_metadata.yaml` | +| `Published/PyBioNetGen/core/tcr` | `tcr.bngl` | `tcr_metadata.yaml` | +| `Published/PyBioNetGen/core/tlbr` | `tlbr.bngl` | `tlbr_metadata.yaml` | +| `Published/PyBioNetGen/tests/ErrNoFrees` | `ErrNoFrees.bngl` | `ErrNoFrees_metadata.yaml` | +| `Published/PyBioNetGen/tests/LilyIgE` | `LilyIgE.bngl` | `LilyIgE_metadata.yaml` | +| `Published/PyBioNetGen/tests/NFmodel` | `NFmodel.bngl` | `NFmodel_metadata.yaml` | +| `Published/PyBioNetGen/tests/ParamsEverywhere` | `ParamsEverywhere.bngl` | `ParamsEverywhere_metadata.yaml` | +| `Published/PyBioNetGen/tests/Simple` | `Simple.bngl` | `Simple_metadata.yaml` | +| `Published/PyBioNetGen/tests/SimpleAddActions` | `Simple_AddActions.bngl` | `Simple_AddActions_metadata.yaml` | +| `Published/PyBioNetGen/tests/SimpleAnswer` | `Simple_Answer.bngl` | `Simple_Answer_metadata.yaml` | +| `Published/PyBioNetGen/tests/SimpleGenOnly` | `Simple_GenOnly.bngl` | `Simple_GenOnly_metadata.yaml` | +| `Published/PyBioNetGen/tests/Simplenogen` | `Simple_nogen.bngl` | `Simple_nogen_metadata.yaml` | +| `Published/PyBioNetGen/tests/Tricky` | `Tricky.bngl` | `Tricky_metadata.yaml` | +| `Published/PyBioNetGen/tests/TrickyUS` | `TrickyUS.bngl` | `TrickyUS_metadata.yaml` | +| `Published/PyBioNetGen/tests/actionssyntax` | `actions_syntax.bngl` | `actions_syntax_metadata.yaml` | +| `Published/PyBioNetGen/tests/bngerror` | `bng_error.bngl` | `bng_error_metadata.yaml` | +| `Published/PyBioNetGen/tests/egg` | `egg.bngl` | `egg_metadata.yaml` | +| `Published/PyBioNetGen/tests/freemissing` | `free_missing.bngl` | `free_missing_metadata.yaml` | +| `Published/PyBioNetGen/tests/nofrees` | `no_frees.bngl` | `no_frees_metadata.yaml` | +| `Published/PyBioNetGen/tests/nogeneratenetwork` | `no_generate_network.bngl` | `no_generate_network_metadata.yaml` | +| `Published/PyBioNetGen/tests/nosuffix` | `no_suffix.bngl` | `no_suffix_metadata.yaml` | +| `Published/PyBioNetGen/tests/parabola` | `parabola.bngl` | `parabola_metadata.yaml` | +| `Published/PyBioNetGen/tests/parabola2` | `parabola2.bngl` | `parabola2_metadata.yaml` | +| `Published/PyBioNetGen/tests/parabola_bngl_files` | `parabola.bngl` | `parabola_metadata.yaml` | +| `Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check` | `parabola.bngl` | `parabola_metadata.yaml` | +| `Published/PyBioNetGen/tests/polynomial` | `polynomial.bngl` | `polynomial_metadata.yaml` | +| `Published/PyBioNetGen/tests/polynomial_full_tests_T6-check` | `polynomial.bngl` | `polynomial_metadata.yaml` | +| `Published/PyBioNetGen/tests/receptornf` | `receptor_nf.bngl` | `receptor_nf_metadata.yaml` | +| `Published/PyBioNetGen/tests/simplenfseed` | `simple_nf_seed.bngl` | `simple_nf_seed_metadata.yaml` | +| `Published/PyBioNetGen/tests/trivial` | `trivial.bngl` | `trivial_metadata.yaml` | +| `Published/Salazar-Cavazos2019/PyBNF-fitting-setup` | `190127_CHO_EGFR_forBNF.bngl` | `190127_CHO_EGFR_forBNF_metadata.yaml` | +| `Published/Thomas2016/example1_BNFfiles` | `example1.bngl` | `example1_metadata.yaml` | +| `Published/Thomas2016/example2_BNFfiles` | `example2.bngl` | `example2_metadata.yaml` | +| `Published/Thomas2016/example3_BNFfiles` | `example3.bngl` | `example3_metadata.yaml` | +| `Published/Thomas2016/example4_BNFfiles` | `example4.bngl` | `example4_metadata.yaml` | +| `Published/Thomas2016/example5_BNFfiles` | `example5.bngl` | `example5_metadata.yaml` | +| `Published/Thomas2016/example6_BNFfiles` | `example6.bngl` | `example6_metadata.yaml` | +| `Published/VaxAndVariants/Dallas` | `Dallas.bngl` | `Dallas_metadata.yaml` | +| `Published/VaxAndVariants/Houston` | `Houston.bngl` | `Houston_metadata.yaml` | +| `Published/VaxAndVariants/NYC` | `NYC.bngl` | `NYC_metadata.yaml` | +| `Published/VaxAndVariants/Phoenix` | `Phoenix.bngl` | `Phoenix_metadata.yaml` | +| `Published/Yang2008` | `tlbr_yang2008.bngl` | `tlbr_yang2008_metadata.yaml` | +| `Examples/biology/ampksignaling` | `ampk-signaling.bngl` | `ampk-signaling_metadata.yaml` | +| `Examples/biology/apoptosiscascade` | `apoptosis-cascade.bngl` | `apoptosis-cascade_metadata.yaml` | +| `Examples/biology/autoactivationloop` | `auto-activation-loop.bngl` | `auto-activation-loop_metadata.yaml` | +| `Examples/biology/bcrsignaling` | `bcr-signaling.bngl` | `bcr-signaling_metadata.yaml` | +| `Examples/biology/bistabletoggleswitch` | `bistable-toggle-switch.bngl` | `bistable-toggle-switch_metadata.yaml` | +| `Examples/biology/bmpsignaling` | `bmp-signaling.bngl` | `bmp-signaling_metadata.yaml` | +| `Examples/biology/calcineurinnfatpathway` | `calcineurin-nfat-pathway.bngl` | `calcineurin-nfat-pathway_metadata.yaml` | +| `Examples/biology/calciumspikesignaling` | `calcium-spike-signaling.bngl` | `calcium-spike-signaling_metadata.yaml` | +| `Examples/biology/chemotaxissignaltransduction` | `chemotaxis-signal-transduction.bngl` | `chemotaxis-signal-transduction_metadata.yaml` | +| `Examples/biology/circadianoscillator` | `circadian-oscillator.bngl` | `circadian-oscillator_metadata.yaml` | +| `Examples/biology/clockbmal1genecircuit` | `clock-bmal1-gene-circuit.bngl` | `clock-bmal1-gene-circuit_metadata.yaml` | +| `Examples/biology/egfrsignalingpathway` | `egfr-signaling-pathway.bngl` | `egfr-signaling-pathway_metadata.yaml` | +| `Examples/biology/eif2astressresponse` | `eif2a-stress-response.bngl` | `eif2a-stress-response_metadata.yaml` | +| `Examples/biology/endosomalsortingrab` | `endosomal-sorting-rab.bngl` | `endosomal-sorting-rab_metadata.yaml` | +| `Examples/biology/erknucleartranslocation` | `erk-nuclear-translocation.bngl` | `erk-nuclear-translocation_metadata.yaml` | +| `Examples/biology/erstressresponse` | `er-stress-response.bngl` | `er-stress-response_metadata.yaml` | +| `Examples/biology/fgfsignalingpathway` | `fgf-signaling-pathway.bngl` | `fgf-signaling-pathway_metadata.yaml` | +| `Examples/biology/gas6axlsignaling` | `gas6-axl-signaling.bngl` | `gas6-axl-signaling_metadata.yaml` | +| `Examples/biology/geneexpressiontoggle` | `gene-expression-toggle.bngl` | `gene-expression-toggle_metadata.yaml` | +| `Examples/biology/glioblastomaegfrviiisignaling` | `glioblastoma-egfrviii-signaling.bngl` | `glioblastoma-egfrviii-signaling_metadata.yaml` | +| `Examples/biology/glycolysisbranchpoint` | `glycolysis-branch-point.bngl` | `glycolysis-branch-point_metadata.yaml` | +| `Examples/biology/gpcrdesensitizationarrestin` | `gpcr-desensitization-arrestin.bngl` | `gpcr-desensitization-arrestin_metadata.yaml` | +| `Examples/biology/hedgehogsignalingpathway` | `hedgehog-signaling-pathway.bngl` | `hedgehog-signaling-pathway_metadata.yaml` | +| `Examples/biology/hematopoieticgrowthfactor` | `hematopoietic-growth-factor.bngl` | `hematopoietic-growth-factor_metadata.yaml` | +| `Examples/biology/hif1adegradationloop` | `hif1a_degradation_loop.bngl` | `hif1a_degradation_loop_metadata.yaml` | +| `Examples/biology/hypoxiaresponsesignaling` | `hypoxia-response-signaling.bngl` | `hypoxia-response-signaling_metadata.yaml` | +| `Examples/biology/il1bsignaling` | `il1b-signaling.bngl` | `il1b-signaling_metadata.yaml` | +| `Examples/biology/il6jakstatpathway` | `il6-jak-stat-pathway.bngl` | `il6-jak-stat-pathway_metadata.yaml` | +| `Examples/biology/immunesynapseformation` | `immune-synapse-formation.bngl` | `immune-synapse-formation_metadata.yaml` | +| `Examples/biology/inflammasomeactivation` | `inflammasome-activation.bngl` | `inflammasome-activation_metadata.yaml` | +| `Examples/biology/inositolphosphatemetabolism` | `inositol-phosphate-metabolism.bngl` | `inositol-phosphate-metabolism_metadata.yaml` | +| `Examples/biology/insulinglucosehomeostasis` | `insulin-glucose-homeostasis.bngl` | `insulin-glucose-homeostasis_metadata.yaml` | +| `Examples/biology/lipidmediatedpip3signaling` | `lipid-mediated-pip3-signaling.bngl` | `lipid-mediated-pip3-signaling_metadata.yaml` | +| `Examples/biology/ltypecalciumchanneldynamics` | `l-type-calcium-channel-dynamics.bngl` | `l-type-calcium-channel-dynamics_metadata.yaml` | +| `Examples/biology/mapksignalingcascade` | `mapk-signaling-cascade.bngl` | `mapk-signaling-cascade_metadata.yaml` | +| `Examples/biology/quorumsensingcircuit` | `quorum-sensing-circuit.bngl` | `quorum-sensing-circuit_metadata.yaml` | +| `Examples/biology/stat3mediatedtranscription` | `stat3-mediated-transcription.bngl` | `stat3-mediated-transcription_metadata.yaml` | +| `Examples/biology/stressresponseadaptation` | `stress-response-adaptation.bngl` | `stress-response-adaptation_metadata.yaml` | +| `Examples/biology/synapticplasticityltp` | `synaptic-plasticity-ltp.bngl` | `synaptic-plasticity-ltp_metadata.yaml` | +| `Examples/biology/tcellactivation` | `t-cell-activation.bngl` | `t-cell-activation_metadata.yaml` | +| `Examples/biology/tlr3dsrnasensing` | `tlr3-dsrna-sensing.bngl` | `tlr3-dsrna-sensing_metadata.yaml` | +| `Examples/biology/tnfinducedapoptosis` | `tnf-induced-apoptosis.bngl` | `tnf-induced-apoptosis_metadata.yaml` | +| `Examples/biology/twocomponentsystem` | `two-component-system.bngl` | `two-component-system_metadata.yaml` | +| `Examples/biology/vegfangiogenesis` | `vegf-angiogenesis.bngl` | `vegf-angiogenesis_metadata.yaml` | +| `Examples/biology/viralsensinginnateimmunity` | `viral-sensing-innate-immunity.bngl` | `viral-sensing-innate-immunity_metadata.yaml` | +| `Examples/biology/wntbetacateninsignaling` | `wnt-beta-catenin-signaling.bngl` | `wnt-beta-catenin-signaling_metadata.yaml` | +| `Examples/biology/woundhealingpdgfsignaling` | `wound-healing-pdgf-signaling.bngl` | `wound-healing-pdgf-signaling_metadata.yaml` | +| `Examples/compartments/compartmentendocytosis` | `compartment_endocytosis.bngl` | `compartment_endocytosis_metadata.yaml` | +| `Examples/compartments/compartmentmembranebound` | `compartment_membrane_bound.bngl` | `compartment_membrane_bound_metadata.yaml` | +| `Examples/compartments/compartmentnestedtransport` | `compartment_nested_transport.bngl` | `compartment_nested_transport_metadata.yaml` | +| `Examples/compartments/compartmentnucleartransport` | `compartment_nuclear_transport.bngl` | `compartment_nuclear_transport_metadata.yaml` | +| `Examples/compartments/compartmentorganelleexchange` | `compartment_organelle_exchange.bngl` | `compartment_organelle_exchange_metadata.yaml` | +| `Examples/cs/csdiffiehellman` | `cs_diffie_hellman.bngl` | `cs_diffie_hellman_metadata.yaml` | +| `Examples/cs/cshashfunction` | `cs_hash_function.bngl` | `cs_hash_function_metadata.yaml` | +| `Examples/cs/cshuffman` | `cs_huffman.bngl` | `cs_huffman_metadata.yaml` | +| `Examples/cs/csmontecarlopi` | `cs_monte_carlo_pi.bngl` | `cs_monte_carlo_pi_metadata.yaml` | +| `Examples/cs/cspagerank` | `cs_pagerank.bngl` | `cs_pagerank_metadata.yaml` | +| `Examples/cs/cspidcontroller` | `cs_pid_controller.bngl` | `cs_pid_controller_metadata.yaml` | +| `Examples/cs/csregexnfa` | `cs_regex_nfa.bngl` | `cs_regex_nfa_metadata.yaml` | +| `Examples/ecology/ecocoevolutionhostparasite` | `eco_coevolution_host_parasite.bngl` | `eco_coevolution_host_parasite_metadata.yaml` | +| `Examples/ecology/ecofoodwebchaos3sp` | `eco_food_web_chaos_3sp.bngl` | `eco_food_web_chaos_3sp_metadata.yaml` | +| `Examples/ecology/ecolotkavolterragrid` | `eco_lotka_volterra_grid.bngl` | `eco_lotka_volterra_grid_metadata.yaml` | +| `Examples/ecology/ecomutualismobligate` | `eco_mutualism_obligate.bngl` | `eco_mutualism_obligate_metadata.yaml` | +| `Examples/ecology/ecorockpaperscissorsspatial` | `eco_rock_paper_scissors_spatial.bngl` | `eco_rock_paper_scissors_spatial_metadata.yaml` | +| `Examples/energy/energyallosterymwc` | `energy_allostery_mwc.bngl` | `energy_allostery_mwc_metadata.yaml` | +| `Examples/energy/energycatalysismm` | `energy_catalysis_mm.bngl` | `energy_catalysis_mm_metadata.yaml` | +| `Examples/energy/energycooperativityadh` | `energy_cooperativity_adh.bngl` | `energy_cooperativity_adh_metadata.yaml` | +| `Examples/energy/energylinearchain` | `energy_linear_chain.bngl` | `energy_linear_chain_metadata.yaml` | +| `Examples/energy/energytransportpump` | `energy_transport_pump.bngl` | `energy_transport_pump_metadata.yaml` | +| `Examples/feature-demos/featurefunctionalratesvolume` | `feature_functional_rates_volume.bngl` | `feature_functional_rates_volume_metadata.yaml` | +| `Examples/feature-demos/featureglobalfunctionsscan` | `feature_global_functions_scan.bngl` | `feature_global_functions_scan_metadata.yaml` | +| `Examples/feature-demos/featurelocalfunctionsexplicit` | `feature_local_functions_explicit.bngl` | `feature_local_functions_explicit_metadata.yaml` | +| `Examples/feature-demos/featuresymmetryfactorscyclic` | `feature_symmetry_factors_cyclic.bngl` | `feature_symmetry_factors_cyclic_metadata.yaml` | +| `Examples/feature-demos/featuresynthesisdegradationss` | `feature_synthesis_degradation_ss.bngl` | `feature_synthesis_degradation_ss_metadata.yaml` | +| `Examples/generative/gmgameoflife` | `gm_game_of_life.bngl` | `gm_game_of_life_metadata.yaml` | +| `Examples/generative/gmraymarcher` | `gm_ray_marcher.bngl` | `gm_ray_marcher_metadata.yaml` | +| `Examples/genetics/geneticbistabilityenergy` | `genetic_bistability_energy.bngl` | `genetic_bistability_energy_metadata.yaml` | +| `Examples/genetics/geneticdnareplicationstochastic` | `genetic_dna_replication_stochastic.bngl` | `genetic_dna_replication_stochastic_metadata.yaml` | +| `Examples/genetics/geneticgoodwinoscillator` | `genetic_goodwin_oscillator.bngl` | `genetic_goodwin_oscillator_metadata.yaml` | +| `Examples/genetics/genetictranslationkinetics` | `genetic_translation_kinetics.bngl` | `genetic_translation_kinetics_metadata.yaml` | +| `Examples/genetics/geneticturingpattern1d` | `genetic_turing_pattern_1d.bngl` | `genetic_turing_pattern_1d_metadata.yaml` | +| `Examples/meta/metaformalgametheory` | `meta_formal_game_theory.bngl` | `meta_formal_game_theory_metadata.yaml` | +| `Examples/meta/metaformalmolecularclock` | `meta_formal_molecular_clock.bngl` | `meta_formal_molecular_clock_metadata.yaml` | +| `Examples/meta/metaformalpetrinet` | `meta_formal_petri_net.bngl` | `meta_formal_petri_net_metadata.yaml` | +| `Examples/meta/mtarithmeticcompiler` | `mt_arithmetic_compiler.bngl` | `mt_arithmetic_compiler_metadata.yaml` | +| `Examples/meta/mtbnglinterpreter` | `mt_bngl_interpreter.bngl` | `mt_bngl_interpreter_metadata.yaml` | +| `Examples/meta/mtmusicsequencer` | `mt_music_sequencer.bngl` | `mt_music_sequencer_metadata.yaml` | +| `Examples/meta/mtpascaltriangle` | `mt_pascal_triangle.bngl` | `mt_pascal_triangle_metadata.yaml` | +| `Examples/meta/mtquine` | `mt_quine.bngl` | `mt_quine_metadata.yaml` | +| `Examples/ml/mlgradientdescent` | `ml_gradient_descent.bngl` | `ml_gradient_descent_metadata.yaml` | +| `Examples/ml/mlhopfield` | `ml_hopfield.bngl` | `ml_hopfield_metadata.yaml` | +| `Examples/ml/mlkmeans` | `ml_kmeans.bngl` | `ml_kmeans_metadata.yaml` | +| `Examples/ml/mlqlearning` | `ml_q_learning.bngl` | `ml_q_learning_metadata.yaml` | +| `Examples/ml/mlsvm` | `ml_svm.bngl` | `ml_svm_metadata.yaml` | +| `Examples/ml/nnxor` | `nn_xor.bngl` | `nn_xor_metadata.yaml` | +| `Examples/nfsim/nfsimcoarsegraining` | `nfsim_coarse_graining.bngl` | `nfsim_coarse_graining_metadata.yaml` | +| `Examples/nfsim/nfsimdynamiccompartments` | `nfsim_dynamic_compartments.bngl` | `nfsim_dynamic_compartments_metadata.yaml` | +| `Examples/nfsim/nfsimringclosurepolymer` | `nfsim_ring_closure_polymer.bngl` | `nfsim_ring_closure_polymer_metadata.yaml` | +| `Examples/physics/phlorenzattractor` | `ph_lorenz_attractor.bngl` | `ph_lorenz_attractor_metadata.yaml` | +| `Examples/physics/phnbodygravity` | `ph_nbody_gravity.bngl` | `ph_nbody_gravity_metadata.yaml` | +| `Examples/physics/phschrodinger` | `ph_schrodinger.bngl` | `ph_schrodinger_metadata.yaml` | +| `Examples/physics/phwaveequation` | `ph_wave_equation.bngl` | `ph_wave_equation_metadata.yaml` | +| `Examples/processes/processactintreadmilling` | `process_actin_treadmilling.bngl` | `process_actin_treadmilling_metadata.yaml` | +| `Examples/processes/processautophagyflux` | `process_autophagy_flux.bngl` | `process_autophagy_flux_metadata.yaml` | +| `Examples/processes/processcelladhesionstrength` | `process_cell_adhesion_strength.bngl` | `process_cell_adhesion_strength_metadata.yaml` | +| `Examples/processes/processkineticproofreadingtcr` | `process_kinetic_proofreading_tcr.bngl` | `process_kinetic_proofreading_tcr_metadata.yaml` | +| `Examples/processes/processquorumsensingswitch` | `process_quorum_sensing_switch.bngl` | `process_quorum_sensing_switch_metadata.yaml` | +| `Examples/signal-processing/spfouriersynthesizer` | `sp_fourier_synthesizer.bngl` | `sp_fourier_synthesizer_metadata.yaml` | +| `Examples/signal-processing/spimageconvolution` | `sp_image_convolution.bngl` | `sp_image_convolution_metadata.yaml` | +| `Examples/signal-processing/spkalmanfilter` | `sp_kalman_filter.bngl` | `sp_kalman_filter_metadata.yaml` | +| `Examples/synbio/synbiobandpassfilter` | `synbio_band_pass_filter.bngl` | `synbio_band_pass_filter_metadata.yaml` | +| `Examples/synbio/synbiocountermolecular` | `synbio_counter_molecular.bngl` | `synbio_counter_molecular_metadata.yaml` | +| `Examples/synbio/synbioedgedetector` | `synbio_edge_detector.bngl` | `synbio_edge_detector_metadata.yaml` | +| `Examples/synbio/synbiologicgatesenzymatic` | `synbio_logic_gates_enzymatic.bngl` | `synbio_logic_gates_enzymatic_metadata.yaml` | +| `Examples/synbio/synbiooscillatorsynchronization` | `synbio_oscillator_synchronization.bngl` | `synbio_oscillator_synchronization_metadata.yaml` | +| `Examples/wacky/wackyalchemystone` | `wacky_alchemy_stone.bngl` | `wacky_alchemy_stone_metadata.yaml` | +| `Examples/wacky/wackyblackhole` | `wacky_black_hole.bngl` | `wacky_black_hole_metadata.yaml` | +| `Examples/wacky/wackybouncingball` | `wacky_bouncing_ball.bngl` | `wacky_bouncing_ball_metadata.yaml` | +| `Examples/wacky/wackytrafficjamasep` | `wacky_traffic_jam_asep.bngl` | `wacky_traffic_jam_asep_metadata.yaml` | +| `Examples/wacky/wackyzombieinfection` | `wacky_zombie_infection.bngl` | `wacky_zombie_infection_metadata.yaml` | +| `Tutorials/CaOscillateFunc` | `CaOscillate_Func.bngl` | `CaOscillate_Func_metadata.yaml` | +| `Tutorials/CaOscillateSat` | `CaOscillate_Sat.bngl` | `CaOscillate_Sat_metadata.yaml` | +| `Tutorials/General/polymerdraft` | `polymer_draft.bngl` | `polymer_draft_metadata.yaml` | +| `Tutorials/General/quasiequilibrium` | `quasi_equilibrium.bngl` | `quasi_equilibrium_metadata.yaml` | +| `Tutorials/General/simple` | `simple.bngl` | `simple_metadata.yaml` | +| `Tutorials/Haugh2b` | `Haugh2b.bngl` | `Haugh2b_metadata.yaml` | +| `Tutorials/Kiefhaberemodel` | `Kiefhaber_emodel.bngl` | `Kiefhaber_emodel_metadata.yaml` | +| `Tutorials/Motivatingexample` | `Motivating_example.bngl` | `Motivating_example_metadata.yaml` | +| `Tutorials/MotivatingexamplecBNGL` | `Motivating_example_cBNGL.bngl` | `Motivating_example_cBNGL_metadata.yaml` | +| `Tutorials/NativeTutorials/AB` | `AB.bngl` | `AB_metadata.yaml` | +| `Tutorials/NativeTutorials/ABC` | `ABC.bngl` | `ABC_metadata.yaml` | +| `Tutorials/NativeTutorials/ABCscan` | `ABC_scan.bngl` | `ABC_scan_metadata.yaml` | +| `Tutorials/NativeTutorials/ABCssa` | `ABC_ssa.bngl` | `ABC_ssa_metadata.yaml` | +| `Tutorials/NativeTutorials/ABp` | `ABp.bngl` | `ABp_metadata.yaml` | +| `Tutorials/NativeTutorials/ABpapprox` | `ABp_approx.bngl` | `ABp_approx_metadata.yaml` | +| `Tutorials/NativeTutorials/BAB` | `BAB.bngl` | `BAB_metadata.yaml` | +| `Tutorials/NativeTutorials/BABcoop` | `BAB_coop.bngl` | `BAB_coop_metadata.yaml` | +| `Tutorials/NativeTutorials/BABscan` | `BAB_scan.bngl` | `BAB_scan_metadata.yaml` | +| `Tutorials/NativeTutorials/BLBR` | `BLBR.bngl` | `BLBR_metadata.yaml` | +| `Tutorials/NativeTutorials/Chyleklibrary` | `Chylek_library.bngl` | `Chylek_library_metadata.yaml` | +| `Tutorials/NativeTutorials/CircadianOscillator` | `CircadianOscillator.bngl` | `CircadianOscillator_metadata.yaml` | +| `Tutorials/NativeTutorials/ComplexDegradation` | `ComplexDegradation.bngl` | `ComplexDegradation_metadata.yaml` | +| `Tutorials/NativeTutorials/Creamer2012` | `Creamer_2012.bngl` | `Creamer_2012_metadata.yaml` | +| `Tutorials/NativeTutorials/FceRIji` | `FceRI_ji.bngl` | `FceRI_ji_metadata.yaml` | +| `Tutorials/NativeTutorials/FceRIviz` | `FceRI_viz.bngl` | `FceRI_viz_metadata.yaml` | +| `Tutorials/NativeTutorials/GK` | `GK.bngl` | `GK_metadata.yaml` | +| `Tutorials/NativeTutorials/LR` | `LR.bngl` | `LR_metadata.yaml` | +| `Tutorials/NativeTutorials/LRR` | `LRR.bngl` | `LRR_metadata.yaml` | +| `Tutorials/NativeTutorials/LRRcomp` | `LRR_comp.bngl` | `LRR_comp_metadata.yaml` | +| `Tutorials/NativeTutorials/LRcomp` | `LR_comp.bngl` | `LR_comp_metadata.yaml` | +| `Tutorials/NativeTutorials/LV` | `LV.bngl` | `LV_metadata.yaml` | +| `Tutorials/NativeTutorials/LVcomp` | `LV_comp.bngl` | `LV_comp_metadata.yaml` | +| `Tutorials/NativeTutorials/Lisman` | `Lisman.bngl` | `Lisman_metadata.yaml` | +| `Tutorials/NativeTutorials/Lismanbifurcate` | `Lisman_bifurcate.bngl` | `Lisman_bifurcate_metadata.yaml` | +| `Tutorials/NativeTutorials/Repressilator` | `Repressilator.bngl` | `Repressilator_metadata.yaml` | +| `Tutorials/NativeTutorials/SIR` | `SIR.bngl` | `SIR_metadata.yaml` | +| `Tutorials/NativeTutorials/Suderman2013` | `Suderman_2013.bngl` | `Suderman_2013_metadata.yaml` | +| `Tutorials/NativeTutorials/birthdeath` | `birth-death.bngl` | `birth-death_metadata.yaml` | +| `Tutorials/NativeTutorials/cBNGLsimple` | `cBNGL_simple.bngl` | `cBNGL_simple_metadata.yaml` | +| `Tutorials/NativeTutorials/egfrsimple` | `egfr_simple.bngl` | `egfr_simple_metadata.yaml` | +| `Tutorials/NativeTutorials/organelletransport` | `organelle_transport.bngl` | `organelle_transport_metadata.yaml` | +| `Tutorials/NativeTutorials/organelletransportstruct` | `organelle_transport_struct.bngl` | `organelle_transport_struct_metadata.yaml` | +| `Tutorials/NativeTutorials/toggle` | `toggle.bngl` | `toggle_metadata.yaml` | +| `Tutorials/NativeTutorials/translateSBML` | `translateSBML.bngl` | `translateSBML_metadata.yaml` | +| `Tutorials/NativeTutorials/visualize` | `visualize.bngl` | `visualize_metadata.yaml` | +| `Tutorials/SHP2basemodel` | `SHP2_base_model.bngl` | `SHP2_base_model_metadata.yaml` | +| `Tutorials/catalysis` | `catalysis.bngl` | `catalysis_metadata.yaml` | +| `Tutorials/continue` | `continue.bngl` | `continue_metadata.yaml` | +| `Tutorials/egfrnet` | `egfr_net.bngl` | `egfr_net_metadata.yaml` | +| `Tutorials/egfrnetred` | `egfr_net_red.bngl` | `egfr_net_red_metadata.yaml` | +| `Tutorials/egfrpath` | `egfr_path.bngl` | `egfr_path_metadata.yaml` | +| `Tutorials/energyexample1` | `energy_example1.bngl` | `energy_example1_metadata.yaml` | +| `Tutorials/example1` | `example1.bngl` | `example1_metadata.yaml` | +| `Tutorials/fcerijicomp` | `fceri_ji_comp.bngl` | `fceri_ji_comp_metadata.yaml` | +| `Tutorials/heise` | `heise.bngl` | `heise_metadata.yaml` | +| `Tutorials/issue198short` | `issue_198_short.bngl` | `issue_198_short_metadata.yaml` | +| `Tutorials/localfunc` | `localfunc.bngl` | `localfunc_metadata.yaml` | +| `Tutorials/michment` | `michment.bngl` | `michment_metadata.yaml` | +| `Tutorials/michmentcont` | `michment_cont.bngl` | `michment_cont_metadata.yaml` | +| `Tutorials/motor` | `motor.bngl` | `motor_metadata.yaml` | +| `Tutorials/mwc` | `mwc.bngl` | `mwc_metadata.yaml` | +| `Tutorials/nfkb` | `nfkb.bngl` | `nfkb_metadata.yaml` | +| `Tutorials/nfkbillustratingprotocols` | `nfkb_illustrating_protocols.bngl` | `nfkb_illustrating_protocols_metadata.yaml` | +| `Tutorials/polymerfixed` | `polymer_fixed.bngl` | `polymer_fixed_metadata.yaml` | +| `Tutorials/recdim` | `rec_dim.bngl` | `rec_dim_metadata.yaml` | +| `Tutorials/recdimcomp` | `rec_dim_comp.bngl` | `rec_dim_comp_metadata.yaml` | +| `Tutorials/simplenfsimtest` | `simple_nfsim_test.bngl` | `simple_nfsim_test_metadata.yaml` | +| `Tutorials/simplesbmlimport` | `simple_sbml_import.bngl` | `simple_sbml_import_metadata.yaml` | +| `Tutorials/simplesystem` | `simple_system.bngl` | `simple_system_metadata.yaml` | +| `Tutorials/testANGsynthesissimple` | `test_ANG_synthesis_simple.bngl` | `test_ANG_synthesis_simple_metadata.yaml` | +| `Tutorials/testMM` | `test_MM.bngl` | `test_MM_metadata.yaml` | +| `Tutorials/testfixed` | `test_fixed.bngl` | `test_fixed_metadata.yaml` | +| `Tutorials/testmratio` | `test_mratio.bngl` | `test_mratio_metadata.yaml` | +| `Tutorials/testnetworkgen` | `test_network_gen.bngl` | `test_network_gen_metadata.yaml` | +| `Tutorials/testsat` | `test_sat.bngl` | `test_sat_metadata.yaml` | +| `Tutorials/testsynthesiscBNGLsimple` | `test_synthesis_cBNGL_simple.bngl` | `test_synthesis_cBNGL_simple_metadata.yaml` | +| `Tutorials/testsynthesiscomplex` | `test_synthesis_complex.bngl` | `test_synthesis_complex_metadata.yaml` | +| `Tutorials/testsynthesiscomplex0cBNGL` | `test_synthesis_complex_0_cBNGL.bngl` | `test_synthesis_complex_0_cBNGL_metadata.yaml` | +| `Tutorials/testsynthesiscomplexsourcecBNGL` | `test_synthesis_complex_source_cBNGL.bngl` | `test_synthesis_complex_source_cBNGL_metadata.yaml` | +| `Tutorials/testsynthesissimple` | `test_synthesis_simple.bngl` | `test_synthesis_simple_metadata.yaml` | +| `Tutorials/tlmr` | `tlmr.bngl` | `tlmr_metadata.yaml` | +| `Tutorials/toyjim` | `toy-jim.bngl` | `toy-jim_metadata.yaml` | +| `Tutorials/univsynth` | `univ_synth.bngl` | `univ_synth_metadata.yaml` | + +## Already correct (unchanged) + +| Directory | BNGL file | Existing metadata copy | +|---|---|---| +| `Published/An2009` | `An_2009.bngl` | `An_2009_metadata.yaml` | +| `Published/Barua2007` | `Barua_2007.bngl` | `Barua_2007_metadata.yaml` | +| `Published/Barua2009` | `Barua_2009.bngl` | `Barua_2009_metadata.yaml` | +| `Published/Barua2013` | `Barua_2013.bngl` | `Barua_2013_metadata.yaml` | +| `Published/BaruaBCR2012` | `BaruaBCR_2012.bngl` | `BaruaBCR_2012_metadata.yaml` | +| `Published/BaruaFceRI2012` | `BaruaFceRI_2012.bngl` | `BaruaFceRI_2012_metadata.yaml` | +| `Published/Blinov2006` | `Blinov_2006.bngl` | `Blinov_2006_metadata.yaml` | +| `Published/Blinovegfr` | `Blinov_egfr.bngl` | `Blinov_egfr_metadata.yaml` | +| `Published/Blinovran` | `Blinov_ran.bngl` | `Blinov_ran_metadata.yaml` | +| `Published/Chattaraj2021` | `Chattaraj_2021.bngl` | `Chattaraj_2021_metadata.yaml` | +| `Published/ChylekFceRI2014` | `ChylekFceRI_2014.bngl` | `ChylekFceRI_2014_metadata.yaml` | +| `Published/ChylekTCR2014` | `ChylekTCR_2014.bngl` | `ChylekTCR_2014_metadata.yaml` | +| `Published/Dolan2015` | `Dolan_2015.bngl` | `Dolan_2015_metadata.yaml` | +| `Published/Dushek2011` | `Dushek_2011.bngl` | `Dushek_2011_metadata.yaml` | +| `Published/Dushek2014` | `Dushek_2014.bngl` | `Dushek_2014_metadata.yaml` | +| `Published/Erdem2021` | `Erdem_2021.bngl` | `Erdem_2021_metadata.yaml` | +| `Published/Hat2016` | `Hat_2016.bngl` | `Hat_2016_metadata.yaml` | +| `Published/JaruszewiczBlonska2023` | `Jaruszewicz-Blonska_2023.bngl` | `Jaruszewicz-Blonska_2023_metadata.yaml` | +| `Published/Jung2017` | `Jung_2017.bngl` | `Jung_2017_metadata.yaml` | +| `Published/Kesseler2013` | `Kesseler_2013.bngl` | `Kesseler_2013_metadata.yaml` | +| `Published/Kocieniewski2012` | `Kocieniewski_2012.bngl` | `Kocieniewski_2012_metadata.yaml` | +| `Published/Korwek2023` | `Korwek_2023.bngl` | `Korwek_2023_metadata.yaml` | +| `Published/Kozer2013` | `Kozer_2013.bngl` | `Kozer_2013_metadata.yaml` | +| `Published/Kozer2014` | `Kozer_2014.bngl` | `Kozer_2014_metadata.yaml` | +| `Published/Lang2024` | `Lang_2024.bngl` | `Lang_2024_metadata.yaml` | +| `Published/Ligon2014` | `Ligon_2014.bngl` | `Ligon_2014_metadata.yaml` | +| `Published/LinERK2019` | `Lin_ERK_2019.bngl` | `Lin_ERK_2019_metadata.yaml` | +| `Published/LinPrion2019` | `Lin_Prion_2019.bngl` | `Lin_Prion_2019_metadata.yaml` | +| `Published/LinTCR2019` | `Lin_TCR_2019.bngl` | `Lin_TCR_2019_metadata.yaml` | +| `Published/Massole2023` | `Massole_2023.bngl` | `Massole_2023_metadata.yaml` | +| `Published/McMillan2021` | `McMillan_2021.bngl` | `McMillan_2021_metadata.yaml` | +| `Published/Mertins2023` | `Mertins_2023.bngl` | `Mertins_2023_metadata.yaml` | +| `Published/ModelZAP` | `Model_ZAP.bngl` | `Model_ZAP_metadata.yaml` | +| `Published/Mukhopadhyay2013` | `Mukhopadhyay_2013.bngl` | `Mukhopadhyay_2013_metadata.yaml` | +| `Published/MyrtleBeachConwayNorthMyrtleBeachSCNC` | `Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl` | `Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC_metadata.yaml` | +| `Published/Nag2009` | `Nag_2009.bngl` | `Nag_2009_metadata.yaml` | +| `Published/Nosbisch2022` | `Nosbisch_2022.bngl` | `Nosbisch_2022_metadata.yaml` | +| `Published/Pekalski2013` | `Pekalski_2013.bngl` | `Pekalski_2013_metadata.yaml` | +| `Published/RulebasedRantransport` | `Rule_based_Ran_transport.bngl` | `Rule_based_Ran_transport_metadata.yaml` | +| `Published/RulebasedRantransportdraft` | `Rule_based_Ran_transport_draft.bngl` | `Rule_based_Ran_transport_draft_metadata.yaml` | +| `Published/Rulebasedegfrcompart` | `Rule_based_egfr_compart.bngl` | `Rule_based_egfr_compart_metadata.yaml` | +| `Published/Rulebasedegfrtutorial` | `Rule_based_egfr_tutorial.bngl` | `Rule_based_egfr_tutorial_metadata.yaml` | +| `Published/Zhang2021` | `Zhang_2021.bngl` | `Zhang_2021_metadata.yaml` | +| `Published/Zhang2023` | `Zhang_2023.bngl` | `Zhang_2023_metadata.yaml` | +| `Published/fcerifyn` | `fceri_fyn.bngl` | `fceri_fyn_metadata.yaml` | +| `Published/innateimmunity` | `innate_immunity.bngl` | `innate_immunity_metadata.yaml` | +| `Published/mapkdimers` | `mapk-dimers.bngl` | `mapk-dimers_metadata.yaml` | +| `Published/mapkmonomers` | `mapk-monomers.bngl` | `mapk-monomers_metadata.yaml` | +| `Published/notch` | `notch.bngl` | `notch_metadata.yaml` | +| `Published/tlbr` | `tlbr.bngl` | `tlbr_metadata.yaml` | +| `Published/vilar2002` | `vilar_2002.bngl` | `vilar_2002_metadata.yaml` | +| `Published/vilar2002b` | `vilar_2002b.bngl` | `vilar_2002b_metadata.yaml` | +| `Published/vilar2002c` | `vilar_2002c.bngl` | `vilar_2002c_metadata.yaml` | +| `Published/wnt` | `wnt.bngl` | `wnt_metadata.yaml` | +| `Examples/biology/aktsignaling` | `akt-signaling.bngl` | `akt-signaling_metadata.yaml` | +| `Examples/biology/allostericactivation` | `allosteric-activation.bngl` | `allosteric-activation_metadata.yaml` | +| `Examples/biology/autophagyregulation` | `autophagy-regulation.bngl` | `autophagy-regulation_metadata.yaml` | +| `Examples/biology/betaadrenergicresponse` | `beta-adrenergic-response.bngl` | `beta-adrenergic-response_metadata.yaml` | +| `Examples/biology/bloodcoagulationthrombin` | `blood-coagulation-thrombin.bngl` | `blood-coagulation-thrombin_metadata.yaml` | +| `Examples/biology/brusselatoroscillator` | `brusselator-oscillator.bngl` | `brusselator-oscillator_metadata.yaml` | +| `Examples/biology/caspaseactivationloop` | `caspase-activation-loop.bngl` | `caspase-activation-loop_metadata.yaml` | +| `Examples/biology/cd40signaling` | `cd40-signaling.bngl` | `cd40-signaling_metadata.yaml` | +| `Examples/biology/cellcyclecheckpoint` | `cell-cycle-checkpoint.bngl` | `cell-cycle-checkpoint_metadata.yaml` | +| `Examples/biology/checkpointkinasesignaling` | `checkpoint-kinase-signaling.bngl` | `checkpoint-kinase-signaling_metadata.yaml` | +| `Examples/biology/competitiveenzymeinhibition` | `competitive-enzyme-inhibition.bngl` | `competitive-enzyme-inhibition_metadata.yaml` | +| `Examples/biology/complementactivationcascade` | `complement-activation-cascade.bngl` | `complement-activation-cascade_metadata.yaml` | +| `Examples/biology/contactinhibitionhippoyap` | `contact-inhibition-hippo-yap.bngl` | `contact-inhibition-hippo-yap_metadata.yaml` | +| `Examples/biology/cooperativebinding` | `cooperative-binding.bngl` | `cooperative-binding_metadata.yaml` | +| `Examples/biology/dnadamagerepair` | `dna-damage-repair.bngl` | `dna-damage-repair_metadata.yaml` | +| `Examples/biology/dnamethylationdynamics` | `dna-methylation-dynamics.bngl` | `dna-methylation-dynamics_metadata.yaml` | +| `Examples/biology/dr5apoptosissignaling` | `dr5-apoptosis-signaling.bngl` | `dr5-apoptosis-signaling_metadata.yaml` | +| `Examples/biology/dualsitephosphorylation` | `dual-site-phosphorylation.bngl` | `dual-site-phosphorylation_metadata.yaml` | +| `Examples/biology/e2frbcellcycleswitch` | `e2f-rb-cell-cycle-switch.bngl` | `e2f-rb-cell-cycle-switch_metadata.yaml` | +| `Examples/biology/interferonsignaling` | `interferon-signaling.bngl` | `interferon-signaling_metadata.yaml` | +| `Examples/biology/ire1axbp1erstress` | `ire1a-xbp1-er-stress.bngl` | `ire1a-xbp1-er-stress_metadata.yaml` | +| `Examples/biology/jakstatcytokinesignaling` | `jak-stat-cytokine-signaling.bngl` | `jak-stat-cytokine-signaling_metadata.yaml` | +| `Examples/biology/jnkmapksignaling` | `jnk-mapk-signaling.bngl` | `jnk-mapk-signaling_metadata.yaml` | +| `Examples/biology/kirchannelregulation` | `kir-channel-regulation.bngl` | `kir-channel-regulation_metadata.yaml` | +| `Examples/biology/lacoperonregulation` | `lac-operon-regulation.bngl` | `lac-operon-regulation_metadata.yaml` | +| `Examples/biology/michaelismentenkinetics` | `michaelis-menten-kinetics.bngl` | `michaelis-menten-kinetics_metadata.yaml` | +| `Examples/biology/mtorc2signaling` | `mtorc2-signaling.bngl` | `mtorc2-signaling_metadata.yaml` | +| `Examples/biology/mtorsignaling` | `mtor-signaling.bngl` | `mtor-signaling_metadata.yaml` | +| `Examples/biology/myogenicdifferentiation` | `myogenic-differentiation.bngl` | `myogenic-differentiation_metadata.yaml` | +| `Examples/biology/negativefeedbackloop` | `negative-feedback-loop.bngl` | `negative-feedback-loop_metadata.yaml` | +| `Examples/biology/neurotransmitterrelease` | `neurotransmitter-release.bngl` | `neurotransmitter-release_metadata.yaml` | +| `Examples/biology/nfkbfeedback` | `nfkb-feedback.bngl` | `nfkb-feedback_metadata.yaml` | +| `Examples/biology/nocgmpsignaling` | `no-cgmp-signaling.bngl` | `no-cgmp-signaling_metadata.yaml` | +| `Examples/biology/notchdeltalateralinhibition` | `notch-delta-lateral-inhibition.bngl` | `notch-delta-lateral-inhibition_metadata.yaml` | +| `Examples/biology/oxidativestressresponse` | `oxidative-stress-response.bngl` | `oxidative-stress-response_metadata.yaml` | +| `Examples/biology/p38mapksignaling` | `p38-mapk-signaling.bngl` | `p38-mapk-signaling_metadata.yaml` | +| `Examples/biology/p53mdm2oscillator` | `p53-mdm2-oscillator.bngl` | `p53-mdm2-oscillator_metadata.yaml` | +| `Examples/biology/parp1mediateddnarepair` | `parp1-mediated-dna-repair.bngl` | `parp1-mediated-dna-repair_metadata.yaml` | +| `Examples/biology/phosphorelaychain` | `phosphorelay-chain.bngl` | `phosphorelay-chain_metadata.yaml` | +| `Examples/biology/plateletactivation` | `platelet-activation.bngl` | `platelet-activation_metadata.yaml` | +| `Examples/biology/predatorpreydynamics` | `predator-prey-dynamics.bngl` | `predator-prey-dynamics_metadata.yaml` | +| `Examples/biology/rabgtpasecycle` | `rab-gtpase-cycle.bngl` | `rab-gtpase-cycle_metadata.yaml` | +| `Examples/biology/ranklranksignaling` | `rankl-rank-signaling.bngl` | `rankl-rank-signaling_metadata.yaml` | +| `Examples/biology/rasgefgapcycle` | `ras-gef-gap-cycle.bngl` | `ras-gef-gap-cycle_metadata.yaml` | +| `Examples/biology/repressilatoroscillator` | `repressilator-oscillator.bngl` | `repressilator-oscillator_metadata.yaml` | +| `Examples/biology/retinoicacidsignaling` | `retinoic-acid-signaling.bngl` | `retinoic-acid-signaling_metadata.yaml` | +| `Examples/biology/rhogtpaseactincytoskeleton` | `rho-gtpase-actin-cytoskeleton.bngl` | `rho-gtpase-actin-cytoskeleton_metadata.yaml` | +| `Examples/biology/shp2phosphataseregulation` | `shp2-phosphatase-regulation.bngl` | `shp2-phosphatase-regulation_metadata.yaml` | +| `Examples/biology/signalamplificationcascade` | `signal-amplification-cascade.bngl` | `signal-amplification-cascade_metadata.yaml` | +| `Examples/biology/simpledimerization` | `simple-dimerization.bngl` | `simple-dimerization_metadata.yaml` | +| `Examples/biology/sirepidemicmodel` | `sir-epidemic-model.bngl` | `sir-epidemic-model_metadata.yaml` | +| `Examples/biology/smadtgfbetasignaling` | `smad-tgf-beta-signaling.bngl` | `smad-tgf-beta-signaling_metadata.yaml` | +| `Examples/biology/sonichedgehoggradient` | `sonic-hedgehog-gradient.bngl` | `sonic-hedgehog-gradient_metadata.yaml` | +| `Examples/nfsim/nfsimhybridparticlefield` | `nfsim_hybrid_particle_field.bngl` | `nfsim_hybrid_particle_field_metadata.yaml` | +| `Tutorials/General/chemistry` | `chemistry.bngl` | `chemistry_metadata.yaml` | +| `Tutorials/General/polymer` | `polymer.bngl` | `polymer_metadata.yaml` | +| `Tutorials/General/toy1` | `toy1.bngl` | `toy1_metadata.yaml` | +| `Tutorials/General/toy2` | `toy2.bngl` | `toy2_metadata.yaml` | + +## Ambiguous directories (skipped) + +No new metadata copy was created in these directories because one `metadata.yaml` could not be paired unambiguously with a single BNGL file. + +| Directory | BNGL count | +|---|---:| +| `Published/Faeder2003` | 2 | +| `Published/Hlavacek2018Elephant` | 2 | +| `Published/Hlavacek2018Restructuration` | 7 | +| `Published/Lin2019` | 3 | +| `Published/Mallela2021` | 50 | +| `Published/Mallela2021_Cities` | 15 | +| `Published/Mallela2022_MSAs` | 281 | +| `Published/Miller2022_NavajoNation` | 5 | +| `Published/Miller2025_MEK` | 10 | +| `Published/Mitra2019/02-egfr` | 2 | +| `Published/Mitra2019/05-threestep` | 2 | +| `Published/Mitra2019/13-receptor` | 2 | +| `Published/Mitra2019/17-egfr-ssa` | 2 | +| `Published/Mitra2019/18-mapk` | 2 | +| `Published/Mitra2019/28-mapk` | 2 | +| `Published/Mitra2019/30-jobs` | 2 | +| `Published/Mitra2019Rab` | 4 | +| `Published/Mitra2019Rab/pybnf_files` | 4 | +| `Published/Salazar-Cavazos2019` | 7 | +| `Published/Thomas2016` | 7 | + +## Earlier ambiguous copies removed + +| Removed file | Reason | +|---|---| +| `Published/Hlavacek2018Elephant/Hlavacek_2018_Elephant_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Hlavacek2018Restructuration/Hlavacek_2018_Restructuration_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Lin2019/Lin_2019_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Mallela2021/Mallela_2021_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Mallela2021_Cities/Mallela2021_Cities_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Mallela2022_MSAs/Mallela2022_MSAs_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Miller2022_NavajoNation/Miller2022_NavajoNation_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Miller2025_MEK/Miller2025_MEK_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Mitra2019Rab/Mitra_2019_Rab_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Salazar-Cavazos2019/Salazar-Cavazos_2019_metadata.yaml` | Parent directory contains multiple BNGL files. | +| `Published/Thomas2016/Thomas_2016_metadata.yaml` | Parent directory contains multiple BNGL files. | + +## Directories without a same-directory BNGL file (skipped) + +None. diff --git a/data/summaries_brief/An2009_ai_simple.md b/data/summaries_brief/An2009_ai_simple.md new file mode 100644 index 00000000..62069c26 --- /dev/null +++ b/data/summaries_brief/An2009_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: An 2009 + +## One-sentence summary + +Toll-like receptor 4 signaling from LPS recognition to NF-kB-driven inflammatory gene expression. + +## What the model shows + +This model shows how an LPS stimulus can be assembled on CD14, MD2, and TLR4, then routed through TRAM/TRIF and MAL/MyD88 adaptor arms to activate TAK1, the IKK complex, and NF-kB. It also shows feedback through newly produced A20 and IkB, so the inflammatory response is not simply turned on but is later restrained. + +## Biological story + +An 2009 is best read as a receptor-to-transcription cascade. It begins with microbial LPS recognition, passes through two adaptor routes, and ends with NF-kB-dependent inflammatory outputs that are later restrained by the very genes NF-kB helps induce. + +## Main biological players + +LPS, CD14, MD2, TLR4, TRAM, TRIF, MAL, MyD88, IRAK1, IRAK4, TRAF6, TAK1, IKK complex, NF-kB, IkB, A20, TNF. + +## Mechanism in plain English + +LPS is first captured by MD2 and CD14 and presented to TLR4. TLR4 complexes recruit TRAM/TRIF or MAL/MyD88 adaptors, which gather kinases and adaptor proteins such as IRAK and TRAF6. These assemblies activate TAK1 and then the IKK complex. Active IKK promotes release and activation of NF-kB, allowing NF-kB to enter the nucleus and drive transcription of inflammatory outputs such as TNF and regulatory outputs such as A20 and IkB. A20 and IkB then provide negative feedback by breaking signaling complexes, turning off IKK activity, recapturing NF-kB, or promoting degradation of signaling intermediates. + +## Key modeled events + +- LPS is assembled with CD14 and MD2 before engaging TLR4, so receptor activation depends on coreceptor-mediated ligand presentation. +- TLR4 complexes branch through TRAM/TRIF and MAL/MyD88 adaptor routes, allowing the same stimulus to feed multiple inflammatory signaling arms. +- IKK-driven NF-kB activation is countered by A20 and IkB feedback, so the model can show both signal rise and signal shutoff. + +## What the model measures + +The readouts follow TNF production, activated TAK1, activated IKK, A20 abundance, nuclear/active NF-kB, and NF-kB bound to IkB. A biologist should read the plots as a timed inflammatory signaling response with built-in delayed negative feedback. + +## Expected behavior in plots + +The most informative plots would show an early rise in TAK1 and IKK activity, followed by NF-kB activation and later accumulation of TNF, A20, and IkB. A20 or IkB rising after NF-kB indicates delayed negative feedback rather than a separate stimulus. + +## Caveats + +This summary treats the model as a pathway-level TLR4/NF-kB explanation. It does not claim that every possible TLR4 adaptor, cytokine, or cell-type-specific regulator is represented. diff --git a/data/summaries_brief/An2009_aigenerated.md b/data/summaries_brief/An2009_aigenerated.md new file mode 100644 index 00000000..62069c26 --- /dev/null +++ b/data/summaries_brief/An2009_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: An 2009 + +## One-sentence summary + +Toll-like receptor 4 signaling from LPS recognition to NF-kB-driven inflammatory gene expression. + +## What the model shows + +This model shows how an LPS stimulus can be assembled on CD14, MD2, and TLR4, then routed through TRAM/TRIF and MAL/MyD88 adaptor arms to activate TAK1, the IKK complex, and NF-kB. It also shows feedback through newly produced A20 and IkB, so the inflammatory response is not simply turned on but is later restrained. + +## Biological story + +An 2009 is best read as a receptor-to-transcription cascade. It begins with microbial LPS recognition, passes through two adaptor routes, and ends with NF-kB-dependent inflammatory outputs that are later restrained by the very genes NF-kB helps induce. + +## Main biological players + +LPS, CD14, MD2, TLR4, TRAM, TRIF, MAL, MyD88, IRAK1, IRAK4, TRAF6, TAK1, IKK complex, NF-kB, IkB, A20, TNF. + +## Mechanism in plain English + +LPS is first captured by MD2 and CD14 and presented to TLR4. TLR4 complexes recruit TRAM/TRIF or MAL/MyD88 adaptors, which gather kinases and adaptor proteins such as IRAK and TRAF6. These assemblies activate TAK1 and then the IKK complex. Active IKK promotes release and activation of NF-kB, allowing NF-kB to enter the nucleus and drive transcription of inflammatory outputs such as TNF and regulatory outputs such as A20 and IkB. A20 and IkB then provide negative feedback by breaking signaling complexes, turning off IKK activity, recapturing NF-kB, or promoting degradation of signaling intermediates. + +## Key modeled events + +- LPS is assembled with CD14 and MD2 before engaging TLR4, so receptor activation depends on coreceptor-mediated ligand presentation. +- TLR4 complexes branch through TRAM/TRIF and MAL/MyD88 adaptor routes, allowing the same stimulus to feed multiple inflammatory signaling arms. +- IKK-driven NF-kB activation is countered by A20 and IkB feedback, so the model can show both signal rise and signal shutoff. + +## What the model measures + +The readouts follow TNF production, activated TAK1, activated IKK, A20 abundance, nuclear/active NF-kB, and NF-kB bound to IkB. A biologist should read the plots as a timed inflammatory signaling response with built-in delayed negative feedback. + +## Expected behavior in plots + +The most informative plots would show an early rise in TAK1 and IKK activity, followed by NF-kB activation and later accumulation of TNF, A20, and IkB. A20 or IkB rising after NF-kB indicates delayed negative feedback rather than a separate stimulus. + +## Caveats + +This summary treats the model as a pathway-level TLR4/NF-kB explanation. It does not claim that every possible TLR4 adaptor, cytokine, or cell-type-specific regulator is represented. diff --git a/data/summaries_brief/Barua2007_ai_simple.md b/data/summaries_brief/Barua2007_ai_simple.md new file mode 100644 index 00000000..7de7b1f2 --- /dev/null +++ b/data/summaries_brief/Barua2007_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2007 + +## One-sentence summary + +SHP2 regulation by phosphorylated receptor dimers and intracomplex SH2-domain engagement. + +## What the model shows + +This model shows how a pre-dimerized receptor can recruit SHP2 and shift SHP2 from a closed, inhibited form toward an open, receptor-bound, catalytically productive form. The central question is how many receptor contacts SHP2 makes, and how those contacts affect receptor dephosphorylation. + +## Biological story + +Barua 2007 focuses on receptor-scaffold control of SHP2. The biological story is not just receptor phosphorylation, but how receptor geometry and SHP2 domain engagement can relieve autoinhibition and turn a recruited enzyme into an active local phosphatase. + +## Main biological players + +A receptor dimer with phosphorylated sites, SHP2 with C-terminal SH2, N-terminal SH2, and phosphatase domains, plus open and closed SHP2 conformations. + +## Mechanism in plain English + +Phosphorylated receptor sites recruit SHP2. SHP2 can bind through different domains, and once one domain is tethered, other parts of the same SHP2 molecule can engage nearby sites on the same receptor dimer. The model distinguishes simple recruitment from stronger intracomplex engagement. Opening SHP2 exposes catalytic function, allowing SHP2 to remove phosphate groups from receptor sites. + +## Key modeled events + +- Phosphorylated receptor dimers recruit SHP2 through SH2-domain contacts, creating receptor-bound phosphatase complexes. +- SHP2 can transition from a closed inhibited form toward an open form when receptor binding stabilizes active conformations. +- Open SHP2 removes phosphate groups from receptor sites, creating a negative-feedback loop on the receptor scaffold itself. + +## What the model measures + +The readouts distinguish free receptor, receptor bound to SHP2, multiply engaged receptor-SHP2 complexes, open SHP2, and phosphorylated receptor. They show how receptor scaffolding and SHP2 conformational opening control the amount of active phosphatase complex. + +## Expected behavior in plots + +Useful plots would compare phosphorylated receptor, receptor-bound SHP2, and open SHP2. A rise in open or multiply engaged SHP2 together with falling receptor phosphorylation would support the intended feedback mechanism. + +## Caveats + +The model abstracts SHP2 regulation into receptor-binding and conformational states. It should not be read as a complete map of all SHP2 partners or all receptor-family signaling outputs. diff --git a/data/summaries_brief/Barua2007_aigenerated.md b/data/summaries_brief/Barua2007_aigenerated.md new file mode 100644 index 00000000..7de7b1f2 --- /dev/null +++ b/data/summaries_brief/Barua2007_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2007 + +## One-sentence summary + +SHP2 regulation by phosphorylated receptor dimers and intracomplex SH2-domain engagement. + +## What the model shows + +This model shows how a pre-dimerized receptor can recruit SHP2 and shift SHP2 from a closed, inhibited form toward an open, receptor-bound, catalytically productive form. The central question is how many receptor contacts SHP2 makes, and how those contacts affect receptor dephosphorylation. + +## Biological story + +Barua 2007 focuses on receptor-scaffold control of SHP2. The biological story is not just receptor phosphorylation, but how receptor geometry and SHP2 domain engagement can relieve autoinhibition and turn a recruited enzyme into an active local phosphatase. + +## Main biological players + +A receptor dimer with phosphorylated sites, SHP2 with C-terminal SH2, N-terminal SH2, and phosphatase domains, plus open and closed SHP2 conformations. + +## Mechanism in plain English + +Phosphorylated receptor sites recruit SHP2. SHP2 can bind through different domains, and once one domain is tethered, other parts of the same SHP2 molecule can engage nearby sites on the same receptor dimer. The model distinguishes simple recruitment from stronger intracomplex engagement. Opening SHP2 exposes catalytic function, allowing SHP2 to remove phosphate groups from receptor sites. + +## Key modeled events + +- Phosphorylated receptor dimers recruit SHP2 through SH2-domain contacts, creating receptor-bound phosphatase complexes. +- SHP2 can transition from a closed inhibited form toward an open form when receptor binding stabilizes active conformations. +- Open SHP2 removes phosphate groups from receptor sites, creating a negative-feedback loop on the receptor scaffold itself. + +## What the model measures + +The readouts distinguish free receptor, receptor bound to SHP2, multiply engaged receptor-SHP2 complexes, open SHP2, and phosphorylated receptor. They show how receptor scaffolding and SHP2 conformational opening control the amount of active phosphatase complex. + +## Expected behavior in plots + +Useful plots would compare phosphorylated receptor, receptor-bound SHP2, and open SHP2. A rise in open or multiply engaged SHP2 together with falling receptor phosphorylation would support the intended feedback mechanism. + +## Caveats + +The model abstracts SHP2 regulation into receptor-binding and conformational states. It should not be read as a complete map of all SHP2 partners or all receptor-family signaling outputs. diff --git a/data/summaries_brief/Barua2009_ai_simple.md b/data/summaries_brief/Barua2009_ai_simple.md new file mode 100644 index 00000000..2a245aca --- /dev/null +++ b/data/summaries_brief/Barua2009_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2009 + +## One-sentence summary + +SH2B dimerization as a scaffold for JAK2 phosphorylation. + +## What the model shows + +This compact model shows how SH2B can bring JAK2 molecules together. It focuses on the idea that dimerized SH2B creates a platform where JAK2 molecules are held close enough for phosphorylation to occur more efficiently. + +## Biological story + +Barua 2009 is a minimal scaffold-amplification story. SH2B does not merely bind JAK2; by dimerizing, it changes the spatial organization of JAK2 and makes phosphorylation more efficient inside a shared complex. + +## Main biological players + +JAK2, represented with a recruitment site and a phosphorylation state, and SH2B, represented with an SH2 binding region and a dimerization region. + +## Mechanism in plain English + +Phosphorylated JAK2 recruits SH2B through the SH2 region. SH2B molecules dimerize, which can bring two JAK2 molecules into one shared complex. JAK2 phosphorylation is slower when both JAK2 molecules are unphosphorylated and faster when one JAK2 is already phosphorylated, capturing cooperative signal amplification. + +## Key modeled events + +- Phosphorylated JAK2 recruits SH2B, linking kinase activation to scaffold binding. +- SH2B dimerization brings two JAK2 molecules into the same assembly, increasing opportunities for JAK2-to-JAK2 phosphorylation. +- A partially activated JAK2-containing complex phosphorylates remaining inactive JAK2 more quickly, representing cooperative amplification. + +## What the model measures + +The readouts track free JAK2, JAK2-SH2B complexes of increasing size, active phosphorylated JAK2, and inactive unphosphorylated JAK2. The model shows how scaffold assembly changes JAK2 activation. + +## Expected behavior in plots + +Plots should be read by comparing inactive JAK2, active JAK2, and JAK2-SH2B assemblies. Accumulation of larger scaffolded complexes should coincide with stronger JAK2 phosphorylation if scaffold amplification dominates. + +## Caveats + +Because the model is intentionally compact, it omits many receptor-level and downstream JAK/STAT details. Its strength is isolating the SH2B dimerization effect. diff --git a/data/summaries_brief/Barua2009_aigenerated.md b/data/summaries_brief/Barua2009_aigenerated.md new file mode 100644 index 00000000..2a245aca --- /dev/null +++ b/data/summaries_brief/Barua2009_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2009 + +## One-sentence summary + +SH2B dimerization as a scaffold for JAK2 phosphorylation. + +## What the model shows + +This compact model shows how SH2B can bring JAK2 molecules together. It focuses on the idea that dimerized SH2B creates a platform where JAK2 molecules are held close enough for phosphorylation to occur more efficiently. + +## Biological story + +Barua 2009 is a minimal scaffold-amplification story. SH2B does not merely bind JAK2; by dimerizing, it changes the spatial organization of JAK2 and makes phosphorylation more efficient inside a shared complex. + +## Main biological players + +JAK2, represented with a recruitment site and a phosphorylation state, and SH2B, represented with an SH2 binding region and a dimerization region. + +## Mechanism in plain English + +Phosphorylated JAK2 recruits SH2B through the SH2 region. SH2B molecules dimerize, which can bring two JAK2 molecules into one shared complex. JAK2 phosphorylation is slower when both JAK2 molecules are unphosphorylated and faster when one JAK2 is already phosphorylated, capturing cooperative signal amplification. + +## Key modeled events + +- Phosphorylated JAK2 recruits SH2B, linking kinase activation to scaffold binding. +- SH2B dimerization brings two JAK2 molecules into the same assembly, increasing opportunities for JAK2-to-JAK2 phosphorylation. +- A partially activated JAK2-containing complex phosphorylates remaining inactive JAK2 more quickly, representing cooperative amplification. + +## What the model measures + +The readouts track free JAK2, JAK2-SH2B complexes of increasing size, active phosphorylated JAK2, and inactive unphosphorylated JAK2. The model shows how scaffold assembly changes JAK2 activation. + +## Expected behavior in plots + +Plots should be read by comparing inactive JAK2, active JAK2, and JAK2-SH2B assemblies. Accumulation of larger scaffolded complexes should coincide with stronger JAK2 phosphorylation if scaffold amplification dominates. + +## Caveats + +Because the model is intentionally compact, it omits many receptor-level and downstream JAK/STAT details. Its strength is isolating the SH2B dimerization effect. diff --git a/data/summaries_brief/Barua2013_ai_simple.md b/data/summaries_brief/Barua2013_ai_simple.md new file mode 100644 index 00000000..08ef711a --- /dev/null +++ b/data/summaries_brief/Barua2013_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2013 + +## One-sentence summary + +Beta-catenin control by the Axin/APC/GSK3/CK1 destruction complex. + +## What the model shows + +This model shows how beta-catenin is captured by a destruction complex, phosphorylated at specific regulatory sites, released or degraded, and replenished by synthesis. It emphasizes how Axin and APC organize beta-catenin with the kinases CK1 and GSK3. + +## Biological story + +Barua 2013 tells a destruction-complex cycle: beta-catenin is recruited to Axin/APC scaffolds, primed and phosphorylated by kinases, removed by degradation, and then replaced by new synthesis. + +## Main biological players + +Beta-catenin, APC, Axin, GSK3 beta, CK1 alpha, and degraded beta-catenin. + +## Mechanism in plain English + +Beta-catenin binds APC and Axin through different interaction surfaces. APC binds Axin, GSK3 binds Axin, and CK1 also binds Axin, assembling a phosphorylation-competent destruction complex. CK1 phosphorylates beta-catenin first, GSK3 phosphorylates additional beta-catenin sites, APC can also be phosphorylated, and phosphatase-like reactions reverse those modifications. Beta-catenin can be synthesized, degraded slowly when not appropriately phosphorylated, or degraded faster after phosphorylation. Degradation releases the associated complex members. + +## Key modeled events + +- Beta-catenin binds APC and Axin, placing it into the destruction-complex environment. +- CK1 and GSK3 phosphorylate beta-catenin in sequence, converting it into a form that is removed more rapidly. +- When beta-catenin is degraded, associated APC or Axin partners are released so the scaffold can participate in another cycle. + +## What the model measures + +The readouts track total live beta-catenin, beta-catenin phosphorylated at CK1 and GSK3 target sites, phosphorylated APC, and beta-catenin bound to Axin. The model shows how destruction-complex assembly controls the balance between beta-catenin persistence and removal. + +## Expected behavior in plots + +Plots should show whether beta-catenin remains mostly live and unmodified or shifts into phosphorylated and degraded forms. Increased beta-catenin-Axin association followed by phosphorylated beta-catenin supports destruction-complex processing. + +## Caveats + +The summary focuses on scaffolded beta-catenin control. It does not imply that the entire Wnt pathway, transcriptional beta-catenin output, or upstream ligand regulation is included. diff --git a/data/summaries_brief/Barua2013_aigenerated.md b/data/summaries_brief/Barua2013_aigenerated.md new file mode 100644 index 00000000..08ef711a --- /dev/null +++ b/data/summaries_brief/Barua2013_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2013 + +## One-sentence summary + +Beta-catenin control by the Axin/APC/GSK3/CK1 destruction complex. + +## What the model shows + +This model shows how beta-catenin is captured by a destruction complex, phosphorylated at specific regulatory sites, released or degraded, and replenished by synthesis. It emphasizes how Axin and APC organize beta-catenin with the kinases CK1 and GSK3. + +## Biological story + +Barua 2013 tells a destruction-complex cycle: beta-catenin is recruited to Axin/APC scaffolds, primed and phosphorylated by kinases, removed by degradation, and then replaced by new synthesis. + +## Main biological players + +Beta-catenin, APC, Axin, GSK3 beta, CK1 alpha, and degraded beta-catenin. + +## Mechanism in plain English + +Beta-catenin binds APC and Axin through different interaction surfaces. APC binds Axin, GSK3 binds Axin, and CK1 also binds Axin, assembling a phosphorylation-competent destruction complex. CK1 phosphorylates beta-catenin first, GSK3 phosphorylates additional beta-catenin sites, APC can also be phosphorylated, and phosphatase-like reactions reverse those modifications. Beta-catenin can be synthesized, degraded slowly when not appropriately phosphorylated, or degraded faster after phosphorylation. Degradation releases the associated complex members. + +## Key modeled events + +- Beta-catenin binds APC and Axin, placing it into the destruction-complex environment. +- CK1 and GSK3 phosphorylate beta-catenin in sequence, converting it into a form that is removed more rapidly. +- When beta-catenin is degraded, associated APC or Axin partners are released so the scaffold can participate in another cycle. + +## What the model measures + +The readouts track total live beta-catenin, beta-catenin phosphorylated at CK1 and GSK3 target sites, phosphorylated APC, and beta-catenin bound to Axin. The model shows how destruction-complex assembly controls the balance between beta-catenin persistence and removal. + +## Expected behavior in plots + +Plots should show whether beta-catenin remains mostly live and unmodified or shifts into phosphorylated and degraded forms. Increased beta-catenin-Axin association followed by phosphorylated beta-catenin supports destruction-complex processing. + +## Caveats + +The summary focuses on scaffolded beta-catenin control. It does not imply that the entire Wnt pathway, transcriptional beta-catenin output, or upstream ligand regulation is included. diff --git a/data/summaries_brief/BaruaBCR2012_ai_simple.md b/data/summaries_brief/BaruaBCR2012_ai_simple.md new file mode 100644 index 00000000..b0a73666 --- /dev/null +++ b/data/summaries_brief/BaruaBCR2012_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2012 + +## One-sentence summary + +Early B-cell receptor signaling with Lyn, Fyn, Syk, Csk, PAG, CD22, and phosphatase feedback. + +## What the model shows + +This model shows how tonic or antigen-induced B-cell receptor signaling is shaped by receptor ITAM phosphorylation, Src-family kinases, Syk recruitment, and multiple negative regulators. It is designed to compare how different kinase and phosphatase interactions tune early BCR output. + +## Biological story + +Barua BCR 2012 is a balance-of-forces model for early B-cell receptor signaling. Antigen, Lyn/Fyn, and Syk drive activation, while Csk/PAG, CD22, SHP1, SHIP, Dok, and RasGAP create multiple braking routes. + +## Main biological players + +B-cell receptor, Lyn, Fyn, Csk, PAG, Syk, CD22, SHP1, SHIP, Dok, RasGAP, Grb2, SOS, and antigen signal input. + +## Mechanism in plain English + +Antigen strengthens receptor clustering and receptor phosphorylation. Lyn and Fyn switch between activating and inhibitory phosphorylation states and phosphorylate receptor ITAMs. Doubly phosphorylated receptor sites recruit Syk, allowing Syk activation. Csk and PAG restrain Src-family kinases, while CD22, SHP1, SHIP, Dok, and RasGAP provide inhibitory routes. Adaptor binding links receptor-proximal phosphorylation to downstream signaling modules. + +## Key modeled events + +- Antigen input strengthens B-cell receptor signaling by promoting receptor phosphorylation and receptor-proximal complex assembly. +- Lyn and Fyn phosphorylate receptor ITAMs and themselves switch between activating and inhibitory phosphorylation states. +- Syk recruitment and activation provide positive signaling, while Csk, PAG, CD22, SHP1, SHIP, Dok, and RasGAP restrain the response. + +## What the model measures + +The readouts follow receptor phosphorylation, active Lyn/Fyn/Syk states, inhibitory complexes, and downstream adaptor recruitment. The model shows how BCR signal strength emerges from a balance of positive kinase action and negative feedback. + +## Expected behavior in plots + +Plots should be interpreted by comparing receptor phosphorylation and Syk activation against inhibitory species. Strong receptor phosphorylation with weak inhibitory buildup suggests activation; rising inhibitory complexes suggest signal damping. + +## Caveats + +The model is detailed for early receptor-proximal BCR signaling, but it should not be treated as a full B-cell fate or transcriptional-response model. diff --git a/data/summaries_brief/BaruaBCR2012_aigenerated.md b/data/summaries_brief/BaruaBCR2012_aigenerated.md new file mode 100644 index 00000000..b0a73666 --- /dev/null +++ b/data/summaries_brief/BaruaBCR2012_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Barua 2012 + +## One-sentence summary + +Early B-cell receptor signaling with Lyn, Fyn, Syk, Csk, PAG, CD22, and phosphatase feedback. + +## What the model shows + +This model shows how tonic or antigen-induced B-cell receptor signaling is shaped by receptor ITAM phosphorylation, Src-family kinases, Syk recruitment, and multiple negative regulators. It is designed to compare how different kinase and phosphatase interactions tune early BCR output. + +## Biological story + +Barua BCR 2012 is a balance-of-forces model for early B-cell receptor signaling. Antigen, Lyn/Fyn, and Syk drive activation, while Csk/PAG, CD22, SHP1, SHIP, Dok, and RasGAP create multiple braking routes. + +## Main biological players + +B-cell receptor, Lyn, Fyn, Csk, PAG, Syk, CD22, SHP1, SHIP, Dok, RasGAP, Grb2, SOS, and antigen signal input. + +## Mechanism in plain English + +Antigen strengthens receptor clustering and receptor phosphorylation. Lyn and Fyn switch between activating and inhibitory phosphorylation states and phosphorylate receptor ITAMs. Doubly phosphorylated receptor sites recruit Syk, allowing Syk activation. Csk and PAG restrain Src-family kinases, while CD22, SHP1, SHIP, Dok, and RasGAP provide inhibitory routes. Adaptor binding links receptor-proximal phosphorylation to downstream signaling modules. + +## Key modeled events + +- Antigen input strengthens B-cell receptor signaling by promoting receptor phosphorylation and receptor-proximal complex assembly. +- Lyn and Fyn phosphorylate receptor ITAMs and themselves switch between activating and inhibitory phosphorylation states. +- Syk recruitment and activation provide positive signaling, while Csk, PAG, CD22, SHP1, SHIP, Dok, and RasGAP restrain the response. + +## What the model measures + +The readouts follow receptor phosphorylation, active Lyn/Fyn/Syk states, inhibitory complexes, and downstream adaptor recruitment. The model shows how BCR signal strength emerges from a balance of positive kinase action and negative feedback. + +## Expected behavior in plots + +Plots should be interpreted by comparing receptor phosphorylation and Syk activation against inhibitory species. Strong receptor phosphorylation with weak inhibitory buildup suggests activation; rising inhibitory complexes suggest signal damping. + +## Caveats + +The model is detailed for early receptor-proximal BCR signaling, but it should not be treated as a full B-cell fate or transcriptional-response model. diff --git a/data/summaries_brief/BaruaFceRI2012_ai_simple.md b/data/summaries_brief/BaruaFceRI2012_ai_simple.md new file mode 100644 index 00000000..23300e60 --- /dev/null +++ b/data/summaries_brief/BaruaFceRI2012_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: BaruaFceRI 2012 + +## One-sentence summary + +FcεRI signaling regulated by ligand crosslinking, Lyn/Syk activation, LAT signaling, and raft localization. + +## What the model shows + +This model shows how multivalent ligand and hapten binding crosslink FcεRI receptors and how that receptor clustering is translated into phosphorylation of receptor chains, Syk, and LAT. It also asks how membrane raft localization changes signaling by altering phosphorylation and dephosphorylation rates. + +## Biological story + +BaruaFceRI 2012 connects receptor crosslinking to membrane-context-dependent signaling. The central story is that FcεRI aggregation enables Lyn and Syk activation, while raft localization changes how strongly phosphorylation is sustained. + +## Main biological players + +FcεRI receptor, multivalent ligand or hapten, Lyn, Syk, LAT, Grb2, and raft versus non-raft localization states. + +## Mechanism in plain English + +Ligand binds receptor-associated antibody arms and crosslinks receptors. Lyn binds receptors and phosphorylates receptor ITAMs. Phosphorylated receptors recruit Syk, Syk becomes activated, and active Syk phosphorylates LAT. LAT recruits Grb2-containing complexes. Proteins can move between raft and non-raft environments, changing how readily they are phosphorylated or dephosphorylated. + +## Key modeled events + +- Ligand and hapten binding crosslink FcεRI, converting receptor occupancy into receptor clustering. +- Lyn phosphorylates receptor chains, allowing Syk recruitment and activation at the membrane. +- LAT phosphorylation and Grb2 recruitment transmit the receptor signal downstream, while raft localization changes the effective strength of phosphorylation and dephosphorylation. + +## What the model measures + +The readouts track receptor aggregates, phosphorylated receptor, receptor-bound Syk, phosphorylated Syk, phosphorylated LAT, and raft-associated signaling species. The model shows how receptor clustering and membrane microenvironment jointly control early FcεRI output. + +## Expected behavior in plots + +Useful plots would show receptor aggregates first, then phosphorylated receptor/Syk/LAT species. Differences between raft and non-raft species indicate how membrane localization changes signaling efficiency. + +## Caveats + +The model emphasizes early FcεRI signaling and raft effects. Later mast-cell outputs such as secretion, transcription, or long-term adaptation are outside its main scope. diff --git a/data/summaries_brief/BaruaFceRI2012_aigenerated.md b/data/summaries_brief/BaruaFceRI2012_aigenerated.md new file mode 100644 index 00000000..23300e60 --- /dev/null +++ b/data/summaries_brief/BaruaFceRI2012_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: BaruaFceRI 2012 + +## One-sentence summary + +FcεRI signaling regulated by ligand crosslinking, Lyn/Syk activation, LAT signaling, and raft localization. + +## What the model shows + +This model shows how multivalent ligand and hapten binding crosslink FcεRI receptors and how that receptor clustering is translated into phosphorylation of receptor chains, Syk, and LAT. It also asks how membrane raft localization changes signaling by altering phosphorylation and dephosphorylation rates. + +## Biological story + +BaruaFceRI 2012 connects receptor crosslinking to membrane-context-dependent signaling. The central story is that FcεRI aggregation enables Lyn and Syk activation, while raft localization changes how strongly phosphorylation is sustained. + +## Main biological players + +FcεRI receptor, multivalent ligand or hapten, Lyn, Syk, LAT, Grb2, and raft versus non-raft localization states. + +## Mechanism in plain English + +Ligand binds receptor-associated antibody arms and crosslinks receptors. Lyn binds receptors and phosphorylates receptor ITAMs. Phosphorylated receptors recruit Syk, Syk becomes activated, and active Syk phosphorylates LAT. LAT recruits Grb2-containing complexes. Proteins can move between raft and non-raft environments, changing how readily they are phosphorylated or dephosphorylated. + +## Key modeled events + +- Ligand and hapten binding crosslink FcεRI, converting receptor occupancy into receptor clustering. +- Lyn phosphorylates receptor chains, allowing Syk recruitment and activation at the membrane. +- LAT phosphorylation and Grb2 recruitment transmit the receptor signal downstream, while raft localization changes the effective strength of phosphorylation and dephosphorylation. + +## What the model measures + +The readouts track receptor aggregates, phosphorylated receptor, receptor-bound Syk, phosphorylated Syk, phosphorylated LAT, and raft-associated signaling species. The model shows how receptor clustering and membrane microenvironment jointly control early FcεRI output. + +## Expected behavior in plots + +Useful plots would show receptor aggregates first, then phosphorylated receptor/Syk/LAT species. Differences between raft and non-raft species indicate how membrane localization changes signaling efficiency. + +## Caveats + +The model emphasizes early FcεRI signaling and raft effects. Later mast-cell outputs such as secretion, transcription, or long-term adaptation are outside its main scope. diff --git a/data/summaries_brief/Blinov2006_ai_simple.md b/data/summaries_brief/Blinov2006_ai_simple.md new file mode 100644 index 00000000..199ec3f0 --- /dev/null +++ b/data/summaries_brief/Blinov2006_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Blinov 2006 + +## One-sentence summary + +EGF receptor signaling through ligand binding, receptor aggregation, receptor phosphorylation, and Shc adaptor recruitment. + +## What the model shows + +This model shows the earliest combinatorial events after EGF stimulation: ligand binds EGFR, receptors aggregate, receptors phosphorylate one another, and phosphorylated receptor sites recruit Shc and downstream adaptor complexes. + +## Biological story + +Blinov 2006 follows EGFR from ligand binding to adaptor recruitment. The biological story is how receptor clustering creates phosphorylated docking sites that pull Shc, Grb2, and SOS into signaling-competent complexes. + +## Main biological players + +EGF ligand, EGFR receptor, Shc, Grb2, SOS, and phosphorylated receptor docking sites. + +## Mechanism in plain English + +EGF binds EGFR and promotes receptor aggregation. Aggregated receptors phosphorylate each other on tyrosine sites. Different phosphorylated sites have different abilities to recruit Shc or adaptor complexes. Shc itself can be phosphorylated, creating additional docking opportunities for Grb2 and SOS. Dephosphorylation reactions reverse receptor and Shc activation. + +## Key modeled events + +- EGF binding creates ligand-bound EGFR complexes that can aggregate with other receptors. +- Aggregated receptors phosphorylate one another on docking sites, creating binding platforms for adaptor proteins. +- Shc recruitment, Shc phosphorylation, and Grb2/SOS assembly connect receptor phosphorylation to downstream signaling. + +## What the model measures + +The readouts follow ligand-bound receptor, receptor aggregates, phosphorylated receptor sites, Shc recruitment, Shc phosphorylation, and Grb2/SOS adaptor complexes. The model shows how EGFR activation is converted into adaptor assembly. + +## Expected behavior in plots + +Plots should show ligand-bound receptor and receptor phosphorylation rising before Shc and Grb2/SOS-containing complexes. Loss of phosphorylation or adaptor complexes indicates dephosphorylation and complex turnover. + +## Caveats + +This is an early EGFR signaling model. It should not be read as a complete Ras/MAPK pathway simulation unless downstream modules are explicitly represented by readouts. diff --git a/data/summaries_brief/Blinov2006_aigenerated.md b/data/summaries_brief/Blinov2006_aigenerated.md new file mode 100644 index 00000000..199ec3f0 --- /dev/null +++ b/data/summaries_brief/Blinov2006_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Blinov 2006 + +## One-sentence summary + +EGF receptor signaling through ligand binding, receptor aggregation, receptor phosphorylation, and Shc adaptor recruitment. + +## What the model shows + +This model shows the earliest combinatorial events after EGF stimulation: ligand binds EGFR, receptors aggregate, receptors phosphorylate one another, and phosphorylated receptor sites recruit Shc and downstream adaptor complexes. + +## Biological story + +Blinov 2006 follows EGFR from ligand binding to adaptor recruitment. The biological story is how receptor clustering creates phosphorylated docking sites that pull Shc, Grb2, and SOS into signaling-competent complexes. + +## Main biological players + +EGF ligand, EGFR receptor, Shc, Grb2, SOS, and phosphorylated receptor docking sites. + +## Mechanism in plain English + +EGF binds EGFR and promotes receptor aggregation. Aggregated receptors phosphorylate each other on tyrosine sites. Different phosphorylated sites have different abilities to recruit Shc or adaptor complexes. Shc itself can be phosphorylated, creating additional docking opportunities for Grb2 and SOS. Dephosphorylation reactions reverse receptor and Shc activation. + +## Key modeled events + +- EGF binding creates ligand-bound EGFR complexes that can aggregate with other receptors. +- Aggregated receptors phosphorylate one another on docking sites, creating binding platforms for adaptor proteins. +- Shc recruitment, Shc phosphorylation, and Grb2/SOS assembly connect receptor phosphorylation to downstream signaling. + +## What the model measures + +The readouts follow ligand-bound receptor, receptor aggregates, phosphorylated receptor sites, Shc recruitment, Shc phosphorylation, and Grb2/SOS adaptor complexes. The model shows how EGFR activation is converted into adaptor assembly. + +## Expected behavior in plots + +Plots should show ligand-bound receptor and receptor phosphorylation rising before Shc and Grb2/SOS-containing complexes. Loss of phosphorylation or adaptor complexes indicates dephosphorylation and complex turnover. + +## Caveats + +This is an early EGFR signaling model. It should not be read as a complete Ras/MAPK pathway simulation unless downstream modules are explicitly represented by readouts. diff --git a/data/summaries_brief/Blinovegfr_ai_simple.md b/data/summaries_brief/Blinovegfr_ai_simple.md new file mode 100644 index 00000000..84cfa257 --- /dev/null +++ b/data/summaries_brief/Blinovegfr_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Blinov egfr + +## One-sentence summary + +A compact EGFR example showing receptor-ligand binding and receptor complex formation. + +## What the model shows + +This model is a small EGFR-centered rule-based example. It shows how ligand engagement and receptor binding states can be represented as receptor complexes rather than as a single on/off variable. + +## Biological story + +Blinov egfr is a compact receptor-complex example. It is useful for understanding how EGFR occupancy and receptor association can be modeled without including a large downstream network. + +## Main biological players + +EGF ligand, EGFR receptor, receptor binding sites, and compartment or membrane context if used by the model. + +## Mechanism in plain English + +Ligand associates with receptor, receptors can occupy different binding states, and the model tracks the formation and loss of receptor-containing complexes. The purpose is to demonstrate EGFR complex formation in a compact form rather than a full downstream signaling network. + +## Key modeled events + +- Ligand binding shifts EGFR from free receptor toward ligand-associated receptor complexes. +- Receptor interaction states are tracked as complexes rather than as a single active/inactive switch. +- The model emphasizes the formation and loss of receptor-containing assemblies as the central EGFR behavior. + +## What the model measures + +The readouts follow receptor or ligand-containing patterns and show how much receptor is free, ligand-associated, or complexed over time. + +## Expected behavior in plots + +Plots mainly distinguish free receptor from ligand-associated or complexed receptor. The important behavior is redistribution among receptor states, not a full signaling cascade. + +## Caveats + +Because this is a small EGFR example, biological interpretation should stay close to receptor binding and complex formation. diff --git a/data/summaries_brief/Blinovegfr_aigenerated.md b/data/summaries_brief/Blinovegfr_aigenerated.md new file mode 100644 index 00000000..84cfa257 --- /dev/null +++ b/data/summaries_brief/Blinovegfr_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Blinov egfr + +## One-sentence summary + +A compact EGFR example showing receptor-ligand binding and receptor complex formation. + +## What the model shows + +This model is a small EGFR-centered rule-based example. It shows how ligand engagement and receptor binding states can be represented as receptor complexes rather than as a single on/off variable. + +## Biological story + +Blinov egfr is a compact receptor-complex example. It is useful for understanding how EGFR occupancy and receptor association can be modeled without including a large downstream network. + +## Main biological players + +EGF ligand, EGFR receptor, receptor binding sites, and compartment or membrane context if used by the model. + +## Mechanism in plain English + +Ligand associates with receptor, receptors can occupy different binding states, and the model tracks the formation and loss of receptor-containing complexes. The purpose is to demonstrate EGFR complex formation in a compact form rather than a full downstream signaling network. + +## Key modeled events + +- Ligand binding shifts EGFR from free receptor toward ligand-associated receptor complexes. +- Receptor interaction states are tracked as complexes rather than as a single active/inactive switch. +- The model emphasizes the formation and loss of receptor-containing assemblies as the central EGFR behavior. + +## What the model measures + +The readouts follow receptor or ligand-containing patterns and show how much receptor is free, ligand-associated, or complexed over time. + +## Expected behavior in plots + +Plots mainly distinguish free receptor from ligand-associated or complexed receptor. The important behavior is redistribution among receptor states, not a full signaling cascade. + +## Caveats + +Because this is a small EGFR example, biological interpretation should stay close to receptor binding and complex formation. diff --git a/data/summaries_brief/Blinovran_ai_simple.md b/data/summaries_brief/Blinovran_ai_simple.md new file mode 100644 index 00000000..fba79cc5 --- /dev/null +++ b/data/summaries_brief/Blinovran_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Blinov ran + +## One-sentence summary + +A compact Ran-system example focused on nucleotide-state and compartment-related molecular cycling. + +## What the model shows + +This model is a small Ran-centered rule-based example. It shows how Ran-like molecular states and interactions can be represented with compartments and state transitions. + +## Biological story + +Blinov ran is a compact transport-cycle example. Its story is how Ran-like molecules change state and location through partner-dependent cycling rather than through a single linear reaction. + +## Main biological players + +Ran-related molecular species, binding partners, nucleotide or activity states, and compartment labels. + +## Mechanism in plain English + +The model follows molecular cycling between states and locations. Binding partners recognize particular Ran states, reactions convert Ran between forms, and compartment-aware rules constrain where events can occur. + +## Key modeled events + +- Ran-related species move through state changes that represent molecular cycling. +- Binding partners recognize particular Ran states, making interaction dependent on the current molecular form. +- Compartment-aware transitions shape where each Ran-related state accumulates. + +## What the model measures + +The readouts track the distribution of Ran-related species across states or compartments, showing how cycling changes the abundance of each form. + +## Expected behavior in plots + +Plots should be read as distributions of Ran-related forms across states or compartments. A shift in one form usually means cycling has moved material into a different molecular or spatial state. + +## Caveats + +The molecule names are compact, so this summary avoids assigning extra biological functions beyond Ran-state cycling and localization. diff --git a/data/summaries_brief/Blinovran_aigenerated.md b/data/summaries_brief/Blinovran_aigenerated.md new file mode 100644 index 00000000..fba79cc5 --- /dev/null +++ b/data/summaries_brief/Blinovran_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Blinov ran + +## One-sentence summary + +A compact Ran-system example focused on nucleotide-state and compartment-related molecular cycling. + +## What the model shows + +This model is a small Ran-centered rule-based example. It shows how Ran-like molecular states and interactions can be represented with compartments and state transitions. + +## Biological story + +Blinov ran is a compact transport-cycle example. Its story is how Ran-like molecules change state and location through partner-dependent cycling rather than through a single linear reaction. + +## Main biological players + +Ran-related molecular species, binding partners, nucleotide or activity states, and compartment labels. + +## Mechanism in plain English + +The model follows molecular cycling between states and locations. Binding partners recognize particular Ran states, reactions convert Ran between forms, and compartment-aware rules constrain where events can occur. + +## Key modeled events + +- Ran-related species move through state changes that represent molecular cycling. +- Binding partners recognize particular Ran states, making interaction dependent on the current molecular form. +- Compartment-aware transitions shape where each Ran-related state accumulates. + +## What the model measures + +The readouts track the distribution of Ran-related species across states or compartments, showing how cycling changes the abundance of each form. + +## Expected behavior in plots + +Plots should be read as distributions of Ran-related forms across states or compartments. A shift in one form usually means cycling has moved material into a different molecular or spatial state. + +## Caveats + +The molecule names are compact, so this summary avoids assigning extra biological functions beyond Ran-state cycling and localization. diff --git a/data/summaries_brief/Chattaraj2021_ai_simple.md b/data/summaries_brief/Chattaraj2021_ai_simple.md new file mode 100644 index 00000000..72914e0e --- /dev/null +++ b/data/summaries_brief/Chattaraj2021_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Chattaraj 2021 + +## One-sentence summary + +Multivalent Nephrin-Nck-NWASP clustering as a model of heterotypic biomolecular condensate formation. + +## What the model shows + +This model shows how three multivalent signaling molecules can assemble into clusters through repeated binding interactions. It is tied to the idea that condensate formation depends on binding affinities and the availability of multiple interaction sites. + +## Biological story + +Chattaraj 2021 is about multivalency and phase-like assembly. Nephrin, Nck, and NWASP create clusters because each molecule can make several simultaneous contacts, allowing small complexes to grow cooperatively. + +## Main biological players + +Nephrin, Nck, NWASP, and their repeated binding modules. + +## Mechanism in plain English + +Nephrin provides multiple binding sites for Nck. Nck provides domains that connect Nephrin to NWASP. NWASP contributes additional multivalent sites, allowing small complexes to grow into larger heterogeneous clusters. Binding and unbinding rates determine whether the system remains mostly dispersed or shifts toward larger assemblies. + +## Key modeled events + +- Nephrin recruits Nck through repeated binding modules, creating multivalent receptor-proximal assemblies. +- Nck links Nephrin to NWASP, and NWASP adds more interaction sites that enlarge clusters. +- Binding affinity and the number of available sites determine whether molecules remain dispersed or form larger condensate-like clusters. + +## What the model measures + +The readouts track free molecules and clustered complexes. The model shows how multivalency and affinity can create a threshold-like transition into condensate-like signaling assemblies. + +## Expected behavior in plots + +Plots should distinguish dispersed molecules from clustered assemblies. A sharp increase in large complexes or clustered material indicates crossing into a condensate-like regime. + +## Caveats + +The model addresses clustering logic and solubility-product behavior; it does not by itself prove liquid-like material properties or downstream actin remodeling outcomes. diff --git a/data/summaries_brief/Chattaraj2021_aigenerated.md b/data/summaries_brief/Chattaraj2021_aigenerated.md new file mode 100644 index 00000000..72914e0e --- /dev/null +++ b/data/summaries_brief/Chattaraj2021_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Chattaraj 2021 + +## One-sentence summary + +Multivalent Nephrin-Nck-NWASP clustering as a model of heterotypic biomolecular condensate formation. + +## What the model shows + +This model shows how three multivalent signaling molecules can assemble into clusters through repeated binding interactions. It is tied to the idea that condensate formation depends on binding affinities and the availability of multiple interaction sites. + +## Biological story + +Chattaraj 2021 is about multivalency and phase-like assembly. Nephrin, Nck, and NWASP create clusters because each molecule can make several simultaneous contacts, allowing small complexes to grow cooperatively. + +## Main biological players + +Nephrin, Nck, NWASP, and their repeated binding modules. + +## Mechanism in plain English + +Nephrin provides multiple binding sites for Nck. Nck provides domains that connect Nephrin to NWASP. NWASP contributes additional multivalent sites, allowing small complexes to grow into larger heterogeneous clusters. Binding and unbinding rates determine whether the system remains mostly dispersed or shifts toward larger assemblies. + +## Key modeled events + +- Nephrin recruits Nck through repeated binding modules, creating multivalent receptor-proximal assemblies. +- Nck links Nephrin to NWASP, and NWASP adds more interaction sites that enlarge clusters. +- Binding affinity and the number of available sites determine whether molecules remain dispersed or form larger condensate-like clusters. + +## What the model measures + +The readouts track free molecules and clustered complexes. The model shows how multivalency and affinity can create a threshold-like transition into condensate-like signaling assemblies. + +## Expected behavior in plots + +Plots should distinguish dispersed molecules from clustered assemblies. A sharp increase in large complexes or clustered material indicates crossing into a condensate-like regime. + +## Caveats + +The model addresses clustering logic and solubility-product behavior; it does not by itself prove liquid-like material properties or downstream actin remodeling outcomes. diff --git a/data/summaries_brief/CheemalavaguJAKSTAT_ai_simple.md b/data/summaries_brief/CheemalavaguJAKSTAT_ai_simple.md new file mode 100644 index 00000000..258a9d91 --- /dev/null +++ b/data/summaries_brief/CheemalavaguJAKSTAT_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Cheemalavagu 2024 + +## One-sentence summary + +IL-6 and IL-10 JAK/STAT signaling with STAT activation and SOCS-mediated inhibition. + +## What the model shows + +This model shows how IL-6 and IL-10 receptor systems activate JAK kinases and STAT transcription factors while SOCS proteins inhibit parts of the pathway. It captures pathway crosstalk because shared JAK/STAT machinery can be engaged by distinct cytokine receptors. + +## Biological story + +Cheemalavagu JAK/STAT is a cytokine-crosstalk story. IL-6 and IL-10 use receptor/JAK assemblies to activate STATs, while SOCS proteins form inducible brakes that can reshape subsequent signaling. + +## Main biological players + +IL-6, IL-10, their receptors, JAK1, JAK2, STAT1, STAT3, SOCS1, and SOCS3. + +## Mechanism in plain English + +Cytokines bind their receptors, receptor complexes recruit JAK proteins, and JAK-bound complexes phosphorylate STAT1 or STAT3. Phosphorylated STATs leave receptor complexes and represent activated transcription-factor output. SOCS proteins bind JAK- or receptor-associated complexes and reduce further STAT activation. + +## Key modeled events + +- IL-6 and IL-10 first assemble receptor complexes that can recruit JAK kinases. +- JAK-associated receptor complexes phosphorylate STAT1 or STAT3, producing the activated transcription-factor signal. +- SOCS proteins bind pathway components and inhibit further signaling, creating cytokine-induced negative regulation. + +## What the model measures + +The readouts track cytokine-receptor complexes, phosphorylated STAT1 and STAT3, inhibited receptor/JAK complexes, and SOCS-associated states. The model shows how cytokine stimulation can be amplified through STAT phosphorylation and restrained by inducible inhibitors. + +## Expected behavior in plots + +Plots should compare phosphorylated STAT1/STAT3 with SOCS-associated inhibition. STAT activation followed by SOCS buildup suggests a pulse-like response with delayed negative regulation. + +## Caveats + +The model focuses on JAK/STAT activation and inhibition. It does not automatically describe all transcriptional genes downstream of STAT1 or STAT3. diff --git a/data/summaries_brief/CheemalavaguJAKSTAT_aigenerated.md b/data/summaries_brief/CheemalavaguJAKSTAT_aigenerated.md new file mode 100644 index 00000000..258a9d91 --- /dev/null +++ b/data/summaries_brief/CheemalavaguJAKSTAT_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Cheemalavagu 2024 + +## One-sentence summary + +IL-6 and IL-10 JAK/STAT signaling with STAT activation and SOCS-mediated inhibition. + +## What the model shows + +This model shows how IL-6 and IL-10 receptor systems activate JAK kinases and STAT transcription factors while SOCS proteins inhibit parts of the pathway. It captures pathway crosstalk because shared JAK/STAT machinery can be engaged by distinct cytokine receptors. + +## Biological story + +Cheemalavagu JAK/STAT is a cytokine-crosstalk story. IL-6 and IL-10 use receptor/JAK assemblies to activate STATs, while SOCS proteins form inducible brakes that can reshape subsequent signaling. + +## Main biological players + +IL-6, IL-10, their receptors, JAK1, JAK2, STAT1, STAT3, SOCS1, and SOCS3. + +## Mechanism in plain English + +Cytokines bind their receptors, receptor complexes recruit JAK proteins, and JAK-bound complexes phosphorylate STAT1 or STAT3. Phosphorylated STATs leave receptor complexes and represent activated transcription-factor output. SOCS proteins bind JAK- or receptor-associated complexes and reduce further STAT activation. + +## Key modeled events + +- IL-6 and IL-10 first assemble receptor complexes that can recruit JAK kinases. +- JAK-associated receptor complexes phosphorylate STAT1 or STAT3, producing the activated transcription-factor signal. +- SOCS proteins bind pathway components and inhibit further signaling, creating cytokine-induced negative regulation. + +## What the model measures + +The readouts track cytokine-receptor complexes, phosphorylated STAT1 and STAT3, inhibited receptor/JAK complexes, and SOCS-associated states. The model shows how cytokine stimulation can be amplified through STAT phosphorylation and restrained by inducible inhibitors. + +## Expected behavior in plots + +Plots should compare phosphorylated STAT1/STAT3 with SOCS-associated inhibition. STAT activation followed by SOCS buildup suggests a pulse-like response with delayed negative regulation. + +## Caveats + +The model focuses on JAK/STAT activation and inhibition. It does not automatically describe all transcriptional genes downstream of STAT1 or STAT3. diff --git a/data/summaries_brief/ChylekFceRI2014_ai_simple.md b/data/summaries_brief/ChylekFceRI2014_ai_simple.md new file mode 100644 index 00000000..ab407f28 --- /dev/null +++ b/data/summaries_brief/ChylekFceRI2014_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Chylek 2014 (FceRI) + +## One-sentence summary + +Detailed early FcεRI signaling from antigen crosslinking to Lyn, Fyn, Syk, PAG, Csk, and phosphatase regulation. + +## What the model shows + +This model shows a detailed receptor-proximal FcεRI signaling network. It follows how DNP-BSA crosslinks IgE-FcεRI, how receptor ITAMs are phosphorylated, and how Src-family kinases, Syk, adaptors, and phosphatases shape the early mast-cell signaling response. + +## Biological story + +Chylek FcεRI 2014 is a detailed early mast-cell receptor network. The story begins with antigen crosslinking of IgE-FcεRI and then follows competing kinase, adaptor, and phosphatase mechanisms that determine signaling strength. + +## Main biological players + +DNP-BSA ligand, IgE-FcεRI receptor, Lyn, Fyn, Syk, PAG1, Csk, SHP1, SHIP1, and receptor beta/gamma ITAM sites. + +## Mechanism in plain English + +Ligand exposes hapten sites that bind IgE arms and crosslink receptors. Lyn and Fyn associate with receptors and switch between activating and inhibitory phosphorylation states. Receptor ITAM phosphorylation recruits Syk, and Syk activation promotes downstream signaling. PAG1 recruits Csk to inhibit Src-family kinases, while SHP1 and SHIP1 remove activating signals. + +## Key modeled events + +- DNP-BSA crosslinks IgE-FcεRI through exposed hapten sites, initiating receptor aggregation. +- Lyn and Fyn phosphorylate receptor ITAMs and regulate their own activity through activating and inhibitory phosphorylation. +- Syk recruitment amplifies signaling, while PAG/Csk, SHP1, and SHIP1 create counteracting inhibitory control. + +## What the model measures + +The readouts follow receptor aggregation, ITAM phosphorylation, active Lyn/Fyn/Syk, PAG/Csk inhibitory complexes, and phosphatase-associated states. The model shows how FcεRI output emerges from receptor clustering plus competing positive and negative regulatory loops. + +## Expected behavior in plots + +Plots should be interpreted as layers: receptor aggregation first, ITAM phosphorylation next, Syk activation and adaptor recruitment after that, and inhibitory PAG/Csk or phosphatase species as counterweights. + +## Caveats + +The model is rich for receptor-proximal events, but later cellular outcomes are only implied if the corresponding readouts are present. diff --git a/data/summaries_brief/ChylekFceRI2014_aigenerated.md b/data/summaries_brief/ChylekFceRI2014_aigenerated.md new file mode 100644 index 00000000..ab407f28 --- /dev/null +++ b/data/summaries_brief/ChylekFceRI2014_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Chylek 2014 (FceRI) + +## One-sentence summary + +Detailed early FcεRI signaling from antigen crosslinking to Lyn, Fyn, Syk, PAG, Csk, and phosphatase regulation. + +## What the model shows + +This model shows a detailed receptor-proximal FcεRI signaling network. It follows how DNP-BSA crosslinks IgE-FcεRI, how receptor ITAMs are phosphorylated, and how Src-family kinases, Syk, adaptors, and phosphatases shape the early mast-cell signaling response. + +## Biological story + +Chylek FcεRI 2014 is a detailed early mast-cell receptor network. The story begins with antigen crosslinking of IgE-FcεRI and then follows competing kinase, adaptor, and phosphatase mechanisms that determine signaling strength. + +## Main biological players + +DNP-BSA ligand, IgE-FcεRI receptor, Lyn, Fyn, Syk, PAG1, Csk, SHP1, SHIP1, and receptor beta/gamma ITAM sites. + +## Mechanism in plain English + +Ligand exposes hapten sites that bind IgE arms and crosslink receptors. Lyn and Fyn associate with receptors and switch between activating and inhibitory phosphorylation states. Receptor ITAM phosphorylation recruits Syk, and Syk activation promotes downstream signaling. PAG1 recruits Csk to inhibit Src-family kinases, while SHP1 and SHIP1 remove activating signals. + +## Key modeled events + +- DNP-BSA crosslinks IgE-FcεRI through exposed hapten sites, initiating receptor aggregation. +- Lyn and Fyn phosphorylate receptor ITAMs and regulate their own activity through activating and inhibitory phosphorylation. +- Syk recruitment amplifies signaling, while PAG/Csk, SHP1, and SHIP1 create counteracting inhibitory control. + +## What the model measures + +The readouts follow receptor aggregation, ITAM phosphorylation, active Lyn/Fyn/Syk, PAG/Csk inhibitory complexes, and phosphatase-associated states. The model shows how FcεRI output emerges from receptor clustering plus competing positive and negative regulatory loops. + +## Expected behavior in plots + +Plots should be interpreted as layers: receptor aggregation first, ITAM phosphorylation next, Syk activation and adaptor recruitment after that, and inhibitory PAG/Csk or phosphatase species as counterweights. + +## Caveats + +The model is rich for receptor-proximal events, but later cellular outcomes are only implied if the corresponding readouts are present. diff --git a/data/summaries_brief/ChylekTCR2014_ai_simple.md b/data/summaries_brief/ChylekTCR2014_ai_simple.md new file mode 100644 index 00000000..c98dd1a3 --- /dev/null +++ b/data/summaries_brief/ChylekTCR2014_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Chylek 2014 (TCR) + +## One-sentence summary + +Early T-cell receptor phosphorylation-site dynamics and adaptor assembly. + +## What the model shows + +This model shows how early TCR signaling is controlled by site-specific phosphorylation, kinase and phosphatase activity, and recruitment of adaptor proteins. It is designed to represent many receptor-proximal molecular states rather than a single generic TCR activation variable. + +## Biological story + +Chylek TCR 2014 is a phosphorylation-site dynamics model. It asks how early TCR signaling emerges from many site-specific phosphorylation and dephosphorylation events rather than from a simple receptor on/off switch. + +## Main biological players + +TCR/CD3 signaling chains, LCK, ZAP70, PTPN6/SHP1, CSK, PAG, LAT, LCP2/SLP76, GRB2, SOS, PLCG1, and other proximal TCR adaptors. + +## Mechanism in plain English + +TCR engagement creates opportunities for LCK-mediated phosphorylation of receptor sites. Phosphorylated receptor motifs recruit ZAP70, which becomes activated and helps phosphorylate adaptor proteins such as LAT and LCP2. Adaptors recruit additional signaling proteins to form larger complexes. Phosphatases and inhibitory kinases counterbalance activation by removing phosphates or restraining Src-family kinase activity. + +## Key modeled events + +- LCK phosphorylates TCR/CD3 sites, creating docking sites for ZAP70. +- Activated ZAP70 phosphorylates adaptor proteins such as LAT and LCP2, enabling larger signaling assemblies. +- Phosphatases and inhibitory kinases oppose activation, so the model can show how site-specific phosphorylation patterns are shaped by competing enzymes. + +## What the model measures + +The readouts track phosphorylated receptor and adaptor sites, active kinases, phosphatase-regulated states, and assembled signaling complexes. The model shows how the pattern of phosphorylation sites controls early T-cell signaling output. + +## Expected behavior in plots + +Plots should be read as a map of signaling-site occupancy. Rising phosphorylated TCR, ZAP70, LAT, or LCP2 states indicate assembly of a productive T-cell signaling platform; inhibitory states show pathway restraint. + +## Caveats + +The model is strongest for early receptor-proximal TCR events. It should not be interpreted as a complete T-cell activation, cytokine production, or proliferation model. diff --git a/data/summaries_brief/ChylekTCR2014_aigenerated.md b/data/summaries_brief/ChylekTCR2014_aigenerated.md new file mode 100644 index 00000000..c98dd1a3 --- /dev/null +++ b/data/summaries_brief/ChylekTCR2014_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Chylek 2014 (TCR) + +## One-sentence summary + +Early T-cell receptor phosphorylation-site dynamics and adaptor assembly. + +## What the model shows + +This model shows how early TCR signaling is controlled by site-specific phosphorylation, kinase and phosphatase activity, and recruitment of adaptor proteins. It is designed to represent many receptor-proximal molecular states rather than a single generic TCR activation variable. + +## Biological story + +Chylek TCR 2014 is a phosphorylation-site dynamics model. It asks how early TCR signaling emerges from many site-specific phosphorylation and dephosphorylation events rather than from a simple receptor on/off switch. + +## Main biological players + +TCR/CD3 signaling chains, LCK, ZAP70, PTPN6/SHP1, CSK, PAG, LAT, LCP2/SLP76, GRB2, SOS, PLCG1, and other proximal TCR adaptors. + +## Mechanism in plain English + +TCR engagement creates opportunities for LCK-mediated phosphorylation of receptor sites. Phosphorylated receptor motifs recruit ZAP70, which becomes activated and helps phosphorylate adaptor proteins such as LAT and LCP2. Adaptors recruit additional signaling proteins to form larger complexes. Phosphatases and inhibitory kinases counterbalance activation by removing phosphates or restraining Src-family kinase activity. + +## Key modeled events + +- LCK phosphorylates TCR/CD3 sites, creating docking sites for ZAP70. +- Activated ZAP70 phosphorylates adaptor proteins such as LAT and LCP2, enabling larger signaling assemblies. +- Phosphatases and inhibitory kinases oppose activation, so the model can show how site-specific phosphorylation patterns are shaped by competing enzymes. + +## What the model measures + +The readouts track phosphorylated receptor and adaptor sites, active kinases, phosphatase-regulated states, and assembled signaling complexes. The model shows how the pattern of phosphorylation sites controls early T-cell signaling output. + +## Expected behavior in plots + +Plots should be read as a map of signaling-site occupancy. Rising phosphorylated TCR, ZAP70, LAT, or LCP2 states indicate assembly of a productive T-cell signaling platform; inhibitory states show pathway restraint. + +## Caveats + +The model is strongest for early receptor-proximal TCR events. It should not be interpreted as a complete T-cell activation, cytokine production, or proliferation model. diff --git a/data/summaries_brief/Dembo1978_ai_simple.md b/data/summaries_brief/Dembo1978_ai_simple.md new file mode 100644 index 00000000..fe261112 --- /dev/null +++ b/data/summaries_brief/Dembo1978_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Dembo 1978 + +## One-sentence summary + +Symmetric bivalent hapten-receptor crosslinking without ring formation. + +## What the model shows + +This model shows how a bivalent hapten binds bivalent cell-surface antibody receptors to form linear crosslinked chains. It illustrates the prozone effect: too little ligand gives few bridges, optimal ligand gives many crosslinks, and excess ligand saturates receptors without efficiently linking them. + +## Biological story + +Dembo 1978 is a physical crosslinking story. Bivalent ligand can bridge bivalent receptors into chains, but the same ligand can also block crosslinking when present in excess. + +## Main biological players + +Bivalent hapten, bivalent cell-surface antibody receptor, free ligand pool, receptor chains, and crosslinked receptor complexes. + +## Mechanism in plain English + +A free hapten arm binds a receptor site. A receptor-bound hapten can then bind a receptor site on another complex, joining complexes into longer chains. Any hapten-receptor bond can also break. The model deliberately excludes intracomplex ring formation, so the main structures are linear chains. + +## Key modeled events + +- A free bivalent hapten arm binds one receptor site, creating a singly bound intermediate. +- The second hapten arm can bind a receptor on another complex, forming a linear crosslink between receptors. +- At very high ligand abundance, receptors become occupied without being efficiently bridged, producing the prozone drop in crosslinking. + +## What the model measures + +The readouts track free receptors, ligand-bound receptors, crosslinked polymers, and the fraction of receptors in polymers. The model shows the bell-shaped crosslinking response expected for bivalent ligand-receptor systems. + +## Expected behavior in plots + +Plots should show a bell-shaped relationship between ligand dose and receptor polymerization: low ligand gives little bridging, intermediate ligand gives maximal crosslinking, and high ligand reduces bridging. + +## Caveats + +The model deliberately excludes ring formation and receptor heterogeneity, so it captures the clean symmetric linear-chain case. diff --git a/data/summaries_brief/Dembo1978_aigenerated.md b/data/summaries_brief/Dembo1978_aigenerated.md new file mode 100644 index 00000000..fe261112 --- /dev/null +++ b/data/summaries_brief/Dembo1978_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Dembo 1978 + +## One-sentence summary + +Symmetric bivalent hapten-receptor crosslinking without ring formation. + +## What the model shows + +This model shows how a bivalent hapten binds bivalent cell-surface antibody receptors to form linear crosslinked chains. It illustrates the prozone effect: too little ligand gives few bridges, optimal ligand gives many crosslinks, and excess ligand saturates receptors without efficiently linking them. + +## Biological story + +Dembo 1978 is a physical crosslinking story. Bivalent ligand can bridge bivalent receptors into chains, but the same ligand can also block crosslinking when present in excess. + +## Main biological players + +Bivalent hapten, bivalent cell-surface antibody receptor, free ligand pool, receptor chains, and crosslinked receptor complexes. + +## Mechanism in plain English + +A free hapten arm binds a receptor site. A receptor-bound hapten can then bind a receptor site on another complex, joining complexes into longer chains. Any hapten-receptor bond can also break. The model deliberately excludes intracomplex ring formation, so the main structures are linear chains. + +## Key modeled events + +- A free bivalent hapten arm binds one receptor site, creating a singly bound intermediate. +- The second hapten arm can bind a receptor on another complex, forming a linear crosslink between receptors. +- At very high ligand abundance, receptors become occupied without being efficiently bridged, producing the prozone drop in crosslinking. + +## What the model measures + +The readouts track free receptors, ligand-bound receptors, crosslinked polymers, and the fraction of receptors in polymers. The model shows the bell-shaped crosslinking response expected for bivalent ligand-receptor systems. + +## Expected behavior in plots + +Plots should show a bell-shaped relationship between ligand dose and receptor polymerization: low ligand gives little bridging, intermediate ligand gives maximal crosslinking, and high ligand reduces bridging. + +## Caveats + +The model deliberately excludes ring formation and receptor heterogeneity, so it captures the clean symmetric linear-chain case. diff --git a/data/summaries_brief/Dreisigmeyer2008_ai_simple.md b/data/summaries_brief/Dreisigmeyer2008_ai_simple.md new file mode 100644 index 00000000..c7a02dc6 --- /dev/null +++ b/data/summaries_brief/Dreisigmeyer2008_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Dreisigmeyer 2008 + +## One-sentence summary + +Lactose induction of the E. coli lac operon through transport, metabolism, allolactose, and beta-galactosidase expression. + +## What the model shows + +This model shows how extracellular lactose can induce the lac operon by raising intracellular lactose and allolactose, which increases beta-galactosidase expression. It represents the system as a small set of continuous variables rather than detailed molecular binding events. + +## Biological story + +Dreisigmeyer 2008 presents lactose induction as a coupled transport-metabolism-expression loop. Lactose import feeds allolactose production, allolactose induces beta-galactosidase, and beta-galactosidase changes the metabolite pool it depends on. + +## Main biological players + +Extracellular lactose, intracellular lactose, allolactose, beta-galactosidase, permease-mediated import, metabolic conversion, and dilution by growth. + +## Mechanism in plain English + +Lactose enters the cell through an asymmetric transport process. Beta-galactosidase metabolizes lactose and allolactose, and a fraction of lactose metabolism produces allolactose. Allolactose relieves repression in a cooperative manner, increasing beta-galactosidase production. Growth dilution lowers intracellular species over time. + +## Key modeled events + +- Lactose import increases intracellular lactose, with transport asymmetry affecting how strongly extracellular lactose drives the system. +- Lactose metabolism creates allolactose, which induces beta-galactosidase expression through cooperative regulation. +- Beta-galactosidase both rises as an output and consumes lactose/allolactose, creating a coupled induction-and-metabolism loop. + +## What the model measures + +The readouts track intracellular lactose, allolactose, beta-galactosidase, and induction as lactose input changes. The model shows a graded lactose-induction curve rather than a strongly bistable switch for the chosen lactose conditions. + +## Expected behavior in plots + +Plots should show intracellular lactose and allolactose changing before or alongside beta-galactosidase. A smooth increase in beta-galactosidase with lactose input indicates graded induction under the modeled conditions. + +## Caveats + +This model is an ODE-style lac-operon abstraction. It is not intended to show every operator-binding microstate or single-cell stochastic switching event. diff --git a/data/summaries_brief/Dreisigmeyer2008_aigenerated.md b/data/summaries_brief/Dreisigmeyer2008_aigenerated.md new file mode 100644 index 00000000..c7a02dc6 --- /dev/null +++ b/data/summaries_brief/Dreisigmeyer2008_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Dreisigmeyer 2008 + +## One-sentence summary + +Lactose induction of the E. coli lac operon through transport, metabolism, allolactose, and beta-galactosidase expression. + +## What the model shows + +This model shows how extracellular lactose can induce the lac operon by raising intracellular lactose and allolactose, which increases beta-galactosidase expression. It represents the system as a small set of continuous variables rather than detailed molecular binding events. + +## Biological story + +Dreisigmeyer 2008 presents lactose induction as a coupled transport-metabolism-expression loop. Lactose import feeds allolactose production, allolactose induces beta-galactosidase, and beta-galactosidase changes the metabolite pool it depends on. + +## Main biological players + +Extracellular lactose, intracellular lactose, allolactose, beta-galactosidase, permease-mediated import, metabolic conversion, and dilution by growth. + +## Mechanism in plain English + +Lactose enters the cell through an asymmetric transport process. Beta-galactosidase metabolizes lactose and allolactose, and a fraction of lactose metabolism produces allolactose. Allolactose relieves repression in a cooperative manner, increasing beta-galactosidase production. Growth dilution lowers intracellular species over time. + +## Key modeled events + +- Lactose import increases intracellular lactose, with transport asymmetry affecting how strongly extracellular lactose drives the system. +- Lactose metabolism creates allolactose, which induces beta-galactosidase expression through cooperative regulation. +- Beta-galactosidase both rises as an output and consumes lactose/allolactose, creating a coupled induction-and-metabolism loop. + +## What the model measures + +The readouts track intracellular lactose, allolactose, beta-galactosidase, and induction as lactose input changes. The model shows a graded lactose-induction curve rather than a strongly bistable switch for the chosen lactose conditions. + +## Expected behavior in plots + +Plots should show intracellular lactose and allolactose changing before or alongside beta-galactosidase. A smooth increase in beta-galactosidase with lactose input indicates graded induction under the modeled conditions. + +## Caveats + +This model is an ODE-style lac-operon abstraction. It is not intended to show every operator-binding microstate or single-cell stochastic switching event. diff --git a/data/summaries_brief/Dushek2011_ai_simple.md b/data/summaries_brief/Dushek2011_ai_simple.md new file mode 100644 index 00000000..bc28a7cf --- /dev/null +++ b/data/summaries_brief/Dushek2011_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Dushek 2011 + +## One-sentence summary + +Encounter-complex control of a kinase/phosphatase modifying a substrate with many sites. + +## What the model shows + +This model shows how a substrate carrying many modification sites is phosphorylated and dephosphorylated through a two-step encounter mechanism. It is designed to study how repeated encounter binding and enzyme refractory periods affect multisite modification. + +## Biological story + +Dushek 2011 is about processivity-like behavior without assuming a permanently bound enzyme. Enzymes repeatedly enter encounter complexes with a multisite substrate, modify it, pause, and re-engage. + +## Main biological players + +A multisite substrate, a kinase, a phosphatase, encounter complexes, active and inactive enzyme states, and a count of modified substrate sites. + +## Mechanism in plain English + +Kinase or phosphatase first enters an encounter complex with the substrate. Within that temporary encounter complex, the enzyme can bind productively and modify one site. After catalysis, the enzyme becomes temporarily inactive, creating a refractory period before it can act again. The substrate state records how many sites are phosphorylated rather than treating each site as a separate named residue. + +## Key modeled events + +- Kinase or phosphatase first enters an encounter complex with the multisite substrate before productive catalysis occurs. +- A catalytic event changes the substrate modification count and temporarily inactivates the enzyme. +- Repeated encounter, modification, release, and reactivation events shape the distribution of substrate molecules across phosphorylation levels. + +## What the model measures + +The readouts track substrate molecules with different numbers of modified sites and enzyme encounter states. The model shows how enzyme rebinding and temporary inactivation shape the distribution of phosphorylation levels. + +## Expected behavior in plots + +Plots should show how substrate molecules distribute across modification levels. Broad distributions indicate heterogeneous multisite processing; accumulation near high modification states indicates efficient repeated modification. + +## Caveats + +The model compresses many individual substrate sites into a modification count, so it is best for overall multisite modification patterns rather than residue-specific biology. diff --git a/data/summaries_brief/Dushek2011_aigenerated.md b/data/summaries_brief/Dushek2011_aigenerated.md new file mode 100644 index 00000000..bc28a7cf --- /dev/null +++ b/data/summaries_brief/Dushek2011_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Dushek 2011 + +## One-sentence summary + +Encounter-complex control of a kinase/phosphatase modifying a substrate with many sites. + +## What the model shows + +This model shows how a substrate carrying many modification sites is phosphorylated and dephosphorylated through a two-step encounter mechanism. It is designed to study how repeated encounter binding and enzyme refractory periods affect multisite modification. + +## Biological story + +Dushek 2011 is about processivity-like behavior without assuming a permanently bound enzyme. Enzymes repeatedly enter encounter complexes with a multisite substrate, modify it, pause, and re-engage. + +## Main biological players + +A multisite substrate, a kinase, a phosphatase, encounter complexes, active and inactive enzyme states, and a count of modified substrate sites. + +## Mechanism in plain English + +Kinase or phosphatase first enters an encounter complex with the substrate. Within that temporary encounter complex, the enzyme can bind productively and modify one site. After catalysis, the enzyme becomes temporarily inactive, creating a refractory period before it can act again. The substrate state records how many sites are phosphorylated rather than treating each site as a separate named residue. + +## Key modeled events + +- Kinase or phosphatase first enters an encounter complex with the multisite substrate before productive catalysis occurs. +- A catalytic event changes the substrate modification count and temporarily inactivates the enzyme. +- Repeated encounter, modification, release, and reactivation events shape the distribution of substrate molecules across phosphorylation levels. + +## What the model measures + +The readouts track substrate molecules with different numbers of modified sites and enzyme encounter states. The model shows how enzyme rebinding and temporary inactivation shape the distribution of phosphorylation levels. + +## Expected behavior in plots + +Plots should show how substrate molecules distribute across modification levels. Broad distributions indicate heterogeneous multisite processing; accumulation near high modification states indicates efficient repeated modification. + +## Caveats + +The model compresses many individual substrate sites into a modification count, so it is best for overall multisite modification patterns rather than residue-specific biology. diff --git a/data/summaries_brief/Dushek2014_ai_simple.md b/data/summaries_brief/Dushek2014_ai_simple.md new file mode 100644 index 00000000..90ef9f7a --- /dev/null +++ b/data/summaries_brief/Dushek2014_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Dushek 2014 + +## One-sentence summary + +Kinase/phosphatase control of a biosensor with intra- and intermolecular signaling states. + +## What the model shows + +This model shows how a biosensor changes state when acted on by a kinase and a phosphatase. It compares modification, intramolecular binding, intermolecular binding, and sequestration of a signaling protein. + +## Biological story + +Dushek 2014 focuses on how biosensor architecture affects signaling readout. The same enzymatic modification can lead to different sensor states depending on whether the modified sensor folds internally, binds externally, or is limited by sequestration. + +## Main biological players + +Biosensor, kinase, phosphatase, modified biosensor state, intramolecularly folded state, intermolecular complex state, and sequestered signaling protein. + +## Mechanism in plain English + +The kinase modifies the biosensor, while the phosphatase reverses that modification. Modified biosensor can change conformation internally or bind another molecule externally, creating distinct sensor states. Some signaling protein can be sequestered, limiting the amount available for complex formation. + +## Key modeled events + +- Kinase activity pushes the biosensor toward a modified state, while phosphatase activity reverses that state. +- The modified biosensor can adopt distinct intramolecular or intermolecular configurations, creating multiple sensor outputs. +- Sequestration limits available signaling protein and changes how much biosensor can enter signaling-competent states. + +## What the model measures + +The readouts distinguish biosensor state 1, state 2, state 3, and sequestered signaling protein. The model shows how enzymatic modification and binding architecture influence biosensor output. + +## Expected behavior in plots + +Plots should compare the named biosensor states rather than only total biosensor. A rise in one state at the expense of another indicates which sensor architecture dominates under the modeled conditions. + +## Caveats + +The model explains sensor behavior, not necessarily the full upstream pathway that activates the kinase or phosphatase. diff --git a/data/summaries_brief/Dushek2014_aigenerated.md b/data/summaries_brief/Dushek2014_aigenerated.md new file mode 100644 index 00000000..90ef9f7a --- /dev/null +++ b/data/summaries_brief/Dushek2014_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Dushek 2014 + +## One-sentence summary + +Kinase/phosphatase control of a biosensor with intra- and intermolecular signaling states. + +## What the model shows + +This model shows how a biosensor changes state when acted on by a kinase and a phosphatase. It compares modification, intramolecular binding, intermolecular binding, and sequestration of a signaling protein. + +## Biological story + +Dushek 2014 focuses on how biosensor architecture affects signaling readout. The same enzymatic modification can lead to different sensor states depending on whether the modified sensor folds internally, binds externally, or is limited by sequestration. + +## Main biological players + +Biosensor, kinase, phosphatase, modified biosensor state, intramolecularly folded state, intermolecular complex state, and sequestered signaling protein. + +## Mechanism in plain English + +The kinase modifies the biosensor, while the phosphatase reverses that modification. Modified biosensor can change conformation internally or bind another molecule externally, creating distinct sensor states. Some signaling protein can be sequestered, limiting the amount available for complex formation. + +## Key modeled events + +- Kinase activity pushes the biosensor toward a modified state, while phosphatase activity reverses that state. +- The modified biosensor can adopt distinct intramolecular or intermolecular configurations, creating multiple sensor outputs. +- Sequestration limits available signaling protein and changes how much biosensor can enter signaling-competent states. + +## What the model measures + +The readouts distinguish biosensor state 1, state 2, state 3, and sequestered signaling protein. The model shows how enzymatic modification and binding architecture influence biosensor output. + +## Expected behavior in plots + +Plots should compare the named biosensor states rather than only total biosensor. A rise in one state at the expense of another indicates which sensor architecture dominates under the modeled conditions. + +## Caveats + +The model explains sensor behavior, not necessarily the full upstream pathway that activates the kinase or phosphatase. diff --git a/data/summaries_brief/Erdem2021_ai_simple.md b/data/summaries_brief/Erdem2021_ai_simple.md new file mode 100644 index 00000000..b3456243 --- /dev/null +++ b/data/summaries_brief/Erdem2021_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Erdem 2021 + +## One-sentence summary + +Early insulin and IGF1 receptor signaling in MCF7 cells fit to RPPA-style signaling data. + +## What the model shows + +This model shows how insulin and IGF1 separately engage their receptors and activate early downstream signaling in MCF7 breast cancer cells. It includes receptor phosphorylation, downstream adaptor signaling, feedback, resensitization, and receptor recycling. + +## Biological story + +Erdem 2021 is a receptor-family signaling comparison in MCF7 cells. Insulin and IGF1 engage related receptors, produce receptor phosphorylation, and feed downstream outputs while feedback and recycling shape signal duration. + +## Main biological players + +Insulin, IGF1, insulin receptor, IGF1 receptor, phosphorylated receptor states, IRS/adapter-like downstream species, ERK/AKT-related outputs, feedback regulators, and recycled receptors. + +## Mechanism in plain English + +Insulin binds insulin receptor and IGF1 binds IGF1 receptor. Ligand-bound receptors become phosphorylated and signal to downstream nodes. Feedback reactions reduce signaling after activation, while resensitization and recycling restore receptor availability. The model uses fitted rate relationships to capture measured early signaling behavior. + +## Key modeled events + +- Insulin and IGF1 bind their matching receptors, producing receptor phosphorylation rather than a generic growth-factor signal. +- Phosphorylated receptors drive downstream signaling outputs through adaptor-like steps calibrated to MCF7 signaling measurements. +- Feedback, resensitization, and receptor recycling allow signaling to decline and receptor responsiveness to recover. + +## What the model measures + +The readouts follow receptor phosphorylation and downstream signaling outputs. The model shows how two related growth-factor inputs produce receptor-specific but overlapping signaling dynamics. + +## Expected behavior in plots + +Plots should compare insulin-receptor and IGF1-receptor phosphorylation with downstream signals. Recovery or decline after an initial peak suggests feedback, resensitization, or receptor recycling. + +## Caveats + +The model is fitted to early signaling behavior in a specific cellular context, so interpretation should not be generalized to every cell type without refitting or validation. diff --git a/data/summaries_brief/Erdem2021_aigenerated.md b/data/summaries_brief/Erdem2021_aigenerated.md new file mode 100644 index 00000000..b3456243 --- /dev/null +++ b/data/summaries_brief/Erdem2021_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Erdem 2021 + +## One-sentence summary + +Early insulin and IGF1 receptor signaling in MCF7 cells fit to RPPA-style signaling data. + +## What the model shows + +This model shows how insulin and IGF1 separately engage their receptors and activate early downstream signaling in MCF7 breast cancer cells. It includes receptor phosphorylation, downstream adaptor signaling, feedback, resensitization, and receptor recycling. + +## Biological story + +Erdem 2021 is a receptor-family signaling comparison in MCF7 cells. Insulin and IGF1 engage related receptors, produce receptor phosphorylation, and feed downstream outputs while feedback and recycling shape signal duration. + +## Main biological players + +Insulin, IGF1, insulin receptor, IGF1 receptor, phosphorylated receptor states, IRS/adapter-like downstream species, ERK/AKT-related outputs, feedback regulators, and recycled receptors. + +## Mechanism in plain English + +Insulin binds insulin receptor and IGF1 binds IGF1 receptor. Ligand-bound receptors become phosphorylated and signal to downstream nodes. Feedback reactions reduce signaling after activation, while resensitization and recycling restore receptor availability. The model uses fitted rate relationships to capture measured early signaling behavior. + +## Key modeled events + +- Insulin and IGF1 bind their matching receptors, producing receptor phosphorylation rather than a generic growth-factor signal. +- Phosphorylated receptors drive downstream signaling outputs through adaptor-like steps calibrated to MCF7 signaling measurements. +- Feedback, resensitization, and receptor recycling allow signaling to decline and receptor responsiveness to recover. + +## What the model measures + +The readouts follow receptor phosphorylation and downstream signaling outputs. The model shows how two related growth-factor inputs produce receptor-specific but overlapping signaling dynamics. + +## Expected behavior in plots + +Plots should compare insulin-receptor and IGF1-receptor phosphorylation with downstream signals. Recovery or decline after an initial peak suggests feedback, resensitization, or receptor recycling. + +## Caveats + +The model is fitted to early signaling behavior in a specific cellular context, so interpretation should not be generalized to every cell type without refitting or validation. diff --git a/data/summaries_brief/Gardner2000_ai_simple.md b/data/summaries_brief/Gardner2000_ai_simple.md new file mode 100644 index 00000000..1853ccb0 --- /dev/null +++ b/data/summaries_brief/Gardner2000_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Gardner 2000 + +## One-sentence summary + +A bistable genetic toggle switch made from two mutually repressing gene products. + +## What the model shows + +This model shows how two genes that repress each other can create a memory-like switch. Depending on the starting condition, one gene product remains high while the other remains low, or the reverse state is maintained. + +## Biological story + +Gardner 2000 is a gene-circuit memory model. Two mutually repressing gene products create alternative stable expression states, so history and starting conditions matter. + +## Main biological players + +Two abstract gene products, mutual repression, cooperative promoter control, and first-order degradation. + +## Mechanism in plain English + +Each gene product inhibits production of the other. Because repression is cooperative, intermediate states can be unstable: a small bias toward one product pushes the system toward a stable state dominated by that product. Degradation prevents unbounded accumulation and sets the time scale. + +## Key modeled events + +- Each gene product represses production of the other, creating mutual antagonism. +- Cooperative repression makes intermediate states unstable, so the system tends to commit to one dominant gene-expression state. +- Protein degradation prevents unlimited accumulation and helps set the time scale for switching or maintenance. + +## What the model measures + +The readouts track the two gene-product levels. The model shows bistability: two stable expression states separated by an unstable boundary. + +## Expected behavior in plots + +Plots should show one gene product becoming high while the other stays low. If trajectories starting from different initial states settle into different endpoints, the toggle is acting bistably. + +## Caveats + +The model is intentionally abstract and dimensionless; the two gene products represent a circuit design rather than a full natural regulatory locus. diff --git a/data/summaries_brief/Gardner2000_aigenerated.md b/data/summaries_brief/Gardner2000_aigenerated.md new file mode 100644 index 00000000..1853ccb0 --- /dev/null +++ b/data/summaries_brief/Gardner2000_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Gardner 2000 + +## One-sentence summary + +A bistable genetic toggle switch made from two mutually repressing gene products. + +## What the model shows + +This model shows how two genes that repress each other can create a memory-like switch. Depending on the starting condition, one gene product remains high while the other remains low, or the reverse state is maintained. + +## Biological story + +Gardner 2000 is a gene-circuit memory model. Two mutually repressing gene products create alternative stable expression states, so history and starting conditions matter. + +## Main biological players + +Two abstract gene products, mutual repression, cooperative promoter control, and first-order degradation. + +## Mechanism in plain English + +Each gene product inhibits production of the other. Because repression is cooperative, intermediate states can be unstable: a small bias toward one product pushes the system toward a stable state dominated by that product. Degradation prevents unbounded accumulation and sets the time scale. + +## Key modeled events + +- Each gene product represses production of the other, creating mutual antagonism. +- Cooperative repression makes intermediate states unstable, so the system tends to commit to one dominant gene-expression state. +- Protein degradation prevents unlimited accumulation and helps set the time scale for switching or maintenance. + +## What the model measures + +The readouts track the two gene-product levels. The model shows bistability: two stable expression states separated by an unstable boundary. + +## Expected behavior in plots + +Plots should show one gene product becoming high while the other stays low. If trajectories starting from different initial states settle into different endpoints, the toggle is acting bistably. + +## Caveats + +The model is intentionally abstract and dimensionless; the two gene products represent a circuit design rather than a full natural regulatory locus. diff --git a/data/summaries_brief/Goldstein1980_ai_simple.md b/data/summaries_brief/Goldstein1980_ai_simple.md new file mode 100644 index 00000000..3078fb0f --- /dev/null +++ b/data/summaries_brief/Goldstein1980_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Goldstein 1980 + +## One-sentence summary + +Bivalent hapten crosslinking of a heterogeneous antibody-receptor population. + +## What the model shows + +This model extends bivalent hapten-receptor crosslinking to two receptor classes with different affinities. It shows how receptor heterogeneity shifts and distorts the crosslinking response compared with a single uniform receptor population. + +## Biological story + +Goldstein 1980 adds receptor heterogeneity to bivalent crosslinking. Instead of one receptor affinity class, two receptor populations compete for ligand and alter the crosslinking dose response. + +## Main biological players + +Bivalent hapten, high-affinity and low-affinity bivalent receptors, receptor chains, ligand bath, and crosslinked polymers. + +## Mechanism in plain English + +Hapten binds either receptor class, and a receptor-bound hapten can bridge to a receptor on another complex. Bonds can break. Because the two receptor classes bind ligand differently, the amount of crosslinking no longer peaks symmetrically at one simple ligand concentration. + +## Key modeled events + +- Bivalent hapten binds either high-affinity or low-affinity receptor populations. +- A receptor-bound hapten can bridge to another receptor complex, producing polymers across a mixed receptor population. +- Different receptor affinities distort the crosslinking dose-response compared with a homogeneous receptor system. + +## What the model measures + +The readouts track crosslinked receptor polymers and receptor occupancy for each receptor type. The model shows how affinity heterogeneity changes the ligand dose-response for receptor aggregation. + +## Expected behavior in plots + +Plots should compare polymer formation and receptor occupancy across ligand concentrations. Shifts or asymmetry in the crosslinking peak indicate the effect of mixed receptor affinities. + +## Caveats + +The model focuses on affinity heterogeneity and excludes other cellular processes such as receptor trafficking, signaling, or active cytoskeletal organization. diff --git a/data/summaries_brief/Goldstein1980_aigenerated.md b/data/summaries_brief/Goldstein1980_aigenerated.md new file mode 100644 index 00000000..3078fb0f --- /dev/null +++ b/data/summaries_brief/Goldstein1980_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Goldstein 1980 + +## One-sentence summary + +Bivalent hapten crosslinking of a heterogeneous antibody-receptor population. + +## What the model shows + +This model extends bivalent hapten-receptor crosslinking to two receptor classes with different affinities. It shows how receptor heterogeneity shifts and distorts the crosslinking response compared with a single uniform receptor population. + +## Biological story + +Goldstein 1980 adds receptor heterogeneity to bivalent crosslinking. Instead of one receptor affinity class, two receptor populations compete for ligand and alter the crosslinking dose response. + +## Main biological players + +Bivalent hapten, high-affinity and low-affinity bivalent receptors, receptor chains, ligand bath, and crosslinked polymers. + +## Mechanism in plain English + +Hapten binds either receptor class, and a receptor-bound hapten can bridge to a receptor on another complex. Bonds can break. Because the two receptor classes bind ligand differently, the amount of crosslinking no longer peaks symmetrically at one simple ligand concentration. + +## Key modeled events + +- Bivalent hapten binds either high-affinity or low-affinity receptor populations. +- A receptor-bound hapten can bridge to another receptor complex, producing polymers across a mixed receptor population. +- Different receptor affinities distort the crosslinking dose-response compared with a homogeneous receptor system. + +## What the model measures + +The readouts track crosslinked receptor polymers and receptor occupancy for each receptor type. The model shows how affinity heterogeneity changes the ligand dose-response for receptor aggregation. + +## Expected behavior in plots + +Plots should compare polymer formation and receptor occupancy across ligand concentrations. Shifts or asymmetry in the crosslinking peak indicate the effect of mixed receptor affinities. + +## Caveats + +The model focuses on affinity heterogeneity and excludes other cellular processes such as receptor trafficking, signaling, or active cytoskeletal organization. diff --git a/data/summaries_brief/Harmon2017_ai_simple.md b/data/summaries_brief/Harmon2017_ai_simple.md new file mode 100644 index 00000000..b045b5f5 --- /dev/null +++ b/data/summaries_brief/Harmon2017_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Harmon 2017 + +## One-sentence summary + +History-dependent FcεRI mast-cell responses to pulsed antigen stimulation. + +## What the model shows + +This model shows why mast cells can respond differently to repeated antigen pulses depending on the time since the previous pulse. Fast Syk activation and slower Ship1-associated negative regulation create memory of recent stimulation. + +## Biological story + +Harmon 2017 is a signaling-history model. The same antigen pulse can produce different mast-cell responses depending on how much fast positive signaling and slower negative regulation remain from earlier stimulation. + +## Main biological players + +FcεRI-IgE receptor, multivalent antigen, Syk, Ship1, cofactor X, PIP3, degranulation output, and pulse/wash antigen input. + +## Mechanism in plain English + +Antigen binds and crosslinks FcεRI, producing a rapid Syk-positive signal. A slower Ship1/X negative branch develops and affects PIP3 signaling. Degranulation integrates these signals. If pulses arrive close together, the inhibitory branch can dominate and reduce the second response; if pulses are separated longer, the system can become primed for a larger response. + +## Key modeled events + +- Antigen pulses rapidly create a Syk-positive FcεRI activation signal. +- A slower Ship1/X negative branch changes PIP3 signaling and stores information about recent stimulation. +- Short pulse intervals can yield desensitization, while longer intervals can permit priming and stronger degranulation. + +## What the model measures + +The readouts track receptor stimulation, Syk activity, Ship1/X negative signaling, PIP3, and degranulation. The model shows desensitization or priming depending on pulse timing. + +## Expected behavior in plots + +Plots should be read across pulse timing. Close pulses should reveal residual inhibition and desensitization, while longer gaps can allow recovery or priming before the next degranulation response. + +## Caveats + +The model is tailored to pulsed FcεRI stimulation and fitted response behavior; it should not be treated as a universal model of every mast-cell stimulus. diff --git a/data/summaries_brief/Harmon2017_aigenerated.md b/data/summaries_brief/Harmon2017_aigenerated.md new file mode 100644 index 00000000..b045b5f5 --- /dev/null +++ b/data/summaries_brief/Harmon2017_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Harmon 2017 + +## One-sentence summary + +History-dependent FcεRI mast-cell responses to pulsed antigen stimulation. + +## What the model shows + +This model shows why mast cells can respond differently to repeated antigen pulses depending on the time since the previous pulse. Fast Syk activation and slower Ship1-associated negative regulation create memory of recent stimulation. + +## Biological story + +Harmon 2017 is a signaling-history model. The same antigen pulse can produce different mast-cell responses depending on how much fast positive signaling and slower negative regulation remain from earlier stimulation. + +## Main biological players + +FcεRI-IgE receptor, multivalent antigen, Syk, Ship1, cofactor X, PIP3, degranulation output, and pulse/wash antigen input. + +## Mechanism in plain English + +Antigen binds and crosslinks FcεRI, producing a rapid Syk-positive signal. A slower Ship1/X negative branch develops and affects PIP3 signaling. Degranulation integrates these signals. If pulses arrive close together, the inhibitory branch can dominate and reduce the second response; if pulses are separated longer, the system can become primed for a larger response. + +## Key modeled events + +- Antigen pulses rapidly create a Syk-positive FcεRI activation signal. +- A slower Ship1/X negative branch changes PIP3 signaling and stores information about recent stimulation. +- Short pulse intervals can yield desensitization, while longer intervals can permit priming and stronger degranulation. + +## What the model measures + +The readouts track receptor stimulation, Syk activity, Ship1/X negative signaling, PIP3, and degranulation. The model shows desensitization or priming depending on pulse timing. + +## Expected behavior in plots + +Plots should be read across pulse timing. Close pulses should reveal residual inhibition and desensitization, while longer gaps can allow recovery or priming before the next degranulation response. + +## Caveats + +The model is tailored to pulsed FcεRI stimulation and fitted response behavior; it should not be treated as a universal model of every mast-cell stimulus. diff --git a/data/summaries_brief/Hat2016_ai_simple.md b/data/summaries_brief/Hat2016_ai_simple.md new file mode 100644 index 00000000..897e3afe --- /dev/null +++ b/data/summaries_brief/Hat2016_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Hat 2016 + +## One-sentence summary + +p53 feedback, bifurcation, and cell-fate decision behavior after DNA damage. + +## What the model shows + +This model shows how p53 pathway feedbacks can convert DNA damage signals into different cell-fate regimes. It includes damage sensing, p53 stabilization, Mdm2-mediated negative feedback, transcriptional outputs, and switches that can support survival or death decisions. + +## Biological story + +Hat 2016 treats p53 as a feedback-driven decision system. DNA damage does not simply raise p53; feedback loops can create thresholds, oscillations, or high-p53 regimes associated with different fates. + +## Main biological players + +DNA damage, repair modules, p53, Mdm2, ATM/ATR-like damage signaling, p53 target genes, pro-survival and pro-death regulatory branches. + +## Mechanism in plain English + +DNA damage activates upstream signaling that stabilizes p53. p53 drives transcription of regulators, including negative-feedback components such as Mdm2 and other fate-associated outputs. Feedback loops create nonlinear behavior, so gradual parameter changes can shift the system between low-p53 survival-like states, oscillatory responses, or high-p53 cell-death-associated states. + +## Key modeled events + +- DNA damage activates upstream signaling that stabilizes and elevates p53. +- p53 induces regulators such as Mdm2 and other target genes, creating both negative feedback and fate-related outputs. +- Feedback and threshold effects allow the same pathway to support low-p53, oscillatory, or high-p53 response regimes. + +## What the model measures + +The readouts track p53, Mdm2, damage, repair, and selected p53 target outputs. The model shows how feedback architecture can create thresholds and alternative cell-fate outcomes. + +## Expected behavior in plots + +Plots should compare DNA damage, p53, Mdm2, and target outputs. Oscillations, sustained high p53, or return to baseline indicate different feedback regimes in the modeled cell-fate landscape. + +## Caveats + +The model summarizes a p53 decision network and depends on selected switches and parameters; it is not a complete molecular inventory of all p53 biology. diff --git a/data/summaries_brief/Hat2016_aigenerated.md b/data/summaries_brief/Hat2016_aigenerated.md new file mode 100644 index 00000000..897e3afe --- /dev/null +++ b/data/summaries_brief/Hat2016_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Hat 2016 + +## One-sentence summary + +p53 feedback, bifurcation, and cell-fate decision behavior after DNA damage. + +## What the model shows + +This model shows how p53 pathway feedbacks can convert DNA damage signals into different cell-fate regimes. It includes damage sensing, p53 stabilization, Mdm2-mediated negative feedback, transcriptional outputs, and switches that can support survival or death decisions. + +## Biological story + +Hat 2016 treats p53 as a feedback-driven decision system. DNA damage does not simply raise p53; feedback loops can create thresholds, oscillations, or high-p53 regimes associated with different fates. + +## Main biological players + +DNA damage, repair modules, p53, Mdm2, ATM/ATR-like damage signaling, p53 target genes, pro-survival and pro-death regulatory branches. + +## Mechanism in plain English + +DNA damage activates upstream signaling that stabilizes p53. p53 drives transcription of regulators, including negative-feedback components such as Mdm2 and other fate-associated outputs. Feedback loops create nonlinear behavior, so gradual parameter changes can shift the system between low-p53 survival-like states, oscillatory responses, or high-p53 cell-death-associated states. + +## Key modeled events + +- DNA damage activates upstream signaling that stabilizes and elevates p53. +- p53 induces regulators such as Mdm2 and other target genes, creating both negative feedback and fate-related outputs. +- Feedback and threshold effects allow the same pathway to support low-p53, oscillatory, or high-p53 response regimes. + +## What the model measures + +The readouts track p53, Mdm2, damage, repair, and selected p53 target outputs. The model shows how feedback architecture can create thresholds and alternative cell-fate outcomes. + +## Expected behavior in plots + +Plots should compare DNA damage, p53, Mdm2, and target outputs. Oscillations, sustained high p53, or return to baseline indicate different feedback regimes in the modeled cell-fate landscape. + +## Caveats + +The model summarizes a p53 decision network and depends on selected switches and parameters; it is not a complete molecular inventory of all p53 biology. diff --git a/data/summaries_brief/Hlavacek1999_ai_simple.md b/data/summaries_brief/Hlavacek1999_ai_simple.md new file mode 100644 index 00000000..f9018c79 --- /dev/null +++ b/data/summaries_brief/Hlavacek1999_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Hlavacek 1999 + +## One-sentence summary + +Steric hindrance in multivalent ligand binding to cell-surface receptors. + +## What the model shows + +This model shows how receptor binding to a multivalent ligand becomes progressively harder as already-bound receptors physically occupy space on the ligand surface. It is a steric-exclusion model rather than a detailed signaling pathway. + +## Biological story + +Hlavacek 1999 is a physical accessibility model. As receptors occupy a multivalent ligand surface, they make nearby binding sites harder to use, so binding capacity falls below the naive independent-site expectation. + +## Main biological players + +A multivalent ligand with many equivalent binding sites, monovalent cell-surface receptors, receptor occupancy classes, and steric hindrance. + +## Mechanism in plain English + +Free ligand binds receptors one at a time. Each bound receptor covers part of the ligand surface, reducing the probability that another receptor can bind nearby. As occupancy increases, the effective number of available sites drops below the simple count of unoccupied sites. + +## Key modeled events + +- A multivalent ligand gains receptors one at a time as receptor sites bind to available ligand surface. +- Each bound receptor covers physical space, reducing the chance that another nearby receptor can attach. +- The model therefore predicts less high-occupancy binding than would be expected from independent identical sites. + +## What the model measures + +The readouts track ligand species with different numbers of bound receptors. The model shows how steric crowding limits high-occupancy multivalent binding. + +## Expected behavior in plots + +Plots should show occupancy classes of ligand. If high-occupancy classes are suppressed compared with a non-steric model, that is the steric hindrance effect. + +## Caveats + +The model addresses geometric crowding in multivalent binding. It does not include downstream signaling or receptor movement beyond the steric approximation. diff --git a/data/summaries_brief/Hlavacek1999_aigenerated.md b/data/summaries_brief/Hlavacek1999_aigenerated.md new file mode 100644 index 00000000..f9018c79 --- /dev/null +++ b/data/summaries_brief/Hlavacek1999_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Hlavacek 1999 + +## One-sentence summary + +Steric hindrance in multivalent ligand binding to cell-surface receptors. + +## What the model shows + +This model shows how receptor binding to a multivalent ligand becomes progressively harder as already-bound receptors physically occupy space on the ligand surface. It is a steric-exclusion model rather than a detailed signaling pathway. + +## Biological story + +Hlavacek 1999 is a physical accessibility model. As receptors occupy a multivalent ligand surface, they make nearby binding sites harder to use, so binding capacity falls below the naive independent-site expectation. + +## Main biological players + +A multivalent ligand with many equivalent binding sites, monovalent cell-surface receptors, receptor occupancy classes, and steric hindrance. + +## Mechanism in plain English + +Free ligand binds receptors one at a time. Each bound receptor covers part of the ligand surface, reducing the probability that another receptor can bind nearby. As occupancy increases, the effective number of available sites drops below the simple count of unoccupied sites. + +## Key modeled events + +- A multivalent ligand gains receptors one at a time as receptor sites bind to available ligand surface. +- Each bound receptor covers physical space, reducing the chance that another nearby receptor can attach. +- The model therefore predicts less high-occupancy binding than would be expected from independent identical sites. + +## What the model measures + +The readouts track ligand species with different numbers of bound receptors. The model shows how steric crowding limits high-occupancy multivalent binding. + +## Expected behavior in plots + +Plots should show occupancy classes of ligand. If high-occupancy classes are suppressed compared with a non-steric model, that is the steric hindrance effect. + +## Caveats + +The model addresses geometric crowding in multivalent binding. It does not include downstream signaling or receptor movement beyond the steric approximation. diff --git a/data/summaries_brief/Hlavacek2001_ai_simple.md b/data/summaries_brief/Hlavacek2001_ai_simple.md new file mode 100644 index 00000000..54e334c9 --- /dev/null +++ b/data/summaries_brief/Hlavacek2001_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Hlavacek 2001 + +## One-sentence summary + +Kinetic proofreading by receptor dimers that must survive sequential modification steps. + +## What the model shows + +This model shows how signaling can discriminate between ligands by requiring a receptor complex to remain intact through several irreversible modification steps. Short-lived complexes tend to fall apart before reaching the final signaling state. + +## Biological story + +Hlavacek 2001 is a kinetic-discrimination model. Receptor dimers must stay intact long enough to pass through several modification steps, making signaling disproportionately sensitive to ligand lifetime. + +## Main biological players + +Bivalent ligand, monovalent receptors, receptor dimers, sequential modification counter, and dissociation reset. + +## Mechanism in plain English + +A bivalent ligand binds two receptors to form a signaling dimer. The dimer then progresses through a chain of modification steps. If either receptor-ligand bond breaks before the final step, the complex loses its accumulated progress and returns to an unmodified state. Longer-lived ligand-receptor interactions therefore generate more fully processed signaling complexes. + +## Key modeled events + +- A bivalent ligand forms a receptor dimer that can begin a sequence of signaling modifications. +- The dimer must remain intact through multiple steps to reach the terminal signaling state. +- If either receptor bond breaks too early, accumulated progress is reset, allowing long-lived ligand complexes to signal disproportionately well. + +## What the model measures + +The readouts track dimers at each modification stage and the terminally modified signaling state. The model shows exponential-like discrimination between weak and strong ligand binding. + +## Expected behavior in plots + +Plots should show early dimer states feeding later modified states. Strong ligands should populate terminal states much more effectively than weak ligands that dissociate and reset. + +## Caveats + +The model idealizes proofreading as sequential modification with reset on dissociation; real pathways may include additional branches or partial memory. diff --git a/data/summaries_brief/Hlavacek2001_aigenerated.md b/data/summaries_brief/Hlavacek2001_aigenerated.md new file mode 100644 index 00000000..54e334c9 --- /dev/null +++ b/data/summaries_brief/Hlavacek2001_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Hlavacek 2001 + +## One-sentence summary + +Kinetic proofreading by receptor dimers that must survive sequential modification steps. + +## What the model shows + +This model shows how signaling can discriminate between ligands by requiring a receptor complex to remain intact through several irreversible modification steps. Short-lived complexes tend to fall apart before reaching the final signaling state. + +## Biological story + +Hlavacek 2001 is a kinetic-discrimination model. Receptor dimers must stay intact long enough to pass through several modification steps, making signaling disproportionately sensitive to ligand lifetime. + +## Main biological players + +Bivalent ligand, monovalent receptors, receptor dimers, sequential modification counter, and dissociation reset. + +## Mechanism in plain English + +A bivalent ligand binds two receptors to form a signaling dimer. The dimer then progresses through a chain of modification steps. If either receptor-ligand bond breaks before the final step, the complex loses its accumulated progress and returns to an unmodified state. Longer-lived ligand-receptor interactions therefore generate more fully processed signaling complexes. + +## Key modeled events + +- A bivalent ligand forms a receptor dimer that can begin a sequence of signaling modifications. +- The dimer must remain intact through multiple steps to reach the terminal signaling state. +- If either receptor bond breaks too early, accumulated progress is reset, allowing long-lived ligand complexes to signal disproportionately well. + +## What the model measures + +The readouts track dimers at each modification stage and the terminally modified signaling state. The model shows exponential-like discrimination between weak and strong ligand binding. + +## Expected behavior in plots + +Plots should show early dimer states feeding later modified states. Strong ligands should populate terminal states much more effectively than weak ligands that dissociate and reset. + +## Caveats + +The model idealizes proofreading as sequential modification with reset on dissociation; real pathways may include additional branches or partial memory. diff --git a/data/summaries_brief/Hlavacek2018Egg_ai_simple.md b/data/summaries_brief/Hlavacek2018Egg_ai_simple.md new file mode 100644 index 00000000..859c3680 --- /dev/null +++ b/data/summaries_brief/Hlavacek2018Egg_ai_simple.md @@ -0,0 +1,39 @@ +# Model Explanation: Hlavacek2018Egg + +## One-sentence summary + +A small parameterized example model used to demonstrate fitted or transformed rate expressions. + +## What the model shows + +This model appears to be a compact example built around adjustable numerical parameters and simple state variables rather than a named biological pathway. It is best read as a demonstration of how a small rule-based model can encode parameter changes and resulting dynamics. + +## Biological story + +Hlavacek2018 Egg is an abstract example rather than a named pathway. Its story is about how a compact model can express parameter-dependent dynamics for toy species. + +## Main biological players + +Abstract species and parameters named with short labels rather than clear biological identities. + +## Mechanism in plain English + +The model changes abstract species according to fitted or transformed parameter values. Because the molecule names are not biologically descriptive, the safest interpretation is that it demonstrates model mechanics rather than a curated biological mechanism. + +## Key modeled events + +- Abstract species change according to fitted or transformed numerical relationships. +- The model demonstrates how a compact rule-based system can encode a sequence of parameter-dependent changes. +- Because the species are not biologically named, the useful behavior is the example dynamics rather than a specific pathway claim. + +## What the model measures + +The readouts track the abstract species defined in the model. The model shows numerical behavior of the toy system, but the biological identities of the species are not specified. + +## Expected behavior in plots + +Plots should be interpreted as behavior of abstract variables. The useful signal is whether the toy system approaches, leaves, or oscillates around particular numerical states. + +## Caveats + +Because the species are not biologically named, any pathway-level interpretation would be speculative; the model is best treated as a demonstration case. diff --git a/data/summaries_brief/Hlavacek2018Egg_aigenerated.md b/data/summaries_brief/Hlavacek2018Egg_aigenerated.md new file mode 100644 index 00000000..859c3680 --- /dev/null +++ b/data/summaries_brief/Hlavacek2018Egg_aigenerated.md @@ -0,0 +1,39 @@ +# Model Explanation: Hlavacek2018Egg + +## One-sentence summary + +A small parameterized example model used to demonstrate fitted or transformed rate expressions. + +## What the model shows + +This model appears to be a compact example built around adjustable numerical parameters and simple state variables rather than a named biological pathway. It is best read as a demonstration of how a small rule-based model can encode parameter changes and resulting dynamics. + +## Biological story + +Hlavacek2018 Egg is an abstract example rather than a named pathway. Its story is about how a compact model can express parameter-dependent dynamics for toy species. + +## Main biological players + +Abstract species and parameters named with short labels rather than clear biological identities. + +## Mechanism in plain English + +The model changes abstract species according to fitted or transformed parameter values. Because the molecule names are not biologically descriptive, the safest interpretation is that it demonstrates model mechanics rather than a curated biological mechanism. + +## Key modeled events + +- Abstract species change according to fitted or transformed numerical relationships. +- The model demonstrates how a compact rule-based system can encode a sequence of parameter-dependent changes. +- Because the species are not biologically named, the useful behavior is the example dynamics rather than a specific pathway claim. + +## What the model measures + +The readouts track the abstract species defined in the model. The model shows numerical behavior of the toy system, but the biological identities of the species are not specified. + +## Expected behavior in plots + +Plots should be interpreted as behavior of abstract variables. The useful signal is whether the toy system approaches, leaves, or oscillates around particular numerical states. + +## Caveats + +Because the species are not biologically named, any pathway-level interpretation would be speculative; the model is best treated as a demonstration case. diff --git a/data/summaries_detailed/Barua2009_ai_coder.md b/data/summaries_detailed/Barua2009_ai_coder.md new file mode 100644 index 00000000..2f66718e --- /dev/null +++ b/data/summaries_detailed/Barua2009_ai_coder.md @@ -0,0 +1,79 @@ +# Coder Model Explanation: Barua 2009 + +## 1. Model identity and scope + +- **Model id:** `Barua_2009` +- **Title:** Barua 2009 +- **BNGL path:** `Published/Barua2009/Barua_2009.bngl` +- **YAML path:** `Published/Barua2009/metadata.yaml` +- **Scope:** This signaling model represents JAK2-SH2B complex assembly. It focuses on SH2-mediated recruitment of SH2B to phosphorylated JAK2, SH2B dimerization through a dimerization domain, and JAK2 phosphorylation within a two-JAK2 scaffolded complex. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 8 kinetic/abundance parameters. | +| Compartments | No | No compartment declarations. | +| Molecule types | Yes | 2 molecule types: `S` and `J`. | +| Seed species | Yes | 2 initial species: free SH2B and singly phosphorylated JAK2. | +| Observables | Yes | 6 molecule-count readouts. | +| Functions | No | No function block. | +| Reaction rules | Yes | 4 reaction rules. | +| Actions | Inline commands | Network generation plus ODE simulation. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value | Role | +| --- | ---: | --- | +| `kon_dimer` | 1.0 | Association rate for SH2B dimerization through `DD`. | +| `koff_dimer` | 0.1 | Dissociation rate for the SH2B dimer. | +| `kon_SH2` | 1.0 | Association rate for SH2B `SH2` binding to JAK2 `Y1`. | +| `koff_SH2` | 0.1 | Dissociation rate for the JAK2-SH2B SH2 interaction. | +| `kphos_slow` | 0.1 | Slow phosphorylation rate when the opposite JAK2 in the dimer scaffold remains unphosphorylated at `Y`. | +| `kphos_fast` | 1.0 | Fast phosphorylation rate when the opposite JAK2 is already phosphorylated at `Y`. | +| `Jtot` | 0.000014 | Initial total JAK2 concentration. | +| `Stot` | 0.1 | Initial total SH2B concentration. | + +There are no BNGL functions. All rules use direct mass-action constants. The two phosphorylation rules differ only in the phosphorylation state of the partner JAK2, making the second JAK2 phosphorylation faster once one JAK2 in the SH2B dimer assembly is already active. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `S` | 2 | `SH2`, `DD` | None | `SH2` binds the `Y1` site of JAK2; `DD` dimerizes two SH2B molecules. | Metadata describes this as SH2B. | +| `J` | 2 | `Y1`, `Y` | `Y1`: `P`; `Y`: `U`, `P` | `Y1` is the SH2B docking site and is initialized phosphorylated; `Y` is the regulated JAK2 activation/phosphorylation site. | `Y1` is declared only with state `P`, so the model does not represent unphosphorylated `Y1`. | + +## 5. Initial species, compartments, and setup + +The model starts with free SH2B, `S(SH2,DD)`, at `Stot`, and JAK2 with `Y1` phosphorylated and `Y` unphosphorylated at `Jtot`. There are no compartments. The initial setup therefore assumes that the JAK2 docking tyrosine is already in the state that can recruit SH2B, while the second JAK2 phosphorylation site is initially inactive. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | JAK2-SH2B interaction | Reversible | `J.Y1` in state `P` binds `S.SH2` | `kon_SH2`, `koff_SH2` | Adds or removes a JAK2-SH2B bond | SH2B can dock onto phosphorylated JAK2 through its SH2 domain. | +| 2 | SH2B dimerization | Reversible | `S.DD` binds another `S.DD` | `kon_dimer`, `koff_dimer` | Adds or removes an SH2B-SH2B dimer bond | Two SH2B molecules can form a dimeric scaffold through their dimerization domains. | +| 3 | JAK2 phosphorylation, slow | One-way | In a JAK2-SH2B-SH2B-JAK2 complex, one JAK2 has `Y~U`; the partner JAK2 also has `Y~U` | `kphos_slow` | Converts one JAK2 `Y` site from `U` to `P` | A fully scaffolded but not-yet-activated two-JAK2 complex can slowly phosphorylate one JAK2 activation site. | +| 4 | JAK2 phosphorylation, fast | One-way | Same scaffolded complex, but the partner JAK2 already has `Y~P` | `kphos_fast` | Converts the remaining JAK2 `Y` site from `U` to `P` | Once one JAK2 in the scaffold is phosphorylated, phosphorylation of the second JAK2 is accelerated. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `J_mono` | `Molecules` | JAK2 with phosphorylated `Y1` | Counts JAK2 molecules that retain the SH2B docking state, regardless of whether they are bound. | +| `JS` | `Molecules` | JAK2 bound to one SH2B through `Y1`/`SH2`, with SH2B `DD` free | Reports the singly recruited JAK2-SH2B complex before SH2B dimerization. | +| `JSS` | `Molecules` | JAK2-SH2B-SH2B complex with one JAK2 | Reports the scaffold after SH2B dimerization but before the second JAK2 is necessarily recruited. | +| `JSSJ` | `Molecules` | Any complex containing two `J` molecules | Reports two-JAK2 assemblies, the structural context required by the phosphorylation rules. | +| `J_active` | `Molecules` | JAK2 with `Y~P` | Counts activated/phosphorylated JAK2 at the regulated `Y` site. | +| `J_inactive` | `Molecules` | JAK2 with `Y~U` | Counts inactive/unphosphorylated JAK2 at the regulated `Y` site. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1, max_stoich=>{J=>2}})` generates a reaction network while limiting generated species to at most two JAK2 molecules per complex. +2. `simulate_ode({t_end=>10000, n_steps=>10000, atoll=>1e-08, rtol=>1e-08, sparse=>1})` runs a long ODE simulation with tight tolerances and sparse linear algebra. + +## 9. Technical caveats and ambiguities + +- The model assumes JAK2 `Y1` is always phosphorylated; no rule creates or removes that state. +- `JSSJ` is a broad two-JAK2 observable and does not specify which JAK2 activation states are present. +- The YAML marks the model as not BNG2-compatible even though the source uses standard BNGL blocks plus inline actions. diff --git a/data/summaries_detailed/Barua2009_coder.md b/data/summaries_detailed/Barua2009_coder.md new file mode 100644 index 00000000..2f66718e --- /dev/null +++ b/data/summaries_detailed/Barua2009_coder.md @@ -0,0 +1,79 @@ +# Coder Model Explanation: Barua 2009 + +## 1. Model identity and scope + +- **Model id:** `Barua_2009` +- **Title:** Barua 2009 +- **BNGL path:** `Published/Barua2009/Barua_2009.bngl` +- **YAML path:** `Published/Barua2009/metadata.yaml` +- **Scope:** This signaling model represents JAK2-SH2B complex assembly. It focuses on SH2-mediated recruitment of SH2B to phosphorylated JAK2, SH2B dimerization through a dimerization domain, and JAK2 phosphorylation within a two-JAK2 scaffolded complex. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 8 kinetic/abundance parameters. | +| Compartments | No | No compartment declarations. | +| Molecule types | Yes | 2 molecule types: `S` and `J`. | +| Seed species | Yes | 2 initial species: free SH2B and singly phosphorylated JAK2. | +| Observables | Yes | 6 molecule-count readouts. | +| Functions | No | No function block. | +| Reaction rules | Yes | 4 reaction rules. | +| Actions | Inline commands | Network generation plus ODE simulation. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value | Role | +| --- | ---: | --- | +| `kon_dimer` | 1.0 | Association rate for SH2B dimerization through `DD`. | +| `koff_dimer` | 0.1 | Dissociation rate for the SH2B dimer. | +| `kon_SH2` | 1.0 | Association rate for SH2B `SH2` binding to JAK2 `Y1`. | +| `koff_SH2` | 0.1 | Dissociation rate for the JAK2-SH2B SH2 interaction. | +| `kphos_slow` | 0.1 | Slow phosphorylation rate when the opposite JAK2 in the dimer scaffold remains unphosphorylated at `Y`. | +| `kphos_fast` | 1.0 | Fast phosphorylation rate when the opposite JAK2 is already phosphorylated at `Y`. | +| `Jtot` | 0.000014 | Initial total JAK2 concentration. | +| `Stot` | 0.1 | Initial total SH2B concentration. | + +There are no BNGL functions. All rules use direct mass-action constants. The two phosphorylation rules differ only in the phosphorylation state of the partner JAK2, making the second JAK2 phosphorylation faster once one JAK2 in the SH2B dimer assembly is already active. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `S` | 2 | `SH2`, `DD` | None | `SH2` binds the `Y1` site of JAK2; `DD` dimerizes two SH2B molecules. | Metadata describes this as SH2B. | +| `J` | 2 | `Y1`, `Y` | `Y1`: `P`; `Y`: `U`, `P` | `Y1` is the SH2B docking site and is initialized phosphorylated; `Y` is the regulated JAK2 activation/phosphorylation site. | `Y1` is declared only with state `P`, so the model does not represent unphosphorylated `Y1`. | + +## 5. Initial species, compartments, and setup + +The model starts with free SH2B, `S(SH2,DD)`, at `Stot`, and JAK2 with `Y1` phosphorylated and `Y` unphosphorylated at `Jtot`. There are no compartments. The initial setup therefore assumes that the JAK2 docking tyrosine is already in the state that can recruit SH2B, while the second JAK2 phosphorylation site is initially inactive. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | JAK2-SH2B interaction | Reversible | `J.Y1` in state `P` binds `S.SH2` | `kon_SH2`, `koff_SH2` | Adds or removes a JAK2-SH2B bond | SH2B can dock onto phosphorylated JAK2 through its SH2 domain. | +| 2 | SH2B dimerization | Reversible | `S.DD` binds another `S.DD` | `kon_dimer`, `koff_dimer` | Adds or removes an SH2B-SH2B dimer bond | Two SH2B molecules can form a dimeric scaffold through their dimerization domains. | +| 3 | JAK2 phosphorylation, slow | One-way | In a JAK2-SH2B-SH2B-JAK2 complex, one JAK2 has `Y~U`; the partner JAK2 also has `Y~U` | `kphos_slow` | Converts one JAK2 `Y` site from `U` to `P` | A fully scaffolded but not-yet-activated two-JAK2 complex can slowly phosphorylate one JAK2 activation site. | +| 4 | JAK2 phosphorylation, fast | One-way | Same scaffolded complex, but the partner JAK2 already has `Y~P` | `kphos_fast` | Converts the remaining JAK2 `Y` site from `U` to `P` | Once one JAK2 in the scaffold is phosphorylated, phosphorylation of the second JAK2 is accelerated. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `J_mono` | `Molecules` | JAK2 with phosphorylated `Y1` | Counts JAK2 molecules that retain the SH2B docking state, regardless of whether they are bound. | +| `JS` | `Molecules` | JAK2 bound to one SH2B through `Y1`/`SH2`, with SH2B `DD` free | Reports the singly recruited JAK2-SH2B complex before SH2B dimerization. | +| `JSS` | `Molecules` | JAK2-SH2B-SH2B complex with one JAK2 | Reports the scaffold after SH2B dimerization but before the second JAK2 is necessarily recruited. | +| `JSSJ` | `Molecules` | Any complex containing two `J` molecules | Reports two-JAK2 assemblies, the structural context required by the phosphorylation rules. | +| `J_active` | `Molecules` | JAK2 with `Y~P` | Counts activated/phosphorylated JAK2 at the regulated `Y` site. | +| `J_inactive` | `Molecules` | JAK2 with `Y~U` | Counts inactive/unphosphorylated JAK2 at the regulated `Y` site. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1, max_stoich=>{J=>2}})` generates a reaction network while limiting generated species to at most two JAK2 molecules per complex. +2. `simulate_ode({t_end=>10000, n_steps=>10000, atoll=>1e-08, rtol=>1e-08, sparse=>1})` runs a long ODE simulation with tight tolerances and sparse linear algebra. + +## 9. Technical caveats and ambiguities + +- The model assumes JAK2 `Y1` is always phosphorylated; no rule creates or removes that state. +- `JSSJ` is a broad two-JAK2 observable and does not specify which JAK2 activation states are present. +- The YAML marks the model as not BNG2-compatible even though the source uses standard BNGL blocks plus inline actions. diff --git a/data/summaries_detailed/Blinovran_ai_coder.md b/data/summaries_detailed/Blinovran_ai_coder.md new file mode 100644 index 00000000..6c6deaea --- /dev/null +++ b/data/summaries_detailed/Blinovran_ai_coder.md @@ -0,0 +1,73 @@ +# Coder Model Explanation: Blinov ran + +## 1. Model identity and scope + +- **Model id:** `Blinov_ran` +- **Title:** Blinov ran +- **BNGL path:** `Published/Blinovran/Blinov_ran.bngl` +- **YAML path:** `Published/Blinovran/metadata.yaml` +- **Scope:** This is a compartmental Ran/cargo/RCC1 transport model. It tracks Ran-cargo complex movement between nucleus and cytoplasm, cargo phosphorylation in the cytoplasm, cargo-Ran dissociation/association in both compartments, and RCC1 binding to nuclear Ran. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Compartments | Yes | 5 compartments/surfaces: `nuc`, `cyt`, `EC`, `pm`, and `nm`. | +| Parameters | Yes | Parameter block is present but empty; numeric rates are written directly in rules. | +| Molecule types | Yes | 3 molecule types: `Ran`, `C`, and `RCC1`. | +| Anchors | Yes | `RCC1(nuc)` anchor declaration. | +| Seed species | Yes | 2 numbered nuclear initial species. | +| Observables | Yes | 7 molecule-count readouts. | +| Functions | Yes | Function block is present but empty. | +| Reaction rules | Yes | 7 labeled reversible rules. | +| Actions | Inline command | One NFsim simulation command. | + +## 3. Parameters, functions, and rate laws + +The parameter block is empty, and there are no function definitions. All rate laws are numeric literals placed directly on reaction rules. Transport uses forward rate `2.0 * 602.0` and reverse rate `0.0`, so Ran-cargo transport is effectively one-way from nucleus to cytoplasm. Cargo phosphorylation and dephosphorylation use `10.0` and `1.0`. Ran-cargo and Ran-RCC1 binding rules use `1.0` and `100.0` for the two directions as written. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `Ran` | 1 | `cargo` | None | Binds cargo `C.site` or RCC1 `site`, depending on the rule context. | The single site is reused for cargo and RCC1 interactions in different compartments. | +| `C` | 4 | `site`, `Y1`, `Y2`, `Y3` | `Y1`: `u`, `p`; `Y2`: `u`, `p`; `Y3`: `u`, `p` | `site` binds Ran; `Y1`, `Y2`, and `Y3` are cargo phosphorylation-state sites. | Metadata tag `c` likely refers to cargo, but interpretation comes mainly from molecule and observable names. | +| `RCC1` | 1 | `site` | None | Binds nuclear Ran through `site`. | Anchor declaration associates RCC1 with the nucleus. | + +## 5. Initial species, compartments, and setup + +The model starts with 1000 nuclear Ran-cargo complexes, `@nuc:Ran(cargo!1).C(site!1,Y1~u,Y2~u,Y3~u)`, and 1000 nuclear RCC1 molecules, `@nuc:RCC1(site)`. Cargo begins unphosphorylated at all three `Y` sites. No cytoplasmic species are seeded initially; cytoplasmic Ran/cargo populations arise through transport and cytoplasmic dissociation/phosphorylation rules. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Transport` | Reversible syntax, effectively one-way | Bound Ran-cargo complex in `nuc` and `cyt` compartments | Forward `2.0 * 602.0`, reverse `0.0` | Moves a Ran-cargo complex from nucleus to cytoplasm | Exports bound Ran-cargo complex to the cytoplasm with no return through this rule. | +| 2 | `Ran_C_bind_cyt` | Reversible | Cytoplasmic Ran `cargo` site and cargo `C.site` | `1.0`, `100.0` | Interconverts bound cytoplasmic Ran-cargo complex and separate cytoplasmic Ran plus cargo | Allows cytoplasmic Ran-cargo dissociation and reassociation. As written, the left side is bound and the right side is free. | +| 3 | `C_p1` | Reversible state change | Cytoplasmic cargo `Y3`, regardless of binding status | `10.0`, `1.0` | Converts `Y3` between unphosphorylated and phosphorylated | Phosphorylates and dephosphorylates the third cargo modification site in the cytoplasm. | +| 4 | `C_p2` | Reversible state change | Cytoplasmic cargo `Y2`, regardless of binding status | `10.0`, `1.0` | Converts `Y2` between unphosphorylated and phosphorylated | Phosphorylates and dephosphorylates the second cargo modification site in the cytoplasm. | +| 5 | `C_p3` | Reversible state change | Cytoplasmic cargo `Y1`, regardless of binding status | `10.0`, `1.0` | Converts `Y1` between unphosphorylated and phosphorylated | Phosphorylates and dephosphorylates the first cargo modification site in the cytoplasm. | +| 6 | `Ran_RCC1_bind` | Reversible | Nuclear Ran `cargo` site and nuclear RCC1 `site` | `1.0`, `100.0` | Adds or removes a nuclear Ran-RCC1 bond | Allows RCC1 to bind nuclear Ran through the same Ran site that otherwise binds cargo. | +| 7 | `Ran_C_bind_nuc` | Reversible | Nuclear Ran `cargo` site and nuclear cargo `C.site` | `1.0`, `100.0` | Interconverts bound nuclear Ran-cargo complex and separate nuclear Ran plus cargo | Allows nuclear Ran-cargo dissociation and reassociation. As written, the left side is bound and the right side is free. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Ran_cyt` | `Molecules` | Cytoplasmic Ran | Counts Ran molecules in the cytoplasm. | +| `Cargo_cyt` | `Molecules` | Cytoplasmic cargo `C` | Counts cargo molecules in the cytoplasm. | +| `RCC1_nuc` | `Molecules` | Nuclear RCC1 | Counts RCC1 molecules in the nucleus. | +| `Cargo_phosp_cyt_total` | `Molecules` | Nuclear cargo with `Y1`, `Y2`, or `Y3` phosphorylated | Despite the name, the listed patterns use `@nuc`, so this readout counts phosphorylated cargo patterns in the nucleus, not cytoplasm. | +| `Cargo_nuc` | `Molecules` | Nuclear cargo `C` | Counts cargo molecules in the nucleus. | +| `Cargo_phosp_cyt` | `Molecules` | Cytoplasmic cargo with all three phosphorylation sites marked phosphorylated/possibly bound | Counts cytoplasmic cargo matching phosphorylated-state constraints across `Y1`, `Y2`, and `Y3`. | +| `Ran_bound_cyt` | `Molecules` | Cytoplasmic Ran with `cargo` bound to something | Counts cytoplasmic Ran that remains bound through its cargo site. | + +## 8. Actions and simulation workflow + +The model runs `simulate_nf({t_end=>10.0,n_steps=>200})`. No network generation action is present. Because the model uses compartments, anchored RCC1, wildcard binding constraints, and NFsim-compatible syntax, the intended workflow is direct network-free simulation over 10 time units with 200 output steps. + +## 9. Technical caveats and ambiguities + +- The parameter and function blocks are empty; rule rates are hard-coded numeric literals. +- `Cargo_phosp_cyt_total` is named like a cytoplasmic observable but uses nuclear patterns, so downstream code should not rely on the name alone. +- The Ran `cargo` site is used for both cargo and RCC1 binding in different rules; the model relies on context and compartments rather than distinct Ran sites for these interactions. diff --git a/data/summaries_detailed/Blinovran_ai_coder_update.md b/data/summaries_detailed/Blinovran_ai_coder_update.md new file mode 100644 index 00000000..524f63e3 --- /dev/null +++ b/data/summaries_detailed/Blinovran_ai_coder_update.md @@ -0,0 +1,126 @@ +# Coder Model Explanation: Blinov ran + +## 1. Model identity and scope + +- **Model id:** `Blinov_ran` +- **Title:** Blinov ran +- **Metadata description:** Ran GTPase cycle +- **Local BNGL path:** `Published/Blinovran/Blinov_ran.bngl` +- **Local YAML path:** `Published/Blinovran/metadata.yaml` + +This is a compact NFsim-oriented compartmental rule-based model for Ran/cargo/RCC1 localization. It does not explicitly encode Ran nucleotide states; instead, the executable logic centers on a Ran molecule with one cargo-binding component, a cargo-like molecule `C` with one Ran/RCC1 contact site plus three reversible modification sites, and nuclear RCC1 as an anchored molecule. The model uses VCell-style compartment prefixes such as `@nuc:Ran(...)` and `@cyt:C(...)`, plus an anchors block that constrains `RCC1` to the nucleus. + +## 2. BNGL block inventory + +| BNGL construct | Present? | Active entries | Technical contribution | +| --- | --- | ---: | --- | +| `begin compartments` | yes | 5 | Declares five compartments: three 3D compartments (`nuc`, `cyt`, `EC`) and two 2D compartments (`pm`, `nm`), all with size value `1`. | +| `begin parameters` | yes | 0 | The parameter block is present but empty; all rule rates are literal numeric expressions. | +| `begin molecule types` | yes | 3 | Declares `Ran`, `C`, and `RCC1` with their sites/states. | +| `begin anchors` | yes | 1 | Declares `RCC1(nuc)`, constraining RCC1-containing species/complexes to the nuclear compartment under VCell-style spatial semantics. | +| `begin seed species` | yes | 2 | Starts with a nuclear Ran-C complex and free nuclear RCC1. | +| `begin observables` | yes | 7 | Tracks cytosolic Ran, cytosolic cargo, nuclear RCC1, nuclear/cytosolic cargo, phosphorylated cargo patterns, and cytosolic bound Ran. | +| `begin functions` | yes | 0 | The functions block is present but empty; `uses_functions` should remain true under block-presence metadata semantics even though no active functions are defined. | +| `begin reaction rules` | yes | 7 | Defines transport, Ran-C association/dissociation in cytoplasm and nucleus, cargo phosphorylation-state toggles, and nuclear Ran-RCC1 binding. | +| Inline actions | yes | 1 | Runs `simulate_nf({t_end=>10.0,n_steps=>200})`. | + +Parser note: this model uses **VCell-style compartment-prefix grammar**, e.g. `@nuc:Ran(...)` and `@cyt:C(...)`. It does not use the CBNGL-style suffix grammar `Molecule(...)@Compartment`. + +## 3. Parameters, functions, and rate laws + +The `parameters` block is present but empty. The `functions` block is also present but empty. Therefore, all active rates are written directly in the reaction-rule rows rather than through named parameters or functions. + +| Rate expression | Where used | Technical interpretation | +| --- | --- | --- | +| `2.0 * 602.0, 0.0` | `Transport` | Forward transport of a bound Ran pattern from nucleus to cytoplasm has rate `1204.0`; the reverse rate is zero, so the reversible arrow is syntactically present but dynamically one-way under these values. | +| `1.0, 100.0` | `Ran_C_bind_cyt`, `Ran_RCC1_bind`, `Ran_C_bind_nuc` | Each of these rules is written with a bound complex on the left and separated molecules on the right. The first number applies left-to-right dissociation; the second applies right-to-left association. | +| `10.0, 1.0` | `C_p1`, `C_p2`, `C_p3` | Each cargo modification site toggles from unmodified to phosphorylated at rate `10.0` and from phosphorylated to unmodified at rate `1.0`. | + +No named algebraic functions, parameter scans, or rate-law functions are defined. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Ran` | 1 | `cargo` | none | Not anchored. Explicitly appears in `nuc` and `cyt` patterns. | `cargo` binds either `C.site` or `RCC1.site` depending on the rule. | The model name references Ran GTPase, but the BNGL does not declare GDP/GTP or active/inactive Ran states. | +| `C` | 4 | `site`, `Y1`, `Y2`, `Y3` | `Y1: u,p`; `Y2: u,p`; `Y3: u,p` | Not anchored. Seeded in the nuclear Ran-C complex and later appears in nuclear/cytosolic rules and readouts. | `site` binds `Ran.cargo`; `Y1`, `Y2`, and `Y3` are independently reversible modification sites. | `C` is named only abstractly in the BNGL/YAML; it behaves like cargo with three phosphorylation-like state sites, but the file does not name a specific cargo protein. | +| `RCC1` | 1 | `site` | none | Anchored to `nuc` by `RCC1(nuc)`. | `site` binds `Ran.cargo` in the nuclear Ran-RCC1 rule. | Because of the anchor, RCC1-containing species should be interpreted as nuclear-localized rather than freely transported. | + +There are no repeated identical site names in these molecule-type declarations. + +## 5. Compartments, anchors, initial species, and setup + +### Compartments + +| Compartment | Dimension value | Size value | Role in this model | +| --- | ---: | ---: | --- | +| `nuc` | 3 | 1 | Nuclear volume where the model starts Ran-C and RCC1 and where nuclear binding/unbinding rules occur. | +| `cyt` | 3 | 1 | Cytosolic volume where transported/bound Ran, cargo, and cargo modification readouts are tracked. | +| `EC` | 3 | 1 | Declared but not used by any active species, observable, or rule pattern in this file. | +| `pm` | 2 | 1 | Declared membrane-like compartment, unused by active patterns in this file. | +| `nm` | 2 | 1 | Declared nuclear-membrane-like compartment, unused by active patterns in this file. | + +### Anchors + +| Anchor declaration | Technical meaning | +| --- | --- | +| `RCC1(nuc)` | RCC1 is constrained to the nuclear compartment. The nuclear Ran-RCC1 binding rule should therefore be read as nuclear-localized by construction, and RCC1-containing complexes should not be interpreted as freely cytosolic. | + +### Initial species + +| Initial species | Initial amount | Technical meaning | +| --- | ---: | --- | +| `@nuc:Ran(cargo!1).C(site!1,Y1~u,Y2~u,Y3~u)` | 1000.0 | The model starts with a nuclear Ran-C complex. `Ran.cargo` is bonded to `C.site`; all three cargo modification sites start unmodified. | +| `@nuc:RCC1(site)` | 1000.0 | The model starts with free nuclear RCC1, consistent with the `RCC1(nuc)` anchor. | + +No initial cytosolic Ran, free cargo, or Ran-RCC1 complex is seeded directly; those states are produced through the reaction rules. + +## 6. Complete reaction-rule inventory + +The source contains **7** reaction rules. The table below preserves one row per rule and identifies the exact sites, state changes, compartment placement, and rate direction. + +### Rule-family orientation + +Rules 1, 2, 6, and 7 are compartmental binding/transport rules involving `Ran.cargo`, `C.site`, or `RCC1.site`. Rules 3-5 are independent reversible state toggles on the three cargo sites `Y3`, `Y2`, and `Y1` in the cytoplasm. Because the model uses VCell-style compartment prefixes, compartment movement is represented by changing prefixes such as `@nuc:Ran(...)` to `@cyt:Ran(...)`, rather than by suffix annotations. + +| # | Rule label | Direction | Participants and affected sites | Exact modeled change | Rate expression | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Transport` | reversible syntax, effectively one-way | Bound `Ran` pattern; `Ran.cargo!+`; compartments `nuc` and `cyt` | Changes a bound Ran pattern from `@nuc:Ran(cargo!+)` to `@cyt:Ran(cargo!+)`; the `cargo!+` constraint requires Ran's `cargo` site to already be bound to some partner, but the partner is not named in the pattern. | `2.0 * 602.0, 0.0` | Implements export-like movement of bound Ran from nucleus to cytoplasm. The reverse arrow exists syntactically, but the zero reverse rate prevents cytoplasm-to-nucleus movement through this rule. A coder should note that only the Ran pattern is explicitly compartment-prefixed in the rule; movement of the connected partner depends on the compartmental semantics applied to the bound complex. | +| 2 | `Ran_C_bind_cyt` | reversible | `Ran.cargo` and `C.site` in `cyt` | Left-to-right releases the cytosolic `Ran.cargo!1`-`C.site!1` bond; right-to-left forms the same bond between free cytosolic Ran and free cytosolic C. | `1.0, 100.0` | Controls cytosolic Ran-C association state. Despite the rule name containing `bind`, the written left-to-right direction is dissociation and the reverse direction is association. | +| 3 | `C_p1` | reversible | Cytosolic `C`; site `Y3`; optional bond status `!?` preserved | Toggles `C.Y3` from `u` to `p` left-to-right and from `p` to `u` right-to-left in `cyt`; the `!?` marker means the rule does not require a specific binding state at `Y3`. | `10.0, 1.0` | Implements reversible modification of the cargo `Y3` site in the cytoplasm without changing `C.site`, `Y1`, `Y2`, or compartment placement. | +| 4 | `C_p2` | reversible | Cytosolic `C`; site `Y2`; optional bond status `!?` preserved | Toggles `C.Y2` from `u` to `p` left-to-right and from `p` to `u` right-to-left in `cyt`; binding status at `Y2` is not constrained. | `10.0, 1.0` | Implements reversible modification of the cargo `Y2` site in the cytoplasm independently of the other cargo modification sites. | +| 5 | `C_p3` | reversible | Cytosolic `C`; site `Y1`; optional bond status `!?` preserved | Toggles `C.Y1` from `u` to `p` left-to-right and from `p` to `u` right-to-left in `cyt`; binding status at `Y1` is not constrained. | `10.0, 1.0` | Implements reversible modification of the cargo `Y1` site in the cytoplasm independently of `Y2` and `Y3`. The rule label `C_p3` refers to the third listed phosphorylation rule, not to site `Y3`. | +| 6 | `Ran_RCC1_bind` | reversible | Nuclear `Ran.cargo` and nuclear `RCC1.site`; RCC1 is anchored to `nuc` | Left-to-right forms a `Ran.cargo!1`-`RCC1.site!1` bond in `nuc`; right-to-left releases that bond back to free nuclear Ran and free nuclear RCC1. | `1.0, 100.0` | Implements nuclear Ran-RCC1 association/dissociation. The `RCC1(nuc)` anchor makes the product complex nuclear-localized by construction and prevents interpreting RCC1 as a freely cytosolic binding partner. | +| 7 | `Ran_C_bind_nuc` | reversible | Nuclear `Ran.cargo` and nuclear `C.site` | Left-to-right releases the nuclear `Ran.cargo!1`-`C.site!1` bond; right-to-left forms the same bond between free nuclear Ran and free nuclear C. | `1.0, 100.0` | Controls nuclear Ran-C association state. This rule can generate free nuclear cargo from the seeded nuclear Ran-C complex and can re-form the nuclear complex. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern counted | Technical interpretation | +| --- | --- | --- | --- | +| `Ran_cyt` | `Molecules` | `@cyt:Ran()` | Counts cytosolic Ran pattern matches, regardless of whether `Ran.cargo` is bound. | +| `Cargo_cyt` | `Molecules` | `@cyt:C()` | Counts cytosolic cargo `C`, regardless of `site`, `Y1`, `Y2`, or `Y3` states. | +| `RCC1_nuc` | `Molecules` | `@nuc:RCC1()` | Counts nuclear RCC1, including free and Ran-bound RCC1 patterns under the nuclear anchor. | +| `Cargo_phosp_cyt_total` | `Molecules` | `@nuc:C(Y1~p!?)`, `@nuc:C(Y2~p!?)`, `@nuc:C(Y3~p!?)` | Despite the name containing `cyt`, the patterns are nuclear `@nuc:C(...)` patterns. The observable counts nuclear cargo matches with each phosphorylated site pattern and may count the same molecule multiple times if several listed patterns match. | +| `Cargo_nuc` | `Molecules` | `@nuc:C()` | Counts nuclear cargo regardless of whether it is bound to Ran or which modification states it carries. | +| `Cargo_phosp_cyt` | `Molecules` | `@cyt:C(Y1~p!?,Y2~p!?,Y3~p!?)` | Counts cytosolic cargo molecules whose `Y1`, `Y2`, and `Y3` sites are all in the phosphorylated state; the optional bond markers do not impose specific bonds at those sites. | +| `Ran_bound_cyt` | `Molecules` | `@cyt:Ran(cargo!+)` | Counts cytosolic Ran whose `cargo` site is bound to some partner, without requiring that the partner be explicitly named in the observable. | + +## 8. Actions and simulation workflow + +The only executable action after `end model` is: + +```bngl +simulate_nf({t_end=>10.0,n_steps=>200}) +``` + +This requests an NFsim simulation from time `0` to `10.0` with `200` output steps. There is no explicit `generate_network(...)` action in this file, consistent with the metadata's `simulation_methods: ["nf"]` and `nfsim_compatible: true`. + +## 9. Technical caveats and ambiguities + +- The metadata description says “Ran GTPase cycle,” but the BNGL molecule type `Ran(cargo)` has no declared nucleotide state site. The model should therefore not be read as an explicit GDP/GTP cycle implementation. +- `C` is an abstract cargo-like molecule name in the local files. The model defines its binding and modification behavior, but does not identify a specific biological cargo protein. +- The `functions` block is empty but present. Under the updated metadata-audit rule, this still supports `uses_functions: true`; under executable-rate interpretation, there are no active functions. +- The observable `Cargo_phosp_cyt_total` has a name suggesting cytosolic cargo phosphorylation, but its patterns are nuclear `@nuc:C(...)` patterns. +- The model declares unused compartments `EC`, `pm`, and `nm`; these may reflect a broader VCell compartment template rather than active biology in this compact file. +- The `Transport` rule uses `Ran(cargo!+)` without naming the bound partner. A coder should verify the target simulator's treatment of connected compartmental complexes before assuming exactly which partner species move with Ran. +- The file uses VCell-style compartment-prefix syntax and an anchors block. These constructs may require VCell-aware parsing and should not be reduced to plain non-spatial BNGL without checking localization semantics. diff --git a/data/summaries_detailed/Blinovran_coder.md b/data/summaries_detailed/Blinovran_coder.md new file mode 100644 index 00000000..6c6deaea --- /dev/null +++ b/data/summaries_detailed/Blinovran_coder.md @@ -0,0 +1,73 @@ +# Coder Model Explanation: Blinov ran + +## 1. Model identity and scope + +- **Model id:** `Blinov_ran` +- **Title:** Blinov ran +- **BNGL path:** `Published/Blinovran/Blinov_ran.bngl` +- **YAML path:** `Published/Blinovran/metadata.yaml` +- **Scope:** This is a compartmental Ran/cargo/RCC1 transport model. It tracks Ran-cargo complex movement between nucleus and cytoplasm, cargo phosphorylation in the cytoplasm, cargo-Ran dissociation/association in both compartments, and RCC1 binding to nuclear Ran. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Compartments | Yes | 5 compartments/surfaces: `nuc`, `cyt`, `EC`, `pm`, and `nm`. | +| Parameters | Yes | Parameter block is present but empty; numeric rates are written directly in rules. | +| Molecule types | Yes | 3 molecule types: `Ran`, `C`, and `RCC1`. | +| Anchors | Yes | `RCC1(nuc)` anchor declaration. | +| Seed species | Yes | 2 numbered nuclear initial species. | +| Observables | Yes | 7 molecule-count readouts. | +| Functions | Yes | Function block is present but empty. | +| Reaction rules | Yes | 7 labeled reversible rules. | +| Actions | Inline command | One NFsim simulation command. | + +## 3. Parameters, functions, and rate laws + +The parameter block is empty, and there are no function definitions. All rate laws are numeric literals placed directly on reaction rules. Transport uses forward rate `2.0 * 602.0` and reverse rate `0.0`, so Ran-cargo transport is effectively one-way from nucleus to cytoplasm. Cargo phosphorylation and dephosphorylation use `10.0` and `1.0`. Ran-cargo and Ran-RCC1 binding rules use `1.0` and `100.0` for the two directions as written. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `Ran` | 1 | `cargo` | None | Binds cargo `C.site` or RCC1 `site`, depending on the rule context. | The single site is reused for cargo and RCC1 interactions in different compartments. | +| `C` | 4 | `site`, `Y1`, `Y2`, `Y3` | `Y1`: `u`, `p`; `Y2`: `u`, `p`; `Y3`: `u`, `p` | `site` binds Ran; `Y1`, `Y2`, and `Y3` are cargo phosphorylation-state sites. | Metadata tag `c` likely refers to cargo, but interpretation comes mainly from molecule and observable names. | +| `RCC1` | 1 | `site` | None | Binds nuclear Ran through `site`. | Anchor declaration associates RCC1 with the nucleus. | + +## 5. Initial species, compartments, and setup + +The model starts with 1000 nuclear Ran-cargo complexes, `@nuc:Ran(cargo!1).C(site!1,Y1~u,Y2~u,Y3~u)`, and 1000 nuclear RCC1 molecules, `@nuc:RCC1(site)`. Cargo begins unphosphorylated at all three `Y` sites. No cytoplasmic species are seeded initially; cytoplasmic Ran/cargo populations arise through transport and cytoplasmic dissociation/phosphorylation rules. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Transport` | Reversible syntax, effectively one-way | Bound Ran-cargo complex in `nuc` and `cyt` compartments | Forward `2.0 * 602.0`, reverse `0.0` | Moves a Ran-cargo complex from nucleus to cytoplasm | Exports bound Ran-cargo complex to the cytoplasm with no return through this rule. | +| 2 | `Ran_C_bind_cyt` | Reversible | Cytoplasmic Ran `cargo` site and cargo `C.site` | `1.0`, `100.0` | Interconverts bound cytoplasmic Ran-cargo complex and separate cytoplasmic Ran plus cargo | Allows cytoplasmic Ran-cargo dissociation and reassociation. As written, the left side is bound and the right side is free. | +| 3 | `C_p1` | Reversible state change | Cytoplasmic cargo `Y3`, regardless of binding status | `10.0`, `1.0` | Converts `Y3` between unphosphorylated and phosphorylated | Phosphorylates and dephosphorylates the third cargo modification site in the cytoplasm. | +| 4 | `C_p2` | Reversible state change | Cytoplasmic cargo `Y2`, regardless of binding status | `10.0`, `1.0` | Converts `Y2` between unphosphorylated and phosphorylated | Phosphorylates and dephosphorylates the second cargo modification site in the cytoplasm. | +| 5 | `C_p3` | Reversible state change | Cytoplasmic cargo `Y1`, regardless of binding status | `10.0`, `1.0` | Converts `Y1` between unphosphorylated and phosphorylated | Phosphorylates and dephosphorylates the first cargo modification site in the cytoplasm. | +| 6 | `Ran_RCC1_bind` | Reversible | Nuclear Ran `cargo` site and nuclear RCC1 `site` | `1.0`, `100.0` | Adds or removes a nuclear Ran-RCC1 bond | Allows RCC1 to bind nuclear Ran through the same Ran site that otherwise binds cargo. | +| 7 | `Ran_C_bind_nuc` | Reversible | Nuclear Ran `cargo` site and nuclear cargo `C.site` | `1.0`, `100.0` | Interconverts bound nuclear Ran-cargo complex and separate nuclear Ran plus cargo | Allows nuclear Ran-cargo dissociation and reassociation. As written, the left side is bound and the right side is free. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Ran_cyt` | `Molecules` | Cytoplasmic Ran | Counts Ran molecules in the cytoplasm. | +| `Cargo_cyt` | `Molecules` | Cytoplasmic cargo `C` | Counts cargo molecules in the cytoplasm. | +| `RCC1_nuc` | `Molecules` | Nuclear RCC1 | Counts RCC1 molecules in the nucleus. | +| `Cargo_phosp_cyt_total` | `Molecules` | Nuclear cargo with `Y1`, `Y2`, or `Y3` phosphorylated | Despite the name, the listed patterns use `@nuc`, so this readout counts phosphorylated cargo patterns in the nucleus, not cytoplasm. | +| `Cargo_nuc` | `Molecules` | Nuclear cargo `C` | Counts cargo molecules in the nucleus. | +| `Cargo_phosp_cyt` | `Molecules` | Cytoplasmic cargo with all three phosphorylation sites marked phosphorylated/possibly bound | Counts cytoplasmic cargo matching phosphorylated-state constraints across `Y1`, `Y2`, and `Y3`. | +| `Ran_bound_cyt` | `Molecules` | Cytoplasmic Ran with `cargo` bound to something | Counts cytoplasmic Ran that remains bound through its cargo site. | + +## 8. Actions and simulation workflow + +The model runs `simulate_nf({t_end=>10.0,n_steps=>200})`. No network generation action is present. Because the model uses compartments, anchored RCC1, wildcard binding constraints, and NFsim-compatible syntax, the intended workflow is direct network-free simulation over 10 time units with 200 output steps. + +## 9. Technical caveats and ambiguities + +- The parameter and function blocks are empty; rule rates are hard-coded numeric literals. +- `Cargo_phosp_cyt_total` is named like a cytoplasmic observable but uses nuclear patterns, so downstream code should not rely on the name alone. +- The Ran `cargo` site is used for both cargo and RCC1 binding in different rules; the model relies on context and compartments rather than distinct Ran sites for these interactions. diff --git a/data/summaries_detailed/Chattaraj2021_condensate_ai_coder.md b/data/summaries_detailed/Chattaraj2021_condensate_ai_coder.md new file mode 100644 index 00000000..8fe27639 --- /dev/null +++ b/data/summaries_detailed/Chattaraj2021_condensate_ai_coder.md @@ -0,0 +1,103 @@ +# Coder Model Explanation: Chattaraj 2021 + +## 1. Model identity and scope + +- **Model id:** `Chattaraj_2021` +- **Title:** Chattaraj 2021 +- **BNGL path:** `Published/Chattaraj2021/Chattaraj_2021.bngl` +- **YAML path:** `Published/Chattaraj2021/metadata.yaml` +- **Metadata description:** The YAML says “NFkB oscillations,” but the BNGL comments and model body describe Nephrin/Nck/NWASP multivalent clustering. +- **Scope:** This file is a heterotypic condensate/clustering model with three molecule types. Nephrin contributes three phosphotyrosine-like sites (`pY1`, `pY2`, `pY3`) that bind the Nck `Sh2` site. Nck also contributes three SH3-like sites (`S1`, `S2`, `S3`) that each bind NWASP proline sites (`p1` through `p6`). The entire behavior is encoded as 21 reversible site-to-site binding rules; there are no internal state changes, compartments, anchors, or functions. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 6 parameters: two dissociation constants, two off-rates, and two derived on-rates for Nephrin-Nck and Nck-NWASP binding. | +| Compartments | No | No compartment block. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 3 molecule types: `Nephrin`, `Nck`, and `NWASP`. | +| Seed/species | Yes | 3 initial pools: 300 Nephrin, 900 Nck, 450 NWASP. | +| Observables | Yes | 11 observables for total/free molecules, fully bound molecules, and mixed clusters. | +| Functions | No | No functions block; rate laws are direct parameters. | +| Reaction rules | Yes | 21 reversible binding rules. | +| Actions | Yes | One inline `writeXML()` command after the model. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `kd_12` | `3500` | Nephrin-Nck equilibrium scale for rules binding `Nephrin.pY*` to `Nck.Sh2`. | +| `kd_23` | `3500` | Nck-NWASP equilibrium scale for rules binding `Nck.S*` to `NWASP.p*`. | +| `koff_23` | `1000` | Reverse rate for all Nck SH3-site/NWASP proline-site rules. | +| `kon_23` | `koff_23/kd_23` | Forward rate for all Nck SH3-site/NWASP proline-site rules. | +| `koff_12` | `1000` | Reverse rate for all Nephrin phosphotyrosine/Nck SH2 rules. | +| `kon_12` | `koff_12/kd_12` | Forward rate for all Nephrin phosphotyrosine/Nck SH2 rules. | + +No functions are declared. Every rule uses either `kon_23, koff_23` or `kon_12, koff_12`. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Nephrin` | 3 | `pY1`, `pY2`, `pY3` | none | none | All three sites bind `Nck.Sh2`. | Multivalent upstream scaffold; no phosphorylation state is modeled even though names contain `pY`. | +| `Nck` | 4 | `S1`, `S2`, `S3`, `Sh2` | none | none | `Sh2` binds Nephrin; `S1`, `S2`, `S3` bind NWASP. | Central adaptor connecting Nephrin and NWASP. | +| `NWASP` | 6 | `p1`, `p2`, `p3`, `p4`, `p5`, `p6` | none | none | Every `p*` site can bind Nck `S1`, `S2`, or `S3`. | Six-site multivalent ligand for Nck SH3 sites. | + +## 5. Compartments, anchors, initial species, and setup + +No compartments or anchors are declared. The initial condition starts all three molecules free: `Nephrin(pY1,pY2,pY3)` at 300, `Nck(S1,S2,S3,Sh2)` at 900, and `NWASP(p1,p2,p3,p4,p5,p6)` at 450. Because all rules are reversible and do not change internal states, cluster composition is controlled by multivalent site occupancy and the two affinity classes. + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 1-18 enumerate every allowed Nck SH3-site/NWASP proline-site contact, one Nck site at a time. Rules 19-21 enumerate the three Nephrin/Nck contacts through Nck `Sh2`. Every row below forms or releases exactly one bond and leaves all other sites unchanged. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `_01_S1_P1` | reversible | `Nck.S1` + `NWASP.p1` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p1!1`. | Allows Nck SH3 site `S1` to occupy NWASP proline site `p1`. | +| 2 | `_02_S2_P1` | reversible | `Nck.S2` + `NWASP.p1` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p1!1`. | Allows Nck `S2` to bind the same NWASP `p1` class as an alternative SH3 contact. | +| 3 | `_03_S3_P1` | reversible | `Nck.S3` + `NWASP.p1` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p1!1`. | Allows Nck `S3` to bind NWASP `p1`. | +| 4 | `_06_S3_P2` | reversible | `Nck.S3` + `NWASP.p2` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p2!1`. | Adds the `S3`/`p2` edge to the SH3-proline interaction graph. | +| 5 | `_05_S2_P2` | reversible | `Nck.S2` + `NWASP.p2` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p2!1`. | Adds the `S2`/`p2` edge. | +| 6 | `_04_S1_P2` | reversible | `Nck.S1` + `NWASP.p2` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p2!1`. | Adds the `S1`/`p2` edge. | +| 7 | `_08_S2_P3` | reversible | `Nck.S2` + `NWASP.p3` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p3!1`. | Adds the `S2`/`p3` edge. | +| 8 | `_07_S1_P3` | reversible | `Nck.S1` + `NWASP.p3` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p3!1`. | Adds the `S1`/`p3` edge. | +| 9 | `_09_S3_P3` | reversible | `Nck.S3` + `NWASP.p3` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p3!1`. | Adds the `S3`/`p3` edge. | +| 10 | `_10_S1_P4` | reversible | `Nck.S1` + `NWASP.p4` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p4!1`. | Adds the `S1`/`p4` edge. | +| 11 | `_11_S2_P4` | reversible | `Nck.S2` + `NWASP.p4` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p4!1`. | Adds the `S2`/`p4` edge. | +| 12 | `_12_S3_P4` | reversible | `Nck.S3` + `NWASP.p4` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p4!1`. | Adds the `S3`/`p4` edge. | +| 13 | `_13_S1_P5` | reversible | `Nck.S1` + `NWASP.p5` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p5!1`. | Adds the `S1`/`p5` edge. | +| 14 | `_14_S2_P5` | reversible | `Nck.S2` + `NWASP.p5` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p5!1`. | Adds the `S2`/`p5` edge. | +| 15 | `_15_S3_P5` | reversible | `Nck.S3` + `NWASP.p5` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p5!1`. | Adds the `S3`/`p5` edge. | +| 16 | `_16_S1_P6` | reversible | `Nck.S1` + `NWASP.p6` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p6!1`. | Adds the `S1`/`p6` edge. | +| 17 | `_17_S3_P6` | reversible | `Nck.S3` + `NWASP.p6` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p6!1`. | Adds the `S3`/`p6` edge. | +| 18 | `_18_S2_P6` | reversible | `Nck.S2` + `NWASP.p6` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p6!1`. | Adds the `S2`/`p6` edge; ordering in source places it after `S3`/`p6`. | +| 19 | `_19_pY1_sh2` | reversible | `Nephrin.pY1` + `Nck.Sh2` | `kon_12, koff_12` | Forms/releases `Nephrin.pY1!1`–`Nck.Sh2!1`. | Connects Nephrin site `pY1` to the Nck adaptor through SH2 binding. | +| 20 | `_20_pY2_sh2` | reversible | `Nephrin.pY2` + `Nck.Sh2` | `kon_12, koff_12` | Forms/releases `Nephrin.pY2!1`–`Nck.Sh2!1`. | Connects Nephrin site `pY2` to Nck. | +| 21 | `_21_pY3_sh2` | reversible | `Nephrin.pY3` + `Nck.Sh2` | `kon_12, koff_12` | Forms/releases `Nephrin.pY3!1`–`Nck.Sh2!1`. | Connects Nephrin site `pY3` to Nck, completing the 3-site Nephrin/Nck binding family. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `tot_Nck` | `Molecules` | `Nck()` | Counts all Nck molecules regardless of site occupancy. | +| `free_Nck` | `Molecules` | `Nck(S1,S2,S3,Sh2)` | Counts Nck with all four sites unbound. | +| `tot_NWASP` | `Molecules` | `NWASP()` | Counts all NWASP molecules. | +| `free_NWASP` | `Molecules` | `NWASP(p1,p2,p3,p4,p5,p6)` | Counts NWASP with all six proline sites free. | +| `tot_Nephrin` | `Molecules` | `Nephrin()` | Counts all Nephrin molecules. | +| `free_Nephrin` | `Molecules` | `Nephrin(pY1,pY2,pY3)` | Counts Nephrin with no Nck bound. | +| `fully_bound_Nephrin` | `Molecules` | `Nephrin(pY1!+,pY2!+,pY3!+)` | Counts Nephrin molecules with all three pY sites occupied. | +| `fully_bound_Nck` | `Molecules` | `Nck(S1!+,S2!+,S3!+,Sh2!+)` | Counts Nck molecules whose three SH3 sites and SH2 site are all occupied. | +| `fully_bound_NWASP` | `Molecules` | `NWASP(p1!+,p2!+,p3!+,p4!+,p5!+,p6!+)` | Counts NWASP molecules with all six proline sites occupied. | +| `cluster_neph_nck_nw` | `Molecules` | `Nephrin().Nck().NWASP()` | Counts complexes containing at least one Nephrin, Nck, and NWASP molecule. | +| `cluster_nck_nw` | `Molecules` | `Nck().NWASP()` | Counts Nck/NWASP-containing complexes with or without Nephrin. | + +## 8. Actions and simulation workflow + +`writeXML()` is called after `end model`, so the file is set up to export the model to XML rather than run a simulation inside the BNGL file. + +## 9. Technical caveats and ambiguities + +- The YAML description does not match the BNGL content; the BNGL comments and molecules clearly describe Nephrin/Nck/NWASP clustering. +- Site names such as `pY` and `p` imply biological motifs, but the model contains no internal phosphorylation states; they are binding sites only. +- The 18 Nck/NWASP rules are explicit individual edges, not one wildcard rule, so site-specific occupancy is preserved in generated complexes. diff --git a/data/summaries_detailed/Chattaraj2021_condensate_coder.md b/data/summaries_detailed/Chattaraj2021_condensate_coder.md new file mode 100644 index 00000000..8fe27639 --- /dev/null +++ b/data/summaries_detailed/Chattaraj2021_condensate_coder.md @@ -0,0 +1,103 @@ +# Coder Model Explanation: Chattaraj 2021 + +## 1. Model identity and scope + +- **Model id:** `Chattaraj_2021` +- **Title:** Chattaraj 2021 +- **BNGL path:** `Published/Chattaraj2021/Chattaraj_2021.bngl` +- **YAML path:** `Published/Chattaraj2021/metadata.yaml` +- **Metadata description:** The YAML says “NFkB oscillations,” but the BNGL comments and model body describe Nephrin/Nck/NWASP multivalent clustering. +- **Scope:** This file is a heterotypic condensate/clustering model with three molecule types. Nephrin contributes three phosphotyrosine-like sites (`pY1`, `pY2`, `pY3`) that bind the Nck `Sh2` site. Nck also contributes three SH3-like sites (`S1`, `S2`, `S3`) that each bind NWASP proline sites (`p1` through `p6`). The entire behavior is encoded as 21 reversible site-to-site binding rules; there are no internal state changes, compartments, anchors, or functions. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 6 parameters: two dissociation constants, two off-rates, and two derived on-rates for Nephrin-Nck and Nck-NWASP binding. | +| Compartments | No | No compartment block. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 3 molecule types: `Nephrin`, `Nck`, and `NWASP`. | +| Seed/species | Yes | 3 initial pools: 300 Nephrin, 900 Nck, 450 NWASP. | +| Observables | Yes | 11 observables for total/free molecules, fully bound molecules, and mixed clusters. | +| Functions | No | No functions block; rate laws are direct parameters. | +| Reaction rules | Yes | 21 reversible binding rules. | +| Actions | Yes | One inline `writeXML()` command after the model. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `kd_12` | `3500` | Nephrin-Nck equilibrium scale for rules binding `Nephrin.pY*` to `Nck.Sh2`. | +| `kd_23` | `3500` | Nck-NWASP equilibrium scale for rules binding `Nck.S*` to `NWASP.p*`. | +| `koff_23` | `1000` | Reverse rate for all Nck SH3-site/NWASP proline-site rules. | +| `kon_23` | `koff_23/kd_23` | Forward rate for all Nck SH3-site/NWASP proline-site rules. | +| `koff_12` | `1000` | Reverse rate for all Nephrin phosphotyrosine/Nck SH2 rules. | +| `kon_12` | `koff_12/kd_12` | Forward rate for all Nephrin phosphotyrosine/Nck SH2 rules. | + +No functions are declared. Every rule uses either `kon_23, koff_23` or `kon_12, koff_12`. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Nephrin` | 3 | `pY1`, `pY2`, `pY3` | none | none | All three sites bind `Nck.Sh2`. | Multivalent upstream scaffold; no phosphorylation state is modeled even though names contain `pY`. | +| `Nck` | 4 | `S1`, `S2`, `S3`, `Sh2` | none | none | `Sh2` binds Nephrin; `S1`, `S2`, `S3` bind NWASP. | Central adaptor connecting Nephrin and NWASP. | +| `NWASP` | 6 | `p1`, `p2`, `p3`, `p4`, `p5`, `p6` | none | none | Every `p*` site can bind Nck `S1`, `S2`, or `S3`. | Six-site multivalent ligand for Nck SH3 sites. | + +## 5. Compartments, anchors, initial species, and setup + +No compartments or anchors are declared. The initial condition starts all three molecules free: `Nephrin(pY1,pY2,pY3)` at 300, `Nck(S1,S2,S3,Sh2)` at 900, and `NWASP(p1,p2,p3,p4,p5,p6)` at 450. Because all rules are reversible and do not change internal states, cluster composition is controlled by multivalent site occupancy and the two affinity classes. + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 1-18 enumerate every allowed Nck SH3-site/NWASP proline-site contact, one Nck site at a time. Rules 19-21 enumerate the three Nephrin/Nck contacts through Nck `Sh2`. Every row below forms or releases exactly one bond and leaves all other sites unchanged. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `_01_S1_P1` | reversible | `Nck.S1` + `NWASP.p1` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p1!1`. | Allows Nck SH3 site `S1` to occupy NWASP proline site `p1`. | +| 2 | `_02_S2_P1` | reversible | `Nck.S2` + `NWASP.p1` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p1!1`. | Allows Nck `S2` to bind the same NWASP `p1` class as an alternative SH3 contact. | +| 3 | `_03_S3_P1` | reversible | `Nck.S3` + `NWASP.p1` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p1!1`. | Allows Nck `S3` to bind NWASP `p1`. | +| 4 | `_06_S3_P2` | reversible | `Nck.S3` + `NWASP.p2` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p2!1`. | Adds the `S3`/`p2` edge to the SH3-proline interaction graph. | +| 5 | `_05_S2_P2` | reversible | `Nck.S2` + `NWASP.p2` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p2!1`. | Adds the `S2`/`p2` edge. | +| 6 | `_04_S1_P2` | reversible | `Nck.S1` + `NWASP.p2` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p2!1`. | Adds the `S1`/`p2` edge. | +| 7 | `_08_S2_P3` | reversible | `Nck.S2` + `NWASP.p3` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p3!1`. | Adds the `S2`/`p3` edge. | +| 8 | `_07_S1_P3` | reversible | `Nck.S1` + `NWASP.p3` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p3!1`. | Adds the `S1`/`p3` edge. | +| 9 | `_09_S3_P3` | reversible | `Nck.S3` + `NWASP.p3` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p3!1`. | Adds the `S3`/`p3` edge. | +| 10 | `_10_S1_P4` | reversible | `Nck.S1` + `NWASP.p4` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p4!1`. | Adds the `S1`/`p4` edge. | +| 11 | `_11_S2_P4` | reversible | `Nck.S2` + `NWASP.p4` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p4!1`. | Adds the `S2`/`p4` edge. | +| 12 | `_12_S3_P4` | reversible | `Nck.S3` + `NWASP.p4` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p4!1`. | Adds the `S3`/`p4` edge. | +| 13 | `_13_S1_P5` | reversible | `Nck.S1` + `NWASP.p5` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p5!1`. | Adds the `S1`/`p5` edge. | +| 14 | `_14_S2_P5` | reversible | `Nck.S2` + `NWASP.p5` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p5!1`. | Adds the `S2`/`p5` edge. | +| 15 | `_15_S3_P5` | reversible | `Nck.S3` + `NWASP.p5` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p5!1`. | Adds the `S3`/`p5` edge. | +| 16 | `_16_S1_P6` | reversible | `Nck.S1` + `NWASP.p6` | `kon_23, koff_23` | Forms/releases `Nck.S1!1`–`NWASP.p6!1`. | Adds the `S1`/`p6` edge. | +| 17 | `_17_S3_P6` | reversible | `Nck.S3` + `NWASP.p6` | `kon_23, koff_23` | Forms/releases `Nck.S3!1`–`NWASP.p6!1`. | Adds the `S3`/`p6` edge. | +| 18 | `_18_S2_P6` | reversible | `Nck.S2` + `NWASP.p6` | `kon_23, koff_23` | Forms/releases `Nck.S2!1`–`NWASP.p6!1`. | Adds the `S2`/`p6` edge; ordering in source places it after `S3`/`p6`. | +| 19 | `_19_pY1_sh2` | reversible | `Nephrin.pY1` + `Nck.Sh2` | `kon_12, koff_12` | Forms/releases `Nephrin.pY1!1`–`Nck.Sh2!1`. | Connects Nephrin site `pY1` to the Nck adaptor through SH2 binding. | +| 20 | `_20_pY2_sh2` | reversible | `Nephrin.pY2` + `Nck.Sh2` | `kon_12, koff_12` | Forms/releases `Nephrin.pY2!1`–`Nck.Sh2!1`. | Connects Nephrin site `pY2` to Nck. | +| 21 | `_21_pY3_sh2` | reversible | `Nephrin.pY3` + `Nck.Sh2` | `kon_12, koff_12` | Forms/releases `Nephrin.pY3!1`–`Nck.Sh2!1`. | Connects Nephrin site `pY3` to Nck, completing the 3-site Nephrin/Nck binding family. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `tot_Nck` | `Molecules` | `Nck()` | Counts all Nck molecules regardless of site occupancy. | +| `free_Nck` | `Molecules` | `Nck(S1,S2,S3,Sh2)` | Counts Nck with all four sites unbound. | +| `tot_NWASP` | `Molecules` | `NWASP()` | Counts all NWASP molecules. | +| `free_NWASP` | `Molecules` | `NWASP(p1,p2,p3,p4,p5,p6)` | Counts NWASP with all six proline sites free. | +| `tot_Nephrin` | `Molecules` | `Nephrin()` | Counts all Nephrin molecules. | +| `free_Nephrin` | `Molecules` | `Nephrin(pY1,pY2,pY3)` | Counts Nephrin with no Nck bound. | +| `fully_bound_Nephrin` | `Molecules` | `Nephrin(pY1!+,pY2!+,pY3!+)` | Counts Nephrin molecules with all three pY sites occupied. | +| `fully_bound_Nck` | `Molecules` | `Nck(S1!+,S2!+,S3!+,Sh2!+)` | Counts Nck molecules whose three SH3 sites and SH2 site are all occupied. | +| `fully_bound_NWASP` | `Molecules` | `NWASP(p1!+,p2!+,p3!+,p4!+,p5!+,p6!+)` | Counts NWASP molecules with all six proline sites occupied. | +| `cluster_neph_nck_nw` | `Molecules` | `Nephrin().Nck().NWASP()` | Counts complexes containing at least one Nephrin, Nck, and NWASP molecule. | +| `cluster_nck_nw` | `Molecules` | `Nck().NWASP()` | Counts Nck/NWASP-containing complexes with or without Nephrin. | + +## 8. Actions and simulation workflow + +`writeXML()` is called after `end model`, so the file is set up to export the model to XML rather than run a simulation inside the BNGL file. + +## 9. Technical caveats and ambiguities + +- The YAML description does not match the BNGL content; the BNGL comments and molecules clearly describe Nephrin/Nck/NWASP clustering. +- Site names such as `pY` and `p` imply biological motifs, but the model contains no internal phosphorylation states; they are binding sites only. +- The 18 Nck/NWASP rules are explicit individual edges, not one wildcard rule, so site-specific occupancy is preserved in generated complexes. diff --git a/data/summaries_detailed/Dembo1978_ai_coder.md b/data/summaries_detailed/Dembo1978_ai_coder.md new file mode 100644 index 00000000..2a9f47db --- /dev/null +++ b/data/summaries_detailed/Dembo1978_ai_coder.md @@ -0,0 +1,81 @@ +# Coder Model Explanation: Dembo 1978 + +## 1. Model identity and scope + +- **Model id:** `Dembo_1978` +- **Title:** Dembo 1978 +- **BNGL path:** `Published/Dembo1978/blbr_dembo1978.bngl` +- **YAML path:** `Published/Dembo1978/metadata.yaml` +- **Scope:** This is a symmetric bivalent ligand-bivalent receptor cross-linking model. It represents bivalent hapten `L` and bivalent receptor/IgE `R`, with free ligand capture, inter-complex cross-linking, and bond dissociation. The comments specify that same-complex ring formation is blocked during NFsim execution. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 13 physical, scaling, abundance, and kinetic parameters. | +| Compartments | No | No compartment declarations. | +| Molecule types | Yes | 2 molecule types: bivalent `L` and bivalent `R`. | +| Seed species | Yes | 2 initial species: free ligand and free receptor. | +| Observables | Yes | 5 readouts for free molecules, bonds, and free sites. | +| Functions | No | No function block. | +| Reaction rules | Yes | 3 labeled rules. | +| Actions | Yes | One NFsim simulation action. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value / expression | Role | +| --- | ---: | --- | +| `NA` | 6.02214076e23 | Avogadro constant for concentration-to-molecule scaling. | +| `V_cell` | 1e-9 | Cell volume in liters. | +| `R_per_cell` | 3e5 | Receptor count before simulation down-scaling. | +| `f` | 0.01 | Simulation scaling factor. | +| `V_sim` | `V_cell*f` | Effective simulation volume. | +| `RT` | `R_per_cell*f` | Scaled receptor count, 3000 molecules. | +| `LT_per_cell` | 3e6 | Ligand count before scaling. | +| `LT` | `LT_per_cell*f` | Scaled ligand count. | +| `kon` | 1e6 | Single-site solution association rate. | +| `koff` | 0.01 | Single-bond dissociation rate. | +| `KxRT` | 5 | Dimensionless cross-linking propensity. | +| `kf` | `kon/(NA*V_sim)` | Stochastic ligand-capture rate for two free molecules. | +| `kxf` | `KxRT/RT*koff` | Stochastic cross-linking rate for a tethered ligand arm binding another receptor. | + +There are no BNGL functions. Rule 1 uses `kf`, rule 2 uses `kxf`, and rule 3 uses `koff`. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `L` | 2 | `r`, `r` | None | Each `r` site can bind a receptor `l` site. | The repeated site names encode two identical hapten arms. | +| `R` | 2 | `l`, `l` | None | Each `l` site can bind a ligand `r` site. | The repeated site names encode two identical receptor/IgE binding sites. | + +## 5. Initial species, compartments, and setup + +The initial condition contains only free bivalent ligand, `L(r,r)`, at `LT`, and free bivalent receptor, `R(l,l)`, at `RT`. There are no compartments. The model starts with no ligand-receptor bonds, and aggregation emerges from the capture and cross-linking rules. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `R_capture` | One-way binding | Free `L` with two free `r` sites plus `R` with a free `l` site | `kf` | Creates one `L.r`-`R.l` bond | A free bivalent hapten is captured from solution by a free receptor site. | +| 2 | `R_crosslink` | One-way binding | Ligand already bound through one `r` site and still free at another `r` site plus a receptor with a free `l` site | `kxf` | Adds a second ligand-receptor bond | A tethered ligand arm binds a receptor site in a different complex, extending a chain and creating receptor cross-links. | +| 3 | `R_dissoc` | One-way unbinding | Any `L.r`-`R.l` bond | `koff` | Breaks one ligand-receptor bond | Any hapten-receptor bond can dissociate, producing one free ligand site and one free receptor site. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Free_L` | `Species` | `L(r,r)` | Counts completely free ligand molecules with both arms unbound. | +| `Obs_Free_R` | `Species` | `R(l,l)` | Counts completely free receptor molecules with both sites unbound. | +| `Obs_Bonds` | `Molecules` | One `L.r`-`R.l` bond | Counts total ligand-receptor bonds. | +| `Obs_Free_L_sites` | `Molecules` | Ligand `r` sites that are free | Counts available hapten arms across all ligand molecules. | +| `Obs_Free_R_sites` | `Molecules` | Receptor `l` sites that are free | Counts available receptor binding sites across all receptor molecules. | + +## 8. Actions and simulation workflow + +The action block runs `simulate({method=>"nf", suffix=>"nfr", t_start=>0, t_end=>3000, n_steps=>300, gml=>2147483647, param=>"-bscb"})`. This uses NFsim rather than generated-network ODE simulation because bivalent-bivalent cross-linking can generate unbounded chain species. The `-bscb` flag blocks same-complex binding, enforcing inter-complex cross-linking and preventing ring closure. + +## 9. Technical caveats and ambiguities + +- The YAML says ODE compatibility, but the BNGL action and comments explicitly use NFsim because network generation is infeasible for unbounded chains. +- Repeated site names mean the two ligand arms and two receptor sites are symmetric; the source does not distinguish arm identities. +- The `R_crosslink` rule relies on the NFsim same-complex-binding block to prevent rings; without that execution flag, interpretation of allowed cross-links would differ. diff --git a/data/summaries_detailed/Dembo1978_coder.md b/data/summaries_detailed/Dembo1978_coder.md new file mode 100644 index 00000000..2a9f47db --- /dev/null +++ b/data/summaries_detailed/Dembo1978_coder.md @@ -0,0 +1,81 @@ +# Coder Model Explanation: Dembo 1978 + +## 1. Model identity and scope + +- **Model id:** `Dembo_1978` +- **Title:** Dembo 1978 +- **BNGL path:** `Published/Dembo1978/blbr_dembo1978.bngl` +- **YAML path:** `Published/Dembo1978/metadata.yaml` +- **Scope:** This is a symmetric bivalent ligand-bivalent receptor cross-linking model. It represents bivalent hapten `L` and bivalent receptor/IgE `R`, with free ligand capture, inter-complex cross-linking, and bond dissociation. The comments specify that same-complex ring formation is blocked during NFsim execution. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 13 physical, scaling, abundance, and kinetic parameters. | +| Compartments | No | No compartment declarations. | +| Molecule types | Yes | 2 molecule types: bivalent `L` and bivalent `R`. | +| Seed species | Yes | 2 initial species: free ligand and free receptor. | +| Observables | Yes | 5 readouts for free molecules, bonds, and free sites. | +| Functions | No | No function block. | +| Reaction rules | Yes | 3 labeled rules. | +| Actions | Yes | One NFsim simulation action. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value / expression | Role | +| --- | ---: | --- | +| `NA` | 6.02214076e23 | Avogadro constant for concentration-to-molecule scaling. | +| `V_cell` | 1e-9 | Cell volume in liters. | +| `R_per_cell` | 3e5 | Receptor count before simulation down-scaling. | +| `f` | 0.01 | Simulation scaling factor. | +| `V_sim` | `V_cell*f` | Effective simulation volume. | +| `RT` | `R_per_cell*f` | Scaled receptor count, 3000 molecules. | +| `LT_per_cell` | 3e6 | Ligand count before scaling. | +| `LT` | `LT_per_cell*f` | Scaled ligand count. | +| `kon` | 1e6 | Single-site solution association rate. | +| `koff` | 0.01 | Single-bond dissociation rate. | +| `KxRT` | 5 | Dimensionless cross-linking propensity. | +| `kf` | `kon/(NA*V_sim)` | Stochastic ligand-capture rate for two free molecules. | +| `kxf` | `KxRT/RT*koff` | Stochastic cross-linking rate for a tethered ligand arm binding another receptor. | + +There are no BNGL functions. Rule 1 uses `kf`, rule 2 uses `kxf`, and rule 3 uses `koff`. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `L` | 2 | `r`, `r` | None | Each `r` site can bind a receptor `l` site. | The repeated site names encode two identical hapten arms. | +| `R` | 2 | `l`, `l` | None | Each `l` site can bind a ligand `r` site. | The repeated site names encode two identical receptor/IgE binding sites. | + +## 5. Initial species, compartments, and setup + +The initial condition contains only free bivalent ligand, `L(r,r)`, at `LT`, and free bivalent receptor, `R(l,l)`, at `RT`. There are no compartments. The model starts with no ligand-receptor bonds, and aggregation emerges from the capture and cross-linking rules. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `R_capture` | One-way binding | Free `L` with two free `r` sites plus `R` with a free `l` site | `kf` | Creates one `L.r`-`R.l` bond | A free bivalent hapten is captured from solution by a free receptor site. | +| 2 | `R_crosslink` | One-way binding | Ligand already bound through one `r` site and still free at another `r` site plus a receptor with a free `l` site | `kxf` | Adds a second ligand-receptor bond | A tethered ligand arm binds a receptor site in a different complex, extending a chain and creating receptor cross-links. | +| 3 | `R_dissoc` | One-way unbinding | Any `L.r`-`R.l` bond | `koff` | Breaks one ligand-receptor bond | Any hapten-receptor bond can dissociate, producing one free ligand site and one free receptor site. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Free_L` | `Species` | `L(r,r)` | Counts completely free ligand molecules with both arms unbound. | +| `Obs_Free_R` | `Species` | `R(l,l)` | Counts completely free receptor molecules with both sites unbound. | +| `Obs_Bonds` | `Molecules` | One `L.r`-`R.l` bond | Counts total ligand-receptor bonds. | +| `Obs_Free_L_sites` | `Molecules` | Ligand `r` sites that are free | Counts available hapten arms across all ligand molecules. | +| `Obs_Free_R_sites` | `Molecules` | Receptor `l` sites that are free | Counts available receptor binding sites across all receptor molecules. | + +## 8. Actions and simulation workflow + +The action block runs `simulate({method=>"nf", suffix=>"nfr", t_start=>0, t_end=>3000, n_steps=>300, gml=>2147483647, param=>"-bscb"})`. This uses NFsim rather than generated-network ODE simulation because bivalent-bivalent cross-linking can generate unbounded chain species. The `-bscb` flag blocks same-complex binding, enforcing inter-complex cross-linking and preventing ring closure. + +## 9. Technical caveats and ambiguities + +- The YAML says ODE compatibility, but the BNGL action and comments explicitly use NFsim because network generation is infeasible for unbounded chains. +- Repeated site names mean the two ligand arms and two receptor sites are symmetric; the source does not distinguish arm identities. +- The `R_crosslink` rule relies on the NFsim same-complex-binding block to prevent rings; without that execution flag, interpretation of allowed cross-links would differ. diff --git a/data/summaries_detailed/Dolan2015_ai_coder.md b/data/summaries_detailed/Dolan2015_ai_coder.md new file mode 100644 index 00000000..1574ae3e --- /dev/null +++ b/data/summaries_detailed/Dolan2015_ai_coder.md @@ -0,0 +1,2971 @@ +# Coder Model Explanation: Dolan 2015 + +## 1. Model identity and scope + +- **Model id:** `Dolan_2015` +- **Title:** Dolan 2015 +- **BNGL path:** `Published/Dolan2015/Dolan_2015.bngl` +- **YAML path:** `Published/Dolan2015/metadata.yaml` +- **Metadata description:** Insulin signaling +- **Scope:** A combined DNA-damage, p53/MDM2/p21 stress-response, oxidative damage, non-homologous end joining (NHEJ), PARP/Ligase repair, ATM/H2AX focus, and senescence-switching model. The source explicitly starts as a combined p53 and NHEJ model, then enumerates 50 explicit DNA break loci and many repeated repair-rule families over those loci. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 73 parameter entries. | +| Compartments | No | 0 compartment entries. | +| Anchors | No | 0 anchor entries. | +| Molecule types | Yes | 74 molecule type entries. | +| Seed/species | Yes | 75 initial species entries. | +| Observables | Yes | 176 observable entries. | +| Functions | Yes | 9 function entries. | +| Reaction rules | Yes | 2339 reaction rules. | +| Actions | Yes | 50 action or inline execution commands. | + +## 3. Parameters, functions, and rate laws + +The model uses the following parameter entries. Comment text is preserved when the source provides it; otherwise the role is inferred from the parameter name and where it is used. + +| Parameter | Value/expression | Role / source comment | +| --- | --- | --- | +| `kp53mRNAsyn` | `0.06` | Rate of p53 mRNA Synthesis | +| `kp53mRNAdeg` | `0.006` | Rate of p53 mRNA Degradation | +| `kp53syn` | `0.36` | Rate of p53 Synthesis | +| `kp53deg` | `4.95e-5` | Rate of p53 Degradation | +| `kp53degMDM2dep` | `0.0495` | Rate of p53 Degradation-MDM2 Dependant | +| `kp53phos` | `0.36` | Rate of p53 Phosphorylation | +| `kp53dphos` | `30` | Rate of p53 Dephosphorylation | +| `kMDM2mRNAsyn` | `0.006` | Rate of MDM2 mRNA Synthesis | +| `kMDM2mRNAdeg` | `0.006` | Rate of MDM2 mRNA Degradation | +| `kMDM2syn` | `0.0297` | Rate of MDM2 Synthesis | +| `kMDM2deg` | `0.02598` | Rate of MDM2 Degradation | +| `kMDM2pdeg` | `0.024` | Rate of Phosphorylated MDM2 Degradation | +| `kMDM2phos` | `120` | Rate of MDM2 Phosphorylation | +| `kMDM2dphos` | `30` | Rate of p53 Dephosphorylation | +| `kp53MDM2bind` | `0.0693` | Rate of p53 MDM2 Binding | +| `kp53MDM2dis` | `0.0000693` | Rate of p53 MDM2 Dissociation | +| `kp21mRNAsyn` | `0.0000036` | Rate of p21 mRNA Synthesis (p53) | +| `kp21mRNAsynp` | `0.00036` | Rate of p21 mRNA Synthesis (Phosphorylated p53) | +| `kp21mRNAdeg` | `0.00144` | Rate of p21 mRNA Degradation | +| `kp21synstep1` | `0.024` | Rate of p21 Synthesis Step 1 | +| `kp21synstep2` | `0.0024` | Rate of p21 Synthesis Step 2 | +| `kp21synstep3` | `0.0024` | Rate of p21 Synthesis Step 3 | +| `kp21deg` | `0.0114` | Rate of p21 Degradation | +| `kGADD45act` | `0.00024` | Rate of GADD45 Activation/Production | +| `kGADD45deg` | `0.0006` | Rate of GADD45 Degradation | +| `kp38phos` | `0.48` | Rate of p38 Phosphorylation | +| `kp38dphos` | `6` | Rate of p38 Dephosphorylation | +| `kROSgen` | `1.5` | Rate of ROS Generation by p38 | +| `kIR` | `80` | Kinetic rate or kinetic expression parameter. | +| `kROS` | `50` | Constant rate of ROS production | +| `kdROS` | `5` | ROS degradation rate | +| `kdam1` | `0.000006` | Rate of simple damage production by ROS | +| `kdam2` | `0.000006` | Rate of complex damage production by ROS | +| `kdku1` | `0.5` | Rate of Ku dissociation from a simple break | +| `kdku2` | `0.5` | Rate of Ku dissociation from a complex break | +| `kdku3` | `5` | Rate of oxidised Ku dissociation from a simple break | +| `kdku4` | `5` | Rate of oxidised Ku dissociation from a complex break | +| `kdnapk1` | `0.033` | Rate of DNAPK simple break complex formation | +| `kdnapk2` | `0.0017` | Rate of DNAPK complex break complex formation | +| `kddnapk1` | `0.02` | Rate of DNAPK simple break complex dissociation | +| `kddnapk2` | `0.02` | Rate of DNAPK complex break complex dissociation | +| `kdnapkphos1` | `0.28` | Rate pd DNAPK phosphorylation in a DNAPK complex of a simple break | +| `kdnapkphos2` | `0.28` | Rate pd DNAPK phosphorylation in a DNAPK complex of a complex break | +| `kliIV1` | `0.00071` | Rate of LigaseIV binding to a simple break complex | +| `kliIV2` | `0.00046` | Rate of LigaseIV binding to a complex break complex | +| `kdliIV1` | `0.0001` | Rate of LigaseIV dissociation from a simple break complex | +| `kdliIV2` | `0.0001` | Rate of LigaseIV dissociation from a complex break complex | +| `kfixIV1` | `0.0285` | Rate of DNA repair by LigaseIV of a simple break | +| `kfixIV2` | `0.0285` | Rate of DNA repair by LigaseIV of a complex break | +| `kPARP1` | `0.000077` | Rate of PARP binding to simple break | +| `kPARP2` | `0.000065` | Rate of PARP binding to complex break | +| `kdPARP1` | `0.02` | Rate of PARP dissociation from a simple break | +| `kdPARP2` | `0.02` | Rate of PARP dissociation from a complex break | +| `kliIII1` | `0.0015` | Rate of LigaseIII binding to a simple break | +| `kliIII2` | `0.00024` | Rate of LigaseIII binding to a complex break | +| `kdliIII1` | `0.0001` | Rate of LigaseIII dissociation from a simple break | +| `kdliIII2` | `0.0001` | Rate of LigaseIII dissociation from a complex break | +| `kfixIII1` | `0.0006` | Rate of DNA accurate repair by LigaseIII for a simple break | +| `kfixIII2` | `0.0006` | Rate of DNA accurate repair by LigaseIII for a complex break | +| `kfixIII3` | `0.0009` | Rate of DNA inaccurate repair by LigaseIII for a simple break | +| `kfixIII4` | `0.0009` | Rate of dna inaccurate repair by LigaseIII for a complex break | +| `kATMact` | `0.0012` | Rate of ATM Activation | +| `kATMinact` | `0.03` | Rate of ATM Inactivation | +| `kh2axp1` | `0.1` | Phosphorylation of h2ax via ATM | +| `kh2axp2` | `0.5` | Phosphorylation of h2ax via DNA-PKcs | +| `kh2axu` | `0.01` | Dephosphorylation of h2ax | +| `kh2axfoc` | `0.5` | Creation of damage foci | +| `kfocback` | `0.03` | Resolution of damage foci | +| `kh2axfull` | `0.1` | Creation of complete damage foci | +| `kfocfin` | `0.03` | Resolution of complete damage foci | +| `kox` | `0.000025` | Rate of oxidisation of Ku | +| `kred` | `0.002` | Rate of reduction of Ku | +| `ksen` | `100` | Activation of senescent state | + +**Functions** + +| Function | Technical interpretation | +| --- | --- | +| `kku1() = if(Senescent_Counter>0,0.000000034,0.00034)` | Executable expression used by rules or rate logic. | +| `kku2() = if(Senescent_Counter>0,0.000000021,0.00021)` | Executable expression used by rules or rate logic. | +| `kplus() = if(p21>15,0.04,0)` | Executable expression used by rules or rate logic. | +| `kminus() = if(p21<=15&&Sen_Min<1,0.5,0)` | Executable expression used by rules or rate logic. | +| `kKuDown() = if(Senescent_Counter==1,0.01,0)` | Executable expression used by rules or rate logic. | +| `kKustop() = if(Ku<=250,0,1)` | Executable expression used by rules or rate logic. | +| `kParpDown() = if(Senescent_Counter==1,0.01,0)` | Executable expression used by rules or rate logic. | +| `kParpstop() = if(PARP<=5,0,1)` | Executable expression used by rules or rate logic. | +| `kDelete()= if(Sink<=5,0,10000)` | Executable expression used by rules or rate logic. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Time` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `T` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `P` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `E` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `IR` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `D` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `p53_mRNA` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `p53` | 1 | `Site1` | Site1: u, p | None | Site1 is an internal state/modification coordinate | Declared in molecule types block. | +| `MDM2` | 1 | `Site1` | Site1: u, p | None | Site1 is an internal state/modification coordinate | Declared in molecule types block. | +| `MDM2_mRNA` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `p21_mRNA` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `p21` | 1 | `step` | step: 1, 2, 3 | None | step is an internal state/modification coordinate | Declared in molecule types block. | +| `p38` | 1 | `Site1` | Site1: u, p | None | Site1 is an internal state/modification coordinate | Declared in molecule types block. | +| `GADD45` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `Sink` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `ATM` | 2 | `state`, `h2ax` | state: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 | None | state is an internal state/modification coordinate; h2ax is used as a binding/matching component | Declared in molecule types block. | +| `DNA1` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA2` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA3` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA4` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA5` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA6` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA7` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA8` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA9` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA10` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA11` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA12` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA13` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA14` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA15` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA16` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA17` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA18` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA19` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA20` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA21` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA22` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA23` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA24` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA25` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA26` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA27` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA28` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA29` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA30` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA31` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA32` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA33` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA34` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA35` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA36` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA37` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA38` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA39` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA40` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA41` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA42` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA43` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA44` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA45` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA46` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA47` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA48` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA49` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA50` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `ROS` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `Ku` | 3 | `dna`, `cs`, `cys` | cys: red, ox | None | dna is used as a binding/matching component; cs is used as a binding/matching component; cys is an internal state/modification coordinate | Declared in molecule types block. | +| `DNAPKcs` | 3 | `ku`, `liIV`, `psite` | psite: u, p | None | ku is used as a binding/matching component; liIV is used as a binding/matching component; psite is an internal state/modification coordinate | Declared in molecule types block. | +| `LiIII` | 1 | `PARP` | None | None | PARP is used as a binding/matching component | Declared in molecule types block. | +| `LiIV` | 1 | `cs` | None | None | cs is used as a binding/matching component | Declared in molecule types block. | +| `PARP` | 2 | `dna`, `liIII` | None | None | dna is used as a binding/matching component; liIII is used as a binding/matching component | Declared in molecule types block. | +| `I` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `Sen` | 2 | `int`, `State` | int: 1, 10, PLUS, MINUS; State: normal, sen | None | int is an internal state/modification coordinate; State is an internal state/modification coordinate | Declared in molecule types block. | + +## 5. Compartments, anchors, initial species, and setup + +No BNGL compartment block is declared. + +No anchors block is declared. + +Ionizing radiation and ROS generate simple or complex DNA breaks across explicit DNA loci. ATM and DNA-PKcs signal damage to p53, p38, H2AX, and repair machinery; p53 induces MDM2 and p21, p21 controls a senescence counter, and senescence feeds back by reducing Ku/PARP repair availability. + +| Initial species entry | Initial amount/expression | Technical setup meaning | +| --- | --- | --- | +| `Time()` | `0` | Initial population or concentration for this exact pattern. | +| `P()` | `1` | Initial population or concentration for this exact pattern. | +| `T()` | `1` | Initial population or concentration for this exact pattern. | +| `E()` | `1` | Initial population or concentration for this exact pattern. | +| `IR()` | `0` | Initial population or concentration for this exact pattern. | +| `D()` | `10` | Initial population or concentration for this exact pattern. | +| `p53_mRNA()` | `10` | Initial population or concentration for this exact pattern. | +| `p53(Site1~u)` | `5` | Initial population or concentration for this exact pattern. | +| `MDM2_mRNA()` | `10` | Initial population or concentration for this exact pattern. | +| `MDM2(Site1~u)` | `5` | Initial population or concentration for this exact pattern. | +| `p53(Site1!1~u).MDM2(Site1!1~u)` | `95` | Initial population or concentration for this exact pattern. | +| `p21_mRNA()` | `1` | Initial population or concentration for this exact pattern. | +| `p21(step~1)` | `0` | Initial population or concentration for this exact pattern. | +| `p38(Site1~u)` | `100` | Initial population or concentration for this exact pattern. | +| `$Sink()` | `0` | Initial population or concentration for this exact pattern. | +| `ATM(state~0,h2ax)` | `200` | Initial population or concentration for this exact pattern. | +| `DNA1(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA2(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA3(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA4(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA5(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA6(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA7(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA8(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA9(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA10(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA11(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA12(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA13(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA14(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA15(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA16(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA17(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA18(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA19(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA20(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA21(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA22(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA23(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA24(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA25(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA26(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA27(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA28(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA29(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA30(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA31(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA32(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA33(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA34(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA35(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA36(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA37(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA38(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA39(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA40(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA41(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA42(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA43(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA44(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA45(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA46(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA47(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA48(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA49(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA50(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `ROS()` | `0` | Initial population or concentration for this exact pattern. | +| `Ku(dna,cs,cys~red)` | `450` | Initial population or concentration for this exact pattern. | +| `Ku(dna,cs,cys~ox)` | `50` | Initial population or concentration for this exact pattern. | +| `DNAPKcs(ku,liIV,psite~u)` | `250` | Initial population or concentration for this exact pattern. | +| `LiIII(PARP)` | `300` | Initial population or concentration for this exact pattern. | +| `LiIV(cs)` | `300` | Initial population or concentration for this exact pattern. | +| `PARP(dna,liIII)` | `500` | Initial population or concentration for this exact pattern. | +| `I()` | `1` | Initial population or concentration for this exact pattern. | +| `Sen(int~1,State~normal)` | `1` | Initial population or concentration for this exact pattern. | + +## 6. Complete reaction-rule inventory + +The source contains **2339** reaction rules. The inventory below preserves one row per source rule, grouped only for readability. + +### Rules 1-250 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | D, Sink | `kDelete() (DeleteMolecules)` | stoichiometric pattern rewrite | `D() + Sink() -> D()` | Removes the matched Sink pattern after rewriting the listed products at `kDelete() (DeleteMolecules)`; used as an explicit cleanup/sink operation. | +| 2 | `Unlabeled` | one-way | P, p53_mRNA | `kp53mRNAsyn` | stoichiometric pattern rewrite | `P() -> p53_mRNA() + P()` | Produces p53_mRNA while retaining or consuming P at `kp53mRNAsyn`. | +| 3 | `Unlabeled` | one-way | Sink, p53_mRNA | `kp53mRNAdeg` | sink/degradation/removal | `p53_mRNA() -> Sink()` | Degrades or diverts p53_mRNA into the model sink at `kp53mRNAdeg`, reducing that active species pool. | +| 4 | `Unlabeled` | one-way | p53, p53_mRNA | `kp53syn` | internal-state conversion/modification | `p53_mRNA() -> p53_mRNA() + p53(Site1~u)` | Produces p53 while retaining or consuming p53_mRNA at `kp53syn`. | +| 5 | `Unlabeled` | one-way | Sink, p53 | `kp53deg` | sink/degradation/removal | `p53(Site1~u) -> Sink()` | Degrades or diverts p53 into the model sink at `kp53deg`, reducing that active species pool. | +| 6 | `Unlabeled` | one-way | Sink, p53 | `kp53deg` | sink/degradation/removal | `p53(Site1~p) -> Sink()` | Degrades or diverts p53 into the model sink at `kp53deg`, reducing that active species pool. | +| 7 | `Unlabeled` | one-way | MDM2, p53 | `kp53degMDM2dep (DeleteMolecules)` | state and binding-pattern rewrite | `p53(Site1!1~u).MDM2(Site1!1~u) -> MDM2(Site1~u)` | Removes the matched p53 pattern after rewriting the listed products at `kp53degMDM2dep (DeleteMolecules)`; used as an explicit cleanup/sink operation. | +| 8 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~1,h2ax!?) -> p53(Site1~p) + ATM(state~1,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 9 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~2,h2ax!?) -> p53(Site1~p) + ATM(state~2,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 10 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~3,h2ax!?) -> p53(Site1~p) + ATM(state~3,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 11 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~4,h2ax!?) -> p53(Site1~p) + ATM(state~4,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 12 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~5,h2ax!?) -> p53(Site1~p) + ATM(state~5,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 13 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~6,h2ax!?) -> p53(Site1~p) + ATM(state~6,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 14 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~7,h2ax!?) -> p53(Site1~p) + ATM(state~7,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 15 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~8,h2ax!?) -> p53(Site1~p) + ATM(state~8,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 16 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~9,h2ax!?) -> p53(Site1~p) + ATM(state~9,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 17 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~10,h2ax!?) -> p53(Site1~p) + ATM(state~10,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 18 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~11,h2ax!?) -> p53(Site1~p) + ATM(state~11,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 19 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~12,h2ax!?) -> p53(Site1~p) + ATM(state~12,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 20 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~13,h2ax!?) -> p53(Site1~p) + ATM(state~13,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 21 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~14,h2ax!?) -> p53(Site1~p) + ATM(state~14,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 22 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~15,h2ax!?) -> p53(Site1~p) + ATM(state~15,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 23 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~16,h2ax!?) -> p53(Site1~p) + ATM(state~16,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 24 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~17,h2ax!?) -> p53(Site1~p) + ATM(state~17,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 25 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~18,h2ax!?) -> p53(Site1~p) + ATM(state~18,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 26 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~19,h2ax!?) -> p53(Site1~p) + ATM(state~19,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 27 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~20,h2ax!?) -> p53(Site1~p) + ATM(state~20,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 28 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~21,h2ax!?) -> p53(Site1~p) + ATM(state~21,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 29 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~22,h2ax!?) -> p53(Site1~p) + ATM(state~22,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 30 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~23,h2ax!?) -> p53(Site1~p) + ATM(state~23,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 31 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~24,h2ax!?) -> p53(Site1~p) + ATM(state~24,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 32 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~25,h2ax!?) -> p53(Site1~p) + ATM(state~25,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 33 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~26,h2ax!?) -> p53(Site1~p) + ATM(state~26,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 34 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~27,h2ax!?) -> p53(Site1~p) + ATM(state~27,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 35 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~28,h2ax!?) -> p53(Site1~p) + ATM(state~28,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 36 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~29,h2ax!?) -> p53(Site1~p) + ATM(state~29,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 37 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~30,h2ax!?) -> p53(Site1~p) + ATM(state~30,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 38 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~31,h2ax!?) -> p53(Site1~p) + ATM(state~31,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 39 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~32,h2ax!?) -> p53(Site1~p) + ATM(state~32,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 40 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~33,h2ax!?) -> p53(Site1~p) + ATM(state~33,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 41 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~34,h2ax!?) -> p53(Site1~p) + ATM(state~34,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 42 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~35,h2ax!?) -> p53(Site1~p) + ATM(state~35,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 43 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~36,h2ax!?) -> p53(Site1~p) + ATM(state~36,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 44 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~37,h2ax!?) -> p53(Site1~p) + ATM(state~37,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 45 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~38,h2ax!?) -> p53(Site1~p) + ATM(state~38,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 46 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~39,h2ax!?) -> p53(Site1~p) + ATM(state~39,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 47 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~40,h2ax!?) -> p53(Site1~p) + ATM(state~40,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 48 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~41,h2ax!?) -> p53(Site1~p) + ATM(state~41,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 49 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~42,h2ax!?) -> p53(Site1~p) + ATM(state~42,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 50 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~43,h2ax!?) -> p53(Site1~p) + ATM(state~43,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 51 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~44,h2ax!?) -> p53(Site1~p) + ATM(state~44,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 52 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~45,h2ax!?) -> p53(Site1~p) + ATM(state~45,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 53 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~46,h2ax!?) -> p53(Site1~p) + ATM(state~46,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 54 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~47,h2ax!?) -> p53(Site1~p) + ATM(state~47,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 55 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~48,h2ax!?) -> p53(Site1~p) + ATM(state~48,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 56 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~49,h2ax!?) -> p53(Site1~p) + ATM(state~49,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 57 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~50,h2ax!?) -> p53(Site1~p) + ATM(state~50,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 58 | `Unlabeled` | one-way | p53 | `kp53dphos` | internal-state conversion/modification | `p53(Site1~p) -> p53(Site1~u)` | Changes internal modification/state marks on p53: p53.Site1 p→u at `kp53dphos`. | +| 59 | `Unlabeled` | one-way | MDM2_mRNA, p53 | `kMDM2mRNAsyn` | internal-state conversion/modification | `p53(Site1~u) -> MDM2_mRNA() + p53(Site1~u)` | Produces MDM2_mRNA while retaining or consuming p53 at `kMDM2mRNAsyn`. | +| 60 | `Unlabeled` | one-way | MDM2_mRNA, p53 | `kMDM2mRNAsyn` | internal-state conversion/modification | `p53(Site1~p) -> MDM2_mRNA() + p53(Site1~p)` | Produces MDM2_mRNA while retaining or consuming p53 at `kMDM2mRNAsyn`. | +| 61 | `Unlabeled` | one-way | MDM2_mRNA, Sink | `kMDM2mRNAdeg` | sink/degradation/removal | `MDM2_mRNA() -> Sink()` | Degrades or diverts MDM2_mRNA into the model sink at `kMDM2mRNAdeg`, reducing that active species pool. | +| 62 | `Unlabeled` | one-way | MDM2, MDM2_mRNA | `kMDM2syn` | internal-state conversion/modification | `MDM2_mRNA() -> MDM2_mRNA() + MDM2(Site1~u)` | Produces MDM2 while retaining or consuming MDM2_mRNA at `kMDM2syn`. | +| 63 | `Unlabeled` | one-way | MDM2, Sink | `kMDM2deg` | sink/degradation/removal | `MDM2(Site1~u) -> Sink()` | Degrades or diverts MDM2 into the model sink at `kMDM2deg`, reducing that active species pool. | +| 64 | `Unlabeled` | one-way | MDM2, Sink | `kMDM2pdeg` | sink/degradation/removal | `MDM2(Site1~p) -> Sink()` | Degrades or diverts MDM2 into the model sink at `kMDM2pdeg`, reducing that active species pool. | +| 65 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~1,h2ax!?) -> MDM2(Site1~p) + ATM(state~1,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 66 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~2,h2ax!?) -> MDM2(Site1~p) + ATM(state~2,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 67 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~3,h2ax!?) -> MDM2(Site1~p) + ATM(state~3,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 68 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~4,h2ax!?) -> MDM2(Site1~p) + ATM(state~4,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 69 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~5,h2ax!?) -> MDM2(Site1~p) + ATM(state~5,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 70 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~6,h2ax!?) -> MDM2(Site1~p) + ATM(state~6,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 71 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~7,h2ax!?) -> MDM2(Site1~p) + ATM(state~7,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 72 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~8,h2ax!?) -> MDM2(Site1~p) + ATM(state~8,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 73 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~9,h2ax!?) -> MDM2(Site1~p) + ATM(state~9,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 74 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~10,h2ax!?) -> MDM2(Site1~p) + ATM(state~10,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 75 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~11,h2ax!?) -> MDM2(Site1~p) + ATM(state~11,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 76 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~12,h2ax!?) -> MDM2(Site1~p) + ATM(state~12,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 77 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~13,h2ax!?) -> MDM2(Site1~p) + ATM(state~13,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 78 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~14,h2ax!?) -> MDM2(Site1~p) + ATM(state~14,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 79 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~15,h2ax!?) -> MDM2(Site1~p) + ATM(state~15,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 80 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~16,h2ax!?) -> MDM2(Site1~p) + ATM(state~16,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 81 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~17,h2ax!?) -> MDM2(Site1~p) + ATM(state~17,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 82 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~18,h2ax!?) -> MDM2(Site1~p) + ATM(state~18,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 83 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~19,h2ax!?) -> MDM2(Site1~p) + ATM(state~19,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 84 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~20,h2ax!?) -> MDM2(Site1~p) + ATM(state~20,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 85 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~21,h2ax!?) -> MDM2(Site1~p) + ATM(state~21,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 86 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~22,h2ax!?) -> MDM2(Site1~p) + ATM(state~22,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 87 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~23,h2ax!?) -> MDM2(Site1~p) + ATM(state~23,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 88 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~24,h2ax!?) -> MDM2(Site1~p) + ATM(state~24,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 89 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~25,h2ax!?) -> MDM2(Site1~p) + ATM(state~25,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 90 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~26,h2ax!?) -> MDM2(Site1~p) + ATM(state~26,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 91 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~27,h2ax!?) -> MDM2(Site1~p) + ATM(state~27,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 92 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~28,h2ax!?) -> MDM2(Site1~p) + ATM(state~28,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 93 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~29,h2ax!?) -> MDM2(Site1~p) + ATM(state~29,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 94 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~30,h2ax!?) -> MDM2(Site1~p) + ATM(state~30,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 95 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~31,h2ax!?) -> MDM2(Site1~p) + ATM(state~31,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 96 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~32,h2ax!?) -> MDM2(Site1~p) + ATM(state~32,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 97 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~33,h2ax!?) -> MDM2(Site1~p) + ATM(state~33,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 98 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~34,h2ax!?) -> MDM2(Site1~p) + ATM(state~34,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 99 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~35,h2ax!?) -> MDM2(Site1~p) + ATM(state~35,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 100 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~36,h2ax!?) -> MDM2(Site1~p) + ATM(state~36,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 101 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~37,h2ax!?) -> MDM2(Site1~p) + ATM(state~37,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 102 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~38,h2ax!?) -> MDM2(Site1~p) + ATM(state~38,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 103 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~39,h2ax!?) -> MDM2(Site1~p) + ATM(state~39,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 104 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~40,h2ax!?) -> MDM2(Site1~p) + ATM(state~40,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 105 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~41,h2ax!?) -> MDM2(Site1~p) + ATM(state~41,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 106 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~42,h2ax!?) -> MDM2(Site1~p) + ATM(state~42,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 107 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~43,h2ax!?) -> MDM2(Site1~p) + ATM(state~43,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 108 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~44,h2ax!?) -> MDM2(Site1~p) + ATM(state~44,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 109 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~45,h2ax!?) -> MDM2(Site1~p) + ATM(state~45,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 110 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~46,h2ax!?) -> MDM2(Site1~p) + ATM(state~46,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 111 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~47,h2ax!?) -> MDM2(Site1~p) + ATM(state~47,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 112 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~48,h2ax!?) -> MDM2(Site1~p) + ATM(state~48,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 113 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~49,h2ax!?) -> MDM2(Site1~p) + ATM(state~49,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 114 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~50,h2ax!?) -> MDM2(Site1~p) + ATM(state~50,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 115 | `Unlabeled` | one-way | MDM2 | `kMDM2dphos` | internal-state conversion/modification | `MDM2(Site1~p) -> MDM2(Site1~u)` | Changes internal modification/state marks on MDM2: MDM2.Site1 p→u at `kMDM2dphos`. | +| 116 | `Unlabeled` | one-way | MDM2, p53 | `kp53MDM2bind` | state and binding-pattern rewrite | `p53(Site1~u) + MDM2(Site1~u) -> p53(Site1!1~u).MDM2(Site1!1~u)` | Forms a complex/contact among MDM2, p53 through MDM2.Site1, p53.Site1 at `kp53MDM2bind`. | +| 117 | `Unlabeled` | one-way | MDM2, p53 | `kp53MDM2dis` | state and binding-pattern rewrite | `p53(Site1!1~u).MDM2(Site1!1~u) -> p53(Site1~u) + MDM2(Site1~u)` | Releases a complex/contact among MDM2, p53 by freeing MDM2.Site1, p53.Site1 at `kp53MDM2dis`. | +| 118 | `Unlabeled` | one-way | p21_mRNA, p53 | `kp21mRNAsyn` | internal-state conversion/modification | `p53(Site1~u) -> p21_mRNA() + p53(Site1~u)` | Produces p21_mRNA while retaining or consuming p53 at `kp21mRNAsyn`. | +| 119 | `Unlabeled` | one-way | p21_mRNA, p53 | `kp21mRNAsynp` | internal-state conversion/modification | `p53(Site1~p) -> p21_mRNA() + p53(Site1~p)` | Produces p21_mRNA while retaining or consuming p53 at `kp21mRNAsynp`. | +| 120 | `Unlabeled` | one-way | Sink, p21_mRNA | `kp21mRNAdeg` | sink/degradation/removal | `p21_mRNA() -> Sink()` | Degrades or diverts p21_mRNA into the model sink at `kp21mRNAdeg`, reducing that active species pool. | +| 121 | `Unlabeled` | one-way | p21, p21_mRNA | `kp21synstep1` | internal-state conversion/modification | `p21_mRNA() -> p21(step~1) + p21_mRNA()` | Produces p21 while retaining or consuming p21_mRNA at `kp21synstep1`. | +| 122 | `Unlabeled` | one-way | p21 | `kp21synstep2` | internal-state conversion/modification | `p21(step~1) -> p21(step~2)` | Changes internal modification/state marks on p21: p21.step 1→2 at `kp21synstep2`. | +| 123 | `Unlabeled` | one-way | p21 | `kp21synstep3` | internal-state conversion/modification | `p21(step~2) -> p21(step~3)` | Changes internal modification/state marks on p21: p21.step 2→3 at `kp21synstep3`. | +| 124 | `Unlabeled` | one-way | Sink, p21 | `kp21deg` | sink/degradation/removal | `p21(step~3) -> Sink()` | Degrades or diverts p21 into the model sink at `kp21deg`, reducing that active species pool. | +| 125 | `Unlabeled` | one-way | GADD45, p21 | `kGADD45act` | internal-state conversion/modification | `p21(step~3) -> p21(step~3) + GADD45()` | Produces GADD45 while retaining or consuming p21 at `kGADD45act`. | +| 126 | `Unlabeled` | one-way | GADD45, Sink | `kGADD45deg` | sink/degradation/removal | `GADD45() -> Sink()` | Degrades or diverts GADD45 into the model sink at `kGADD45deg`, reducing that active species pool. | +| 127 | `Unlabeled` | one-way | GADD45, p38 | `kp38phos` | internal-state conversion/modification | `p38(Site1~u) + GADD45() -> p38(Site1~p) + GADD45()` | Changes internal modification/state marks on GADD45, p38: p38.Site1 u→p at `kp38phos`. | +| 128 | `Unlabeled` | one-way | p38 | `kp38dphos` | internal-state conversion/modification | `p38(Site1~p) -> p38(Site1~u)` | Changes internal modification/state marks on p38: p38.Site1 p→u at `kp38dphos`. | +| 129 | `Unlabeled` | one-way | ROS, p38 | `kROSgen` | internal-state conversion/modification | `p38(Site1~p) -> ROS() + p38(Site1~p)` | Produces ROS while retaining or consuming p38 at `kROSgen`. | +| 130 | `Unlabeled` | one-way | DNA1, Ku | `kku1()` | state and binding-pattern rewrite | `DNA1(site~sdsb) + Ku(dna,cs) -> DNA1(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA1, Ku through DNA1.site, Ku.dna at `kku1()`. | +| 131 | `Unlabeled` | one-way | DNA2, Ku | `kku1()` | state and binding-pattern rewrite | `DNA2(site~sdsb) + Ku(dna,cs) -> DNA2(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA2, Ku through DNA2.site, Ku.dna at `kku1()`. | +| 132 | `Unlabeled` | one-way | DNA3, Ku | `kku1()` | state and binding-pattern rewrite | `DNA3(site~sdsb) + Ku(dna,cs) -> DNA3(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA3, Ku through DNA3.site, Ku.dna at `kku1()`. | +| 133 | `Unlabeled` | one-way | DNA4, Ku | `kku1()` | state and binding-pattern rewrite | `DNA4(site~sdsb) + Ku(dna,cs) -> DNA4(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA4, Ku through DNA4.site, Ku.dna at `kku1()`. | +| 134 | `Unlabeled` | one-way | DNA5, Ku | `kku1()` | state and binding-pattern rewrite | `DNA5(site~sdsb) + Ku(dna,cs) -> DNA5(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA5, Ku through DNA5.site, Ku.dna at `kku1()`. | +| 135 | `Unlabeled` | one-way | DNA6, Ku | `kku1()` | state and binding-pattern rewrite | `DNA6(site~sdsb) + Ku(dna,cs) -> DNA6(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA6, Ku through DNA6.site, Ku.dna at `kku1()`. | +| 136 | `Unlabeled` | one-way | DNA7, Ku | `kku1()` | state and binding-pattern rewrite | `DNA7(site~sdsb) + Ku(dna,cs) -> DNA7(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA7, Ku through DNA7.site, Ku.dna at `kku1()`. | +| 137 | `Unlabeled` | one-way | DNA8, Ku | `kku1()` | state and binding-pattern rewrite | `DNA8(site~sdsb) + Ku(dna,cs) -> DNA8(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA8, Ku through DNA8.site, Ku.dna at `kku1()`. | +| 138 | `Unlabeled` | one-way | DNA9, Ku | `kku1()` | state and binding-pattern rewrite | `DNA9(site~sdsb) + Ku(dna,cs) -> DNA9(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA9, Ku through DNA9.site, Ku.dna at `kku1()`. | +| 139 | `Unlabeled` | one-way | DNA10, Ku | `kku1()` | state and binding-pattern rewrite | `DNA10(site~sdsb) + Ku(dna,cs) -> DNA10(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA10, Ku through DNA10.site, Ku.dna at `kku1()`. | +| 140 | `Unlabeled` | one-way | DNA11, Ku | `kku1()` | state and binding-pattern rewrite | `DNA11(site~sdsb) + Ku(dna,cs) -> DNA11(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA11, Ku through DNA11.site, Ku.dna at `kku1()`. | +| 141 | `Unlabeled` | one-way | DNA12, Ku | `kku1()` | state and binding-pattern rewrite | `DNA12(site~sdsb) + Ku(dna,cs) -> DNA12(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA12, Ku through DNA12.site, Ku.dna at `kku1()`. | +| 142 | `Unlabeled` | one-way | DNA13, Ku | `kku1()` | state and binding-pattern rewrite | `DNA13(site~sdsb) + Ku(dna,cs) -> DNA13(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA13, Ku through DNA13.site, Ku.dna at `kku1()`. | +| 143 | `Unlabeled` | one-way | DNA14, Ku | `kku1()` | state and binding-pattern rewrite | `DNA14(site~sdsb) + Ku(dna,cs) -> DNA14(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA14, Ku through DNA14.site, Ku.dna at `kku1()`. | +| 144 | `Unlabeled` | one-way | DNA15, Ku | `kku1()` | state and binding-pattern rewrite | `DNA15(site~sdsb) + Ku(dna,cs) -> DNA15(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA15, Ku through DNA15.site, Ku.dna at `kku1()`. | +| 145 | `Unlabeled` | one-way | DNA16, Ku | `kku1()` | state and binding-pattern rewrite | `DNA16(site~sdsb) + Ku(dna,cs) -> DNA16(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA16, Ku through DNA16.site, Ku.dna at `kku1()`. | +| 146 | `Unlabeled` | one-way | DNA17, Ku | `kku1()` | state and binding-pattern rewrite | `DNA17(site~sdsb) + Ku(dna,cs) -> DNA17(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA17, Ku through DNA17.site, Ku.dna at `kku1()`. | +| 147 | `Unlabeled` | one-way | DNA18, Ku | `kku1()` | state and binding-pattern rewrite | `DNA18(site~sdsb) + Ku(dna,cs) -> DNA18(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA18, Ku through DNA18.site, Ku.dna at `kku1()`. | +| 148 | `Unlabeled` | one-way | DNA19, Ku | `kku1()` | state and binding-pattern rewrite | `DNA19(site~sdsb) + Ku(dna,cs) -> DNA19(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA19, Ku through DNA19.site, Ku.dna at `kku1()`. | +| 149 | `Unlabeled` | one-way | DNA20, Ku | `kku1()` | state and binding-pattern rewrite | `DNA20(site~sdsb) + Ku(dna,cs) -> DNA20(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA20, Ku through DNA20.site, Ku.dna at `kku1()`. | +| 150 | `Unlabeled` | one-way | DNA21, Ku | `kku1()` | state and binding-pattern rewrite | `DNA21(site~sdsb) + Ku(dna,cs) -> DNA21(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA21, Ku through DNA21.site, Ku.dna at `kku1()`. | +| 151 | `Unlabeled` | one-way | DNA22, Ku | `kku1()` | state and binding-pattern rewrite | `DNA22(site~sdsb) + Ku(dna,cs) -> DNA22(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA22, Ku through DNA22.site, Ku.dna at `kku1()`. | +| 152 | `Unlabeled` | one-way | DNA23, Ku | `kku1()` | state and binding-pattern rewrite | `DNA23(site~sdsb) + Ku(dna,cs) -> DNA23(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA23, Ku through DNA23.site, Ku.dna at `kku1()`. | +| 153 | `Unlabeled` | one-way | DNA24, Ku | `kku1()` | state and binding-pattern rewrite | `DNA24(site~sdsb) + Ku(dna,cs) -> DNA24(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA24, Ku through DNA24.site, Ku.dna at `kku1()`. | +| 154 | `Unlabeled` | one-way | DNA25, Ku | `kku1()` | state and binding-pattern rewrite | `DNA25(site~sdsb) + Ku(dna,cs) -> DNA25(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA25, Ku through DNA25.site, Ku.dna at `kku1()`. | +| 155 | `Unlabeled` | one-way | DNA26, Ku | `kku1()` | state and binding-pattern rewrite | `DNA26(site~sdsb) + Ku(dna,cs) -> DNA26(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA26, Ku through DNA26.site, Ku.dna at `kku1()`. | +| 156 | `Unlabeled` | one-way | DNA27, Ku | `kku1()` | state and binding-pattern rewrite | `DNA27(site~sdsb) + Ku(dna,cs) -> DNA27(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA27, Ku through DNA27.site, Ku.dna at `kku1()`. | +| 157 | `Unlabeled` | one-way | DNA28, Ku | `kku1()` | state and binding-pattern rewrite | `DNA28(site~sdsb) + Ku(dna,cs) -> DNA28(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA28, Ku through DNA28.site, Ku.dna at `kku1()`. | +| 158 | `Unlabeled` | one-way | DNA29, Ku | `kku1()` | state and binding-pattern rewrite | `DNA29(site~sdsb) + Ku(dna,cs) -> DNA29(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA29, Ku through DNA29.site, Ku.dna at `kku1()`. | +| 159 | `Unlabeled` | one-way | DNA30, Ku | `kku1()` | state and binding-pattern rewrite | `DNA30(site~sdsb) + Ku(dna,cs) -> DNA30(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA30, Ku through DNA30.site, Ku.dna at `kku1()`. | +| 160 | `Unlabeled` | one-way | DNA31, Ku | `kku1()` | state and binding-pattern rewrite | `DNA31(site~sdsb) + Ku(dna,cs) -> DNA31(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA31, Ku through DNA31.site, Ku.dna at `kku1()`. | +| 161 | `Unlabeled` | one-way | DNA32, Ku | `kku1()` | state and binding-pattern rewrite | `DNA32(site~sdsb) + Ku(dna,cs) -> DNA32(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA32, Ku through DNA32.site, Ku.dna at `kku1()`. | +| 162 | `Unlabeled` | one-way | DNA33, Ku | `kku1()` | state and binding-pattern rewrite | `DNA33(site~sdsb) + Ku(dna,cs) -> DNA33(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA33, Ku through DNA33.site, Ku.dna at `kku1()`. | +| 163 | `Unlabeled` | one-way | DNA34, Ku | `kku1()` | state and binding-pattern rewrite | `DNA34(site~sdsb) + Ku(dna,cs) -> DNA34(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA34, Ku through DNA34.site, Ku.dna at `kku1()`. | +| 164 | `Unlabeled` | one-way | DNA35, Ku | `kku1()` | state and binding-pattern rewrite | `DNA35(site~sdsb) + Ku(dna,cs) -> DNA35(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA35, Ku through DNA35.site, Ku.dna at `kku1()`. | +| 165 | `Unlabeled` | one-way | DNA36, Ku | `kku1()` | state and binding-pattern rewrite | `DNA36(site~sdsb) + Ku(dna,cs) -> DNA36(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA36, Ku through DNA36.site, Ku.dna at `kku1()`. | +| 166 | `Unlabeled` | one-way | DNA37, Ku | `kku1()` | state and binding-pattern rewrite | `DNA37(site~sdsb) + Ku(dna,cs) -> DNA37(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA37, Ku through DNA37.site, Ku.dna at `kku1()`. | +| 167 | `Unlabeled` | one-way | DNA38, Ku | `kku1()` | state and binding-pattern rewrite | `DNA38(site~sdsb) + Ku(dna,cs) -> DNA38(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA38, Ku through DNA38.site, Ku.dna at `kku1()`. | +| 168 | `Unlabeled` | one-way | DNA39, Ku | `kku1()` | state and binding-pattern rewrite | `DNA39(site~sdsb) + Ku(dna,cs) -> DNA39(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA39, Ku through DNA39.site, Ku.dna at `kku1()`. | +| 169 | `Unlabeled` | one-way | DNA40, Ku | `kku1()` | state and binding-pattern rewrite | `DNA40(site~sdsb) + Ku(dna,cs) -> DNA40(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA40, Ku through DNA40.site, Ku.dna at `kku1()`. | +| 170 | `Unlabeled` | one-way | DNA41, Ku | `kku1()` | state and binding-pattern rewrite | `DNA41(site~sdsb) + Ku(dna,cs) -> DNA41(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA41, Ku through DNA41.site, Ku.dna at `kku1()`. | +| 171 | `Unlabeled` | one-way | DNA42, Ku | `kku1()` | state and binding-pattern rewrite | `DNA42(site~sdsb) + Ku(dna,cs) -> DNA42(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA42, Ku through DNA42.site, Ku.dna at `kku1()`. | +| 172 | `Unlabeled` | one-way | DNA43, Ku | `kku1()` | state and binding-pattern rewrite | `DNA43(site~sdsb) + Ku(dna,cs) -> DNA43(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA43, Ku through DNA43.site, Ku.dna at `kku1()`. | +| 173 | `Unlabeled` | one-way | DNA44, Ku | `kku1()` | state and binding-pattern rewrite | `DNA44(site~sdsb) + Ku(dna,cs) -> DNA44(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA44, Ku through DNA44.site, Ku.dna at `kku1()`. | +| 174 | `Unlabeled` | one-way | DNA45, Ku | `kku1()` | state and binding-pattern rewrite | `DNA45(site~sdsb) + Ku(dna,cs) -> DNA45(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA45, Ku through DNA45.site, Ku.dna at `kku1()`. | +| 175 | `Unlabeled` | one-way | DNA46, Ku | `kku1()` | state and binding-pattern rewrite | `DNA46(site~sdsb) + Ku(dna,cs) -> DNA46(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA46, Ku through DNA46.site, Ku.dna at `kku1()`. | +| 176 | `Unlabeled` | one-way | DNA47, Ku | `kku1()` | state and binding-pattern rewrite | `DNA47(site~sdsb) + Ku(dna,cs) -> DNA47(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA47, Ku through DNA47.site, Ku.dna at `kku1()`. | +| 177 | `Unlabeled` | one-way | DNA48, Ku | `kku1()` | state and binding-pattern rewrite | `DNA48(site~sdsb) + Ku(dna,cs) -> DNA48(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA48, Ku through DNA48.site, Ku.dna at `kku1()`. | +| 178 | `Unlabeled` | one-way | DNA49, Ku | `kku1()` | state and binding-pattern rewrite | `DNA49(site~sdsb) + Ku(dna,cs) -> DNA49(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA49, Ku through DNA49.site, Ku.dna at `kku1()`. | +| 179 | `Unlabeled` | one-way | DNA50, Ku | `kku1()` | state and binding-pattern rewrite | `DNA50(site~sdsb) + Ku(dna,cs) -> DNA50(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA50, Ku through DNA50.site, Ku.dna at `kku1()`. | +| 180 | `Unlabeled` | one-way | DNA1, Ku | `kku2()` | state and binding-pattern rewrite | `DNA1(site~cdsb) + Ku(dna,cs) -> DNA1(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA1, Ku through DNA1.site, Ku.dna at `kku2()`. | +| 181 | `Unlabeled` | one-way | DNA2, Ku | `kku2()` | state and binding-pattern rewrite | `DNA2(site~cdsb) + Ku(dna,cs) -> DNA2(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA2, Ku through DNA2.site, Ku.dna at `kku2()`. | +| 182 | `Unlabeled` | one-way | DNA3, Ku | `kku2()` | state and binding-pattern rewrite | `DNA3(site~cdsb) + Ku(dna,cs) -> DNA3(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA3, Ku through DNA3.site, Ku.dna at `kku2()`. | +| 183 | `Unlabeled` | one-way | DNA4, Ku | `kku2()` | state and binding-pattern rewrite | `DNA4(site~cdsb) + Ku(dna,cs) -> DNA4(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA4, Ku through DNA4.site, Ku.dna at `kku2()`. | +| 184 | `Unlabeled` | one-way | DNA5, Ku | `kku2()` | state and binding-pattern rewrite | `DNA5(site~cdsb) + Ku(dna,cs) -> DNA5(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA5, Ku through DNA5.site, Ku.dna at `kku2()`. | +| 185 | `Unlabeled` | one-way | DNA6, Ku | `kku2()` | state and binding-pattern rewrite | `DNA6(site~cdsb) + Ku(dna,cs) -> DNA6(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA6, Ku through DNA6.site, Ku.dna at `kku2()`. | +| 186 | `Unlabeled` | one-way | DNA7, Ku | `kku2()` | state and binding-pattern rewrite | `DNA7(site~cdsb) + Ku(dna,cs) -> DNA7(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA7, Ku through DNA7.site, Ku.dna at `kku2()`. | +| 187 | `Unlabeled` | one-way | DNA8, Ku | `kku2()` | state and binding-pattern rewrite | `DNA8(site~cdsb) + Ku(dna,cs) -> DNA8(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA8, Ku through DNA8.site, Ku.dna at `kku2()`. | +| 188 | `Unlabeled` | one-way | DNA9, Ku | `kku2()` | state and binding-pattern rewrite | `DNA9(site~cdsb) + Ku(dna,cs) -> DNA9(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA9, Ku through DNA9.site, Ku.dna at `kku2()`. | +| 189 | `Unlabeled` | one-way | DNA10, Ku | `kku2()` | state and binding-pattern rewrite | `DNA10(site~cdsb) + Ku(dna,cs) -> DNA10(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA10, Ku through DNA10.site, Ku.dna at `kku2()`. | +| 190 | `Unlabeled` | one-way | DNA11, Ku | `kku2()` | state and binding-pattern rewrite | `DNA11(site~cdsb) + Ku(dna,cs) -> DNA11(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA11, Ku through DNA11.site, Ku.dna at `kku2()`. | +| 191 | `Unlabeled` | one-way | DNA12, Ku | `kku2()` | state and binding-pattern rewrite | `DNA12(site~cdsb) + Ku(dna,cs) -> DNA12(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA12, Ku through DNA12.site, Ku.dna at `kku2()`. | +| 192 | `Unlabeled` | one-way | DNA13, Ku | `kku2()` | state and binding-pattern rewrite | `DNA13(site~cdsb) + Ku(dna,cs) -> DNA13(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA13, Ku through DNA13.site, Ku.dna at `kku2()`. | +| 193 | `Unlabeled` | one-way | DNA14, Ku | `kku2()` | state and binding-pattern rewrite | `DNA14(site~cdsb) + Ku(dna,cs) -> DNA14(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA14, Ku through DNA14.site, Ku.dna at `kku2()`. | +| 194 | `Unlabeled` | one-way | DNA15, Ku | `kku2()` | state and binding-pattern rewrite | `DNA15(site~cdsb) + Ku(dna,cs) -> DNA15(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA15, Ku through DNA15.site, Ku.dna at `kku2()`. | +| 195 | `Unlabeled` | one-way | DNA16, Ku | `kku2()` | state and binding-pattern rewrite | `DNA16(site~cdsb) + Ku(dna,cs) -> DNA16(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA16, Ku through DNA16.site, Ku.dna at `kku2()`. | +| 196 | `Unlabeled` | one-way | DNA17, Ku | `kku2()` | state and binding-pattern rewrite | `DNA17(site~cdsb) + Ku(dna,cs) -> DNA17(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA17, Ku through DNA17.site, Ku.dna at `kku2()`. | +| 197 | `Unlabeled` | one-way | DNA18, Ku | `kku2()` | state and binding-pattern rewrite | `DNA18(site~cdsb) + Ku(dna,cs) -> DNA18(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA18, Ku through DNA18.site, Ku.dna at `kku2()`. | +| 198 | `Unlabeled` | one-way | DNA19, Ku | `kku2()` | state and binding-pattern rewrite | `DNA19(site~cdsb) + Ku(dna,cs) -> DNA19(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA19, Ku through DNA19.site, Ku.dna at `kku2()`. | +| 199 | `Unlabeled` | one-way | DNA20, Ku | `kku2()` | state and binding-pattern rewrite | `DNA20(site~cdsb) + Ku(dna,cs) -> DNA20(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA20, Ku through DNA20.site, Ku.dna at `kku2()`. | +| 200 | `Unlabeled` | one-way | DNA21, Ku | `kku2()` | state and binding-pattern rewrite | `DNA21(site~cdsb) + Ku(dna,cs) -> DNA21(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA21, Ku through DNA21.site, Ku.dna at `kku2()`. | +| 201 | `Unlabeled` | one-way | DNA22, Ku | `kku2()` | state and binding-pattern rewrite | `DNA22(site~cdsb) + Ku(dna,cs) -> DNA22(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA22, Ku through DNA22.site, Ku.dna at `kku2()`. | +| 202 | `Unlabeled` | one-way | DNA23, Ku | `kku2()` | state and binding-pattern rewrite | `DNA23(site~cdsb) + Ku(dna,cs) -> DNA23(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA23, Ku through DNA23.site, Ku.dna at `kku2()`. | +| 203 | `Unlabeled` | one-way | DNA24, Ku | `kku2()` | state and binding-pattern rewrite | `DNA24(site~cdsb) + Ku(dna,cs) -> DNA24(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA24, Ku through DNA24.site, Ku.dna at `kku2()`. | +| 204 | `Unlabeled` | one-way | DNA25, Ku | `kku2()` | state and binding-pattern rewrite | `DNA25(site~cdsb) + Ku(dna,cs) -> DNA25(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA25, Ku through DNA25.site, Ku.dna at `kku2()`. | +| 205 | `Unlabeled` | one-way | DNA26, Ku | `kku2()` | state and binding-pattern rewrite | `DNA26(site~cdsb) + Ku(dna,cs) -> DNA26(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA26, Ku through DNA26.site, Ku.dna at `kku2()`. | +| 206 | `Unlabeled` | one-way | DNA27, Ku | `kku2()` | state and binding-pattern rewrite | `DNA27(site~cdsb) + Ku(dna,cs) -> DNA27(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA27, Ku through DNA27.site, Ku.dna at `kku2()`. | +| 207 | `Unlabeled` | one-way | DNA28, Ku | `kku2()` | state and binding-pattern rewrite | `DNA28(site~cdsb) + Ku(dna,cs) -> DNA28(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA28, Ku through DNA28.site, Ku.dna at `kku2()`. | +| 208 | `Unlabeled` | one-way | DNA29, Ku | `kku2()` | state and binding-pattern rewrite | `DNA29(site~cdsb) + Ku(dna,cs) -> DNA29(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA29, Ku through DNA29.site, Ku.dna at `kku2()`. | +| 209 | `Unlabeled` | one-way | DNA30, Ku | `kku2()` | state and binding-pattern rewrite | `DNA30(site~cdsb) + Ku(dna,cs) -> DNA30(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA30, Ku through DNA30.site, Ku.dna at `kku2()`. | +| 210 | `Unlabeled` | one-way | DNA31, Ku | `kku2()` | state and binding-pattern rewrite | `DNA31(site~cdsb) + Ku(dna,cs) -> DNA31(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA31, Ku through DNA31.site, Ku.dna at `kku2()`. | +| 211 | `Unlabeled` | one-way | DNA32, Ku | `kku2()` | state and binding-pattern rewrite | `DNA32(site~cdsb) + Ku(dna,cs) -> DNA32(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA32, Ku through DNA32.site, Ku.dna at `kku2()`. | +| 212 | `Unlabeled` | one-way | DNA33, Ku | `kku2()` | state and binding-pattern rewrite | `DNA33(site~cdsb) + Ku(dna,cs) -> DNA33(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA33, Ku through DNA33.site, Ku.dna at `kku2()`. | +| 213 | `Unlabeled` | one-way | DNA34, Ku | `kku2()` | state and binding-pattern rewrite | `DNA34(site~cdsb) + Ku(dna,cs) -> DNA34(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA34, Ku through DNA34.site, Ku.dna at `kku2()`. | +| 214 | `Unlabeled` | one-way | DNA35, Ku | `kku2()` | state and binding-pattern rewrite | `DNA35(site~cdsb) + Ku(dna,cs) -> DNA35(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA35, Ku through DNA35.site, Ku.dna at `kku2()`. | +| 215 | `Unlabeled` | one-way | DNA36, Ku | `kku2()` | state and binding-pattern rewrite | `DNA36(site~cdsb) + Ku(dna,cs) -> DNA36(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA36, Ku through DNA36.site, Ku.dna at `kku2()`. | +| 216 | `Unlabeled` | one-way | DNA37, Ku | `kku2()` | state and binding-pattern rewrite | `DNA37(site~cdsb) + Ku(dna,cs) -> DNA37(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA37, Ku through DNA37.site, Ku.dna at `kku2()`. | +| 217 | `Unlabeled` | one-way | DNA38, Ku | `kku2()` | state and binding-pattern rewrite | `DNA38(site~cdsb) + Ku(dna,cs) -> DNA38(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA38, Ku through DNA38.site, Ku.dna at `kku2()`. | +| 218 | `Unlabeled` | one-way | DNA39, Ku | `kku2()` | state and binding-pattern rewrite | `DNA39(site~cdsb) + Ku(dna,cs) -> DNA39(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA39, Ku through DNA39.site, Ku.dna at `kku2()`. | +| 219 | `Unlabeled` | one-way | DNA40, Ku | `kku2()` | state and binding-pattern rewrite | `DNA40(site~cdsb) + Ku(dna,cs) -> DNA40(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA40, Ku through DNA40.site, Ku.dna at `kku2()`. | +| 220 | `Unlabeled` | one-way | DNA41, Ku | `kku2()` | state and binding-pattern rewrite | `DNA41(site~cdsb) + Ku(dna,cs) -> DNA41(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA41, Ku through DNA41.site, Ku.dna at `kku2()`. | +| 221 | `Unlabeled` | one-way | DNA42, Ku | `kku2()` | state and binding-pattern rewrite | `DNA42(site~cdsb) + Ku(dna,cs) -> DNA42(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA42, Ku through DNA42.site, Ku.dna at `kku2()`. | +| 222 | `Unlabeled` | one-way | DNA43, Ku | `kku2()` | state and binding-pattern rewrite | `DNA43(site~cdsb) + Ku(dna,cs) -> DNA43(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA43, Ku through DNA43.site, Ku.dna at `kku2()`. | +| 223 | `Unlabeled` | one-way | DNA44, Ku | `kku2()` | state and binding-pattern rewrite | `DNA44(site~cdsb) + Ku(dna,cs) -> DNA44(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA44, Ku through DNA44.site, Ku.dna at `kku2()`. | +| 224 | `Unlabeled` | one-way | DNA45, Ku | `kku2()` | state and binding-pattern rewrite | `DNA45(site~cdsb) + Ku(dna,cs) -> DNA45(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA45, Ku through DNA45.site, Ku.dna at `kku2()`. | +| 225 | `Unlabeled` | one-way | DNA46, Ku | `kku2()` | state and binding-pattern rewrite | `DNA46(site~cdsb) + Ku(dna,cs) -> DNA46(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA46, Ku through DNA46.site, Ku.dna at `kku2()`. | +| 226 | `Unlabeled` | one-way | DNA47, Ku | `kku2()` | state and binding-pattern rewrite | `DNA47(site~cdsb) + Ku(dna,cs) -> DNA47(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA47, Ku through DNA47.site, Ku.dna at `kku2()`. | +| 227 | `Unlabeled` | one-way | DNA48, Ku | `kku2()` | state and binding-pattern rewrite | `DNA48(site~cdsb) + Ku(dna,cs) -> DNA48(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA48, Ku through DNA48.site, Ku.dna at `kku2()`. | +| 228 | `Unlabeled` | one-way | DNA49, Ku | `kku2()` | state and binding-pattern rewrite | `DNA49(site~cdsb) + Ku(dna,cs) -> DNA49(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA49, Ku through DNA49.site, Ku.dna at `kku2()`. | +| 229 | `Unlabeled` | one-way | DNA50, Ku | `kku2()` | state and binding-pattern rewrite | `DNA50(site~cdsb) + Ku(dna,cs) -> DNA50(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA50, Ku through DNA50.site, Ku.dna at `kku2()`. | +| 230 | `Unlabeled` | one-way | DNA1, Ku | `kdku1` | state and binding-pattern rewrite | `DNA1(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA1(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA1, Ku by freeing DNA1.site, Ku.dna at `kdku1`. | +| 231 | `Unlabeled` | one-way | DNA2, Ku | `kdku1` | state and binding-pattern rewrite | `DNA2(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA2(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA2, Ku by freeing DNA2.site, Ku.dna at `kdku1`. | +| 232 | `Unlabeled` | one-way | DNA3, Ku | `kdku1` | state and binding-pattern rewrite | `DNA3(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA3(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA3, Ku by freeing DNA3.site, Ku.dna at `kdku1`. | +| 233 | `Unlabeled` | one-way | DNA4, Ku | `kdku1` | state and binding-pattern rewrite | `DNA4(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA4(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA4, Ku by freeing DNA4.site, Ku.dna at `kdku1`. | +| 234 | `Unlabeled` | one-way | DNA5, Ku | `kdku1` | state and binding-pattern rewrite | `DNA5(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA5(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA5, Ku by freeing DNA5.site, Ku.dna at `kdku1`. | +| 235 | `Unlabeled` | one-way | DNA6, Ku | `kdku1` | state and binding-pattern rewrite | `DNA6(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA6(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA6, Ku by freeing DNA6.site, Ku.dna at `kdku1`. | +| 236 | `Unlabeled` | one-way | DNA7, Ku | `kdku1` | state and binding-pattern rewrite | `DNA7(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA7(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA7, Ku by freeing DNA7.site, Ku.dna at `kdku1`. | +| 237 | `Unlabeled` | one-way | DNA8, Ku | `kdku1` | state and binding-pattern rewrite | `DNA8(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA8(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA8, Ku by freeing DNA8.site, Ku.dna at `kdku1`. | +| 238 | `Unlabeled` | one-way | DNA9, Ku | `kdku1` | state and binding-pattern rewrite | `DNA9(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA9(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA9, Ku by freeing DNA9.site, Ku.dna at `kdku1`. | +| 239 | `Unlabeled` | one-way | DNA10, Ku | `kdku1` | state and binding-pattern rewrite | `DNA10(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA10(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA10, Ku by freeing DNA10.site, Ku.dna at `kdku1`. | +| 240 | `Unlabeled` | one-way | DNA11, Ku | `kdku1` | state and binding-pattern rewrite | `DNA11(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA11(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA11, Ku by freeing DNA11.site, Ku.dna at `kdku1`. | +| 241 | `Unlabeled` | one-way | DNA12, Ku | `kdku1` | state and binding-pattern rewrite | `DNA12(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA12(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA12, Ku by freeing DNA12.site, Ku.dna at `kdku1`. | +| 242 | `Unlabeled` | one-way | DNA13, Ku | `kdku1` | state and binding-pattern rewrite | `DNA13(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA13(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA13, Ku by freeing DNA13.site, Ku.dna at `kdku1`. | +| 243 | `Unlabeled` | one-way | DNA14, Ku | `kdku1` | state and binding-pattern rewrite | `DNA14(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA14(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA14, Ku by freeing DNA14.site, Ku.dna at `kdku1`. | +| 244 | `Unlabeled` | one-way | DNA15, Ku | `kdku1` | state and binding-pattern rewrite | `DNA15(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA15(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA15, Ku by freeing DNA15.site, Ku.dna at `kdku1`. | +| 245 | `Unlabeled` | one-way | DNA16, Ku | `kdku1` | state and binding-pattern rewrite | `DNA16(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA16(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA16, Ku by freeing DNA16.site, Ku.dna at `kdku1`. | +| 246 | `Unlabeled` | one-way | DNA17, Ku | `kdku1` | state and binding-pattern rewrite | `DNA17(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA17(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA17, Ku by freeing DNA17.site, Ku.dna at `kdku1`. | +| 247 | `Unlabeled` | one-way | DNA18, Ku | `kdku1` | state and binding-pattern rewrite | `DNA18(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA18(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA18, Ku by freeing DNA18.site, Ku.dna at `kdku1`. | +| 248 | `Unlabeled` | one-way | DNA19, Ku | `kdku1` | state and binding-pattern rewrite | `DNA19(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA19(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA19, Ku by freeing DNA19.site, Ku.dna at `kdku1`. | +| 249 | `Unlabeled` | one-way | DNA20, Ku | `kdku1` | state and binding-pattern rewrite | `DNA20(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA20(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA20, Ku by freeing DNA20.site, Ku.dna at `kdku1`. | +| 250 | `Unlabeled` | one-way | DNA21, Ku | `kdku1` | state and binding-pattern rewrite | `DNA21(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA21(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA21, Ku by freeing DNA21.site, Ku.dna at `kdku1`. | + +### Rules 251-500 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 251 | `Unlabeled` | one-way | DNA22, Ku | `kdku1` | state and binding-pattern rewrite | `DNA22(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA22(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA22, Ku by freeing DNA22.site, Ku.dna at `kdku1`. | +| 252 | `Unlabeled` | one-way | DNA23, Ku | `kdku1` | state and binding-pattern rewrite | `DNA23(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA23(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA23, Ku by freeing DNA23.site, Ku.dna at `kdku1`. | +| 253 | `Unlabeled` | one-way | DNA24, Ku | `kdku1` | state and binding-pattern rewrite | `DNA24(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA24(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA24, Ku by freeing DNA24.site, Ku.dna at `kdku1`. | +| 254 | `Unlabeled` | one-way | DNA25, Ku | `kdku1` | state and binding-pattern rewrite | `DNA25(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA25(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA25, Ku by freeing DNA25.site, Ku.dna at `kdku1`. | +| 255 | `Unlabeled` | one-way | DNA26, Ku | `kdku1` | state and binding-pattern rewrite | `DNA26(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA26(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA26, Ku by freeing DNA26.site, Ku.dna at `kdku1`. | +| 256 | `Unlabeled` | one-way | DNA27, Ku | `kdku1` | state and binding-pattern rewrite | `DNA27(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA27(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA27, Ku by freeing DNA27.site, Ku.dna at `kdku1`. | +| 257 | `Unlabeled` | one-way | DNA28, Ku | `kdku1` | state and binding-pattern rewrite | `DNA28(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA28(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA28, Ku by freeing DNA28.site, Ku.dna at `kdku1`. | +| 258 | `Unlabeled` | one-way | DNA29, Ku | `kdku1` | state and binding-pattern rewrite | `DNA29(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA29(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA29, Ku by freeing DNA29.site, Ku.dna at `kdku1`. | +| 259 | `Unlabeled` | one-way | DNA30, Ku | `kdku1` | state and binding-pattern rewrite | `DNA30(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA30(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA30, Ku by freeing DNA30.site, Ku.dna at `kdku1`. | +| 260 | `Unlabeled` | one-way | DNA31, Ku | `kdku1` | state and binding-pattern rewrite | `DNA31(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA31(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA31, Ku by freeing DNA31.site, Ku.dna at `kdku1`. | +| 261 | `Unlabeled` | one-way | DNA32, Ku | `kdku1` | state and binding-pattern rewrite | `DNA32(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA32(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA32, Ku by freeing DNA32.site, Ku.dna at `kdku1`. | +| 262 | `Unlabeled` | one-way | DNA33, Ku | `kdku1` | state and binding-pattern rewrite | `DNA33(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA33(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA33, Ku by freeing DNA33.site, Ku.dna at `kdku1`. | +| 263 | `Unlabeled` | one-way | DNA34, Ku | `kdku1` | state and binding-pattern rewrite | `DNA34(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA34(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA34, Ku by freeing DNA34.site, Ku.dna at `kdku1`. | +| 264 | `Unlabeled` | one-way | DNA35, Ku | `kdku1` | state and binding-pattern rewrite | `DNA35(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA35(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA35, Ku by freeing DNA35.site, Ku.dna at `kdku1`. | +| 265 | `Unlabeled` | one-way | DNA36, Ku | `kdku1` | state and binding-pattern rewrite | `DNA36(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA36(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA36, Ku by freeing DNA36.site, Ku.dna at `kdku1`. | +| 266 | `Unlabeled` | one-way | DNA37, Ku | `kdku1` | state and binding-pattern rewrite | `DNA37(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA37(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA37, Ku by freeing DNA37.site, Ku.dna at `kdku1`. | +| 267 | `Unlabeled` | one-way | DNA38, Ku | `kdku1` | state and binding-pattern rewrite | `DNA38(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA38(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA38, Ku by freeing DNA38.site, Ku.dna at `kdku1`. | +| 268 | `Unlabeled` | one-way | DNA39, Ku | `kdku1` | state and binding-pattern rewrite | `DNA39(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA39(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA39, Ku by freeing DNA39.site, Ku.dna at `kdku1`. | +| 269 | `Unlabeled` | one-way | DNA40, Ku | `kdku1` | state and binding-pattern rewrite | `DNA40(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA40(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA40, Ku by freeing DNA40.site, Ku.dna at `kdku1`. | +| 270 | `Unlabeled` | one-way | DNA41, Ku | `kdku1` | state and binding-pattern rewrite | `DNA41(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA41(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA41, Ku by freeing DNA41.site, Ku.dna at `kdku1`. | +| 271 | `Unlabeled` | one-way | DNA42, Ku | `kdku1` | state and binding-pattern rewrite | `DNA42(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA42(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA42, Ku by freeing DNA42.site, Ku.dna at `kdku1`. | +| 272 | `Unlabeled` | one-way | DNA43, Ku | `kdku1` | state and binding-pattern rewrite | `DNA43(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA43(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA43, Ku by freeing DNA43.site, Ku.dna at `kdku1`. | +| 273 | `Unlabeled` | one-way | DNA44, Ku | `kdku1` | state and binding-pattern rewrite | `DNA44(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA44(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA44, Ku by freeing DNA44.site, Ku.dna at `kdku1`. | +| 274 | `Unlabeled` | one-way | DNA45, Ku | `kdku1` | state and binding-pattern rewrite | `DNA45(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA45(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA45, Ku by freeing DNA45.site, Ku.dna at `kdku1`. | +| 275 | `Unlabeled` | one-way | DNA46, Ku | `kdku1` | state and binding-pattern rewrite | `DNA46(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA46(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA46, Ku by freeing DNA46.site, Ku.dna at `kdku1`. | +| 276 | `Unlabeled` | one-way | DNA47, Ku | `kdku1` | state and binding-pattern rewrite | `DNA47(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA47(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA47, Ku by freeing DNA47.site, Ku.dna at `kdku1`. | +| 277 | `Unlabeled` | one-way | DNA48, Ku | `kdku1` | state and binding-pattern rewrite | `DNA48(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA48(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA48, Ku by freeing DNA48.site, Ku.dna at `kdku1`. | +| 278 | `Unlabeled` | one-way | DNA49, Ku | `kdku1` | state and binding-pattern rewrite | `DNA49(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA49(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA49, Ku by freeing DNA49.site, Ku.dna at `kdku1`. | +| 279 | `Unlabeled` | one-way | DNA50, Ku | `kdku1` | state and binding-pattern rewrite | `DNA50(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA50(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA50, Ku by freeing DNA50.site, Ku.dna at `kdku1`. | +| 280 | `Unlabeled` | one-way | DNA1, Ku | `kdku2` | state and binding-pattern rewrite | `DNA1(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA1(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA1, Ku by freeing DNA1.site, Ku.dna at `kdku2`. | +| 281 | `Unlabeled` | one-way | DNA2, Ku | `kdku2` | state and binding-pattern rewrite | `DNA2(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA2(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA2, Ku by freeing DNA2.site, Ku.dna at `kdku2`. | +| 282 | `Unlabeled` | one-way | DNA3, Ku | `kdku2` | state and binding-pattern rewrite | `DNA3(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA3(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA3, Ku by freeing DNA3.site, Ku.dna at `kdku2`. | +| 283 | `Unlabeled` | one-way | DNA4, Ku | `kdku2` | state and binding-pattern rewrite | `DNA4(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA4(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA4, Ku by freeing DNA4.site, Ku.dna at `kdku2`. | +| 284 | `Unlabeled` | one-way | DNA5, Ku | `kdku2` | state and binding-pattern rewrite | `DNA5(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA5(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA5, Ku by freeing DNA5.site, Ku.dna at `kdku2`. | +| 285 | `Unlabeled` | one-way | DNA6, Ku | `kdku2` | state and binding-pattern rewrite | `DNA6(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA6(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA6, Ku by freeing DNA6.site, Ku.dna at `kdku2`. | +| 286 | `Unlabeled` | one-way | DNA7, Ku | `kdku2` | state and binding-pattern rewrite | `DNA7(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA7(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA7, Ku by freeing DNA7.site, Ku.dna at `kdku2`. | +| 287 | `Unlabeled` | one-way | DNA8, Ku | `kdku2` | state and binding-pattern rewrite | `DNA8(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA8(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA8, Ku by freeing DNA8.site, Ku.dna at `kdku2`. | +| 288 | `Unlabeled` | one-way | DNA9, Ku | `kdku2` | state and binding-pattern rewrite | `DNA9(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA9(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA9, Ku by freeing DNA9.site, Ku.dna at `kdku2`. | +| 289 | `Unlabeled` | one-way | DNA10, Ku | `kdku2` | state and binding-pattern rewrite | `DNA10(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA10(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA10, Ku by freeing DNA10.site, Ku.dna at `kdku2`. | +| 290 | `Unlabeled` | one-way | DNA11, Ku | `kdku2` | state and binding-pattern rewrite | `DNA11(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA11(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA11, Ku by freeing DNA11.site, Ku.dna at `kdku2`. | +| 291 | `Unlabeled` | one-way | DNA12, Ku | `kdku2` | state and binding-pattern rewrite | `DNA12(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA12(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA12, Ku by freeing DNA12.site, Ku.dna at `kdku2`. | +| 292 | `Unlabeled` | one-way | DNA13, Ku | `kdku2` | state and binding-pattern rewrite | `DNA13(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA13(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA13, Ku by freeing DNA13.site, Ku.dna at `kdku2`. | +| 293 | `Unlabeled` | one-way | DNA14, Ku | `kdku2` | state and binding-pattern rewrite | `DNA14(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA14(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA14, Ku by freeing DNA14.site, Ku.dna at `kdku2`. | +| 294 | `Unlabeled` | one-way | DNA15, Ku | `kdku2` | state and binding-pattern rewrite | `DNA15(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA15(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA15, Ku by freeing DNA15.site, Ku.dna at `kdku2`. | +| 295 | `Unlabeled` | one-way | DNA16, Ku | `kdku2` | state and binding-pattern rewrite | `DNA16(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA16(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA16, Ku by freeing DNA16.site, Ku.dna at `kdku2`. | +| 296 | `Unlabeled` | one-way | DNA17, Ku | `kdku2` | state and binding-pattern rewrite | `DNA17(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA17(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA17, Ku by freeing DNA17.site, Ku.dna at `kdku2`. | +| 297 | `Unlabeled` | one-way | DNA18, Ku | `kdku2` | state and binding-pattern rewrite | `DNA18(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA18(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA18, Ku by freeing DNA18.site, Ku.dna at `kdku2`. | +| 298 | `Unlabeled` | one-way | DNA19, Ku | `kdku2` | state and binding-pattern rewrite | `DNA19(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA19(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA19, Ku by freeing DNA19.site, Ku.dna at `kdku2`. | +| 299 | `Unlabeled` | one-way | DNA20, Ku | `kdku2` | state and binding-pattern rewrite | `DNA20(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA20(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA20, Ku by freeing DNA20.site, Ku.dna at `kdku2`. | +| 300 | `Unlabeled` | one-way | DNA21, Ku | `kdku2` | state and binding-pattern rewrite | `DNA21(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA21(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA21, Ku by freeing DNA21.site, Ku.dna at `kdku2`. | +| 301 | `Unlabeled` | one-way | DNA22, Ku | `kdku2` | state and binding-pattern rewrite | `DNA22(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA22(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA22, Ku by freeing DNA22.site, Ku.dna at `kdku2`. | +| 302 | `Unlabeled` | one-way | DNA23, Ku | `kdku2` | state and binding-pattern rewrite | `DNA23(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA23(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA23, Ku by freeing DNA23.site, Ku.dna at `kdku2`. | +| 303 | `Unlabeled` | one-way | DNA24, Ku | `kdku2` | state and binding-pattern rewrite | `DNA24(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA24(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA24, Ku by freeing DNA24.site, Ku.dna at `kdku2`. | +| 304 | `Unlabeled` | one-way | DNA25, Ku | `kdku2` | state and binding-pattern rewrite | `DNA25(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA25(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA25, Ku by freeing DNA25.site, Ku.dna at `kdku2`. | +| 305 | `Unlabeled` | one-way | DNA26, Ku | `kdku2` | state and binding-pattern rewrite | `DNA26(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA26(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA26, Ku by freeing DNA26.site, Ku.dna at `kdku2`. | +| 306 | `Unlabeled` | one-way | DNA27, Ku | `kdku2` | state and binding-pattern rewrite | `DNA27(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA27(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA27, Ku by freeing DNA27.site, Ku.dna at `kdku2`. | +| 307 | `Unlabeled` | one-way | DNA28, Ku | `kdku2` | state and binding-pattern rewrite | `DNA28(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA28(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA28, Ku by freeing DNA28.site, Ku.dna at `kdku2`. | +| 308 | `Unlabeled` | one-way | DNA29, Ku | `kdku2` | state and binding-pattern rewrite | `DNA29(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA29(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA29, Ku by freeing DNA29.site, Ku.dna at `kdku2`. | +| 309 | `Unlabeled` | one-way | DNA30, Ku | `kdku2` | state and binding-pattern rewrite | `DNA30(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA30(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA30, Ku by freeing DNA30.site, Ku.dna at `kdku2`. | +| 310 | `Unlabeled` | one-way | DNA31, Ku | `kdku2` | state and binding-pattern rewrite | `DNA31(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA31(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA31, Ku by freeing DNA31.site, Ku.dna at `kdku2`. | +| 311 | `Unlabeled` | one-way | DNA32, Ku | `kdku2` | state and binding-pattern rewrite | `DNA32(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA32(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA32, Ku by freeing DNA32.site, Ku.dna at `kdku2`. | +| 312 | `Unlabeled` | one-way | DNA33, Ku | `kdku2` | state and binding-pattern rewrite | `DNA33(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA33(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA33, Ku by freeing DNA33.site, Ku.dna at `kdku2`. | +| 313 | `Unlabeled` | one-way | DNA34, Ku | `kdku2` | state and binding-pattern rewrite | `DNA34(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA34(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA34, Ku by freeing DNA34.site, Ku.dna at `kdku2`. | +| 314 | `Unlabeled` | one-way | DNA35, Ku | `kdku2` | state and binding-pattern rewrite | `DNA35(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA35(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA35, Ku by freeing DNA35.site, Ku.dna at `kdku2`. | +| 315 | `Unlabeled` | one-way | DNA36, Ku | `kdku2` | state and binding-pattern rewrite | `DNA36(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA36(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA36, Ku by freeing DNA36.site, Ku.dna at `kdku2`. | +| 316 | `Unlabeled` | one-way | DNA37, Ku | `kdku2` | state and binding-pattern rewrite | `DNA37(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA37(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA37, Ku by freeing DNA37.site, Ku.dna at `kdku2`. | +| 317 | `Unlabeled` | one-way | DNA38, Ku | `kdku2` | state and binding-pattern rewrite | `DNA38(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA38(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA38, Ku by freeing DNA38.site, Ku.dna at `kdku2`. | +| 318 | `Unlabeled` | one-way | DNA39, Ku | `kdku2` | state and binding-pattern rewrite | `DNA39(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA39(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA39, Ku by freeing DNA39.site, Ku.dna at `kdku2`. | +| 319 | `Unlabeled` | one-way | DNA40, Ku | `kdku2` | state and binding-pattern rewrite | `DNA40(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA40(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA40, Ku by freeing DNA40.site, Ku.dna at `kdku2`. | +| 320 | `Unlabeled` | one-way | DNA41, Ku | `kdku2` | state and binding-pattern rewrite | `DNA41(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA41(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA41, Ku by freeing DNA41.site, Ku.dna at `kdku2`. | +| 321 | `Unlabeled` | one-way | DNA42, Ku | `kdku2` | state and binding-pattern rewrite | `DNA42(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA42(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA42, Ku by freeing DNA42.site, Ku.dna at `kdku2`. | +| 322 | `Unlabeled` | one-way | DNA43, Ku | `kdku2` | state and binding-pattern rewrite | `DNA43(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA43(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA43, Ku by freeing DNA43.site, Ku.dna at `kdku2`. | +| 323 | `Unlabeled` | one-way | DNA44, Ku | `kdku2` | state and binding-pattern rewrite | `DNA44(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA44(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA44, Ku by freeing DNA44.site, Ku.dna at `kdku2`. | +| 324 | `Unlabeled` | one-way | DNA45, Ku | `kdku2` | state and binding-pattern rewrite | `DNA45(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA45(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA45, Ku by freeing DNA45.site, Ku.dna at `kdku2`. | +| 325 | `Unlabeled` | one-way | DNA46, Ku | `kdku2` | state and binding-pattern rewrite | `DNA46(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA46(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA46, Ku by freeing DNA46.site, Ku.dna at `kdku2`. | +| 326 | `Unlabeled` | one-way | DNA47, Ku | `kdku2` | state and binding-pattern rewrite | `DNA47(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA47(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA47, Ku by freeing DNA47.site, Ku.dna at `kdku2`. | +| 327 | `Unlabeled` | one-way | DNA48, Ku | `kdku2` | state and binding-pattern rewrite | `DNA48(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA48(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA48, Ku by freeing DNA48.site, Ku.dna at `kdku2`. | +| 328 | `Unlabeled` | one-way | DNA49, Ku | `kdku2` | state and binding-pattern rewrite | `DNA49(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA49(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA49, Ku by freeing DNA49.site, Ku.dna at `kdku2`. | +| 329 | `Unlabeled` | one-way | DNA50, Ku | `kdku2` | state and binding-pattern rewrite | `DNA50(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA50(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA50, Ku by freeing DNA50.site, Ku.dna at `kdku2`. | +| 330 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA1(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA1, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 331 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA2(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA2, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 332 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA3(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA3, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 333 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA4(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA4, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 334 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA5(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA5, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 335 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA6(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA6, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 336 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA7(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA7, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 337 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA8(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA8, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 338 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA9(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA9, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 339 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA10(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA10, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 340 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA11(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA11, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 341 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA12(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA12, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 342 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA13(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA13, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 343 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA14(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA14, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 344 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA15(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA15, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 345 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA16(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA16, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 346 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA17(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA17, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 347 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA18(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA18, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 348 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA19(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA19, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 349 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA20(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA20, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 350 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA21(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA21, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 351 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA22(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA22, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 352 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA23(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA23, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 353 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA24(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA24, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 354 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA25(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA25, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 355 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA26(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA26, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 356 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA27(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA27, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 357 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA28(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA28, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 358 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA29(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA29, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 359 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA30(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA30, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 360 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA31(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA31, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 361 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA32(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA32, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 362 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA33(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA33, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 363 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA34(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA34, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 364 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA35(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA35, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 365 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA36(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA36, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 366 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA37(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA37, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 367 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA38(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA38, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 368 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA39(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA39, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 369 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA40(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA40, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 370 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA41(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA41, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 371 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA42(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA42, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 372 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA43(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA43, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 373 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA44(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA44, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 374 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA45(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA45, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 375 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA46(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA46, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 376 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA47(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA47, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 377 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA48(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA48, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 378 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA49(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA49, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 379 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA50(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA50, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 380 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA1(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA1, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 381 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA2(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA2, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 382 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA3(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA3, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 383 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA4(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA4, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 384 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA5(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA5, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 385 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA6(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA6, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 386 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA7(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA7, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 387 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA8(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA8, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 388 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA9(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA9, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 389 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA10(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA10, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 390 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA11(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA11, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 391 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA12(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA12, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 392 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA13(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA13, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 393 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA14(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA14, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 394 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA15(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA15, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 395 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA16(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA16, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 396 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA17(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA17, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 397 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA18(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA18, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 398 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA19(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA19, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 399 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA20(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA20, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 400 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA21(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA21, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 401 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA22(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA22, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 402 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA23(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA23, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 403 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA24(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA24, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 404 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA25(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA25, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 405 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA26(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA26, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 406 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA27(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA27, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 407 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA28(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA28, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 408 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA29(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA29, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 409 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA30(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA30, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 410 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA31(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA31, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 411 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA32(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA32, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 412 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA33(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA33, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 413 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA34(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA34, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 414 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA35(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA35, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 415 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA36(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA36, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 416 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA37(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA37, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 417 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA38(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA38, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 418 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA39(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA39, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 419 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA40(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA40, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 420 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA41(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA41, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 421 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA42(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA42, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 422 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA43(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA43, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 423 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA44(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA44, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 424 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA45(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA45, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 425 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA46(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA46, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 426 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA47(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA47, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 427 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA48(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA48, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 428 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA49(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA49, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 429 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA50(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA50, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 430 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA1(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA1, DNAPKcs, Ku by freeing DNA1.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 431 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA2(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA2, DNAPKcs, Ku by freeing DNA2.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 432 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA3(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA3, DNAPKcs, Ku by freeing DNA3.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 433 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA4(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA4, DNAPKcs, Ku by freeing DNA4.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 434 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA5(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA5, DNAPKcs, Ku by freeing DNA5.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 435 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA6(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA6, DNAPKcs, Ku by freeing DNA6.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 436 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA7(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA7, DNAPKcs, Ku by freeing DNA7.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 437 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA8(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA8, DNAPKcs, Ku by freeing DNA8.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 438 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA9(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA9, DNAPKcs, Ku by freeing DNA9.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 439 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA10(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA10, DNAPKcs, Ku by freeing DNA10.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 440 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA11(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA11, DNAPKcs, Ku by freeing DNA11.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 441 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA12(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA12, DNAPKcs, Ku by freeing DNA12.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 442 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA13(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA13, DNAPKcs, Ku by freeing DNA13.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 443 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA14(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA14, DNAPKcs, Ku by freeing DNA14.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 444 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA15(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA15, DNAPKcs, Ku by freeing DNA15.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 445 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA16(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA16, DNAPKcs, Ku by freeing DNA16.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 446 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA17(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA17, DNAPKcs, Ku by freeing DNA17.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 447 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA18(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA18, DNAPKcs, Ku by freeing DNA18.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 448 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA19(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA19, DNAPKcs, Ku by freeing DNA19.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 449 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA20(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA20, DNAPKcs, Ku by freeing DNA20.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 450 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA21(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA21, DNAPKcs, Ku by freeing DNA21.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 451 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA22(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA22, DNAPKcs, Ku by freeing DNA22.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 452 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA23(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA23, DNAPKcs, Ku by freeing DNA23.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 453 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA24(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA24, DNAPKcs, Ku by freeing DNA24.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 454 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA25(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA25, DNAPKcs, Ku by freeing DNA25.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 455 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA26(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA26, DNAPKcs, Ku by freeing DNA26.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 456 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA27(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA27, DNAPKcs, Ku by freeing DNA27.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 457 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA28(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA28, DNAPKcs, Ku by freeing DNA28.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 458 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA29(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA29, DNAPKcs, Ku by freeing DNA29.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 459 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA30(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA30, DNAPKcs, Ku by freeing DNA30.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 460 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA31(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA31, DNAPKcs, Ku by freeing DNA31.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 461 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA32(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA32, DNAPKcs, Ku by freeing DNA32.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 462 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA33(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA33, DNAPKcs, Ku by freeing DNA33.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 463 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA34(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA34, DNAPKcs, Ku by freeing DNA34.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 464 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA35(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA35, DNAPKcs, Ku by freeing DNA35.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 465 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA36(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA36, DNAPKcs, Ku by freeing DNA36.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 466 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA37(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA37, DNAPKcs, Ku by freeing DNA37.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 467 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA38(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA38, DNAPKcs, Ku by freeing DNA38.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 468 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA39(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA39, DNAPKcs, Ku by freeing DNA39.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 469 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA40(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA40, DNAPKcs, Ku by freeing DNA40.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 470 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA41(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA41, DNAPKcs, Ku by freeing DNA41.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 471 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA42(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA42, DNAPKcs, Ku by freeing DNA42.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 472 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA43(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA43, DNAPKcs, Ku by freeing DNA43.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 473 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA44(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA44, DNAPKcs, Ku by freeing DNA44.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 474 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA45(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA45, DNAPKcs, Ku by freeing DNA45.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 475 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA46(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA46, DNAPKcs, Ku by freeing DNA46.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 476 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA47(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA47, DNAPKcs, Ku by freeing DNA47.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 477 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA48(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA48, DNAPKcs, Ku by freeing DNA48.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 478 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA49(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA49, DNAPKcs, Ku by freeing DNA49.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 479 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA50(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA50, DNAPKcs, Ku by freeing DNA50.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 480 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA1(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA1, DNAPKcs, Ku by freeing DNA1.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 481 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA2(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA2, DNAPKcs, Ku by freeing DNA2.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 482 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA3(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA3, DNAPKcs, Ku by freeing DNA3.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 483 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA4(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA4, DNAPKcs, Ku by freeing DNA4.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 484 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA5(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA5, DNAPKcs, Ku by freeing DNA5.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 485 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA6(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA6, DNAPKcs, Ku by freeing DNA6.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 486 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA7(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA7, DNAPKcs, Ku by freeing DNA7.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 487 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA8(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA8, DNAPKcs, Ku by freeing DNA8.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 488 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA9(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA9, DNAPKcs, Ku by freeing DNA9.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 489 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA10(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA10, DNAPKcs, Ku by freeing DNA10.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 490 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA11(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA11, DNAPKcs, Ku by freeing DNA11.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 491 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA12(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA12, DNAPKcs, Ku by freeing DNA12.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 492 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA13(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA13, DNAPKcs, Ku by freeing DNA13.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 493 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA14(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA14, DNAPKcs, Ku by freeing DNA14.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 494 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA15(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA15, DNAPKcs, Ku by freeing DNA15.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 495 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA16(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA16, DNAPKcs, Ku by freeing DNA16.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 496 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA17(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA17, DNAPKcs, Ku by freeing DNA17.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 497 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA18(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA18, DNAPKcs, Ku by freeing DNA18.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 498 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA19(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA19, DNAPKcs, Ku by freeing DNA19.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 499 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA20(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA20, DNAPKcs, Ku by freeing DNA20.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 500 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA21(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA21, DNAPKcs, Ku by freeing DNA21.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | + +### Rules 501-750 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 501 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA22(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA22, DNAPKcs, Ku by freeing DNA22.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 502 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA23(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA23, DNAPKcs, Ku by freeing DNA23.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 503 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA24(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA24, DNAPKcs, Ku by freeing DNA24.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 504 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA25(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA25, DNAPKcs, Ku by freeing DNA25.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 505 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA26(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA26, DNAPKcs, Ku by freeing DNA26.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 506 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA27(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA27, DNAPKcs, Ku by freeing DNA27.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 507 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA28(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA28, DNAPKcs, Ku by freeing DNA28.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 508 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA29(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA29, DNAPKcs, Ku by freeing DNA29.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 509 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA30(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA30, DNAPKcs, Ku by freeing DNA30.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 510 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA31(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA31, DNAPKcs, Ku by freeing DNA31.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 511 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA32(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA32, DNAPKcs, Ku by freeing DNA32.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 512 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA33(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA33, DNAPKcs, Ku by freeing DNA33.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 513 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA34(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA34, DNAPKcs, Ku by freeing DNA34.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 514 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA35(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA35, DNAPKcs, Ku by freeing DNA35.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 515 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA36(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA36, DNAPKcs, Ku by freeing DNA36.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 516 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA37(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA37, DNAPKcs, Ku by freeing DNA37.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 517 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA38(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA38, DNAPKcs, Ku by freeing DNA38.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 518 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA39(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA39, DNAPKcs, Ku by freeing DNA39.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 519 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA40(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA40, DNAPKcs, Ku by freeing DNA40.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 520 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA41(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA41, DNAPKcs, Ku by freeing DNA41.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 521 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA42(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA42, DNAPKcs, Ku by freeing DNA42.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 522 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA43(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA43, DNAPKcs, Ku by freeing DNA43.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 523 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA44(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA44, DNAPKcs, Ku by freeing DNA44.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 524 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA45(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA45, DNAPKcs, Ku by freeing DNA45.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 525 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA46(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA46, DNAPKcs, Ku by freeing DNA46.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 526 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA47(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA47, DNAPKcs, Ku by freeing DNA47.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 527 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA48(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA48, DNAPKcs, Ku by freeing DNA48.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 528 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA49(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA49, DNAPKcs, Ku by freeing DNA49.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 529 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA50(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA50, DNAPKcs, Ku by freeing DNA50.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 530 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA1, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 531 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA2, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 532 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA3, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 533 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA4, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 534 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA5, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 535 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA6, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 536 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA7, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 537 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA8, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 538 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA9, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 539 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA10, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 540 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA11, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 541 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA12, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 542 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA13, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 543 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA14, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 544 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA15, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 545 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA16, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 546 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA17, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 547 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA18, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 548 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA19, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 549 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA20, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 550 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA21, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 551 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA22, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 552 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA23, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 553 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA24, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 554 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA25, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 555 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA26, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 556 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA27, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 557 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA28, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 558 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA29, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 559 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA30, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 560 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA31, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 561 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA32, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 562 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA33, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 563 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA34, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 564 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA35, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 565 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA36, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 566 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA37, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 567 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA38, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 568 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA39, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 569 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA40, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 570 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA41, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 571 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA42, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 572 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA43, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 573 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA44, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 574 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA45, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 575 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA46, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 576 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA47, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 577 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA48, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 578 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA49, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 579 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA50, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 580 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA1, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 581 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA2, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 582 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA3, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 583 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA4, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 584 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA5, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 585 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA6, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 586 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA7, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 587 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA8, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 588 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA9, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 589 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA10, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 590 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA11, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 591 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA12, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 592 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA13, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 593 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA14, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 594 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA15, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 595 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA16, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 596 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA17, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 597 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA18, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 598 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA19, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 599 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA20, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 600 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA21, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 601 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA22, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 602 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA23, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 603 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA24, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 604 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA25, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 605 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA26, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 606 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA27, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 607 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA28, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 608 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA29, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 609 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA30, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 610 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA31, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 611 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA32, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 612 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA33, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 613 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA34, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 614 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA35, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 615 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA36, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 616 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA37, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 617 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA38, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 618 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA39, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 619 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA40, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 620 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA41, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 621 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA42, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 622 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA43, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 623 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA44, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 624 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA45, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 625 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA46, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 626 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA47, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 627 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA48, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 628 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA49, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 629 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA50, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 630 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA1, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 631 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA2, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 632 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA3, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 633 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA4, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 634 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA5, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 635 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA6, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 636 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA7, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 637 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA8, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 638 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA9, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 639 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA10, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 640 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA11, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 641 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA12, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 642 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA13, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 643 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA14, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 644 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA15, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 645 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA16, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 646 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA17, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 647 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA18, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 648 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA19, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 649 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA20, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 650 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA21, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 651 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA22, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 652 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA23, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 653 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA24, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 654 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA25, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 655 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA26, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 656 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA27, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 657 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA28, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 658 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA29, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 659 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA30, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 660 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA31, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 661 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA32, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 662 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA33, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 663 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA34, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 664 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA35, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 665 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA36, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 666 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA37, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 667 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA38, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 668 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA39, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 669 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA40, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 670 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA41, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 671 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA42, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 672 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA43, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 673 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA44, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 674 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA45, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 675 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA46, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 676 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA47, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 677 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA48, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 678 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA49, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 679 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA50, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 680 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA1, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 681 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA2, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 682 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA3, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 683 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA4, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 684 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA5, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 685 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA6, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 686 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA7, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 687 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA8, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 688 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA9, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 689 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA10, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 690 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA11, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 691 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA12, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 692 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA13, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 693 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA14, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 694 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA15, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 695 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA16, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 696 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA17, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 697 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA18, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 698 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA19, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 699 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA20, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 700 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA21, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 701 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA22, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 702 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA23, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 703 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA24, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 704 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA25, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 705 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA26, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 706 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA27, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 707 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA28, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 708 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA29, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 709 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA30, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 710 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA31, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 711 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA32, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 712 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA33, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 713 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA34, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 714 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA35, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 715 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA36, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 716 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA37, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 717 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA38, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 718 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA39, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 719 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA40, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 720 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA41, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 721 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA42, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 722 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA43, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 723 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA44, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 724 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA45, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 725 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA46, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 726 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA47, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 727 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA48, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 728 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA49, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 729 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA50, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 730 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA1, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 731 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA2, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 732 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA3, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 733 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA4, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 734 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA5, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 735 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA6, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 736 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA7, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 737 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA8, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 738 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA9, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 739 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA10, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 740 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA11, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 741 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA12, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 742 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA13, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 743 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA14, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 744 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA15, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 745 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA16, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 746 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA17, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 747 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA18, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 748 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA19, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 749 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA20, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 750 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA21, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | + +### Rules 751-1000 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 751 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA22, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 752 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA23, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 753 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA24, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 754 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA25, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 755 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA26, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 756 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA27, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 757 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA28, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 758 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA29, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 759 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA30, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 760 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA31, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 761 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA32, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 762 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA33, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 763 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA34, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 764 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA35, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 765 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA36, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 766 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA37, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 767 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA38, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 768 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA39, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 769 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA40, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 770 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA41, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 771 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA42, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 772 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA43, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 773 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA44, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 774 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA45, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 775 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA46, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 776 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA47, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 777 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA48, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 778 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA49, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 779 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA50, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 780 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA1, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 781 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA2, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 782 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA3, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 783 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA4, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 784 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA5, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 785 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA6, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 786 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA7, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 787 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA8, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 788 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA9, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 789 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA10, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 790 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA11, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 791 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA12, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 792 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA13, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 793 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA14, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 794 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA15, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 795 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA16, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 796 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA17, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 797 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA18, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 798 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA19, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 799 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA20, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 800 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA21, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 801 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA22, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 802 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA23, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 803 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA24, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 804 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA25, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 805 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA26, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 806 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA27, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 807 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA28, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 808 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA29, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 809 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA30, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 810 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA31, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 811 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA32, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 812 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA33, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 813 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA34, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 814 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA35, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 815 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA36, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 816 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA37, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 817 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA38, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 818 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA39, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 819 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA40, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 820 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA41, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 821 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA42, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 822 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA43, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 823 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA44, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 824 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA45, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 825 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA46, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 826 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA47, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 827 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA48, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 828 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA49, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 829 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA50, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 830 | `Unlabeled` | one-way | ATM, DNA1, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA1(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA1.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 831 | `Unlabeled` | one-way | ATM, DNA2, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA2(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA2.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 832 | `Unlabeled` | one-way | ATM, DNA3, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA3(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA3.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 833 | `Unlabeled` | one-way | ATM, DNA4, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA4(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA4.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 834 | `Unlabeled` | one-way | ATM, DNA5, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA5(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA5.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 835 | `Unlabeled` | one-way | ATM, DNA6, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA6(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA6.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 836 | `Unlabeled` | one-way | ATM, DNA7, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA7(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA7.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 837 | `Unlabeled` | one-way | ATM, DNA8, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA8(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA8.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 838 | `Unlabeled` | one-way | ATM, DNA9, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA9(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA9.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 839 | `Unlabeled` | one-way | ATM, DNA10, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA10(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA10.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 840 | `Unlabeled` | one-way | ATM, DNA11, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA11(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA11.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 841 | `Unlabeled` | one-way | ATM, DNA12, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA12(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA12.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 842 | `Unlabeled` | one-way | ATM, DNA13, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA13(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA13.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 843 | `Unlabeled` | one-way | ATM, DNA14, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA14(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA14.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 844 | `Unlabeled` | one-way | ATM, DNA15, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA15(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA15.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 845 | `Unlabeled` | one-way | ATM, DNA16, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA16(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA16.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 846 | `Unlabeled` | one-way | ATM, DNA17, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA17(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA17.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 847 | `Unlabeled` | one-way | ATM, DNA18, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA18(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA18.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 848 | `Unlabeled` | one-way | ATM, DNA19, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA19(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA19.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 849 | `Unlabeled` | one-way | ATM, DNA20, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA20(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA20.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 850 | `Unlabeled` | one-way | ATM, DNA21, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA21(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA21.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 851 | `Unlabeled` | one-way | ATM, DNA22, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA22(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA22.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 852 | `Unlabeled` | one-way | ATM, DNA23, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA23(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA23.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 853 | `Unlabeled` | one-way | ATM, DNA24, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA24(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA24.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 854 | `Unlabeled` | one-way | ATM, DNA25, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA25(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA25.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 855 | `Unlabeled` | one-way | ATM, DNA26, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA26(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA26.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 856 | `Unlabeled` | one-way | ATM, DNA27, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA27(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA27.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 857 | `Unlabeled` | one-way | ATM, DNA28, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA28(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA28.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 858 | `Unlabeled` | one-way | ATM, DNA29, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA29(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA29.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 859 | `Unlabeled` | one-way | ATM, DNA30, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA30(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA30.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 860 | `Unlabeled` | one-way | ATM, DNA31, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA31(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA31.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 861 | `Unlabeled` | one-way | ATM, DNA32, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA32(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA32.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 862 | `Unlabeled` | one-way | ATM, DNA33, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA33(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA33.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 863 | `Unlabeled` | one-way | ATM, DNA34, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA34(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA34.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 864 | `Unlabeled` | one-way | ATM, DNA35, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA35(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA35.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 865 | `Unlabeled` | one-way | ATM, DNA36, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA36(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA36.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 866 | `Unlabeled` | one-way | ATM, DNA37, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA37(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA37.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 867 | `Unlabeled` | one-way | ATM, DNA38, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA38(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA38.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 868 | `Unlabeled` | one-way | ATM, DNA39, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA39(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA39.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 869 | `Unlabeled` | one-way | ATM, DNA40, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA40(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA40.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 870 | `Unlabeled` | one-way | ATM, DNA41, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA41(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA41.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 871 | `Unlabeled` | one-way | ATM, DNA42, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA42(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA42.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 872 | `Unlabeled` | one-way | ATM, DNA43, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA43(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA43.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 873 | `Unlabeled` | one-way | ATM, DNA44, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA44(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA44.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 874 | `Unlabeled` | one-way | ATM, DNA45, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA45(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA45.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 875 | `Unlabeled` | one-way | ATM, DNA46, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA46(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA46.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 876 | `Unlabeled` | one-way | ATM, DNA47, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA47(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA47.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 877 | `Unlabeled` | one-way | ATM, DNA48, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA48(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA48.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 878 | `Unlabeled` | one-way | ATM, DNA49, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA49(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA49.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 879 | `Unlabeled` | one-way | ATM, DNA50, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA50(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA50.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 880 | `Unlabeled` | one-way | ATM, DNA1, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA1(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA1.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 881 | `Unlabeled` | one-way | ATM, DNA2, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA2(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA2.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 882 | `Unlabeled` | one-way | ATM, DNA3, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA3(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA3.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 883 | `Unlabeled` | one-way | ATM, DNA4, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA4(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA4.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 884 | `Unlabeled` | one-way | ATM, DNA5, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA5(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA5.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 885 | `Unlabeled` | one-way | ATM, DNA6, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA6(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA6.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 886 | `Unlabeled` | one-way | ATM, DNA7, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA7(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA7.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 887 | `Unlabeled` | one-way | ATM, DNA8, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA8(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA8.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 888 | `Unlabeled` | one-way | ATM, DNA9, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA9(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA9.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 889 | `Unlabeled` | one-way | ATM, DNA10, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA10(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA10.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 890 | `Unlabeled` | one-way | ATM, DNA11, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA11(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA11.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 891 | `Unlabeled` | one-way | ATM, DNA12, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA12(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA12.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 892 | `Unlabeled` | one-way | ATM, DNA13, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA13(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA13.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 893 | `Unlabeled` | one-way | ATM, DNA14, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA14(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA14.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 894 | `Unlabeled` | one-way | ATM, DNA15, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA15(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA15.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 895 | `Unlabeled` | one-way | ATM, DNA16, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA16(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA16.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 896 | `Unlabeled` | one-way | ATM, DNA17, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA17(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA17.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 897 | `Unlabeled` | one-way | ATM, DNA18, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA18(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA18.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 898 | `Unlabeled` | one-way | ATM, DNA19, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA19(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA19.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 899 | `Unlabeled` | one-way | ATM, DNA20, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA20(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA20.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 900 | `Unlabeled` | one-way | ATM, DNA21, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA21(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA21.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 901 | `Unlabeled` | one-way | ATM, DNA22, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA22(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA22.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 902 | `Unlabeled` | one-way | ATM, DNA23, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA23(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA23.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 903 | `Unlabeled` | one-way | ATM, DNA24, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA24(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA24.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 904 | `Unlabeled` | one-way | ATM, DNA25, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA25(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA25.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 905 | `Unlabeled` | one-way | ATM, DNA26, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA26(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA26.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 906 | `Unlabeled` | one-way | ATM, DNA27, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA27(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA27.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 907 | `Unlabeled` | one-way | ATM, DNA28, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA28(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA28.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 908 | `Unlabeled` | one-way | ATM, DNA29, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA29(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA29.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 909 | `Unlabeled` | one-way | ATM, DNA30, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA30(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA30.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 910 | `Unlabeled` | one-way | ATM, DNA31, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA31(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA31.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 911 | `Unlabeled` | one-way | ATM, DNA32, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA32(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA32.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 912 | `Unlabeled` | one-way | ATM, DNA33, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA33(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA33.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 913 | `Unlabeled` | one-way | ATM, DNA34, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA34(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA34.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 914 | `Unlabeled` | one-way | ATM, DNA35, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA35(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA35.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 915 | `Unlabeled` | one-way | ATM, DNA36, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA36(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA36.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 916 | `Unlabeled` | one-way | ATM, DNA37, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA37(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA37.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 917 | `Unlabeled` | one-way | ATM, DNA38, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA38(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA38.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 918 | `Unlabeled` | one-way | ATM, DNA39, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA39(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA39.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 919 | `Unlabeled` | one-way | ATM, DNA40, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA40(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA40.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 920 | `Unlabeled` | one-way | ATM, DNA41, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA41(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA41.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 921 | `Unlabeled` | one-way | ATM, DNA42, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA42(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA42.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 922 | `Unlabeled` | one-way | ATM, DNA43, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA43(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA43.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 923 | `Unlabeled` | one-way | ATM, DNA44, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA44(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA44.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 924 | `Unlabeled` | one-way | ATM, DNA45, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA45(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA45.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 925 | `Unlabeled` | one-way | ATM, DNA46, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA46(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA46.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 926 | `Unlabeled` | one-way | ATM, DNA47, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA47(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA47.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 927 | `Unlabeled` | one-way | ATM, DNA48, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA48(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA48.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 928 | `Unlabeled` | one-way | ATM, DNA49, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA49(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA49.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 929 | `Unlabeled` | one-way | ATM, DNA50, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA50(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA50.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 930 | `Unlabeled` | one-way | DNA1, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA1(site~sdsb) + PARP(dna,liIII) -> DNA1(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA1, PARP through DNA1.site, PARP.dna at `kPARP1`. | +| 931 | `Unlabeled` | one-way | DNA2, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA2(site~sdsb) + PARP(dna,liIII) -> DNA2(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA2, PARP through DNA2.site, PARP.dna at `kPARP1`. | +| 932 | `Unlabeled` | one-way | DNA3, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA3(site~sdsb) + PARP(dna,liIII) -> DNA3(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA3, PARP through DNA3.site, PARP.dna at `kPARP1`. | +| 933 | `Unlabeled` | one-way | DNA4, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA4(site~sdsb) + PARP(dna,liIII) -> DNA4(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA4, PARP through DNA4.site, PARP.dna at `kPARP1`. | +| 934 | `Unlabeled` | one-way | DNA5, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA5(site~sdsb) + PARP(dna,liIII) -> DNA5(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA5, PARP through DNA5.site, PARP.dna at `kPARP1`. | +| 935 | `Unlabeled` | one-way | DNA6, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA6(site~sdsb) + PARP(dna,liIII) -> DNA6(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA6, PARP through DNA6.site, PARP.dna at `kPARP1`. | +| 936 | `Unlabeled` | one-way | DNA7, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA7(site~sdsb) + PARP(dna,liIII) -> DNA7(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA7, PARP through DNA7.site, PARP.dna at `kPARP1`. | +| 937 | `Unlabeled` | one-way | DNA8, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA8(site~sdsb) + PARP(dna,liIII) -> DNA8(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA8, PARP through DNA8.site, PARP.dna at `kPARP1`. | +| 938 | `Unlabeled` | one-way | DNA9, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA9(site~sdsb) + PARP(dna,liIII) -> DNA9(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA9, PARP through DNA9.site, PARP.dna at `kPARP1`. | +| 939 | `Unlabeled` | one-way | DNA10, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA10(site~sdsb) + PARP(dna,liIII) -> DNA10(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA10, PARP through DNA10.site, PARP.dna at `kPARP1`. | +| 940 | `Unlabeled` | one-way | DNA11, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA11(site~sdsb) + PARP(dna,liIII) -> DNA11(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA11, PARP through DNA11.site, PARP.dna at `kPARP1`. | +| 941 | `Unlabeled` | one-way | DNA12, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA12(site~sdsb) + PARP(dna,liIII) -> DNA12(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA12, PARP through DNA12.site, PARP.dna at `kPARP1`. | +| 942 | `Unlabeled` | one-way | DNA13, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA13(site~sdsb) + PARP(dna,liIII) -> DNA13(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA13, PARP through DNA13.site, PARP.dna at `kPARP1`. | +| 943 | `Unlabeled` | one-way | DNA14, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA14(site~sdsb) + PARP(dna,liIII) -> DNA14(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA14, PARP through DNA14.site, PARP.dna at `kPARP1`. | +| 944 | `Unlabeled` | one-way | DNA15, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA15(site~sdsb) + PARP(dna,liIII) -> DNA15(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA15, PARP through DNA15.site, PARP.dna at `kPARP1`. | +| 945 | `Unlabeled` | one-way | DNA16, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA16(site~sdsb) + PARP(dna,liIII) -> DNA16(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA16, PARP through DNA16.site, PARP.dna at `kPARP1`. | +| 946 | `Unlabeled` | one-way | DNA17, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA17(site~sdsb) + PARP(dna,liIII) -> DNA17(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA17, PARP through DNA17.site, PARP.dna at `kPARP1`. | +| 947 | `Unlabeled` | one-way | DNA18, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA18(site~sdsb) + PARP(dna,liIII) -> DNA18(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA18, PARP through DNA18.site, PARP.dna at `kPARP1`. | +| 948 | `Unlabeled` | one-way | DNA19, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA19(site~sdsb) + PARP(dna,liIII) -> DNA19(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA19, PARP through DNA19.site, PARP.dna at `kPARP1`. | +| 949 | `Unlabeled` | one-way | DNA20, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA20(site~sdsb) + PARP(dna,liIII) -> DNA20(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA20, PARP through DNA20.site, PARP.dna at `kPARP1`. | +| 950 | `Unlabeled` | one-way | DNA21, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA21(site~sdsb) + PARP(dna,liIII) -> DNA21(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA21, PARP through DNA21.site, PARP.dna at `kPARP1`. | +| 951 | `Unlabeled` | one-way | DNA22, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA22(site~sdsb) + PARP(dna,liIII) -> DNA22(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA22, PARP through DNA22.site, PARP.dna at `kPARP1`. | +| 952 | `Unlabeled` | one-way | DNA23, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA23(site~sdsb) + PARP(dna,liIII) -> DNA23(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA23, PARP through DNA23.site, PARP.dna at `kPARP1`. | +| 953 | `Unlabeled` | one-way | DNA24, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA24(site~sdsb) + PARP(dna,liIII) -> DNA24(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA24, PARP through DNA24.site, PARP.dna at `kPARP1`. | +| 954 | `Unlabeled` | one-way | DNA25, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA25(site~sdsb) + PARP(dna,liIII) -> DNA25(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA25, PARP through DNA25.site, PARP.dna at `kPARP1`. | +| 955 | `Unlabeled` | one-way | DNA26, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA26(site~sdsb) + PARP(dna,liIII) -> DNA26(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA26, PARP through DNA26.site, PARP.dna at `kPARP1`. | +| 956 | `Unlabeled` | one-way | DNA27, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA27(site~sdsb) + PARP(dna,liIII) -> DNA27(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA27, PARP through DNA27.site, PARP.dna at `kPARP1`. | +| 957 | `Unlabeled` | one-way | DNA28, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA28(site~sdsb) + PARP(dna,liIII) -> DNA28(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA28, PARP through DNA28.site, PARP.dna at `kPARP1`. | +| 958 | `Unlabeled` | one-way | DNA29, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA29(site~sdsb) + PARP(dna,liIII) -> DNA29(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA29, PARP through DNA29.site, PARP.dna at `kPARP1`. | +| 959 | `Unlabeled` | one-way | DNA30, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA30(site~sdsb) + PARP(dna,liIII) -> DNA30(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA30, PARP through DNA30.site, PARP.dna at `kPARP1`. | +| 960 | `Unlabeled` | one-way | DNA31, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA31(site~sdsb) + PARP(dna,liIII) -> DNA31(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA31, PARP through DNA31.site, PARP.dna at `kPARP1`. | +| 961 | `Unlabeled` | one-way | DNA32, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA32(site~sdsb) + PARP(dna,liIII) -> DNA32(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA32, PARP through DNA32.site, PARP.dna at `kPARP1`. | +| 962 | `Unlabeled` | one-way | DNA33, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA33(site~sdsb) + PARP(dna,liIII) -> DNA33(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA33, PARP through DNA33.site, PARP.dna at `kPARP1`. | +| 963 | `Unlabeled` | one-way | DNA34, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA34(site~sdsb) + PARP(dna,liIII) -> DNA34(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA34, PARP through DNA34.site, PARP.dna at `kPARP1`. | +| 964 | `Unlabeled` | one-way | DNA35, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA35(site~sdsb) + PARP(dna,liIII) -> DNA35(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA35, PARP through DNA35.site, PARP.dna at `kPARP1`. | +| 965 | `Unlabeled` | one-way | DNA36, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA36(site~sdsb) + PARP(dna,liIII) -> DNA36(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA36, PARP through DNA36.site, PARP.dna at `kPARP1`. | +| 966 | `Unlabeled` | one-way | DNA37, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA37(site~sdsb) + PARP(dna,liIII) -> DNA37(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA37, PARP through DNA37.site, PARP.dna at `kPARP1`. | +| 967 | `Unlabeled` | one-way | DNA38, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA38(site~sdsb) + PARP(dna,liIII) -> DNA38(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA38, PARP through DNA38.site, PARP.dna at `kPARP1`. | +| 968 | `Unlabeled` | one-way | DNA39, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA39(site~sdsb) + PARP(dna,liIII) -> DNA39(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA39, PARP through DNA39.site, PARP.dna at `kPARP1`. | +| 969 | `Unlabeled` | one-way | DNA40, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA40(site~sdsb) + PARP(dna,liIII) -> DNA40(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA40, PARP through DNA40.site, PARP.dna at `kPARP1`. | +| 970 | `Unlabeled` | one-way | DNA41, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA41(site~sdsb) + PARP(dna,liIII) -> DNA41(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA41, PARP through DNA41.site, PARP.dna at `kPARP1`. | +| 971 | `Unlabeled` | one-way | DNA42, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA42(site~sdsb) + PARP(dna,liIII) -> DNA42(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA42, PARP through DNA42.site, PARP.dna at `kPARP1`. | +| 972 | `Unlabeled` | one-way | DNA43, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA43(site~sdsb) + PARP(dna,liIII) -> DNA43(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA43, PARP through DNA43.site, PARP.dna at `kPARP1`. | +| 973 | `Unlabeled` | one-way | DNA44, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA44(site~sdsb) + PARP(dna,liIII) -> DNA44(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA44, PARP through DNA44.site, PARP.dna at `kPARP1`. | +| 974 | `Unlabeled` | one-way | DNA45, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA45(site~sdsb) + PARP(dna,liIII) -> DNA45(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA45, PARP through DNA45.site, PARP.dna at `kPARP1`. | +| 975 | `Unlabeled` | one-way | DNA46, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA46(site~sdsb) + PARP(dna,liIII) -> DNA46(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA46, PARP through DNA46.site, PARP.dna at `kPARP1`. | +| 976 | `Unlabeled` | one-way | DNA47, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA47(site~sdsb) + PARP(dna,liIII) -> DNA47(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA47, PARP through DNA47.site, PARP.dna at `kPARP1`. | +| 977 | `Unlabeled` | one-way | DNA48, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA48(site~sdsb) + PARP(dna,liIII) -> DNA48(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA48, PARP through DNA48.site, PARP.dna at `kPARP1`. | +| 978 | `Unlabeled` | one-way | DNA49, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA49(site~sdsb) + PARP(dna,liIII) -> DNA49(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA49, PARP through DNA49.site, PARP.dna at `kPARP1`. | +| 979 | `Unlabeled` | one-way | DNA50, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA50(site~sdsb) + PARP(dna,liIII) -> DNA50(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA50, PARP through DNA50.site, PARP.dna at `kPARP1`. | +| 980 | `Unlabeled` | one-way | DNA1, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA1(site~cdsb) + PARP(dna,liIII) -> DNA1(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA1, PARP through DNA1.site, PARP.dna at `kPARP2`. | +| 981 | `Unlabeled` | one-way | DNA2, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA2(site~cdsb) + PARP(dna,liIII) -> DNA2(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA2, PARP through DNA2.site, PARP.dna at `kPARP2`. | +| 982 | `Unlabeled` | one-way | DNA3, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA3(site~cdsb) + PARP(dna,liIII) -> DNA3(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA3, PARP through DNA3.site, PARP.dna at `kPARP2`. | +| 983 | `Unlabeled` | one-way | DNA4, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA4(site~cdsb) + PARP(dna,liIII) -> DNA4(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA4, PARP through DNA4.site, PARP.dna at `kPARP2`. | +| 984 | `Unlabeled` | one-way | DNA5, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA5(site~cdsb) + PARP(dna,liIII) -> DNA5(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA5, PARP through DNA5.site, PARP.dna at `kPARP2`. | +| 985 | `Unlabeled` | one-way | DNA6, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA6(site~cdsb) + PARP(dna,liIII) -> DNA6(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA6, PARP through DNA6.site, PARP.dna at `kPARP2`. | +| 986 | `Unlabeled` | one-way | DNA7, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA7(site~cdsb) + PARP(dna,liIII) -> DNA7(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA7, PARP through DNA7.site, PARP.dna at `kPARP2`. | +| 987 | `Unlabeled` | one-way | DNA8, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA8(site~cdsb) + PARP(dna,liIII) -> DNA8(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA8, PARP through DNA8.site, PARP.dna at `kPARP2`. | +| 988 | `Unlabeled` | one-way | DNA9, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA9(site~cdsb) + PARP(dna,liIII) -> DNA9(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA9, PARP through DNA9.site, PARP.dna at `kPARP2`. | +| 989 | `Unlabeled` | one-way | DNA10, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA10(site~cdsb) + PARP(dna,liIII) -> DNA10(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA10, PARP through DNA10.site, PARP.dna at `kPARP2`. | +| 990 | `Unlabeled` | one-way | DNA11, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA11(site~cdsb) + PARP(dna,liIII) -> DNA11(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA11, PARP through DNA11.site, PARP.dna at `kPARP2`. | +| 991 | `Unlabeled` | one-way | DNA12, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA12(site~cdsb) + PARP(dna,liIII) -> DNA12(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA12, PARP through DNA12.site, PARP.dna at `kPARP2`. | +| 992 | `Unlabeled` | one-way | DNA13, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA13(site~cdsb) + PARP(dna,liIII) -> DNA13(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA13, PARP through DNA13.site, PARP.dna at `kPARP2`. | +| 993 | `Unlabeled` | one-way | DNA14, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA14(site~cdsb) + PARP(dna,liIII) -> DNA14(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA14, PARP through DNA14.site, PARP.dna at `kPARP2`. | +| 994 | `Unlabeled` | one-way | DNA15, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA15(site~cdsb) + PARP(dna,liIII) -> DNA15(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA15, PARP through DNA15.site, PARP.dna at `kPARP2`. | +| 995 | `Unlabeled` | one-way | DNA16, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA16(site~cdsb) + PARP(dna,liIII) -> DNA16(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA16, PARP through DNA16.site, PARP.dna at `kPARP2`. | +| 996 | `Unlabeled` | one-way | DNA17, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA17(site~cdsb) + PARP(dna,liIII) -> DNA17(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA17, PARP through DNA17.site, PARP.dna at `kPARP2`. | +| 997 | `Unlabeled` | one-way | DNA18, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA18(site~cdsb) + PARP(dna,liIII) -> DNA18(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA18, PARP through DNA18.site, PARP.dna at `kPARP2`. | +| 998 | `Unlabeled` | one-way | DNA19, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA19(site~cdsb) + PARP(dna,liIII) -> DNA19(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA19, PARP through DNA19.site, PARP.dna at `kPARP2`. | +| 999 | `Unlabeled` | one-way | DNA20, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA20(site~cdsb) + PARP(dna,liIII) -> DNA20(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA20, PARP through DNA20.site, PARP.dna at `kPARP2`. | +| 1000 | `Unlabeled` | one-way | DNA21, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA21(site~cdsb) + PARP(dna,liIII) -> DNA21(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA21, PARP through DNA21.site, PARP.dna at `kPARP2`. | + +### Rules 1001-1250 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1001 | `Unlabeled` | one-way | DNA22, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA22(site~cdsb) + PARP(dna,liIII) -> DNA22(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA22, PARP through DNA22.site, PARP.dna at `kPARP2`. | +| 1002 | `Unlabeled` | one-way | DNA23, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA23(site~cdsb) + PARP(dna,liIII) -> DNA23(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA23, PARP through DNA23.site, PARP.dna at `kPARP2`. | +| 1003 | `Unlabeled` | one-way | DNA24, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA24(site~cdsb) + PARP(dna,liIII) -> DNA24(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA24, PARP through DNA24.site, PARP.dna at `kPARP2`. | +| 1004 | `Unlabeled` | one-way | DNA25, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA25(site~cdsb) + PARP(dna,liIII) -> DNA25(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA25, PARP through DNA25.site, PARP.dna at `kPARP2`. | +| 1005 | `Unlabeled` | one-way | DNA26, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA26(site~cdsb) + PARP(dna,liIII) -> DNA26(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA26, PARP through DNA26.site, PARP.dna at `kPARP2`. | +| 1006 | `Unlabeled` | one-way | DNA27, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA27(site~cdsb) + PARP(dna,liIII) -> DNA27(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA27, PARP through DNA27.site, PARP.dna at `kPARP2`. | +| 1007 | `Unlabeled` | one-way | DNA28, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA28(site~cdsb) + PARP(dna,liIII) -> DNA28(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA28, PARP through DNA28.site, PARP.dna at `kPARP2`. | +| 1008 | `Unlabeled` | one-way | DNA29, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA29(site~cdsb) + PARP(dna,liIII) -> DNA29(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA29, PARP through DNA29.site, PARP.dna at `kPARP2`. | +| 1009 | `Unlabeled` | one-way | DNA30, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA30(site~cdsb) + PARP(dna,liIII) -> DNA30(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA30, PARP through DNA30.site, PARP.dna at `kPARP2`. | +| 1010 | `Unlabeled` | one-way | DNA31, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA31(site~cdsb) + PARP(dna,liIII) -> DNA31(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA31, PARP through DNA31.site, PARP.dna at `kPARP2`. | +| 1011 | `Unlabeled` | one-way | DNA32, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA32(site~cdsb) + PARP(dna,liIII) -> DNA32(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA32, PARP through DNA32.site, PARP.dna at `kPARP2`. | +| 1012 | `Unlabeled` | one-way | DNA33, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA33(site~cdsb) + PARP(dna,liIII) -> DNA33(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA33, PARP through DNA33.site, PARP.dna at `kPARP2`. | +| 1013 | `Unlabeled` | one-way | DNA34, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA34(site~cdsb) + PARP(dna,liIII) -> DNA34(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA34, PARP through DNA34.site, PARP.dna at `kPARP2`. | +| 1014 | `Unlabeled` | one-way | DNA35, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA35(site~cdsb) + PARP(dna,liIII) -> DNA35(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA35, PARP through DNA35.site, PARP.dna at `kPARP2`. | +| 1015 | `Unlabeled` | one-way | DNA36, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA36(site~cdsb) + PARP(dna,liIII) -> DNA36(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA36, PARP through DNA36.site, PARP.dna at `kPARP2`. | +| 1016 | `Unlabeled` | one-way | DNA37, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA37(site~cdsb) + PARP(dna,liIII) -> DNA37(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA37, PARP through DNA37.site, PARP.dna at `kPARP2`. | +| 1017 | `Unlabeled` | one-way | DNA38, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA38(site~cdsb) + PARP(dna,liIII) -> DNA38(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA38, PARP through DNA38.site, PARP.dna at `kPARP2`. | +| 1018 | `Unlabeled` | one-way | DNA39, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA39(site~cdsb) + PARP(dna,liIII) -> DNA39(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA39, PARP through DNA39.site, PARP.dna at `kPARP2`. | +| 1019 | `Unlabeled` | one-way | DNA40, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA40(site~cdsb) + PARP(dna,liIII) -> DNA40(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA40, PARP through DNA40.site, PARP.dna at `kPARP2`. | +| 1020 | `Unlabeled` | one-way | DNA41, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA41(site~cdsb) + PARP(dna,liIII) -> DNA41(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA41, PARP through DNA41.site, PARP.dna at `kPARP2`. | +| 1021 | `Unlabeled` | one-way | DNA42, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA42(site~cdsb) + PARP(dna,liIII) -> DNA42(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA42, PARP through DNA42.site, PARP.dna at `kPARP2`. | +| 1022 | `Unlabeled` | one-way | DNA43, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA43(site~cdsb) + PARP(dna,liIII) -> DNA43(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA43, PARP through DNA43.site, PARP.dna at `kPARP2`. | +| 1023 | `Unlabeled` | one-way | DNA44, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA44(site~cdsb) + PARP(dna,liIII) -> DNA44(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA44, PARP through DNA44.site, PARP.dna at `kPARP2`. | +| 1024 | `Unlabeled` | one-way | DNA45, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA45(site~cdsb) + PARP(dna,liIII) -> DNA45(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA45, PARP through DNA45.site, PARP.dna at `kPARP2`. | +| 1025 | `Unlabeled` | one-way | DNA46, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA46(site~cdsb) + PARP(dna,liIII) -> DNA46(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA46, PARP through DNA46.site, PARP.dna at `kPARP2`. | +| 1026 | `Unlabeled` | one-way | DNA47, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA47(site~cdsb) + PARP(dna,liIII) -> DNA47(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA47, PARP through DNA47.site, PARP.dna at `kPARP2`. | +| 1027 | `Unlabeled` | one-way | DNA48, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA48(site~cdsb) + PARP(dna,liIII) -> DNA48(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA48, PARP through DNA48.site, PARP.dna at `kPARP2`. | +| 1028 | `Unlabeled` | one-way | DNA49, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA49(site~cdsb) + PARP(dna,liIII) -> DNA49(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA49, PARP through DNA49.site, PARP.dna at `kPARP2`. | +| 1029 | `Unlabeled` | one-way | DNA50, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA50(site~cdsb) + PARP(dna,liIII) -> DNA50(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA50, PARP through DNA50.site, PARP.dna at `kPARP2`. | +| 1030 | `Unlabeled` | one-way | DNA1, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA1(site!1~sdsb).PARP(dna!1,liIII) -> DNA1(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA1, PARP by freeing DNA1.site, PARP.dna at `kdPARP1`. | +| 1031 | `Unlabeled` | one-way | DNA2, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA2(site!1~sdsb).PARP(dna!1,liIII) -> DNA2(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA2, PARP by freeing DNA2.site, PARP.dna at `kdPARP1`. | +| 1032 | `Unlabeled` | one-way | DNA3, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA3(site!1~sdsb).PARP(dna!1,liIII) -> DNA3(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA3, PARP by freeing DNA3.site, PARP.dna at `kdPARP1`. | +| 1033 | `Unlabeled` | one-way | DNA4, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA4(site!1~sdsb).PARP(dna!1,liIII) -> DNA4(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA4, PARP by freeing DNA4.site, PARP.dna at `kdPARP1`. | +| 1034 | `Unlabeled` | one-way | DNA5, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA5(site!1~sdsb).PARP(dna!1,liIII) -> DNA5(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA5, PARP by freeing DNA5.site, PARP.dna at `kdPARP1`. | +| 1035 | `Unlabeled` | one-way | DNA6, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA6(site!1~sdsb).PARP(dna!1,liIII) -> DNA6(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA6, PARP by freeing DNA6.site, PARP.dna at `kdPARP1`. | +| 1036 | `Unlabeled` | one-way | DNA7, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA7(site!1~sdsb).PARP(dna!1,liIII) -> DNA7(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA7, PARP by freeing DNA7.site, PARP.dna at `kdPARP1`. | +| 1037 | `Unlabeled` | one-way | DNA8, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA8(site!1~sdsb).PARP(dna!1,liIII) -> DNA8(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA8, PARP by freeing DNA8.site, PARP.dna at `kdPARP1`. | +| 1038 | `Unlabeled` | one-way | DNA9, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA9(site!1~sdsb).PARP(dna!1,liIII) -> DNA9(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA9, PARP by freeing DNA9.site, PARP.dna at `kdPARP1`. | +| 1039 | `Unlabeled` | one-way | DNA10, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA10(site!1~sdsb).PARP(dna!1,liIII) -> DNA10(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA10, PARP by freeing DNA10.site, PARP.dna at `kdPARP1`. | +| 1040 | `Unlabeled` | one-way | DNA11, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA11(site!1~sdsb).PARP(dna!1,liIII) -> DNA11(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA11, PARP by freeing DNA11.site, PARP.dna at `kdPARP1`. | +| 1041 | `Unlabeled` | one-way | DNA12, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA12(site!1~sdsb).PARP(dna!1,liIII) -> DNA12(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA12, PARP by freeing DNA12.site, PARP.dna at `kdPARP1`. | +| 1042 | `Unlabeled` | one-way | DNA13, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA13(site!1~sdsb).PARP(dna!1,liIII) -> DNA13(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA13, PARP by freeing DNA13.site, PARP.dna at `kdPARP1`. | +| 1043 | `Unlabeled` | one-way | DNA14, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA14(site!1~sdsb).PARP(dna!1,liIII) -> DNA14(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA14, PARP by freeing DNA14.site, PARP.dna at `kdPARP1`. | +| 1044 | `Unlabeled` | one-way | DNA15, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA15(site!1~sdsb).PARP(dna!1,liIII) -> DNA15(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA15, PARP by freeing DNA15.site, PARP.dna at `kdPARP1`. | +| 1045 | `Unlabeled` | one-way | DNA16, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA16(site!1~sdsb).PARP(dna!1,liIII) -> DNA16(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA16, PARP by freeing DNA16.site, PARP.dna at `kdPARP1`. | +| 1046 | `Unlabeled` | one-way | DNA17, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA17(site!1~sdsb).PARP(dna!1,liIII) -> DNA17(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA17, PARP by freeing DNA17.site, PARP.dna at `kdPARP1`. | +| 1047 | `Unlabeled` | one-way | DNA18, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA18(site!1~sdsb).PARP(dna!1,liIII) -> DNA18(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA18, PARP by freeing DNA18.site, PARP.dna at `kdPARP1`. | +| 1048 | `Unlabeled` | one-way | DNA19, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA19(site!1~sdsb).PARP(dna!1,liIII) -> DNA19(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA19, PARP by freeing DNA19.site, PARP.dna at `kdPARP1`. | +| 1049 | `Unlabeled` | one-way | DNA20, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA20(site!1~sdsb).PARP(dna!1,liIII) -> DNA20(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA20, PARP by freeing DNA20.site, PARP.dna at `kdPARP1`. | +| 1050 | `Unlabeled` | one-way | DNA21, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA21(site!1~sdsb).PARP(dna!1,liIII) -> DNA21(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA21, PARP by freeing DNA21.site, PARP.dna at `kdPARP1`. | +| 1051 | `Unlabeled` | one-way | DNA22, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA22(site!1~sdsb).PARP(dna!1,liIII) -> DNA22(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA22, PARP by freeing DNA22.site, PARP.dna at `kdPARP1`. | +| 1052 | `Unlabeled` | one-way | DNA23, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA23(site!1~sdsb).PARP(dna!1,liIII) -> DNA23(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA23, PARP by freeing DNA23.site, PARP.dna at `kdPARP1`. | +| 1053 | `Unlabeled` | one-way | DNA24, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA24(site!1~sdsb).PARP(dna!1,liIII) -> DNA24(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA24, PARP by freeing DNA24.site, PARP.dna at `kdPARP1`. | +| 1054 | `Unlabeled` | one-way | DNA25, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA25(site!1~sdsb).PARP(dna!1,liIII) -> DNA25(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA25, PARP by freeing DNA25.site, PARP.dna at `kdPARP1`. | +| 1055 | `Unlabeled` | one-way | DNA26, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA26(site!1~sdsb).PARP(dna!1,liIII) -> DNA26(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA26, PARP by freeing DNA26.site, PARP.dna at `kdPARP1`. | +| 1056 | `Unlabeled` | one-way | DNA27, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA27(site!1~sdsb).PARP(dna!1,liIII) -> DNA27(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA27, PARP by freeing DNA27.site, PARP.dna at `kdPARP1`. | +| 1057 | `Unlabeled` | one-way | DNA28, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA28(site!1~sdsb).PARP(dna!1,liIII) -> DNA28(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA28, PARP by freeing DNA28.site, PARP.dna at `kdPARP1`. | +| 1058 | `Unlabeled` | one-way | DNA29, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA29(site!1~sdsb).PARP(dna!1,liIII) -> DNA29(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA29, PARP by freeing DNA29.site, PARP.dna at `kdPARP1`. | +| 1059 | `Unlabeled` | one-way | DNA30, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA30(site!1~sdsb).PARP(dna!1,liIII) -> DNA30(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA30, PARP by freeing DNA30.site, PARP.dna at `kdPARP1`. | +| 1060 | `Unlabeled` | one-way | DNA31, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA31(site!1~sdsb).PARP(dna!1,liIII) -> DNA31(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA31, PARP by freeing DNA31.site, PARP.dna at `kdPARP1`. | +| 1061 | `Unlabeled` | one-way | DNA32, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA32(site!1~sdsb).PARP(dna!1,liIII) -> DNA32(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA32, PARP by freeing DNA32.site, PARP.dna at `kdPARP1`. | +| 1062 | `Unlabeled` | one-way | DNA33, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA33(site!1~sdsb).PARP(dna!1,liIII) -> DNA33(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA33, PARP by freeing DNA33.site, PARP.dna at `kdPARP1`. | +| 1063 | `Unlabeled` | one-way | DNA34, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA34(site!1~sdsb).PARP(dna!1,liIII) -> DNA34(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA34, PARP by freeing DNA34.site, PARP.dna at `kdPARP1`. | +| 1064 | `Unlabeled` | one-way | DNA35, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA35(site!1~sdsb).PARP(dna!1,liIII) -> DNA35(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA35, PARP by freeing DNA35.site, PARP.dna at `kdPARP1`. | +| 1065 | `Unlabeled` | one-way | DNA36, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA36(site!1~sdsb).PARP(dna!1,liIII) -> DNA36(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA36, PARP by freeing DNA36.site, PARP.dna at `kdPARP1`. | +| 1066 | `Unlabeled` | one-way | DNA37, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA37(site!1~sdsb).PARP(dna!1,liIII) -> DNA37(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA37, PARP by freeing DNA37.site, PARP.dna at `kdPARP1`. | +| 1067 | `Unlabeled` | one-way | DNA38, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA38(site!1~sdsb).PARP(dna!1,liIII) -> DNA38(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA38, PARP by freeing DNA38.site, PARP.dna at `kdPARP1`. | +| 1068 | `Unlabeled` | one-way | DNA39, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA39(site!1~sdsb).PARP(dna!1,liIII) -> DNA39(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA39, PARP by freeing DNA39.site, PARP.dna at `kdPARP1`. | +| 1069 | `Unlabeled` | one-way | DNA40, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA40(site!1~sdsb).PARP(dna!1,liIII) -> DNA40(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA40, PARP by freeing DNA40.site, PARP.dna at `kdPARP1`. | +| 1070 | `Unlabeled` | one-way | DNA41, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA41(site!1~sdsb).PARP(dna!1,liIII) -> DNA41(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA41, PARP by freeing DNA41.site, PARP.dna at `kdPARP1`. | +| 1071 | `Unlabeled` | one-way | DNA42, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA42(site!1~sdsb).PARP(dna!1,liIII) -> DNA42(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA42, PARP by freeing DNA42.site, PARP.dna at `kdPARP1`. | +| 1072 | `Unlabeled` | one-way | DNA43, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA43(site!1~sdsb).PARP(dna!1,liIII) -> DNA43(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA43, PARP by freeing DNA43.site, PARP.dna at `kdPARP1`. | +| 1073 | `Unlabeled` | one-way | DNA44, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA44(site!1~sdsb).PARP(dna!1,liIII) -> DNA44(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA44, PARP by freeing DNA44.site, PARP.dna at `kdPARP1`. | +| 1074 | `Unlabeled` | one-way | DNA45, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA45(site!1~sdsb).PARP(dna!1,liIII) -> DNA45(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA45, PARP by freeing DNA45.site, PARP.dna at `kdPARP1`. | +| 1075 | `Unlabeled` | one-way | DNA46, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA46(site!1~sdsb).PARP(dna!1,liIII) -> DNA46(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA46, PARP by freeing DNA46.site, PARP.dna at `kdPARP1`. | +| 1076 | `Unlabeled` | one-way | DNA47, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA47(site!1~sdsb).PARP(dna!1,liIII) -> DNA47(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA47, PARP by freeing DNA47.site, PARP.dna at `kdPARP1`. | +| 1077 | `Unlabeled` | one-way | DNA48, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA48(site!1~sdsb).PARP(dna!1,liIII) -> DNA48(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA48, PARP by freeing DNA48.site, PARP.dna at `kdPARP1`. | +| 1078 | `Unlabeled` | one-way | DNA49, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA49(site!1~sdsb).PARP(dna!1,liIII) -> DNA49(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA49, PARP by freeing DNA49.site, PARP.dna at `kdPARP1`. | +| 1079 | `Unlabeled` | one-way | DNA50, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA50(site!1~sdsb).PARP(dna!1,liIII) -> DNA50(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA50, PARP by freeing DNA50.site, PARP.dna at `kdPARP1`. | +| 1080 | `Unlabeled` | one-way | DNA1, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA1(site!1~cdsb).PARP(dna!1,liIII) -> DNA1(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA1, PARP by freeing DNA1.site, PARP.dna at `kdPARP2`. | +| 1081 | `Unlabeled` | one-way | DNA2, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA2(site!1~cdsb).PARP(dna!1,liIII) -> DNA2(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA2, PARP by freeing DNA2.site, PARP.dna at `kdPARP2`. | +| 1082 | `Unlabeled` | one-way | DNA3, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA3(site!1~cdsb).PARP(dna!1,liIII) -> DNA3(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA3, PARP by freeing DNA3.site, PARP.dna at `kdPARP2`. | +| 1083 | `Unlabeled` | one-way | DNA4, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA4(site!1~cdsb).PARP(dna!1,liIII) -> DNA4(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA4, PARP by freeing DNA4.site, PARP.dna at `kdPARP2`. | +| 1084 | `Unlabeled` | one-way | DNA5, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA5(site!1~cdsb).PARP(dna!1,liIII) -> DNA5(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA5, PARP by freeing DNA5.site, PARP.dna at `kdPARP2`. | +| 1085 | `Unlabeled` | one-way | DNA6, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA6(site!1~cdsb).PARP(dna!1,liIII) -> DNA6(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA6, PARP by freeing DNA6.site, PARP.dna at `kdPARP2`. | +| 1086 | `Unlabeled` | one-way | DNA7, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA7(site!1~cdsb).PARP(dna!1,liIII) -> DNA7(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA7, PARP by freeing DNA7.site, PARP.dna at `kdPARP2`. | +| 1087 | `Unlabeled` | one-way | DNA8, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA8(site!1~cdsb).PARP(dna!1,liIII) -> DNA8(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA8, PARP by freeing DNA8.site, PARP.dna at `kdPARP2`. | +| 1088 | `Unlabeled` | one-way | DNA9, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA9(site!1~cdsb).PARP(dna!1,liIII) -> DNA9(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA9, PARP by freeing DNA9.site, PARP.dna at `kdPARP2`. | +| 1089 | `Unlabeled` | one-way | DNA10, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA10(site!1~cdsb).PARP(dna!1,liIII) -> DNA10(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA10, PARP by freeing DNA10.site, PARP.dna at `kdPARP2`. | +| 1090 | `Unlabeled` | one-way | DNA11, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA11(site!1~cdsb).PARP(dna!1,liIII) -> DNA11(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA11, PARP by freeing DNA11.site, PARP.dna at `kdPARP2`. | +| 1091 | `Unlabeled` | one-way | DNA12, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA12(site!1~cdsb).PARP(dna!1,liIII) -> DNA12(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA12, PARP by freeing DNA12.site, PARP.dna at `kdPARP2`. | +| 1092 | `Unlabeled` | one-way | DNA13, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA13(site!1~cdsb).PARP(dna!1,liIII) -> DNA13(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA13, PARP by freeing DNA13.site, PARP.dna at `kdPARP2`. | +| 1093 | `Unlabeled` | one-way | DNA14, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA14(site!1~cdsb).PARP(dna!1,liIII) -> DNA14(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA14, PARP by freeing DNA14.site, PARP.dna at `kdPARP2`. | +| 1094 | `Unlabeled` | one-way | DNA15, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA15(site!1~cdsb).PARP(dna!1,liIII) -> DNA15(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA15, PARP by freeing DNA15.site, PARP.dna at `kdPARP2`. | +| 1095 | `Unlabeled` | one-way | DNA16, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA16(site!1~cdsb).PARP(dna!1,liIII) -> DNA16(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA16, PARP by freeing DNA16.site, PARP.dna at `kdPARP2`. | +| 1096 | `Unlabeled` | one-way | DNA17, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA17(site!1~cdsb).PARP(dna!1,liIII) -> DNA17(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA17, PARP by freeing DNA17.site, PARP.dna at `kdPARP2`. | +| 1097 | `Unlabeled` | one-way | DNA18, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA18(site!1~cdsb).PARP(dna!1,liIII) -> DNA18(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA18, PARP by freeing DNA18.site, PARP.dna at `kdPARP2`. | +| 1098 | `Unlabeled` | one-way | DNA19, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA19(site!1~cdsb).PARP(dna!1,liIII) -> DNA19(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA19, PARP by freeing DNA19.site, PARP.dna at `kdPARP2`. | +| 1099 | `Unlabeled` | one-way | DNA20, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA20(site!1~cdsb).PARP(dna!1,liIII) -> DNA20(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA20, PARP by freeing DNA20.site, PARP.dna at `kdPARP2`. | +| 1100 | `Unlabeled` | one-way | DNA21, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA21(site!1~cdsb).PARP(dna!1,liIII) -> DNA21(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA21, PARP by freeing DNA21.site, PARP.dna at `kdPARP2`. | +| 1101 | `Unlabeled` | one-way | DNA22, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA22(site!1~cdsb).PARP(dna!1,liIII) -> DNA22(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA22, PARP by freeing DNA22.site, PARP.dna at `kdPARP2`. | +| 1102 | `Unlabeled` | one-way | DNA23, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA23(site!1~cdsb).PARP(dna!1,liIII) -> DNA23(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA23, PARP by freeing DNA23.site, PARP.dna at `kdPARP2`. | +| 1103 | `Unlabeled` | one-way | DNA24, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA24(site!1~cdsb).PARP(dna!1,liIII) -> DNA24(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA24, PARP by freeing DNA24.site, PARP.dna at `kdPARP2`. | +| 1104 | `Unlabeled` | one-way | DNA25, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA25(site!1~cdsb).PARP(dna!1,liIII) -> DNA25(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA25, PARP by freeing DNA25.site, PARP.dna at `kdPARP2`. | +| 1105 | `Unlabeled` | one-way | DNA26, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA26(site!1~cdsb).PARP(dna!1,liIII) -> DNA26(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA26, PARP by freeing DNA26.site, PARP.dna at `kdPARP2`. | +| 1106 | `Unlabeled` | one-way | DNA27, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA27(site!1~cdsb).PARP(dna!1,liIII) -> DNA27(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA27, PARP by freeing DNA27.site, PARP.dna at `kdPARP2`. | +| 1107 | `Unlabeled` | one-way | DNA28, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA28(site!1~cdsb).PARP(dna!1,liIII) -> DNA28(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA28, PARP by freeing DNA28.site, PARP.dna at `kdPARP2`. | +| 1108 | `Unlabeled` | one-way | DNA29, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA29(site!1~cdsb).PARP(dna!1,liIII) -> DNA29(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA29, PARP by freeing DNA29.site, PARP.dna at `kdPARP2`. | +| 1109 | `Unlabeled` | one-way | DNA30, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA30(site!1~cdsb).PARP(dna!1,liIII) -> DNA30(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA30, PARP by freeing DNA30.site, PARP.dna at `kdPARP2`. | +| 1110 | `Unlabeled` | one-way | DNA31, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA31(site!1~cdsb).PARP(dna!1,liIII) -> DNA31(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA31, PARP by freeing DNA31.site, PARP.dna at `kdPARP2`. | +| 1111 | `Unlabeled` | one-way | DNA32, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA32(site!1~cdsb).PARP(dna!1,liIII) -> DNA32(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA32, PARP by freeing DNA32.site, PARP.dna at `kdPARP2`. | +| 1112 | `Unlabeled` | one-way | DNA33, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA33(site!1~cdsb).PARP(dna!1,liIII) -> DNA33(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA33, PARP by freeing DNA33.site, PARP.dna at `kdPARP2`. | +| 1113 | `Unlabeled` | one-way | DNA34, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA34(site!1~cdsb).PARP(dna!1,liIII) -> DNA34(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA34, PARP by freeing DNA34.site, PARP.dna at `kdPARP2`. | +| 1114 | `Unlabeled` | one-way | DNA35, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA35(site!1~cdsb).PARP(dna!1,liIII) -> DNA35(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA35, PARP by freeing DNA35.site, PARP.dna at `kdPARP2`. | +| 1115 | `Unlabeled` | one-way | DNA36, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA36(site!1~cdsb).PARP(dna!1,liIII) -> DNA36(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA36, PARP by freeing DNA36.site, PARP.dna at `kdPARP2`. | +| 1116 | `Unlabeled` | one-way | DNA37, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA37(site!1~cdsb).PARP(dna!1,liIII) -> DNA37(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA37, PARP by freeing DNA37.site, PARP.dna at `kdPARP2`. | +| 1117 | `Unlabeled` | one-way | DNA38, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA38(site!1~cdsb).PARP(dna!1,liIII) -> DNA38(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA38, PARP by freeing DNA38.site, PARP.dna at `kdPARP2`. | +| 1118 | `Unlabeled` | one-way | DNA39, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA39(site!1~cdsb).PARP(dna!1,liIII) -> DNA39(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA39, PARP by freeing DNA39.site, PARP.dna at `kdPARP2`. | +| 1119 | `Unlabeled` | one-way | DNA40, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA40(site!1~cdsb).PARP(dna!1,liIII) -> DNA40(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA40, PARP by freeing DNA40.site, PARP.dna at `kdPARP2`. | +| 1120 | `Unlabeled` | one-way | DNA41, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA41(site!1~cdsb).PARP(dna!1,liIII) -> DNA41(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA41, PARP by freeing DNA41.site, PARP.dna at `kdPARP2`. | +| 1121 | `Unlabeled` | one-way | DNA42, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA42(site!1~cdsb).PARP(dna!1,liIII) -> DNA42(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA42, PARP by freeing DNA42.site, PARP.dna at `kdPARP2`. | +| 1122 | `Unlabeled` | one-way | DNA43, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA43(site!1~cdsb).PARP(dna!1,liIII) -> DNA43(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA43, PARP by freeing DNA43.site, PARP.dna at `kdPARP2`. | +| 1123 | `Unlabeled` | one-way | DNA44, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA44(site!1~cdsb).PARP(dna!1,liIII) -> DNA44(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA44, PARP by freeing DNA44.site, PARP.dna at `kdPARP2`. | +| 1124 | `Unlabeled` | one-way | DNA45, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA45(site!1~cdsb).PARP(dna!1,liIII) -> DNA45(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA45, PARP by freeing DNA45.site, PARP.dna at `kdPARP2`. | +| 1125 | `Unlabeled` | one-way | DNA46, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA46(site!1~cdsb).PARP(dna!1,liIII) -> DNA46(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA46, PARP by freeing DNA46.site, PARP.dna at `kdPARP2`. | +| 1126 | `Unlabeled` | one-way | DNA47, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA47(site!1~cdsb).PARP(dna!1,liIII) -> DNA47(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA47, PARP by freeing DNA47.site, PARP.dna at `kdPARP2`. | +| 1127 | `Unlabeled` | one-way | DNA48, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA48(site!1~cdsb).PARP(dna!1,liIII) -> DNA48(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA48, PARP by freeing DNA48.site, PARP.dna at `kdPARP2`. | +| 1128 | `Unlabeled` | one-way | DNA49, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA49(site!1~cdsb).PARP(dna!1,liIII) -> DNA49(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA49, PARP by freeing DNA49.site, PARP.dna at `kdPARP2`. | +| 1129 | `Unlabeled` | one-way | DNA50, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA50(site!1~cdsb).PARP(dna!1,liIII) -> DNA50(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA50, PARP by freeing DNA50.site, PARP.dna at `kdPARP2`. | +| 1130 | `Unlabeled` | one-way | DNA1, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA1(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA1(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA1, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1131 | `Unlabeled` | one-way | DNA2, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA2(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA2(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA2, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1132 | `Unlabeled` | one-way | DNA3, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA3(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA3(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA3, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1133 | `Unlabeled` | one-way | DNA4, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA4(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA4(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA4, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1134 | `Unlabeled` | one-way | DNA5, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA5(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA5(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA5, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1135 | `Unlabeled` | one-way | DNA6, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA6(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA6(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA6, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1136 | `Unlabeled` | one-way | DNA7, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA7(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA7(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA7, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1137 | `Unlabeled` | one-way | DNA8, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA8(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA8(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA8, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1138 | `Unlabeled` | one-way | DNA9, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA9(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA9(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA9, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1139 | `Unlabeled` | one-way | DNA10, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA10(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA10(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA10, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1140 | `Unlabeled` | one-way | DNA11, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA11(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA11(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA11, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1141 | `Unlabeled` | one-way | DNA12, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA12(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA12(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA12, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1142 | `Unlabeled` | one-way | DNA13, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA13(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA13(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA13, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1143 | `Unlabeled` | one-way | DNA14, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA14(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA14(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA14, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1144 | `Unlabeled` | one-way | DNA15, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA15(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA15(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA15, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1145 | `Unlabeled` | one-way | DNA16, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA16(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA16(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA16, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1146 | `Unlabeled` | one-way | DNA17, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA17(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA17(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA17, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1147 | `Unlabeled` | one-way | DNA18, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA18(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA18(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA18, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1148 | `Unlabeled` | one-way | DNA19, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA19(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA19(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA19, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1149 | `Unlabeled` | one-way | DNA20, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA20(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA20(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA20, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1150 | `Unlabeled` | one-way | DNA21, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA21(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA21(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA21, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1151 | `Unlabeled` | one-way | DNA22, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA22(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA22(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA22, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1152 | `Unlabeled` | one-way | DNA23, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA23(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA23(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA23, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1153 | `Unlabeled` | one-way | DNA24, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA24(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA24(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA24, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1154 | `Unlabeled` | one-way | DNA25, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA25(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA25(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA25, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1155 | `Unlabeled` | one-way | DNA26, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA26(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA26(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA26, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1156 | `Unlabeled` | one-way | DNA27, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA27(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA27(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA27, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1157 | `Unlabeled` | one-way | DNA28, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA28(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA28(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA28, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1158 | `Unlabeled` | one-way | DNA29, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA29(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA29(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA29, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1159 | `Unlabeled` | one-way | DNA30, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA30(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA30(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA30, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1160 | `Unlabeled` | one-way | DNA31, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA31(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA31(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA31, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1161 | `Unlabeled` | one-way | DNA32, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA32(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA32(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA32, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1162 | `Unlabeled` | one-way | DNA33, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA33(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA33(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA33, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1163 | `Unlabeled` | one-way | DNA34, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA34(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA34(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA34, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1164 | `Unlabeled` | one-way | DNA35, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA35(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA35(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA35, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1165 | `Unlabeled` | one-way | DNA36, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA36(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA36(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA36, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1166 | `Unlabeled` | one-way | DNA37, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA37(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA37(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA37, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1167 | `Unlabeled` | one-way | DNA38, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA38(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA38(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA38, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1168 | `Unlabeled` | one-way | DNA39, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA39(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA39(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA39, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1169 | `Unlabeled` | one-way | DNA40, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA40(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA40(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA40, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1170 | `Unlabeled` | one-way | DNA41, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA41(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA41(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA41, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1171 | `Unlabeled` | one-way | DNA42, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA42(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA42(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA42, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1172 | `Unlabeled` | one-way | DNA43, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA43(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA43(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA43, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1173 | `Unlabeled` | one-way | DNA44, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA44(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA44(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA44, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1174 | `Unlabeled` | one-way | DNA45, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA45(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA45(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA45, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1175 | `Unlabeled` | one-way | DNA46, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA46(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA46(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA46, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1176 | `Unlabeled` | one-way | DNA47, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA47(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA47(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA47, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1177 | `Unlabeled` | one-way | DNA48, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA48(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA48(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA48, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1178 | `Unlabeled` | one-way | DNA49, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA49(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA49(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA49, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1179 | `Unlabeled` | one-way | DNA50, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA50(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA50(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA50, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1180 | `Unlabeled` | one-way | DNA1, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA1(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA1(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA1, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1181 | `Unlabeled` | one-way | DNA2, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA2(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA2(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA2, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1182 | `Unlabeled` | one-way | DNA3, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA3(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA3(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA3, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1183 | `Unlabeled` | one-way | DNA4, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA4(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA4(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA4, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1184 | `Unlabeled` | one-way | DNA5, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA5(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA5(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA5, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1185 | `Unlabeled` | one-way | DNA6, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA6(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA6(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA6, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1186 | `Unlabeled` | one-way | DNA7, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA7(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA7(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA7, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1187 | `Unlabeled` | one-way | DNA8, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA8(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA8(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA8, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1188 | `Unlabeled` | one-way | DNA9, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA9(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA9(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA9, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1189 | `Unlabeled` | one-way | DNA10, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA10(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA10(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA10, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1190 | `Unlabeled` | one-way | DNA11, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA11(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA11(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA11, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1191 | `Unlabeled` | one-way | DNA12, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA12(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA12(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA12, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1192 | `Unlabeled` | one-way | DNA13, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA13(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA13(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA13, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1193 | `Unlabeled` | one-way | DNA14, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA14(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA14(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA14, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1194 | `Unlabeled` | one-way | DNA15, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA15(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA15(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA15, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1195 | `Unlabeled` | one-way | DNA16, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA16(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA16(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA16, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1196 | `Unlabeled` | one-way | DNA17, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA17(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA17(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA17, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1197 | `Unlabeled` | one-way | DNA18, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA18(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA18(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA18, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1198 | `Unlabeled` | one-way | DNA19, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA19(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA19(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA19, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1199 | `Unlabeled` | one-way | DNA20, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA20(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA20(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA20, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1200 | `Unlabeled` | one-way | DNA21, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA21(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA21(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA21, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1201 | `Unlabeled` | one-way | DNA22, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA22(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA22(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA22, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1202 | `Unlabeled` | one-way | DNA23, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA23(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA23(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA23, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1203 | `Unlabeled` | one-way | DNA24, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA24(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA24(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA24, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1204 | `Unlabeled` | one-way | DNA25, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA25(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA25(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA25, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1205 | `Unlabeled` | one-way | DNA26, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA26(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA26(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA26, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1206 | `Unlabeled` | one-way | DNA27, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA27(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA27(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA27, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1207 | `Unlabeled` | one-way | DNA28, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA28(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA28(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA28, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1208 | `Unlabeled` | one-way | DNA29, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA29(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA29(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA29, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1209 | `Unlabeled` | one-way | DNA30, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA30(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA30(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA30, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1210 | `Unlabeled` | one-way | DNA31, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA31(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA31(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA31, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1211 | `Unlabeled` | one-way | DNA32, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA32(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA32(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA32, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1212 | `Unlabeled` | one-way | DNA33, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA33(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA33(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA33, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1213 | `Unlabeled` | one-way | DNA34, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA34(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA34(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA34, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1214 | `Unlabeled` | one-way | DNA35, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA35(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA35(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA35, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1215 | `Unlabeled` | one-way | DNA36, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA36(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA36(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA36, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1216 | `Unlabeled` | one-way | DNA37, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA37(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA37(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA37, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1217 | `Unlabeled` | one-way | DNA38, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA38(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA38(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA38, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1218 | `Unlabeled` | one-way | DNA39, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA39(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA39(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA39, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1219 | `Unlabeled` | one-way | DNA40, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA40(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA40(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA40, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1220 | `Unlabeled` | one-way | DNA41, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA41(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA41(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA41, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1221 | `Unlabeled` | one-way | DNA42, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA42(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA42(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA42, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1222 | `Unlabeled` | one-way | DNA43, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA43(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA43(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA43, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1223 | `Unlabeled` | one-way | DNA44, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA44(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA44(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA44, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1224 | `Unlabeled` | one-way | DNA45, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA45(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA45(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA45, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1225 | `Unlabeled` | one-way | DNA46, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA46(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA46(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA46, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1226 | `Unlabeled` | one-way | DNA47, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA47(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA47(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA47, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1227 | `Unlabeled` | one-way | DNA48, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA48(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA48(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA48, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1228 | `Unlabeled` | one-way | DNA49, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA49(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA49(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA49, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1229 | `Unlabeled` | one-way | DNA50, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA50(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA50(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA50, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1230 | `Unlabeled` | one-way | DNA1, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA1(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA1(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA1, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1231 | `Unlabeled` | one-way | DNA2, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA2(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA2(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA2, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1232 | `Unlabeled` | one-way | DNA3, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA3(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA3(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA3, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1233 | `Unlabeled` | one-way | DNA4, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA4(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA4(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA4, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1234 | `Unlabeled` | one-way | DNA5, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA5(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA5(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA5, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1235 | `Unlabeled` | one-way | DNA6, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA6(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA6(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA6, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1236 | `Unlabeled` | one-way | DNA7, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA7(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA7(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA7, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1237 | `Unlabeled` | one-way | DNA8, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA8(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA8(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA8, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1238 | `Unlabeled` | one-way | DNA9, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA9(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA9(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA9, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1239 | `Unlabeled` | one-way | DNA10, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA10(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA10(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA10, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1240 | `Unlabeled` | one-way | DNA11, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA11(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA11(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA11, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1241 | `Unlabeled` | one-way | DNA12, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA12(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA12(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA12, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1242 | `Unlabeled` | one-way | DNA13, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA13(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA13(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA13, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1243 | `Unlabeled` | one-way | DNA14, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA14(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA14(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA14, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1244 | `Unlabeled` | one-way | DNA15, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA15(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA15(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA15, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1245 | `Unlabeled` | one-way | DNA16, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA16(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA16(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA16, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1246 | `Unlabeled` | one-way | DNA17, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA17(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA17(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA17, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1247 | `Unlabeled` | one-way | DNA18, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA18(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA18(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA18, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1248 | `Unlabeled` | one-way | DNA19, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA19(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA19(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA19, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1249 | `Unlabeled` | one-way | DNA20, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA20(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA20(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA20, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1250 | `Unlabeled` | one-way | DNA21, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA21(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA21(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA21, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | + +### Rules 1251-1500 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1251 | `Unlabeled` | one-way | DNA22, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA22(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA22(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA22, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1252 | `Unlabeled` | one-way | DNA23, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA23(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA23(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA23, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1253 | `Unlabeled` | one-way | DNA24, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA24(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA24(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA24, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1254 | `Unlabeled` | one-way | DNA25, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA25(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA25(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA25, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1255 | `Unlabeled` | one-way | DNA26, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA26(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA26(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA26, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1256 | `Unlabeled` | one-way | DNA27, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA27(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA27(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA27, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1257 | `Unlabeled` | one-way | DNA28, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA28(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA28(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA28, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1258 | `Unlabeled` | one-way | DNA29, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA29(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA29(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA29, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1259 | `Unlabeled` | one-way | DNA30, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA30(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA30(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA30, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1260 | `Unlabeled` | one-way | DNA31, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA31(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA31(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA31, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1261 | `Unlabeled` | one-way | DNA32, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA32(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA32(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA32, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1262 | `Unlabeled` | one-way | DNA33, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA33(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA33(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA33, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1263 | `Unlabeled` | one-way | DNA34, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA34(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA34(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA34, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1264 | `Unlabeled` | one-way | DNA35, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA35(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA35(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA35, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1265 | `Unlabeled` | one-way | DNA36, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA36(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA36(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA36, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1266 | `Unlabeled` | one-way | DNA37, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA37(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA37(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA37, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1267 | `Unlabeled` | one-way | DNA38, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA38(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA38(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA38, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1268 | `Unlabeled` | one-way | DNA39, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA39(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA39(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA39, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1269 | `Unlabeled` | one-way | DNA40, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA40(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA40(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA40, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1270 | `Unlabeled` | one-way | DNA41, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA41(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA41(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA41, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1271 | `Unlabeled` | one-way | DNA42, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA42(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA42(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA42, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1272 | `Unlabeled` | one-way | DNA43, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA43(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA43(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA43, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1273 | `Unlabeled` | one-way | DNA44, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA44(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA44(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA44, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1274 | `Unlabeled` | one-way | DNA45, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA45(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA45(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA45, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1275 | `Unlabeled` | one-way | DNA46, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA46(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA46(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA46, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1276 | `Unlabeled` | one-way | DNA47, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA47(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA47(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA47, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1277 | `Unlabeled` | one-way | DNA48, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA48(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA48(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA48, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1278 | `Unlabeled` | one-way | DNA49, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA49(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA49(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA49, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1279 | `Unlabeled` | one-way | DNA50, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA50(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA50(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA50, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1280 | `Unlabeled` | one-way | DNA1, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA1(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA1(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA1, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1281 | `Unlabeled` | one-way | DNA2, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA2(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA2(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA2, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1282 | `Unlabeled` | one-way | DNA3, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA3(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA3(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA3, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1283 | `Unlabeled` | one-way | DNA4, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA4(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA4(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA4, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1284 | `Unlabeled` | one-way | DNA5, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA5(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA5(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA5, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1285 | `Unlabeled` | one-way | DNA6, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA6(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA6(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA6, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1286 | `Unlabeled` | one-way | DNA7, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA7(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA7(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA7, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1287 | `Unlabeled` | one-way | DNA8, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA8(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA8(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA8, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1288 | `Unlabeled` | one-way | DNA9, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA9(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA9(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA9, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1289 | `Unlabeled` | one-way | DNA10, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA10(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA10(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA10, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1290 | `Unlabeled` | one-way | DNA11, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA11(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA11(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA11, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1291 | `Unlabeled` | one-way | DNA12, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA12(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA12(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA12, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1292 | `Unlabeled` | one-way | DNA13, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA13(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA13(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA13, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1293 | `Unlabeled` | one-way | DNA14, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA14(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA14(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA14, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1294 | `Unlabeled` | one-way | DNA15, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA15(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA15(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA15, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1295 | `Unlabeled` | one-way | DNA16, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA16(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA16(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA16, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1296 | `Unlabeled` | one-way | DNA17, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA17(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA17(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA17, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1297 | `Unlabeled` | one-way | DNA18, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA18(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA18(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA18, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1298 | `Unlabeled` | one-way | DNA19, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA19(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA19(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA19, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1299 | `Unlabeled` | one-way | DNA20, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA20(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA20(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA20, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1300 | `Unlabeled` | one-way | DNA21, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA21(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA21(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA21, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1301 | `Unlabeled` | one-way | DNA22, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA22(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA22(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA22, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1302 | `Unlabeled` | one-way | DNA23, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA23(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA23(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA23, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1303 | `Unlabeled` | one-way | DNA24, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA24(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA24(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA24, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1304 | `Unlabeled` | one-way | DNA25, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA25(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA25(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA25, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1305 | `Unlabeled` | one-way | DNA26, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA26(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA26(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA26, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1306 | `Unlabeled` | one-way | DNA27, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA27(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA27(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA27, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1307 | `Unlabeled` | one-way | DNA28, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA28(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA28(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA28, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1308 | `Unlabeled` | one-way | DNA29, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA29(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA29(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA29, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1309 | `Unlabeled` | one-way | DNA30, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA30(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA30(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA30, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1310 | `Unlabeled` | one-way | DNA31, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA31(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA31(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA31, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1311 | `Unlabeled` | one-way | DNA32, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA32(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA32(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA32, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1312 | `Unlabeled` | one-way | DNA33, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA33(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA33(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA33, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1313 | `Unlabeled` | one-way | DNA34, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA34(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA34(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA34, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1314 | `Unlabeled` | one-way | DNA35, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA35(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA35(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA35, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1315 | `Unlabeled` | one-way | DNA36, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA36(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA36(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA36, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1316 | `Unlabeled` | one-way | DNA37, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA37(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA37(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA37, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1317 | `Unlabeled` | one-way | DNA38, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA38(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA38(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA38, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1318 | `Unlabeled` | one-way | DNA39, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA39(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA39(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA39, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1319 | `Unlabeled` | one-way | DNA40, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA40(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA40(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA40, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1320 | `Unlabeled` | one-way | DNA41, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA41(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA41(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA41, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1321 | `Unlabeled` | one-way | DNA42, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA42(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA42(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA42, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1322 | `Unlabeled` | one-way | DNA43, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA43(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA43(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA43, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1323 | `Unlabeled` | one-way | DNA44, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA44(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA44(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA44, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1324 | `Unlabeled` | one-way | DNA45, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA45(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA45(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA45, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1325 | `Unlabeled` | one-way | DNA46, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA46(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA46(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA46, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1326 | `Unlabeled` | one-way | DNA47, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA47(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA47(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA47, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1327 | `Unlabeled` | one-way | DNA48, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA48(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA48(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA48, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1328 | `Unlabeled` | one-way | DNA49, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA49(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA49(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA49, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1329 | `Unlabeled` | one-way | DNA50, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA50(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA50(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA50, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1330 | `Unlabeled` | one-way | ATM, DNA1, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA1(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA1, LiIII, PARP by freeing DNA1.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1331 | `Unlabeled` | one-way | ATM, DNA2, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA2(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA2, LiIII, PARP by freeing DNA2.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1332 | `Unlabeled` | one-way | ATM, DNA3, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA3(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA3, LiIII, PARP by freeing DNA3.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1333 | `Unlabeled` | one-way | ATM, DNA4, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA4(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA4, LiIII, PARP by freeing DNA4.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1334 | `Unlabeled` | one-way | ATM, DNA5, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA5(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA5, LiIII, PARP by freeing DNA5.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1335 | `Unlabeled` | one-way | ATM, DNA6, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA6(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA6, LiIII, PARP by freeing DNA6.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1336 | `Unlabeled` | one-way | ATM, DNA7, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA7(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA7, LiIII, PARP by freeing DNA7.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1337 | `Unlabeled` | one-way | ATM, DNA8, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA8(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA8, LiIII, PARP by freeing DNA8.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1338 | `Unlabeled` | one-way | ATM, DNA9, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA9(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA9, LiIII, PARP by freeing DNA9.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1339 | `Unlabeled` | one-way | ATM, DNA10, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA10(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA10, LiIII, PARP by freeing DNA10.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1340 | `Unlabeled` | one-way | ATM, DNA11, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA11(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA11, LiIII, PARP by freeing DNA11.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1341 | `Unlabeled` | one-way | ATM, DNA12, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA12(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA12, LiIII, PARP by freeing DNA12.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1342 | `Unlabeled` | one-way | ATM, DNA13, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA13(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA13, LiIII, PARP by freeing DNA13.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1343 | `Unlabeled` | one-way | ATM, DNA14, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA14(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA14, LiIII, PARP by freeing DNA14.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1344 | `Unlabeled` | one-way | ATM, DNA15, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA15(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA15, LiIII, PARP by freeing DNA15.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1345 | `Unlabeled` | one-way | ATM, DNA16, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA16(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA16, LiIII, PARP by freeing DNA16.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1346 | `Unlabeled` | one-way | ATM, DNA17, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA17(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA17, LiIII, PARP by freeing DNA17.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1347 | `Unlabeled` | one-way | ATM, DNA18, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA18(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA18, LiIII, PARP by freeing DNA18.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1348 | `Unlabeled` | one-way | ATM, DNA19, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA19(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA19, LiIII, PARP by freeing DNA19.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1349 | `Unlabeled` | one-way | ATM, DNA20, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA20(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA20, LiIII, PARP by freeing DNA20.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1350 | `Unlabeled` | one-way | ATM, DNA21, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA21(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA21, LiIII, PARP by freeing DNA21.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1351 | `Unlabeled` | one-way | ATM, DNA22, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA22(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA22, LiIII, PARP by freeing DNA22.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1352 | `Unlabeled` | one-way | ATM, DNA23, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA23(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA23, LiIII, PARP by freeing DNA23.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1353 | `Unlabeled` | one-way | ATM, DNA24, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA24(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA24, LiIII, PARP by freeing DNA24.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1354 | `Unlabeled` | one-way | ATM, DNA25, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA25(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA25, LiIII, PARP by freeing DNA25.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1355 | `Unlabeled` | one-way | ATM, DNA26, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA26(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA26, LiIII, PARP by freeing DNA26.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1356 | `Unlabeled` | one-way | ATM, DNA27, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA27(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA27, LiIII, PARP by freeing DNA27.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1357 | `Unlabeled` | one-way | ATM, DNA28, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA28(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA28, LiIII, PARP by freeing DNA28.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1358 | `Unlabeled` | one-way | ATM, DNA29, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA29(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA29, LiIII, PARP by freeing DNA29.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1359 | `Unlabeled` | one-way | ATM, DNA30, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA30(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA30, LiIII, PARP by freeing DNA30.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1360 | `Unlabeled` | one-way | ATM, DNA31, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA31(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA31, LiIII, PARP by freeing DNA31.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1361 | `Unlabeled` | one-way | ATM, DNA32, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA32(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA32, LiIII, PARP by freeing DNA32.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1362 | `Unlabeled` | one-way | ATM, DNA33, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA33(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA33, LiIII, PARP by freeing DNA33.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1363 | `Unlabeled` | one-way | ATM, DNA34, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA34(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA34, LiIII, PARP by freeing DNA34.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1364 | `Unlabeled` | one-way | ATM, DNA35, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA35(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA35, LiIII, PARP by freeing DNA35.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1365 | `Unlabeled` | one-way | ATM, DNA36, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA36(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA36, LiIII, PARP by freeing DNA36.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1366 | `Unlabeled` | one-way | ATM, DNA37, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA37(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA37, LiIII, PARP by freeing DNA37.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1367 | `Unlabeled` | one-way | ATM, DNA38, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA38(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA38, LiIII, PARP by freeing DNA38.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1368 | `Unlabeled` | one-way | ATM, DNA39, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA39(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA39, LiIII, PARP by freeing DNA39.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1369 | `Unlabeled` | one-way | ATM, DNA40, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA40(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA40, LiIII, PARP by freeing DNA40.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1370 | `Unlabeled` | one-way | ATM, DNA41, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA41(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA41, LiIII, PARP by freeing DNA41.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1371 | `Unlabeled` | one-way | ATM, DNA42, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA42(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA42, LiIII, PARP by freeing DNA42.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1372 | `Unlabeled` | one-way | ATM, DNA43, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA43(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA43, LiIII, PARP by freeing DNA43.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1373 | `Unlabeled` | one-way | ATM, DNA44, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA44(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA44, LiIII, PARP by freeing DNA44.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1374 | `Unlabeled` | one-way | ATM, DNA45, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA45(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA45, LiIII, PARP by freeing DNA45.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1375 | `Unlabeled` | one-way | ATM, DNA46, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA46(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA46, LiIII, PARP by freeing DNA46.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1376 | `Unlabeled` | one-way | ATM, DNA47, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA47(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA47, LiIII, PARP by freeing DNA47.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1377 | `Unlabeled` | one-way | ATM, DNA48, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA48(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA48, LiIII, PARP by freeing DNA48.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1378 | `Unlabeled` | one-way | ATM, DNA49, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA49(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA49, LiIII, PARP by freeing DNA49.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1379 | `Unlabeled` | one-way | ATM, DNA50, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA50(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA50, LiIII, PARP by freeing DNA50.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1380 | `Unlabeled` | one-way | ATM, DNA1, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA1(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA1, LiIII, PARP by freeing DNA1.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1381 | `Unlabeled` | one-way | ATM, DNA2, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA2(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA2, LiIII, PARP by freeing DNA2.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1382 | `Unlabeled` | one-way | ATM, DNA3, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA3(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA3, LiIII, PARP by freeing DNA3.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1383 | `Unlabeled` | one-way | ATM, DNA4, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA4(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA4, LiIII, PARP by freeing DNA4.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1384 | `Unlabeled` | one-way | ATM, DNA5, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA5(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA5, LiIII, PARP by freeing DNA5.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1385 | `Unlabeled` | one-way | ATM, DNA6, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA6(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA6, LiIII, PARP by freeing DNA6.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1386 | `Unlabeled` | one-way | ATM, DNA7, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA7(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA7, LiIII, PARP by freeing DNA7.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1387 | `Unlabeled` | one-way | ATM, DNA8, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA8(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA8, LiIII, PARP by freeing DNA8.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1388 | `Unlabeled` | one-way | ATM, DNA9, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA9(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA9, LiIII, PARP by freeing DNA9.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1389 | `Unlabeled` | one-way | ATM, DNA10, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA10(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA10, LiIII, PARP by freeing DNA10.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1390 | `Unlabeled` | one-way | ATM, DNA11, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA11(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA11, LiIII, PARP by freeing DNA11.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1391 | `Unlabeled` | one-way | ATM, DNA12, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA12(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA12, LiIII, PARP by freeing DNA12.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1392 | `Unlabeled` | one-way | ATM, DNA13, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA13(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA13, LiIII, PARP by freeing DNA13.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1393 | `Unlabeled` | one-way | ATM, DNA14, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA14(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA14, LiIII, PARP by freeing DNA14.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1394 | `Unlabeled` | one-way | ATM, DNA15, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA15(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA15, LiIII, PARP by freeing DNA15.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1395 | `Unlabeled` | one-way | ATM, DNA16, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA16(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA16, LiIII, PARP by freeing DNA16.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1396 | `Unlabeled` | one-way | ATM, DNA17, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA17(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA17, LiIII, PARP by freeing DNA17.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1397 | `Unlabeled` | one-way | ATM, DNA18, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA18(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA18, LiIII, PARP by freeing DNA18.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1398 | `Unlabeled` | one-way | ATM, DNA19, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA19(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA19, LiIII, PARP by freeing DNA19.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1399 | `Unlabeled` | one-way | ATM, DNA20, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA20(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA20, LiIII, PARP by freeing DNA20.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1400 | `Unlabeled` | one-way | ATM, DNA21, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA21(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA21, LiIII, PARP by freeing DNA21.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1401 | `Unlabeled` | one-way | ATM, DNA22, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA22(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA22, LiIII, PARP by freeing DNA22.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1402 | `Unlabeled` | one-way | ATM, DNA23, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA23(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA23, LiIII, PARP by freeing DNA23.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1403 | `Unlabeled` | one-way | ATM, DNA24, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA24(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA24, LiIII, PARP by freeing DNA24.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1404 | `Unlabeled` | one-way | ATM, DNA25, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA25(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA25, LiIII, PARP by freeing DNA25.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1405 | `Unlabeled` | one-way | ATM, DNA26, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA26(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA26, LiIII, PARP by freeing DNA26.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1406 | `Unlabeled` | one-way | ATM, DNA27, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA27(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA27, LiIII, PARP by freeing DNA27.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1407 | `Unlabeled` | one-way | ATM, DNA28, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA28(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA28, LiIII, PARP by freeing DNA28.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1408 | `Unlabeled` | one-way | ATM, DNA29, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA29(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA29, LiIII, PARP by freeing DNA29.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1409 | `Unlabeled` | one-way | ATM, DNA30, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA30(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA30, LiIII, PARP by freeing DNA30.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1410 | `Unlabeled` | one-way | ATM, DNA31, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA31(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA31, LiIII, PARP by freeing DNA31.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1411 | `Unlabeled` | one-way | ATM, DNA32, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA32(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA32, LiIII, PARP by freeing DNA32.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1412 | `Unlabeled` | one-way | ATM, DNA33, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA33(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA33, LiIII, PARP by freeing DNA33.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1413 | `Unlabeled` | one-way | ATM, DNA34, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA34(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA34, LiIII, PARP by freeing DNA34.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1414 | `Unlabeled` | one-way | ATM, DNA35, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA35(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA35, LiIII, PARP by freeing DNA35.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1415 | `Unlabeled` | one-way | ATM, DNA36, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA36(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA36, LiIII, PARP by freeing DNA36.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1416 | `Unlabeled` | one-way | ATM, DNA37, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA37(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA37, LiIII, PARP by freeing DNA37.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1417 | `Unlabeled` | one-way | ATM, DNA38, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA38(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA38, LiIII, PARP by freeing DNA38.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1418 | `Unlabeled` | one-way | ATM, DNA39, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA39(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA39, LiIII, PARP by freeing DNA39.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1419 | `Unlabeled` | one-way | ATM, DNA40, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA40(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA40, LiIII, PARP by freeing DNA40.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1420 | `Unlabeled` | one-way | ATM, DNA41, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA41(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA41, LiIII, PARP by freeing DNA41.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1421 | `Unlabeled` | one-way | ATM, DNA42, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA42(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA42, LiIII, PARP by freeing DNA42.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1422 | `Unlabeled` | one-way | ATM, DNA43, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA43(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA43, LiIII, PARP by freeing DNA43.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1423 | `Unlabeled` | one-way | ATM, DNA44, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA44(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA44, LiIII, PARP by freeing DNA44.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1424 | `Unlabeled` | one-way | ATM, DNA45, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA45(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA45, LiIII, PARP by freeing DNA45.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1425 | `Unlabeled` | one-way | ATM, DNA46, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA46(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA46, LiIII, PARP by freeing DNA46.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1426 | `Unlabeled` | one-way | ATM, DNA47, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA47(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA47, LiIII, PARP by freeing DNA47.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1427 | `Unlabeled` | one-way | ATM, DNA48, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA48(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA48, LiIII, PARP by freeing DNA48.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1428 | `Unlabeled` | one-way | ATM, DNA49, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA49(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA49, LiIII, PARP by freeing DNA49.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1429 | `Unlabeled` | one-way | ATM, DNA50, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA50(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA50, LiIII, PARP by freeing DNA50.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1430 | `Unlabeled` | one-way | ATM, DNA1, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA1(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA1, LiIII, PARP by freeing DNA1.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1431 | `Unlabeled` | one-way | ATM, DNA2, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA2(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA2, LiIII, PARP by freeing DNA2.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1432 | `Unlabeled` | one-way | ATM, DNA3, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA3(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA3, LiIII, PARP by freeing DNA3.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1433 | `Unlabeled` | one-way | ATM, DNA4, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA4(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA4, LiIII, PARP by freeing DNA4.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1434 | `Unlabeled` | one-way | ATM, DNA5, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA5(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA5, LiIII, PARP by freeing DNA5.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1435 | `Unlabeled` | one-way | ATM, DNA6, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA6(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA6, LiIII, PARP by freeing DNA6.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1436 | `Unlabeled` | one-way | ATM, DNA7, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA7(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA7, LiIII, PARP by freeing DNA7.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1437 | `Unlabeled` | one-way | ATM, DNA8, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA8(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA8, LiIII, PARP by freeing DNA8.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1438 | `Unlabeled` | one-way | ATM, DNA9, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA9(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA9, LiIII, PARP by freeing DNA9.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1439 | `Unlabeled` | one-way | ATM, DNA10, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA10(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA10, LiIII, PARP by freeing DNA10.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1440 | `Unlabeled` | one-way | ATM, DNA11, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA11(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA11, LiIII, PARP by freeing DNA11.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1441 | `Unlabeled` | one-way | ATM, DNA12, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA12(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA12, LiIII, PARP by freeing DNA12.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1442 | `Unlabeled` | one-way | ATM, DNA13, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA13(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA13, LiIII, PARP by freeing DNA13.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1443 | `Unlabeled` | one-way | ATM, DNA14, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA14(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA14, LiIII, PARP by freeing DNA14.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1444 | `Unlabeled` | one-way | ATM, DNA15, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA15(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA15, LiIII, PARP by freeing DNA15.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1445 | `Unlabeled` | one-way | ATM, DNA16, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA16(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA16, LiIII, PARP by freeing DNA16.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1446 | `Unlabeled` | one-way | ATM, DNA17, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA17(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA17, LiIII, PARP by freeing DNA17.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1447 | `Unlabeled` | one-way | ATM, DNA18, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA18(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA18, LiIII, PARP by freeing DNA18.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1448 | `Unlabeled` | one-way | ATM, DNA19, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA19(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA19, LiIII, PARP by freeing DNA19.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1449 | `Unlabeled` | one-way | ATM, DNA20, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA20(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA20, LiIII, PARP by freeing DNA20.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1450 | `Unlabeled` | one-way | ATM, DNA21, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA21(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA21, LiIII, PARP by freeing DNA21.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1451 | `Unlabeled` | one-way | ATM, DNA22, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA22(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA22, LiIII, PARP by freeing DNA22.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1452 | `Unlabeled` | one-way | ATM, DNA23, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA23(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA23, LiIII, PARP by freeing DNA23.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1453 | `Unlabeled` | one-way | ATM, DNA24, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA24(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA24, LiIII, PARP by freeing DNA24.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1454 | `Unlabeled` | one-way | ATM, DNA25, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA25(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA25, LiIII, PARP by freeing DNA25.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1455 | `Unlabeled` | one-way | ATM, DNA26, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA26(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA26, LiIII, PARP by freeing DNA26.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1456 | `Unlabeled` | one-way | ATM, DNA27, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA27(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA27, LiIII, PARP by freeing DNA27.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1457 | `Unlabeled` | one-way | ATM, DNA28, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA28(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA28, LiIII, PARP by freeing DNA28.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1458 | `Unlabeled` | one-way | ATM, DNA29, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA29(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA29, LiIII, PARP by freeing DNA29.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1459 | `Unlabeled` | one-way | ATM, DNA30, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA30(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA30, LiIII, PARP by freeing DNA30.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1460 | `Unlabeled` | one-way | ATM, DNA31, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA31(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA31, LiIII, PARP by freeing DNA31.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1461 | `Unlabeled` | one-way | ATM, DNA32, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA32(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA32, LiIII, PARP by freeing DNA32.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1462 | `Unlabeled` | one-way | ATM, DNA33, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA33(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA33, LiIII, PARP by freeing DNA33.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1463 | `Unlabeled` | one-way | ATM, DNA34, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA34(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA34, LiIII, PARP by freeing DNA34.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1464 | `Unlabeled` | one-way | ATM, DNA35, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA35(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA35, LiIII, PARP by freeing DNA35.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1465 | `Unlabeled` | one-way | ATM, DNA36, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA36(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA36, LiIII, PARP by freeing DNA36.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1466 | `Unlabeled` | one-way | ATM, DNA37, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA37(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA37, LiIII, PARP by freeing DNA37.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1467 | `Unlabeled` | one-way | ATM, DNA38, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA38(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA38, LiIII, PARP by freeing DNA38.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1468 | `Unlabeled` | one-way | ATM, DNA39, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA39(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA39, LiIII, PARP by freeing DNA39.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1469 | `Unlabeled` | one-way | ATM, DNA40, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA40(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA40, LiIII, PARP by freeing DNA40.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1470 | `Unlabeled` | one-way | ATM, DNA41, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA41(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA41, LiIII, PARP by freeing DNA41.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1471 | `Unlabeled` | one-way | ATM, DNA42, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA42(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA42, LiIII, PARP by freeing DNA42.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1472 | `Unlabeled` | one-way | ATM, DNA43, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA43(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA43, LiIII, PARP by freeing DNA43.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1473 | `Unlabeled` | one-way | ATM, DNA44, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA44(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA44, LiIII, PARP by freeing DNA44.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1474 | `Unlabeled` | one-way | ATM, DNA45, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA45(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA45, LiIII, PARP by freeing DNA45.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1475 | `Unlabeled` | one-way | ATM, DNA46, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA46(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA46, LiIII, PARP by freeing DNA46.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1476 | `Unlabeled` | one-way | ATM, DNA47, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA47(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA47, LiIII, PARP by freeing DNA47.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1477 | `Unlabeled` | one-way | ATM, DNA48, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA48(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA48, LiIII, PARP by freeing DNA48.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1478 | `Unlabeled` | one-way | ATM, DNA49, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA49(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA49, LiIII, PARP by freeing DNA49.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1479 | `Unlabeled` | one-way | ATM, DNA50, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA50(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA50, LiIII, PARP by freeing DNA50.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1480 | `Unlabeled` | one-way | ATM, DNA1, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA1(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA1, LiIII, PARP by freeing DNA1.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1481 | `Unlabeled` | one-way | ATM, DNA2, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA2(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA2, LiIII, PARP by freeing DNA2.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1482 | `Unlabeled` | one-way | ATM, DNA3, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA3(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA3, LiIII, PARP by freeing DNA3.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1483 | `Unlabeled` | one-way | ATM, DNA4, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA4(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA4, LiIII, PARP by freeing DNA4.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1484 | `Unlabeled` | one-way | ATM, DNA5, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA5(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA5, LiIII, PARP by freeing DNA5.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1485 | `Unlabeled` | one-way | ATM, DNA6, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA6(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA6, LiIII, PARP by freeing DNA6.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1486 | `Unlabeled` | one-way | ATM, DNA7, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA7(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA7, LiIII, PARP by freeing DNA7.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1487 | `Unlabeled` | one-way | ATM, DNA8, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA8(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA8, LiIII, PARP by freeing DNA8.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1488 | `Unlabeled` | one-way | ATM, DNA9, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA9(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA9, LiIII, PARP by freeing DNA9.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1489 | `Unlabeled` | one-way | ATM, DNA10, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA10(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA10, LiIII, PARP by freeing DNA10.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1490 | `Unlabeled` | one-way | ATM, DNA11, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA11(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA11, LiIII, PARP by freeing DNA11.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1491 | `Unlabeled` | one-way | ATM, DNA12, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA12(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA12, LiIII, PARP by freeing DNA12.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1492 | `Unlabeled` | one-way | ATM, DNA13, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA13(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA13, LiIII, PARP by freeing DNA13.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1493 | `Unlabeled` | one-way | ATM, DNA14, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA14(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA14, LiIII, PARP by freeing DNA14.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1494 | `Unlabeled` | one-way | ATM, DNA15, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA15(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA15, LiIII, PARP by freeing DNA15.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1495 | `Unlabeled` | one-way | ATM, DNA16, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA16(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA16, LiIII, PARP by freeing DNA16.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1496 | `Unlabeled` | one-way | ATM, DNA17, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA17(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA17, LiIII, PARP by freeing DNA17.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1497 | `Unlabeled` | one-way | ATM, DNA18, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA18(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA18, LiIII, PARP by freeing DNA18.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1498 | `Unlabeled` | one-way | ATM, DNA19, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA19(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA19, LiIII, PARP by freeing DNA19.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1499 | `Unlabeled` | one-way | ATM, DNA20, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA20(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA20, LiIII, PARP by freeing DNA20.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1500 | `Unlabeled` | one-way | ATM, DNA21, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA21(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA21, LiIII, PARP by freeing DNA21.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | + +### Rules 1501-1750 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1501 | `Unlabeled` | one-way | ATM, DNA22, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA22(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA22, LiIII, PARP by freeing DNA22.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1502 | `Unlabeled` | one-way | ATM, DNA23, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA23(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA23, LiIII, PARP by freeing DNA23.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1503 | `Unlabeled` | one-way | ATM, DNA24, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA24(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA24, LiIII, PARP by freeing DNA24.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1504 | `Unlabeled` | one-way | ATM, DNA25, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA25(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA25, LiIII, PARP by freeing DNA25.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1505 | `Unlabeled` | one-way | ATM, DNA26, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA26(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA26, LiIII, PARP by freeing DNA26.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1506 | `Unlabeled` | one-way | ATM, DNA27, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA27(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA27, LiIII, PARP by freeing DNA27.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1507 | `Unlabeled` | one-way | ATM, DNA28, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA28(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA28, LiIII, PARP by freeing DNA28.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1508 | `Unlabeled` | one-way | ATM, DNA29, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA29(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA29, LiIII, PARP by freeing DNA29.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1509 | `Unlabeled` | one-way | ATM, DNA30, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA30(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA30, LiIII, PARP by freeing DNA30.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1510 | `Unlabeled` | one-way | ATM, DNA31, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA31(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA31, LiIII, PARP by freeing DNA31.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1511 | `Unlabeled` | one-way | ATM, DNA32, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA32(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA32, LiIII, PARP by freeing DNA32.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1512 | `Unlabeled` | one-way | ATM, DNA33, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA33(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA33, LiIII, PARP by freeing DNA33.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1513 | `Unlabeled` | one-way | ATM, DNA34, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA34(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA34, LiIII, PARP by freeing DNA34.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1514 | `Unlabeled` | one-way | ATM, DNA35, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA35(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA35, LiIII, PARP by freeing DNA35.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1515 | `Unlabeled` | one-way | ATM, DNA36, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA36(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA36, LiIII, PARP by freeing DNA36.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1516 | `Unlabeled` | one-way | ATM, DNA37, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA37(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA37, LiIII, PARP by freeing DNA37.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1517 | `Unlabeled` | one-way | ATM, DNA38, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA38(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA38, LiIII, PARP by freeing DNA38.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1518 | `Unlabeled` | one-way | ATM, DNA39, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA39(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA39, LiIII, PARP by freeing DNA39.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1519 | `Unlabeled` | one-way | ATM, DNA40, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA40(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA40, LiIII, PARP by freeing DNA40.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1520 | `Unlabeled` | one-way | ATM, DNA41, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA41(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA41, LiIII, PARP by freeing DNA41.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1521 | `Unlabeled` | one-way | ATM, DNA42, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA42(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA42, LiIII, PARP by freeing DNA42.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1522 | `Unlabeled` | one-way | ATM, DNA43, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA43(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA43, LiIII, PARP by freeing DNA43.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1523 | `Unlabeled` | one-way | ATM, DNA44, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA44(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA44, LiIII, PARP by freeing DNA44.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1524 | `Unlabeled` | one-way | ATM, DNA45, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA45(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA45, LiIII, PARP by freeing DNA45.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1525 | `Unlabeled` | one-way | ATM, DNA46, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA46(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA46, LiIII, PARP by freeing DNA46.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1526 | `Unlabeled` | one-way | ATM, DNA47, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA47(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA47, LiIII, PARP by freeing DNA47.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1527 | `Unlabeled` | one-way | ATM, DNA48, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA48(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA48, LiIII, PARP by freeing DNA48.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1528 | `Unlabeled` | one-way | ATM, DNA49, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA49(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA49, LiIII, PARP by freeing DNA49.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1529 | `Unlabeled` | one-way | ATM, DNA50, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA50(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA50, LiIII, PARP by freeing DNA50.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1530 | `Unlabeled` | one-way | ATM, DNA1 | `kATMact` | internal-state conversion/modification | `DNA1(site!?~sdsb) + ATM(state~0,h2ax) -> DNA1(site!?~sdsb) + ATM(state~1,h2ax)` | Changes internal modification/state marks on ATM, DNA1: ATM.state 0→1 at `kATMact`. | +| 1531 | `Unlabeled` | one-way | ATM, DNA2 | `kATMact` | internal-state conversion/modification | `DNA2(site!?~sdsb) + ATM(state~0,h2ax) -> DNA2(site!?~sdsb) + ATM(state~2,h2ax)` | Changes internal modification/state marks on ATM, DNA2: ATM.state 0→2 at `kATMact`. | +| 1532 | `Unlabeled` | one-way | ATM, DNA3 | `kATMact` | internal-state conversion/modification | `DNA3(site!?~sdsb) + ATM(state~0,h2ax) -> DNA3(site!?~sdsb) + ATM(state~3,h2ax)` | Changes internal modification/state marks on ATM, DNA3: ATM.state 0→3 at `kATMact`. | +| 1533 | `Unlabeled` | one-way | ATM, DNA4 | `kATMact` | internal-state conversion/modification | `DNA4(site!?~sdsb) + ATM(state~0,h2ax) -> DNA4(site!?~sdsb) + ATM(state~4,h2ax)` | Changes internal modification/state marks on ATM, DNA4: ATM.state 0→4 at `kATMact`. | +| 1534 | `Unlabeled` | one-way | ATM, DNA5 | `kATMact` | internal-state conversion/modification | `DNA5(site!?~sdsb) + ATM(state~0,h2ax) -> DNA5(site!?~sdsb) + ATM(state~5,h2ax)` | Changes internal modification/state marks on ATM, DNA5: ATM.state 0→5 at `kATMact`. | +| 1535 | `Unlabeled` | one-way | ATM, DNA6 | `kATMact` | internal-state conversion/modification | `DNA6(site!?~sdsb) + ATM(state~0,h2ax) -> DNA6(site!?~sdsb) + ATM(state~6,h2ax)` | Changes internal modification/state marks on ATM, DNA6: ATM.state 0→6 at `kATMact`. | +| 1536 | `Unlabeled` | one-way | ATM, DNA7 | `kATMact` | internal-state conversion/modification | `DNA7(site!?~sdsb) + ATM(state~0,h2ax) -> DNA7(site!?~sdsb) + ATM(state~7,h2ax)` | Changes internal modification/state marks on ATM, DNA7: ATM.state 0→7 at `kATMact`. | +| 1537 | `Unlabeled` | one-way | ATM, DNA8 | `kATMact` | internal-state conversion/modification | `DNA8(site!?~sdsb) + ATM(state~0,h2ax) -> DNA8(site!?~sdsb) + ATM(state~8,h2ax)` | Changes internal modification/state marks on ATM, DNA8: ATM.state 0→8 at `kATMact`. | +| 1538 | `Unlabeled` | one-way | ATM, DNA9 | `kATMact` | internal-state conversion/modification | `DNA9(site!?~sdsb) + ATM(state~0,h2ax) -> DNA9(site!?~sdsb) + ATM(state~9,h2ax)` | Changes internal modification/state marks on ATM, DNA9: ATM.state 0→9 at `kATMact`. | +| 1539 | `Unlabeled` | one-way | ATM, DNA10 | `kATMact` | internal-state conversion/modification | `DNA10(site!?~sdsb) + ATM(state~0,h2ax) -> DNA10(site!?~sdsb) + ATM(state~10,h2ax)` | Changes internal modification/state marks on ATM, DNA10: ATM.state 0→10 at `kATMact`. | +| 1540 | `Unlabeled` | one-way | ATM, DNA11 | `kATMact` | internal-state conversion/modification | `DNA11(site!?~sdsb) + ATM(state~0,h2ax) -> DNA11(site!?~sdsb) + ATM(state~11,h2ax)` | Changes internal modification/state marks on ATM, DNA11: ATM.state 0→11 at `kATMact`. | +| 1541 | `Unlabeled` | one-way | ATM, DNA12 | `kATMact` | internal-state conversion/modification | `DNA12(site!?~sdsb) + ATM(state~0,h2ax) -> DNA12(site!?~sdsb) + ATM(state~12,h2ax)` | Changes internal modification/state marks on ATM, DNA12: ATM.state 0→12 at `kATMact`. | +| 1542 | `Unlabeled` | one-way | ATM, DNA13 | `kATMact` | internal-state conversion/modification | `DNA13(site!?~sdsb) + ATM(state~0,h2ax) -> DNA13(site!?~sdsb) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA13: ATM.state 0→13 at `kATMact`. | +| 1543 | `Unlabeled` | one-way | ATM, DNA14 | `kATMact` | internal-state conversion/modification | `DNA14(site!?~sdsb) + ATM(state~0,h2ax) -> DNA14(site!?~sdsb) + ATM(state~14,h2ax)` | Changes internal modification/state marks on ATM, DNA14: ATM.state 0→14 at `kATMact`. | +| 1544 | `Unlabeled` | one-way | ATM, DNA15 | `kATMact` | internal-state conversion/modification | `DNA15(site!?~sdsb) + ATM(state~0,h2ax) -> DNA15(site!?~sdsb) + ATM(state~15,h2ax)` | Changes internal modification/state marks on ATM, DNA15: ATM.state 0→15 at `kATMact`. | +| 1545 | `Unlabeled` | one-way | ATM, DNA16 | `kATMact` | internal-state conversion/modification | `DNA16(site!?~sdsb) + ATM(state~0,h2ax) -> DNA16(site!?~sdsb) + ATM(state~16,h2ax)` | Changes internal modification/state marks on ATM, DNA16: ATM.state 0→16 at `kATMact`. | +| 1546 | `Unlabeled` | one-way | ATM, DNA17 | `kATMact` | internal-state conversion/modification | `DNA17(site!?~sdsb) + ATM(state~0,h2ax) -> DNA17(site!?~sdsb) + ATM(state~17,h2ax)` | Changes internal modification/state marks on ATM, DNA17: ATM.state 0→17 at `kATMact`. | +| 1547 | `Unlabeled` | one-way | ATM, DNA18 | `kATMact` | internal-state conversion/modification | `DNA18(site!?~sdsb) + ATM(state~0,h2ax) -> DNA18(site!?~sdsb) + ATM(state~18,h2ax)` | Changes internal modification/state marks on ATM, DNA18: ATM.state 0→18 at `kATMact`. | +| 1548 | `Unlabeled` | one-way | ATM, DNA19 | `kATMact` | internal-state conversion/modification | `DNA19(site!?~sdsb) + ATM(state~0,h2ax) -> DNA19(site!?~sdsb) + ATM(state~19,h2ax)` | Changes internal modification/state marks on ATM, DNA19: ATM.state 0→19 at `kATMact`. | +| 1549 | `Unlabeled` | one-way | ATM, DNA20 | `kATMact` | internal-state conversion/modification | `DNA20(site!?~sdsb) + ATM(state~0,h2ax) -> DNA20(site!?~sdsb) + ATM(state~20,h2ax)` | Changes internal modification/state marks on ATM, DNA20: ATM.state 0→20 at `kATMact`. | +| 1550 | `Unlabeled` | one-way | ATM, DNA21 | `kATMact` | internal-state conversion/modification | `DNA21(site!?~sdsb) + ATM(state~0,h2ax) -> DNA21(site!?~sdsb) + ATM(state~21,h2ax)` | Changes internal modification/state marks on ATM, DNA21: ATM.state 0→21 at `kATMact`. | +| 1551 | `Unlabeled` | one-way | ATM, DNA22 | `kATMact` | internal-state conversion/modification | `DNA22(site!?~sdsb) + ATM(state~0,h2ax) -> DNA22(site!?~sdsb) + ATM(state~22,h2ax)` | Changes internal modification/state marks on ATM, DNA22: ATM.state 0→22 at `kATMact`. | +| 1552 | `Unlabeled` | one-way | ATM, DNA23 | `kATMact` | internal-state conversion/modification | `DNA23(site!?~sdsb) + ATM(state~0,h2ax) -> DNA23(site!?~sdsb) + ATM(state~23,h2ax)` | Changes internal modification/state marks on ATM, DNA23: ATM.state 0→23 at `kATMact`. | +| 1553 | `Unlabeled` | one-way | ATM, DNA24 | `kATMact` | internal-state conversion/modification | `DNA24(site!?~sdsb) + ATM(state~0,h2ax) -> DNA24(site!?~sdsb) + ATM(state~24,h2ax)` | Changes internal modification/state marks on ATM, DNA24: ATM.state 0→24 at `kATMact`. | +| 1554 | `Unlabeled` | one-way | ATM, DNA25 | `kATMact` | internal-state conversion/modification | `DNA25(site!?~sdsb) + ATM(state~0,h2ax) -> DNA25(site!?~sdsb) + ATM(state~25,h2ax)` | Changes internal modification/state marks on ATM, DNA25: ATM.state 0→25 at `kATMact`. | +| 1555 | `Unlabeled` | one-way | ATM, DNA26 | `kATMact` | internal-state conversion/modification | `DNA26(site!?~sdsb) + ATM(state~0,h2ax) -> DNA26(site!?~sdsb) + ATM(state~26,h2ax)` | Changes internal modification/state marks on ATM, DNA26: ATM.state 0→26 at `kATMact`. | +| 1556 | `Unlabeled` | one-way | ATM, DNA27 | `kATMact` | internal-state conversion/modification | `DNA27(site!?~sdsb) + ATM(state~0,h2ax) -> DNA27(site!?~sdsb) + ATM(state~27,h2ax)` | Changes internal modification/state marks on ATM, DNA27: ATM.state 0→27 at `kATMact`. | +| 1557 | `Unlabeled` | one-way | ATM, DNA28 | `kATMact` | internal-state conversion/modification | `DNA28(site!?~sdsb) + ATM(state~0,h2ax) -> DNA28(site!?~sdsb) + ATM(state~28,h2ax)` | Changes internal modification/state marks on ATM, DNA28: ATM.state 0→28 at `kATMact`. | +| 1558 | `Unlabeled` | one-way | ATM, DNA29 | `kATMact` | internal-state conversion/modification | `DNA29(site!?~sdsb) + ATM(state~0,h2ax) -> DNA29(site!?~sdsb) + ATM(state~29,h2ax)` | Changes internal modification/state marks on ATM, DNA29: ATM.state 0→29 at `kATMact`. | +| 1559 | `Unlabeled` | one-way | ATM, DNA30 | `kATMact` | internal-state conversion/modification | `DNA30(site!?~sdsb) + ATM(state~0,h2ax) -> DNA30(site!?~sdsb) + ATM(state~30,h2ax)` | Changes internal modification/state marks on ATM, DNA30: ATM.state 0→30 at `kATMact`. | +| 1560 | `Unlabeled` | one-way | ATM, DNA31 | `kATMact` | internal-state conversion/modification | `DNA31(site!?~sdsb) + ATM(state~0,h2ax) -> DNA31(site!?~sdsb) + ATM(state~31,h2ax)` | Changes internal modification/state marks on ATM, DNA31: ATM.state 0→31 at `kATMact`. | +| 1561 | `Unlabeled` | one-way | ATM, DNA32 | `kATMact` | internal-state conversion/modification | `DNA32(site!?~sdsb) + ATM(state~0,h2ax) -> DNA32(site!?~sdsb) + ATM(state~32,h2ax)` | Changes internal modification/state marks on ATM, DNA32: ATM.state 0→32 at `kATMact`. | +| 1562 | `Unlabeled` | one-way | ATM, DNA33 | `kATMact` | internal-state conversion/modification | `DNA33(site!?~sdsb) + ATM(state~0,h2ax) -> DNA33(site!?~sdsb) + ATM(state~33,h2ax)` | Changes internal modification/state marks on ATM, DNA33: ATM.state 0→33 at `kATMact`. | +| 1563 | `Unlabeled` | one-way | ATM, DNA34 | `kATMact` | internal-state conversion/modification | `DNA34(site!?~sdsb) + ATM(state~0,h2ax) -> DNA34(site!?~sdsb) + ATM(state~34,h2ax)` | Changes internal modification/state marks on ATM, DNA34: ATM.state 0→34 at `kATMact`. | +| 1564 | `Unlabeled` | one-way | ATM, DNA35 | `kATMact` | internal-state conversion/modification | `DNA35(site!?~sdsb) + ATM(state~0,h2ax) -> DNA35(site!?~sdsb) + ATM(state~35,h2ax)` | Changes internal modification/state marks on ATM, DNA35: ATM.state 0→35 at `kATMact`. | +| 1565 | `Unlabeled` | one-way | ATM, DNA36 | `kATMact` | internal-state conversion/modification | `DNA36(site!?~sdsb) + ATM(state~0,h2ax) -> DNA36(site!?~sdsb) + ATM(state~36,h2ax)` | Changes internal modification/state marks on ATM, DNA36: ATM.state 0→36 at `kATMact`. | +| 1566 | `Unlabeled` | one-way | ATM, DNA37 | `kATMact` | internal-state conversion/modification | `DNA37(site!?~sdsb) + ATM(state~0,h2ax) -> DNA37(site!?~sdsb) + ATM(state~37,h2ax)` | Changes internal modification/state marks on ATM, DNA37: ATM.state 0→37 at `kATMact`. | +| 1567 | `Unlabeled` | one-way | ATM, DNA38 | `kATMact` | internal-state conversion/modification | `DNA38(site!?~sdsb) + ATM(state~0,h2ax) -> DNA38(site!?~sdsb) + ATM(state~38,h2ax)` | Changes internal modification/state marks on ATM, DNA38: ATM.state 0→38 at `kATMact`. | +| 1568 | `Unlabeled` | one-way | ATM, DNA39 | `kATMact` | internal-state conversion/modification | `DNA39(site!?~sdsb) + ATM(state~0,h2ax) -> DNA39(site!?~sdsb) + ATM(state~39,h2ax)` | Changes internal modification/state marks on ATM, DNA39: ATM.state 0→39 at `kATMact`. | +| 1569 | `Unlabeled` | one-way | ATM, DNA40 | `kATMact` | internal-state conversion/modification | `DNA40(site!?~sdsb) + ATM(state~0,h2ax) -> DNA40(site!?~sdsb) + ATM(state~40,h2ax)` | Changes internal modification/state marks on ATM, DNA40: ATM.state 0→40 at `kATMact`. | +| 1570 | `Unlabeled` | one-way | ATM, DNA41 | `kATMact` | internal-state conversion/modification | `DNA41(site!?~sdsb) + ATM(state~0,h2ax) -> DNA41(site!?~sdsb) + ATM(state~41,h2ax)` | Changes internal modification/state marks on ATM, DNA41: ATM.state 0→41 at `kATMact`. | +| 1571 | `Unlabeled` | one-way | ATM, DNA42 | `kATMact` | internal-state conversion/modification | `DNA42(site!?~sdsb) + ATM(state~0,h2ax) -> DNA42(site!?~sdsb) + ATM(state~42,h2ax)` | Changes internal modification/state marks on ATM, DNA42: ATM.state 0→42 at `kATMact`. | +| 1572 | `Unlabeled` | one-way | ATM, DNA43 | `kATMact` | internal-state conversion/modification | `DNA43(site!?~sdsb) + ATM(state~0,h2ax) -> DNA43(site!?~sdsb) + ATM(state~43,h2ax)` | Changes internal modification/state marks on ATM, DNA43: ATM.state 0→43 at `kATMact`. | +| 1573 | `Unlabeled` | one-way | ATM, DNA44 | `kATMact` | internal-state conversion/modification | `DNA44(site!?~sdsb) + ATM(state~0,h2ax) -> DNA44(site!?~sdsb) + ATM(state~44,h2ax)` | Changes internal modification/state marks on ATM, DNA44: ATM.state 0→44 at `kATMact`. | +| 1574 | `Unlabeled` | one-way | ATM, DNA45 | `kATMact` | internal-state conversion/modification | `DNA45(site!?~sdsb) + ATM(state~0,h2ax) -> DNA45(site!?~sdsb) + ATM(state~45,h2ax)` | Changes internal modification/state marks on ATM, DNA45: ATM.state 0→45 at `kATMact`. | +| 1575 | `Unlabeled` | one-way | ATM, DNA46 | `kATMact` | internal-state conversion/modification | `DNA46(site!?~sdsb) + ATM(state~0,h2ax) -> DNA46(site!?~sdsb) + ATM(state~46,h2ax)` | Changes internal modification/state marks on ATM, DNA46: ATM.state 0→46 at `kATMact`. | +| 1576 | `Unlabeled` | one-way | ATM, DNA47 | `kATMact` | internal-state conversion/modification | `DNA47(site!?~sdsb) + ATM(state~0,h2ax) -> DNA47(site!?~sdsb) + ATM(state~47,h2ax)` | Changes internal modification/state marks on ATM, DNA47: ATM.state 0→47 at `kATMact`. | +| 1577 | `Unlabeled` | one-way | ATM, DNA48 | `kATMact` | internal-state conversion/modification | `DNA48(site!?~sdsb) + ATM(state~0,h2ax) -> DNA48(site!?~sdsb) + ATM(state~48,h2ax)` | Changes internal modification/state marks on ATM, DNA48: ATM.state 0→48 at `kATMact`. | +| 1578 | `Unlabeled` | one-way | ATM, DNA49 | `kATMact` | internal-state conversion/modification | `DNA49(site!?~sdsb) + ATM(state~0,h2ax) -> DNA49(site!?~sdsb) + ATM(state~49,h2ax)` | Changes internal modification/state marks on ATM, DNA49: ATM.state 0→49 at `kATMact`. | +| 1579 | `Unlabeled` | one-way | ATM, DNA50 | `kATMact` | internal-state conversion/modification | `DNA50(site!?~sdsb) + ATM(state~0,h2ax) -> DNA50(site!?~sdsb) + ATM(state~50,h2ax)` | Changes internal modification/state marks on ATM, DNA50: ATM.state 0→50 at `kATMact`. | +| 1580 | `Unlabeled` | one-way | ATM, DNA1 | `kATMact` | internal-state conversion/modification | `DNA1(site!?~cdsb) + ATM(state~0,h2ax) -> DNA1(site!?~cdsb) + ATM(state~1,h2ax)` | Changes internal modification/state marks on ATM, DNA1: ATM.state 0→1 at `kATMact`. | +| 1581 | `Unlabeled` | one-way | ATM, DNA2 | `kATMact` | internal-state conversion/modification | `DNA2(site!?~cdsb) + ATM(state~0,h2ax) -> DNA2(site!?~cdsb) + ATM(state~2,h2ax)` | Changes internal modification/state marks on ATM, DNA2: ATM.state 0→2 at `kATMact`. | +| 1582 | `Unlabeled` | one-way | ATM, DNA3 | `kATMact` | internal-state conversion/modification | `DNA3(site!?~cdsb) + ATM(state~0,h2ax) -> DNA3(site!?~cdsb) + ATM(state~3,h2ax)` | Changes internal modification/state marks on ATM, DNA3: ATM.state 0→3 at `kATMact`. | +| 1583 | `Unlabeled` | one-way | ATM, DNA4 | `kATMact` | internal-state conversion/modification | `DNA4(site!?~cdsb) + ATM(state~0,h2ax) -> DNA4(site!?~cdsb) + ATM(state~4,h2ax)` | Changes internal modification/state marks on ATM, DNA4: ATM.state 0→4 at `kATMact`. | +| 1584 | `Unlabeled` | one-way | ATM, DNA5 | `kATMact` | internal-state conversion/modification | `DNA5(site!?~cdsb) + ATM(state~0,h2ax) -> DNA5(site!?~cdsb) + ATM(state~5,h2ax)` | Changes internal modification/state marks on ATM, DNA5: ATM.state 0→5 at `kATMact`. | +| 1585 | `Unlabeled` | one-way | ATM, DNA6 | `kATMact` | internal-state conversion/modification | `DNA6(site!?~cdsb) + ATM(state~0,h2ax) -> DNA6(site!?~cdsb) + ATM(state~6,h2ax)` | Changes internal modification/state marks on ATM, DNA6: ATM.state 0→6 at `kATMact`. | +| 1586 | `Unlabeled` | one-way | ATM, DNA7 | `kATMact` | internal-state conversion/modification | `DNA7(site!?~cdsb) + ATM(state~0,h2ax) -> DNA7(site!?~cdsb) + ATM(state~7,h2ax)` | Changes internal modification/state marks on ATM, DNA7: ATM.state 0→7 at `kATMact`. | +| 1587 | `Unlabeled` | one-way | ATM, DNA8 | `kATMact` | internal-state conversion/modification | `DNA8(site!?~cdsb) + ATM(state~0,h2ax) -> DNA8(site!?~cdsb) + ATM(state~8,h2ax)` | Changes internal modification/state marks on ATM, DNA8: ATM.state 0→8 at `kATMact`. | +| 1588 | `Unlabeled` | one-way | ATM, DNA9 | `kATMact` | internal-state conversion/modification | `DNA9(site!?~cdsb) + ATM(state~0,h2ax) -> DNA9(site!?~cdsb) + ATM(state~9,h2ax)` | Changes internal modification/state marks on ATM, DNA9: ATM.state 0→9 at `kATMact`. | +| 1589 | `Unlabeled` | one-way | ATM, DNA10 | `kATMact` | internal-state conversion/modification | `DNA10(site!?~cdsb) + ATM(state~0,h2ax) -> DNA10(site!?~cdsb) + ATM(state~10,h2ax)` | Changes internal modification/state marks on ATM, DNA10: ATM.state 0→10 at `kATMact`. | +| 1590 | `Unlabeled` | one-way | ATM, DNA11 | `kATMact` | internal-state conversion/modification | `DNA11(site!?~cdsb) + ATM(state~0,h2ax) -> DNA11(site!?~cdsb) + ATM(state~12,h2ax)` | Changes internal modification/state marks on ATM, DNA11: ATM.state 0→12 at `kATMact`. | +| 1591 | `Unlabeled` | one-way | ATM, DNA12 | `kATMact` | internal-state conversion/modification | `DNA12(site!?~cdsb) + ATM(state~0,h2ax) -> DNA12(site!?~cdsb) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA12: ATM.state 0→13 at `kATMact`. | +| 1592 | `Unlabeled` | one-way | ATM, DNA13 | `kATMact` | internal-state conversion/modification | `DNA13(site!?~cdsb) + ATM(state~0,h2ax) -> DNA13(site!?~cdsb) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA13: ATM.state 0→13 at `kATMact`. | +| 1593 | `Unlabeled` | one-way | ATM, DNA14 | `kATMact` | internal-state conversion/modification | `DNA14(site!?~cdsb) + ATM(state~0,h2ax) -> DNA14(site!?~cdsb) + ATM(state~14,h2ax)` | Changes internal modification/state marks on ATM, DNA14: ATM.state 0→14 at `kATMact`. | +| 1594 | `Unlabeled` | one-way | ATM, DNA15 | `kATMact` | internal-state conversion/modification | `DNA15(site!?~cdsb) + ATM(state~0,h2ax) -> DNA15(site!?~cdsb) + ATM(state~15,h2ax)` | Changes internal modification/state marks on ATM, DNA15: ATM.state 0→15 at `kATMact`. | +| 1595 | `Unlabeled` | one-way | ATM, DNA16 | `kATMact` | internal-state conversion/modification | `DNA16(site!?~cdsb) + ATM(state~0,h2ax) -> DNA16(site!?~cdsb) + ATM(state~16,h2ax)` | Changes internal modification/state marks on ATM, DNA16: ATM.state 0→16 at `kATMact`. | +| 1596 | `Unlabeled` | one-way | ATM, DNA17 | `kATMact` | internal-state conversion/modification | `DNA17(site!?~cdsb) + ATM(state~0,h2ax) -> DNA17(site!?~cdsb) + ATM(state~17,h2ax)` | Changes internal modification/state marks on ATM, DNA17: ATM.state 0→17 at `kATMact`. | +| 1597 | `Unlabeled` | one-way | ATM, DNA18 | `kATMact` | internal-state conversion/modification | `DNA18(site!?~cdsb) + ATM(state~0,h2ax) -> DNA18(site!?~cdsb) + ATM(state~18,h2ax)` | Changes internal modification/state marks on ATM, DNA18: ATM.state 0→18 at `kATMact`. | +| 1598 | `Unlabeled` | one-way | ATM, DNA19 | `kATMact` | internal-state conversion/modification | `DNA19(site!?~cdsb) + ATM(state~0,h2ax) -> DNA19(site!?~cdsb) + ATM(state~19,h2ax)` | Changes internal modification/state marks on ATM, DNA19: ATM.state 0→19 at `kATMact`. | +| 1599 | `Unlabeled` | one-way | ATM, DNA20 | `kATMact` | internal-state conversion/modification | `DNA20(site!?~cdsb) + ATM(state~0,h2ax) -> DNA20(site!?~cdsb) + ATM(state~20,h2ax)` | Changes internal modification/state marks on ATM, DNA20: ATM.state 0→20 at `kATMact`. | +| 1600 | `Unlabeled` | one-way | ATM, DNA21 | `kATMact` | internal-state conversion/modification | `DNA21(site!?~cdsb) + ATM(state~0,h2ax) -> DNA21(site!?~cdsb) + ATM(state~21,h2ax)` | Changes internal modification/state marks on ATM, DNA21: ATM.state 0→21 at `kATMact`. | +| 1601 | `Unlabeled` | one-way | ATM, DNA22 | `kATMact` | internal-state conversion/modification | `DNA22(site!?~cdsb) + ATM(state~0,h2ax) -> DNA22(site!?~cdsb) + ATM(state~22,h2ax)` | Changes internal modification/state marks on ATM, DNA22: ATM.state 0→22 at `kATMact`. | +| 1602 | `Unlabeled` | one-way | ATM, DNA23 | `kATMact` | internal-state conversion/modification | `DNA23(site!?~cdsb) + ATM(state~0,h2ax) -> DNA23(site!?~cdsb) + ATM(state~23,h2ax)` | Changes internal modification/state marks on ATM, DNA23: ATM.state 0→23 at `kATMact`. | +| 1603 | `Unlabeled` | one-way | ATM, DNA24 | `kATMact` | internal-state conversion/modification | `DNA24(site!?~cdsb) + ATM(state~0,h2ax) -> DNA24(site!?~cdsb) + ATM(state~24,h2ax)` | Changes internal modification/state marks on ATM, DNA24: ATM.state 0→24 at `kATMact`. | +| 1604 | `Unlabeled` | one-way | ATM, DNA25 | `kATMact` | internal-state conversion/modification | `DNA25(site!?~cdsb) + ATM(state~0,h2ax) -> DNA25(site!?~cdsb) + ATM(state~25,h2ax)` | Changes internal modification/state marks on ATM, DNA25: ATM.state 0→25 at `kATMact`. | +| 1605 | `Unlabeled` | one-way | ATM, DNA26 | `kATMact` | internal-state conversion/modification | `DNA26(site!?~cdsb) + ATM(state~0,h2ax) -> DNA26(site!?~cdsb) + ATM(state~26,h2ax)` | Changes internal modification/state marks on ATM, DNA26: ATM.state 0→26 at `kATMact`. | +| 1606 | `Unlabeled` | one-way | ATM, DNA27 | `kATMact` | internal-state conversion/modification | `DNA27(site!?~cdsb) + ATM(state~0,h2ax) -> DNA27(site!?~cdsb) + ATM(state~27,h2ax)` | Changes internal modification/state marks on ATM, DNA27: ATM.state 0→27 at `kATMact`. | +| 1607 | `Unlabeled` | one-way | ATM, DNA28 | `kATMact` | internal-state conversion/modification | `DNA28(site!?~cdsb) + ATM(state~0,h2ax) -> DNA28(site!?~cdsb) + ATM(state~28,h2ax)` | Changes internal modification/state marks on ATM, DNA28: ATM.state 0→28 at `kATMact`. | +| 1608 | `Unlabeled` | one-way | ATM, DNA29 | `kATMact` | internal-state conversion/modification | `DNA29(site!?~cdsb) + ATM(state~0,h2ax) -> DNA29(site!?~cdsb) + ATM(state~29,h2ax)` | Changes internal modification/state marks on ATM, DNA29: ATM.state 0→29 at `kATMact`. | +| 1609 | `Unlabeled` | one-way | ATM, DNA30 | `kATMact` | internal-state conversion/modification | `DNA30(site!?~cdsb) + ATM(state~0,h2ax) -> DNA30(site!?~cdsb) + ATM(state~30,h2ax)` | Changes internal modification/state marks on ATM, DNA30: ATM.state 0→30 at `kATMact`. | +| 1610 | `Unlabeled` | one-way | ATM, DNA31 | `kATMact` | internal-state conversion/modification | `DNA31(site!?~cdsb) + ATM(state~0,h2ax) -> DNA31(site!?~cdsb) + ATM(state~31,h2ax)` | Changes internal modification/state marks on ATM, DNA31: ATM.state 0→31 at `kATMact`. | +| 1611 | `Unlabeled` | one-way | ATM, DNA32 | `kATMact` | internal-state conversion/modification | `DNA32(site!?~cdsb) + ATM(state~0,h2ax) -> DNA32(site!?~cdsb) + ATM(state~32,h2ax)` | Changes internal modification/state marks on ATM, DNA32: ATM.state 0→32 at `kATMact`. | +| 1612 | `Unlabeled` | one-way | ATM, DNA33 | `kATMact` | internal-state conversion/modification | `DNA33(site!?~cdsb) + ATM(state~0,h2ax) -> DNA33(site!?~cdsb) + ATM(state~33,h2ax)` | Changes internal modification/state marks on ATM, DNA33: ATM.state 0→33 at `kATMact`. | +| 1613 | `Unlabeled` | one-way | ATM, DNA34 | `kATMact` | internal-state conversion/modification | `DNA34(site!?~cdsb) + ATM(state~0,h2ax) -> DNA34(site!?~cdsb) + ATM(state~34,h2ax)` | Changes internal modification/state marks on ATM, DNA34: ATM.state 0→34 at `kATMact`. | +| 1614 | `Unlabeled` | one-way | ATM, DNA35 | `kATMact` | internal-state conversion/modification | `DNA35(site!?~cdsb) + ATM(state~0,h2ax) -> DNA35(site!?~cdsb) + ATM(state~35,h2ax)` | Changes internal modification/state marks on ATM, DNA35: ATM.state 0→35 at `kATMact`. | +| 1615 | `Unlabeled` | one-way | ATM, DNA36 | `kATMact` | internal-state conversion/modification | `DNA36(site!?~cdsb) + ATM(state~0,h2ax) -> DNA36(site!?~cdsb) + ATM(state~36,h2ax)` | Changes internal modification/state marks on ATM, DNA36: ATM.state 0→36 at `kATMact`. | +| 1616 | `Unlabeled` | one-way | ATM, DNA37 | `kATMact` | internal-state conversion/modification | `DNA37(site!?~cdsb) + ATM(state~0,h2ax) -> DNA37(site!?~cdsb) + ATM(state~37,h2ax)` | Changes internal modification/state marks on ATM, DNA37: ATM.state 0→37 at `kATMact`. | +| 1617 | `Unlabeled` | one-way | ATM, DNA38 | `kATMact` | internal-state conversion/modification | `DNA38(site!?~cdsb) + ATM(state~0,h2ax) -> DNA38(site!?~cdsb) + ATM(state~38,h2ax)` | Changes internal modification/state marks on ATM, DNA38: ATM.state 0→38 at `kATMact`. | +| 1618 | `Unlabeled` | one-way | ATM, DNA39 | `kATMact` | internal-state conversion/modification | `DNA39(site!?~cdsb) + ATM(state~0,h2ax) -> DNA39(site!?~cdsb) + ATM(state~39,h2ax)` | Changes internal modification/state marks on ATM, DNA39: ATM.state 0→39 at `kATMact`. | +| 1619 | `Unlabeled` | one-way | ATM, DNA40 | `kATMact` | internal-state conversion/modification | `DNA40(site!?~cdsb) + ATM(state~0,h2ax) -> DNA40(site!?~cdsb) + ATM(state~40,h2ax)` | Changes internal modification/state marks on ATM, DNA40: ATM.state 0→40 at `kATMact`. | +| 1620 | `Unlabeled` | one-way | ATM, DNA41 | `kATMact` | internal-state conversion/modification | `DNA41(site!?~cdsb) + ATM(state~0,h2ax) -> DNA41(site!?~cdsb) + ATM(state~41,h2ax)` | Changes internal modification/state marks on ATM, DNA41: ATM.state 0→41 at `kATMact`. | +| 1621 | `Unlabeled` | one-way | ATM, DNA42 | `kATMact` | internal-state conversion/modification | `DNA42(site!?~cdsb) + ATM(state~0,h2ax) -> DNA42(site!?~cdsb) + ATM(state~42,h2ax)` | Changes internal modification/state marks on ATM, DNA42: ATM.state 0→42 at `kATMact`. | +| 1622 | `Unlabeled` | one-way | ATM, DNA43 | `kATMact` | internal-state conversion/modification | `DNA43(site!?~cdsb) + ATM(state~0,h2ax) -> DNA43(site!?~cdsb) + ATM(state~43,h2ax)` | Changes internal modification/state marks on ATM, DNA43: ATM.state 0→43 at `kATMact`. | +| 1623 | `Unlabeled` | one-way | ATM, DNA44 | `kATMact` | internal-state conversion/modification | `DNA44(site!?~cdsb) + ATM(state~0,h2ax) -> DNA44(site!?~cdsb) + ATM(state~44,h2ax)` | Changes internal modification/state marks on ATM, DNA44: ATM.state 0→44 at `kATMact`. | +| 1624 | `Unlabeled` | one-way | ATM, DNA45 | `kATMact` | internal-state conversion/modification | `DNA45(site!?~cdsb) + ATM(state~0,h2ax) -> DNA45(site!?~cdsb) + ATM(state~45,h2ax)` | Changes internal modification/state marks on ATM, DNA45: ATM.state 0→45 at `kATMact`. | +| 1625 | `Unlabeled` | one-way | ATM, DNA46 | `kATMact` | internal-state conversion/modification | `DNA46(site!?~cdsb) + ATM(state~0,h2ax) -> DNA46(site!?~cdsb) + ATM(state~46,h2ax)` | Changes internal modification/state marks on ATM, DNA46: ATM.state 0→46 at `kATMact`. | +| 1626 | `Unlabeled` | one-way | ATM, DNA47 | `kATMact` | internal-state conversion/modification | `DNA47(site!?~cdsb) + ATM(state~0,h2ax) -> DNA47(site!?~cdsb) + ATM(state~47,h2ax)` | Changes internal modification/state marks on ATM, DNA47: ATM.state 0→47 at `kATMact`. | +| 1627 | `Unlabeled` | one-way | ATM, DNA48 | `kATMact` | internal-state conversion/modification | `DNA48(site!?~cdsb) + ATM(state~0,h2ax) -> DNA48(site!?~cdsb) + ATM(state~48,h2ax)` | Changes internal modification/state marks on ATM, DNA48: ATM.state 0→48 at `kATMact`. | +| 1628 | `Unlabeled` | one-way | ATM, DNA49 | `kATMact` | internal-state conversion/modification | `DNA49(site!?~cdsb) + ATM(state~0,h2ax) -> DNA49(site!?~cdsb) + ATM(state~49,h2ax)` | Changes internal modification/state marks on ATM, DNA49: ATM.state 0→49 at `kATMact`. | +| 1629 | `Unlabeled` | one-way | ATM, DNA50 | `kATMact` | internal-state conversion/modification | `DNA50(site!?~cdsb) + ATM(state~0,h2ax) -> DNA50(site!?~cdsb) + ATM(state~50,h2ax)` | Changes internal modification/state marks on ATM, DNA50: ATM.state 0→50 at `kATMact`. | +| 1630 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~1,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 1→0 at `kATMinact`. | +| 1631 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~2,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 2→0 at `kATMinact`. | +| 1632 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~3,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 3→0 at `kATMinact`. | +| 1633 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~4,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 4→0 at `kATMinact`. | +| 1634 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~5,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 5→0 at `kATMinact`. | +| 1635 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~6,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 6→0 at `kATMinact`. | +| 1636 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~7,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 7→0 at `kATMinact`. | +| 1637 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~8,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 8→0 at `kATMinact`. | +| 1638 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~9,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 9→0 at `kATMinact`. | +| 1639 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~10,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 10→0 at `kATMinact`. | +| 1640 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~11,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 11→0 at `kATMinact`. | +| 1641 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~12,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 12→0 at `kATMinact`. | +| 1642 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~13,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 13→0 at `kATMinact`. | +| 1643 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~14,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 14→0 at `kATMinact`. | +| 1644 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~15,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 15→0 at `kATMinact`. | +| 1645 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~16,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 16→0 at `kATMinact`. | +| 1646 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~17,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 17→0 at `kATMinact`. | +| 1647 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~18,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 18→0 at `kATMinact`. | +| 1648 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~19,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 19→0 at `kATMinact`. | +| 1649 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~20,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 20→0 at `kATMinact`. | +| 1650 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~21,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 21→0 at `kATMinact`. | +| 1651 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~22,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 22→0 at `kATMinact`. | +| 1652 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~23,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 23→0 at `kATMinact`. | +| 1653 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~24,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 24→0 at `kATMinact`. | +| 1654 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~25,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 25→0 at `kATMinact`. | +| 1655 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~26,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 26→0 at `kATMinact`. | +| 1656 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~27,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 27→0 at `kATMinact`. | +| 1657 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~28,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 28→0 at `kATMinact`. | +| 1658 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~29,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 29→0 at `kATMinact`. | +| 1659 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~30,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 30→0 at `kATMinact`. | +| 1660 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~31,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 31→0 at `kATMinact`. | +| 1661 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~32,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 32→0 at `kATMinact`. | +| 1662 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~33,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 33→0 at `kATMinact`. | +| 1663 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~34,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 34→0 at `kATMinact`. | +| 1664 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~35,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 35→0 at `kATMinact`. | +| 1665 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~36,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 36→0 at `kATMinact`. | +| 1666 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~37,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 37→0 at `kATMinact`. | +| 1667 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~38,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 38→0 at `kATMinact`. | +| 1668 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~39,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 39→0 at `kATMinact`. | +| 1669 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~40,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 40→0 at `kATMinact`. | +| 1670 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~41,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 41→0 at `kATMinact`. | +| 1671 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~42,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 42→0 at `kATMinact`. | +| 1672 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~43,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 43→0 at `kATMinact`. | +| 1673 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~44,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 44→0 at `kATMinact`. | +| 1674 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~45,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 45→0 at `kATMinact`. | +| 1675 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~46,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 46→0 at `kATMinact`. | +| 1676 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~47,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 47→0 at `kATMinact`. | +| 1677 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~48,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 48→0 at `kATMinact`. | +| 1678 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~49,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 49→0 at `kATMinact`. | +| 1679 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~50,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 50→0 at `kATMinact`. | +| 1680 | `Unlabeled` | one-way | ATM, DNA1 | `kh2axp1` | internal-state conversion/modification | `DNA1(site!?~sdsb,h2ax~u) + ATM(state~1,h2ax) -> DNA1(site!?~sdsb,h2ax~p) + ATM(state~1,h2ax)` | Changes internal modification/state marks on ATM, DNA1: DNA1.h2ax u→p at `kh2axp1`. | +| 1681 | `Unlabeled` | one-way | ATM, DNA2 | `kh2axp1` | internal-state conversion/modification | `DNA2(site!?~sdsb,h2ax~u) + ATM(state~2,h2ax) -> DNA2(site!?~sdsb,h2ax~p) + ATM(state~2,h2ax)` | Changes internal modification/state marks on ATM, DNA2: DNA2.h2ax u→p at `kh2axp1`. | +| 1682 | `Unlabeled` | one-way | ATM, DNA3 | `kh2axp1` | internal-state conversion/modification | `DNA3(site!?~sdsb,h2ax~u) + ATM(state~3,h2ax) -> DNA3(site!?~sdsb,h2ax~p) + ATM(state~3,h2ax)` | Changes internal modification/state marks on ATM, DNA3: DNA3.h2ax u→p at `kh2axp1`. | +| 1683 | `Unlabeled` | one-way | ATM, DNA4 | `kh2axp1` | internal-state conversion/modification | `DNA4(site!?~sdsb,h2ax~u) + ATM(state~4,h2ax) -> DNA4(site!?~sdsb,h2ax~p) + ATM(state~4,h2ax)` | Changes internal modification/state marks on ATM, DNA4: DNA4.h2ax u→p at `kh2axp1`. | +| 1684 | `Unlabeled` | one-way | ATM, DNA5 | `kh2axp1` | internal-state conversion/modification | `DNA5(site!?~sdsb,h2ax~u) + ATM(state~5,h2ax) -> DNA5(site!?~sdsb,h2ax~p) + ATM(state~5,h2ax)` | Changes internal modification/state marks on ATM, DNA5: DNA5.h2ax u→p at `kh2axp1`. | +| 1685 | `Unlabeled` | one-way | ATM, DNA6 | `kh2axp1` | internal-state conversion/modification | `DNA6(site!?~sdsb,h2ax~u) + ATM(state~6,h2ax) -> DNA6(site!?~sdsb,h2ax~p) + ATM(state~6,h2ax)` | Changes internal modification/state marks on ATM, DNA6: DNA6.h2ax u→p at `kh2axp1`. | +| 1686 | `Unlabeled` | one-way | ATM, DNA7 | `kh2axp1` | internal-state conversion/modification | `DNA7(site!?~sdsb,h2ax~u) + ATM(state~7,h2ax) -> DNA7(site!?~sdsb,h2ax~p) + ATM(state~7,h2ax)` | Changes internal modification/state marks on ATM, DNA7: DNA7.h2ax u→p at `kh2axp1`. | +| 1687 | `Unlabeled` | one-way | ATM, DNA8 | `kh2axp1` | internal-state conversion/modification | `DNA8(site!?~sdsb,h2ax~u) + ATM(state~8,h2ax) -> DNA8(site!?~sdsb,h2ax~p) + ATM(state~8,h2ax)` | Changes internal modification/state marks on ATM, DNA8: DNA8.h2ax u→p at `kh2axp1`. | +| 1688 | `Unlabeled` | one-way | ATM, DNA9 | `kh2axp1` | internal-state conversion/modification | `DNA9(site!?~sdsb,h2ax~u) + ATM(state~9,h2ax) -> DNA9(site!?~sdsb,h2ax~p) + ATM(state~9,h2ax)` | Changes internal modification/state marks on ATM, DNA9: DNA9.h2ax u→p at `kh2axp1`. | +| 1689 | `Unlabeled` | one-way | ATM, DNA10 | `kh2axp1` | internal-state conversion/modification | `DNA10(site!?~sdsb,h2ax~u) + ATM(state~10,h2ax) -> DNA10(site!?~sdsb,h2ax~p) + ATM(state~10,h2ax)` | Changes internal modification/state marks on ATM, DNA10: DNA10.h2ax u→p at `kh2axp1`. | +| 1690 | `Unlabeled` | one-way | ATM, DNA11 | `kh2axp1` | internal-state conversion/modification | `DNA11(site!?~sdsb,h2ax~u) + ATM(state~11,h2ax) -> DNA11(site!?~sdsb,h2ax~p) + ATM(state~11,h2ax)` | Changes internal modification/state marks on ATM, DNA11: DNA11.h2ax u→p at `kh2axp1`. | +| 1691 | `Unlabeled` | one-way | ATM, DNA12 | `kh2axp1` | internal-state conversion/modification | `DNA12(site!?~sdsb,h2ax~u) + ATM(state~12,h2ax) -> DNA12(site!?~sdsb,h2ax~p) + ATM(state~12,h2ax)` | Changes internal modification/state marks on ATM, DNA12: DNA12.h2ax u→p at `kh2axp1`. | +| 1692 | `Unlabeled` | one-way | ATM, DNA13 | `kh2axp1` | internal-state conversion/modification | `DNA13(site!?~sdsb,h2ax~u) + ATM(state~13,h2ax) -> DNA13(site!?~sdsb,h2ax~p) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA13: DNA13.h2ax u→p at `kh2axp1`. | +| 1693 | `Unlabeled` | one-way | ATM, DNA14 | `kh2axp1` | internal-state conversion/modification | `DNA14(site!?~sdsb,h2ax~u) + ATM(state~14,h2ax) -> DNA14(site!?~sdsb,h2ax~p) + ATM(state~14,h2ax)` | Changes internal modification/state marks on ATM, DNA14: DNA14.h2ax u→p at `kh2axp1`. | +| 1694 | `Unlabeled` | one-way | ATM, DNA15 | `kh2axp1` | internal-state conversion/modification | `DNA15(site!?~sdsb,h2ax~u) + ATM(state~15,h2ax) -> DNA15(site!?~sdsb,h2ax~p) + ATM(state~15,h2ax)` | Changes internal modification/state marks on ATM, DNA15: DNA15.h2ax u→p at `kh2axp1`. | +| 1695 | `Unlabeled` | one-way | ATM, DNA16 | `kh2axp1` | internal-state conversion/modification | `DNA16(site!?~sdsb,h2ax~u) + ATM(state~16,h2ax) -> DNA16(site!?~sdsb,h2ax~p) + ATM(state~16,h2ax)` | Changes internal modification/state marks on ATM, DNA16: DNA16.h2ax u→p at `kh2axp1`. | +| 1696 | `Unlabeled` | one-way | ATM, DNA17 | `kh2axp1` | internal-state conversion/modification | `DNA17(site!?~sdsb,h2ax~u) + ATM(state~17,h2ax) -> DNA17(site!?~sdsb,h2ax~p) + ATM(state~17,h2ax)` | Changes internal modification/state marks on ATM, DNA17: DNA17.h2ax u→p at `kh2axp1`. | +| 1697 | `Unlabeled` | one-way | ATM, DNA18 | `kh2axp1` | internal-state conversion/modification | `DNA18(site!?~sdsb,h2ax~u) + ATM(state~18,h2ax) -> DNA18(site!?~sdsb,h2ax~p) + ATM(state~18,h2ax)` | Changes internal modification/state marks on ATM, DNA18: DNA18.h2ax u→p at `kh2axp1`. | +| 1698 | `Unlabeled` | one-way | ATM, DNA19 | `kh2axp1` | internal-state conversion/modification | `DNA19(site!?~sdsb,h2ax~u) + ATM(state~19,h2ax) -> DNA19(site!?~sdsb,h2ax~p) + ATM(state~19,h2ax)` | Changes internal modification/state marks on ATM, DNA19: DNA19.h2ax u→p at `kh2axp1`. | +| 1699 | `Unlabeled` | one-way | ATM, DNA20 | `kh2axp1` | internal-state conversion/modification | `DNA20(site!?~sdsb,h2ax~u) + ATM(state~20,h2ax) -> DNA20(site!?~sdsb,h2ax~p) + ATM(state~20,h2ax)` | Changes internal modification/state marks on ATM, DNA20: DNA20.h2ax u→p at `kh2axp1`. | +| 1700 | `Unlabeled` | one-way | ATM, DNA21 | `kh2axp1` | internal-state conversion/modification | `DNA21(site!?~sdsb,h2ax~u) + ATM(state~21,h2ax) -> DNA21(site!?~sdsb,h2ax~p) + ATM(state~21,h2ax)` | Changes internal modification/state marks on ATM, DNA21: DNA21.h2ax u→p at `kh2axp1`. | +| 1701 | `Unlabeled` | one-way | ATM, DNA22 | `kh2axp1` | internal-state conversion/modification | `DNA22(site!?~sdsb,h2ax~u) + ATM(state~22,h2ax) -> DNA22(site!?~sdsb,h2ax~p) + ATM(state~22,h2ax)` | Changes internal modification/state marks on ATM, DNA22: DNA22.h2ax u→p at `kh2axp1`. | +| 1702 | `Unlabeled` | one-way | ATM, DNA23 | `kh2axp1` | internal-state conversion/modification | `DNA23(site!?~sdsb,h2ax~u) + ATM(state~23,h2ax) -> DNA23(site!?~sdsb,h2ax~p) + ATM(state~23,h2ax)` | Changes internal modification/state marks on ATM, DNA23: DNA23.h2ax u→p at `kh2axp1`. | +| 1703 | `Unlabeled` | one-way | ATM, DNA24 | `kh2axp1` | internal-state conversion/modification | `DNA24(site!?~sdsb,h2ax~u) + ATM(state~24,h2ax) -> DNA24(site!?~sdsb,h2ax~p) + ATM(state~24,h2ax)` | Changes internal modification/state marks on ATM, DNA24: DNA24.h2ax u→p at `kh2axp1`. | +| 1704 | `Unlabeled` | one-way | ATM, DNA25 | `kh2axp1` | internal-state conversion/modification | `DNA25(site!?~sdsb,h2ax~u) + ATM(state~25,h2ax) -> DNA25(site!?~sdsb,h2ax~p) + ATM(state~25,h2ax)` | Changes internal modification/state marks on ATM, DNA25: DNA25.h2ax u→p at `kh2axp1`. | +| 1705 | `Unlabeled` | one-way | ATM, DNA26 | `kh2axp1` | internal-state conversion/modification | `DNA26(site!?~sdsb,h2ax~u) + ATM(state~26,h2ax) -> DNA26(site!?~sdsb,h2ax~p) + ATM(state~26,h2ax)` | Changes internal modification/state marks on ATM, DNA26: DNA26.h2ax u→p at `kh2axp1`. | +| 1706 | `Unlabeled` | one-way | ATM, DNA27 | `kh2axp1` | internal-state conversion/modification | `DNA27(site!?~sdsb,h2ax~u) + ATM(state~27,h2ax) -> DNA27(site!?~sdsb,h2ax~p) + ATM(state~27,h2ax)` | Changes internal modification/state marks on ATM, DNA27: DNA27.h2ax u→p at `kh2axp1`. | +| 1707 | `Unlabeled` | one-way | ATM, DNA28 | `kh2axp1` | internal-state conversion/modification | `DNA28(site!?~sdsb,h2ax~u) + ATM(state~28,h2ax) -> DNA28(site!?~sdsb,h2ax~p) + ATM(state~28,h2ax)` | Changes internal modification/state marks on ATM, DNA28: DNA28.h2ax u→p at `kh2axp1`. | +| 1708 | `Unlabeled` | one-way | ATM, DNA29 | `kh2axp1` | internal-state conversion/modification | `DNA29(site!?~sdsb,h2ax~u) + ATM(state~29,h2ax) -> DNA29(site!?~sdsb,h2ax~p) + ATM(state~29,h2ax)` | Changes internal modification/state marks on ATM, DNA29: DNA29.h2ax u→p at `kh2axp1`. | +| 1709 | `Unlabeled` | one-way | ATM, DNA30 | `kh2axp1` | internal-state conversion/modification | `DNA30(site!?~sdsb,h2ax~u) + ATM(state~30,h2ax) -> DNA30(site!?~sdsb,h2ax~p) + ATM(state~30,h2ax)` | Changes internal modification/state marks on ATM, DNA30: DNA30.h2ax u→p at `kh2axp1`. | +| 1710 | `Unlabeled` | one-way | ATM, DNA31 | `kh2axp1` | internal-state conversion/modification | `DNA31(site!?~sdsb,h2ax~u) + ATM(state~31,h2ax) -> DNA31(site!?~sdsb,h2ax~p) + ATM(state~31,h2ax)` | Changes internal modification/state marks on ATM, DNA31: DNA31.h2ax u→p at `kh2axp1`. | +| 1711 | `Unlabeled` | one-way | ATM, DNA32 | `kh2axp1` | internal-state conversion/modification | `DNA32(site!?~sdsb,h2ax~u) + ATM(state~32,h2ax) -> DNA32(site!?~sdsb,h2ax~p) + ATM(state~32,h2ax)` | Changes internal modification/state marks on ATM, DNA32: DNA32.h2ax u→p at `kh2axp1`. | +| 1712 | `Unlabeled` | one-way | ATM, DNA33 | `kh2axp1` | internal-state conversion/modification | `DNA33(site!?~sdsb,h2ax~u) + ATM(state~33,h2ax) -> DNA33(site!?~sdsb,h2ax~p) + ATM(state~33,h2ax)` | Changes internal modification/state marks on ATM, DNA33: DNA33.h2ax u→p at `kh2axp1`. | +| 1713 | `Unlabeled` | one-way | ATM, DNA34 | `kh2axp1` | internal-state conversion/modification | `DNA34(site!?~sdsb,h2ax~u) + ATM(state~34,h2ax) -> DNA34(site!?~sdsb,h2ax~p) + ATM(state~34,h2ax)` | Changes internal modification/state marks on ATM, DNA34: DNA34.h2ax u→p at `kh2axp1`. | +| 1714 | `Unlabeled` | one-way | ATM, DNA35 | `kh2axp1` | internal-state conversion/modification | `DNA35(site!?~sdsb,h2ax~u) + ATM(state~35,h2ax) -> DNA35(site!?~sdsb,h2ax~p) + ATM(state~35,h2ax)` | Changes internal modification/state marks on ATM, DNA35: DNA35.h2ax u→p at `kh2axp1`. | +| 1715 | `Unlabeled` | one-way | ATM, DNA36 | `kh2axp1` | internal-state conversion/modification | `DNA36(site!?~sdsb,h2ax~u) + ATM(state~36,h2ax) -> DNA36(site!?~sdsb,h2ax~p) + ATM(state~36,h2ax)` | Changes internal modification/state marks on ATM, DNA36: DNA36.h2ax u→p at `kh2axp1`. | +| 1716 | `Unlabeled` | one-way | ATM, DNA37 | `kh2axp1` | internal-state conversion/modification | `DNA37(site!?~sdsb,h2ax~u) + ATM(state~37,h2ax) -> DNA37(site!?~sdsb,h2ax~p) + ATM(state~37,h2ax)` | Changes internal modification/state marks on ATM, DNA37: DNA37.h2ax u→p at `kh2axp1`. | +| 1717 | `Unlabeled` | one-way | ATM, DNA38 | `kh2axp1` | internal-state conversion/modification | `DNA38(site!?~sdsb,h2ax~u) + ATM(state~38,h2ax) -> DNA38(site!?~sdsb,h2ax~p) + ATM(state~38,h2ax)` | Changes internal modification/state marks on ATM, DNA38: DNA38.h2ax u→p at `kh2axp1`. | +| 1718 | `Unlabeled` | one-way | ATM, DNA39 | `kh2axp1` | internal-state conversion/modification | `DNA39(site!?~sdsb,h2ax~u) + ATM(state~39,h2ax) -> DNA39(site!?~sdsb,h2ax~p) + ATM(state~39,h2ax)` | Changes internal modification/state marks on ATM, DNA39: DNA39.h2ax u→p at `kh2axp1`. | +| 1719 | `Unlabeled` | one-way | ATM, DNA40 | `kh2axp1` | internal-state conversion/modification | `DNA40(site!?~sdsb,h2ax~u) + ATM(state~40,h2ax) -> DNA40(site!?~sdsb,h2ax~p) + ATM(state~40,h2ax)` | Changes internal modification/state marks on ATM, DNA40: DNA40.h2ax u→p at `kh2axp1`. | +| 1720 | `Unlabeled` | one-way | ATM, DNA41 | `kh2axp1` | internal-state conversion/modification | `DNA41(site!?~sdsb,h2ax~u) + ATM(state~41,h2ax) -> DNA41(site!?~sdsb,h2ax~p) + ATM(state~41,h2ax)` | Changes internal modification/state marks on ATM, DNA41: DNA41.h2ax u→p at `kh2axp1`. | +| 1721 | `Unlabeled` | one-way | ATM, DNA42 | `kh2axp1` | internal-state conversion/modification | `DNA42(site!?~sdsb,h2ax~u) + ATM(state~42,h2ax) -> DNA42(site!?~sdsb,h2ax~p) + ATM(state~42,h2ax)` | Changes internal modification/state marks on ATM, DNA42: DNA42.h2ax u→p at `kh2axp1`. | +| 1722 | `Unlabeled` | one-way | ATM, DNA43 | `kh2axp1` | internal-state conversion/modification | `DNA43(site!?~sdsb,h2ax~u) + ATM(state~43,h2ax) -> DNA43(site!?~sdsb,h2ax~p) + ATM(state~43,h2ax)` | Changes internal modification/state marks on ATM, DNA43: DNA43.h2ax u→p at `kh2axp1`. | +| 1723 | `Unlabeled` | one-way | ATM, DNA44 | `kh2axp1` | internal-state conversion/modification | `DNA44(site!?~sdsb,h2ax~u) + ATM(state~44,h2ax) -> DNA44(site!?~sdsb,h2ax~p) + ATM(state~44,h2ax)` | Changes internal modification/state marks on ATM, DNA44: DNA44.h2ax u→p at `kh2axp1`. | +| 1724 | `Unlabeled` | one-way | ATM, DNA45 | `kh2axp1` | internal-state conversion/modification | `DNA45(site!?~sdsb,h2ax~u) + ATM(state~45,h2ax) -> DNA45(site!?~sdsb,h2ax~p) + ATM(state~45,h2ax)` | Changes internal modification/state marks on ATM, DNA45: DNA45.h2ax u→p at `kh2axp1`. | +| 1725 | `Unlabeled` | one-way | ATM, DNA46 | `kh2axp1` | internal-state conversion/modification | `DNA46(site!?~sdsb,h2ax~u) + ATM(state~46,h2ax) -> DNA46(site!?~sdsb,h2ax~p) + ATM(state~46,h2ax)` | Changes internal modification/state marks on ATM, DNA46: DNA46.h2ax u→p at `kh2axp1`. | +| 1726 | `Unlabeled` | one-way | ATM, DNA47 | `kh2axp1` | internal-state conversion/modification | `DNA47(site!?~sdsb,h2ax~u) + ATM(state~47,h2ax) -> DNA47(site!?~sdsb,h2ax~p) + ATM(state~47,h2ax)` | Changes internal modification/state marks on ATM, DNA47: DNA47.h2ax u→p at `kh2axp1`. | +| 1727 | `Unlabeled` | one-way | ATM, DNA48 | `kh2axp1` | internal-state conversion/modification | `DNA48(site!?~sdsb,h2ax~u) + ATM(state~48,h2ax) -> DNA48(site!?~sdsb,h2ax~p) + ATM(state~48,h2ax)` | Changes internal modification/state marks on ATM, DNA48: DNA48.h2ax u→p at `kh2axp1`. | +| 1728 | `Unlabeled` | one-way | ATM, DNA49 | `kh2axp1` | internal-state conversion/modification | `DNA49(site!?~sdsb,h2ax~u) + ATM(state~49,h2ax) -> DNA49(site!?~sdsb,h2ax~p) + ATM(state~49,h2ax)` | Changes internal modification/state marks on ATM, DNA49: DNA49.h2ax u→p at `kh2axp1`. | +| 1729 | `Unlabeled` | one-way | ATM, DNA50 | `kh2axp1` | internal-state conversion/modification | `DNA50(site!?~sdsb,h2ax~u) + ATM(state~50,h2ax) -> DNA50(site!?~sdsb,h2ax~p) + ATM(state~50,h2ax)` | Changes internal modification/state marks on ATM, DNA50: DNA50.h2ax u→p at `kh2axp1`. | +| 1730 | `Unlabeled` | one-way | ATM, DNA1 | `kh2axp1` | internal-state conversion/modification | `DNA1(site!?~cdsb,h2ax~u) + ATM(state~1,h2ax) -> DNA1(site!?~cdsb,h2ax~p) + ATM(state~1,h2ax)` | Changes internal modification/state marks on ATM, DNA1: DNA1.h2ax u→p at `kh2axp1`. | +| 1731 | `Unlabeled` | one-way | ATM, DNA2 | `kh2axp1` | internal-state conversion/modification | `DNA2(site!?~cdsb,h2ax~u) + ATM(state~2,h2ax) -> DNA2(site!?~cdsb,h2ax~p) + ATM(state~2,h2ax)` | Changes internal modification/state marks on ATM, DNA2: DNA2.h2ax u→p at `kh2axp1`. | +| 1732 | `Unlabeled` | one-way | ATM, DNA3 | `kh2axp1` | internal-state conversion/modification | `DNA3(site!?~cdsb,h2ax~u) + ATM(state~3,h2ax) -> DNA3(site!?~cdsb,h2ax~p) + ATM(state~3,h2ax)` | Changes internal modification/state marks on ATM, DNA3: DNA3.h2ax u→p at `kh2axp1`. | +| 1733 | `Unlabeled` | one-way | ATM, DNA4 | `kh2axp1` | internal-state conversion/modification | `DNA4(site!?~cdsb,h2ax~u) + ATM(state~4,h2ax) -> DNA4(site!?~cdsb,h2ax~p) + ATM(state~4,h2ax)` | Changes internal modification/state marks on ATM, DNA4: DNA4.h2ax u→p at `kh2axp1`. | +| 1734 | `Unlabeled` | one-way | ATM, DNA5 | `kh2axp1` | internal-state conversion/modification | `DNA5(site!?~cdsb,h2ax~u) + ATM(state~5,h2ax) -> DNA5(site!?~cdsb,h2ax~p) + ATM(state~5,h2ax)` | Changes internal modification/state marks on ATM, DNA5: DNA5.h2ax u→p at `kh2axp1`. | +| 1735 | `Unlabeled` | one-way | ATM, DNA6 | `kh2axp1` | internal-state conversion/modification | `DNA6(site!?~cdsb,h2ax~u) + ATM(state~6,h2ax) -> DNA6(site!?~cdsb,h2ax~p) + ATM(state~6,h2ax)` | Changes internal modification/state marks on ATM, DNA6: DNA6.h2ax u→p at `kh2axp1`. | +| 1736 | `Unlabeled` | one-way | ATM, DNA7 | `kh2axp1` | internal-state conversion/modification | `DNA7(site!?~cdsb,h2ax~u) + ATM(state~7,h2ax) -> DNA7(site!?~cdsb,h2ax~p) + ATM(state~7,h2ax)` | Changes internal modification/state marks on ATM, DNA7: DNA7.h2ax u→p at `kh2axp1`. | +| 1737 | `Unlabeled` | one-way | ATM, DNA8 | `kh2axp1` | internal-state conversion/modification | `DNA8(site!?~cdsb,h2ax~u) + ATM(state~8,h2ax) -> DNA8(site!?~cdsb,h2ax~p) + ATM(state~8,h2ax)` | Changes internal modification/state marks on ATM, DNA8: DNA8.h2ax u→p at `kh2axp1`. | +| 1738 | `Unlabeled` | one-way | ATM, DNA9 | `kh2axp1` | internal-state conversion/modification | `DNA9(site!?~cdsb,h2ax~u) + ATM(state~9,h2ax) -> DNA9(site!?~cdsb,h2ax~p) + ATM(state~9,h2ax)` | Changes internal modification/state marks on ATM, DNA9: DNA9.h2ax u→p at `kh2axp1`. | +| 1739 | `Unlabeled` | one-way | ATM, DNA10 | `kh2axp1` | internal-state conversion/modification | `DNA10(site!?~cdsb,h2ax~u) + ATM(state~10,h2ax) -> DNA10(site!?~cdsb,h2ax~p) + ATM(state~10,h2ax)` | Changes internal modification/state marks on ATM, DNA10: DNA10.h2ax u→p at `kh2axp1`. | +| 1740 | `Unlabeled` | one-way | ATM, DNA11 | `kh2axp1` | internal-state conversion/modification | `DNA11(site!?~cdsb,h2ax~u) + ATM(state~11,h2ax) -> DNA11(site!?~cdsb,h2ax~p) + ATM(state~11,h2ax)` | Changes internal modification/state marks on ATM, DNA11: DNA11.h2ax u→p at `kh2axp1`. | +| 1741 | `Unlabeled` | one-way | ATM, DNA12 | `kh2axp1` | internal-state conversion/modification | `DNA12(site!?~cdsb,h2ax~u) + ATM(state~12,h2ax) -> DNA12(site!?~cdsb,h2ax~p) + ATM(state~12,h2ax)` | Changes internal modification/state marks on ATM, DNA12: DNA12.h2ax u→p at `kh2axp1`. | +| 1742 | `Unlabeled` | one-way | ATM, DNA13 | `kh2axp1` | internal-state conversion/modification | `DNA13(site!?~cdsb,h2ax~u) + ATM(state~13,h2ax) -> DNA13(site!?~cdsb,h2ax~p) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA13: DNA13.h2ax u→p at `kh2axp1`. | +| 1743 | `Unlabeled` | one-way | ATM, DNA14 | `kh2axp1` | internal-state conversion/modification | `DNA14(site!?~cdsb,h2ax~u) + ATM(state~14,h2ax) -> DNA14(site!?~cdsb,h2ax~p) + ATM(state~14,h2ax)` | Changes internal modification/state marks on ATM, DNA14: DNA14.h2ax u→p at `kh2axp1`. | +| 1744 | `Unlabeled` | one-way | ATM, DNA15 | `kh2axp1` | internal-state conversion/modification | `DNA15(site!?~cdsb,h2ax~u) + ATM(state~15,h2ax) -> DNA15(site!?~cdsb,h2ax~p) + ATM(state~15,h2ax)` | Changes internal modification/state marks on ATM, DNA15: DNA15.h2ax u→p at `kh2axp1`. | +| 1745 | `Unlabeled` | one-way | ATM, DNA16 | `kh2axp1` | internal-state conversion/modification | `DNA16(site!?~cdsb,h2ax~u) + ATM(state~16,h2ax) -> DNA16(site!?~cdsb,h2ax~p) + ATM(state~16,h2ax)` | Changes internal modification/state marks on ATM, DNA16: DNA16.h2ax u→p at `kh2axp1`. | +| 1746 | `Unlabeled` | one-way | ATM, DNA17 | `kh2axp1` | internal-state conversion/modification | `DNA17(site!?~cdsb,h2ax~u) + ATM(state~17,h2ax) -> DNA17(site!?~cdsb,h2ax~p) + ATM(state~17,h2ax)` | Changes internal modification/state marks on ATM, DNA17: DNA17.h2ax u→p at `kh2axp1`. | +| 1747 | `Unlabeled` | one-way | ATM, DNA18 | `kh2axp1` | internal-state conversion/modification | `DNA18(site!?~cdsb,h2ax~u) + ATM(state~18,h2ax) -> DNA18(site!?~cdsb,h2ax~p) + ATM(state~18,h2ax)` | Changes internal modification/state marks on ATM, DNA18: DNA18.h2ax u→p at `kh2axp1`. | +| 1748 | `Unlabeled` | one-way | ATM, DNA19 | `kh2axp1` | internal-state conversion/modification | `DNA19(site!?~cdsb,h2ax~u) + ATM(state~19,h2ax) -> DNA19(site!?~cdsb,h2ax~p) + ATM(state~19,h2ax)` | Changes internal modification/state marks on ATM, DNA19: DNA19.h2ax u→p at `kh2axp1`. | +| 1749 | `Unlabeled` | one-way | ATM, DNA20 | `kh2axp1` | internal-state conversion/modification | `DNA20(site!?~cdsb,h2ax~u) + ATM(state~20,h2ax) -> DNA20(site!?~cdsb,h2ax~p) + ATM(state~20,h2ax)` | Changes internal modification/state marks on ATM, DNA20: DNA20.h2ax u→p at `kh2axp1`. | +| 1750 | `Unlabeled` | one-way | ATM, DNA21 | `kh2axp1` | internal-state conversion/modification | `DNA21(site!?~cdsb,h2ax~u) + ATM(state~21,h2ax) -> DNA21(site!?~cdsb,h2ax~p) + ATM(state~21,h2ax)` | Changes internal modification/state marks on ATM, DNA21: DNA21.h2ax u→p at `kh2axp1`. | + +### Rules 1751-2000 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1751 | `Unlabeled` | one-way | ATM, DNA22 | `kh2axp1` | internal-state conversion/modification | `DNA22(site!?~cdsb,h2ax~u) + ATM(state~22,h2ax) -> DNA22(site!?~cdsb,h2ax~p) + ATM(state~22,h2ax)` | Changes internal modification/state marks on ATM, DNA22: DNA22.h2ax u→p at `kh2axp1`. | +| 1752 | `Unlabeled` | one-way | ATM, DNA23 | `kh2axp1` | internal-state conversion/modification | `DNA23(site!?~cdsb,h2ax~u) + ATM(state~23,h2ax) -> DNA23(site!?~cdsb,h2ax~p) + ATM(state~23,h2ax)` | Changes internal modification/state marks on ATM, DNA23: DNA23.h2ax u→p at `kh2axp1`. | +| 1753 | `Unlabeled` | one-way | ATM, DNA24 | `kh2axp1` | internal-state conversion/modification | `DNA24(site!?~cdsb,h2ax~u) + ATM(state~24,h2ax) -> DNA24(site!?~cdsb,h2ax~p) + ATM(state~24,h2ax)` | Changes internal modification/state marks on ATM, DNA24: DNA24.h2ax u→p at `kh2axp1`. | +| 1754 | `Unlabeled` | one-way | ATM, DNA25 | `kh2axp1` | internal-state conversion/modification | `DNA25(site!?~cdsb,h2ax~u) + ATM(state~25,h2ax) -> DNA25(site!?~cdsb,h2ax~p) + ATM(state~25,h2ax)` | Changes internal modification/state marks on ATM, DNA25: DNA25.h2ax u→p at `kh2axp1`. | +| 1755 | `Unlabeled` | one-way | ATM, DNA26 | `kh2axp1` | internal-state conversion/modification | `DNA26(site!?~cdsb,h2ax~u) + ATM(state~26,h2ax) -> DNA26(site!?~cdsb,h2ax~p) + ATM(state~26,h2ax)` | Changes internal modification/state marks on ATM, DNA26: DNA26.h2ax u→p at `kh2axp1`. | +| 1756 | `Unlabeled` | one-way | ATM, DNA27 | `kh2axp1` | internal-state conversion/modification | `DNA27(site!?~cdsb,h2ax~u) + ATM(state~27,h2ax) -> DNA27(site!?~cdsb,h2ax~p) + ATM(state~27,h2ax)` | Changes internal modification/state marks on ATM, DNA27: DNA27.h2ax u→p at `kh2axp1`. | +| 1757 | `Unlabeled` | one-way | ATM, DNA28 | `kh2axp1` | internal-state conversion/modification | `DNA28(site!?~cdsb,h2ax~u) + ATM(state~28,h2ax) -> DNA28(site!?~cdsb,h2ax~p) + ATM(state~28,h2ax)` | Changes internal modification/state marks on ATM, DNA28: DNA28.h2ax u→p at `kh2axp1`. | +| 1758 | `Unlabeled` | one-way | ATM, DNA29 | `kh2axp1` | internal-state conversion/modification | `DNA29(site!?~cdsb,h2ax~u) + ATM(state~29,h2ax) -> DNA29(site!?~cdsb,h2ax~p) + ATM(state~29,h2ax)` | Changes internal modification/state marks on ATM, DNA29: DNA29.h2ax u→p at `kh2axp1`. | +| 1759 | `Unlabeled` | one-way | ATM, DNA30 | `kh2axp1` | internal-state conversion/modification | `DNA30(site!?~cdsb,h2ax~u) + ATM(state~30,h2ax) -> DNA30(site!?~cdsb,h2ax~p) + ATM(state~30,h2ax)` | Changes internal modification/state marks on ATM, DNA30: DNA30.h2ax u→p at `kh2axp1`. | +| 1760 | `Unlabeled` | one-way | ATM, DNA31 | `kh2axp1` | internal-state conversion/modification | `DNA31(site!?~cdsb,h2ax~u) + ATM(state~31,h2ax) -> DNA31(site!?~cdsb,h2ax~p) + ATM(state~31,h2ax)` | Changes internal modification/state marks on ATM, DNA31: DNA31.h2ax u→p at `kh2axp1`. | +| 1761 | `Unlabeled` | one-way | ATM, DNA32 | `kh2axp1` | internal-state conversion/modification | `DNA32(site!?~cdsb,h2ax~u) + ATM(state~32,h2ax) -> DNA32(site!?~cdsb,h2ax~p) + ATM(state~32,h2ax)` | Changes internal modification/state marks on ATM, DNA32: DNA32.h2ax u→p at `kh2axp1`. | +| 1762 | `Unlabeled` | one-way | ATM, DNA33 | `kh2axp1` | internal-state conversion/modification | `DNA33(site!?~cdsb,h2ax~u) + ATM(state~33,h2ax) -> DNA33(site!?~cdsb,h2ax~p) + ATM(state~33,h2ax)` | Changes internal modification/state marks on ATM, DNA33: DNA33.h2ax u→p at `kh2axp1`. | +| 1763 | `Unlabeled` | one-way | ATM, DNA34 | `kh2axp1` | internal-state conversion/modification | `DNA34(site!?~cdsb,h2ax~u) + ATM(state~34,h2ax) -> DNA34(site!?~cdsb,h2ax~p) + ATM(state~34,h2ax)` | Changes internal modification/state marks on ATM, DNA34: DNA34.h2ax u→p at `kh2axp1`. | +| 1764 | `Unlabeled` | one-way | ATM, DNA35 | `kh2axp1` | internal-state conversion/modification | `DNA35(site!?~cdsb,h2ax~u) + ATM(state~35,h2ax) -> DNA35(site!?~cdsb,h2ax~p) + ATM(state~35,h2ax)` | Changes internal modification/state marks on ATM, DNA35: DNA35.h2ax u→p at `kh2axp1`. | +| 1765 | `Unlabeled` | one-way | ATM, DNA36 | `kh2axp1` | internal-state conversion/modification | `DNA36(site!?~cdsb,h2ax~u) + ATM(state~36,h2ax) -> DNA36(site!?~cdsb,h2ax~p) + ATM(state~36,h2ax)` | Changes internal modification/state marks on ATM, DNA36: DNA36.h2ax u→p at `kh2axp1`. | +| 1766 | `Unlabeled` | one-way | ATM, DNA37 | `kh2axp1` | internal-state conversion/modification | `DNA37(site!?~cdsb,h2ax~u) + ATM(state~37,h2ax) -> DNA37(site!?~cdsb,h2ax~p) + ATM(state~37,h2ax)` | Changes internal modification/state marks on ATM, DNA37: DNA37.h2ax u→p at `kh2axp1`. | +| 1767 | `Unlabeled` | one-way | ATM, DNA38 | `kh2axp1` | internal-state conversion/modification | `DNA38(site!?~cdsb,h2ax~u) + ATM(state~38,h2ax) -> DNA38(site!?~cdsb,h2ax~p) + ATM(state~38,h2ax)` | Changes internal modification/state marks on ATM, DNA38: DNA38.h2ax u→p at `kh2axp1`. | +| 1768 | `Unlabeled` | one-way | ATM, DNA39 | `kh2axp1` | internal-state conversion/modification | `DNA39(site!?~cdsb,h2ax~u) + ATM(state~39,h2ax) -> DNA39(site!?~cdsb,h2ax~p) + ATM(state~39,h2ax)` | Changes internal modification/state marks on ATM, DNA39: DNA39.h2ax u→p at `kh2axp1`. | +| 1769 | `Unlabeled` | one-way | ATM, DNA40 | `kh2axp1` | internal-state conversion/modification | `DNA40(site!?~cdsb,h2ax~u) + ATM(state~40,h2ax) -> DNA40(site!?~cdsb,h2ax~p) + ATM(state~40,h2ax)` | Changes internal modification/state marks on ATM, DNA40: DNA40.h2ax u→p at `kh2axp1`. | +| 1770 | `Unlabeled` | one-way | ATM, DNA41 | `kh2axp1` | internal-state conversion/modification | `DNA41(site!?~cdsb,h2ax~u) + ATM(state~41,h2ax) -> DNA41(site!?~cdsb,h2ax~p) + ATM(state~41,h2ax)` | Changes internal modification/state marks on ATM, DNA41: DNA41.h2ax u→p at `kh2axp1`. | +| 1771 | `Unlabeled` | one-way | ATM, DNA42 | `kh2axp1` | internal-state conversion/modification | `DNA42(site!?~cdsb,h2ax~u) + ATM(state~42,h2ax) -> DNA42(site!?~cdsb,h2ax~p) + ATM(state~42,h2ax)` | Changes internal modification/state marks on ATM, DNA42: DNA42.h2ax u→p at `kh2axp1`. | +| 1772 | `Unlabeled` | one-way | ATM, DNA43 | `kh2axp1` | internal-state conversion/modification | `DNA43(site!?~cdsb,h2ax~u) + ATM(state~43,h2ax) -> DNA43(site!?~cdsb,h2ax~p) + ATM(state~43,h2ax)` | Changes internal modification/state marks on ATM, DNA43: DNA43.h2ax u→p at `kh2axp1`. | +| 1773 | `Unlabeled` | one-way | ATM, DNA44 | `kh2axp1` | internal-state conversion/modification | `DNA44(site!?~cdsb,h2ax~u) + ATM(state~44,h2ax) -> DNA44(site!?~cdsb,h2ax~p) + ATM(state~44,h2ax)` | Changes internal modification/state marks on ATM, DNA44: DNA44.h2ax u→p at `kh2axp1`. | +| 1774 | `Unlabeled` | one-way | ATM, DNA45 | `kh2axp1` | internal-state conversion/modification | `DNA45(site!?~cdsb,h2ax~u) + ATM(state~45,h2ax) -> DNA45(site!?~cdsb,h2ax~p) + ATM(state~45,h2ax)` | Changes internal modification/state marks on ATM, DNA45: DNA45.h2ax u→p at `kh2axp1`. | +| 1775 | `Unlabeled` | one-way | ATM, DNA46 | `kh2axp1` | internal-state conversion/modification | `DNA46(site!?~cdsb,h2ax~u) + ATM(state~46,h2ax) -> DNA46(site!?~cdsb,h2ax~p) + ATM(state~46,h2ax)` | Changes internal modification/state marks on ATM, DNA46: DNA46.h2ax u→p at `kh2axp1`. | +| 1776 | `Unlabeled` | one-way | ATM, DNA47 | `kh2axp1` | internal-state conversion/modification | `DNA47(site!?~cdsb,h2ax~u) + ATM(state~47,h2ax) -> DNA47(site!?~cdsb,h2ax~p) + ATM(state~47,h2ax)` | Changes internal modification/state marks on ATM, DNA47: DNA47.h2ax u→p at `kh2axp1`. | +| 1777 | `Unlabeled` | one-way | ATM, DNA48 | `kh2axp1` | internal-state conversion/modification | `DNA48(site!?~cdsb,h2ax~u) + ATM(state~48,h2ax) -> DNA48(site!?~cdsb,h2ax~p) + ATM(state~48,h2ax)` | Changes internal modification/state marks on ATM, DNA48: DNA48.h2ax u→p at `kh2axp1`. | +| 1778 | `Unlabeled` | one-way | ATM, DNA49 | `kh2axp1` | internal-state conversion/modification | `DNA49(site!?~cdsb,h2ax~u) + ATM(state~49,h2ax) -> DNA49(site!?~cdsb,h2ax~p) + ATM(state~49,h2ax)` | Changes internal modification/state marks on ATM, DNA49: DNA49.h2ax u→p at `kh2axp1`. | +| 1779 | `Unlabeled` | one-way | ATM, DNA50 | `kh2axp1` | internal-state conversion/modification | `DNA50(site!?~cdsb,h2ax~u) + ATM(state~50,h2ax) -> DNA50(site!?~cdsb,h2ax~p) + ATM(state~50,h2ax)` | Changes internal modification/state marks on ATM, DNA50: DNA50.h2ax u→p at `kh2axp1`. | +| 1780 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA1(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA1(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA1, DNAPKcs, Ku: DNA1.h2ax u→p at `kh2axp2`. | +| 1781 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA2(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA2(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA2, DNAPKcs, Ku: DNA2.h2ax u→p at `kh2axp2`. | +| 1782 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA3(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA3(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA3, DNAPKcs, Ku: DNA3.h2ax u→p at `kh2axp2`. | +| 1783 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA4(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA4(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA4, DNAPKcs, Ku: DNA4.h2ax u→p at `kh2axp2`. | +| 1784 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA5(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA5(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA5, DNAPKcs, Ku: DNA5.h2ax u→p at `kh2axp2`. | +| 1785 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA6(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA6(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA6, DNAPKcs, Ku: DNA6.h2ax u→p at `kh2axp2`. | +| 1786 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA7(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA7(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA7, DNAPKcs, Ku: DNA7.h2ax u→p at `kh2axp2`. | +| 1787 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA8(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA8(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA8, DNAPKcs, Ku: DNA8.h2ax u→p at `kh2axp2`. | +| 1788 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA9(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA9(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA9, DNAPKcs, Ku: DNA9.h2ax u→p at `kh2axp2`. | +| 1789 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA10(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA10(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA10, DNAPKcs, Ku: DNA10.h2ax u→p at `kh2axp2`. | +| 1790 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA11(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA11(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA11, DNAPKcs, Ku: DNA11.h2ax u→p at `kh2axp2`. | +| 1791 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA12(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA12(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA12, DNAPKcs, Ku: DNA12.h2ax u→p at `kh2axp2`. | +| 1792 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA13(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA13(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA13, DNAPKcs, Ku: DNA13.h2ax u→p at `kh2axp2`. | +| 1793 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA14(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA14(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA14, DNAPKcs, Ku: DNA14.h2ax u→p at `kh2axp2`. | +| 1794 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA15(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA15(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA15, DNAPKcs, Ku: DNA15.h2ax u→p at `kh2axp2`. | +| 1795 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA16(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA16(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA16, DNAPKcs, Ku: DNA16.h2ax u→p at `kh2axp2`. | +| 1796 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA17(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA17(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA17, DNAPKcs, Ku: DNA17.h2ax u→p at `kh2axp2`. | +| 1797 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA18(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA18(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA18, DNAPKcs, Ku: DNA18.h2ax u→p at `kh2axp2`. | +| 1798 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA19(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA19(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA19, DNAPKcs, Ku: DNA19.h2ax u→p at `kh2axp2`. | +| 1799 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA20(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA20(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA20, DNAPKcs, Ku: DNA20.h2ax u→p at `kh2axp2`. | +| 1800 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA21(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA21(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA21, DNAPKcs, Ku: DNA21.h2ax u→p at `kh2axp2`. | +| 1801 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA22(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA22(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA22, DNAPKcs, Ku: DNA22.h2ax u→p at `kh2axp2`. | +| 1802 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA23(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA23(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA23, DNAPKcs, Ku: DNA23.h2ax u→p at `kh2axp2`. | +| 1803 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA24(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA24(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA24, DNAPKcs, Ku: DNA24.h2ax u→p at `kh2axp2`. | +| 1804 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA25(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA25(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA25, DNAPKcs, Ku: DNA25.h2ax u→p at `kh2axp2`. | +| 1805 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA26(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA26(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA26, DNAPKcs, Ku: DNA26.h2ax u→p at `kh2axp2`. | +| 1806 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA27(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA27(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA27, DNAPKcs, Ku: DNA27.h2ax u→p at `kh2axp2`. | +| 1807 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA28(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA28(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA28, DNAPKcs, Ku: DNA28.h2ax u→p at `kh2axp2`. | +| 1808 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA29(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA29(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA29, DNAPKcs, Ku: DNA29.h2ax u→p at `kh2axp2`. | +| 1809 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA30(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA30(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA30, DNAPKcs, Ku: DNA30.h2ax u→p at `kh2axp2`. | +| 1810 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA31(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA31(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA31, DNAPKcs, Ku: DNA31.h2ax u→p at `kh2axp2`. | +| 1811 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA32(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA32(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA32, DNAPKcs, Ku: DNA32.h2ax u→p at `kh2axp2`. | +| 1812 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA33(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA33(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA33, DNAPKcs, Ku: DNA33.h2ax u→p at `kh2axp2`. | +| 1813 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA34(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA34(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA34, DNAPKcs, Ku: DNA34.h2ax u→p at `kh2axp2`. | +| 1814 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA35(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA35(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA35, DNAPKcs, Ku: DNA35.h2ax u→p at `kh2axp2`. | +| 1815 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA36(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA36(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA36, DNAPKcs, Ku: DNA36.h2ax u→p at `kh2axp2`. | +| 1816 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA37(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA37(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA37, DNAPKcs, Ku: DNA37.h2ax u→p at `kh2axp2`. | +| 1817 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA38(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA38(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA38, DNAPKcs, Ku: DNA38.h2ax u→p at `kh2axp2`. | +| 1818 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA39(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA39(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA39, DNAPKcs, Ku: DNA39.h2ax u→p at `kh2axp2`. | +| 1819 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA40(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA40(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA40, DNAPKcs, Ku: DNA40.h2ax u→p at `kh2axp2`. | +| 1820 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA41(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA41(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA41, DNAPKcs, Ku: DNA41.h2ax u→p at `kh2axp2`. | +| 1821 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA42(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA42(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA42, DNAPKcs, Ku: DNA42.h2ax u→p at `kh2axp2`. | +| 1822 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA43(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA43(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA43, DNAPKcs, Ku: DNA43.h2ax u→p at `kh2axp2`. | +| 1823 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA44(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA44(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA44, DNAPKcs, Ku: DNA44.h2ax u→p at `kh2axp2`. | +| 1824 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA45(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA45(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA45, DNAPKcs, Ku: DNA45.h2ax u→p at `kh2axp2`. | +| 1825 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA46(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA46(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA46, DNAPKcs, Ku: DNA46.h2ax u→p at `kh2axp2`. | +| 1826 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA47(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA47(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA47, DNAPKcs, Ku: DNA47.h2ax u→p at `kh2axp2`. | +| 1827 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA48(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA48(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA48, DNAPKcs, Ku: DNA48.h2ax u→p at `kh2axp2`. | +| 1828 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA49(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA49(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA49, DNAPKcs, Ku: DNA49.h2ax u→p at `kh2axp2`. | +| 1829 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA50(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA50(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA50, DNAPKcs, Ku: DNA50.h2ax u→p at `kh2axp2`. | +| 1830 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA1(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA1(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA1, DNAPKcs, Ku: DNA1.h2ax u→p at `kh2axp2`. | +| 1831 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA2(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA2(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA2, DNAPKcs, Ku: DNA2.h2ax u→p at `kh2axp2`. | +| 1832 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA3(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA3(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA3, DNAPKcs, Ku: DNA3.h2ax u→p at `kh2axp2`. | +| 1833 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA4(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA4(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA4, DNAPKcs, Ku: DNA4.h2ax u→p at `kh2axp2`. | +| 1834 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA5(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA5(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA5, DNAPKcs, Ku: DNA5.h2ax u→p at `kh2axp2`. | +| 1835 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA6(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA6(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA6, DNAPKcs, Ku: DNA6.h2ax u→p at `kh2axp2`. | +| 1836 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA7(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA7(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA7, DNAPKcs, Ku: DNA7.h2ax u→p at `kh2axp2`. | +| 1837 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA8(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA8(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA8, DNAPKcs, Ku: DNA8.h2ax u→p at `kh2axp2`. | +| 1838 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA9(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA9(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA9, DNAPKcs, Ku: DNA9.h2ax u→p at `kh2axp2`. | +| 1839 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA10(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA10(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA10, DNAPKcs, Ku: DNA10.h2ax u→p at `kh2axp2`. | +| 1840 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA11(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA11(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA11, DNAPKcs, Ku: DNA11.h2ax u→p at `kh2axp2`. | +| 1841 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA12(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA12(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA12, DNAPKcs, Ku: DNA12.h2ax u→p at `kh2axp2`. | +| 1842 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA13(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA13(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA13, DNAPKcs, Ku: DNA13.h2ax u→p at `kh2axp2`. | +| 1843 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA14(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA14(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA14, DNAPKcs, Ku: DNA14.h2ax u→p at `kh2axp2`. | +| 1844 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA15(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA15(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA15, DNAPKcs, Ku: DNA15.h2ax u→p at `kh2axp2`. | +| 1845 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA16(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA16(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA16, DNAPKcs, Ku: DNA16.h2ax u→p at `kh2axp2`. | +| 1846 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA17(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA17(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA17, DNAPKcs, Ku: DNA17.h2ax u→p at `kh2axp2`. | +| 1847 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA18(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA18(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA18, DNAPKcs, Ku: DNA18.h2ax u→p at `kh2axp2`. | +| 1848 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA19(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA19(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA19, DNAPKcs, Ku: DNA19.h2ax u→p at `kh2axp2`. | +| 1849 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA20(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA20(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA20, DNAPKcs, Ku: DNA20.h2ax u→p at `kh2axp2`. | +| 1850 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA21(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA21(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA21, DNAPKcs, Ku: DNA21.h2ax u→p at `kh2axp2`. | +| 1851 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA22(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA22(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA22, DNAPKcs, Ku: DNA22.h2ax u→p at `kh2axp2`. | +| 1852 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA23(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA23(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA23, DNAPKcs, Ku: DNA23.h2ax u→p at `kh2axp2`. | +| 1853 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA24(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA24(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA24, DNAPKcs, Ku: DNA24.h2ax u→p at `kh2axp2`. | +| 1854 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA25(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA25(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA25, DNAPKcs, Ku: DNA25.h2ax u→p at `kh2axp2`. | +| 1855 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA26(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA26(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA26, DNAPKcs, Ku: DNA26.h2ax u→p at `kh2axp2`. | +| 1856 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA27(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA27(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA27, DNAPKcs, Ku: DNA27.h2ax u→p at `kh2axp2`. | +| 1857 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA28(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA28(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA28, DNAPKcs, Ku: DNA28.h2ax u→p at `kh2axp2`. | +| 1858 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA29(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA29(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA29, DNAPKcs, Ku: DNA29.h2ax u→p at `kh2axp2`. | +| 1859 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA30(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA30(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA30, DNAPKcs, Ku: DNA30.h2ax u→p at `kh2axp2`. | +| 1860 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA31(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA31(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA31, DNAPKcs, Ku: DNA31.h2ax u→p at `kh2axp2`. | +| 1861 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA32(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA32(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA32, DNAPKcs, Ku: DNA32.h2ax u→p at `kh2axp2`. | +| 1862 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA33(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA33(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA33, DNAPKcs, Ku: DNA33.h2ax u→p at `kh2axp2`. | +| 1863 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA34(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA34(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA34, DNAPKcs, Ku: DNA34.h2ax u→p at `kh2axp2`. | +| 1864 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA35(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA35(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA35, DNAPKcs, Ku: DNA35.h2ax u→p at `kh2axp2`. | +| 1865 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA36(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA36(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA36, DNAPKcs, Ku: DNA36.h2ax u→p at `kh2axp2`. | +| 1866 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA37(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA37(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA37, DNAPKcs, Ku: DNA37.h2ax u→p at `kh2axp2`. | +| 1867 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA38(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA38(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA38, DNAPKcs, Ku: DNA38.h2ax u→p at `kh2axp2`. | +| 1868 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA39(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA39(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA39, DNAPKcs, Ku: DNA39.h2ax u→p at `kh2axp2`. | +| 1869 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA40(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA40(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA40, DNAPKcs, Ku: DNA40.h2ax u→p at `kh2axp2`. | +| 1870 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA41(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA41(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA41, DNAPKcs, Ku: DNA41.h2ax u→p at `kh2axp2`. | +| 1871 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA42(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA42(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA42, DNAPKcs, Ku: DNA42.h2ax u→p at `kh2axp2`. | +| 1872 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA43(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA43(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA43, DNAPKcs, Ku: DNA43.h2ax u→p at `kh2axp2`. | +| 1873 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA44(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA44(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA44, DNAPKcs, Ku: DNA44.h2ax u→p at `kh2axp2`. | +| 1874 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA45(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA45(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA45, DNAPKcs, Ku: DNA45.h2ax u→p at `kh2axp2`. | +| 1875 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA46(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA46(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA46, DNAPKcs, Ku: DNA46.h2ax u→p at `kh2axp2`. | +| 1876 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA47(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA47(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA47, DNAPKcs, Ku: DNA47.h2ax u→p at `kh2axp2`. | +| 1877 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA48(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA48(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA48, DNAPKcs, Ku: DNA48.h2ax u→p at `kh2axp2`. | +| 1878 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA49(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA49(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA49, DNAPKcs, Ku: DNA49.h2ax u→p at `kh2axp2`. | +| 1879 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA50(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA50(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA50, DNAPKcs, Ku: DNA50.h2ax u→p at `kh2axp2`. | +| 1880 | `Unlabeled` | one-way | DNA1 | `kh2axu` | internal-state conversion/modification | `DNA1(h2ax~p) -> DNA1(h2ax~u)` | Changes internal modification/state marks on DNA1: DNA1.h2ax p→u at `kh2axu`. | +| 1881 | `Unlabeled` | one-way | DNA2 | `kh2axu` | internal-state conversion/modification | `DNA2(h2ax~p) -> DNA2(h2ax~u)` | Changes internal modification/state marks on DNA2: DNA2.h2ax p→u at `kh2axu`. | +| 1882 | `Unlabeled` | one-way | DNA3 | `kh2axu` | internal-state conversion/modification | `DNA3(h2ax~p) -> DNA3(h2ax~u)` | Changes internal modification/state marks on DNA3: DNA3.h2ax p→u at `kh2axu`. | +| 1883 | `Unlabeled` | one-way | DNA4 | `kh2axu` | internal-state conversion/modification | `DNA4(h2ax~p) -> DNA4(h2ax~u)` | Changes internal modification/state marks on DNA4: DNA4.h2ax p→u at `kh2axu`. | +| 1884 | `Unlabeled` | one-way | DNA5 | `kh2axu` | internal-state conversion/modification | `DNA5(h2ax~p) -> DNA5(h2ax~u)` | Changes internal modification/state marks on DNA5: DNA5.h2ax p→u at `kh2axu`. | +| 1885 | `Unlabeled` | one-way | DNA6 | `kh2axu` | internal-state conversion/modification | `DNA6(h2ax~p) -> DNA6(h2ax~u)` | Changes internal modification/state marks on DNA6: DNA6.h2ax p→u at `kh2axu`. | +| 1886 | `Unlabeled` | one-way | DNA7 | `kh2axu` | internal-state conversion/modification | `DNA7(h2ax~p) -> DNA7(h2ax~u)` | Changes internal modification/state marks on DNA7: DNA7.h2ax p→u at `kh2axu`. | +| 1887 | `Unlabeled` | one-way | DNA8 | `kh2axu` | internal-state conversion/modification | `DNA8(h2ax~p) -> DNA8(h2ax~u)` | Changes internal modification/state marks on DNA8: DNA8.h2ax p→u at `kh2axu`. | +| 1888 | `Unlabeled` | one-way | DNA9 | `kh2axu` | internal-state conversion/modification | `DNA9(h2ax~p) -> DNA9(h2ax~u)` | Changes internal modification/state marks on DNA9: DNA9.h2ax p→u at `kh2axu`. | +| 1889 | `Unlabeled` | one-way | DNA10 | `kh2axu` | internal-state conversion/modification | `DNA10(h2ax~p) -> DNA10(h2ax~u)` | Changes internal modification/state marks on DNA10: DNA10.h2ax p→u at `kh2axu`. | +| 1890 | `Unlabeled` | one-way | DNA11 | `kh2axu` | internal-state conversion/modification | `DNA11(h2ax~p) -> DNA11(h2ax~u)` | Changes internal modification/state marks on DNA11: DNA11.h2ax p→u at `kh2axu`. | +| 1891 | `Unlabeled` | one-way | DNA12 | `kh2axu` | internal-state conversion/modification | `DNA12(h2ax~p) -> DNA12(h2ax~u)` | Changes internal modification/state marks on DNA12: DNA12.h2ax p→u at `kh2axu`. | +| 1892 | `Unlabeled` | one-way | DNA13 | `kh2axu` | internal-state conversion/modification | `DNA13(h2ax~p) -> DNA13(h2ax~u)` | Changes internal modification/state marks on DNA13: DNA13.h2ax p→u at `kh2axu`. | +| 1893 | `Unlabeled` | one-way | DNA14 | `kh2axu` | internal-state conversion/modification | `DNA14(h2ax~p) -> DNA14(h2ax~u)` | Changes internal modification/state marks on DNA14: DNA14.h2ax p→u at `kh2axu`. | +| 1894 | `Unlabeled` | one-way | DNA15 | `kh2axu` | internal-state conversion/modification | `DNA15(h2ax~p) -> DNA15(h2ax~u)` | Changes internal modification/state marks on DNA15: DNA15.h2ax p→u at `kh2axu`. | +| 1895 | `Unlabeled` | one-way | DNA16 | `kh2axu` | internal-state conversion/modification | `DNA16(h2ax~p) -> DNA16(h2ax~u)` | Changes internal modification/state marks on DNA16: DNA16.h2ax p→u at `kh2axu`. | +| 1896 | `Unlabeled` | one-way | DNA17 | `kh2axu` | internal-state conversion/modification | `DNA17(h2ax~p) -> DNA17(h2ax~u)` | Changes internal modification/state marks on DNA17: DNA17.h2ax p→u at `kh2axu`. | +| 1897 | `Unlabeled` | one-way | DNA18 | `kh2axu` | internal-state conversion/modification | `DNA18(h2ax~p) -> DNA18(h2ax~u)` | Changes internal modification/state marks on DNA18: DNA18.h2ax p→u at `kh2axu`. | +| 1898 | `Unlabeled` | one-way | DNA19 | `kh2axu` | internal-state conversion/modification | `DNA19(h2ax~p) -> DNA19(h2ax~u)` | Changes internal modification/state marks on DNA19: DNA19.h2ax p→u at `kh2axu`. | +| 1899 | `Unlabeled` | one-way | DNA20 | `kh2axu` | internal-state conversion/modification | `DNA20(h2ax~p) -> DNA20(h2ax~u)` | Changes internal modification/state marks on DNA20: DNA20.h2ax p→u at `kh2axu`. | +| 1900 | `Unlabeled` | one-way | DNA21 | `kh2axu` | internal-state conversion/modification | `DNA21(h2ax~p) -> DNA21(h2ax~u)` | Changes internal modification/state marks on DNA21: DNA21.h2ax p→u at `kh2axu`. | +| 1901 | `Unlabeled` | one-way | DNA22 | `kh2axu` | internal-state conversion/modification | `DNA22(h2ax~p) -> DNA22(h2ax~u)` | Changes internal modification/state marks on DNA22: DNA22.h2ax p→u at `kh2axu`. | +| 1902 | `Unlabeled` | one-way | DNA23 | `kh2axu` | internal-state conversion/modification | `DNA23(h2ax~p) -> DNA23(h2ax~u)` | Changes internal modification/state marks on DNA23: DNA23.h2ax p→u at `kh2axu`. | +| 1903 | `Unlabeled` | one-way | DNA24 | `kh2axu` | internal-state conversion/modification | `DNA24(h2ax~p) -> DNA24(h2ax~u)` | Changes internal modification/state marks on DNA24: DNA24.h2ax p→u at `kh2axu`. | +| 1904 | `Unlabeled` | one-way | DNA25 | `kh2axu` | internal-state conversion/modification | `DNA25(h2ax~p) -> DNA25(h2ax~u)` | Changes internal modification/state marks on DNA25: DNA25.h2ax p→u at `kh2axu`. | +| 1905 | `Unlabeled` | one-way | DNA26 | `kh2axu` | internal-state conversion/modification | `DNA26(h2ax~p) -> DNA26(h2ax~u)` | Changes internal modification/state marks on DNA26: DNA26.h2ax p→u at `kh2axu`. | +| 1906 | `Unlabeled` | one-way | DNA27 | `kh2axu` | internal-state conversion/modification | `DNA27(h2ax~p) -> DNA27(h2ax~u)` | Changes internal modification/state marks on DNA27: DNA27.h2ax p→u at `kh2axu`. | +| 1907 | `Unlabeled` | one-way | DNA28 | `kh2axu` | internal-state conversion/modification | `DNA28(h2ax~p) -> DNA28(h2ax~u)` | Changes internal modification/state marks on DNA28: DNA28.h2ax p→u at `kh2axu`. | +| 1908 | `Unlabeled` | one-way | DNA29 | `kh2axu` | internal-state conversion/modification | `DNA29(h2ax~p) -> DNA29(h2ax~u)` | Changes internal modification/state marks on DNA29: DNA29.h2ax p→u at `kh2axu`. | +| 1909 | `Unlabeled` | one-way | DNA30 | `kh2axu` | internal-state conversion/modification | `DNA30(h2ax~p) -> DNA30(h2ax~u)` | Changes internal modification/state marks on DNA30: DNA30.h2ax p→u at `kh2axu`. | +| 1910 | `Unlabeled` | one-way | DNA31 | `kh2axu` | internal-state conversion/modification | `DNA31(h2ax~p) -> DNA31(h2ax~u)` | Changes internal modification/state marks on DNA31: DNA31.h2ax p→u at `kh2axu`. | +| 1911 | `Unlabeled` | one-way | DNA32 | `kh2axu` | internal-state conversion/modification | `DNA32(h2ax~p) -> DNA32(h2ax~u)` | Changes internal modification/state marks on DNA32: DNA32.h2ax p→u at `kh2axu`. | +| 1912 | `Unlabeled` | one-way | DNA33 | `kh2axu` | internal-state conversion/modification | `DNA33(h2ax~p) -> DNA33(h2ax~u)` | Changes internal modification/state marks on DNA33: DNA33.h2ax p→u at `kh2axu`. | +| 1913 | `Unlabeled` | one-way | DNA34 | `kh2axu` | internal-state conversion/modification | `DNA34(h2ax~p) -> DNA34(h2ax~u)` | Changes internal modification/state marks on DNA34: DNA34.h2ax p→u at `kh2axu`. | +| 1914 | `Unlabeled` | one-way | DNA35 | `kh2axu` | internal-state conversion/modification | `DNA35(h2ax~p) -> DNA35(h2ax~u)` | Changes internal modification/state marks on DNA35: DNA35.h2ax p→u at `kh2axu`. | +| 1915 | `Unlabeled` | one-way | DNA36 | `kh2axu` | internal-state conversion/modification | `DNA36(h2ax~p) -> DNA36(h2ax~u)` | Changes internal modification/state marks on DNA36: DNA36.h2ax p→u at `kh2axu`. | +| 1916 | `Unlabeled` | one-way | DNA37 | `kh2axu` | internal-state conversion/modification | `DNA37(h2ax~p) -> DNA37(h2ax~u)` | Changes internal modification/state marks on DNA37: DNA37.h2ax p→u at `kh2axu`. | +| 1917 | `Unlabeled` | one-way | DNA38 | `kh2axu` | internal-state conversion/modification | `DNA38(h2ax~p) -> DNA38(h2ax~u)` | Changes internal modification/state marks on DNA38: DNA38.h2ax p→u at `kh2axu`. | +| 1918 | `Unlabeled` | one-way | DNA39 | `kh2axu` | internal-state conversion/modification | `DNA39(h2ax~p) -> DNA39(h2ax~u)` | Changes internal modification/state marks on DNA39: DNA39.h2ax p→u at `kh2axu`. | +| 1919 | `Unlabeled` | one-way | DNA40 | `kh2axu` | internal-state conversion/modification | `DNA40(h2ax~p) -> DNA40(h2ax~u)` | Changes internal modification/state marks on DNA40: DNA40.h2ax p→u at `kh2axu`. | +| 1920 | `Unlabeled` | one-way | DNA41 | `kh2axu` | internal-state conversion/modification | `DNA41(h2ax~p) -> DNA41(h2ax~u)` | Changes internal modification/state marks on DNA41: DNA41.h2ax p→u at `kh2axu`. | +| 1921 | `Unlabeled` | one-way | DNA42 | `kh2axu` | internal-state conversion/modification | `DNA42(h2ax~p) -> DNA42(h2ax~u)` | Changes internal modification/state marks on DNA42: DNA42.h2ax p→u at `kh2axu`. | +| 1922 | `Unlabeled` | one-way | DNA43 | `kh2axu` | internal-state conversion/modification | `DNA43(h2ax~p) -> DNA43(h2ax~u)` | Changes internal modification/state marks on DNA43: DNA43.h2ax p→u at `kh2axu`. | +| 1923 | `Unlabeled` | one-way | DNA44 | `kh2axu` | internal-state conversion/modification | `DNA44(h2ax~p) -> DNA44(h2ax~u)` | Changes internal modification/state marks on DNA44: DNA44.h2ax p→u at `kh2axu`. | +| 1924 | `Unlabeled` | one-way | DNA45 | `kh2axu` | internal-state conversion/modification | `DNA45(h2ax~p) -> DNA45(h2ax~u)` | Changes internal modification/state marks on DNA45: DNA45.h2ax p→u at `kh2axu`. | +| 1925 | `Unlabeled` | one-way | DNA46 | `kh2axu` | internal-state conversion/modification | `DNA46(h2ax~p) -> DNA46(h2ax~u)` | Changes internal modification/state marks on DNA46: DNA46.h2ax p→u at `kh2axu`. | +| 1926 | `Unlabeled` | one-way | DNA47 | `kh2axu` | internal-state conversion/modification | `DNA47(h2ax~p) -> DNA47(h2ax~u)` | Changes internal modification/state marks on DNA47: DNA47.h2ax p→u at `kh2axu`. | +| 1927 | `Unlabeled` | one-way | DNA48 | `kh2axu` | internal-state conversion/modification | `DNA48(h2ax~p) -> DNA48(h2ax~u)` | Changes internal modification/state marks on DNA48: DNA48.h2ax p→u at `kh2axu`. | +| 1928 | `Unlabeled` | one-way | DNA49 | `kh2axu` | internal-state conversion/modification | `DNA49(h2ax~p) -> DNA49(h2ax~u)` | Changes internal modification/state marks on DNA49: DNA49.h2ax p→u at `kh2axu`. | +| 1929 | `Unlabeled` | one-way | DNA50 | `kh2axu` | internal-state conversion/modification | `DNA50(h2ax~p) -> DNA50(h2ax~u)` | Changes internal modification/state marks on DNA50: DNA50.h2ax p→u at `kh2axu`. | +| 1930 | `Unlabeled` | one-way | DNA1 | `kh2axfoc` | internal-state conversion/modification | `DNA1(h2ax~p) -> DNA1(h2ax~foc)` | Changes internal modification/state marks on DNA1: DNA1.h2ax p→foc at `kh2axfoc`. | +| 1931 | `Unlabeled` | one-way | DNA2 | `kh2axfoc` | internal-state conversion/modification | `DNA2(h2ax~p) -> DNA2(h2ax~foc)` | Changes internal modification/state marks on DNA2: DNA2.h2ax p→foc at `kh2axfoc`. | +| 1932 | `Unlabeled` | one-way | DNA3 | `kh2axfoc` | internal-state conversion/modification | `DNA3(h2ax~p) -> DNA3(h2ax~foc)` | Changes internal modification/state marks on DNA3: DNA3.h2ax p→foc at `kh2axfoc`. | +| 1933 | `Unlabeled` | one-way | DNA4 | `kh2axfoc` | internal-state conversion/modification | `DNA4(h2ax~p) -> DNA4(h2ax~foc)` | Changes internal modification/state marks on DNA4: DNA4.h2ax p→foc at `kh2axfoc`. | +| 1934 | `Unlabeled` | one-way | DNA5 | `kh2axfoc` | internal-state conversion/modification | `DNA5(h2ax~p) -> DNA5(h2ax~foc)` | Changes internal modification/state marks on DNA5: DNA5.h2ax p→foc at `kh2axfoc`. | +| 1935 | `Unlabeled` | one-way | DNA6 | `kh2axfoc` | internal-state conversion/modification | `DNA6(h2ax~p) -> DNA6(h2ax~foc)` | Changes internal modification/state marks on DNA6: DNA6.h2ax p→foc at `kh2axfoc`. | +| 1936 | `Unlabeled` | one-way | DNA7 | `kh2axfoc` | internal-state conversion/modification | `DNA7(h2ax~p) -> DNA7(h2ax~foc)` | Changes internal modification/state marks on DNA7: DNA7.h2ax p→foc at `kh2axfoc`. | +| 1937 | `Unlabeled` | one-way | DNA8 | `kh2axfoc` | internal-state conversion/modification | `DNA8(h2ax~p) -> DNA8(h2ax~foc)` | Changes internal modification/state marks on DNA8: DNA8.h2ax p→foc at `kh2axfoc`. | +| 1938 | `Unlabeled` | one-way | DNA9 | `kh2axfoc` | internal-state conversion/modification | `DNA9(h2ax~p) -> DNA9(h2ax~foc)` | Changes internal modification/state marks on DNA9: DNA9.h2ax p→foc at `kh2axfoc`. | +| 1939 | `Unlabeled` | one-way | DNA10 | `kh2axfoc` | internal-state conversion/modification | `DNA10(h2ax~p) -> DNA10(h2ax~foc)` | Changes internal modification/state marks on DNA10: DNA10.h2ax p→foc at `kh2axfoc`. | +| 1940 | `Unlabeled` | one-way | DNA11 | `kh2axfoc` | internal-state conversion/modification | `DNA11(h2ax~p) -> DNA11(h2ax~foc)` | Changes internal modification/state marks on DNA11: DNA11.h2ax p→foc at `kh2axfoc`. | +| 1941 | `Unlabeled` | one-way | DNA12 | `kh2axfoc` | internal-state conversion/modification | `DNA12(h2ax~p) -> DNA12(h2ax~foc)` | Changes internal modification/state marks on DNA12: DNA12.h2ax p→foc at `kh2axfoc`. | +| 1942 | `Unlabeled` | one-way | DNA13 | `kh2axfoc` | internal-state conversion/modification | `DNA13(h2ax~p) -> DNA13(h2ax~foc)` | Changes internal modification/state marks on DNA13: DNA13.h2ax p→foc at `kh2axfoc`. | +| 1943 | `Unlabeled` | one-way | DNA14 | `kh2axfoc` | internal-state conversion/modification | `DNA14(h2ax~p) -> DNA14(h2ax~foc)` | Changes internal modification/state marks on DNA14: DNA14.h2ax p→foc at `kh2axfoc`. | +| 1944 | `Unlabeled` | one-way | DNA15 | `kh2axfoc` | internal-state conversion/modification | `DNA15(h2ax~p) -> DNA15(h2ax~foc)` | Changes internal modification/state marks on DNA15: DNA15.h2ax p→foc at `kh2axfoc`. | +| 1945 | `Unlabeled` | one-way | DNA16 | `kh2axfoc` | internal-state conversion/modification | `DNA16(h2ax~p) -> DNA16(h2ax~foc)` | Changes internal modification/state marks on DNA16: DNA16.h2ax p→foc at `kh2axfoc`. | +| 1946 | `Unlabeled` | one-way | DNA17 | `kh2axfoc` | internal-state conversion/modification | `DNA17(h2ax~p) -> DNA17(h2ax~foc)` | Changes internal modification/state marks on DNA17: DNA17.h2ax p→foc at `kh2axfoc`. | +| 1947 | `Unlabeled` | one-way | DNA18 | `kh2axfoc` | internal-state conversion/modification | `DNA18(h2ax~p) -> DNA18(h2ax~foc)` | Changes internal modification/state marks on DNA18: DNA18.h2ax p→foc at `kh2axfoc`. | +| 1948 | `Unlabeled` | one-way | DNA19 | `kh2axfoc` | internal-state conversion/modification | `DNA19(h2ax~p) -> DNA19(h2ax~foc)` | Changes internal modification/state marks on DNA19: DNA19.h2ax p→foc at `kh2axfoc`. | +| 1949 | `Unlabeled` | one-way | DNA20 | `kh2axfoc` | internal-state conversion/modification | `DNA20(h2ax~p) -> DNA20(h2ax~foc)` | Changes internal modification/state marks on DNA20: DNA20.h2ax p→foc at `kh2axfoc`. | +| 1950 | `Unlabeled` | one-way | DNA21 | `kh2axfoc` | internal-state conversion/modification | `DNA21(h2ax~p) -> DNA21(h2ax~foc)` | Changes internal modification/state marks on DNA21: DNA21.h2ax p→foc at `kh2axfoc`. | +| 1951 | `Unlabeled` | one-way | DNA22 | `kh2axfoc` | internal-state conversion/modification | `DNA22(h2ax~p) -> DNA22(h2ax~foc)` | Changes internal modification/state marks on DNA22: DNA22.h2ax p→foc at `kh2axfoc`. | +| 1952 | `Unlabeled` | one-way | DNA23 | `kh2axfoc` | internal-state conversion/modification | `DNA23(h2ax~p) -> DNA23(h2ax~foc)` | Changes internal modification/state marks on DNA23: DNA23.h2ax p→foc at `kh2axfoc`. | +| 1953 | `Unlabeled` | one-way | DNA24 | `kh2axfoc` | internal-state conversion/modification | `DNA24(h2ax~p) -> DNA24(h2ax~foc)` | Changes internal modification/state marks on DNA24: DNA24.h2ax p→foc at `kh2axfoc`. | +| 1954 | `Unlabeled` | one-way | DNA25 | `kh2axfoc` | internal-state conversion/modification | `DNA25(h2ax~p) -> DNA25(h2ax~foc)` | Changes internal modification/state marks on DNA25: DNA25.h2ax p→foc at `kh2axfoc`. | +| 1955 | `Unlabeled` | one-way | DNA26 | `kh2axfoc` | internal-state conversion/modification | `DNA26(h2ax~p) -> DNA26(h2ax~foc)` | Changes internal modification/state marks on DNA26: DNA26.h2ax p→foc at `kh2axfoc`. | +| 1956 | `Unlabeled` | one-way | DNA27 | `kh2axfoc` | internal-state conversion/modification | `DNA27(h2ax~p) -> DNA27(h2ax~foc)` | Changes internal modification/state marks on DNA27: DNA27.h2ax p→foc at `kh2axfoc`. | +| 1957 | `Unlabeled` | one-way | DNA28 | `kh2axfoc` | internal-state conversion/modification | `DNA28(h2ax~p) -> DNA28(h2ax~foc)` | Changes internal modification/state marks on DNA28: DNA28.h2ax p→foc at `kh2axfoc`. | +| 1958 | `Unlabeled` | one-way | DNA29 | `kh2axfoc` | internal-state conversion/modification | `DNA29(h2ax~p) -> DNA29(h2ax~foc)` | Changes internal modification/state marks on DNA29: DNA29.h2ax p→foc at `kh2axfoc`. | +| 1959 | `Unlabeled` | one-way | DNA30 | `kh2axfoc` | internal-state conversion/modification | `DNA30(h2ax~p) -> DNA30(h2ax~foc)` | Changes internal modification/state marks on DNA30: DNA30.h2ax p→foc at `kh2axfoc`. | +| 1960 | `Unlabeled` | one-way | DNA31 | `kh2axfoc` | internal-state conversion/modification | `DNA31(h2ax~p) -> DNA31(h2ax~foc)` | Changes internal modification/state marks on DNA31: DNA31.h2ax p→foc at `kh2axfoc`. | +| 1961 | `Unlabeled` | one-way | DNA32 | `kh2axfoc` | internal-state conversion/modification | `DNA32(h2ax~p) -> DNA32(h2ax~foc)` | Changes internal modification/state marks on DNA32: DNA32.h2ax p→foc at `kh2axfoc`. | +| 1962 | `Unlabeled` | one-way | DNA33 | `kh2axfoc` | internal-state conversion/modification | `DNA33(h2ax~p) -> DNA33(h2ax~foc)` | Changes internal modification/state marks on DNA33: DNA33.h2ax p→foc at `kh2axfoc`. | +| 1963 | `Unlabeled` | one-way | DNA34 | `kh2axfoc` | internal-state conversion/modification | `DNA34(h2ax~p) -> DNA34(h2ax~foc)` | Changes internal modification/state marks on DNA34: DNA34.h2ax p→foc at `kh2axfoc`. | +| 1964 | `Unlabeled` | one-way | DNA35 | `kh2axfoc` | internal-state conversion/modification | `DNA35(h2ax~p) -> DNA35(h2ax~foc)` | Changes internal modification/state marks on DNA35: DNA35.h2ax p→foc at `kh2axfoc`. | +| 1965 | `Unlabeled` | one-way | DNA36 | `kh2axfoc` | internal-state conversion/modification | `DNA36(h2ax~p) -> DNA36(h2ax~foc)` | Changes internal modification/state marks on DNA36: DNA36.h2ax p→foc at `kh2axfoc`. | +| 1966 | `Unlabeled` | one-way | DNA37 | `kh2axfoc` | internal-state conversion/modification | `DNA37(h2ax~p) -> DNA37(h2ax~foc)` | Changes internal modification/state marks on DNA37: DNA37.h2ax p→foc at `kh2axfoc`. | +| 1967 | `Unlabeled` | one-way | DNA38 | `kh2axfoc` | internal-state conversion/modification | `DNA38(h2ax~p) -> DNA38(h2ax~foc)` | Changes internal modification/state marks on DNA38: DNA38.h2ax p→foc at `kh2axfoc`. | +| 1968 | `Unlabeled` | one-way | DNA39 | `kh2axfoc` | internal-state conversion/modification | `DNA39(h2ax~p) -> DNA39(h2ax~foc)` | Changes internal modification/state marks on DNA39: DNA39.h2ax p→foc at `kh2axfoc`. | +| 1969 | `Unlabeled` | one-way | DNA40 | `kh2axfoc` | internal-state conversion/modification | `DNA40(h2ax~p) -> DNA40(h2ax~foc)` | Changes internal modification/state marks on DNA40: DNA40.h2ax p→foc at `kh2axfoc`. | +| 1970 | `Unlabeled` | one-way | DNA41 | `kh2axfoc` | internal-state conversion/modification | `DNA41(h2ax~p) -> DNA41(h2ax~foc)` | Changes internal modification/state marks on DNA41: DNA41.h2ax p→foc at `kh2axfoc`. | +| 1971 | `Unlabeled` | one-way | DNA42 | `kh2axfoc` | internal-state conversion/modification | `DNA42(h2ax~p) -> DNA42(h2ax~foc)` | Changes internal modification/state marks on DNA42: DNA42.h2ax p→foc at `kh2axfoc`. | +| 1972 | `Unlabeled` | one-way | DNA43 | `kh2axfoc` | internal-state conversion/modification | `DNA43(h2ax~p) -> DNA43(h2ax~foc)` | Changes internal modification/state marks on DNA43: DNA43.h2ax p→foc at `kh2axfoc`. | +| 1973 | `Unlabeled` | one-way | DNA44 | `kh2axfoc` | internal-state conversion/modification | `DNA44(h2ax~p) -> DNA44(h2ax~foc)` | Changes internal modification/state marks on DNA44: DNA44.h2ax p→foc at `kh2axfoc`. | +| 1974 | `Unlabeled` | one-way | DNA45 | `kh2axfoc` | internal-state conversion/modification | `DNA45(h2ax~p) -> DNA45(h2ax~foc)` | Changes internal modification/state marks on DNA45: DNA45.h2ax p→foc at `kh2axfoc`. | +| 1975 | `Unlabeled` | one-way | DNA46 | `kh2axfoc` | internal-state conversion/modification | `DNA46(h2ax~p) -> DNA46(h2ax~foc)` | Changes internal modification/state marks on DNA46: DNA46.h2ax p→foc at `kh2axfoc`. | +| 1976 | `Unlabeled` | one-way | DNA47 | `kh2axfoc` | internal-state conversion/modification | `DNA47(h2ax~p) -> DNA47(h2ax~foc)` | Changes internal modification/state marks on DNA47: DNA47.h2ax p→foc at `kh2axfoc`. | +| 1977 | `Unlabeled` | one-way | DNA48 | `kh2axfoc` | internal-state conversion/modification | `DNA48(h2ax~p) -> DNA48(h2ax~foc)` | Changes internal modification/state marks on DNA48: DNA48.h2ax p→foc at `kh2axfoc`. | +| 1978 | `Unlabeled` | one-way | DNA49 | `kh2axfoc` | internal-state conversion/modification | `DNA49(h2ax~p) -> DNA49(h2ax~foc)` | Changes internal modification/state marks on DNA49: DNA49.h2ax p→foc at `kh2axfoc`. | +| 1979 | `Unlabeled` | one-way | DNA50 | `kh2axfoc` | internal-state conversion/modification | `DNA50(h2ax~p) -> DNA50(h2ax~foc)` | Changes internal modification/state marks on DNA50: DNA50.h2ax p→foc at `kh2axfoc`. | +| 1980 | `Unlabeled` | one-way | DNA1 | `kfocback` | internal-state conversion/modification | `DNA1(h2ax~foc) -> DNA1(h2ax~u)` | Changes internal modification/state marks on DNA1: DNA1.h2ax foc→u at `kfocback`. | +| 1981 | `Unlabeled` | one-way | DNA2 | `kfocback` | internal-state conversion/modification | `DNA2(h2ax~foc) -> DNA2(h2ax~u)` | Changes internal modification/state marks on DNA2: DNA2.h2ax foc→u at `kfocback`. | +| 1982 | `Unlabeled` | one-way | DNA3 | `kfocback` | internal-state conversion/modification | `DNA3(h2ax~foc) -> DNA3(h2ax~u)` | Changes internal modification/state marks on DNA3: DNA3.h2ax foc→u at `kfocback`. | +| 1983 | `Unlabeled` | one-way | DNA4 | `kfocback` | internal-state conversion/modification | `DNA4(h2ax~foc) -> DNA4(h2ax~u)` | Changes internal modification/state marks on DNA4: DNA4.h2ax foc→u at `kfocback`. | +| 1984 | `Unlabeled` | one-way | DNA5 | `kfocback` | internal-state conversion/modification | `DNA5(h2ax~foc) -> DNA5(h2ax~u)` | Changes internal modification/state marks on DNA5: DNA5.h2ax foc→u at `kfocback`. | +| 1985 | `Unlabeled` | one-way | DNA6 | `kfocback` | internal-state conversion/modification | `DNA6(h2ax~foc) -> DNA6(h2ax~u)` | Changes internal modification/state marks on DNA6: DNA6.h2ax foc→u at `kfocback`. | +| 1986 | `Unlabeled` | one-way | DNA7 | `kfocback` | internal-state conversion/modification | `DNA7(h2ax~foc) -> DNA7(h2ax~u)` | Changes internal modification/state marks on DNA7: DNA7.h2ax foc→u at `kfocback`. | +| 1987 | `Unlabeled` | one-way | DNA8 | `kfocback` | internal-state conversion/modification | `DNA8(h2ax~foc) -> DNA8(h2ax~u)` | Changes internal modification/state marks on DNA8: DNA8.h2ax foc→u at `kfocback`. | +| 1988 | `Unlabeled` | one-way | DNA9 | `kfocback` | internal-state conversion/modification | `DNA9(h2ax~foc) -> DNA9(h2ax~u)` | Changes internal modification/state marks on DNA9: DNA9.h2ax foc→u at `kfocback`. | +| 1989 | `Unlabeled` | one-way | DNA10 | `kfocback` | internal-state conversion/modification | `DNA10(h2ax~foc) -> DNA10(h2ax~u)` | Changes internal modification/state marks on DNA10: DNA10.h2ax foc→u at `kfocback`. | +| 1990 | `Unlabeled` | one-way | DNA11 | `kfocback` | internal-state conversion/modification | `DNA11(h2ax~foc) -> DNA11(h2ax~u)` | Changes internal modification/state marks on DNA11: DNA11.h2ax foc→u at `kfocback`. | +| 1991 | `Unlabeled` | one-way | DNA12 | `kfocback` | internal-state conversion/modification | `DNA12(h2ax~foc) -> DNA12(h2ax~u)` | Changes internal modification/state marks on DNA12: DNA12.h2ax foc→u at `kfocback`. | +| 1992 | `Unlabeled` | one-way | DNA13 | `kfocback` | internal-state conversion/modification | `DNA13(h2ax~foc) -> DNA13(h2ax~u)` | Changes internal modification/state marks on DNA13: DNA13.h2ax foc→u at `kfocback`. | +| 1993 | `Unlabeled` | one-way | DNA14 | `kfocback` | internal-state conversion/modification | `DNA14(h2ax~foc) -> DNA14(h2ax~u)` | Changes internal modification/state marks on DNA14: DNA14.h2ax foc→u at `kfocback`. | +| 1994 | `Unlabeled` | one-way | DNA15 | `kfocback` | internal-state conversion/modification | `DNA15(h2ax~foc) -> DNA15(h2ax~u)` | Changes internal modification/state marks on DNA15: DNA15.h2ax foc→u at `kfocback`. | +| 1995 | `Unlabeled` | one-way | DNA16 | `kfocback` | internal-state conversion/modification | `DNA16(h2ax~foc) -> DNA16(h2ax~u)` | Changes internal modification/state marks on DNA16: DNA16.h2ax foc→u at `kfocback`. | +| 1996 | `Unlabeled` | one-way | DNA17 | `kfocback` | internal-state conversion/modification | `DNA17(h2ax~foc) -> DNA17(h2ax~u)` | Changes internal modification/state marks on DNA17: DNA17.h2ax foc→u at `kfocback`. | +| 1997 | `Unlabeled` | one-way | DNA18 | `kfocback` | internal-state conversion/modification | `DNA18(h2ax~foc) -> DNA18(h2ax~u)` | Changes internal modification/state marks on DNA18: DNA18.h2ax foc→u at `kfocback`. | +| 1998 | `Unlabeled` | one-way | DNA19 | `kfocback` | internal-state conversion/modification | `DNA19(h2ax~foc) -> DNA19(h2ax~u)` | Changes internal modification/state marks on DNA19: DNA19.h2ax foc→u at `kfocback`. | +| 1999 | `Unlabeled` | one-way | DNA20 | `kfocback` | internal-state conversion/modification | `DNA20(h2ax~foc) -> DNA20(h2ax~u)` | Changes internal modification/state marks on DNA20: DNA20.h2ax foc→u at `kfocback`. | +| 2000 | `Unlabeled` | one-way | DNA21 | `kfocback` | internal-state conversion/modification | `DNA21(h2ax~foc) -> DNA21(h2ax~u)` | Changes internal modification/state marks on DNA21: DNA21.h2ax foc→u at `kfocback`. | + +### Rules 2001-2250 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 2001 | `Unlabeled` | one-way | DNA22 | `kfocback` | internal-state conversion/modification | `DNA22(h2ax~foc) -> DNA22(h2ax~u)` | Changes internal modification/state marks on DNA22: DNA22.h2ax foc→u at `kfocback`. | +| 2002 | `Unlabeled` | one-way | DNA23 | `kfocback` | internal-state conversion/modification | `DNA23(h2ax~foc) -> DNA23(h2ax~u)` | Changes internal modification/state marks on DNA23: DNA23.h2ax foc→u at `kfocback`. | +| 2003 | `Unlabeled` | one-way | DNA24 | `kfocback` | internal-state conversion/modification | `DNA24(h2ax~foc) -> DNA24(h2ax~u)` | Changes internal modification/state marks on DNA24: DNA24.h2ax foc→u at `kfocback`. | +| 2004 | `Unlabeled` | one-way | DNA25 | `kfocback` | internal-state conversion/modification | `DNA25(h2ax~foc) -> DNA25(h2ax~u)` | Changes internal modification/state marks on DNA25: DNA25.h2ax foc→u at `kfocback`. | +| 2005 | `Unlabeled` | one-way | DNA26 | `kfocback` | internal-state conversion/modification | `DNA26(h2ax~foc) -> DNA26(h2ax~u)` | Changes internal modification/state marks on DNA26: DNA26.h2ax foc→u at `kfocback`. | +| 2006 | `Unlabeled` | one-way | DNA27 | `kfocback` | internal-state conversion/modification | `DNA27(h2ax~foc) -> DNA27(h2ax~u)` | Changes internal modification/state marks on DNA27: DNA27.h2ax foc→u at `kfocback`. | +| 2007 | `Unlabeled` | one-way | DNA28 | `kfocback` | internal-state conversion/modification | `DNA28(h2ax~foc) -> DNA28(h2ax~u)` | Changes internal modification/state marks on DNA28: DNA28.h2ax foc→u at `kfocback`. | +| 2008 | `Unlabeled` | one-way | DNA29 | `kfocback` | internal-state conversion/modification | `DNA29(h2ax~foc) -> DNA29(h2ax~u)` | Changes internal modification/state marks on DNA29: DNA29.h2ax foc→u at `kfocback`. | +| 2009 | `Unlabeled` | one-way | DNA30 | `kfocback` | internal-state conversion/modification | `DNA30(h2ax~foc) -> DNA30(h2ax~u)` | Changes internal modification/state marks on DNA30: DNA30.h2ax foc→u at `kfocback`. | +| 2010 | `Unlabeled` | one-way | DNA31 | `kfocback` | internal-state conversion/modification | `DNA31(h2ax~foc) -> DNA31(h2ax~u)` | Changes internal modification/state marks on DNA31: DNA31.h2ax foc→u at `kfocback`. | +| 2011 | `Unlabeled` | one-way | DNA32 | `kfocback` | internal-state conversion/modification | `DNA32(h2ax~foc) -> DNA32(h2ax~u)` | Changes internal modification/state marks on DNA32: DNA32.h2ax foc→u at `kfocback`. | +| 2012 | `Unlabeled` | one-way | DNA33 | `kfocback` | internal-state conversion/modification | `DNA33(h2ax~foc) -> DNA33(h2ax~u)` | Changes internal modification/state marks on DNA33: DNA33.h2ax foc→u at `kfocback`. | +| 2013 | `Unlabeled` | one-way | DNA34 | `kfocback` | internal-state conversion/modification | `DNA34(h2ax~foc) -> DNA34(h2ax~u)` | Changes internal modification/state marks on DNA34: DNA34.h2ax foc→u at `kfocback`. | +| 2014 | `Unlabeled` | one-way | DNA35 | `kfocback` | internal-state conversion/modification | `DNA35(h2ax~foc) -> DNA35(h2ax~u)` | Changes internal modification/state marks on DNA35: DNA35.h2ax foc→u at `kfocback`. | +| 2015 | `Unlabeled` | one-way | DNA36 | `kfocback` | internal-state conversion/modification | `DNA36(h2ax~foc) -> DNA36(h2ax~u)` | Changes internal modification/state marks on DNA36: DNA36.h2ax foc→u at `kfocback`. | +| 2016 | `Unlabeled` | one-way | DNA37 | `kfocback` | internal-state conversion/modification | `DNA37(h2ax~foc) -> DNA37(h2ax~u)` | Changes internal modification/state marks on DNA37: DNA37.h2ax foc→u at `kfocback`. | +| 2017 | `Unlabeled` | one-way | DNA38 | `kfocback` | internal-state conversion/modification | `DNA38(h2ax~foc) -> DNA38(h2ax~u)` | Changes internal modification/state marks on DNA38: DNA38.h2ax foc→u at `kfocback`. | +| 2018 | `Unlabeled` | one-way | DNA39 | `kfocback` | internal-state conversion/modification | `DNA39(h2ax~foc) -> DNA39(h2ax~u)` | Changes internal modification/state marks on DNA39: DNA39.h2ax foc→u at `kfocback`. | +| 2019 | `Unlabeled` | one-way | DNA40 | `kfocback` | internal-state conversion/modification | `DNA40(h2ax~foc) -> DNA40(h2ax~u)` | Changes internal modification/state marks on DNA40: DNA40.h2ax foc→u at `kfocback`. | +| 2020 | `Unlabeled` | one-way | DNA41 | `kfocback` | internal-state conversion/modification | `DNA41(h2ax~foc) -> DNA41(h2ax~u)` | Changes internal modification/state marks on DNA41: DNA41.h2ax foc→u at `kfocback`. | +| 2021 | `Unlabeled` | one-way | DNA42 | `kfocback` | internal-state conversion/modification | `DNA42(h2ax~foc) -> DNA42(h2ax~u)` | Changes internal modification/state marks on DNA42: DNA42.h2ax foc→u at `kfocback`. | +| 2022 | `Unlabeled` | one-way | DNA43 | `kfocback` | internal-state conversion/modification | `DNA43(h2ax~foc) -> DNA43(h2ax~u)` | Changes internal modification/state marks on DNA43: DNA43.h2ax foc→u at `kfocback`. | +| 2023 | `Unlabeled` | one-way | DNA44 | `kfocback` | internal-state conversion/modification | `DNA44(h2ax~foc) -> DNA44(h2ax~u)` | Changes internal modification/state marks on DNA44: DNA44.h2ax foc→u at `kfocback`. | +| 2024 | `Unlabeled` | one-way | DNA45 | `kfocback` | internal-state conversion/modification | `DNA45(h2ax~foc) -> DNA45(h2ax~u)` | Changes internal modification/state marks on DNA45: DNA45.h2ax foc→u at `kfocback`. | +| 2025 | `Unlabeled` | one-way | DNA46 | `kfocback` | internal-state conversion/modification | `DNA46(h2ax~foc) -> DNA46(h2ax~u)` | Changes internal modification/state marks on DNA46: DNA46.h2ax foc→u at `kfocback`. | +| 2026 | `Unlabeled` | one-way | DNA47 | `kfocback` | internal-state conversion/modification | `DNA47(h2ax~foc) -> DNA47(h2ax~u)` | Changes internal modification/state marks on DNA47: DNA47.h2ax foc→u at `kfocback`. | +| 2027 | `Unlabeled` | one-way | DNA48 | `kfocback` | internal-state conversion/modification | `DNA48(h2ax~foc) -> DNA48(h2ax~u)` | Changes internal modification/state marks on DNA48: DNA48.h2ax foc→u at `kfocback`. | +| 2028 | `Unlabeled` | one-way | DNA49 | `kfocback` | internal-state conversion/modification | `DNA49(h2ax~foc) -> DNA49(h2ax~u)` | Changes internal modification/state marks on DNA49: DNA49.h2ax foc→u at `kfocback`. | +| 2029 | `Unlabeled` | one-way | DNA50 | `kfocback` | internal-state conversion/modification | `DNA50(h2ax~foc) -> DNA50(h2ax~u)` | Changes internal modification/state marks on DNA50: DNA50.h2ax foc→u at `kfocback`. | +| 2030 | `Unlabeled` | one-way | ATM, DNA1 | `kh2axfull` | state and binding-pattern rewrite | `DNA1(h2ax~foc) + ATM(state~1,h2ax) -> DNA1(h2ax!1~foc).ATM(state~1,h2ax!1)` | Forms a complex/contact among ATM, DNA1 through ATM.h2ax, DNA1.h2ax at `kh2axfull`. | +| 2031 | `Unlabeled` | one-way | ATM, DNA2 | `kh2axfull` | state and binding-pattern rewrite | `DNA2(h2ax~foc) + ATM(state~2,h2ax) -> DNA2(h2ax!1~foc).ATM(state~2,h2ax!1)` | Forms a complex/contact among ATM, DNA2 through ATM.h2ax, DNA2.h2ax at `kh2axfull`. | +| 2032 | `Unlabeled` | one-way | ATM, DNA3 | `kh2axfull` | state and binding-pattern rewrite | `DNA3(h2ax~foc) + ATM(state~3,h2ax) -> DNA3(h2ax!1~foc).ATM(state~3,h2ax!1)` | Forms a complex/contact among ATM, DNA3 through ATM.h2ax, DNA3.h2ax at `kh2axfull`. | +| 2033 | `Unlabeled` | one-way | ATM, DNA4 | `kh2axfull` | state and binding-pattern rewrite | `DNA4(h2ax~foc) + ATM(state~4,h2ax) -> DNA4(h2ax!1~foc).ATM(state~4,h2ax!1)` | Forms a complex/contact among ATM, DNA4 through ATM.h2ax, DNA4.h2ax at `kh2axfull`. | +| 2034 | `Unlabeled` | one-way | ATM, DNA5 | `kh2axfull` | state and binding-pattern rewrite | `DNA5(h2ax~foc) + ATM(state~5,h2ax) -> DNA5(h2ax!1~foc).ATM(state~5,h2ax!1)` | Forms a complex/contact among ATM, DNA5 through ATM.h2ax, DNA5.h2ax at `kh2axfull`. | +| 2035 | `Unlabeled` | one-way | ATM, DNA6 | `kh2axfull` | state and binding-pattern rewrite | `DNA6(h2ax~foc) + ATM(state~6,h2ax) -> DNA6(h2ax!1~foc).ATM(state~6,h2ax!1)` | Forms a complex/contact among ATM, DNA6 through ATM.h2ax, DNA6.h2ax at `kh2axfull`. | +| 2036 | `Unlabeled` | one-way | ATM, DNA7 | `kh2axfull` | state and binding-pattern rewrite | `DNA7(h2ax~foc) + ATM(state~7,h2ax) -> DNA7(h2ax!1~foc).ATM(state~7,h2ax!1)` | Forms a complex/contact among ATM, DNA7 through ATM.h2ax, DNA7.h2ax at `kh2axfull`. | +| 2037 | `Unlabeled` | one-way | ATM, DNA8 | `kh2axfull` | state and binding-pattern rewrite | `DNA8(h2ax~foc) + ATM(state~8,h2ax) -> DNA8(h2ax!1~foc).ATM(state~8,h2ax!1)` | Forms a complex/contact among ATM, DNA8 through ATM.h2ax, DNA8.h2ax at `kh2axfull`. | +| 2038 | `Unlabeled` | one-way | ATM, DNA9 | `kh2axfull` | state and binding-pattern rewrite | `DNA9(h2ax~foc) + ATM(state~9,h2ax) -> DNA9(h2ax!1~foc).ATM(state~9,h2ax!1)` | Forms a complex/contact among ATM, DNA9 through ATM.h2ax, DNA9.h2ax at `kh2axfull`. | +| 2039 | `Unlabeled` | one-way | ATM, DNA10 | `kh2axfull` | state and binding-pattern rewrite | `DNA10(h2ax~foc) + ATM(state~10,h2ax) -> DNA10(h2ax!1~foc).ATM(state~10,h2ax!1)` | Forms a complex/contact among ATM, DNA10 through ATM.h2ax, DNA10.h2ax at `kh2axfull`. | +| 2040 | `Unlabeled` | one-way | ATM, DNA11 | `kh2axfull` | state and binding-pattern rewrite | `DNA11(h2ax~foc) + ATM(state~11,h2ax) -> DNA11(h2ax!1~foc).ATM(state~11,h2ax!1)` | Forms a complex/contact among ATM, DNA11 through ATM.h2ax, DNA11.h2ax at `kh2axfull`. | +| 2041 | `Unlabeled` | one-way | ATM, DNA12 | `kh2axfull` | state and binding-pattern rewrite | `DNA12(h2ax~foc) + ATM(state~12,h2ax) -> DNA12(h2ax!1~foc).ATM(state~12,h2ax!1)` | Forms a complex/contact among ATM, DNA12 through ATM.h2ax, DNA12.h2ax at `kh2axfull`. | +| 2042 | `Unlabeled` | one-way | ATM, DNA13 | `kh2axfull` | state and binding-pattern rewrite | `DNA13(h2ax~foc) + ATM(state~13,h2ax) -> DNA13(h2ax!1~foc).ATM(state~13,h2ax!1)` | Forms a complex/contact among ATM, DNA13 through ATM.h2ax, DNA13.h2ax at `kh2axfull`. | +| 2043 | `Unlabeled` | one-way | ATM, DNA14 | `kh2axfull` | state and binding-pattern rewrite | `DNA14(h2ax~foc) + ATM(state~14,h2ax) -> DNA14(h2ax!1~foc).ATM(state~14,h2ax!1)` | Forms a complex/contact among ATM, DNA14 through ATM.h2ax, DNA14.h2ax at `kh2axfull`. | +| 2044 | `Unlabeled` | one-way | ATM, DNA15 | `kh2axfull` | state and binding-pattern rewrite | `DNA15(h2ax~foc) + ATM(state~15,h2ax) -> DNA15(h2ax!1~foc).ATM(state~15,h2ax!1)` | Forms a complex/contact among ATM, DNA15 through ATM.h2ax, DNA15.h2ax at `kh2axfull`. | +| 2045 | `Unlabeled` | one-way | ATM, DNA16 | `kh2axfull` | state and binding-pattern rewrite | `DNA16(h2ax~foc) + ATM(state~16,h2ax) -> DNA16(h2ax!1~foc).ATM(state~16,h2ax!1)` | Forms a complex/contact among ATM, DNA16 through ATM.h2ax, DNA16.h2ax at `kh2axfull`. | +| 2046 | `Unlabeled` | one-way | ATM, DNA17 | `kh2axfull` | state and binding-pattern rewrite | `DNA17(h2ax~foc) + ATM(state~17,h2ax) -> DNA17(h2ax!1~foc).ATM(state~17,h2ax!1)` | Forms a complex/contact among ATM, DNA17 through ATM.h2ax, DNA17.h2ax at `kh2axfull`. | +| 2047 | `Unlabeled` | one-way | ATM, DNA18 | `kh2axfull` | state and binding-pattern rewrite | `DNA18(h2ax~foc) + ATM(state~18,h2ax) -> DNA18(h2ax!1~foc).ATM(state~18,h2ax!1)` | Forms a complex/contact among ATM, DNA18 through ATM.h2ax, DNA18.h2ax at `kh2axfull`. | +| 2048 | `Unlabeled` | one-way | ATM, DNA19 | `kh2axfull` | state and binding-pattern rewrite | `DNA19(h2ax~foc) + ATM(state~19,h2ax) -> DNA19(h2ax!1~foc).ATM(state~19,h2ax!1)` | Forms a complex/contact among ATM, DNA19 through ATM.h2ax, DNA19.h2ax at `kh2axfull`. | +| 2049 | `Unlabeled` | one-way | ATM, DNA20 | `kh2axfull` | state and binding-pattern rewrite | `DNA20(h2ax~foc) + ATM(state~20,h2ax) -> DNA20(h2ax!1~foc).ATM(state~20,h2ax!1)` | Forms a complex/contact among ATM, DNA20 through ATM.h2ax, DNA20.h2ax at `kh2axfull`. | +| 2050 | `Unlabeled` | one-way | ATM, DNA21 | `kh2axfull` | state and binding-pattern rewrite | `DNA21(h2ax~foc) + ATM(state~21,h2ax) -> DNA21(h2ax!1~foc).ATM(state~21,h2ax!1)` | Forms a complex/contact among ATM, DNA21 through ATM.h2ax, DNA21.h2ax at `kh2axfull`. | +| 2051 | `Unlabeled` | one-way | ATM, DNA22 | `kh2axfull` | state and binding-pattern rewrite | `DNA22(h2ax~foc) + ATM(state~22,h2ax) -> DNA22(h2ax!1~foc).ATM(state~22,h2ax!1)` | Forms a complex/contact among ATM, DNA22 through ATM.h2ax, DNA22.h2ax at `kh2axfull`. | +| 2052 | `Unlabeled` | one-way | ATM, DNA23 | `kh2axfull` | state and binding-pattern rewrite | `DNA23(h2ax~foc) + ATM(state~23,h2ax) -> DNA23(h2ax!1~foc).ATM(state~23,h2ax!1)` | Forms a complex/contact among ATM, DNA23 through ATM.h2ax, DNA23.h2ax at `kh2axfull`. | +| 2053 | `Unlabeled` | one-way | ATM, DNA24 | `kh2axfull` | state and binding-pattern rewrite | `DNA24(h2ax~foc) + ATM(state~24,h2ax) -> DNA24(h2ax!1~foc).ATM(state~24,h2ax!1)` | Forms a complex/contact among ATM, DNA24 through ATM.h2ax, DNA24.h2ax at `kh2axfull`. | +| 2054 | `Unlabeled` | one-way | ATM, DNA25 | `kh2axfull` | state and binding-pattern rewrite | `DNA25(h2ax~foc) + ATM(state~25,h2ax) -> DNA25(h2ax!1~foc).ATM(state~25,h2ax!1)` | Forms a complex/contact among ATM, DNA25 through ATM.h2ax, DNA25.h2ax at `kh2axfull`. | +| 2055 | `Unlabeled` | one-way | ATM, DNA26 | `kh2axfull` | state and binding-pattern rewrite | `DNA26(h2ax~foc) + ATM(state~26,h2ax) -> DNA26(h2ax!1~foc).ATM(state~26,h2ax!1)` | Forms a complex/contact among ATM, DNA26 through ATM.h2ax, DNA26.h2ax at `kh2axfull`. | +| 2056 | `Unlabeled` | one-way | ATM, DNA27 | `kh2axfull` | state and binding-pattern rewrite | `DNA27(h2ax~foc) + ATM(state~27,h2ax) -> DNA27(h2ax!1~foc).ATM(state~27,h2ax!1)` | Forms a complex/contact among ATM, DNA27 through ATM.h2ax, DNA27.h2ax at `kh2axfull`. | +| 2057 | `Unlabeled` | one-way | ATM, DNA28 | `kh2axfull` | state and binding-pattern rewrite | `DNA28(h2ax~foc) + ATM(state~28,h2ax) -> DNA28(h2ax!1~foc).ATM(state~28,h2ax!1)` | Forms a complex/contact among ATM, DNA28 through ATM.h2ax, DNA28.h2ax at `kh2axfull`. | +| 2058 | `Unlabeled` | one-way | ATM, DNA29 | `kh2axfull` | state and binding-pattern rewrite | `DNA29(h2ax~foc) + ATM(state~29,h2ax) -> DNA29(h2ax!1~foc).ATM(state~29,h2ax!1)` | Forms a complex/contact among ATM, DNA29 through ATM.h2ax, DNA29.h2ax at `kh2axfull`. | +| 2059 | `Unlabeled` | one-way | ATM, DNA30 | `kh2axfull` | state and binding-pattern rewrite | `DNA30(h2ax~foc) + ATM(state~30,h2ax) -> DNA30(h2ax!1~foc).ATM(state~30,h2ax!1)` | Forms a complex/contact among ATM, DNA30 through ATM.h2ax, DNA30.h2ax at `kh2axfull`. | +| 2060 | `Unlabeled` | one-way | ATM, DNA31 | `kh2axfull` | state and binding-pattern rewrite | `DNA31(h2ax~foc) + ATM(state~31,h2ax) -> DNA31(h2ax!1~foc).ATM(state~31,h2ax!1)` | Forms a complex/contact among ATM, DNA31 through ATM.h2ax, DNA31.h2ax at `kh2axfull`. | +| 2061 | `Unlabeled` | one-way | ATM, DNA32 | `kh2axfull` | state and binding-pattern rewrite | `DNA32(h2ax~foc) + ATM(state~32,h2ax) -> DNA32(h2ax!1~foc).ATM(state~32,h2ax!1)` | Forms a complex/contact among ATM, DNA32 through ATM.h2ax, DNA32.h2ax at `kh2axfull`. | +| 2062 | `Unlabeled` | one-way | ATM, DNA33 | `kh2axfull` | state and binding-pattern rewrite | `DNA33(h2ax~foc) + ATM(state~33,h2ax) -> DNA33(h2ax!1~foc).ATM(state~33,h2ax!1)` | Forms a complex/contact among ATM, DNA33 through ATM.h2ax, DNA33.h2ax at `kh2axfull`. | +| 2063 | `Unlabeled` | one-way | ATM, DNA34 | `kh2axfull` | state and binding-pattern rewrite | `DNA34(h2ax~foc) + ATM(state~34,h2ax) -> DNA34(h2ax!1~foc).ATM(state~34,h2ax!1)` | Forms a complex/contact among ATM, DNA34 through ATM.h2ax, DNA34.h2ax at `kh2axfull`. | +| 2064 | `Unlabeled` | one-way | ATM, DNA35 | `kh2axfull` | state and binding-pattern rewrite | `DNA35(h2ax~foc) + ATM(state~35,h2ax) -> DNA35(h2ax!1~foc).ATM(state~35,h2ax!1)` | Forms a complex/contact among ATM, DNA35 through ATM.h2ax, DNA35.h2ax at `kh2axfull`. | +| 2065 | `Unlabeled` | one-way | ATM, DNA36 | `kh2axfull` | state and binding-pattern rewrite | `DNA36(h2ax~foc) + ATM(state~36,h2ax) -> DNA36(h2ax!1~foc).ATM(state~36,h2ax!1)` | Forms a complex/contact among ATM, DNA36 through ATM.h2ax, DNA36.h2ax at `kh2axfull`. | +| 2066 | `Unlabeled` | one-way | ATM, DNA37 | `kh2axfull` | state and binding-pattern rewrite | `DNA37(h2ax~foc) + ATM(state~37,h2ax) -> DNA37(h2ax!1~foc).ATM(state~37,h2ax!1)` | Forms a complex/contact among ATM, DNA37 through ATM.h2ax, DNA37.h2ax at `kh2axfull`. | +| 2067 | `Unlabeled` | one-way | ATM, DNA38 | `kh2axfull` | state and binding-pattern rewrite | `DNA38(h2ax~foc) + ATM(state~38,h2ax) -> DNA38(h2ax!1~foc).ATM(state~38,h2ax!1)` | Forms a complex/contact among ATM, DNA38 through ATM.h2ax, DNA38.h2ax at `kh2axfull`. | +| 2068 | `Unlabeled` | one-way | ATM, DNA39 | `kh2axfull` | state and binding-pattern rewrite | `DNA39(h2ax~foc) + ATM(state~39,h2ax) -> DNA39(h2ax!1~foc).ATM(state~39,h2ax!1)` | Forms a complex/contact among ATM, DNA39 through ATM.h2ax, DNA39.h2ax at `kh2axfull`. | +| 2069 | `Unlabeled` | one-way | ATM, DNA40 | `kh2axfull` | state and binding-pattern rewrite | `DNA40(h2ax~foc) + ATM(state~40,h2ax) -> DNA40(h2ax!1~foc).ATM(state~40,h2ax!1)` | Forms a complex/contact among ATM, DNA40 through ATM.h2ax, DNA40.h2ax at `kh2axfull`. | +| 2070 | `Unlabeled` | one-way | ATM, DNA41 | `kh2axfull` | state and binding-pattern rewrite | `DNA41(h2ax~foc) + ATM(state~41,h2ax) -> DNA41(h2ax!1~foc).ATM(state~41,h2ax!1)` | Forms a complex/contact among ATM, DNA41 through ATM.h2ax, DNA41.h2ax at `kh2axfull`. | +| 2071 | `Unlabeled` | one-way | ATM, DNA42 | `kh2axfull` | state and binding-pattern rewrite | `DNA42(h2ax~foc) + ATM(state~42,h2ax) -> DNA42(h2ax!1~foc).ATM(state~42,h2ax!1)` | Forms a complex/contact among ATM, DNA42 through ATM.h2ax, DNA42.h2ax at `kh2axfull`. | +| 2072 | `Unlabeled` | one-way | ATM, DNA43 | `kh2axfull` | state and binding-pattern rewrite | `DNA43(h2ax~foc) + ATM(state~43,h2ax) -> DNA43(h2ax!1~foc).ATM(state~43,h2ax!1)` | Forms a complex/contact among ATM, DNA43 through ATM.h2ax, DNA43.h2ax at `kh2axfull`. | +| 2073 | `Unlabeled` | one-way | ATM, DNA44 | `kh2axfull` | state and binding-pattern rewrite | `DNA44(h2ax~foc) + ATM(state~44,h2ax) -> DNA44(h2ax!1~foc).ATM(state~44,h2ax!1)` | Forms a complex/contact among ATM, DNA44 through ATM.h2ax, DNA44.h2ax at `kh2axfull`. | +| 2074 | `Unlabeled` | one-way | ATM, DNA45 | `kh2axfull` | state and binding-pattern rewrite | `DNA45(h2ax~foc) + ATM(state~45,h2ax) -> DNA45(h2ax!1~foc).ATM(state~45,h2ax!1)` | Forms a complex/contact among ATM, DNA45 through ATM.h2ax, DNA45.h2ax at `kh2axfull`. | +| 2075 | `Unlabeled` | one-way | ATM, DNA46 | `kh2axfull` | state and binding-pattern rewrite | `DNA46(h2ax~foc) + ATM(state~46,h2ax) -> DNA46(h2ax!1~foc).ATM(state~46,h2ax!1)` | Forms a complex/contact among ATM, DNA46 through ATM.h2ax, DNA46.h2ax at `kh2axfull`. | +| 2076 | `Unlabeled` | one-way | ATM, DNA47 | `kh2axfull` | state and binding-pattern rewrite | `DNA47(h2ax~foc) + ATM(state~47,h2ax) -> DNA47(h2ax!1~foc).ATM(state~47,h2ax!1)` | Forms a complex/contact among ATM, DNA47 through ATM.h2ax, DNA47.h2ax at `kh2axfull`. | +| 2077 | `Unlabeled` | one-way | ATM, DNA48 | `kh2axfull` | state and binding-pattern rewrite | `DNA48(h2ax~foc) + ATM(state~48,h2ax) -> DNA48(h2ax!1~foc).ATM(state~48,h2ax!1)` | Forms a complex/contact among ATM, DNA48 through ATM.h2ax, DNA48.h2ax at `kh2axfull`. | +| 2078 | `Unlabeled` | one-way | ATM, DNA49 | `kh2axfull` | state and binding-pattern rewrite | `DNA49(h2ax~foc) + ATM(state~49,h2ax) -> DNA49(h2ax!1~foc).ATM(state~49,h2ax!1)` | Forms a complex/contact among ATM, DNA49 through ATM.h2ax, DNA49.h2ax at `kh2axfull`. | +| 2079 | `Unlabeled` | one-way | ATM, DNA50 | `kh2axfull` | state and binding-pattern rewrite | `DNA50(h2ax~foc) + ATM(state~50,h2ax) -> DNA50(h2ax!1~foc).ATM(state~50,h2ax!1)` | Forms a complex/contact among ATM, DNA50 through ATM.h2ax, DNA50.h2ax at `kh2axfull`. | +| 2080 | `Unlabeled` | one-way | ATM, DNA1 | `kfocfin` | state and binding-pattern rewrite | `DNA1(h2ax!1~foc).ATM(state~1,h2ax!1) -> DNA1(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 1→0) with binding-site changes (removes ATM.h2ax, DNA1.h2ax) at `kfocfin`. | +| 2081 | `Unlabeled` | one-way | ATM, DNA2 | `kfocfin` | state and binding-pattern rewrite | `DNA2(h2ax!1~foc).ATM(state~2,h2ax!1) -> DNA2(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 2→0) with binding-site changes (removes ATM.h2ax, DNA2.h2ax) at `kfocfin`. | +| 2082 | `Unlabeled` | one-way | ATM, DNA3 | `kfocfin` | state and binding-pattern rewrite | `DNA3(h2ax!1~foc).ATM(state~3,h2ax!1) -> DNA3(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 3→0) with binding-site changes (removes ATM.h2ax, DNA3.h2ax) at `kfocfin`. | +| 2083 | `Unlabeled` | one-way | ATM, DNA4 | `kfocfin` | state and binding-pattern rewrite | `DNA4(h2ax!1~foc).ATM(state~4,h2ax!1) -> DNA4(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 4→0) with binding-site changes (removes ATM.h2ax, DNA4.h2ax) at `kfocfin`. | +| 2084 | `Unlabeled` | one-way | ATM, DNA5 | `kfocfin` | state and binding-pattern rewrite | `DNA5(h2ax!1~foc).ATM(state~5,h2ax!1) -> DNA5(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 5→0) with binding-site changes (removes ATM.h2ax, DNA5.h2ax) at `kfocfin`. | +| 2085 | `Unlabeled` | one-way | ATM, DNA6 | `kfocfin` | state and binding-pattern rewrite | `DNA6(h2ax!1~foc).ATM(state~6,h2ax!1) -> DNA6(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 6→0) with binding-site changes (removes ATM.h2ax, DNA6.h2ax) at `kfocfin`. | +| 2086 | `Unlabeled` | one-way | ATM, DNA7 | `kfocfin` | state and binding-pattern rewrite | `DNA7(h2ax!1~foc).ATM(state~7,h2ax!1) -> DNA7(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 7→0) with binding-site changes (removes ATM.h2ax, DNA7.h2ax) at `kfocfin`. | +| 2087 | `Unlabeled` | one-way | ATM, DNA8 | `kfocfin` | state and binding-pattern rewrite | `DNA8(h2ax!1~foc).ATM(state~8,h2ax!1) -> DNA8(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 8→0) with binding-site changes (removes ATM.h2ax, DNA8.h2ax) at `kfocfin`. | +| 2088 | `Unlabeled` | one-way | ATM, DNA9 | `kfocfin` | state and binding-pattern rewrite | `DNA9(h2ax!1~foc).ATM(state~9,h2ax!1) -> DNA9(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 9→0) with binding-site changes (removes ATM.h2ax, DNA9.h2ax) at `kfocfin`. | +| 2089 | `Unlabeled` | one-way | ATM, DNA10 | `kfocfin` | state and binding-pattern rewrite | `DNA10(h2ax!1~foc).ATM(state~10,h2ax!1) -> DNA10(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 10→0) with binding-site changes (removes ATM.h2ax, DNA10.h2ax) at `kfocfin`. | +| 2090 | `Unlabeled` | one-way | ATM, DNA11 | `kfocfin` | state and binding-pattern rewrite | `DNA11(h2ax!1~foc).ATM(state~11,h2ax!1) -> DNA11(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 11→0) with binding-site changes (removes ATM.h2ax, DNA11.h2ax) at `kfocfin`. | +| 2091 | `Unlabeled` | one-way | ATM, DNA12 | `kfocfin` | state and binding-pattern rewrite | `DNA12(h2ax!1~foc).ATM(state~12,h2ax!1) -> DNA12(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 12→0) with binding-site changes (removes ATM.h2ax, DNA12.h2ax) at `kfocfin`. | +| 2092 | `Unlabeled` | one-way | ATM, DNA13 | `kfocfin` | state and binding-pattern rewrite | `DNA13(h2ax!1~foc).ATM(state~13,h2ax!1) -> DNA13(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 13→0) with binding-site changes (removes ATM.h2ax, DNA13.h2ax) at `kfocfin`. | +| 2093 | `Unlabeled` | one-way | ATM, DNA14 | `kfocfin` | state and binding-pattern rewrite | `DNA14(h2ax!1~foc).ATM(state~14,h2ax!1) -> DNA14(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 14→0) with binding-site changes (removes ATM.h2ax, DNA14.h2ax) at `kfocfin`. | +| 2094 | `Unlabeled` | one-way | ATM, DNA15 | `kfocfin` | state and binding-pattern rewrite | `DNA15(h2ax!1~foc).ATM(state~15,h2ax!1) -> DNA15(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 15→0) with binding-site changes (removes ATM.h2ax, DNA15.h2ax) at `kfocfin`. | +| 2095 | `Unlabeled` | one-way | ATM, DNA16 | `kfocfin` | state and binding-pattern rewrite | `DNA16(h2ax!1~foc).ATM(state~16,h2ax!1) -> DNA16(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 16→0) with binding-site changes (removes ATM.h2ax, DNA16.h2ax) at `kfocfin`. | +| 2096 | `Unlabeled` | one-way | ATM, DNA17 | `kfocfin` | state and binding-pattern rewrite | `DNA17(h2ax!1~foc).ATM(state~17,h2ax!1) -> DNA17(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 17→0) with binding-site changes (removes ATM.h2ax, DNA17.h2ax) at `kfocfin`. | +| 2097 | `Unlabeled` | one-way | ATM, DNA18 | `kfocfin` | state and binding-pattern rewrite | `DNA18(h2ax!1~foc).ATM(state~18,h2ax!1) -> DNA18(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 18→0) with binding-site changes (removes ATM.h2ax, DNA18.h2ax) at `kfocfin`. | +| 2098 | `Unlabeled` | one-way | ATM, DNA19 | `kfocfin` | state and binding-pattern rewrite | `DNA19(h2ax!1~foc).ATM(state~19,h2ax!1) -> DNA19(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 19→0) with binding-site changes (removes ATM.h2ax, DNA19.h2ax) at `kfocfin`. | +| 2099 | `Unlabeled` | one-way | ATM, DNA20 | `kfocfin` | state and binding-pattern rewrite | `DNA20(h2ax!1~foc).ATM(state~20,h2ax!1) -> DNA20(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 20→0) with binding-site changes (removes ATM.h2ax, DNA20.h2ax) at `kfocfin`. | +| 2100 | `Unlabeled` | one-way | ATM, DNA21 | `kfocfin` | state and binding-pattern rewrite | `DNA21(h2ax!1~foc).ATM(state~21,h2ax!1) -> DNA21(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 21→0) with binding-site changes (removes ATM.h2ax, DNA21.h2ax) at `kfocfin`. | +| 2101 | `Unlabeled` | one-way | ATM, DNA22 | `kfocfin` | state and binding-pattern rewrite | `DNA22(h2ax!1~foc).ATM(state~22,h2ax!1) -> DNA22(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 22→0) with binding-site changes (removes ATM.h2ax, DNA22.h2ax) at `kfocfin`. | +| 2102 | `Unlabeled` | one-way | ATM, DNA23 | `kfocfin` | state and binding-pattern rewrite | `DNA23(h2ax!1~foc).ATM(state~23,h2ax!1) -> DNA23(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 23→0) with binding-site changes (removes ATM.h2ax, DNA23.h2ax) at `kfocfin`. | +| 2103 | `Unlabeled` | one-way | ATM, DNA24 | `kfocfin` | state and binding-pattern rewrite | `DNA24(h2ax!1~foc).ATM(state~24,h2ax!1) -> DNA24(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 24→0) with binding-site changes (removes ATM.h2ax, DNA24.h2ax) at `kfocfin`. | +| 2104 | `Unlabeled` | one-way | ATM, DNA25 | `kfocfin` | state and binding-pattern rewrite | `DNA25(h2ax!1~foc).ATM(state~25,h2ax!1) -> DNA25(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 25→0) with binding-site changes (removes ATM.h2ax, DNA25.h2ax) at `kfocfin`. | +| 2105 | `Unlabeled` | one-way | ATM, DNA26 | `kfocfin` | state and binding-pattern rewrite | `DNA26(h2ax!1~foc).ATM(state~26,h2ax!1) -> DNA26(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 26→0) with binding-site changes (removes ATM.h2ax, DNA26.h2ax) at `kfocfin`. | +| 2106 | `Unlabeled` | one-way | ATM, DNA27 | `kfocfin` | state and binding-pattern rewrite | `DNA27(h2ax!1~foc).ATM(state~27,h2ax!1) -> DNA27(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 27→0) with binding-site changes (removes ATM.h2ax, DNA27.h2ax) at `kfocfin`. | +| 2107 | `Unlabeled` | one-way | ATM, DNA28 | `kfocfin` | state and binding-pattern rewrite | `DNA28(h2ax!1~foc).ATM(state~28,h2ax!1) -> DNA28(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 28→0) with binding-site changes (removes ATM.h2ax, DNA28.h2ax) at `kfocfin`. | +| 2108 | `Unlabeled` | one-way | ATM, DNA29 | `kfocfin` | state and binding-pattern rewrite | `DNA29(h2ax!1~foc).ATM(state~29,h2ax!1) -> DNA29(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 29→0) with binding-site changes (removes ATM.h2ax, DNA29.h2ax) at `kfocfin`. | +| 2109 | `Unlabeled` | one-way | ATM, DNA30 | `kfocfin` | state and binding-pattern rewrite | `DNA30(h2ax!1~foc).ATM(state~30,h2ax!1) -> DNA30(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 30→0) with binding-site changes (removes ATM.h2ax, DNA30.h2ax) at `kfocfin`. | +| 2110 | `Unlabeled` | one-way | ATM, DNA31 | `kfocfin` | state and binding-pattern rewrite | `DNA31(h2ax!1~foc).ATM(state~31,h2ax!1) -> DNA31(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 31→0) with binding-site changes (removes ATM.h2ax, DNA31.h2ax) at `kfocfin`. | +| 2111 | `Unlabeled` | one-way | ATM, DNA32 | `kfocfin` | state and binding-pattern rewrite | `DNA32(h2ax!1~foc).ATM(state~32,h2ax!1) -> DNA32(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 32→0) with binding-site changes (removes ATM.h2ax, DNA32.h2ax) at `kfocfin`. | +| 2112 | `Unlabeled` | one-way | ATM, DNA33 | `kfocfin` | state and binding-pattern rewrite | `DNA33(h2ax!1~foc).ATM(state~33,h2ax!1) -> DNA33(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 33→0) with binding-site changes (removes ATM.h2ax, DNA33.h2ax) at `kfocfin`. | +| 2113 | `Unlabeled` | one-way | ATM, DNA34 | `kfocfin` | state and binding-pattern rewrite | `DNA34(h2ax!1~foc).ATM(state~34,h2ax!1) -> DNA34(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 34→0) with binding-site changes (removes ATM.h2ax, DNA34.h2ax) at `kfocfin`. | +| 2114 | `Unlabeled` | one-way | ATM, DNA35 | `kfocfin` | state and binding-pattern rewrite | `DNA35(h2ax!1~foc).ATM(state~35,h2ax!1) -> DNA35(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 35→0) with binding-site changes (removes ATM.h2ax, DNA35.h2ax) at `kfocfin`. | +| 2115 | `Unlabeled` | one-way | ATM, DNA36 | `kfocfin` | state and binding-pattern rewrite | `DNA36(h2ax!1~foc).ATM(state~36,h2ax!1) -> DNA36(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 36→0) with binding-site changes (removes ATM.h2ax, DNA36.h2ax) at `kfocfin`. | +| 2116 | `Unlabeled` | one-way | ATM, DNA37 | `kfocfin` | state and binding-pattern rewrite | `DNA37(h2ax!1~foc).ATM(state~37,h2ax!1) -> DNA37(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 37→0) with binding-site changes (removes ATM.h2ax, DNA37.h2ax) at `kfocfin`. | +| 2117 | `Unlabeled` | one-way | ATM, DNA38 | `kfocfin` | state and binding-pattern rewrite | `DNA38(h2ax!1~foc).ATM(state~38,h2ax!1) -> DNA38(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 38→0) with binding-site changes (removes ATM.h2ax, DNA38.h2ax) at `kfocfin`. | +| 2118 | `Unlabeled` | one-way | ATM, DNA39 | `kfocfin` | state and binding-pattern rewrite | `DNA39(h2ax!1~foc).ATM(state~39,h2ax!1) -> DNA39(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 39→0) with binding-site changes (removes ATM.h2ax, DNA39.h2ax) at `kfocfin`. | +| 2119 | `Unlabeled` | one-way | ATM, DNA40 | `kfocfin` | state and binding-pattern rewrite | `DNA40(h2ax!1~foc).ATM(state~40,h2ax!1) -> DNA40(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 40→0) with binding-site changes (removes ATM.h2ax, DNA40.h2ax) at `kfocfin`. | +| 2120 | `Unlabeled` | one-way | ATM, DNA41 | `kfocfin` | state and binding-pattern rewrite | `DNA41(h2ax!1~foc).ATM(state~41,h2ax!1) -> DNA41(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 41→0) with binding-site changes (removes ATM.h2ax, DNA41.h2ax) at `kfocfin`. | +| 2121 | `Unlabeled` | one-way | ATM, DNA42 | `kfocfin` | state and binding-pattern rewrite | `DNA42(h2ax!1~foc).ATM(state~42,h2ax!1) -> DNA42(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 42→0) with binding-site changes (removes ATM.h2ax, DNA42.h2ax) at `kfocfin`. | +| 2122 | `Unlabeled` | one-way | ATM, DNA43 | `kfocfin` | state and binding-pattern rewrite | `DNA43(h2ax!1~foc).ATM(state~43,h2ax!1) -> DNA43(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 43→0) with binding-site changes (removes ATM.h2ax, DNA43.h2ax) at `kfocfin`. | +| 2123 | `Unlabeled` | one-way | ATM, DNA44 | `kfocfin` | state and binding-pattern rewrite | `DNA44(h2ax!1~foc).ATM(state~44,h2ax!1) -> DNA44(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 44→0) with binding-site changes (removes ATM.h2ax, DNA44.h2ax) at `kfocfin`. | +| 2124 | `Unlabeled` | one-way | ATM, DNA45 | `kfocfin` | state and binding-pattern rewrite | `DNA45(h2ax!1~foc).ATM(state~45,h2ax!1) -> DNA45(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 45→0) with binding-site changes (removes ATM.h2ax, DNA45.h2ax) at `kfocfin`. | +| 2125 | `Unlabeled` | one-way | ATM, DNA46 | `kfocfin` | state and binding-pattern rewrite | `DNA46(h2ax!1~foc).ATM(state~46,h2ax!1) -> DNA46(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 46→0) with binding-site changes (removes ATM.h2ax, DNA46.h2ax) at `kfocfin`. | +| 2126 | `Unlabeled` | one-way | ATM, DNA47 | `kfocfin` | state and binding-pattern rewrite | `DNA47(h2ax!1~foc).ATM(state~47,h2ax!1) -> DNA47(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 47→0) with binding-site changes (removes ATM.h2ax, DNA47.h2ax) at `kfocfin`. | +| 2127 | `Unlabeled` | one-way | ATM, DNA48 | `kfocfin` | state and binding-pattern rewrite | `DNA48(h2ax!1~foc).ATM(state~48,h2ax!1) -> DNA48(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 48→0) with binding-site changes (removes ATM.h2ax, DNA48.h2ax) at `kfocfin`. | +| 2128 | `Unlabeled` | one-way | ATM, DNA49 | `kfocfin` | state and binding-pattern rewrite | `DNA49(h2ax!1~foc).ATM(state~49,h2ax!1) -> DNA49(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 49→0) with binding-site changes (removes ATM.h2ax, DNA49.h2ax) at `kfocfin`. | +| 2129 | `Unlabeled` | one-way | ATM, DNA50 | `kfocfin` | state and binding-pattern rewrite | `DNA50(h2ax!1~foc).ATM(state~50,h2ax!1) -> DNA50(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 50→0) with binding-site changes (removes ATM.h2ax, DNA50.h2ax) at `kfocfin`. | +| 2130 | `Unlabeled` | one-way | I, ROS | `kROS` | source/synthesis or algebraic source term | `I() -> I() + ROS()` | Produces ROS while retaining or consuming I at `kROS`. | +| 2131 | `Unlabeled` | one-way | ROS, Sink | `kdROS` | sink/degradation/removal | `ROS() -> Sink()` | Degrades or diverts ROS into the model sink at `kdROS`, reducing that active species pool. | +| 2132 | `Unlabeled` | one-way | IR, ROS | `kIR` | stoichiometric pattern rewrite | `IR() -> IR() + ROS()` | Produces ROS while retaining or consuming IR at `kIR`. | +| 2133 | `Unlabeled` | one-way | DNA1, ROS | `kdam1` | internal-state conversion/modification | `DNA1(site~ok) + ROS() -> DNA1(site~sdsb)` | Changes internal modification/state marks on DNA1, ROS: DNA1.site ok→sdsb at `kdam1`. | +| 2134 | `Unlabeled` | one-way | DNA2, ROS | `kdam1` | internal-state conversion/modification | `DNA2(site~ok) + ROS() -> DNA2(site~sdsb)` | Changes internal modification/state marks on DNA2, ROS: DNA2.site ok→sdsb at `kdam1`. | +| 2135 | `Unlabeled` | one-way | DNA3, ROS | `kdam1` | internal-state conversion/modification | `DNA3(site~ok) + ROS() -> DNA3(site~sdsb)` | Changes internal modification/state marks on DNA3, ROS: DNA3.site ok→sdsb at `kdam1`. | +| 2136 | `Unlabeled` | one-way | DNA4, ROS | `kdam1` | internal-state conversion/modification | `DNA4(site~ok) + ROS() -> DNA4(site~sdsb)` | Changes internal modification/state marks on DNA4, ROS: DNA4.site ok→sdsb at `kdam1`. | +| 2137 | `Unlabeled` | one-way | DNA5, ROS | `kdam1` | internal-state conversion/modification | `DNA5(site~ok) + ROS() -> DNA5(site~sdsb)` | Changes internal modification/state marks on DNA5, ROS: DNA5.site ok→sdsb at `kdam1`. | +| 2138 | `Unlabeled` | one-way | DNA6, ROS | `kdam1` | internal-state conversion/modification | `DNA6(site~ok) + ROS() -> DNA6(site~sdsb)` | Changes internal modification/state marks on DNA6, ROS: DNA6.site ok→sdsb at `kdam1`. | +| 2139 | `Unlabeled` | one-way | DNA7, ROS | `kdam1` | internal-state conversion/modification | `DNA7(site~ok) + ROS() -> DNA7(site~sdsb)` | Changes internal modification/state marks on DNA7, ROS: DNA7.site ok→sdsb at `kdam1`. | +| 2140 | `Unlabeled` | one-way | DNA8, ROS | `kdam1` | internal-state conversion/modification | `DNA8(site~ok) + ROS() -> DNA8(site~sdsb)` | Changes internal modification/state marks on DNA8, ROS: DNA8.site ok→sdsb at `kdam1`. | +| 2141 | `Unlabeled` | one-way | DNA9, ROS | `kdam1` | internal-state conversion/modification | `DNA9(site~ok) + ROS() -> DNA9(site~sdsb)` | Changes internal modification/state marks on DNA9, ROS: DNA9.site ok→sdsb at `kdam1`. | +| 2142 | `Unlabeled` | one-way | DNA10, ROS | `kdam1` | internal-state conversion/modification | `DNA10(site~ok) + ROS() -> DNA10(site~sdsb)` | Changes internal modification/state marks on DNA10, ROS: DNA10.site ok→sdsb at `kdam1`. | +| 2143 | `Unlabeled` | one-way | DNA11, ROS | `kdam1` | internal-state conversion/modification | `DNA11(site~ok) + ROS() -> DNA11(site~sdsb)` | Changes internal modification/state marks on DNA11, ROS: DNA11.site ok→sdsb at `kdam1`. | +| 2144 | `Unlabeled` | one-way | DNA12, ROS | `kdam1` | internal-state conversion/modification | `DNA12(site~ok) + ROS() -> DNA12(site~sdsb)` | Changes internal modification/state marks on DNA12, ROS: DNA12.site ok→sdsb at `kdam1`. | +| 2145 | `Unlabeled` | one-way | DNA13, ROS | `kdam1` | internal-state conversion/modification | `DNA13(site~ok) + ROS() -> DNA13(site~sdsb)` | Changes internal modification/state marks on DNA13, ROS: DNA13.site ok→sdsb at `kdam1`. | +| 2146 | `Unlabeled` | one-way | DNA14, ROS | `kdam1` | internal-state conversion/modification | `DNA14(site~ok) + ROS() -> DNA14(site~sdsb)` | Changes internal modification/state marks on DNA14, ROS: DNA14.site ok→sdsb at `kdam1`. | +| 2147 | `Unlabeled` | one-way | DNA15, ROS | `kdam1` | internal-state conversion/modification | `DNA15(site~ok) + ROS() -> DNA15(site~sdsb)` | Changes internal modification/state marks on DNA15, ROS: DNA15.site ok→sdsb at `kdam1`. | +| 2148 | `Unlabeled` | one-way | DNA16, ROS | `kdam1` | internal-state conversion/modification | `DNA16(site~ok) + ROS() -> DNA16(site~sdsb)` | Changes internal modification/state marks on DNA16, ROS: DNA16.site ok→sdsb at `kdam1`. | +| 2149 | `Unlabeled` | one-way | DNA17, ROS | `kdam1` | internal-state conversion/modification | `DNA17(site~ok) + ROS() -> DNA17(site~sdsb)` | Changes internal modification/state marks on DNA17, ROS: DNA17.site ok→sdsb at `kdam1`. | +| 2150 | `Unlabeled` | one-way | DNA18, ROS | `kdam1` | internal-state conversion/modification | `DNA18(site~ok) + ROS() -> DNA18(site~sdsb)` | Changes internal modification/state marks on DNA18, ROS: DNA18.site ok→sdsb at `kdam1`. | +| 2151 | `Unlabeled` | one-way | DNA19, ROS | `kdam1` | internal-state conversion/modification | `DNA19(site~ok) + ROS() -> DNA19(site~sdsb)` | Changes internal modification/state marks on DNA19, ROS: DNA19.site ok→sdsb at `kdam1`. | +| 2152 | `Unlabeled` | one-way | DNA20, ROS | `kdam1` | internal-state conversion/modification | `DNA20(site~ok) + ROS() -> DNA20(site~sdsb)` | Changes internal modification/state marks on DNA20, ROS: DNA20.site ok→sdsb at `kdam1`. | +| 2153 | `Unlabeled` | one-way | DNA21, ROS | `kdam1` | internal-state conversion/modification | `DNA21(site~ok) + ROS() -> DNA21(site~sdsb)` | Changes internal modification/state marks on DNA21, ROS: DNA21.site ok→sdsb at `kdam1`. | +| 2154 | `Unlabeled` | one-way | DNA22, ROS | `kdam1` | internal-state conversion/modification | `DNA22(site~ok) + ROS() -> DNA22(site~sdsb)` | Changes internal modification/state marks on DNA22, ROS: DNA22.site ok→sdsb at `kdam1`. | +| 2155 | `Unlabeled` | one-way | DNA23, ROS | `kdam1` | internal-state conversion/modification | `DNA23(site~ok) + ROS() -> DNA23(site~sdsb)` | Changes internal modification/state marks on DNA23, ROS: DNA23.site ok→sdsb at `kdam1`. | +| 2156 | `Unlabeled` | one-way | DNA24, ROS | `kdam1` | internal-state conversion/modification | `DNA24(site~ok) + ROS() -> DNA24(site~sdsb)` | Changes internal modification/state marks on DNA24, ROS: DNA24.site ok→sdsb at `kdam1`. | +| 2157 | `Unlabeled` | one-way | DNA25, ROS | `kdam1` | internal-state conversion/modification | `DNA25(site~ok) + ROS() -> DNA25(site~sdsb)` | Changes internal modification/state marks on DNA25, ROS: DNA25.site ok→sdsb at `kdam1`. | +| 2158 | `Unlabeled` | one-way | DNA26, ROS | `kdam1` | internal-state conversion/modification | `DNA26(site~ok) + ROS() -> DNA26(site~sdsb)` | Changes internal modification/state marks on DNA26, ROS: DNA26.site ok→sdsb at `kdam1`. | +| 2159 | `Unlabeled` | one-way | DNA27, ROS | `kdam1` | internal-state conversion/modification | `DNA27(site~ok) + ROS() -> DNA27(site~sdsb)` | Changes internal modification/state marks on DNA27, ROS: DNA27.site ok→sdsb at `kdam1`. | +| 2160 | `Unlabeled` | one-way | DNA28, ROS | `kdam1` | internal-state conversion/modification | `DNA28(site~ok) + ROS() -> DNA28(site~sdsb)` | Changes internal modification/state marks on DNA28, ROS: DNA28.site ok→sdsb at `kdam1`. | +| 2161 | `Unlabeled` | one-way | DNA29, ROS | `kdam1` | internal-state conversion/modification | `DNA29(site~ok) + ROS() -> DNA29(site~sdsb)` | Changes internal modification/state marks on DNA29, ROS: DNA29.site ok→sdsb at `kdam1`. | +| 2162 | `Unlabeled` | one-way | DNA30, ROS | `kdam1` | internal-state conversion/modification | `DNA30(site~ok) + ROS() -> DNA30(site~sdsb)` | Changes internal modification/state marks on DNA30, ROS: DNA30.site ok→sdsb at `kdam1`. | +| 2163 | `Unlabeled` | one-way | DNA31, ROS | `kdam1` | internal-state conversion/modification | `DNA31(site~ok) + ROS() -> DNA31(site~sdsb)` | Changes internal modification/state marks on DNA31, ROS: DNA31.site ok→sdsb at `kdam1`. | +| 2164 | `Unlabeled` | one-way | DNA32, ROS | `kdam1` | internal-state conversion/modification | `DNA32(site~ok) + ROS() -> DNA32(site~sdsb)` | Changes internal modification/state marks on DNA32, ROS: DNA32.site ok→sdsb at `kdam1`. | +| 2165 | `Unlabeled` | one-way | DNA33, ROS | `kdam1` | internal-state conversion/modification | `DNA33(site~ok) + ROS() -> DNA33(site~sdsb)` | Changes internal modification/state marks on DNA33, ROS: DNA33.site ok→sdsb at `kdam1`. | +| 2166 | `Unlabeled` | one-way | DNA34, ROS | `kdam1` | internal-state conversion/modification | `DNA34(site~ok) + ROS() -> DNA34(site~sdsb)` | Changes internal modification/state marks on DNA34, ROS: DNA34.site ok→sdsb at `kdam1`. | +| 2167 | `Unlabeled` | one-way | DNA35, ROS | `kdam1` | internal-state conversion/modification | `DNA35(site~ok) + ROS() -> DNA35(site~sdsb)` | Changes internal modification/state marks on DNA35, ROS: DNA35.site ok→sdsb at `kdam1`. | +| 2168 | `Unlabeled` | one-way | DNA36, ROS | `kdam1` | internal-state conversion/modification | `DNA36(site~ok) + ROS() -> DNA36(site~sdsb)` | Changes internal modification/state marks on DNA36, ROS: DNA36.site ok→sdsb at `kdam1`. | +| 2169 | `Unlabeled` | one-way | DNA37, ROS | `kdam1` | internal-state conversion/modification | `DNA37(site~ok) + ROS() -> DNA37(site~sdsb)` | Changes internal modification/state marks on DNA37, ROS: DNA37.site ok→sdsb at `kdam1`. | +| 2170 | `Unlabeled` | one-way | DNA38, ROS | `kdam1` | internal-state conversion/modification | `DNA38(site~ok) + ROS() -> DNA38(site~sdsb)` | Changes internal modification/state marks on DNA38, ROS: DNA38.site ok→sdsb at `kdam1`. | +| 2171 | `Unlabeled` | one-way | DNA39, ROS | `kdam1` | internal-state conversion/modification | `DNA39(site~ok) + ROS() -> DNA39(site~sdsb)` | Changes internal modification/state marks on DNA39, ROS: DNA39.site ok→sdsb at `kdam1`. | +| 2172 | `Unlabeled` | one-way | DNA40, ROS | `kdam1` | internal-state conversion/modification | `DNA40(site~ok) + ROS() -> DNA40(site~sdsb)` | Changes internal modification/state marks on DNA40, ROS: DNA40.site ok→sdsb at `kdam1`. | +| 2173 | `Unlabeled` | one-way | DNA41, ROS | `kdam1` | internal-state conversion/modification | `DNA41(site~ok) + ROS() -> DNA41(site~sdsb)` | Changes internal modification/state marks on DNA41, ROS: DNA41.site ok→sdsb at `kdam1`. | +| 2174 | `Unlabeled` | one-way | DNA42, ROS | `kdam1` | internal-state conversion/modification | `DNA42(site~ok) + ROS() -> DNA42(site~sdsb)` | Changes internal modification/state marks on DNA42, ROS: DNA42.site ok→sdsb at `kdam1`. | +| 2175 | `Unlabeled` | one-way | DNA43, ROS | `kdam1` | internal-state conversion/modification | `DNA43(site~ok) + ROS() -> DNA43(site~sdsb)` | Changes internal modification/state marks on DNA43, ROS: DNA43.site ok→sdsb at `kdam1`. | +| 2176 | `Unlabeled` | one-way | DNA44, ROS | `kdam1` | internal-state conversion/modification | `DNA44(site~ok) + ROS() -> DNA44(site~sdsb)` | Changes internal modification/state marks on DNA44, ROS: DNA44.site ok→sdsb at `kdam1`. | +| 2177 | `Unlabeled` | one-way | DNA45, ROS | `kdam1` | internal-state conversion/modification | `DNA45(site~ok) + ROS() -> DNA45(site~sdsb)` | Changes internal modification/state marks on DNA45, ROS: DNA45.site ok→sdsb at `kdam1`. | +| 2178 | `Unlabeled` | one-way | DNA46, ROS | `kdam1` | internal-state conversion/modification | `DNA46(site~ok) + ROS() -> DNA46(site~sdsb)` | Changes internal modification/state marks on DNA46, ROS: DNA46.site ok→sdsb at `kdam1`. | +| 2179 | `Unlabeled` | one-way | DNA47, ROS | `kdam1` | internal-state conversion/modification | `DNA47(site~ok) + ROS() -> DNA47(site~sdsb)` | Changes internal modification/state marks on DNA47, ROS: DNA47.site ok→sdsb at `kdam1`. | +| 2180 | `Unlabeled` | one-way | DNA48, ROS | `kdam1` | internal-state conversion/modification | `DNA48(site~ok) + ROS() -> DNA48(site~sdsb)` | Changes internal modification/state marks on DNA48, ROS: DNA48.site ok→sdsb at `kdam1`. | +| 2181 | `Unlabeled` | one-way | DNA49, ROS | `kdam1` | internal-state conversion/modification | `DNA49(site~ok) + ROS() -> DNA49(site~sdsb)` | Changes internal modification/state marks on DNA49, ROS: DNA49.site ok→sdsb at `kdam1`. | +| 2182 | `Unlabeled` | one-way | DNA50, ROS | `kdam1` | internal-state conversion/modification | `DNA50(site~ok) + ROS() -> DNA50(site~sdsb)` | Changes internal modification/state marks on DNA50, ROS: DNA50.site ok→sdsb at `kdam1`. | +| 2183 | `Unlabeled` | one-way | DNA1, ROS | `kdam2` | internal-state conversion/modification | `DNA1(site~ok) + ROS() -> DNA1(site~cdsb)` | Changes internal modification/state marks on DNA1, ROS: DNA1.site ok→cdsb at `kdam2`. | +| 2184 | `Unlabeled` | one-way | DNA2, ROS | `kdam2` | internal-state conversion/modification | `DNA2(site~ok) + ROS() -> DNA2(site~cdsb)` | Changes internal modification/state marks on DNA2, ROS: DNA2.site ok→cdsb at `kdam2`. | +| 2185 | `Unlabeled` | one-way | DNA3, ROS | `kdam2` | internal-state conversion/modification | `DNA3(site~ok) + ROS() -> DNA3(site~cdsb)` | Changes internal modification/state marks on DNA3, ROS: DNA3.site ok→cdsb at `kdam2`. | +| 2186 | `Unlabeled` | one-way | DNA4, ROS | `kdam2` | internal-state conversion/modification | `DNA4(site~ok) + ROS() -> DNA4(site~cdsb)` | Changes internal modification/state marks on DNA4, ROS: DNA4.site ok→cdsb at `kdam2`. | +| 2187 | `Unlabeled` | one-way | DNA5, ROS | `kdam2` | internal-state conversion/modification | `DNA5(site~ok) + ROS() -> DNA5(site~cdsb)` | Changes internal modification/state marks on DNA5, ROS: DNA5.site ok→cdsb at `kdam2`. | +| 2188 | `Unlabeled` | one-way | DNA6, ROS | `kdam2` | internal-state conversion/modification | `DNA6(site~ok) + ROS() -> DNA6(site~cdsb)` | Changes internal modification/state marks on DNA6, ROS: DNA6.site ok→cdsb at `kdam2`. | +| 2189 | `Unlabeled` | one-way | DNA7, ROS | `kdam2` | internal-state conversion/modification | `DNA7(site~ok) + ROS() -> DNA7(site~cdsb)` | Changes internal modification/state marks on DNA7, ROS: DNA7.site ok→cdsb at `kdam2`. | +| 2190 | `Unlabeled` | one-way | DNA8, ROS | `kdam2` | internal-state conversion/modification | `DNA8(site~ok) + ROS() -> DNA8(site~cdsb)` | Changes internal modification/state marks on DNA8, ROS: DNA8.site ok→cdsb at `kdam2`. | +| 2191 | `Unlabeled` | one-way | DNA9, ROS | `kdam2` | internal-state conversion/modification | `DNA9(site~ok) + ROS() -> DNA9(site~cdsb)` | Changes internal modification/state marks on DNA9, ROS: DNA9.site ok→cdsb at `kdam2`. | +| 2192 | `Unlabeled` | one-way | DNA10, ROS | `kdam2` | internal-state conversion/modification | `DNA10(site~ok) + ROS() -> DNA10(site~cdsb)` | Changes internal modification/state marks on DNA10, ROS: DNA10.site ok→cdsb at `kdam2`. | +| 2193 | `Unlabeled` | one-way | DNA11, ROS | `kdam2` | internal-state conversion/modification | `DNA11(site~ok) + ROS() -> DNA11(site~cdsb)` | Changes internal modification/state marks on DNA11, ROS: DNA11.site ok→cdsb at `kdam2`. | +| 2194 | `Unlabeled` | one-way | DNA12, ROS | `kdam2` | internal-state conversion/modification | `DNA12(site~ok) + ROS() -> DNA12(site~cdsb)` | Changes internal modification/state marks on DNA12, ROS: DNA12.site ok→cdsb at `kdam2`. | +| 2195 | `Unlabeled` | one-way | DNA13, ROS | `kdam2` | internal-state conversion/modification | `DNA13(site~ok) + ROS() -> DNA13(site~cdsb)` | Changes internal modification/state marks on DNA13, ROS: DNA13.site ok→cdsb at `kdam2`. | +| 2196 | `Unlabeled` | one-way | DNA14, ROS | `kdam2` | internal-state conversion/modification | `DNA14(site~ok) + ROS() -> DNA14(site~cdsb)` | Changes internal modification/state marks on DNA14, ROS: DNA14.site ok→cdsb at `kdam2`. | +| 2197 | `Unlabeled` | one-way | DNA15, ROS | `kdam2` | internal-state conversion/modification | `DNA15(site~ok) + ROS() -> DNA15(site~cdsb)` | Changes internal modification/state marks on DNA15, ROS: DNA15.site ok→cdsb at `kdam2`. | +| 2198 | `Unlabeled` | one-way | DNA16, ROS | `kdam2` | internal-state conversion/modification | `DNA16(site~ok) + ROS() -> DNA16(site~cdsb)` | Changes internal modification/state marks on DNA16, ROS: DNA16.site ok→cdsb at `kdam2`. | +| 2199 | `Unlabeled` | one-way | DNA17, ROS | `kdam2` | internal-state conversion/modification | `DNA17(site~ok) + ROS() -> DNA17(site~cdsb)` | Changes internal modification/state marks on DNA17, ROS: DNA17.site ok→cdsb at `kdam2`. | +| 2200 | `Unlabeled` | one-way | DNA18, ROS | `kdam2` | internal-state conversion/modification | `DNA18(site~ok) + ROS() -> DNA18(site~cdsb)` | Changes internal modification/state marks on DNA18, ROS: DNA18.site ok→cdsb at `kdam2`. | +| 2201 | `Unlabeled` | one-way | DNA19, ROS | `kdam2` | internal-state conversion/modification | `DNA19(site~ok) + ROS() -> DNA19(site~cdsb)` | Changes internal modification/state marks on DNA19, ROS: DNA19.site ok→cdsb at `kdam2`. | +| 2202 | `Unlabeled` | one-way | DNA20, ROS | `kdam2` | internal-state conversion/modification | `DNA20(site~ok) + ROS() -> DNA20(site~cdsb)` | Changes internal modification/state marks on DNA20, ROS: DNA20.site ok→cdsb at `kdam2`. | +| 2203 | `Unlabeled` | one-way | DNA21, ROS | `kdam2` | internal-state conversion/modification | `DNA21(site~ok) + ROS() -> DNA21(site~cdsb)` | Changes internal modification/state marks on DNA21, ROS: DNA21.site ok→cdsb at `kdam2`. | +| 2204 | `Unlabeled` | one-way | DNA22, ROS | `kdam2` | internal-state conversion/modification | `DNA22(site~ok) + ROS() -> DNA22(site~cdsb)` | Changes internal modification/state marks on DNA22, ROS: DNA22.site ok→cdsb at `kdam2`. | +| 2205 | `Unlabeled` | one-way | DNA23, ROS | `kdam2` | internal-state conversion/modification | `DNA23(site~ok) + ROS() -> DNA23(site~cdsb)` | Changes internal modification/state marks on DNA23, ROS: DNA23.site ok→cdsb at `kdam2`. | +| 2206 | `Unlabeled` | one-way | DNA24, ROS | `kdam2` | internal-state conversion/modification | `DNA24(site~ok) + ROS() -> DNA24(site~cdsb)` | Changes internal modification/state marks on DNA24, ROS: DNA24.site ok→cdsb at `kdam2`. | +| 2207 | `Unlabeled` | one-way | DNA25, ROS | `kdam2` | internal-state conversion/modification | `DNA25(site~ok) + ROS() -> DNA25(site~cdsb)` | Changes internal modification/state marks on DNA25, ROS: DNA25.site ok→cdsb at `kdam2`. | +| 2208 | `Unlabeled` | one-way | DNA26, ROS | `kdam2` | internal-state conversion/modification | `DNA26(site~ok) + ROS() -> DNA26(site~cdsb)` | Changes internal modification/state marks on DNA26, ROS: DNA26.site ok→cdsb at `kdam2`. | +| 2209 | `Unlabeled` | one-way | DNA27, ROS | `kdam2` | internal-state conversion/modification | `DNA27(site~ok) + ROS() -> DNA27(site~cdsb)` | Changes internal modification/state marks on DNA27, ROS: DNA27.site ok→cdsb at `kdam2`. | +| 2210 | `Unlabeled` | one-way | DNA28, ROS | `kdam2` | internal-state conversion/modification | `DNA28(site~ok) + ROS() -> DNA28(site~cdsb)` | Changes internal modification/state marks on DNA28, ROS: DNA28.site ok→cdsb at `kdam2`. | +| 2211 | `Unlabeled` | one-way | DNA29, ROS | `kdam2` | internal-state conversion/modification | `DNA29(site~ok) + ROS() -> DNA29(site~cdsb)` | Changes internal modification/state marks on DNA29, ROS: DNA29.site ok→cdsb at `kdam2`. | +| 2212 | `Unlabeled` | one-way | DNA30, ROS | `kdam2` | internal-state conversion/modification | `DNA30(site~ok) + ROS() -> DNA30(site~cdsb)` | Changes internal modification/state marks on DNA30, ROS: DNA30.site ok→cdsb at `kdam2`. | +| 2213 | `Unlabeled` | one-way | DNA31, ROS | `kdam2` | internal-state conversion/modification | `DNA31(site~ok) + ROS() -> DNA31(site~cdsb)` | Changes internal modification/state marks on DNA31, ROS: DNA31.site ok→cdsb at `kdam2`. | +| 2214 | `Unlabeled` | one-way | DNA32, ROS | `kdam2` | internal-state conversion/modification | `DNA32(site~ok) + ROS() -> DNA32(site~cdsb)` | Changes internal modification/state marks on DNA32, ROS: DNA32.site ok→cdsb at `kdam2`. | +| 2215 | `Unlabeled` | one-way | DNA33, ROS | `kdam2` | internal-state conversion/modification | `DNA33(site~ok) + ROS() -> DNA33(site~cdsb)` | Changes internal modification/state marks on DNA33, ROS: DNA33.site ok→cdsb at `kdam2`. | +| 2216 | `Unlabeled` | one-way | DNA34, ROS | `kdam2` | internal-state conversion/modification | `DNA34(site~ok) + ROS() -> DNA34(site~cdsb)` | Changes internal modification/state marks on DNA34, ROS: DNA34.site ok→cdsb at `kdam2`. | +| 2217 | `Unlabeled` | one-way | DNA35, ROS | `kdam2` | internal-state conversion/modification | `DNA35(site~ok) + ROS() -> DNA35(site~cdsb)` | Changes internal modification/state marks on DNA35, ROS: DNA35.site ok→cdsb at `kdam2`. | +| 2218 | `Unlabeled` | one-way | DNA36, ROS | `kdam2` | internal-state conversion/modification | `DNA36(site~ok) + ROS() -> DNA36(site~cdsb)` | Changes internal modification/state marks on DNA36, ROS: DNA36.site ok→cdsb at `kdam2`. | +| 2219 | `Unlabeled` | one-way | DNA37, ROS | `kdam2` | internal-state conversion/modification | `DNA37(site~ok) + ROS() -> DNA37(site~cdsb)` | Changes internal modification/state marks on DNA37, ROS: DNA37.site ok→cdsb at `kdam2`. | +| 2220 | `Unlabeled` | one-way | DNA38, ROS | `kdam2` | internal-state conversion/modification | `DNA38(site~ok) + ROS() -> DNA38(site~cdsb)` | Changes internal modification/state marks on DNA38, ROS: DNA38.site ok→cdsb at `kdam2`. | +| 2221 | `Unlabeled` | one-way | DNA39, ROS | `kdam2` | internal-state conversion/modification | `DNA39(site~ok) + ROS() -> DNA39(site~cdsb)` | Changes internal modification/state marks on DNA39, ROS: DNA39.site ok→cdsb at `kdam2`. | +| 2222 | `Unlabeled` | one-way | DNA40, ROS | `kdam2` | internal-state conversion/modification | `DNA40(site~ok) + ROS() -> DNA40(site~cdsb)` | Changes internal modification/state marks on DNA40, ROS: DNA40.site ok→cdsb at `kdam2`. | +| 2223 | `Unlabeled` | one-way | DNA41, ROS | `kdam2` | internal-state conversion/modification | `DNA41(site~ok) + ROS() -> DNA41(site~cdsb)` | Changes internal modification/state marks on DNA41, ROS: DNA41.site ok→cdsb at `kdam2`. | +| 2224 | `Unlabeled` | one-way | DNA42, ROS | `kdam2` | internal-state conversion/modification | `DNA42(site~ok) + ROS() -> DNA42(site~cdsb)` | Changes internal modification/state marks on DNA42, ROS: DNA42.site ok→cdsb at `kdam2`. | +| 2225 | `Unlabeled` | one-way | DNA43, ROS | `kdam2` | internal-state conversion/modification | `DNA43(site~ok) + ROS() -> DNA43(site~cdsb)` | Changes internal modification/state marks on DNA43, ROS: DNA43.site ok→cdsb at `kdam2`. | +| 2226 | `Unlabeled` | one-way | DNA44, ROS | `kdam2` | internal-state conversion/modification | `DNA44(site~ok) + ROS() -> DNA44(site~cdsb)` | Changes internal modification/state marks on DNA44, ROS: DNA44.site ok→cdsb at `kdam2`. | +| 2227 | `Unlabeled` | one-way | DNA45, ROS | `kdam2` | internal-state conversion/modification | `DNA45(site~ok) + ROS() -> DNA45(site~cdsb)` | Changes internal modification/state marks on DNA45, ROS: DNA45.site ok→cdsb at `kdam2`. | +| 2228 | `Unlabeled` | one-way | DNA46, ROS | `kdam2` | internal-state conversion/modification | `DNA46(site~ok) + ROS() -> DNA46(site~cdsb)` | Changes internal modification/state marks on DNA46, ROS: DNA46.site ok→cdsb at `kdam2`. | +| 2229 | `Unlabeled` | one-way | DNA47, ROS | `kdam2` | internal-state conversion/modification | `DNA47(site~ok) + ROS() -> DNA47(site~cdsb)` | Changes internal modification/state marks on DNA47, ROS: DNA47.site ok→cdsb at `kdam2`. | +| 2230 | `Unlabeled` | one-way | DNA48, ROS | `kdam2` | internal-state conversion/modification | `DNA48(site~ok) + ROS() -> DNA48(site~cdsb)` | Changes internal modification/state marks on DNA48, ROS: DNA48.site ok→cdsb at `kdam2`. | +| 2231 | `Unlabeled` | one-way | DNA49, ROS | `kdam2` | internal-state conversion/modification | `DNA49(site~ok) + ROS() -> DNA49(site~cdsb)` | Changes internal modification/state marks on DNA49, ROS: DNA49.site ok→cdsb at `kdam2`. | +| 2232 | `Unlabeled` | one-way | DNA50, ROS | `kdam2` | internal-state conversion/modification | `DNA50(site~ok) + ROS() -> DNA50(site~cdsb)` | Changes internal modification/state marks on DNA50, ROS: DNA50.site ok→cdsb at `kdam2`. | +| 2233 | `Unlabeled` | one-way | Ku, ROS | `kox` | internal-state conversion/modification | `Ku(dna,cs,cys~red) + ROS() -> Ku(dna,cs,cys~ox) + ROS()` | Changes internal modification/state marks on Ku, ROS: Ku.cys red→ox at `kox`. | +| 2234 | `Unlabeled` | one-way | Ku | `kred` | internal-state conversion/modification | `Ku(dna,cs,cys~ox) -> Ku(dna,cs,cys~red)` | Changes internal modification/state marks on Ku: Ku.cys ox→red at `kred`. | +| 2235 | `Unlabeled` | one-way | DNA1, Ku | `kdku3` | state and binding-pattern rewrite | `DNA1(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA1(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA1, Ku by freeing DNA1.site, Ku.dna at `kdku3`. | +| 2236 | `Unlabeled` | one-way | DNA2, Ku | `kdku3` | state and binding-pattern rewrite | `DNA2(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA2(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA2, Ku by freeing DNA2.site, Ku.dna at `kdku3`. | +| 2237 | `Unlabeled` | one-way | DNA3, Ku | `kdku3` | state and binding-pattern rewrite | `DNA3(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA3(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA3, Ku by freeing DNA3.site, Ku.dna at `kdku3`. | +| 2238 | `Unlabeled` | one-way | DNA4, Ku | `kdku3` | state and binding-pattern rewrite | `DNA4(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA4(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA4, Ku by freeing DNA4.site, Ku.dna at `kdku3`. | +| 2239 | `Unlabeled` | one-way | DNA5, Ku | `kdku3` | state and binding-pattern rewrite | `DNA5(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA5(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA5, Ku by freeing DNA5.site, Ku.dna at `kdku3`. | +| 2240 | `Unlabeled` | one-way | DNA6, Ku | `kdku3` | state and binding-pattern rewrite | `DNA6(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA6(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA6, Ku by freeing DNA6.site, Ku.dna at `kdku3`. | +| 2241 | `Unlabeled` | one-way | DNA7, Ku | `kdku3` | state and binding-pattern rewrite | `DNA7(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA7(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA7, Ku by freeing DNA7.site, Ku.dna at `kdku3`. | +| 2242 | `Unlabeled` | one-way | DNA8, Ku | `kdku3` | state and binding-pattern rewrite | `DNA8(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA8(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA8, Ku by freeing DNA8.site, Ku.dna at `kdku3`. | +| 2243 | `Unlabeled` | one-way | DNA9, Ku | `kdku3` | state and binding-pattern rewrite | `DNA9(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA9(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA9, Ku by freeing DNA9.site, Ku.dna at `kdku3`. | +| 2244 | `Unlabeled` | one-way | DNA10, Ku | `kdku3` | state and binding-pattern rewrite | `DNA10(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA10(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA10, Ku by freeing DNA10.site, Ku.dna at `kdku3`. | +| 2245 | `Unlabeled` | one-way | DNA11, Ku | `kdku3` | state and binding-pattern rewrite | `DNA11(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA11(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA11, Ku by freeing DNA11.site, Ku.dna at `kdku3`. | +| 2246 | `Unlabeled` | one-way | DNA12, Ku | `kdku3` | state and binding-pattern rewrite | `DNA12(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA12(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA12, Ku by freeing DNA12.site, Ku.dna at `kdku3`. | +| 2247 | `Unlabeled` | one-way | DNA13, Ku | `kdku3` | state and binding-pattern rewrite | `DNA13(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA13(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA13, Ku by freeing DNA13.site, Ku.dna at `kdku3`. | +| 2248 | `Unlabeled` | one-way | DNA14, Ku | `kdku3` | state and binding-pattern rewrite | `DNA14(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA14(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA14, Ku by freeing DNA14.site, Ku.dna at `kdku3`. | +| 2249 | `Unlabeled` | one-way | DNA15, Ku | `kdku3` | state and binding-pattern rewrite | `DNA15(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA15(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA15, Ku by freeing DNA15.site, Ku.dna at `kdku3`. | +| 2250 | `Unlabeled` | one-way | DNA16, Ku | `kdku3` | state and binding-pattern rewrite | `DNA16(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA16(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA16, Ku by freeing DNA16.site, Ku.dna at `kdku3`. | + +### Rules 2251-2339 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 2251 | `Unlabeled` | one-way | DNA17, Ku | `kdku3` | state and binding-pattern rewrite | `DNA17(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA17(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA17, Ku by freeing DNA17.site, Ku.dna at `kdku3`. | +| 2252 | `Unlabeled` | one-way | DNA18, Ku | `kdku3` | state and binding-pattern rewrite | `DNA18(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA18(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA18, Ku by freeing DNA18.site, Ku.dna at `kdku3`. | +| 2253 | `Unlabeled` | one-way | DNA19, Ku | `kdku3` | state and binding-pattern rewrite | `DNA19(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA19(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA19, Ku by freeing DNA19.site, Ku.dna at `kdku3`. | +| 2254 | `Unlabeled` | one-way | DNA20, Ku | `kdku3` | state and binding-pattern rewrite | `DNA20(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA20(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA20, Ku by freeing DNA20.site, Ku.dna at `kdku3`. | +| 2255 | `Unlabeled` | one-way | DNA21, Ku | `kdku3` | state and binding-pattern rewrite | `DNA21(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA21(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA21, Ku by freeing DNA21.site, Ku.dna at `kdku3`. | +| 2256 | `Unlabeled` | one-way | DNA22, Ku | `kdku3` | state and binding-pattern rewrite | `DNA22(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA22(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA22, Ku by freeing DNA22.site, Ku.dna at `kdku3`. | +| 2257 | `Unlabeled` | one-way | DNA23, Ku | `kdku3` | state and binding-pattern rewrite | `DNA23(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA23(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA23, Ku by freeing DNA23.site, Ku.dna at `kdku3`. | +| 2258 | `Unlabeled` | one-way | DNA24, Ku | `kdku3` | state and binding-pattern rewrite | `DNA24(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA24(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA24, Ku by freeing DNA24.site, Ku.dna at `kdku3`. | +| 2259 | `Unlabeled` | one-way | DNA25, Ku | `kdku3` | state and binding-pattern rewrite | `DNA25(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA25(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA25, Ku by freeing DNA25.site, Ku.dna at `kdku3`. | +| 2260 | `Unlabeled` | one-way | DNA26, Ku | `kdku3` | state and binding-pattern rewrite | `DNA26(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA26(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA26, Ku by freeing DNA26.site, Ku.dna at `kdku3`. | +| 2261 | `Unlabeled` | one-way | DNA27, Ku | `kdku3` | state and binding-pattern rewrite | `DNA27(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA27(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA27, Ku by freeing DNA27.site, Ku.dna at `kdku3`. | +| 2262 | `Unlabeled` | one-way | DNA28, Ku | `kdku3` | state and binding-pattern rewrite | `DNA28(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA28(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA28, Ku by freeing DNA28.site, Ku.dna at `kdku3`. | +| 2263 | `Unlabeled` | one-way | DNA29, Ku | `kdku3` | state and binding-pattern rewrite | `DNA29(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA29(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA29, Ku by freeing DNA29.site, Ku.dna at `kdku3`. | +| 2264 | `Unlabeled` | one-way | DNA30, Ku | `kdku3` | state and binding-pattern rewrite | `DNA30(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA30(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA30, Ku by freeing DNA30.site, Ku.dna at `kdku3`. | +| 2265 | `Unlabeled` | one-way | DNA31, Ku | `kdku3` | state and binding-pattern rewrite | `DNA31(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA31(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA31, Ku by freeing DNA31.site, Ku.dna at `kdku3`. | +| 2266 | `Unlabeled` | one-way | DNA32, Ku | `kdku3` | state and binding-pattern rewrite | `DNA32(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA32(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA32, Ku by freeing DNA32.site, Ku.dna at `kdku3`. | +| 2267 | `Unlabeled` | one-way | DNA33, Ku | `kdku3` | state and binding-pattern rewrite | `DNA33(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA33(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA33, Ku by freeing DNA33.site, Ku.dna at `kdku3`. | +| 2268 | `Unlabeled` | one-way | DNA34, Ku | `kdku3` | state and binding-pattern rewrite | `DNA34(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA34(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA34, Ku by freeing DNA34.site, Ku.dna at `kdku3`. | +| 2269 | `Unlabeled` | one-way | DNA35, Ku | `kdku3` | state and binding-pattern rewrite | `DNA35(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA35(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA35, Ku by freeing DNA35.site, Ku.dna at `kdku3`. | +| 2270 | `Unlabeled` | one-way | DNA36, Ku | `kdku3` | state and binding-pattern rewrite | `DNA36(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA36(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA36, Ku by freeing DNA36.site, Ku.dna at `kdku3`. | +| 2271 | `Unlabeled` | one-way | DNA37, Ku | `kdku3` | state and binding-pattern rewrite | `DNA37(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA37(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA37, Ku by freeing DNA37.site, Ku.dna at `kdku3`. | +| 2272 | `Unlabeled` | one-way | DNA38, Ku | `kdku3` | state and binding-pattern rewrite | `DNA38(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA38(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA38, Ku by freeing DNA38.site, Ku.dna at `kdku3`. | +| 2273 | `Unlabeled` | one-way | DNA39, Ku | `kdku3` | state and binding-pattern rewrite | `DNA39(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA39(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA39, Ku by freeing DNA39.site, Ku.dna at `kdku3`. | +| 2274 | `Unlabeled` | one-way | DNA40, Ku | `kdku3` | state and binding-pattern rewrite | `DNA40(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA40(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA40, Ku by freeing DNA40.site, Ku.dna at `kdku3`. | +| 2275 | `Unlabeled` | one-way | DNA41, Ku | `kdku3` | state and binding-pattern rewrite | `DNA41(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA41(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA41, Ku by freeing DNA41.site, Ku.dna at `kdku3`. | +| 2276 | `Unlabeled` | one-way | DNA42, Ku | `kdku3` | state and binding-pattern rewrite | `DNA42(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA42(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA42, Ku by freeing DNA42.site, Ku.dna at `kdku3`. | +| 2277 | `Unlabeled` | one-way | DNA43, Ku | `kdku3` | state and binding-pattern rewrite | `DNA43(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA43(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA43, Ku by freeing DNA43.site, Ku.dna at `kdku3`. | +| 2278 | `Unlabeled` | one-way | DNA44, Ku | `kdku3` | state and binding-pattern rewrite | `DNA44(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA44(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA44, Ku by freeing DNA44.site, Ku.dna at `kdku3`. | +| 2279 | `Unlabeled` | one-way | DNA45, Ku | `kdku3` | state and binding-pattern rewrite | `DNA45(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA45(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA45, Ku by freeing DNA45.site, Ku.dna at `kdku3`. | +| 2280 | `Unlabeled` | one-way | DNA46, Ku | `kdku3` | state and binding-pattern rewrite | `DNA46(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA46(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA46, Ku by freeing DNA46.site, Ku.dna at `kdku3`. | +| 2281 | `Unlabeled` | one-way | DNA47, Ku | `kdku3` | state and binding-pattern rewrite | `DNA47(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA47(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA47, Ku by freeing DNA47.site, Ku.dna at `kdku3`. | +| 2282 | `Unlabeled` | one-way | DNA48, Ku | `kdku3` | state and binding-pattern rewrite | `DNA48(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA48(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA48, Ku by freeing DNA48.site, Ku.dna at `kdku3`. | +| 2283 | `Unlabeled` | one-way | DNA49, Ku | `kdku3` | state and binding-pattern rewrite | `DNA49(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA49(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA49, Ku by freeing DNA49.site, Ku.dna at `kdku3`. | +| 2284 | `Unlabeled` | one-way | DNA50, Ku | `kdku3` | state and binding-pattern rewrite | `DNA50(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA50(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA50, Ku by freeing DNA50.site, Ku.dna at `kdku3`. | +| 2285 | `Unlabeled` | one-way | DNA1, Ku | `kdku4` | state and binding-pattern rewrite | `DNA1(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA1(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA1, Ku by freeing DNA1.site, Ku.dna at `kdku4`. | +| 2286 | `Unlabeled` | one-way | DNA2, Ku | `kdku4` | state and binding-pattern rewrite | `DNA2(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA2(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA2, Ku by freeing DNA2.site, Ku.dna at `kdku4`. | +| 2287 | `Unlabeled` | one-way | DNA3, Ku | `kdku4` | state and binding-pattern rewrite | `DNA3(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA3(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA3, Ku by freeing DNA3.site, Ku.dna at `kdku4`. | +| 2288 | `Unlabeled` | one-way | DNA4, Ku | `kdku4` | state and binding-pattern rewrite | `DNA4(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA4(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA4, Ku by freeing DNA4.site, Ku.dna at `kdku4`. | +| 2289 | `Unlabeled` | one-way | DNA5, Ku | `kdku4` | state and binding-pattern rewrite | `DNA5(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA5(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA5, Ku by freeing DNA5.site, Ku.dna at `kdku4`. | +| 2290 | `Unlabeled` | one-way | DNA6, Ku | `kdku4` | state and binding-pattern rewrite | `DNA6(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA6(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA6, Ku by freeing DNA6.site, Ku.dna at `kdku4`. | +| 2291 | `Unlabeled` | one-way | DNA7, Ku | `kdku4` | state and binding-pattern rewrite | `DNA7(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA7(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA7, Ku by freeing DNA7.site, Ku.dna at `kdku4`. | +| 2292 | `Unlabeled` | one-way | DNA8, Ku | `kdku4` | state and binding-pattern rewrite | `DNA8(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA8(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA8, Ku by freeing DNA8.site, Ku.dna at `kdku4`. | +| 2293 | `Unlabeled` | one-way | DNA9, Ku | `kdku4` | state and binding-pattern rewrite | `DNA9(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA9(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA9, Ku by freeing DNA9.site, Ku.dna at `kdku4`. | +| 2294 | `Unlabeled` | one-way | DNA10, Ku | `kdku4` | state and binding-pattern rewrite | `DNA10(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA10(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA10, Ku by freeing DNA10.site, Ku.dna at `kdku4`. | +| 2295 | `Unlabeled` | one-way | DNA11, Ku | `kdku4` | state and binding-pattern rewrite | `DNA11(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA11(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA11, Ku by freeing DNA11.site, Ku.dna at `kdku4`. | +| 2296 | `Unlabeled` | one-way | DNA12, Ku | `kdku4` | state and binding-pattern rewrite | `DNA12(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA12(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA12, Ku by freeing DNA12.site, Ku.dna at `kdku4`. | +| 2297 | `Unlabeled` | one-way | DNA13, Ku | `kdku4` | state and binding-pattern rewrite | `DNA13(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA13(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA13, Ku by freeing DNA13.site, Ku.dna at `kdku4`. | +| 2298 | `Unlabeled` | one-way | DNA14, Ku | `kdku4` | state and binding-pattern rewrite | `DNA14(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA14(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA14, Ku by freeing DNA14.site, Ku.dna at `kdku4`. | +| 2299 | `Unlabeled` | one-way | DNA15, Ku | `kdku4` | state and binding-pattern rewrite | `DNA15(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA15(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA15, Ku by freeing DNA15.site, Ku.dna at `kdku4`. | +| 2300 | `Unlabeled` | one-way | DNA16, Ku | `kdku4` | state and binding-pattern rewrite | `DNA16(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA16(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA16, Ku by freeing DNA16.site, Ku.dna at `kdku4`. | +| 2301 | `Unlabeled` | one-way | DNA17, Ku | `kdku4` | state and binding-pattern rewrite | `DNA17(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA17(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA17, Ku by freeing DNA17.site, Ku.dna at `kdku4`. | +| 2302 | `Unlabeled` | one-way | DNA18, Ku | `kdku4` | state and binding-pattern rewrite | `DNA18(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA18(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA18, Ku by freeing DNA18.site, Ku.dna at `kdku4`. | +| 2303 | `Unlabeled` | one-way | DNA19, Ku | `kdku4` | state and binding-pattern rewrite | `DNA19(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA19(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA19, Ku by freeing DNA19.site, Ku.dna at `kdku4`. | +| 2304 | `Unlabeled` | one-way | DNA20, Ku | `kdku4` | state and binding-pattern rewrite | `DNA20(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA20(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA20, Ku by freeing DNA20.site, Ku.dna at `kdku4`. | +| 2305 | `Unlabeled` | one-way | DNA21, Ku | `kdku4` | state and binding-pattern rewrite | `DNA21(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA21(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA21, Ku by freeing DNA21.site, Ku.dna at `kdku4`. | +| 2306 | `Unlabeled` | one-way | DNA22, Ku | `kdku4` | state and binding-pattern rewrite | `DNA22(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA22(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA22, Ku by freeing DNA22.site, Ku.dna at `kdku4`. | +| 2307 | `Unlabeled` | one-way | DNA23, Ku | `kdku4` | state and binding-pattern rewrite | `DNA23(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA23(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA23, Ku by freeing DNA23.site, Ku.dna at `kdku4`. | +| 2308 | `Unlabeled` | one-way | DNA24, Ku | `kdku4` | state and binding-pattern rewrite | `DNA24(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA24(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA24, Ku by freeing DNA24.site, Ku.dna at `kdku4`. | +| 2309 | `Unlabeled` | one-way | DNA25, Ku | `kdku4` | state and binding-pattern rewrite | `DNA25(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA25(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA25, Ku by freeing DNA25.site, Ku.dna at `kdku4`. | +| 2310 | `Unlabeled` | one-way | DNA26, Ku | `kdku4` | state and binding-pattern rewrite | `DNA26(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA26(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA26, Ku by freeing DNA26.site, Ku.dna at `kdku4`. | +| 2311 | `Unlabeled` | one-way | DNA27, Ku | `kdku4` | state and binding-pattern rewrite | `DNA27(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA27(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA27, Ku by freeing DNA27.site, Ku.dna at `kdku4`. | +| 2312 | `Unlabeled` | one-way | DNA28, Ku | `kdku4` | state and binding-pattern rewrite | `DNA28(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA28(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA28, Ku by freeing DNA28.site, Ku.dna at `kdku4`. | +| 2313 | `Unlabeled` | one-way | DNA29, Ku | `kdku4` | state and binding-pattern rewrite | `DNA29(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA29(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA29, Ku by freeing DNA29.site, Ku.dna at `kdku4`. | +| 2314 | `Unlabeled` | one-way | DNA30, Ku | `kdku4` | state and binding-pattern rewrite | `DNA30(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA30(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA30, Ku by freeing DNA30.site, Ku.dna at `kdku4`. | +| 2315 | `Unlabeled` | one-way | DNA31, Ku | `kdku4` | state and binding-pattern rewrite | `DNA31(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA31(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA31, Ku by freeing DNA31.site, Ku.dna at `kdku4`. | +| 2316 | `Unlabeled` | one-way | DNA32, Ku | `kdku4` | state and binding-pattern rewrite | `DNA32(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA32(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA32, Ku by freeing DNA32.site, Ku.dna at `kdku4`. | +| 2317 | `Unlabeled` | one-way | DNA33, Ku | `kdku4` | state and binding-pattern rewrite | `DNA33(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA33(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA33, Ku by freeing DNA33.site, Ku.dna at `kdku4`. | +| 2318 | `Unlabeled` | one-way | DNA34, Ku | `kdku4` | state and binding-pattern rewrite | `DNA34(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA34(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA34, Ku by freeing DNA34.site, Ku.dna at `kdku4`. | +| 2319 | `Unlabeled` | one-way | DNA35, Ku | `kdku4` | state and binding-pattern rewrite | `DNA35(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA35(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA35, Ku by freeing DNA35.site, Ku.dna at `kdku4`. | +| 2320 | `Unlabeled` | one-way | DNA36, Ku | `kdku4` | state and binding-pattern rewrite | `DNA36(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA36(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA36, Ku by freeing DNA36.site, Ku.dna at `kdku4`. | +| 2321 | `Unlabeled` | one-way | DNA37, Ku | `kdku4` | state and binding-pattern rewrite | `DNA37(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA37(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA37, Ku by freeing DNA37.site, Ku.dna at `kdku4`. | +| 2322 | `Unlabeled` | one-way | DNA38, Ku | `kdku4` | state and binding-pattern rewrite | `DNA38(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA38(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA38, Ku by freeing DNA38.site, Ku.dna at `kdku4`. | +| 2323 | `Unlabeled` | one-way | DNA39, Ku | `kdku4` | state and binding-pattern rewrite | `DNA39(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA39(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA39, Ku by freeing DNA39.site, Ku.dna at `kdku4`. | +| 2324 | `Unlabeled` | one-way | DNA40, Ku | `kdku4` | state and binding-pattern rewrite | `DNA40(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA40(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA40, Ku by freeing DNA40.site, Ku.dna at `kdku4`. | +| 2325 | `Unlabeled` | one-way | DNA41, Ku | `kdku4` | state and binding-pattern rewrite | `DNA41(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA41(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA41, Ku by freeing DNA41.site, Ku.dna at `kdku4`. | +| 2326 | `Unlabeled` | one-way | DNA42, Ku | `kdku4` | state and binding-pattern rewrite | `DNA42(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA42(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA42, Ku by freeing DNA42.site, Ku.dna at `kdku4`. | +| 2327 | `Unlabeled` | one-way | DNA43, Ku | `kdku4` | state and binding-pattern rewrite | `DNA43(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA43(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA43, Ku by freeing DNA43.site, Ku.dna at `kdku4`. | +| 2328 | `Unlabeled` | one-way | DNA44, Ku | `kdku4` | state and binding-pattern rewrite | `DNA44(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA44(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA44, Ku by freeing DNA44.site, Ku.dna at `kdku4`. | +| 2329 | `Unlabeled` | one-way | DNA45, Ku | `kdku4` | state and binding-pattern rewrite | `DNA45(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA45(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA45, Ku by freeing DNA45.site, Ku.dna at `kdku4`. | +| 2330 | `Unlabeled` | one-way | DNA46, Ku | `kdku4` | state and binding-pattern rewrite | `DNA46(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA46(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA46, Ku by freeing DNA46.site, Ku.dna at `kdku4`. | +| 2331 | `Unlabeled` | one-way | DNA47, Ku | `kdku4` | state and binding-pattern rewrite | `DNA47(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA47(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA47, Ku by freeing DNA47.site, Ku.dna at `kdku4`. | +| 2332 | `Unlabeled` | one-way | DNA48, Ku | `kdku4` | state and binding-pattern rewrite | `DNA48(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA48(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA48, Ku by freeing DNA48.site, Ku.dna at `kdku4`. | +| 2333 | `Unlabeled` | one-way | DNA49, Ku | `kdku4` | state and binding-pattern rewrite | `DNA49(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA49(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA49, Ku by freeing DNA49.site, Ku.dna at `kdku4`. | +| 2334 | `Unlabeled` | one-way | DNA50, Ku | `kdku4` | state and binding-pattern rewrite | `DNA50(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA50(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA50, Ku by freeing DNA50.site, Ku.dna at `kdku4`. | +| 2335 | `Unlabeled` | one-way | Sen | `kplus()` | internal-state conversion/modification | `Sen(int~?,State~normal) -> Sen(int~PLUS,State~normal)` | Rewrites the matched Sen pattern without an obvious state or bond-count change at `kplus()`; the table row preserves the exact implementation pattern. | +| 2336 | `Unlabeled` | one-way | Sen | `kminus()` | internal-state conversion/modification | `Sen(int~?,State~normal) -> Sen(int~MINUS,State~normal)` | Rewrites the matched Sen pattern without an obvious state or bond-count change at `kminus()`; the table row preserves the exact implementation pattern. | +| 2337 | `Unlabeled` | one-way | Sen | `ksen` | internal-state conversion/modification | `Sen(int~10,State~normal) -> Sen(int~10,State~sen)` | Changes internal modification/state marks on Sen: Sen.State normal→sen at `ksen`. | +| 2338 | `Unlabeled` | one-way | Ku, Sink, kKuDown | `kKustop()` | sink/degradation/removal | `Ku(dna,cs,cys~?) -> Sink() kKuDown() *` | Degrades or diverts Ku into the model sink at `kKustop()`, reducing that active species pool. | +| 2339 | `Unlabeled` | one-way | PARP, Sink, kParpDown | `kParpstop()` | sink/degradation/removal | `PARP(dna,liIII) -> Sink() kParpDown() *` | Degrades or diverts PARP into the model sink at `kParpstop()`, reducing that active species pool. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Time` | `Molecules` | `Time()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p53` | `Molecules` | `p53()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p53_Bound` | `Molecules` | `p53(Site1!1~u).MDM2(Site1!1~u)` | Reports bound or complexed species matching the pattern. | +| `p53_Phos` | `Molecules` | `p53(Site1~p)` | Reports phosphorylated or modified species matching the pattern. | +| `p53_Unphos` | `Molecules` | `p53(Site1~u)` | Reports phosphorylated or modified species matching the pattern. | +| `p21` | `Molecules` | `p21(step~3)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p38p` | `Molecules` | `p38(Site1~p)` | Reports phosphorylated or modified species matching the pattern. | +| `p38u` | `Molecules` | `p38(Site1~u)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ROS` | `Molecules` | `ROS()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p53_mRNA` | `Molecules` | `p53_mRNA()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `MDM2_Phos` | `Molecules` | `MDM2(Site1~p)` | Reports phosphorylated or modified species matching the pattern. | +| `MDM2_Unphos` | `Molecules` | `MDM2(Site1~u)` | Reports phosphorylated or modified species matching the pattern. | +| `MDM2_mRNA` | `Molecules` | `MDM2_mRNA()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p21_mRNA` | `Molecules` | `p21_mRNA()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `GADD45` | `Molecules` | `GADD45()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM0` | `Molecules` | `ATM(state~0)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM1` | `Molecules` | `ATM(state~1)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM2` | `Molecules` | `ATM(state~2)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM3` | `Molecules` | `ATM(state~3)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM4` | `Molecules` | `ATM(state~4)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM5` | `Molecules` | `ATM(state~5)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM6` | `Molecules` | `ATM(state~6)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM7` | `Molecules` | `ATM(state~7)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM8` | `Molecules` | `ATM(state~8)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM9` | `Molecules` | `ATM(state~9)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM10` | `Molecules` | `ATM(state~10)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM11` | `Molecules` | `ATM(state~11)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM12` | `Molecules` | `ATM(state~12)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM13` | `Molecules` | `ATM(state~13)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM14` | `Molecules` | `ATM(state~14)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM15` | `Molecules` | `ATM(state~15)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM16` | `Molecules` | `ATM(state~16)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM17` | `Molecules` | `ATM(state~17)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM18` | `Molecules` | `ATM(state~18)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM19` | `Molecules` | `ATM(state~19)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM20` | `Molecules` | `ATM(state~20)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM21` | `Molecules` | `ATM(state~21)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM22` | `Molecules` | `ATM(state~22)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM23` | `Molecules` | `ATM(state~23)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM24` | `Molecules` | `ATM(state~24)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM25` | `Molecules` | `ATM(state~25)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM26` | `Molecules` | `ATM(state~26)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM27` | `Molecules` | `ATM(state~27)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM28` | `Molecules` | `ATM(state~28)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM29` | `Molecules` | `ATM(state~29)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM30` | `Molecules` | `ATM(state~30)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM31` | `Molecules` | `ATM(state~31)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM32` | `Molecules` | `ATM(state~32)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM33` | `Molecules` | `ATM(state~33)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM34` | `Molecules` | `ATM(state~34)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM35` | `Molecules` | `ATM(state~35)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM36` | `Molecules` | `ATM(state~36)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM37` | `Molecules` | `ATM(state~37)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM38` | `Molecules` | `ATM(state~38)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM39` | `Molecules` | `ATM(state~39)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM40` | `Molecules` | `ATM(state~40)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM41` | `Molecules` | `ATM(state~41)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM42` | `Molecules` | `ATM(state~42)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM43` | `Molecules` | `ATM(state~43)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM44` | `Molecules` | `ATM(state~44)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM45` | `Molecules` | `ATM(state~45)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM46` | `Molecules` | `ATM(state~46)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM47` | `Molecules` | `ATM(state~47)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM48` | `Molecules` | `ATM(state~48)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM49` | `Molecules` | `ATM(state~49)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM50` | `Molecules` | `ATM(state~50)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Damage_Foci_1` | `Molecules` | `DNA1(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_1` | `Molecules` | `DNA1(h2ax!1~foc).ATM(state~1,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_2` | `Molecules` | `DNA2(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_2` | `Molecules` | `DNA2(h2ax!1~foc).ATM(state~2,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_3` | `Molecules` | `DNA3(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_3` | `Molecules` | `DNA3(h2ax!1~foc).ATM(state~3,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_4` | `Molecules` | `DNA4(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_4` | `Molecules` | `DNA4(h2ax!1~foc).ATM(state~4,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_5` | `Molecules` | `DNA5(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_5` | `Molecules` | `DNA5(h2ax!1~foc).ATM(state~5,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_6` | `Molecules` | `DNA6(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_6` | `Molecules` | `DNA6(h2ax!1~foc).ATM(state~6,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_7` | `Molecules` | `DNA7(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_7` | `Molecules` | `DNA7(h2ax!1~foc).ATM(state~7,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_8` | `Molecules` | `DNA8(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_8` | `Molecules` | `DNA8(h2ax!1~foc).ATM(state~8,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_9` | `Molecules` | `DNA9(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_9` | `Molecules` | `DNA9(h2ax!1~foc).ATM(state~9,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_10` | `Molecules` | `DNA10(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_10` | `Molecules` | `DNA10(h2ax!1~foc).ATM(state~10,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_11` | `Molecules` | `DNA11(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_11` | `Molecules` | `DNA11(h2ax!1~foc).ATM(state~11,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_12` | `Molecules` | `DNA12(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_12` | `Molecules` | `DNA12(h2ax!1~foc).ATM(state~12,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_13` | `Molecules` | `DNA13(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_13` | `Molecules` | `DNA13(h2ax!1~foc).ATM(state~13,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_14` | `Molecules` | `DNA14(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_14` | `Molecules` | `DNA14(h2ax!1~foc).ATM(state~14,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_15` | `Molecules` | `DNA15(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_15` | `Molecules` | `DNA15(h2ax!1~foc).ATM(state~15,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_16` | `Molecules` | `DNA16(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_16` | `Molecules` | `DNA16(h2ax!1~foc).ATM(state~16,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_17` | `Molecules` | `DNA17(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_17` | `Molecules` | `DNA17(h2ax!1~foc).ATM(state~17,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_18` | `Molecules` | `DNA18(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_18` | `Molecules` | `DNA18(h2ax!1~foc).ATM(state~18,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_19` | `Molecules` | `DNA19(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_19` | `Molecules` | `DNA19(h2ax!1~foc).ATM(state~19,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_20` | `Molecules` | `DNA20(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_20` | `Molecules` | `DNA20(h2ax!1~foc).ATM(state~20,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_21` | `Molecules` | `DNA21(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_21` | `Molecules` | `DNA21(h2ax!1~foc).ATM(state~21,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_22` | `Molecules` | `DNA22(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_22` | `Molecules` | `DNA22(h2ax!1~foc).ATM(state~22,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_23` | `Molecules` | `DNA23(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_23` | `Molecules` | `DNA23(h2ax!1~foc).ATM(state~23,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_24` | `Molecules` | `DNA24(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_24` | `Molecules` | `DNA24(h2ax!1~foc).ATM(state~24,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_25` | `Molecules` | `DNA25(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_25` | `Molecules` | `DNA25(h2ax!1~foc).ATM(state~25,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_26` | `Molecules` | `DNA26(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_26` | `Molecules` | `DNA26(h2ax!1~foc).ATM(state~26,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_27` | `Molecules` | `DNA27(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_27` | `Molecules` | `DNA27(h2ax!1~foc).ATM(state~27,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_28` | `Molecules` | `DNA28(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_28` | `Molecules` | `DNA28(h2ax!1~foc).ATM(state~28,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_29` | `Molecules` | `DNA29(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_29` | `Molecules` | `DNA29(h2ax!1~foc).ATM(state~29,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_30` | `Molecules` | `DNA30(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_30` | `Molecules` | `DNA30(h2ax!1~foc).ATM(state~30,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_31` | `Molecules` | `DNA31(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_31` | `Molecules` | `DNA31(h2ax!1~foc).ATM(state~31,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_32` | `Molecules` | `DNA32(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_32` | `Molecules` | `DNA32(h2ax!1~foc).ATM(state~32,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_33` | `Molecules` | `DNA33(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_33` | `Molecules` | `DNA33(h2ax!1~foc).ATM(state~33,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_34` | `Molecules` | `DNA34(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_34` | `Molecules` | `DNA34(h2ax!1~foc).ATM(state~34,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_35` | `Molecules` | `DNA35(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_35` | `Molecules` | `DNA35(h2ax!1~foc).ATM(state~35,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_36` | `Molecules` | `DNA36(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_36` | `Molecules` | `DNA36(h2ax!1~foc).ATM(state~36,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_37` | `Molecules` | `DNA37(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_37` | `Molecules` | `DNA37(h2ax!1~foc).ATM(state~37,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_38` | `Molecules` | `DNA38(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_38` | `Molecules` | `DNA38(h2ax!1~foc).ATM(state~38,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_39` | `Molecules` | `DNA39(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_39` | `Molecules` | `DNA39(h2ax!1~foc).ATM(state~39,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_40` | `Molecules` | `DNA40(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_40` | `Molecules` | `DNA40(h2ax!1~foc).ATM(state~40,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_41` | `Molecules` | `DNA41(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_41` | `Molecules` | `DNA41(h2ax!1~foc).ATM(state~41,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_42` | `Molecules` | `DNA42(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_42` | `Molecules` | `DNA42(h2ax!1~foc).ATM(state~42,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_43` | `Molecules` | `DNA43(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_43` | `Molecules` | `DNA43(h2ax!1~foc).ATM(state~43,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_44` | `Molecules` | `DNA44(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_44` | `Molecules` | `DNA44(h2ax!1~foc).ATM(state~44,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_45` | `Molecules` | `DNA45(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_45` | `Molecules` | `DNA45(h2ax!1~foc).ATM(state~45,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_46` | `Molecules` | `DNA46(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_46` | `Molecules` | `DNA46(h2ax!1~foc).ATM(state~46,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_47` | `Molecules` | `DNA47(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_47` | `Molecules` | `DNA47(h2ax!1~foc).ATM(state~47,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_48` | `Molecules` | `DNA48(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_48` | `Molecules` | `DNA48(h2ax!1~foc).ATM(state~48,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_49` | `Molecules` | `DNA49(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_49` | `Molecules` | `DNA49(h2ax!1~foc).ATM(state~49,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_50` | `Molecules` | `DNA50(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_50` | `Molecules` | `DNA50(h2ax!1~foc).ATM(state~50,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Ku` | `Molecules` | `Ku(dna,cs,cys~?)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `PARP` | `Molecules` | `PARP(dna,liIII)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Ku_Red` | `Molecules` | `Ku(dna,cs,cys~red)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Ku_Ox` | `Molecules` | `Ku(dna,cs,cys~ox)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `DNA_PKcs` | `Molecules` | `DNAPKcs(ku,liIV,psite~u)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `LiIII` | `Molecules` | `LiIII(PARP)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `LiIV` | `Molecules` | `LiIV(cs)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Senescent_Counter` | `Molecules` | `Sen(int~?,State~sen)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Sen_Min` | `Molecules` | `Sen(int~1,State~?)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Sink` | `Molecules` | `Sink()` | Reports the BNGL pattern for downstream plotting or rate expressions. | + +## 8. Actions and simulation workflow + +1. `simulate_nf({suffix=>"nf_run1",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +2. `simulate_nf({suffix=>"nf_run2",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +3. `simulate_nf({suffix=>"nf_run3",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +4. `simulate_nf({suffix=>"nf_run4",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +5. `simulate_nf({suffix=>"nf_run5",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +6. `simulate_nf({suffix=>"nf_run6",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +7. `simulate_nf({suffix=>"nf_run7",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +8. `simulate_nf({suffix=>"nf_run8",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +9. `simulate_nf({suffix=>"nf_run9",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +10. `simulate_nf({suffix=>"nf_run10",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +11. `simulate_nf({suffix=>"nf_run11",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +12. `simulate_nf({suffix=>"nf_run12",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +13. `simulate_nf({suffix=>"nf_run13",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +14. `simulate_nf({suffix=>"nf_run14",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +15. `simulate_nf({suffix=>"nf_run15",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +16. `simulate_nf({suffix=>"nf_run16",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +17. `simulate_nf({suffix=>"nf_run17",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +18. `simulate_nf({suffix=>"nf_run18",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +19. `simulate_nf({suffix=>"nf_run19",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +20. `simulate_nf({suffix=>"nf_run20",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +21. `simulate_nf({suffix=>"nf_run21",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +22. `simulate_nf({suffix=>"nf_run22",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +23. `simulate_nf({suffix=>"nf_run23",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +24. `simulate_nf({suffix=>"nf_run24",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +25. `simulate_nf({suffix=>"nf_run25",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +26. `simulate_nf({suffix=>"nf_run26",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +27. `simulate_nf({suffix=>"nf_run27",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +28. `simulate_nf({suffix=>"nf_run28",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +29. `simulate_nf({suffix=>"nf_run29",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +30. `simulate_nf({suffix=>"nf_run30",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +31. `simulate_nf({suffix=>"nf_run31",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +32. `simulate_nf({suffix=>"nf_run32",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +33. `simulate_nf({suffix=>"nf_run33",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +34. `simulate_nf({suffix=>"nf_run34",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +35. `simulate_nf({suffix=>"nf_run35",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +36. `simulate_nf({suffix=>"nf_run36",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +37. `simulate_nf({suffix=>"nf_run37",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +38. `simulate_nf({suffix=>"nf_run38",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +39. `simulate_nf({suffix=>"nf_run39",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +40. `simulate_nf({suffix=>"nf_run40",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +41. `simulate_nf({suffix=>"nf_run41",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +42. `simulate_nf({suffix=>"nf_run42",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +43. `simulate_nf({suffix=>"nf_run43",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +44. `simulate_nf({suffix=>"nf_run44",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +45. `simulate_nf({suffix=>"nf_run45",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +46. `simulate_nf({suffix=>"nf_run46",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +47. `simulate_nf({suffix=>"nf_run47",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +48. `simulate_nf({suffix=>"nf_run48",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +49. `simulate_nf({suffix=>"nf_run49",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +50. `simulate_nf({suffix=>"nf_run50",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +## 9. Technical caveats and ambiguities + +- No compartments or anchors are declared; all spatial interpretation is abstract. + +- The 50 DNA molecule types are explicit copies, so many rule families repeat once per DNA locus rather than using a single generic DNA molecule. + +- The reaction-rule inventory is intentionally very large because the source file literally enumerates each locus-specific rule. + +- The complete rule inventory has 2339 rows; downstream review should compare this count with the `begin reaction rules` block after any source edits. + +- The summary keeps raw molecule, site, state, and parameter names because this is the coder-facing version and those identifiers are necessary for implementation review. diff --git a/data/summaries_detailed/Dolan2015_coder.md b/data/summaries_detailed/Dolan2015_coder.md new file mode 100644 index 00000000..1574ae3e --- /dev/null +++ b/data/summaries_detailed/Dolan2015_coder.md @@ -0,0 +1,2971 @@ +# Coder Model Explanation: Dolan 2015 + +## 1. Model identity and scope + +- **Model id:** `Dolan_2015` +- **Title:** Dolan 2015 +- **BNGL path:** `Published/Dolan2015/Dolan_2015.bngl` +- **YAML path:** `Published/Dolan2015/metadata.yaml` +- **Metadata description:** Insulin signaling +- **Scope:** A combined DNA-damage, p53/MDM2/p21 stress-response, oxidative damage, non-homologous end joining (NHEJ), PARP/Ligase repair, ATM/H2AX focus, and senescence-switching model. The source explicitly starts as a combined p53 and NHEJ model, then enumerates 50 explicit DNA break loci and many repeated repair-rule families over those loci. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 73 parameter entries. | +| Compartments | No | 0 compartment entries. | +| Anchors | No | 0 anchor entries. | +| Molecule types | Yes | 74 molecule type entries. | +| Seed/species | Yes | 75 initial species entries. | +| Observables | Yes | 176 observable entries. | +| Functions | Yes | 9 function entries. | +| Reaction rules | Yes | 2339 reaction rules. | +| Actions | Yes | 50 action or inline execution commands. | + +## 3. Parameters, functions, and rate laws + +The model uses the following parameter entries. Comment text is preserved when the source provides it; otherwise the role is inferred from the parameter name and where it is used. + +| Parameter | Value/expression | Role / source comment | +| --- | --- | --- | +| `kp53mRNAsyn` | `0.06` | Rate of p53 mRNA Synthesis | +| `kp53mRNAdeg` | `0.006` | Rate of p53 mRNA Degradation | +| `kp53syn` | `0.36` | Rate of p53 Synthesis | +| `kp53deg` | `4.95e-5` | Rate of p53 Degradation | +| `kp53degMDM2dep` | `0.0495` | Rate of p53 Degradation-MDM2 Dependant | +| `kp53phos` | `0.36` | Rate of p53 Phosphorylation | +| `kp53dphos` | `30` | Rate of p53 Dephosphorylation | +| `kMDM2mRNAsyn` | `0.006` | Rate of MDM2 mRNA Synthesis | +| `kMDM2mRNAdeg` | `0.006` | Rate of MDM2 mRNA Degradation | +| `kMDM2syn` | `0.0297` | Rate of MDM2 Synthesis | +| `kMDM2deg` | `0.02598` | Rate of MDM2 Degradation | +| `kMDM2pdeg` | `0.024` | Rate of Phosphorylated MDM2 Degradation | +| `kMDM2phos` | `120` | Rate of MDM2 Phosphorylation | +| `kMDM2dphos` | `30` | Rate of p53 Dephosphorylation | +| `kp53MDM2bind` | `0.0693` | Rate of p53 MDM2 Binding | +| `kp53MDM2dis` | `0.0000693` | Rate of p53 MDM2 Dissociation | +| `kp21mRNAsyn` | `0.0000036` | Rate of p21 mRNA Synthesis (p53) | +| `kp21mRNAsynp` | `0.00036` | Rate of p21 mRNA Synthesis (Phosphorylated p53) | +| `kp21mRNAdeg` | `0.00144` | Rate of p21 mRNA Degradation | +| `kp21synstep1` | `0.024` | Rate of p21 Synthesis Step 1 | +| `kp21synstep2` | `0.0024` | Rate of p21 Synthesis Step 2 | +| `kp21synstep3` | `0.0024` | Rate of p21 Synthesis Step 3 | +| `kp21deg` | `0.0114` | Rate of p21 Degradation | +| `kGADD45act` | `0.00024` | Rate of GADD45 Activation/Production | +| `kGADD45deg` | `0.0006` | Rate of GADD45 Degradation | +| `kp38phos` | `0.48` | Rate of p38 Phosphorylation | +| `kp38dphos` | `6` | Rate of p38 Dephosphorylation | +| `kROSgen` | `1.5` | Rate of ROS Generation by p38 | +| `kIR` | `80` | Kinetic rate or kinetic expression parameter. | +| `kROS` | `50` | Constant rate of ROS production | +| `kdROS` | `5` | ROS degradation rate | +| `kdam1` | `0.000006` | Rate of simple damage production by ROS | +| `kdam2` | `0.000006` | Rate of complex damage production by ROS | +| `kdku1` | `0.5` | Rate of Ku dissociation from a simple break | +| `kdku2` | `0.5` | Rate of Ku dissociation from a complex break | +| `kdku3` | `5` | Rate of oxidised Ku dissociation from a simple break | +| `kdku4` | `5` | Rate of oxidised Ku dissociation from a complex break | +| `kdnapk1` | `0.033` | Rate of DNAPK simple break complex formation | +| `kdnapk2` | `0.0017` | Rate of DNAPK complex break complex formation | +| `kddnapk1` | `0.02` | Rate of DNAPK simple break complex dissociation | +| `kddnapk2` | `0.02` | Rate of DNAPK complex break complex dissociation | +| `kdnapkphos1` | `0.28` | Rate pd DNAPK phosphorylation in a DNAPK complex of a simple break | +| `kdnapkphos2` | `0.28` | Rate pd DNAPK phosphorylation in a DNAPK complex of a complex break | +| `kliIV1` | `0.00071` | Rate of LigaseIV binding to a simple break complex | +| `kliIV2` | `0.00046` | Rate of LigaseIV binding to a complex break complex | +| `kdliIV1` | `0.0001` | Rate of LigaseIV dissociation from a simple break complex | +| `kdliIV2` | `0.0001` | Rate of LigaseIV dissociation from a complex break complex | +| `kfixIV1` | `0.0285` | Rate of DNA repair by LigaseIV of a simple break | +| `kfixIV2` | `0.0285` | Rate of DNA repair by LigaseIV of a complex break | +| `kPARP1` | `0.000077` | Rate of PARP binding to simple break | +| `kPARP2` | `0.000065` | Rate of PARP binding to complex break | +| `kdPARP1` | `0.02` | Rate of PARP dissociation from a simple break | +| `kdPARP2` | `0.02` | Rate of PARP dissociation from a complex break | +| `kliIII1` | `0.0015` | Rate of LigaseIII binding to a simple break | +| `kliIII2` | `0.00024` | Rate of LigaseIII binding to a complex break | +| `kdliIII1` | `0.0001` | Rate of LigaseIII dissociation from a simple break | +| `kdliIII2` | `0.0001` | Rate of LigaseIII dissociation from a complex break | +| `kfixIII1` | `0.0006` | Rate of DNA accurate repair by LigaseIII for a simple break | +| `kfixIII2` | `0.0006` | Rate of DNA accurate repair by LigaseIII for a complex break | +| `kfixIII3` | `0.0009` | Rate of DNA inaccurate repair by LigaseIII for a simple break | +| `kfixIII4` | `0.0009` | Rate of dna inaccurate repair by LigaseIII for a complex break | +| `kATMact` | `0.0012` | Rate of ATM Activation | +| `kATMinact` | `0.03` | Rate of ATM Inactivation | +| `kh2axp1` | `0.1` | Phosphorylation of h2ax via ATM | +| `kh2axp2` | `0.5` | Phosphorylation of h2ax via DNA-PKcs | +| `kh2axu` | `0.01` | Dephosphorylation of h2ax | +| `kh2axfoc` | `0.5` | Creation of damage foci | +| `kfocback` | `0.03` | Resolution of damage foci | +| `kh2axfull` | `0.1` | Creation of complete damage foci | +| `kfocfin` | `0.03` | Resolution of complete damage foci | +| `kox` | `0.000025` | Rate of oxidisation of Ku | +| `kred` | `0.002` | Rate of reduction of Ku | +| `ksen` | `100` | Activation of senescent state | + +**Functions** + +| Function | Technical interpretation | +| --- | --- | +| `kku1() = if(Senescent_Counter>0,0.000000034,0.00034)` | Executable expression used by rules or rate logic. | +| `kku2() = if(Senescent_Counter>0,0.000000021,0.00021)` | Executable expression used by rules or rate logic. | +| `kplus() = if(p21>15,0.04,0)` | Executable expression used by rules or rate logic. | +| `kminus() = if(p21<=15&&Sen_Min<1,0.5,0)` | Executable expression used by rules or rate logic. | +| `kKuDown() = if(Senescent_Counter==1,0.01,0)` | Executable expression used by rules or rate logic. | +| `kKustop() = if(Ku<=250,0,1)` | Executable expression used by rules or rate logic. | +| `kParpDown() = if(Senescent_Counter==1,0.01,0)` | Executable expression used by rules or rate logic. | +| `kParpstop() = if(PARP<=5,0,1)` | Executable expression used by rules or rate logic. | +| `kDelete()= if(Sink<=5,0,10000)` | Executable expression used by rules or rate logic. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Time` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `T` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `P` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `E` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `IR` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `D` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `p53_mRNA` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `p53` | 1 | `Site1` | Site1: u, p | None | Site1 is an internal state/modification coordinate | Declared in molecule types block. | +| `MDM2` | 1 | `Site1` | Site1: u, p | None | Site1 is an internal state/modification coordinate | Declared in molecule types block. | +| `MDM2_mRNA` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `p21_mRNA` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `p21` | 1 | `step` | step: 1, 2, 3 | None | step is an internal state/modification coordinate | Declared in molecule types block. | +| `p38` | 1 | `Site1` | Site1: u, p | None | Site1 is an internal state/modification coordinate | Declared in molecule types block. | +| `GADD45` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `Sink` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `ATM` | 2 | `state`, `h2ax` | state: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 | None | state is an internal state/modification coordinate; h2ax is used as a binding/matching component | Declared in molecule types block. | +| `DNA1` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA2` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA3` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA4` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA5` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA6` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA7` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA8` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA9` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA10` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA11` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA12` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA13` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA14` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA15` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA16` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA17` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA18` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA19` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA20` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA21` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA22` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA23` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA24` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA25` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA26` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA27` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA28` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA29` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA30` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA31` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA32` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA33` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA34` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA35` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA36` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA37` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA38` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA39` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA40` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA41` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA42` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA43` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA44` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA45` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA46` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA47` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA48` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA49` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `DNA50` | 2 | `site`, `h2ax` | site: ok, sdsb, cdsb; h2ax: u, p, foc | None | site is an internal state/modification coordinate; h2ax is an internal state/modification coordinate | Declared in molecule types block. | +| `ROS` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `Ku` | 3 | `dna`, `cs`, `cys` | cys: red, ox | None | dna is used as a binding/matching component; cs is used as a binding/matching component; cys is an internal state/modification coordinate | Declared in molecule types block. | +| `DNAPKcs` | 3 | `ku`, `liIV`, `psite` | psite: u, p | None | ku is used as a binding/matching component; liIV is used as a binding/matching component; psite is an internal state/modification coordinate | Declared in molecule types block. | +| `LiIII` | 1 | `PARP` | None | None | PARP is used as a binding/matching component | Declared in molecule types block. | +| `LiIV` | 1 | `cs` | None | None | cs is used as a binding/matching component | Declared in molecule types block. | +| `PARP` | 2 | `dna`, `liIII` | None | None | dna is used as a binding/matching component; liIII is used as a binding/matching component | Declared in molecule types block. | +| `I` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `Sen` | 2 | `int`, `State` | int: 1, 10, PLUS, MINUS; State: normal, sen | None | int is an internal state/modification coordinate; State is an internal state/modification coordinate | Declared in molecule types block. | + +## 5. Compartments, anchors, initial species, and setup + +No BNGL compartment block is declared. + +No anchors block is declared. + +Ionizing radiation and ROS generate simple or complex DNA breaks across explicit DNA loci. ATM and DNA-PKcs signal damage to p53, p38, H2AX, and repair machinery; p53 induces MDM2 and p21, p21 controls a senescence counter, and senescence feeds back by reducing Ku/PARP repair availability. + +| Initial species entry | Initial amount/expression | Technical setup meaning | +| --- | --- | --- | +| `Time()` | `0` | Initial population or concentration for this exact pattern. | +| `P()` | `1` | Initial population or concentration for this exact pattern. | +| `T()` | `1` | Initial population or concentration for this exact pattern. | +| `E()` | `1` | Initial population or concentration for this exact pattern. | +| `IR()` | `0` | Initial population or concentration for this exact pattern. | +| `D()` | `10` | Initial population or concentration for this exact pattern. | +| `p53_mRNA()` | `10` | Initial population or concentration for this exact pattern. | +| `p53(Site1~u)` | `5` | Initial population or concentration for this exact pattern. | +| `MDM2_mRNA()` | `10` | Initial population or concentration for this exact pattern. | +| `MDM2(Site1~u)` | `5` | Initial population or concentration for this exact pattern. | +| `p53(Site1!1~u).MDM2(Site1!1~u)` | `95` | Initial population or concentration for this exact pattern. | +| `p21_mRNA()` | `1` | Initial population or concentration for this exact pattern. | +| `p21(step~1)` | `0` | Initial population or concentration for this exact pattern. | +| `p38(Site1~u)` | `100` | Initial population or concentration for this exact pattern. | +| `$Sink()` | `0` | Initial population or concentration for this exact pattern. | +| `ATM(state~0,h2ax)` | `200` | Initial population or concentration for this exact pattern. | +| `DNA1(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA2(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA3(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA4(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA5(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA6(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA7(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA8(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA9(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA10(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA11(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA12(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA13(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA14(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA15(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA16(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA17(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA18(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA19(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA20(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA21(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA22(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA23(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA24(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA25(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA26(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA27(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA28(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA29(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA30(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA31(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA32(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA33(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA34(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA35(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA36(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA37(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA38(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA39(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA40(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA41(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA42(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA43(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA44(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA45(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA46(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA47(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA48(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA49(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `DNA50(site~ok,h2ax~u)` | `1` | Initial population or concentration for this exact pattern. | +| `ROS()` | `0` | Initial population or concentration for this exact pattern. | +| `Ku(dna,cs,cys~red)` | `450` | Initial population or concentration for this exact pattern. | +| `Ku(dna,cs,cys~ox)` | `50` | Initial population or concentration for this exact pattern. | +| `DNAPKcs(ku,liIV,psite~u)` | `250` | Initial population or concentration for this exact pattern. | +| `LiIII(PARP)` | `300` | Initial population or concentration for this exact pattern. | +| `LiIV(cs)` | `300` | Initial population or concentration for this exact pattern. | +| `PARP(dna,liIII)` | `500` | Initial population or concentration for this exact pattern. | +| `I()` | `1` | Initial population or concentration for this exact pattern. | +| `Sen(int~1,State~normal)` | `1` | Initial population or concentration for this exact pattern. | + +## 6. Complete reaction-rule inventory + +The source contains **2339** reaction rules. The inventory below preserves one row per source rule, grouped only for readability. + +### Rules 1-250 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | D, Sink | `kDelete() (DeleteMolecules)` | stoichiometric pattern rewrite | `D() + Sink() -> D()` | Removes the matched Sink pattern after rewriting the listed products at `kDelete() (DeleteMolecules)`; used as an explicit cleanup/sink operation. | +| 2 | `Unlabeled` | one-way | P, p53_mRNA | `kp53mRNAsyn` | stoichiometric pattern rewrite | `P() -> p53_mRNA() + P()` | Produces p53_mRNA while retaining or consuming P at `kp53mRNAsyn`. | +| 3 | `Unlabeled` | one-way | Sink, p53_mRNA | `kp53mRNAdeg` | sink/degradation/removal | `p53_mRNA() -> Sink()` | Degrades or diverts p53_mRNA into the model sink at `kp53mRNAdeg`, reducing that active species pool. | +| 4 | `Unlabeled` | one-way | p53, p53_mRNA | `kp53syn` | internal-state conversion/modification | `p53_mRNA() -> p53_mRNA() + p53(Site1~u)` | Produces p53 while retaining or consuming p53_mRNA at `kp53syn`. | +| 5 | `Unlabeled` | one-way | Sink, p53 | `kp53deg` | sink/degradation/removal | `p53(Site1~u) -> Sink()` | Degrades or diverts p53 into the model sink at `kp53deg`, reducing that active species pool. | +| 6 | `Unlabeled` | one-way | Sink, p53 | `kp53deg` | sink/degradation/removal | `p53(Site1~p) -> Sink()` | Degrades or diverts p53 into the model sink at `kp53deg`, reducing that active species pool. | +| 7 | `Unlabeled` | one-way | MDM2, p53 | `kp53degMDM2dep (DeleteMolecules)` | state and binding-pattern rewrite | `p53(Site1!1~u).MDM2(Site1!1~u) -> MDM2(Site1~u)` | Removes the matched p53 pattern after rewriting the listed products at `kp53degMDM2dep (DeleteMolecules)`; used as an explicit cleanup/sink operation. | +| 8 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~1,h2ax!?) -> p53(Site1~p) + ATM(state~1,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 9 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~2,h2ax!?) -> p53(Site1~p) + ATM(state~2,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 10 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~3,h2ax!?) -> p53(Site1~p) + ATM(state~3,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 11 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~4,h2ax!?) -> p53(Site1~p) + ATM(state~4,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 12 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~5,h2ax!?) -> p53(Site1~p) + ATM(state~5,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 13 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~6,h2ax!?) -> p53(Site1~p) + ATM(state~6,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 14 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~7,h2ax!?) -> p53(Site1~p) + ATM(state~7,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 15 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~8,h2ax!?) -> p53(Site1~p) + ATM(state~8,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 16 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~9,h2ax!?) -> p53(Site1~p) + ATM(state~9,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 17 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~10,h2ax!?) -> p53(Site1~p) + ATM(state~10,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 18 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~11,h2ax!?) -> p53(Site1~p) + ATM(state~11,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 19 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~12,h2ax!?) -> p53(Site1~p) + ATM(state~12,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 20 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~13,h2ax!?) -> p53(Site1~p) + ATM(state~13,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 21 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~14,h2ax!?) -> p53(Site1~p) + ATM(state~14,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 22 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~15,h2ax!?) -> p53(Site1~p) + ATM(state~15,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 23 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~16,h2ax!?) -> p53(Site1~p) + ATM(state~16,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 24 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~17,h2ax!?) -> p53(Site1~p) + ATM(state~17,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 25 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~18,h2ax!?) -> p53(Site1~p) + ATM(state~18,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 26 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~19,h2ax!?) -> p53(Site1~p) + ATM(state~19,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 27 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~20,h2ax!?) -> p53(Site1~p) + ATM(state~20,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 28 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~21,h2ax!?) -> p53(Site1~p) + ATM(state~21,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 29 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~22,h2ax!?) -> p53(Site1~p) + ATM(state~22,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 30 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~23,h2ax!?) -> p53(Site1~p) + ATM(state~23,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 31 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~24,h2ax!?) -> p53(Site1~p) + ATM(state~24,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 32 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~25,h2ax!?) -> p53(Site1~p) + ATM(state~25,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 33 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~26,h2ax!?) -> p53(Site1~p) + ATM(state~26,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 34 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~27,h2ax!?) -> p53(Site1~p) + ATM(state~27,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 35 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~28,h2ax!?) -> p53(Site1~p) + ATM(state~28,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 36 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~29,h2ax!?) -> p53(Site1~p) + ATM(state~29,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 37 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~30,h2ax!?) -> p53(Site1~p) + ATM(state~30,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 38 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~31,h2ax!?) -> p53(Site1~p) + ATM(state~31,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 39 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~32,h2ax!?) -> p53(Site1~p) + ATM(state~32,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 40 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~33,h2ax!?) -> p53(Site1~p) + ATM(state~33,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 41 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~34,h2ax!?) -> p53(Site1~p) + ATM(state~34,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 42 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~35,h2ax!?) -> p53(Site1~p) + ATM(state~35,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 43 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~36,h2ax!?) -> p53(Site1~p) + ATM(state~36,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 44 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~37,h2ax!?) -> p53(Site1~p) + ATM(state~37,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 45 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~38,h2ax!?) -> p53(Site1~p) + ATM(state~38,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 46 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~39,h2ax!?) -> p53(Site1~p) + ATM(state~39,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 47 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~40,h2ax!?) -> p53(Site1~p) + ATM(state~40,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 48 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~41,h2ax!?) -> p53(Site1~p) + ATM(state~41,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 49 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~42,h2ax!?) -> p53(Site1~p) + ATM(state~42,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 50 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~43,h2ax!?) -> p53(Site1~p) + ATM(state~43,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 51 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~44,h2ax!?) -> p53(Site1~p) + ATM(state~44,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 52 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~45,h2ax!?) -> p53(Site1~p) + ATM(state~45,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 53 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~46,h2ax!?) -> p53(Site1~p) + ATM(state~46,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 54 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~47,h2ax!?) -> p53(Site1~p) + ATM(state~47,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 55 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~48,h2ax!?) -> p53(Site1~p) + ATM(state~48,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 56 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~49,h2ax!?) -> p53(Site1~p) + ATM(state~49,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 57 | `Unlabeled` | one-way | ATM, p53 | `kp53phos` | internal-state conversion/modification | `p53(Site1~u) + ATM(state~50,h2ax!?) -> p53(Site1~p) + ATM(state~50,h2ax!?)` | Changes internal modification/state marks on ATM, p53: p53.Site1 u→p at `kp53phos`. | +| 58 | `Unlabeled` | one-way | p53 | `kp53dphos` | internal-state conversion/modification | `p53(Site1~p) -> p53(Site1~u)` | Changes internal modification/state marks on p53: p53.Site1 p→u at `kp53dphos`. | +| 59 | `Unlabeled` | one-way | MDM2_mRNA, p53 | `kMDM2mRNAsyn` | internal-state conversion/modification | `p53(Site1~u) -> MDM2_mRNA() + p53(Site1~u)` | Produces MDM2_mRNA while retaining or consuming p53 at `kMDM2mRNAsyn`. | +| 60 | `Unlabeled` | one-way | MDM2_mRNA, p53 | `kMDM2mRNAsyn` | internal-state conversion/modification | `p53(Site1~p) -> MDM2_mRNA() + p53(Site1~p)` | Produces MDM2_mRNA while retaining or consuming p53 at `kMDM2mRNAsyn`. | +| 61 | `Unlabeled` | one-way | MDM2_mRNA, Sink | `kMDM2mRNAdeg` | sink/degradation/removal | `MDM2_mRNA() -> Sink()` | Degrades or diverts MDM2_mRNA into the model sink at `kMDM2mRNAdeg`, reducing that active species pool. | +| 62 | `Unlabeled` | one-way | MDM2, MDM2_mRNA | `kMDM2syn` | internal-state conversion/modification | `MDM2_mRNA() -> MDM2_mRNA() + MDM2(Site1~u)` | Produces MDM2 while retaining or consuming MDM2_mRNA at `kMDM2syn`. | +| 63 | `Unlabeled` | one-way | MDM2, Sink | `kMDM2deg` | sink/degradation/removal | `MDM2(Site1~u) -> Sink()` | Degrades or diverts MDM2 into the model sink at `kMDM2deg`, reducing that active species pool. | +| 64 | `Unlabeled` | one-way | MDM2, Sink | `kMDM2pdeg` | sink/degradation/removal | `MDM2(Site1~p) -> Sink()` | Degrades or diverts MDM2 into the model sink at `kMDM2pdeg`, reducing that active species pool. | +| 65 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~1,h2ax!?) -> MDM2(Site1~p) + ATM(state~1,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 66 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~2,h2ax!?) -> MDM2(Site1~p) + ATM(state~2,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 67 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~3,h2ax!?) -> MDM2(Site1~p) + ATM(state~3,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 68 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~4,h2ax!?) -> MDM2(Site1~p) + ATM(state~4,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 69 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~5,h2ax!?) -> MDM2(Site1~p) + ATM(state~5,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 70 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~6,h2ax!?) -> MDM2(Site1~p) + ATM(state~6,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 71 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~7,h2ax!?) -> MDM2(Site1~p) + ATM(state~7,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 72 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~8,h2ax!?) -> MDM2(Site1~p) + ATM(state~8,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 73 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~9,h2ax!?) -> MDM2(Site1~p) + ATM(state~9,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 74 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~10,h2ax!?) -> MDM2(Site1~p) + ATM(state~10,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 75 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~11,h2ax!?) -> MDM2(Site1~p) + ATM(state~11,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 76 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~12,h2ax!?) -> MDM2(Site1~p) + ATM(state~12,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 77 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~13,h2ax!?) -> MDM2(Site1~p) + ATM(state~13,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 78 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~14,h2ax!?) -> MDM2(Site1~p) + ATM(state~14,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 79 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~15,h2ax!?) -> MDM2(Site1~p) + ATM(state~15,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 80 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~16,h2ax!?) -> MDM2(Site1~p) + ATM(state~16,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 81 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~17,h2ax!?) -> MDM2(Site1~p) + ATM(state~17,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 82 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~18,h2ax!?) -> MDM2(Site1~p) + ATM(state~18,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 83 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~19,h2ax!?) -> MDM2(Site1~p) + ATM(state~19,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 84 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~20,h2ax!?) -> MDM2(Site1~p) + ATM(state~20,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 85 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~21,h2ax!?) -> MDM2(Site1~p) + ATM(state~21,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 86 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~22,h2ax!?) -> MDM2(Site1~p) + ATM(state~22,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 87 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~23,h2ax!?) -> MDM2(Site1~p) + ATM(state~23,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 88 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~24,h2ax!?) -> MDM2(Site1~p) + ATM(state~24,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 89 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~25,h2ax!?) -> MDM2(Site1~p) + ATM(state~25,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 90 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~26,h2ax!?) -> MDM2(Site1~p) + ATM(state~26,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 91 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~27,h2ax!?) -> MDM2(Site1~p) + ATM(state~27,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 92 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~28,h2ax!?) -> MDM2(Site1~p) + ATM(state~28,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 93 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~29,h2ax!?) -> MDM2(Site1~p) + ATM(state~29,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 94 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~30,h2ax!?) -> MDM2(Site1~p) + ATM(state~30,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 95 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~31,h2ax!?) -> MDM2(Site1~p) + ATM(state~31,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 96 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~32,h2ax!?) -> MDM2(Site1~p) + ATM(state~32,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 97 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~33,h2ax!?) -> MDM2(Site1~p) + ATM(state~33,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 98 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~34,h2ax!?) -> MDM2(Site1~p) + ATM(state~34,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 99 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~35,h2ax!?) -> MDM2(Site1~p) + ATM(state~35,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 100 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~36,h2ax!?) -> MDM2(Site1~p) + ATM(state~36,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 101 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~37,h2ax!?) -> MDM2(Site1~p) + ATM(state~37,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 102 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~38,h2ax!?) -> MDM2(Site1~p) + ATM(state~38,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 103 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~39,h2ax!?) -> MDM2(Site1~p) + ATM(state~39,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 104 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~40,h2ax!?) -> MDM2(Site1~p) + ATM(state~40,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 105 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~41,h2ax!?) -> MDM2(Site1~p) + ATM(state~41,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 106 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~42,h2ax!?) -> MDM2(Site1~p) + ATM(state~42,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 107 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~43,h2ax!?) -> MDM2(Site1~p) + ATM(state~43,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 108 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~44,h2ax!?) -> MDM2(Site1~p) + ATM(state~44,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 109 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~45,h2ax!?) -> MDM2(Site1~p) + ATM(state~45,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 110 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~46,h2ax!?) -> MDM2(Site1~p) + ATM(state~46,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 111 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~47,h2ax!?) -> MDM2(Site1~p) + ATM(state~47,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 112 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~48,h2ax!?) -> MDM2(Site1~p) + ATM(state~48,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 113 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~49,h2ax!?) -> MDM2(Site1~p) + ATM(state~49,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 114 | `Unlabeled` | one-way | ATM, MDM2 | `kMDM2phos` | internal-state conversion/modification | `MDM2(Site1~u) + ATM(state~50,h2ax!?) -> MDM2(Site1~p) + ATM(state~50,h2ax!?)` | Changes internal modification/state marks on ATM, MDM2: MDM2.Site1 u→p at `kMDM2phos`. | +| 115 | `Unlabeled` | one-way | MDM2 | `kMDM2dphos` | internal-state conversion/modification | `MDM2(Site1~p) -> MDM2(Site1~u)` | Changes internal modification/state marks on MDM2: MDM2.Site1 p→u at `kMDM2dphos`. | +| 116 | `Unlabeled` | one-way | MDM2, p53 | `kp53MDM2bind` | state and binding-pattern rewrite | `p53(Site1~u) + MDM2(Site1~u) -> p53(Site1!1~u).MDM2(Site1!1~u)` | Forms a complex/contact among MDM2, p53 through MDM2.Site1, p53.Site1 at `kp53MDM2bind`. | +| 117 | `Unlabeled` | one-way | MDM2, p53 | `kp53MDM2dis` | state and binding-pattern rewrite | `p53(Site1!1~u).MDM2(Site1!1~u) -> p53(Site1~u) + MDM2(Site1~u)` | Releases a complex/contact among MDM2, p53 by freeing MDM2.Site1, p53.Site1 at `kp53MDM2dis`. | +| 118 | `Unlabeled` | one-way | p21_mRNA, p53 | `kp21mRNAsyn` | internal-state conversion/modification | `p53(Site1~u) -> p21_mRNA() + p53(Site1~u)` | Produces p21_mRNA while retaining or consuming p53 at `kp21mRNAsyn`. | +| 119 | `Unlabeled` | one-way | p21_mRNA, p53 | `kp21mRNAsynp` | internal-state conversion/modification | `p53(Site1~p) -> p21_mRNA() + p53(Site1~p)` | Produces p21_mRNA while retaining or consuming p53 at `kp21mRNAsynp`. | +| 120 | `Unlabeled` | one-way | Sink, p21_mRNA | `kp21mRNAdeg` | sink/degradation/removal | `p21_mRNA() -> Sink()` | Degrades or diverts p21_mRNA into the model sink at `kp21mRNAdeg`, reducing that active species pool. | +| 121 | `Unlabeled` | one-way | p21, p21_mRNA | `kp21synstep1` | internal-state conversion/modification | `p21_mRNA() -> p21(step~1) + p21_mRNA()` | Produces p21 while retaining or consuming p21_mRNA at `kp21synstep1`. | +| 122 | `Unlabeled` | one-way | p21 | `kp21synstep2` | internal-state conversion/modification | `p21(step~1) -> p21(step~2)` | Changes internal modification/state marks on p21: p21.step 1→2 at `kp21synstep2`. | +| 123 | `Unlabeled` | one-way | p21 | `kp21synstep3` | internal-state conversion/modification | `p21(step~2) -> p21(step~3)` | Changes internal modification/state marks on p21: p21.step 2→3 at `kp21synstep3`. | +| 124 | `Unlabeled` | one-way | Sink, p21 | `kp21deg` | sink/degradation/removal | `p21(step~3) -> Sink()` | Degrades or diverts p21 into the model sink at `kp21deg`, reducing that active species pool. | +| 125 | `Unlabeled` | one-way | GADD45, p21 | `kGADD45act` | internal-state conversion/modification | `p21(step~3) -> p21(step~3) + GADD45()` | Produces GADD45 while retaining or consuming p21 at `kGADD45act`. | +| 126 | `Unlabeled` | one-way | GADD45, Sink | `kGADD45deg` | sink/degradation/removal | `GADD45() -> Sink()` | Degrades or diverts GADD45 into the model sink at `kGADD45deg`, reducing that active species pool. | +| 127 | `Unlabeled` | one-way | GADD45, p38 | `kp38phos` | internal-state conversion/modification | `p38(Site1~u) + GADD45() -> p38(Site1~p) + GADD45()` | Changes internal modification/state marks on GADD45, p38: p38.Site1 u→p at `kp38phos`. | +| 128 | `Unlabeled` | one-way | p38 | `kp38dphos` | internal-state conversion/modification | `p38(Site1~p) -> p38(Site1~u)` | Changes internal modification/state marks on p38: p38.Site1 p→u at `kp38dphos`. | +| 129 | `Unlabeled` | one-way | ROS, p38 | `kROSgen` | internal-state conversion/modification | `p38(Site1~p) -> ROS() + p38(Site1~p)` | Produces ROS while retaining or consuming p38 at `kROSgen`. | +| 130 | `Unlabeled` | one-way | DNA1, Ku | `kku1()` | state and binding-pattern rewrite | `DNA1(site~sdsb) + Ku(dna,cs) -> DNA1(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA1, Ku through DNA1.site, Ku.dna at `kku1()`. | +| 131 | `Unlabeled` | one-way | DNA2, Ku | `kku1()` | state and binding-pattern rewrite | `DNA2(site~sdsb) + Ku(dna,cs) -> DNA2(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA2, Ku through DNA2.site, Ku.dna at `kku1()`. | +| 132 | `Unlabeled` | one-way | DNA3, Ku | `kku1()` | state and binding-pattern rewrite | `DNA3(site~sdsb) + Ku(dna,cs) -> DNA3(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA3, Ku through DNA3.site, Ku.dna at `kku1()`. | +| 133 | `Unlabeled` | one-way | DNA4, Ku | `kku1()` | state and binding-pattern rewrite | `DNA4(site~sdsb) + Ku(dna,cs) -> DNA4(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA4, Ku through DNA4.site, Ku.dna at `kku1()`. | +| 134 | `Unlabeled` | one-way | DNA5, Ku | `kku1()` | state and binding-pattern rewrite | `DNA5(site~sdsb) + Ku(dna,cs) -> DNA5(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA5, Ku through DNA5.site, Ku.dna at `kku1()`. | +| 135 | `Unlabeled` | one-way | DNA6, Ku | `kku1()` | state and binding-pattern rewrite | `DNA6(site~sdsb) + Ku(dna,cs) -> DNA6(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA6, Ku through DNA6.site, Ku.dna at `kku1()`. | +| 136 | `Unlabeled` | one-way | DNA7, Ku | `kku1()` | state and binding-pattern rewrite | `DNA7(site~sdsb) + Ku(dna,cs) -> DNA7(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA7, Ku through DNA7.site, Ku.dna at `kku1()`. | +| 137 | `Unlabeled` | one-way | DNA8, Ku | `kku1()` | state and binding-pattern rewrite | `DNA8(site~sdsb) + Ku(dna,cs) -> DNA8(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA8, Ku through DNA8.site, Ku.dna at `kku1()`. | +| 138 | `Unlabeled` | one-way | DNA9, Ku | `kku1()` | state and binding-pattern rewrite | `DNA9(site~sdsb) + Ku(dna,cs) -> DNA9(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA9, Ku through DNA9.site, Ku.dna at `kku1()`. | +| 139 | `Unlabeled` | one-way | DNA10, Ku | `kku1()` | state and binding-pattern rewrite | `DNA10(site~sdsb) + Ku(dna,cs) -> DNA10(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA10, Ku through DNA10.site, Ku.dna at `kku1()`. | +| 140 | `Unlabeled` | one-way | DNA11, Ku | `kku1()` | state and binding-pattern rewrite | `DNA11(site~sdsb) + Ku(dna,cs) -> DNA11(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA11, Ku through DNA11.site, Ku.dna at `kku1()`. | +| 141 | `Unlabeled` | one-way | DNA12, Ku | `kku1()` | state and binding-pattern rewrite | `DNA12(site~sdsb) + Ku(dna,cs) -> DNA12(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA12, Ku through DNA12.site, Ku.dna at `kku1()`. | +| 142 | `Unlabeled` | one-way | DNA13, Ku | `kku1()` | state and binding-pattern rewrite | `DNA13(site~sdsb) + Ku(dna,cs) -> DNA13(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA13, Ku through DNA13.site, Ku.dna at `kku1()`. | +| 143 | `Unlabeled` | one-way | DNA14, Ku | `kku1()` | state and binding-pattern rewrite | `DNA14(site~sdsb) + Ku(dna,cs) -> DNA14(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA14, Ku through DNA14.site, Ku.dna at `kku1()`. | +| 144 | `Unlabeled` | one-way | DNA15, Ku | `kku1()` | state and binding-pattern rewrite | `DNA15(site~sdsb) + Ku(dna,cs) -> DNA15(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA15, Ku through DNA15.site, Ku.dna at `kku1()`. | +| 145 | `Unlabeled` | one-way | DNA16, Ku | `kku1()` | state and binding-pattern rewrite | `DNA16(site~sdsb) + Ku(dna,cs) -> DNA16(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA16, Ku through DNA16.site, Ku.dna at `kku1()`. | +| 146 | `Unlabeled` | one-way | DNA17, Ku | `kku1()` | state and binding-pattern rewrite | `DNA17(site~sdsb) + Ku(dna,cs) -> DNA17(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA17, Ku through DNA17.site, Ku.dna at `kku1()`. | +| 147 | `Unlabeled` | one-way | DNA18, Ku | `kku1()` | state and binding-pattern rewrite | `DNA18(site~sdsb) + Ku(dna,cs) -> DNA18(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA18, Ku through DNA18.site, Ku.dna at `kku1()`. | +| 148 | `Unlabeled` | one-way | DNA19, Ku | `kku1()` | state and binding-pattern rewrite | `DNA19(site~sdsb) + Ku(dna,cs) -> DNA19(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA19, Ku through DNA19.site, Ku.dna at `kku1()`. | +| 149 | `Unlabeled` | one-way | DNA20, Ku | `kku1()` | state and binding-pattern rewrite | `DNA20(site~sdsb) + Ku(dna,cs) -> DNA20(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA20, Ku through DNA20.site, Ku.dna at `kku1()`. | +| 150 | `Unlabeled` | one-way | DNA21, Ku | `kku1()` | state and binding-pattern rewrite | `DNA21(site~sdsb) + Ku(dna,cs) -> DNA21(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA21, Ku through DNA21.site, Ku.dna at `kku1()`. | +| 151 | `Unlabeled` | one-way | DNA22, Ku | `kku1()` | state and binding-pattern rewrite | `DNA22(site~sdsb) + Ku(dna,cs) -> DNA22(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA22, Ku through DNA22.site, Ku.dna at `kku1()`. | +| 152 | `Unlabeled` | one-way | DNA23, Ku | `kku1()` | state and binding-pattern rewrite | `DNA23(site~sdsb) + Ku(dna,cs) -> DNA23(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA23, Ku through DNA23.site, Ku.dna at `kku1()`. | +| 153 | `Unlabeled` | one-way | DNA24, Ku | `kku1()` | state and binding-pattern rewrite | `DNA24(site~sdsb) + Ku(dna,cs) -> DNA24(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA24, Ku through DNA24.site, Ku.dna at `kku1()`. | +| 154 | `Unlabeled` | one-way | DNA25, Ku | `kku1()` | state and binding-pattern rewrite | `DNA25(site~sdsb) + Ku(dna,cs) -> DNA25(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA25, Ku through DNA25.site, Ku.dna at `kku1()`. | +| 155 | `Unlabeled` | one-way | DNA26, Ku | `kku1()` | state and binding-pattern rewrite | `DNA26(site~sdsb) + Ku(dna,cs) -> DNA26(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA26, Ku through DNA26.site, Ku.dna at `kku1()`. | +| 156 | `Unlabeled` | one-way | DNA27, Ku | `kku1()` | state and binding-pattern rewrite | `DNA27(site~sdsb) + Ku(dna,cs) -> DNA27(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA27, Ku through DNA27.site, Ku.dna at `kku1()`. | +| 157 | `Unlabeled` | one-way | DNA28, Ku | `kku1()` | state and binding-pattern rewrite | `DNA28(site~sdsb) + Ku(dna,cs) -> DNA28(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA28, Ku through DNA28.site, Ku.dna at `kku1()`. | +| 158 | `Unlabeled` | one-way | DNA29, Ku | `kku1()` | state and binding-pattern rewrite | `DNA29(site~sdsb) + Ku(dna,cs) -> DNA29(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA29, Ku through DNA29.site, Ku.dna at `kku1()`. | +| 159 | `Unlabeled` | one-way | DNA30, Ku | `kku1()` | state and binding-pattern rewrite | `DNA30(site~sdsb) + Ku(dna,cs) -> DNA30(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA30, Ku through DNA30.site, Ku.dna at `kku1()`. | +| 160 | `Unlabeled` | one-way | DNA31, Ku | `kku1()` | state and binding-pattern rewrite | `DNA31(site~sdsb) + Ku(dna,cs) -> DNA31(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA31, Ku through DNA31.site, Ku.dna at `kku1()`. | +| 161 | `Unlabeled` | one-way | DNA32, Ku | `kku1()` | state and binding-pattern rewrite | `DNA32(site~sdsb) + Ku(dna,cs) -> DNA32(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA32, Ku through DNA32.site, Ku.dna at `kku1()`. | +| 162 | `Unlabeled` | one-way | DNA33, Ku | `kku1()` | state and binding-pattern rewrite | `DNA33(site~sdsb) + Ku(dna,cs) -> DNA33(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA33, Ku through DNA33.site, Ku.dna at `kku1()`. | +| 163 | `Unlabeled` | one-way | DNA34, Ku | `kku1()` | state and binding-pattern rewrite | `DNA34(site~sdsb) + Ku(dna,cs) -> DNA34(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA34, Ku through DNA34.site, Ku.dna at `kku1()`. | +| 164 | `Unlabeled` | one-way | DNA35, Ku | `kku1()` | state and binding-pattern rewrite | `DNA35(site~sdsb) + Ku(dna,cs) -> DNA35(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA35, Ku through DNA35.site, Ku.dna at `kku1()`. | +| 165 | `Unlabeled` | one-way | DNA36, Ku | `kku1()` | state and binding-pattern rewrite | `DNA36(site~sdsb) + Ku(dna,cs) -> DNA36(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA36, Ku through DNA36.site, Ku.dna at `kku1()`. | +| 166 | `Unlabeled` | one-way | DNA37, Ku | `kku1()` | state and binding-pattern rewrite | `DNA37(site~sdsb) + Ku(dna,cs) -> DNA37(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA37, Ku through DNA37.site, Ku.dna at `kku1()`. | +| 167 | `Unlabeled` | one-way | DNA38, Ku | `kku1()` | state and binding-pattern rewrite | `DNA38(site~sdsb) + Ku(dna,cs) -> DNA38(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA38, Ku through DNA38.site, Ku.dna at `kku1()`. | +| 168 | `Unlabeled` | one-way | DNA39, Ku | `kku1()` | state and binding-pattern rewrite | `DNA39(site~sdsb) + Ku(dna,cs) -> DNA39(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA39, Ku through DNA39.site, Ku.dna at `kku1()`. | +| 169 | `Unlabeled` | one-way | DNA40, Ku | `kku1()` | state and binding-pattern rewrite | `DNA40(site~sdsb) + Ku(dna,cs) -> DNA40(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA40, Ku through DNA40.site, Ku.dna at `kku1()`. | +| 170 | `Unlabeled` | one-way | DNA41, Ku | `kku1()` | state and binding-pattern rewrite | `DNA41(site~sdsb) + Ku(dna,cs) -> DNA41(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA41, Ku through DNA41.site, Ku.dna at `kku1()`. | +| 171 | `Unlabeled` | one-way | DNA42, Ku | `kku1()` | state and binding-pattern rewrite | `DNA42(site~sdsb) + Ku(dna,cs) -> DNA42(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA42, Ku through DNA42.site, Ku.dna at `kku1()`. | +| 172 | `Unlabeled` | one-way | DNA43, Ku | `kku1()` | state and binding-pattern rewrite | `DNA43(site~sdsb) + Ku(dna,cs) -> DNA43(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA43, Ku through DNA43.site, Ku.dna at `kku1()`. | +| 173 | `Unlabeled` | one-way | DNA44, Ku | `kku1()` | state and binding-pattern rewrite | `DNA44(site~sdsb) + Ku(dna,cs) -> DNA44(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA44, Ku through DNA44.site, Ku.dna at `kku1()`. | +| 174 | `Unlabeled` | one-way | DNA45, Ku | `kku1()` | state and binding-pattern rewrite | `DNA45(site~sdsb) + Ku(dna,cs) -> DNA45(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA45, Ku through DNA45.site, Ku.dna at `kku1()`. | +| 175 | `Unlabeled` | one-way | DNA46, Ku | `kku1()` | state and binding-pattern rewrite | `DNA46(site~sdsb) + Ku(dna,cs) -> DNA46(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA46, Ku through DNA46.site, Ku.dna at `kku1()`. | +| 176 | `Unlabeled` | one-way | DNA47, Ku | `kku1()` | state and binding-pattern rewrite | `DNA47(site~sdsb) + Ku(dna,cs) -> DNA47(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA47, Ku through DNA47.site, Ku.dna at `kku1()`. | +| 177 | `Unlabeled` | one-way | DNA48, Ku | `kku1()` | state and binding-pattern rewrite | `DNA48(site~sdsb) + Ku(dna,cs) -> DNA48(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA48, Ku through DNA48.site, Ku.dna at `kku1()`. | +| 178 | `Unlabeled` | one-way | DNA49, Ku | `kku1()` | state and binding-pattern rewrite | `DNA49(site~sdsb) + Ku(dna,cs) -> DNA49(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA49, Ku through DNA49.site, Ku.dna at `kku1()`. | +| 179 | `Unlabeled` | one-way | DNA50, Ku | `kku1()` | state and binding-pattern rewrite | `DNA50(site~sdsb) + Ku(dna,cs) -> DNA50(site!1~sdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA50, Ku through DNA50.site, Ku.dna at `kku1()`. | +| 180 | `Unlabeled` | one-way | DNA1, Ku | `kku2()` | state and binding-pattern rewrite | `DNA1(site~cdsb) + Ku(dna,cs) -> DNA1(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA1, Ku through DNA1.site, Ku.dna at `kku2()`. | +| 181 | `Unlabeled` | one-way | DNA2, Ku | `kku2()` | state and binding-pattern rewrite | `DNA2(site~cdsb) + Ku(dna,cs) -> DNA2(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA2, Ku through DNA2.site, Ku.dna at `kku2()`. | +| 182 | `Unlabeled` | one-way | DNA3, Ku | `kku2()` | state and binding-pattern rewrite | `DNA3(site~cdsb) + Ku(dna,cs) -> DNA3(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA3, Ku through DNA3.site, Ku.dna at `kku2()`. | +| 183 | `Unlabeled` | one-way | DNA4, Ku | `kku2()` | state and binding-pattern rewrite | `DNA4(site~cdsb) + Ku(dna,cs) -> DNA4(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA4, Ku through DNA4.site, Ku.dna at `kku2()`. | +| 184 | `Unlabeled` | one-way | DNA5, Ku | `kku2()` | state and binding-pattern rewrite | `DNA5(site~cdsb) + Ku(dna,cs) -> DNA5(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA5, Ku through DNA5.site, Ku.dna at `kku2()`. | +| 185 | `Unlabeled` | one-way | DNA6, Ku | `kku2()` | state and binding-pattern rewrite | `DNA6(site~cdsb) + Ku(dna,cs) -> DNA6(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA6, Ku through DNA6.site, Ku.dna at `kku2()`. | +| 186 | `Unlabeled` | one-way | DNA7, Ku | `kku2()` | state and binding-pattern rewrite | `DNA7(site~cdsb) + Ku(dna,cs) -> DNA7(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA7, Ku through DNA7.site, Ku.dna at `kku2()`. | +| 187 | `Unlabeled` | one-way | DNA8, Ku | `kku2()` | state and binding-pattern rewrite | `DNA8(site~cdsb) + Ku(dna,cs) -> DNA8(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA8, Ku through DNA8.site, Ku.dna at `kku2()`. | +| 188 | `Unlabeled` | one-way | DNA9, Ku | `kku2()` | state and binding-pattern rewrite | `DNA9(site~cdsb) + Ku(dna,cs) -> DNA9(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA9, Ku through DNA9.site, Ku.dna at `kku2()`. | +| 189 | `Unlabeled` | one-way | DNA10, Ku | `kku2()` | state and binding-pattern rewrite | `DNA10(site~cdsb) + Ku(dna,cs) -> DNA10(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA10, Ku through DNA10.site, Ku.dna at `kku2()`. | +| 190 | `Unlabeled` | one-way | DNA11, Ku | `kku2()` | state and binding-pattern rewrite | `DNA11(site~cdsb) + Ku(dna,cs) -> DNA11(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA11, Ku through DNA11.site, Ku.dna at `kku2()`. | +| 191 | `Unlabeled` | one-way | DNA12, Ku | `kku2()` | state and binding-pattern rewrite | `DNA12(site~cdsb) + Ku(dna,cs) -> DNA12(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA12, Ku through DNA12.site, Ku.dna at `kku2()`. | +| 192 | `Unlabeled` | one-way | DNA13, Ku | `kku2()` | state and binding-pattern rewrite | `DNA13(site~cdsb) + Ku(dna,cs) -> DNA13(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA13, Ku through DNA13.site, Ku.dna at `kku2()`. | +| 193 | `Unlabeled` | one-way | DNA14, Ku | `kku2()` | state and binding-pattern rewrite | `DNA14(site~cdsb) + Ku(dna,cs) -> DNA14(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA14, Ku through DNA14.site, Ku.dna at `kku2()`. | +| 194 | `Unlabeled` | one-way | DNA15, Ku | `kku2()` | state and binding-pattern rewrite | `DNA15(site~cdsb) + Ku(dna,cs) -> DNA15(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA15, Ku through DNA15.site, Ku.dna at `kku2()`. | +| 195 | `Unlabeled` | one-way | DNA16, Ku | `kku2()` | state and binding-pattern rewrite | `DNA16(site~cdsb) + Ku(dna,cs) -> DNA16(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA16, Ku through DNA16.site, Ku.dna at `kku2()`. | +| 196 | `Unlabeled` | one-way | DNA17, Ku | `kku2()` | state and binding-pattern rewrite | `DNA17(site~cdsb) + Ku(dna,cs) -> DNA17(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA17, Ku through DNA17.site, Ku.dna at `kku2()`. | +| 197 | `Unlabeled` | one-way | DNA18, Ku | `kku2()` | state and binding-pattern rewrite | `DNA18(site~cdsb) + Ku(dna,cs) -> DNA18(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA18, Ku through DNA18.site, Ku.dna at `kku2()`. | +| 198 | `Unlabeled` | one-way | DNA19, Ku | `kku2()` | state and binding-pattern rewrite | `DNA19(site~cdsb) + Ku(dna,cs) -> DNA19(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA19, Ku through DNA19.site, Ku.dna at `kku2()`. | +| 199 | `Unlabeled` | one-way | DNA20, Ku | `kku2()` | state and binding-pattern rewrite | `DNA20(site~cdsb) + Ku(dna,cs) -> DNA20(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA20, Ku through DNA20.site, Ku.dna at `kku2()`. | +| 200 | `Unlabeled` | one-way | DNA21, Ku | `kku2()` | state and binding-pattern rewrite | `DNA21(site~cdsb) + Ku(dna,cs) -> DNA21(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA21, Ku through DNA21.site, Ku.dna at `kku2()`. | +| 201 | `Unlabeled` | one-way | DNA22, Ku | `kku2()` | state and binding-pattern rewrite | `DNA22(site~cdsb) + Ku(dna,cs) -> DNA22(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA22, Ku through DNA22.site, Ku.dna at `kku2()`. | +| 202 | `Unlabeled` | one-way | DNA23, Ku | `kku2()` | state and binding-pattern rewrite | `DNA23(site~cdsb) + Ku(dna,cs) -> DNA23(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA23, Ku through DNA23.site, Ku.dna at `kku2()`. | +| 203 | `Unlabeled` | one-way | DNA24, Ku | `kku2()` | state and binding-pattern rewrite | `DNA24(site~cdsb) + Ku(dna,cs) -> DNA24(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA24, Ku through DNA24.site, Ku.dna at `kku2()`. | +| 204 | `Unlabeled` | one-way | DNA25, Ku | `kku2()` | state and binding-pattern rewrite | `DNA25(site~cdsb) + Ku(dna,cs) -> DNA25(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA25, Ku through DNA25.site, Ku.dna at `kku2()`. | +| 205 | `Unlabeled` | one-way | DNA26, Ku | `kku2()` | state and binding-pattern rewrite | `DNA26(site~cdsb) + Ku(dna,cs) -> DNA26(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA26, Ku through DNA26.site, Ku.dna at `kku2()`. | +| 206 | `Unlabeled` | one-way | DNA27, Ku | `kku2()` | state and binding-pattern rewrite | `DNA27(site~cdsb) + Ku(dna,cs) -> DNA27(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA27, Ku through DNA27.site, Ku.dna at `kku2()`. | +| 207 | `Unlabeled` | one-way | DNA28, Ku | `kku2()` | state and binding-pattern rewrite | `DNA28(site~cdsb) + Ku(dna,cs) -> DNA28(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA28, Ku through DNA28.site, Ku.dna at `kku2()`. | +| 208 | `Unlabeled` | one-way | DNA29, Ku | `kku2()` | state and binding-pattern rewrite | `DNA29(site~cdsb) + Ku(dna,cs) -> DNA29(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA29, Ku through DNA29.site, Ku.dna at `kku2()`. | +| 209 | `Unlabeled` | one-way | DNA30, Ku | `kku2()` | state and binding-pattern rewrite | `DNA30(site~cdsb) + Ku(dna,cs) -> DNA30(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA30, Ku through DNA30.site, Ku.dna at `kku2()`. | +| 210 | `Unlabeled` | one-way | DNA31, Ku | `kku2()` | state and binding-pattern rewrite | `DNA31(site~cdsb) + Ku(dna,cs) -> DNA31(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA31, Ku through DNA31.site, Ku.dna at `kku2()`. | +| 211 | `Unlabeled` | one-way | DNA32, Ku | `kku2()` | state and binding-pattern rewrite | `DNA32(site~cdsb) + Ku(dna,cs) -> DNA32(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA32, Ku through DNA32.site, Ku.dna at `kku2()`. | +| 212 | `Unlabeled` | one-way | DNA33, Ku | `kku2()` | state and binding-pattern rewrite | `DNA33(site~cdsb) + Ku(dna,cs) -> DNA33(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA33, Ku through DNA33.site, Ku.dna at `kku2()`. | +| 213 | `Unlabeled` | one-way | DNA34, Ku | `kku2()` | state and binding-pattern rewrite | `DNA34(site~cdsb) + Ku(dna,cs) -> DNA34(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA34, Ku through DNA34.site, Ku.dna at `kku2()`. | +| 214 | `Unlabeled` | one-way | DNA35, Ku | `kku2()` | state and binding-pattern rewrite | `DNA35(site~cdsb) + Ku(dna,cs) -> DNA35(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA35, Ku through DNA35.site, Ku.dna at `kku2()`. | +| 215 | `Unlabeled` | one-way | DNA36, Ku | `kku2()` | state and binding-pattern rewrite | `DNA36(site~cdsb) + Ku(dna,cs) -> DNA36(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA36, Ku through DNA36.site, Ku.dna at `kku2()`. | +| 216 | `Unlabeled` | one-way | DNA37, Ku | `kku2()` | state and binding-pattern rewrite | `DNA37(site~cdsb) + Ku(dna,cs) -> DNA37(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA37, Ku through DNA37.site, Ku.dna at `kku2()`. | +| 217 | `Unlabeled` | one-way | DNA38, Ku | `kku2()` | state and binding-pattern rewrite | `DNA38(site~cdsb) + Ku(dna,cs) -> DNA38(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA38, Ku through DNA38.site, Ku.dna at `kku2()`. | +| 218 | `Unlabeled` | one-way | DNA39, Ku | `kku2()` | state and binding-pattern rewrite | `DNA39(site~cdsb) + Ku(dna,cs) -> DNA39(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA39, Ku through DNA39.site, Ku.dna at `kku2()`. | +| 219 | `Unlabeled` | one-way | DNA40, Ku | `kku2()` | state and binding-pattern rewrite | `DNA40(site~cdsb) + Ku(dna,cs) -> DNA40(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA40, Ku through DNA40.site, Ku.dna at `kku2()`. | +| 220 | `Unlabeled` | one-way | DNA41, Ku | `kku2()` | state and binding-pattern rewrite | `DNA41(site~cdsb) + Ku(dna,cs) -> DNA41(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA41, Ku through DNA41.site, Ku.dna at `kku2()`. | +| 221 | `Unlabeled` | one-way | DNA42, Ku | `kku2()` | state and binding-pattern rewrite | `DNA42(site~cdsb) + Ku(dna,cs) -> DNA42(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA42, Ku through DNA42.site, Ku.dna at `kku2()`. | +| 222 | `Unlabeled` | one-way | DNA43, Ku | `kku2()` | state and binding-pattern rewrite | `DNA43(site~cdsb) + Ku(dna,cs) -> DNA43(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA43, Ku through DNA43.site, Ku.dna at `kku2()`. | +| 223 | `Unlabeled` | one-way | DNA44, Ku | `kku2()` | state and binding-pattern rewrite | `DNA44(site~cdsb) + Ku(dna,cs) -> DNA44(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA44, Ku through DNA44.site, Ku.dna at `kku2()`. | +| 224 | `Unlabeled` | one-way | DNA45, Ku | `kku2()` | state and binding-pattern rewrite | `DNA45(site~cdsb) + Ku(dna,cs) -> DNA45(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA45, Ku through DNA45.site, Ku.dna at `kku2()`. | +| 225 | `Unlabeled` | one-way | DNA46, Ku | `kku2()` | state and binding-pattern rewrite | `DNA46(site~cdsb) + Ku(dna,cs) -> DNA46(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA46, Ku through DNA46.site, Ku.dna at `kku2()`. | +| 226 | `Unlabeled` | one-way | DNA47, Ku | `kku2()` | state and binding-pattern rewrite | `DNA47(site~cdsb) + Ku(dna,cs) -> DNA47(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA47, Ku through DNA47.site, Ku.dna at `kku2()`. | +| 227 | `Unlabeled` | one-way | DNA48, Ku | `kku2()` | state and binding-pattern rewrite | `DNA48(site~cdsb) + Ku(dna,cs) -> DNA48(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA48, Ku through DNA48.site, Ku.dna at `kku2()`. | +| 228 | `Unlabeled` | one-way | DNA49, Ku | `kku2()` | state and binding-pattern rewrite | `DNA49(site~cdsb) + Ku(dna,cs) -> DNA49(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA49, Ku through DNA49.site, Ku.dna at `kku2()`. | +| 229 | `Unlabeled` | one-way | DNA50, Ku | `kku2()` | state and binding-pattern rewrite | `DNA50(site~cdsb) + Ku(dna,cs) -> DNA50(site!1~cdsb).Ku(dna!1,cs)` | Forms a complex/contact among DNA50, Ku through DNA50.site, Ku.dna at `kku2()`. | +| 230 | `Unlabeled` | one-way | DNA1, Ku | `kdku1` | state and binding-pattern rewrite | `DNA1(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA1(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA1, Ku by freeing DNA1.site, Ku.dna at `kdku1`. | +| 231 | `Unlabeled` | one-way | DNA2, Ku | `kdku1` | state and binding-pattern rewrite | `DNA2(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA2(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA2, Ku by freeing DNA2.site, Ku.dna at `kdku1`. | +| 232 | `Unlabeled` | one-way | DNA3, Ku | `kdku1` | state and binding-pattern rewrite | `DNA3(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA3(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA3, Ku by freeing DNA3.site, Ku.dna at `kdku1`. | +| 233 | `Unlabeled` | one-way | DNA4, Ku | `kdku1` | state and binding-pattern rewrite | `DNA4(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA4(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA4, Ku by freeing DNA4.site, Ku.dna at `kdku1`. | +| 234 | `Unlabeled` | one-way | DNA5, Ku | `kdku1` | state and binding-pattern rewrite | `DNA5(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA5(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA5, Ku by freeing DNA5.site, Ku.dna at `kdku1`. | +| 235 | `Unlabeled` | one-way | DNA6, Ku | `kdku1` | state and binding-pattern rewrite | `DNA6(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA6(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA6, Ku by freeing DNA6.site, Ku.dna at `kdku1`. | +| 236 | `Unlabeled` | one-way | DNA7, Ku | `kdku1` | state and binding-pattern rewrite | `DNA7(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA7(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA7, Ku by freeing DNA7.site, Ku.dna at `kdku1`. | +| 237 | `Unlabeled` | one-way | DNA8, Ku | `kdku1` | state and binding-pattern rewrite | `DNA8(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA8(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA8, Ku by freeing DNA8.site, Ku.dna at `kdku1`. | +| 238 | `Unlabeled` | one-way | DNA9, Ku | `kdku1` | state and binding-pattern rewrite | `DNA9(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA9(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA9, Ku by freeing DNA9.site, Ku.dna at `kdku1`. | +| 239 | `Unlabeled` | one-way | DNA10, Ku | `kdku1` | state and binding-pattern rewrite | `DNA10(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA10(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA10, Ku by freeing DNA10.site, Ku.dna at `kdku1`. | +| 240 | `Unlabeled` | one-way | DNA11, Ku | `kdku1` | state and binding-pattern rewrite | `DNA11(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA11(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA11, Ku by freeing DNA11.site, Ku.dna at `kdku1`. | +| 241 | `Unlabeled` | one-way | DNA12, Ku | `kdku1` | state and binding-pattern rewrite | `DNA12(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA12(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA12, Ku by freeing DNA12.site, Ku.dna at `kdku1`. | +| 242 | `Unlabeled` | one-way | DNA13, Ku | `kdku1` | state and binding-pattern rewrite | `DNA13(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA13(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA13, Ku by freeing DNA13.site, Ku.dna at `kdku1`. | +| 243 | `Unlabeled` | one-way | DNA14, Ku | `kdku1` | state and binding-pattern rewrite | `DNA14(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA14(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA14, Ku by freeing DNA14.site, Ku.dna at `kdku1`. | +| 244 | `Unlabeled` | one-way | DNA15, Ku | `kdku1` | state and binding-pattern rewrite | `DNA15(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA15(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA15, Ku by freeing DNA15.site, Ku.dna at `kdku1`. | +| 245 | `Unlabeled` | one-way | DNA16, Ku | `kdku1` | state and binding-pattern rewrite | `DNA16(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA16(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA16, Ku by freeing DNA16.site, Ku.dna at `kdku1`. | +| 246 | `Unlabeled` | one-way | DNA17, Ku | `kdku1` | state and binding-pattern rewrite | `DNA17(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA17(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA17, Ku by freeing DNA17.site, Ku.dna at `kdku1`. | +| 247 | `Unlabeled` | one-way | DNA18, Ku | `kdku1` | state and binding-pattern rewrite | `DNA18(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA18(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA18, Ku by freeing DNA18.site, Ku.dna at `kdku1`. | +| 248 | `Unlabeled` | one-way | DNA19, Ku | `kdku1` | state and binding-pattern rewrite | `DNA19(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA19(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA19, Ku by freeing DNA19.site, Ku.dna at `kdku1`. | +| 249 | `Unlabeled` | one-way | DNA20, Ku | `kdku1` | state and binding-pattern rewrite | `DNA20(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA20(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA20, Ku by freeing DNA20.site, Ku.dna at `kdku1`. | +| 250 | `Unlabeled` | one-way | DNA21, Ku | `kdku1` | state and binding-pattern rewrite | `DNA21(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA21(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA21, Ku by freeing DNA21.site, Ku.dna at `kdku1`. | + +### Rules 251-500 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 251 | `Unlabeled` | one-way | DNA22, Ku | `kdku1` | state and binding-pattern rewrite | `DNA22(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA22(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA22, Ku by freeing DNA22.site, Ku.dna at `kdku1`. | +| 252 | `Unlabeled` | one-way | DNA23, Ku | `kdku1` | state and binding-pattern rewrite | `DNA23(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA23(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA23, Ku by freeing DNA23.site, Ku.dna at `kdku1`. | +| 253 | `Unlabeled` | one-way | DNA24, Ku | `kdku1` | state and binding-pattern rewrite | `DNA24(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA24(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA24, Ku by freeing DNA24.site, Ku.dna at `kdku1`. | +| 254 | `Unlabeled` | one-way | DNA25, Ku | `kdku1` | state and binding-pattern rewrite | `DNA25(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA25(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA25, Ku by freeing DNA25.site, Ku.dna at `kdku1`. | +| 255 | `Unlabeled` | one-way | DNA26, Ku | `kdku1` | state and binding-pattern rewrite | `DNA26(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA26(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA26, Ku by freeing DNA26.site, Ku.dna at `kdku1`. | +| 256 | `Unlabeled` | one-way | DNA27, Ku | `kdku1` | state and binding-pattern rewrite | `DNA27(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA27(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA27, Ku by freeing DNA27.site, Ku.dna at `kdku1`. | +| 257 | `Unlabeled` | one-way | DNA28, Ku | `kdku1` | state and binding-pattern rewrite | `DNA28(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA28(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA28, Ku by freeing DNA28.site, Ku.dna at `kdku1`. | +| 258 | `Unlabeled` | one-way | DNA29, Ku | `kdku1` | state and binding-pattern rewrite | `DNA29(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA29(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA29, Ku by freeing DNA29.site, Ku.dna at `kdku1`. | +| 259 | `Unlabeled` | one-way | DNA30, Ku | `kdku1` | state and binding-pattern rewrite | `DNA30(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA30(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA30, Ku by freeing DNA30.site, Ku.dna at `kdku1`. | +| 260 | `Unlabeled` | one-way | DNA31, Ku | `kdku1` | state and binding-pattern rewrite | `DNA31(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA31(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA31, Ku by freeing DNA31.site, Ku.dna at `kdku1`. | +| 261 | `Unlabeled` | one-way | DNA32, Ku | `kdku1` | state and binding-pattern rewrite | `DNA32(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA32(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA32, Ku by freeing DNA32.site, Ku.dna at `kdku1`. | +| 262 | `Unlabeled` | one-way | DNA33, Ku | `kdku1` | state and binding-pattern rewrite | `DNA33(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA33(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA33, Ku by freeing DNA33.site, Ku.dna at `kdku1`. | +| 263 | `Unlabeled` | one-way | DNA34, Ku | `kdku1` | state and binding-pattern rewrite | `DNA34(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA34(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA34, Ku by freeing DNA34.site, Ku.dna at `kdku1`. | +| 264 | `Unlabeled` | one-way | DNA35, Ku | `kdku1` | state and binding-pattern rewrite | `DNA35(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA35(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA35, Ku by freeing DNA35.site, Ku.dna at `kdku1`. | +| 265 | `Unlabeled` | one-way | DNA36, Ku | `kdku1` | state and binding-pattern rewrite | `DNA36(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA36(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA36, Ku by freeing DNA36.site, Ku.dna at `kdku1`. | +| 266 | `Unlabeled` | one-way | DNA37, Ku | `kdku1` | state and binding-pattern rewrite | `DNA37(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA37(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA37, Ku by freeing DNA37.site, Ku.dna at `kdku1`. | +| 267 | `Unlabeled` | one-way | DNA38, Ku | `kdku1` | state and binding-pattern rewrite | `DNA38(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA38(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA38, Ku by freeing DNA38.site, Ku.dna at `kdku1`. | +| 268 | `Unlabeled` | one-way | DNA39, Ku | `kdku1` | state and binding-pattern rewrite | `DNA39(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA39(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA39, Ku by freeing DNA39.site, Ku.dna at `kdku1`. | +| 269 | `Unlabeled` | one-way | DNA40, Ku | `kdku1` | state and binding-pattern rewrite | `DNA40(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA40(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA40, Ku by freeing DNA40.site, Ku.dna at `kdku1`. | +| 270 | `Unlabeled` | one-way | DNA41, Ku | `kdku1` | state and binding-pattern rewrite | `DNA41(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA41(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA41, Ku by freeing DNA41.site, Ku.dna at `kdku1`. | +| 271 | `Unlabeled` | one-way | DNA42, Ku | `kdku1` | state and binding-pattern rewrite | `DNA42(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA42(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA42, Ku by freeing DNA42.site, Ku.dna at `kdku1`. | +| 272 | `Unlabeled` | one-way | DNA43, Ku | `kdku1` | state and binding-pattern rewrite | `DNA43(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA43(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA43, Ku by freeing DNA43.site, Ku.dna at `kdku1`. | +| 273 | `Unlabeled` | one-way | DNA44, Ku | `kdku1` | state and binding-pattern rewrite | `DNA44(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA44(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA44, Ku by freeing DNA44.site, Ku.dna at `kdku1`. | +| 274 | `Unlabeled` | one-way | DNA45, Ku | `kdku1` | state and binding-pattern rewrite | `DNA45(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA45(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA45, Ku by freeing DNA45.site, Ku.dna at `kdku1`. | +| 275 | `Unlabeled` | one-way | DNA46, Ku | `kdku1` | state and binding-pattern rewrite | `DNA46(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA46(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA46, Ku by freeing DNA46.site, Ku.dna at `kdku1`. | +| 276 | `Unlabeled` | one-way | DNA47, Ku | `kdku1` | state and binding-pattern rewrite | `DNA47(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA47(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA47, Ku by freeing DNA47.site, Ku.dna at `kdku1`. | +| 277 | `Unlabeled` | one-way | DNA48, Ku | `kdku1` | state and binding-pattern rewrite | `DNA48(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA48(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA48, Ku by freeing DNA48.site, Ku.dna at `kdku1`. | +| 278 | `Unlabeled` | one-way | DNA49, Ku | `kdku1` | state and binding-pattern rewrite | `DNA49(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA49(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA49, Ku by freeing DNA49.site, Ku.dna at `kdku1`. | +| 279 | `Unlabeled` | one-way | DNA50, Ku | `kdku1` | state and binding-pattern rewrite | `DNA50(site!1~sdsb).Ku(dna!1,cs,cys~red) -> DNA50(site~sdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA50, Ku by freeing DNA50.site, Ku.dna at `kdku1`. | +| 280 | `Unlabeled` | one-way | DNA1, Ku | `kdku2` | state and binding-pattern rewrite | `DNA1(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA1(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA1, Ku by freeing DNA1.site, Ku.dna at `kdku2`. | +| 281 | `Unlabeled` | one-way | DNA2, Ku | `kdku2` | state and binding-pattern rewrite | `DNA2(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA2(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA2, Ku by freeing DNA2.site, Ku.dna at `kdku2`. | +| 282 | `Unlabeled` | one-way | DNA3, Ku | `kdku2` | state and binding-pattern rewrite | `DNA3(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA3(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA3, Ku by freeing DNA3.site, Ku.dna at `kdku2`. | +| 283 | `Unlabeled` | one-way | DNA4, Ku | `kdku2` | state and binding-pattern rewrite | `DNA4(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA4(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA4, Ku by freeing DNA4.site, Ku.dna at `kdku2`. | +| 284 | `Unlabeled` | one-way | DNA5, Ku | `kdku2` | state and binding-pattern rewrite | `DNA5(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA5(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA5, Ku by freeing DNA5.site, Ku.dna at `kdku2`. | +| 285 | `Unlabeled` | one-way | DNA6, Ku | `kdku2` | state and binding-pattern rewrite | `DNA6(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA6(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA6, Ku by freeing DNA6.site, Ku.dna at `kdku2`. | +| 286 | `Unlabeled` | one-way | DNA7, Ku | `kdku2` | state and binding-pattern rewrite | `DNA7(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA7(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA7, Ku by freeing DNA7.site, Ku.dna at `kdku2`. | +| 287 | `Unlabeled` | one-way | DNA8, Ku | `kdku2` | state and binding-pattern rewrite | `DNA8(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA8(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA8, Ku by freeing DNA8.site, Ku.dna at `kdku2`. | +| 288 | `Unlabeled` | one-way | DNA9, Ku | `kdku2` | state and binding-pattern rewrite | `DNA9(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA9(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA9, Ku by freeing DNA9.site, Ku.dna at `kdku2`. | +| 289 | `Unlabeled` | one-way | DNA10, Ku | `kdku2` | state and binding-pattern rewrite | `DNA10(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA10(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA10, Ku by freeing DNA10.site, Ku.dna at `kdku2`. | +| 290 | `Unlabeled` | one-way | DNA11, Ku | `kdku2` | state and binding-pattern rewrite | `DNA11(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA11(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA11, Ku by freeing DNA11.site, Ku.dna at `kdku2`. | +| 291 | `Unlabeled` | one-way | DNA12, Ku | `kdku2` | state and binding-pattern rewrite | `DNA12(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA12(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA12, Ku by freeing DNA12.site, Ku.dna at `kdku2`. | +| 292 | `Unlabeled` | one-way | DNA13, Ku | `kdku2` | state and binding-pattern rewrite | `DNA13(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA13(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA13, Ku by freeing DNA13.site, Ku.dna at `kdku2`. | +| 293 | `Unlabeled` | one-way | DNA14, Ku | `kdku2` | state and binding-pattern rewrite | `DNA14(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA14(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA14, Ku by freeing DNA14.site, Ku.dna at `kdku2`. | +| 294 | `Unlabeled` | one-way | DNA15, Ku | `kdku2` | state and binding-pattern rewrite | `DNA15(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA15(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA15, Ku by freeing DNA15.site, Ku.dna at `kdku2`. | +| 295 | `Unlabeled` | one-way | DNA16, Ku | `kdku2` | state and binding-pattern rewrite | `DNA16(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA16(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA16, Ku by freeing DNA16.site, Ku.dna at `kdku2`. | +| 296 | `Unlabeled` | one-way | DNA17, Ku | `kdku2` | state and binding-pattern rewrite | `DNA17(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA17(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA17, Ku by freeing DNA17.site, Ku.dna at `kdku2`. | +| 297 | `Unlabeled` | one-way | DNA18, Ku | `kdku2` | state and binding-pattern rewrite | `DNA18(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA18(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA18, Ku by freeing DNA18.site, Ku.dna at `kdku2`. | +| 298 | `Unlabeled` | one-way | DNA19, Ku | `kdku2` | state and binding-pattern rewrite | `DNA19(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA19(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA19, Ku by freeing DNA19.site, Ku.dna at `kdku2`. | +| 299 | `Unlabeled` | one-way | DNA20, Ku | `kdku2` | state and binding-pattern rewrite | `DNA20(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA20(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA20, Ku by freeing DNA20.site, Ku.dna at `kdku2`. | +| 300 | `Unlabeled` | one-way | DNA21, Ku | `kdku2` | state and binding-pattern rewrite | `DNA21(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA21(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA21, Ku by freeing DNA21.site, Ku.dna at `kdku2`. | +| 301 | `Unlabeled` | one-way | DNA22, Ku | `kdku2` | state and binding-pattern rewrite | `DNA22(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA22(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA22, Ku by freeing DNA22.site, Ku.dna at `kdku2`. | +| 302 | `Unlabeled` | one-way | DNA23, Ku | `kdku2` | state and binding-pattern rewrite | `DNA23(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA23(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA23, Ku by freeing DNA23.site, Ku.dna at `kdku2`. | +| 303 | `Unlabeled` | one-way | DNA24, Ku | `kdku2` | state and binding-pattern rewrite | `DNA24(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA24(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA24, Ku by freeing DNA24.site, Ku.dna at `kdku2`. | +| 304 | `Unlabeled` | one-way | DNA25, Ku | `kdku2` | state and binding-pattern rewrite | `DNA25(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA25(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA25, Ku by freeing DNA25.site, Ku.dna at `kdku2`. | +| 305 | `Unlabeled` | one-way | DNA26, Ku | `kdku2` | state and binding-pattern rewrite | `DNA26(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA26(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA26, Ku by freeing DNA26.site, Ku.dna at `kdku2`. | +| 306 | `Unlabeled` | one-way | DNA27, Ku | `kdku2` | state and binding-pattern rewrite | `DNA27(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA27(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA27, Ku by freeing DNA27.site, Ku.dna at `kdku2`. | +| 307 | `Unlabeled` | one-way | DNA28, Ku | `kdku2` | state and binding-pattern rewrite | `DNA28(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA28(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA28, Ku by freeing DNA28.site, Ku.dna at `kdku2`. | +| 308 | `Unlabeled` | one-way | DNA29, Ku | `kdku2` | state and binding-pattern rewrite | `DNA29(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA29(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA29, Ku by freeing DNA29.site, Ku.dna at `kdku2`. | +| 309 | `Unlabeled` | one-way | DNA30, Ku | `kdku2` | state and binding-pattern rewrite | `DNA30(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA30(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA30, Ku by freeing DNA30.site, Ku.dna at `kdku2`. | +| 310 | `Unlabeled` | one-way | DNA31, Ku | `kdku2` | state and binding-pattern rewrite | `DNA31(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA31(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA31, Ku by freeing DNA31.site, Ku.dna at `kdku2`. | +| 311 | `Unlabeled` | one-way | DNA32, Ku | `kdku2` | state and binding-pattern rewrite | `DNA32(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA32(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA32, Ku by freeing DNA32.site, Ku.dna at `kdku2`. | +| 312 | `Unlabeled` | one-way | DNA33, Ku | `kdku2` | state and binding-pattern rewrite | `DNA33(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA33(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA33, Ku by freeing DNA33.site, Ku.dna at `kdku2`. | +| 313 | `Unlabeled` | one-way | DNA34, Ku | `kdku2` | state and binding-pattern rewrite | `DNA34(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA34(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA34, Ku by freeing DNA34.site, Ku.dna at `kdku2`. | +| 314 | `Unlabeled` | one-way | DNA35, Ku | `kdku2` | state and binding-pattern rewrite | `DNA35(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA35(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA35, Ku by freeing DNA35.site, Ku.dna at `kdku2`. | +| 315 | `Unlabeled` | one-way | DNA36, Ku | `kdku2` | state and binding-pattern rewrite | `DNA36(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA36(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA36, Ku by freeing DNA36.site, Ku.dna at `kdku2`. | +| 316 | `Unlabeled` | one-way | DNA37, Ku | `kdku2` | state and binding-pattern rewrite | `DNA37(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA37(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA37, Ku by freeing DNA37.site, Ku.dna at `kdku2`. | +| 317 | `Unlabeled` | one-way | DNA38, Ku | `kdku2` | state and binding-pattern rewrite | `DNA38(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA38(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA38, Ku by freeing DNA38.site, Ku.dna at `kdku2`. | +| 318 | `Unlabeled` | one-way | DNA39, Ku | `kdku2` | state and binding-pattern rewrite | `DNA39(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA39(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA39, Ku by freeing DNA39.site, Ku.dna at `kdku2`. | +| 319 | `Unlabeled` | one-way | DNA40, Ku | `kdku2` | state and binding-pattern rewrite | `DNA40(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA40(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA40, Ku by freeing DNA40.site, Ku.dna at `kdku2`. | +| 320 | `Unlabeled` | one-way | DNA41, Ku | `kdku2` | state and binding-pattern rewrite | `DNA41(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA41(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA41, Ku by freeing DNA41.site, Ku.dna at `kdku2`. | +| 321 | `Unlabeled` | one-way | DNA42, Ku | `kdku2` | state and binding-pattern rewrite | `DNA42(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA42(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA42, Ku by freeing DNA42.site, Ku.dna at `kdku2`. | +| 322 | `Unlabeled` | one-way | DNA43, Ku | `kdku2` | state and binding-pattern rewrite | `DNA43(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA43(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA43, Ku by freeing DNA43.site, Ku.dna at `kdku2`. | +| 323 | `Unlabeled` | one-way | DNA44, Ku | `kdku2` | state and binding-pattern rewrite | `DNA44(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA44(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA44, Ku by freeing DNA44.site, Ku.dna at `kdku2`. | +| 324 | `Unlabeled` | one-way | DNA45, Ku | `kdku2` | state and binding-pattern rewrite | `DNA45(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA45(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA45, Ku by freeing DNA45.site, Ku.dna at `kdku2`. | +| 325 | `Unlabeled` | one-way | DNA46, Ku | `kdku2` | state and binding-pattern rewrite | `DNA46(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA46(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA46, Ku by freeing DNA46.site, Ku.dna at `kdku2`. | +| 326 | `Unlabeled` | one-way | DNA47, Ku | `kdku2` | state and binding-pattern rewrite | `DNA47(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA47(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA47, Ku by freeing DNA47.site, Ku.dna at `kdku2`. | +| 327 | `Unlabeled` | one-way | DNA48, Ku | `kdku2` | state and binding-pattern rewrite | `DNA48(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA48(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA48, Ku by freeing DNA48.site, Ku.dna at `kdku2`. | +| 328 | `Unlabeled` | one-way | DNA49, Ku | `kdku2` | state and binding-pattern rewrite | `DNA49(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA49(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA49, Ku by freeing DNA49.site, Ku.dna at `kdku2`. | +| 329 | `Unlabeled` | one-way | DNA50, Ku | `kdku2` | state and binding-pattern rewrite | `DNA50(site!1~cdsb).Ku(dna!1,cs,cys~red) -> DNA50(site~cdsb) + Ku(dna,cs,cys~red)` | Releases a complex/contact among DNA50, Ku by freeing DNA50.site, Ku.dna at `kdku2`. | +| 330 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA1(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA1, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 331 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA2(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA2, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 332 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA3(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA3, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 333 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA4(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA4, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 334 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA5(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA5, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 335 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA6(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA6, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 336 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA7(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA7, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 337 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA8(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA8, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 338 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA9(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA9, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 339 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA10(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA10, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 340 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA11(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA11, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 341 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA12(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA12, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 342 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA13(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA13, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 343 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA14(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA14, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 344 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA15(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA15, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 345 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA16(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA16, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 346 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA17(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA17, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 347 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA18(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA18, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 348 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA19(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA19, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 349 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA20(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA20, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 350 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA21(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA21, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 351 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA22(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA22, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 352 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA23(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA23, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 353 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA24(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA24, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 354 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA25(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA25, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 355 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA26(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA26, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 356 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA27(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA27, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 357 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA28(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA28, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 358 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA29(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA29, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 359 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA30(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA30, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 360 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA31(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA31, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 361 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA32(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA32, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 362 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA33(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA33, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 363 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA34(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA34, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 364 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA35(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA35, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 365 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA36(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA36, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 366 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA37(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA37, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 367 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA38(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA38, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 368 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA39(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA39, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 369 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA40(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA40, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 370 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA41(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA41, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 371 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA42(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA42, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 372 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA43(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA43, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 373 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA44(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA44, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 374 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA45(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA45, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 375 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA46(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA46, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 376 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA47(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA47, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 377 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA48(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA48, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 378 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA49(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA49, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 379 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kdnapk1` | internal-state conversion/modification | `DNA50(site!1~sdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA50, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk1`. | +| 380 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA1(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA1, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 381 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA2(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA2, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 382 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA3(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA3, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 383 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA4(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA4, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 384 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA5(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA5, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 385 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA6(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA6, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 386 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA7(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA7, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 387 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA8(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA8, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 388 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA9(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA9, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 389 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA10(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA10, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 390 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA11(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA11, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 391 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA12(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA12, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 392 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA13(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA13, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 393 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA14(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA14, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 394 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA15(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA15, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 395 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA16(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA16, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 396 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA17(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA17, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 397 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA18(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA18, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 398 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA19(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA19, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 399 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA20(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA20, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 400 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA21(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA21, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 401 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA22(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA22, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 402 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA23(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA23, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 403 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA24(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA24, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 404 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA25(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA25, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 405 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA26(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA26, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 406 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA27(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA27, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 407 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA28(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA28, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 408 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA29(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA29, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 409 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA30(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA30, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 410 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA31(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA31, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 411 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA32(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA32, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 412 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA33(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA33, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 413 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA34(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA34, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 414 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA35(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA35, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 415 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA36(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA36, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 416 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA37(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA37, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 417 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA38(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA38, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 418 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA39(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA39, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 419 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA40(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA40, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 420 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA41(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA41, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 421 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA42(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA42, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 422 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA43(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA43, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 423 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA44(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA44, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 424 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA45(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA45, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 425 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA46(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA46, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 426 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA47(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA47, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 427 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA48(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA48, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 428 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA49(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA49, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 429 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kdnapk2` | internal-state conversion/modification | `DNA50(site!1~cdsb).Ku(dna!1,cs) + DNAPKcs(ku,liIV,psite~u) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u)` | Forms a complex/contact among DNA50, DNAPKcs, Ku through DNAPKcs.ku, Ku.cs at `kdnapk2`. | +| 430 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA1(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA1, DNAPKcs, Ku by freeing DNA1.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 431 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA2(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA2, DNAPKcs, Ku by freeing DNA2.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 432 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA3(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA3, DNAPKcs, Ku by freeing DNA3.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 433 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA4(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA4, DNAPKcs, Ku by freeing DNA4.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 434 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA5(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA5, DNAPKcs, Ku by freeing DNA5.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 435 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA6(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA6, DNAPKcs, Ku by freeing DNA6.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 436 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA7(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA7, DNAPKcs, Ku by freeing DNA7.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 437 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA8(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA8, DNAPKcs, Ku by freeing DNA8.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 438 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA9(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA9, DNAPKcs, Ku by freeing DNA9.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 439 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA10(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA10, DNAPKcs, Ku by freeing DNA10.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 440 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA11(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA11, DNAPKcs, Ku by freeing DNA11.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 441 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA12(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA12, DNAPKcs, Ku by freeing DNA12.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 442 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA13(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA13, DNAPKcs, Ku by freeing DNA13.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 443 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA14(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA14, DNAPKcs, Ku by freeing DNA14.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 444 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA15(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA15, DNAPKcs, Ku by freeing DNA15.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 445 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA16(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA16, DNAPKcs, Ku by freeing DNA16.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 446 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA17(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA17, DNAPKcs, Ku by freeing DNA17.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 447 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA18(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA18, DNAPKcs, Ku by freeing DNA18.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 448 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA19(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA19, DNAPKcs, Ku by freeing DNA19.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 449 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA20(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA20, DNAPKcs, Ku by freeing DNA20.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 450 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA21(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA21, DNAPKcs, Ku by freeing DNA21.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 451 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA22(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA22, DNAPKcs, Ku by freeing DNA22.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 452 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA23(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA23, DNAPKcs, Ku by freeing DNA23.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 453 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA24(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA24, DNAPKcs, Ku by freeing DNA24.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 454 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA25(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA25, DNAPKcs, Ku by freeing DNA25.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 455 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA26(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA26, DNAPKcs, Ku by freeing DNA26.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 456 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA27(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA27, DNAPKcs, Ku by freeing DNA27.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 457 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA28(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA28, DNAPKcs, Ku by freeing DNA28.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 458 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA29(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA29, DNAPKcs, Ku by freeing DNA29.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 459 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA30(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA30, DNAPKcs, Ku by freeing DNA30.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 460 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA31(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA31, DNAPKcs, Ku by freeing DNA31.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 461 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA32(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA32, DNAPKcs, Ku by freeing DNA32.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 462 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA33(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA33, DNAPKcs, Ku by freeing DNA33.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 463 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA34(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA34, DNAPKcs, Ku by freeing DNA34.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 464 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA35(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA35, DNAPKcs, Ku by freeing DNA35.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 465 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA36(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA36, DNAPKcs, Ku by freeing DNA36.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 466 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA37(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA37, DNAPKcs, Ku by freeing DNA37.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 467 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA38(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA38, DNAPKcs, Ku by freeing DNA38.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 468 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA39(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA39, DNAPKcs, Ku by freeing DNA39.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 469 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA40(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA40, DNAPKcs, Ku by freeing DNA40.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 470 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA41(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA41, DNAPKcs, Ku by freeing DNA41.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 471 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA42(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA42, DNAPKcs, Ku by freeing DNA42.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 472 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA43(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA43, DNAPKcs, Ku by freeing DNA43.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 473 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA44(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA44, DNAPKcs, Ku by freeing DNA44.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 474 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA45(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA45, DNAPKcs, Ku by freeing DNA45.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 475 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA46(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA46, DNAPKcs, Ku by freeing DNA46.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 476 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA47(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA47, DNAPKcs, Ku by freeing DNA47.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 477 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA48(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA48, DNAPKcs, Ku by freeing DNA48.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 478 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA49(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA49, DNAPKcs, Ku by freeing DNA49.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 479 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kddnapk1` | state and binding-pattern rewrite | `DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA50(site~sdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA50, DNAPKcs, Ku by freeing DNA50.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk1`. | +| 480 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA1(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA1, DNAPKcs, Ku by freeing DNA1.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 481 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA2(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA2, DNAPKcs, Ku by freeing DNA2.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 482 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA3(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA3, DNAPKcs, Ku by freeing DNA3.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 483 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA4(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA4, DNAPKcs, Ku by freeing DNA4.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 484 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA5(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA5, DNAPKcs, Ku by freeing DNA5.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 485 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA6(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA6, DNAPKcs, Ku by freeing DNA6.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 486 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA7(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA7, DNAPKcs, Ku by freeing DNA7.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 487 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA8(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA8, DNAPKcs, Ku by freeing DNA8.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 488 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA9(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA9, DNAPKcs, Ku by freeing DNA9.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 489 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA10(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA10, DNAPKcs, Ku by freeing DNA10.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 490 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA11(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA11, DNAPKcs, Ku by freeing DNA11.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 491 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA12(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA12, DNAPKcs, Ku by freeing DNA12.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 492 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA13(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA13, DNAPKcs, Ku by freeing DNA13.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 493 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA14(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA14, DNAPKcs, Ku by freeing DNA14.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 494 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA15(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA15, DNAPKcs, Ku by freeing DNA15.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 495 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA16(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA16, DNAPKcs, Ku by freeing DNA16.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 496 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA17(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA17, DNAPKcs, Ku by freeing DNA17.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 497 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA18(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA18, DNAPKcs, Ku by freeing DNA18.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 498 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA19(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA19, DNAPKcs, Ku by freeing DNA19.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 499 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA20(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA20, DNAPKcs, Ku by freeing DNA20.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 500 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA21(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA21, DNAPKcs, Ku by freeing DNA21.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | + +### Rules 501-750 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 501 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA22(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA22, DNAPKcs, Ku by freeing DNA22.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 502 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA23(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA23, DNAPKcs, Ku by freeing DNA23.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 503 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA24(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA24, DNAPKcs, Ku by freeing DNA24.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 504 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA25(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA25, DNAPKcs, Ku by freeing DNA25.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 505 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA26(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA26, DNAPKcs, Ku by freeing DNA26.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 506 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA27(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA27, DNAPKcs, Ku by freeing DNA27.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 507 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA28(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA28, DNAPKcs, Ku by freeing DNA28.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 508 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA29(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA29, DNAPKcs, Ku by freeing DNA29.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 509 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA30(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA30, DNAPKcs, Ku by freeing DNA30.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 510 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA31(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA31, DNAPKcs, Ku by freeing DNA31.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 511 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA32(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA32, DNAPKcs, Ku by freeing DNA32.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 512 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA33(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA33, DNAPKcs, Ku by freeing DNA33.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 513 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA34(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA34, DNAPKcs, Ku by freeing DNA34.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 514 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA35(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA35, DNAPKcs, Ku by freeing DNA35.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 515 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA36(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA36, DNAPKcs, Ku by freeing DNA36.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 516 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA37(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA37, DNAPKcs, Ku by freeing DNA37.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 517 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA38(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA38, DNAPKcs, Ku by freeing DNA38.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 518 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA39(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA39, DNAPKcs, Ku by freeing DNA39.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 519 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA40(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA40, DNAPKcs, Ku by freeing DNA40.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 520 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA41(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA41, DNAPKcs, Ku by freeing DNA41.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 521 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA42(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA42, DNAPKcs, Ku by freeing DNA42.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 522 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA43(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA43, DNAPKcs, Ku by freeing DNA43.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 523 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA44(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA44, DNAPKcs, Ku by freeing DNA44.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 524 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA45(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA45, DNAPKcs, Ku by freeing DNA45.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 525 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA46(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA46, DNAPKcs, Ku by freeing DNA46.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 526 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA47(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA47, DNAPKcs, Ku by freeing DNA47.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 527 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA48(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA48, DNAPKcs, Ku by freeing DNA48.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 528 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA49(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA49, DNAPKcs, Ku by freeing DNA49.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 529 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kddnapk2` | state and binding-pattern rewrite | `DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~?) -> DNA50(site~cdsb) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u)` | Releases a complex/contact among DNA50, DNAPKcs, Ku by freeing DNA50.site, DNAPKcs.ku, Ku.cs, Ku.dna at `kddnapk2`. | +| 530 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA1, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 531 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA2, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 532 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA3, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 533 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA4, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 534 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA5, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 535 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA6, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 536 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA7, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 537 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA8, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 538 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA9, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 539 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA10, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 540 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA11, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 541 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA12, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 542 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA13, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 543 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA14, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 544 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA15, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 545 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA16, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 546 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA17, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 547 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA18, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 548 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA19, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 549 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA20, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 550 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA21, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 551 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA22, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 552 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA23, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 553 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA24, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 554 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA25, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 555 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA26, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 556 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA27, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 557 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA28, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 558 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA29, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 559 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA30, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 560 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA31, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 561 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA32, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 562 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA33, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 563 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA34, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 564 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA35, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 565 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA36, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 566 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA37, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 567 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA38, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 568 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA39, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 569 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA40, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 570 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA41, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 571 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA42, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 572 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA43, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 573 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA44, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 574 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA45, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 575 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA46, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 576 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA47, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 577 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA48, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 578 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA49, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 579 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kdnapkphos1` | internal-state conversion/modification | `DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA50, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos1`. | +| 580 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA1, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 581 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA2, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 582 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA3, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 583 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA4, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 584 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA5, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 585 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA6, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 586 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA7, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 587 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA8, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 588 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA9, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 589 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA10, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 590 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA11, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 591 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA12, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 592 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA13, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 593 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA14, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 594 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA15, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 595 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA16, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 596 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA17, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 597 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA18, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 598 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA19, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 599 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA20, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 600 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA21, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 601 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA22, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 602 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA23, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 603 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA24, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 604 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA25, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 605 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA26, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 606 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA27, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 607 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA28, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 608 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA29, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 609 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA30, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 610 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA31, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 611 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA32, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 612 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA33, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 613 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA34, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 614 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA35, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 615 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA36, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 616 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA37, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 617 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA38, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 618 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA39, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 619 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA40, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 620 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA41, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 621 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA42, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 622 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA43, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 623 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA44, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 624 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA45, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 625 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA46, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 626 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA47, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 627 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA48, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 628 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA49, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 629 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kdnapkphos2` | internal-state conversion/modification | `DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~u) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA50, DNAPKcs, Ku: DNAPKcs.psite u→p at `kdnapkphos2`. | +| 630 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA1, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 631 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA2, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 632 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA3, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 633 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA4, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 634 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA5, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 635 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA6, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 636 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA7, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 637 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA8, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 638 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA9, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 639 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA10, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 640 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA11, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 641 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA12, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 642 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA13, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 643 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA14, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 644 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA15, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 645 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA16, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 646 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA17, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 647 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA18, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 648 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA19, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 649 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA20, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 650 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA21, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 651 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA22, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 652 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA23, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 653 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA24, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 654 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA25, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 655 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA26, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 656 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA27, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 657 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA28, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 658 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA29, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 659 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA30, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 660 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA31, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 661 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA32, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 662 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA33, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 663 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA34, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 664 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA35, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 665 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA36, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 666 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA37, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 667 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA38, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 668 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA39, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 669 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA40, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 670 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA41, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 671 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA42, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 672 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA43, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 673 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA44, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 674 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA45, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 675 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA46, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 676 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA47, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 677 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA48, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 678 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA49, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 679 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku, LiIV | `kliIV1` | internal-state conversion/modification | `DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA50, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV1`. | +| 680 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA1, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 681 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA2, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 682 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA3, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 683 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA4, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 684 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA5, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 685 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA6, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 686 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA7, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 687 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA8, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 688 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA9, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 689 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA10, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 690 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA11, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 691 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA12, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 692 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA13, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 693 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA14, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 694 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA15, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 695 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA16, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 696 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA17, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 697 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA18, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 698 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA19, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 699 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA20, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 700 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA21, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 701 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA22, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 702 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA23, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 703 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA24, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 704 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA25, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 705 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA26, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 706 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA27, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 707 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA28, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 708 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA29, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 709 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA30, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 710 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA31, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 711 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA32, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 712 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA33, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 713 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA34, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 714 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA35, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 715 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA36, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 716 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA37, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 717 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA38, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 718 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA39, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 719 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA40, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 720 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA41, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 721 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA42, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 722 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA43, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 723 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA44, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 724 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA45, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 725 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA46, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 726 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA47, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 727 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA48, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 728 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA49, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 729 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku, LiIV | `kliIV2` | internal-state conversion/modification | `DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3)` | Forms a complex/contact among DNA50, DNAPKcs, Ku, LiIV through DNAPKcs.liIV, LiIV.cs at `kliIV2`. | +| 730 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA1(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA1, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 731 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA2(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA2, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 732 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA3(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA3, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 733 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA4(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA4, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 734 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA5(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA5, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 735 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA6(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA6, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 736 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA7(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA7, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 737 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA8(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA8, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 738 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA9(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA9, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 739 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA10(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA10, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 740 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA11(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA11, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 741 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA12(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA12, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 742 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA13(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA13, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 743 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA14(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA14, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 744 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA15(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA15, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 745 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA16(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA16, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 746 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA17(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA17, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 747 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA18(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA18, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 748 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA19(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA19, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 749 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA20(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA20, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 750 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA21(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA21, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | + +### Rules 751-1000 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 751 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA22(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA22, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 752 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA23(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA23, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 753 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA24(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA24, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 754 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA25(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA25, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 755 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA26(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA26, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 756 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA27(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA27, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 757 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA28(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA28, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 758 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA29(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA29, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 759 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA30(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA30, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 760 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA31(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA31, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 761 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA32(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA32, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 762 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA33(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA33, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 763 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA34(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA34, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 764 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA35(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA35, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 765 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA36(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA36, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 766 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA37(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA37, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 767 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA38(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA38, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 768 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA39(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA39, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 769 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA40(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA40, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 770 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA41(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA41, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 771 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA42(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA42, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 772 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA43(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA43, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 773 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA44(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA44, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 774 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA45(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA45, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 775 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA46(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA46, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 776 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA47(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA47, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 777 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA48(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA48, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 778 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA49(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA49, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 779 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku, LiIV | `kdliIV1` | internal-state conversion/modification | `DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA50(site!1~sdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA50, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV1`. | +| 780 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA1(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA1, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 781 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA2(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA2, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 782 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA3(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA3, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 783 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA4(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA4, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 784 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA5(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA5, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 785 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA6(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA6, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 786 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA7(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA7, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 787 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA8(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA8, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 788 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA9(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA9, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 789 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA10(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA10, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 790 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA11(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA11, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 791 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA12(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA12, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 792 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA13(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA13, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 793 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA14(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA14, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 794 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA15(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA15, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 795 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA16(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA16, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 796 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA17(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA17, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 797 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA18(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA18, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 798 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA19(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA19, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 799 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA20(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA20, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 800 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA21(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA21, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 801 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA22(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA22, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 802 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA23(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA23, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 803 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA24(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA24, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 804 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA25(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA25, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 805 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA26(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA26, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 806 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA27(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA27, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 807 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA28(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA28, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 808 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA29(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA29, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 809 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA30(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA30, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 810 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA31(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA31, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 811 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA32(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA32, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 812 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA33(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA33, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 813 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA34(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA34, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 814 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA35(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA35, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 815 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA36(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA36, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 816 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA37(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA37, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 817 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA38(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA38, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 818 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA39(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA39, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 819 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA40(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA40, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 820 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA41(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA41, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 821 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA42(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA42, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 822 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA43(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA43, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 823 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA44(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA44, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 824 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA45(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA45, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 825 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA46(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA46, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 826 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA47(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA47, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 827 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA48(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA48, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 828 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA49(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA49, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 829 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku, LiIV | `kdliIV2` | internal-state conversion/modification | `DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3) -> DNA50(site!1~cdsb).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) + LiIV(cs)` | Releases a complex/contact among DNA50, DNAPKcs, Ku, LiIV by freeing DNAPKcs.liIV, LiIV.cs at `kdliIV2`. | +| 830 | `Unlabeled` | one-way | ATM, DNA1, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA1(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA1.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 831 | `Unlabeled` | one-way | ATM, DNA2, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA2(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA2.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 832 | `Unlabeled` | one-way | ATM, DNA3, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA3(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA3.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 833 | `Unlabeled` | one-way | ATM, DNA4, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA4(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA4.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 834 | `Unlabeled` | one-way | ATM, DNA5, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA5(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA5.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 835 | `Unlabeled` | one-way | ATM, DNA6, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA6(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA6.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 836 | `Unlabeled` | one-way | ATM, DNA7, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA7(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA7.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 837 | `Unlabeled` | one-way | ATM, DNA8, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA8(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA8.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 838 | `Unlabeled` | one-way | ATM, DNA9, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA9(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA9.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 839 | `Unlabeled` | one-way | ATM, DNA10, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA10(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA10.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 840 | `Unlabeled` | one-way | ATM, DNA11, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA11(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA11.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 841 | `Unlabeled` | one-way | ATM, DNA12, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA12(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA12.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 842 | `Unlabeled` | one-way | ATM, DNA13, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA13(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA13.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 843 | `Unlabeled` | one-way | ATM, DNA14, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA14(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA14.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 844 | `Unlabeled` | one-way | ATM, DNA15, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA15(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA15.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 845 | `Unlabeled` | one-way | ATM, DNA16, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA16(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA16.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 846 | `Unlabeled` | one-way | ATM, DNA17, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA17(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA17.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 847 | `Unlabeled` | one-way | ATM, DNA18, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA18(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA18.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 848 | `Unlabeled` | one-way | ATM, DNA19, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA19(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA19.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 849 | `Unlabeled` | one-way | ATM, DNA20, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA20(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA20.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 850 | `Unlabeled` | one-way | ATM, DNA21, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA21(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA21.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 851 | `Unlabeled` | one-way | ATM, DNA22, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA22(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA22.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 852 | `Unlabeled` | one-way | ATM, DNA23, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA23(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA23.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 853 | `Unlabeled` | one-way | ATM, DNA24, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA24(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA24.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 854 | `Unlabeled` | one-way | ATM, DNA25, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA25(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA25.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 855 | `Unlabeled` | one-way | ATM, DNA26, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA26(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA26.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 856 | `Unlabeled` | one-way | ATM, DNA27, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA27(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA27.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 857 | `Unlabeled` | one-way | ATM, DNA28, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA28(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA28.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 858 | `Unlabeled` | one-way | ATM, DNA29, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA29(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA29.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 859 | `Unlabeled` | one-way | ATM, DNA30, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA30(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA30.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 860 | `Unlabeled` | one-way | ATM, DNA31, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA31(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA31.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 861 | `Unlabeled` | one-way | ATM, DNA32, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA32(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA32.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 862 | `Unlabeled` | one-way | ATM, DNA33, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA33(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA33.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 863 | `Unlabeled` | one-way | ATM, DNA34, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA34(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA34.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 864 | `Unlabeled` | one-way | ATM, DNA35, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA35(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA35.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 865 | `Unlabeled` | one-way | ATM, DNA36, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA36(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA36.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 866 | `Unlabeled` | one-way | ATM, DNA37, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA37(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA37.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 867 | `Unlabeled` | one-way | ATM, DNA38, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA38(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA38.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 868 | `Unlabeled` | one-way | ATM, DNA39, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA39(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA39.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 869 | `Unlabeled` | one-way | ATM, DNA40, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA40(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA40.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 870 | `Unlabeled` | one-way | ATM, DNA41, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA41(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA41.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 871 | `Unlabeled` | one-way | ATM, DNA42, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA42(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA42.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 872 | `Unlabeled` | one-way | ATM, DNA43, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA43(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA43.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 873 | `Unlabeled` | one-way | ATM, DNA44, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA44(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA44.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 874 | `Unlabeled` | one-way | ATM, DNA45, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA45(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA45.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 875 | `Unlabeled` | one-way | ATM, DNA46, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA46(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA46.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 876 | `Unlabeled` | one-way | ATM, DNA47, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA47(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA47.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 877 | `Unlabeled` | one-way | ATM, DNA48, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA48(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA48.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 878 | `Unlabeled` | one-way | ATM, DNA49, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA49(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA49.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 879 | `Unlabeled` | one-way | ATM, DNA50, DNAPKcs, Ku, LiIV | `kfixIV1` | internal-state conversion/modification | `DNA50(site!1~sdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA50.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV1`. | +| 880 | `Unlabeled` | one-way | ATM, DNA1, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA1(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA1.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 881 | `Unlabeled` | one-way | ATM, DNA2, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA2(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA2.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 882 | `Unlabeled` | one-way | ATM, DNA3, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA3(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA3.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 883 | `Unlabeled` | one-way | ATM, DNA4, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA4(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA4.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 884 | `Unlabeled` | one-way | ATM, DNA5, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA5(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA5.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 885 | `Unlabeled` | one-way | ATM, DNA6, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA6(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA6.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 886 | `Unlabeled` | one-way | ATM, DNA7, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA7(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA7.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 887 | `Unlabeled` | one-way | ATM, DNA8, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA8(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA8.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 888 | `Unlabeled` | one-way | ATM, DNA9, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA9(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA9.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 889 | `Unlabeled` | one-way | ATM, DNA10, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA10(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA10.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 890 | `Unlabeled` | one-way | ATM, DNA11, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA11(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA11.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 891 | `Unlabeled` | one-way | ATM, DNA12, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA12(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA12.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 892 | `Unlabeled` | one-way | ATM, DNA13, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA13(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA13.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 893 | `Unlabeled` | one-way | ATM, DNA14, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA14(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA14.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 894 | `Unlabeled` | one-way | ATM, DNA15, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA15(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA15.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 895 | `Unlabeled` | one-way | ATM, DNA16, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA16(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA16.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 896 | `Unlabeled` | one-way | ATM, DNA17, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA17(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA17.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 897 | `Unlabeled` | one-way | ATM, DNA18, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA18(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA18.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 898 | `Unlabeled` | one-way | ATM, DNA19, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA19(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA19.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 899 | `Unlabeled` | one-way | ATM, DNA20, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA20(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA20.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 900 | `Unlabeled` | one-way | ATM, DNA21, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA21(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA21.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 901 | `Unlabeled` | one-way | ATM, DNA22, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA22(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA22.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 902 | `Unlabeled` | one-way | ATM, DNA23, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA23(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA23.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 903 | `Unlabeled` | one-way | ATM, DNA24, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA24(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA24.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 904 | `Unlabeled` | one-way | ATM, DNA25, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA25(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA25.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 905 | `Unlabeled` | one-way | ATM, DNA26, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA26(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA26.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 906 | `Unlabeled` | one-way | ATM, DNA27, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA27(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA27.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 907 | `Unlabeled` | one-way | ATM, DNA28, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA28(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA28.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 908 | `Unlabeled` | one-way | ATM, DNA29, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA29(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA29.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 909 | `Unlabeled` | one-way | ATM, DNA30, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA30(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA30.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 910 | `Unlabeled` | one-way | ATM, DNA31, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA31(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA31.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 911 | `Unlabeled` | one-way | ATM, DNA32, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA32(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA32.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 912 | `Unlabeled` | one-way | ATM, DNA33, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA33(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA33.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 913 | `Unlabeled` | one-way | ATM, DNA34, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA34(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA34.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 914 | `Unlabeled` | one-way | ATM, DNA35, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA35(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA35.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 915 | `Unlabeled` | one-way | ATM, DNA36, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA36(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA36.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 916 | `Unlabeled` | one-way | ATM, DNA37, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA37(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA37.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 917 | `Unlabeled` | one-way | ATM, DNA38, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA38(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA38.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 918 | `Unlabeled` | one-way | ATM, DNA39, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA39(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA39.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 919 | `Unlabeled` | one-way | ATM, DNA40, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA40(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA40.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 920 | `Unlabeled` | one-way | ATM, DNA41, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA41(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA41.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 921 | `Unlabeled` | one-way | ATM, DNA42, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA42(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA42.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 922 | `Unlabeled` | one-way | ATM, DNA43, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA43(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA43.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 923 | `Unlabeled` | one-way | ATM, DNA44, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA44(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA44.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 924 | `Unlabeled` | one-way | ATM, DNA45, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA45(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA45.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 925 | `Unlabeled` | one-way | ATM, DNA46, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA46(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA46.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 926 | `Unlabeled` | one-way | ATM, DNA47, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA47(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA47.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 927 | `Unlabeled` | one-way | ATM, DNA48, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA48(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA48.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 928 | `Unlabeled` | one-way | ATM, DNA49, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA49(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA49.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 929 | `Unlabeled` | one-way | ATM, DNA50, DNAPKcs, Ku, LiIV | `kfixIV2` | internal-state conversion/modification | `DNA50(site!1~cdsb,h2ax!4~foc).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV!3,psite~p).LiIV(cs!3).ATM(h2ax!4) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + Ku(dna,cs) + DNAPKcs(ku,liIV,psite~u) + LiIV(cs)` | Couples site-state changes (DNAPKcs.psite p→u) with binding-site changes (removes DNA50.site, DNAPKcs.ku, DNAPKcs.liIV, Ku.cs, Ku.dna, LiIV.cs) at `kfixIV2`. | +| 930 | `Unlabeled` | one-way | DNA1, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA1(site~sdsb) + PARP(dna,liIII) -> DNA1(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA1, PARP through DNA1.site, PARP.dna at `kPARP1`. | +| 931 | `Unlabeled` | one-way | DNA2, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA2(site~sdsb) + PARP(dna,liIII) -> DNA2(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA2, PARP through DNA2.site, PARP.dna at `kPARP1`. | +| 932 | `Unlabeled` | one-way | DNA3, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA3(site~sdsb) + PARP(dna,liIII) -> DNA3(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA3, PARP through DNA3.site, PARP.dna at `kPARP1`. | +| 933 | `Unlabeled` | one-way | DNA4, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA4(site~sdsb) + PARP(dna,liIII) -> DNA4(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA4, PARP through DNA4.site, PARP.dna at `kPARP1`. | +| 934 | `Unlabeled` | one-way | DNA5, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA5(site~sdsb) + PARP(dna,liIII) -> DNA5(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA5, PARP through DNA5.site, PARP.dna at `kPARP1`. | +| 935 | `Unlabeled` | one-way | DNA6, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA6(site~sdsb) + PARP(dna,liIII) -> DNA6(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA6, PARP through DNA6.site, PARP.dna at `kPARP1`. | +| 936 | `Unlabeled` | one-way | DNA7, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA7(site~sdsb) + PARP(dna,liIII) -> DNA7(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA7, PARP through DNA7.site, PARP.dna at `kPARP1`. | +| 937 | `Unlabeled` | one-way | DNA8, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA8(site~sdsb) + PARP(dna,liIII) -> DNA8(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA8, PARP through DNA8.site, PARP.dna at `kPARP1`. | +| 938 | `Unlabeled` | one-way | DNA9, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA9(site~sdsb) + PARP(dna,liIII) -> DNA9(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA9, PARP through DNA9.site, PARP.dna at `kPARP1`. | +| 939 | `Unlabeled` | one-way | DNA10, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA10(site~sdsb) + PARP(dna,liIII) -> DNA10(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA10, PARP through DNA10.site, PARP.dna at `kPARP1`. | +| 940 | `Unlabeled` | one-way | DNA11, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA11(site~sdsb) + PARP(dna,liIII) -> DNA11(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA11, PARP through DNA11.site, PARP.dna at `kPARP1`. | +| 941 | `Unlabeled` | one-way | DNA12, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA12(site~sdsb) + PARP(dna,liIII) -> DNA12(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA12, PARP through DNA12.site, PARP.dna at `kPARP1`. | +| 942 | `Unlabeled` | one-way | DNA13, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA13(site~sdsb) + PARP(dna,liIII) -> DNA13(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA13, PARP through DNA13.site, PARP.dna at `kPARP1`. | +| 943 | `Unlabeled` | one-way | DNA14, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA14(site~sdsb) + PARP(dna,liIII) -> DNA14(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA14, PARP through DNA14.site, PARP.dna at `kPARP1`. | +| 944 | `Unlabeled` | one-way | DNA15, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA15(site~sdsb) + PARP(dna,liIII) -> DNA15(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA15, PARP through DNA15.site, PARP.dna at `kPARP1`. | +| 945 | `Unlabeled` | one-way | DNA16, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA16(site~sdsb) + PARP(dna,liIII) -> DNA16(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA16, PARP through DNA16.site, PARP.dna at `kPARP1`. | +| 946 | `Unlabeled` | one-way | DNA17, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA17(site~sdsb) + PARP(dna,liIII) -> DNA17(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA17, PARP through DNA17.site, PARP.dna at `kPARP1`. | +| 947 | `Unlabeled` | one-way | DNA18, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA18(site~sdsb) + PARP(dna,liIII) -> DNA18(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA18, PARP through DNA18.site, PARP.dna at `kPARP1`. | +| 948 | `Unlabeled` | one-way | DNA19, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA19(site~sdsb) + PARP(dna,liIII) -> DNA19(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA19, PARP through DNA19.site, PARP.dna at `kPARP1`. | +| 949 | `Unlabeled` | one-way | DNA20, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA20(site~sdsb) + PARP(dna,liIII) -> DNA20(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA20, PARP through DNA20.site, PARP.dna at `kPARP1`. | +| 950 | `Unlabeled` | one-way | DNA21, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA21(site~sdsb) + PARP(dna,liIII) -> DNA21(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA21, PARP through DNA21.site, PARP.dna at `kPARP1`. | +| 951 | `Unlabeled` | one-way | DNA22, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA22(site~sdsb) + PARP(dna,liIII) -> DNA22(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA22, PARP through DNA22.site, PARP.dna at `kPARP1`. | +| 952 | `Unlabeled` | one-way | DNA23, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA23(site~sdsb) + PARP(dna,liIII) -> DNA23(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA23, PARP through DNA23.site, PARP.dna at `kPARP1`. | +| 953 | `Unlabeled` | one-way | DNA24, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA24(site~sdsb) + PARP(dna,liIII) -> DNA24(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA24, PARP through DNA24.site, PARP.dna at `kPARP1`. | +| 954 | `Unlabeled` | one-way | DNA25, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA25(site~sdsb) + PARP(dna,liIII) -> DNA25(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA25, PARP through DNA25.site, PARP.dna at `kPARP1`. | +| 955 | `Unlabeled` | one-way | DNA26, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA26(site~sdsb) + PARP(dna,liIII) -> DNA26(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA26, PARP through DNA26.site, PARP.dna at `kPARP1`. | +| 956 | `Unlabeled` | one-way | DNA27, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA27(site~sdsb) + PARP(dna,liIII) -> DNA27(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA27, PARP through DNA27.site, PARP.dna at `kPARP1`. | +| 957 | `Unlabeled` | one-way | DNA28, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA28(site~sdsb) + PARP(dna,liIII) -> DNA28(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA28, PARP through DNA28.site, PARP.dna at `kPARP1`. | +| 958 | `Unlabeled` | one-way | DNA29, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA29(site~sdsb) + PARP(dna,liIII) -> DNA29(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA29, PARP through DNA29.site, PARP.dna at `kPARP1`. | +| 959 | `Unlabeled` | one-way | DNA30, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA30(site~sdsb) + PARP(dna,liIII) -> DNA30(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA30, PARP through DNA30.site, PARP.dna at `kPARP1`. | +| 960 | `Unlabeled` | one-way | DNA31, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA31(site~sdsb) + PARP(dna,liIII) -> DNA31(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA31, PARP through DNA31.site, PARP.dna at `kPARP1`. | +| 961 | `Unlabeled` | one-way | DNA32, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA32(site~sdsb) + PARP(dna,liIII) -> DNA32(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA32, PARP through DNA32.site, PARP.dna at `kPARP1`. | +| 962 | `Unlabeled` | one-way | DNA33, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA33(site~sdsb) + PARP(dna,liIII) -> DNA33(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA33, PARP through DNA33.site, PARP.dna at `kPARP1`. | +| 963 | `Unlabeled` | one-way | DNA34, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA34(site~sdsb) + PARP(dna,liIII) -> DNA34(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA34, PARP through DNA34.site, PARP.dna at `kPARP1`. | +| 964 | `Unlabeled` | one-way | DNA35, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA35(site~sdsb) + PARP(dna,liIII) -> DNA35(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA35, PARP through DNA35.site, PARP.dna at `kPARP1`. | +| 965 | `Unlabeled` | one-way | DNA36, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA36(site~sdsb) + PARP(dna,liIII) -> DNA36(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA36, PARP through DNA36.site, PARP.dna at `kPARP1`. | +| 966 | `Unlabeled` | one-way | DNA37, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA37(site~sdsb) + PARP(dna,liIII) -> DNA37(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA37, PARP through DNA37.site, PARP.dna at `kPARP1`. | +| 967 | `Unlabeled` | one-way | DNA38, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA38(site~sdsb) + PARP(dna,liIII) -> DNA38(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA38, PARP through DNA38.site, PARP.dna at `kPARP1`. | +| 968 | `Unlabeled` | one-way | DNA39, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA39(site~sdsb) + PARP(dna,liIII) -> DNA39(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA39, PARP through DNA39.site, PARP.dna at `kPARP1`. | +| 969 | `Unlabeled` | one-way | DNA40, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA40(site~sdsb) + PARP(dna,liIII) -> DNA40(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA40, PARP through DNA40.site, PARP.dna at `kPARP1`. | +| 970 | `Unlabeled` | one-way | DNA41, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA41(site~sdsb) + PARP(dna,liIII) -> DNA41(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA41, PARP through DNA41.site, PARP.dna at `kPARP1`. | +| 971 | `Unlabeled` | one-way | DNA42, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA42(site~sdsb) + PARP(dna,liIII) -> DNA42(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA42, PARP through DNA42.site, PARP.dna at `kPARP1`. | +| 972 | `Unlabeled` | one-way | DNA43, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA43(site~sdsb) + PARP(dna,liIII) -> DNA43(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA43, PARP through DNA43.site, PARP.dna at `kPARP1`. | +| 973 | `Unlabeled` | one-way | DNA44, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA44(site~sdsb) + PARP(dna,liIII) -> DNA44(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA44, PARP through DNA44.site, PARP.dna at `kPARP1`. | +| 974 | `Unlabeled` | one-way | DNA45, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA45(site~sdsb) + PARP(dna,liIII) -> DNA45(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA45, PARP through DNA45.site, PARP.dna at `kPARP1`. | +| 975 | `Unlabeled` | one-way | DNA46, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA46(site~sdsb) + PARP(dna,liIII) -> DNA46(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA46, PARP through DNA46.site, PARP.dna at `kPARP1`. | +| 976 | `Unlabeled` | one-way | DNA47, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA47(site~sdsb) + PARP(dna,liIII) -> DNA47(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA47, PARP through DNA47.site, PARP.dna at `kPARP1`. | +| 977 | `Unlabeled` | one-way | DNA48, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA48(site~sdsb) + PARP(dna,liIII) -> DNA48(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA48, PARP through DNA48.site, PARP.dna at `kPARP1`. | +| 978 | `Unlabeled` | one-way | DNA49, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA49(site~sdsb) + PARP(dna,liIII) -> DNA49(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA49, PARP through DNA49.site, PARP.dna at `kPARP1`. | +| 979 | `Unlabeled` | one-way | DNA50, PARP | `kPARP1` | state and binding-pattern rewrite | `DNA50(site~sdsb) + PARP(dna,liIII) -> DNA50(site!1~sdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA50, PARP through DNA50.site, PARP.dna at `kPARP1`. | +| 980 | `Unlabeled` | one-way | DNA1, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA1(site~cdsb) + PARP(dna,liIII) -> DNA1(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA1, PARP through DNA1.site, PARP.dna at `kPARP2`. | +| 981 | `Unlabeled` | one-way | DNA2, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA2(site~cdsb) + PARP(dna,liIII) -> DNA2(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA2, PARP through DNA2.site, PARP.dna at `kPARP2`. | +| 982 | `Unlabeled` | one-way | DNA3, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA3(site~cdsb) + PARP(dna,liIII) -> DNA3(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA3, PARP through DNA3.site, PARP.dna at `kPARP2`. | +| 983 | `Unlabeled` | one-way | DNA4, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA4(site~cdsb) + PARP(dna,liIII) -> DNA4(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA4, PARP through DNA4.site, PARP.dna at `kPARP2`. | +| 984 | `Unlabeled` | one-way | DNA5, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA5(site~cdsb) + PARP(dna,liIII) -> DNA5(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA5, PARP through DNA5.site, PARP.dna at `kPARP2`. | +| 985 | `Unlabeled` | one-way | DNA6, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA6(site~cdsb) + PARP(dna,liIII) -> DNA6(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA6, PARP through DNA6.site, PARP.dna at `kPARP2`. | +| 986 | `Unlabeled` | one-way | DNA7, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA7(site~cdsb) + PARP(dna,liIII) -> DNA7(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA7, PARP through DNA7.site, PARP.dna at `kPARP2`. | +| 987 | `Unlabeled` | one-way | DNA8, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA8(site~cdsb) + PARP(dna,liIII) -> DNA8(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA8, PARP through DNA8.site, PARP.dna at `kPARP2`. | +| 988 | `Unlabeled` | one-way | DNA9, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA9(site~cdsb) + PARP(dna,liIII) -> DNA9(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA9, PARP through DNA9.site, PARP.dna at `kPARP2`. | +| 989 | `Unlabeled` | one-way | DNA10, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA10(site~cdsb) + PARP(dna,liIII) -> DNA10(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA10, PARP through DNA10.site, PARP.dna at `kPARP2`. | +| 990 | `Unlabeled` | one-way | DNA11, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA11(site~cdsb) + PARP(dna,liIII) -> DNA11(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA11, PARP through DNA11.site, PARP.dna at `kPARP2`. | +| 991 | `Unlabeled` | one-way | DNA12, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA12(site~cdsb) + PARP(dna,liIII) -> DNA12(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA12, PARP through DNA12.site, PARP.dna at `kPARP2`. | +| 992 | `Unlabeled` | one-way | DNA13, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA13(site~cdsb) + PARP(dna,liIII) -> DNA13(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA13, PARP through DNA13.site, PARP.dna at `kPARP2`. | +| 993 | `Unlabeled` | one-way | DNA14, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA14(site~cdsb) + PARP(dna,liIII) -> DNA14(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA14, PARP through DNA14.site, PARP.dna at `kPARP2`. | +| 994 | `Unlabeled` | one-way | DNA15, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA15(site~cdsb) + PARP(dna,liIII) -> DNA15(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA15, PARP through DNA15.site, PARP.dna at `kPARP2`. | +| 995 | `Unlabeled` | one-way | DNA16, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA16(site~cdsb) + PARP(dna,liIII) -> DNA16(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA16, PARP through DNA16.site, PARP.dna at `kPARP2`. | +| 996 | `Unlabeled` | one-way | DNA17, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA17(site~cdsb) + PARP(dna,liIII) -> DNA17(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA17, PARP through DNA17.site, PARP.dna at `kPARP2`. | +| 997 | `Unlabeled` | one-way | DNA18, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA18(site~cdsb) + PARP(dna,liIII) -> DNA18(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA18, PARP through DNA18.site, PARP.dna at `kPARP2`. | +| 998 | `Unlabeled` | one-way | DNA19, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA19(site~cdsb) + PARP(dna,liIII) -> DNA19(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA19, PARP through DNA19.site, PARP.dna at `kPARP2`. | +| 999 | `Unlabeled` | one-way | DNA20, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA20(site~cdsb) + PARP(dna,liIII) -> DNA20(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA20, PARP through DNA20.site, PARP.dna at `kPARP2`. | +| 1000 | `Unlabeled` | one-way | DNA21, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA21(site~cdsb) + PARP(dna,liIII) -> DNA21(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA21, PARP through DNA21.site, PARP.dna at `kPARP2`. | + +### Rules 1001-1250 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1001 | `Unlabeled` | one-way | DNA22, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA22(site~cdsb) + PARP(dna,liIII) -> DNA22(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA22, PARP through DNA22.site, PARP.dna at `kPARP2`. | +| 1002 | `Unlabeled` | one-way | DNA23, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA23(site~cdsb) + PARP(dna,liIII) -> DNA23(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA23, PARP through DNA23.site, PARP.dna at `kPARP2`. | +| 1003 | `Unlabeled` | one-way | DNA24, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA24(site~cdsb) + PARP(dna,liIII) -> DNA24(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA24, PARP through DNA24.site, PARP.dna at `kPARP2`. | +| 1004 | `Unlabeled` | one-way | DNA25, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA25(site~cdsb) + PARP(dna,liIII) -> DNA25(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA25, PARP through DNA25.site, PARP.dna at `kPARP2`. | +| 1005 | `Unlabeled` | one-way | DNA26, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA26(site~cdsb) + PARP(dna,liIII) -> DNA26(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA26, PARP through DNA26.site, PARP.dna at `kPARP2`. | +| 1006 | `Unlabeled` | one-way | DNA27, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA27(site~cdsb) + PARP(dna,liIII) -> DNA27(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA27, PARP through DNA27.site, PARP.dna at `kPARP2`. | +| 1007 | `Unlabeled` | one-way | DNA28, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA28(site~cdsb) + PARP(dna,liIII) -> DNA28(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA28, PARP through DNA28.site, PARP.dna at `kPARP2`. | +| 1008 | `Unlabeled` | one-way | DNA29, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA29(site~cdsb) + PARP(dna,liIII) -> DNA29(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA29, PARP through DNA29.site, PARP.dna at `kPARP2`. | +| 1009 | `Unlabeled` | one-way | DNA30, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA30(site~cdsb) + PARP(dna,liIII) -> DNA30(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA30, PARP through DNA30.site, PARP.dna at `kPARP2`. | +| 1010 | `Unlabeled` | one-way | DNA31, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA31(site~cdsb) + PARP(dna,liIII) -> DNA31(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA31, PARP through DNA31.site, PARP.dna at `kPARP2`. | +| 1011 | `Unlabeled` | one-way | DNA32, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA32(site~cdsb) + PARP(dna,liIII) -> DNA32(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA32, PARP through DNA32.site, PARP.dna at `kPARP2`. | +| 1012 | `Unlabeled` | one-way | DNA33, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA33(site~cdsb) + PARP(dna,liIII) -> DNA33(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA33, PARP through DNA33.site, PARP.dna at `kPARP2`. | +| 1013 | `Unlabeled` | one-way | DNA34, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA34(site~cdsb) + PARP(dna,liIII) -> DNA34(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA34, PARP through DNA34.site, PARP.dna at `kPARP2`. | +| 1014 | `Unlabeled` | one-way | DNA35, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA35(site~cdsb) + PARP(dna,liIII) -> DNA35(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA35, PARP through DNA35.site, PARP.dna at `kPARP2`. | +| 1015 | `Unlabeled` | one-way | DNA36, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA36(site~cdsb) + PARP(dna,liIII) -> DNA36(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA36, PARP through DNA36.site, PARP.dna at `kPARP2`. | +| 1016 | `Unlabeled` | one-way | DNA37, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA37(site~cdsb) + PARP(dna,liIII) -> DNA37(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA37, PARP through DNA37.site, PARP.dna at `kPARP2`. | +| 1017 | `Unlabeled` | one-way | DNA38, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA38(site~cdsb) + PARP(dna,liIII) -> DNA38(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA38, PARP through DNA38.site, PARP.dna at `kPARP2`. | +| 1018 | `Unlabeled` | one-way | DNA39, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA39(site~cdsb) + PARP(dna,liIII) -> DNA39(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA39, PARP through DNA39.site, PARP.dna at `kPARP2`. | +| 1019 | `Unlabeled` | one-way | DNA40, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA40(site~cdsb) + PARP(dna,liIII) -> DNA40(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA40, PARP through DNA40.site, PARP.dna at `kPARP2`. | +| 1020 | `Unlabeled` | one-way | DNA41, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA41(site~cdsb) + PARP(dna,liIII) -> DNA41(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA41, PARP through DNA41.site, PARP.dna at `kPARP2`. | +| 1021 | `Unlabeled` | one-way | DNA42, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA42(site~cdsb) + PARP(dna,liIII) -> DNA42(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA42, PARP through DNA42.site, PARP.dna at `kPARP2`. | +| 1022 | `Unlabeled` | one-way | DNA43, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA43(site~cdsb) + PARP(dna,liIII) -> DNA43(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA43, PARP through DNA43.site, PARP.dna at `kPARP2`. | +| 1023 | `Unlabeled` | one-way | DNA44, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA44(site~cdsb) + PARP(dna,liIII) -> DNA44(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA44, PARP through DNA44.site, PARP.dna at `kPARP2`. | +| 1024 | `Unlabeled` | one-way | DNA45, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA45(site~cdsb) + PARP(dna,liIII) -> DNA45(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA45, PARP through DNA45.site, PARP.dna at `kPARP2`. | +| 1025 | `Unlabeled` | one-way | DNA46, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA46(site~cdsb) + PARP(dna,liIII) -> DNA46(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA46, PARP through DNA46.site, PARP.dna at `kPARP2`. | +| 1026 | `Unlabeled` | one-way | DNA47, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA47(site~cdsb) + PARP(dna,liIII) -> DNA47(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA47, PARP through DNA47.site, PARP.dna at `kPARP2`. | +| 1027 | `Unlabeled` | one-way | DNA48, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA48(site~cdsb) + PARP(dna,liIII) -> DNA48(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA48, PARP through DNA48.site, PARP.dna at `kPARP2`. | +| 1028 | `Unlabeled` | one-way | DNA49, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA49(site~cdsb) + PARP(dna,liIII) -> DNA49(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA49, PARP through DNA49.site, PARP.dna at `kPARP2`. | +| 1029 | `Unlabeled` | one-way | DNA50, PARP | `kPARP2` | state and binding-pattern rewrite | `DNA50(site~cdsb) + PARP(dna,liIII) -> DNA50(site!1~cdsb).PARP(dna!1,liIII)` | Forms a complex/contact among DNA50, PARP through DNA50.site, PARP.dna at `kPARP2`. | +| 1030 | `Unlabeled` | one-way | DNA1, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA1(site!1~sdsb).PARP(dna!1,liIII) -> DNA1(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA1, PARP by freeing DNA1.site, PARP.dna at `kdPARP1`. | +| 1031 | `Unlabeled` | one-way | DNA2, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA2(site!1~sdsb).PARP(dna!1,liIII) -> DNA2(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA2, PARP by freeing DNA2.site, PARP.dna at `kdPARP1`. | +| 1032 | `Unlabeled` | one-way | DNA3, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA3(site!1~sdsb).PARP(dna!1,liIII) -> DNA3(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA3, PARP by freeing DNA3.site, PARP.dna at `kdPARP1`. | +| 1033 | `Unlabeled` | one-way | DNA4, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA4(site!1~sdsb).PARP(dna!1,liIII) -> DNA4(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA4, PARP by freeing DNA4.site, PARP.dna at `kdPARP1`. | +| 1034 | `Unlabeled` | one-way | DNA5, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA5(site!1~sdsb).PARP(dna!1,liIII) -> DNA5(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA5, PARP by freeing DNA5.site, PARP.dna at `kdPARP1`. | +| 1035 | `Unlabeled` | one-way | DNA6, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA6(site!1~sdsb).PARP(dna!1,liIII) -> DNA6(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA6, PARP by freeing DNA6.site, PARP.dna at `kdPARP1`. | +| 1036 | `Unlabeled` | one-way | DNA7, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA7(site!1~sdsb).PARP(dna!1,liIII) -> DNA7(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA7, PARP by freeing DNA7.site, PARP.dna at `kdPARP1`. | +| 1037 | `Unlabeled` | one-way | DNA8, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA8(site!1~sdsb).PARP(dna!1,liIII) -> DNA8(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA8, PARP by freeing DNA8.site, PARP.dna at `kdPARP1`. | +| 1038 | `Unlabeled` | one-way | DNA9, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA9(site!1~sdsb).PARP(dna!1,liIII) -> DNA9(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA9, PARP by freeing DNA9.site, PARP.dna at `kdPARP1`. | +| 1039 | `Unlabeled` | one-way | DNA10, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA10(site!1~sdsb).PARP(dna!1,liIII) -> DNA10(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA10, PARP by freeing DNA10.site, PARP.dna at `kdPARP1`. | +| 1040 | `Unlabeled` | one-way | DNA11, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA11(site!1~sdsb).PARP(dna!1,liIII) -> DNA11(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA11, PARP by freeing DNA11.site, PARP.dna at `kdPARP1`. | +| 1041 | `Unlabeled` | one-way | DNA12, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA12(site!1~sdsb).PARP(dna!1,liIII) -> DNA12(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA12, PARP by freeing DNA12.site, PARP.dna at `kdPARP1`. | +| 1042 | `Unlabeled` | one-way | DNA13, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA13(site!1~sdsb).PARP(dna!1,liIII) -> DNA13(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA13, PARP by freeing DNA13.site, PARP.dna at `kdPARP1`. | +| 1043 | `Unlabeled` | one-way | DNA14, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA14(site!1~sdsb).PARP(dna!1,liIII) -> DNA14(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA14, PARP by freeing DNA14.site, PARP.dna at `kdPARP1`. | +| 1044 | `Unlabeled` | one-way | DNA15, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA15(site!1~sdsb).PARP(dna!1,liIII) -> DNA15(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA15, PARP by freeing DNA15.site, PARP.dna at `kdPARP1`. | +| 1045 | `Unlabeled` | one-way | DNA16, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA16(site!1~sdsb).PARP(dna!1,liIII) -> DNA16(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA16, PARP by freeing DNA16.site, PARP.dna at `kdPARP1`. | +| 1046 | `Unlabeled` | one-way | DNA17, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA17(site!1~sdsb).PARP(dna!1,liIII) -> DNA17(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA17, PARP by freeing DNA17.site, PARP.dna at `kdPARP1`. | +| 1047 | `Unlabeled` | one-way | DNA18, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA18(site!1~sdsb).PARP(dna!1,liIII) -> DNA18(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA18, PARP by freeing DNA18.site, PARP.dna at `kdPARP1`. | +| 1048 | `Unlabeled` | one-way | DNA19, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA19(site!1~sdsb).PARP(dna!1,liIII) -> DNA19(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA19, PARP by freeing DNA19.site, PARP.dna at `kdPARP1`. | +| 1049 | `Unlabeled` | one-way | DNA20, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA20(site!1~sdsb).PARP(dna!1,liIII) -> DNA20(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA20, PARP by freeing DNA20.site, PARP.dna at `kdPARP1`. | +| 1050 | `Unlabeled` | one-way | DNA21, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA21(site!1~sdsb).PARP(dna!1,liIII) -> DNA21(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA21, PARP by freeing DNA21.site, PARP.dna at `kdPARP1`. | +| 1051 | `Unlabeled` | one-way | DNA22, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA22(site!1~sdsb).PARP(dna!1,liIII) -> DNA22(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA22, PARP by freeing DNA22.site, PARP.dna at `kdPARP1`. | +| 1052 | `Unlabeled` | one-way | DNA23, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA23(site!1~sdsb).PARP(dna!1,liIII) -> DNA23(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA23, PARP by freeing DNA23.site, PARP.dna at `kdPARP1`. | +| 1053 | `Unlabeled` | one-way | DNA24, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA24(site!1~sdsb).PARP(dna!1,liIII) -> DNA24(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA24, PARP by freeing DNA24.site, PARP.dna at `kdPARP1`. | +| 1054 | `Unlabeled` | one-way | DNA25, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA25(site!1~sdsb).PARP(dna!1,liIII) -> DNA25(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA25, PARP by freeing DNA25.site, PARP.dna at `kdPARP1`. | +| 1055 | `Unlabeled` | one-way | DNA26, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA26(site!1~sdsb).PARP(dna!1,liIII) -> DNA26(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA26, PARP by freeing DNA26.site, PARP.dna at `kdPARP1`. | +| 1056 | `Unlabeled` | one-way | DNA27, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA27(site!1~sdsb).PARP(dna!1,liIII) -> DNA27(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA27, PARP by freeing DNA27.site, PARP.dna at `kdPARP1`. | +| 1057 | `Unlabeled` | one-way | DNA28, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA28(site!1~sdsb).PARP(dna!1,liIII) -> DNA28(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA28, PARP by freeing DNA28.site, PARP.dna at `kdPARP1`. | +| 1058 | `Unlabeled` | one-way | DNA29, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA29(site!1~sdsb).PARP(dna!1,liIII) -> DNA29(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA29, PARP by freeing DNA29.site, PARP.dna at `kdPARP1`. | +| 1059 | `Unlabeled` | one-way | DNA30, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA30(site!1~sdsb).PARP(dna!1,liIII) -> DNA30(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA30, PARP by freeing DNA30.site, PARP.dna at `kdPARP1`. | +| 1060 | `Unlabeled` | one-way | DNA31, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA31(site!1~sdsb).PARP(dna!1,liIII) -> DNA31(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA31, PARP by freeing DNA31.site, PARP.dna at `kdPARP1`. | +| 1061 | `Unlabeled` | one-way | DNA32, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA32(site!1~sdsb).PARP(dna!1,liIII) -> DNA32(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA32, PARP by freeing DNA32.site, PARP.dna at `kdPARP1`. | +| 1062 | `Unlabeled` | one-way | DNA33, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA33(site!1~sdsb).PARP(dna!1,liIII) -> DNA33(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA33, PARP by freeing DNA33.site, PARP.dna at `kdPARP1`. | +| 1063 | `Unlabeled` | one-way | DNA34, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA34(site!1~sdsb).PARP(dna!1,liIII) -> DNA34(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA34, PARP by freeing DNA34.site, PARP.dna at `kdPARP1`. | +| 1064 | `Unlabeled` | one-way | DNA35, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA35(site!1~sdsb).PARP(dna!1,liIII) -> DNA35(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA35, PARP by freeing DNA35.site, PARP.dna at `kdPARP1`. | +| 1065 | `Unlabeled` | one-way | DNA36, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA36(site!1~sdsb).PARP(dna!1,liIII) -> DNA36(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA36, PARP by freeing DNA36.site, PARP.dna at `kdPARP1`. | +| 1066 | `Unlabeled` | one-way | DNA37, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA37(site!1~sdsb).PARP(dna!1,liIII) -> DNA37(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA37, PARP by freeing DNA37.site, PARP.dna at `kdPARP1`. | +| 1067 | `Unlabeled` | one-way | DNA38, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA38(site!1~sdsb).PARP(dna!1,liIII) -> DNA38(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA38, PARP by freeing DNA38.site, PARP.dna at `kdPARP1`. | +| 1068 | `Unlabeled` | one-way | DNA39, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA39(site!1~sdsb).PARP(dna!1,liIII) -> DNA39(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA39, PARP by freeing DNA39.site, PARP.dna at `kdPARP1`. | +| 1069 | `Unlabeled` | one-way | DNA40, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA40(site!1~sdsb).PARP(dna!1,liIII) -> DNA40(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA40, PARP by freeing DNA40.site, PARP.dna at `kdPARP1`. | +| 1070 | `Unlabeled` | one-way | DNA41, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA41(site!1~sdsb).PARP(dna!1,liIII) -> DNA41(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA41, PARP by freeing DNA41.site, PARP.dna at `kdPARP1`. | +| 1071 | `Unlabeled` | one-way | DNA42, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA42(site!1~sdsb).PARP(dna!1,liIII) -> DNA42(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA42, PARP by freeing DNA42.site, PARP.dna at `kdPARP1`. | +| 1072 | `Unlabeled` | one-way | DNA43, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA43(site!1~sdsb).PARP(dna!1,liIII) -> DNA43(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA43, PARP by freeing DNA43.site, PARP.dna at `kdPARP1`. | +| 1073 | `Unlabeled` | one-way | DNA44, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA44(site!1~sdsb).PARP(dna!1,liIII) -> DNA44(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA44, PARP by freeing DNA44.site, PARP.dna at `kdPARP1`. | +| 1074 | `Unlabeled` | one-way | DNA45, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA45(site!1~sdsb).PARP(dna!1,liIII) -> DNA45(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA45, PARP by freeing DNA45.site, PARP.dna at `kdPARP1`. | +| 1075 | `Unlabeled` | one-way | DNA46, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA46(site!1~sdsb).PARP(dna!1,liIII) -> DNA46(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA46, PARP by freeing DNA46.site, PARP.dna at `kdPARP1`. | +| 1076 | `Unlabeled` | one-way | DNA47, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA47(site!1~sdsb).PARP(dna!1,liIII) -> DNA47(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA47, PARP by freeing DNA47.site, PARP.dna at `kdPARP1`. | +| 1077 | `Unlabeled` | one-way | DNA48, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA48(site!1~sdsb).PARP(dna!1,liIII) -> DNA48(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA48, PARP by freeing DNA48.site, PARP.dna at `kdPARP1`. | +| 1078 | `Unlabeled` | one-way | DNA49, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA49(site!1~sdsb).PARP(dna!1,liIII) -> DNA49(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA49, PARP by freeing DNA49.site, PARP.dna at `kdPARP1`. | +| 1079 | `Unlabeled` | one-way | DNA50, PARP | `kdPARP1` | state and binding-pattern rewrite | `DNA50(site!1~sdsb).PARP(dna!1,liIII) -> DNA50(site~sdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA50, PARP by freeing DNA50.site, PARP.dna at `kdPARP1`. | +| 1080 | `Unlabeled` | one-way | DNA1, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA1(site!1~cdsb).PARP(dna!1,liIII) -> DNA1(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA1, PARP by freeing DNA1.site, PARP.dna at `kdPARP2`. | +| 1081 | `Unlabeled` | one-way | DNA2, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA2(site!1~cdsb).PARP(dna!1,liIII) -> DNA2(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA2, PARP by freeing DNA2.site, PARP.dna at `kdPARP2`. | +| 1082 | `Unlabeled` | one-way | DNA3, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA3(site!1~cdsb).PARP(dna!1,liIII) -> DNA3(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA3, PARP by freeing DNA3.site, PARP.dna at `kdPARP2`. | +| 1083 | `Unlabeled` | one-way | DNA4, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA4(site!1~cdsb).PARP(dna!1,liIII) -> DNA4(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA4, PARP by freeing DNA4.site, PARP.dna at `kdPARP2`. | +| 1084 | `Unlabeled` | one-way | DNA5, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA5(site!1~cdsb).PARP(dna!1,liIII) -> DNA5(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA5, PARP by freeing DNA5.site, PARP.dna at `kdPARP2`. | +| 1085 | `Unlabeled` | one-way | DNA6, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA6(site!1~cdsb).PARP(dna!1,liIII) -> DNA6(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA6, PARP by freeing DNA6.site, PARP.dna at `kdPARP2`. | +| 1086 | `Unlabeled` | one-way | DNA7, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA7(site!1~cdsb).PARP(dna!1,liIII) -> DNA7(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA7, PARP by freeing DNA7.site, PARP.dna at `kdPARP2`. | +| 1087 | `Unlabeled` | one-way | DNA8, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA8(site!1~cdsb).PARP(dna!1,liIII) -> DNA8(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA8, PARP by freeing DNA8.site, PARP.dna at `kdPARP2`. | +| 1088 | `Unlabeled` | one-way | DNA9, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA9(site!1~cdsb).PARP(dna!1,liIII) -> DNA9(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA9, PARP by freeing DNA9.site, PARP.dna at `kdPARP2`. | +| 1089 | `Unlabeled` | one-way | DNA10, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA10(site!1~cdsb).PARP(dna!1,liIII) -> DNA10(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA10, PARP by freeing DNA10.site, PARP.dna at `kdPARP2`. | +| 1090 | `Unlabeled` | one-way | DNA11, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA11(site!1~cdsb).PARP(dna!1,liIII) -> DNA11(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA11, PARP by freeing DNA11.site, PARP.dna at `kdPARP2`. | +| 1091 | `Unlabeled` | one-way | DNA12, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA12(site!1~cdsb).PARP(dna!1,liIII) -> DNA12(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA12, PARP by freeing DNA12.site, PARP.dna at `kdPARP2`. | +| 1092 | `Unlabeled` | one-way | DNA13, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA13(site!1~cdsb).PARP(dna!1,liIII) -> DNA13(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA13, PARP by freeing DNA13.site, PARP.dna at `kdPARP2`. | +| 1093 | `Unlabeled` | one-way | DNA14, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA14(site!1~cdsb).PARP(dna!1,liIII) -> DNA14(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA14, PARP by freeing DNA14.site, PARP.dna at `kdPARP2`. | +| 1094 | `Unlabeled` | one-way | DNA15, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA15(site!1~cdsb).PARP(dna!1,liIII) -> DNA15(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA15, PARP by freeing DNA15.site, PARP.dna at `kdPARP2`. | +| 1095 | `Unlabeled` | one-way | DNA16, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA16(site!1~cdsb).PARP(dna!1,liIII) -> DNA16(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA16, PARP by freeing DNA16.site, PARP.dna at `kdPARP2`. | +| 1096 | `Unlabeled` | one-way | DNA17, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA17(site!1~cdsb).PARP(dna!1,liIII) -> DNA17(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA17, PARP by freeing DNA17.site, PARP.dna at `kdPARP2`. | +| 1097 | `Unlabeled` | one-way | DNA18, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA18(site!1~cdsb).PARP(dna!1,liIII) -> DNA18(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA18, PARP by freeing DNA18.site, PARP.dna at `kdPARP2`. | +| 1098 | `Unlabeled` | one-way | DNA19, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA19(site!1~cdsb).PARP(dna!1,liIII) -> DNA19(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA19, PARP by freeing DNA19.site, PARP.dna at `kdPARP2`. | +| 1099 | `Unlabeled` | one-way | DNA20, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA20(site!1~cdsb).PARP(dna!1,liIII) -> DNA20(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA20, PARP by freeing DNA20.site, PARP.dna at `kdPARP2`. | +| 1100 | `Unlabeled` | one-way | DNA21, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA21(site!1~cdsb).PARP(dna!1,liIII) -> DNA21(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA21, PARP by freeing DNA21.site, PARP.dna at `kdPARP2`. | +| 1101 | `Unlabeled` | one-way | DNA22, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA22(site!1~cdsb).PARP(dna!1,liIII) -> DNA22(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA22, PARP by freeing DNA22.site, PARP.dna at `kdPARP2`. | +| 1102 | `Unlabeled` | one-way | DNA23, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA23(site!1~cdsb).PARP(dna!1,liIII) -> DNA23(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA23, PARP by freeing DNA23.site, PARP.dna at `kdPARP2`. | +| 1103 | `Unlabeled` | one-way | DNA24, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA24(site!1~cdsb).PARP(dna!1,liIII) -> DNA24(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA24, PARP by freeing DNA24.site, PARP.dna at `kdPARP2`. | +| 1104 | `Unlabeled` | one-way | DNA25, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA25(site!1~cdsb).PARP(dna!1,liIII) -> DNA25(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA25, PARP by freeing DNA25.site, PARP.dna at `kdPARP2`. | +| 1105 | `Unlabeled` | one-way | DNA26, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA26(site!1~cdsb).PARP(dna!1,liIII) -> DNA26(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA26, PARP by freeing DNA26.site, PARP.dna at `kdPARP2`. | +| 1106 | `Unlabeled` | one-way | DNA27, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA27(site!1~cdsb).PARP(dna!1,liIII) -> DNA27(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA27, PARP by freeing DNA27.site, PARP.dna at `kdPARP2`. | +| 1107 | `Unlabeled` | one-way | DNA28, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA28(site!1~cdsb).PARP(dna!1,liIII) -> DNA28(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA28, PARP by freeing DNA28.site, PARP.dna at `kdPARP2`. | +| 1108 | `Unlabeled` | one-way | DNA29, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA29(site!1~cdsb).PARP(dna!1,liIII) -> DNA29(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA29, PARP by freeing DNA29.site, PARP.dna at `kdPARP2`. | +| 1109 | `Unlabeled` | one-way | DNA30, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA30(site!1~cdsb).PARP(dna!1,liIII) -> DNA30(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA30, PARP by freeing DNA30.site, PARP.dna at `kdPARP2`. | +| 1110 | `Unlabeled` | one-way | DNA31, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA31(site!1~cdsb).PARP(dna!1,liIII) -> DNA31(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA31, PARP by freeing DNA31.site, PARP.dna at `kdPARP2`. | +| 1111 | `Unlabeled` | one-way | DNA32, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA32(site!1~cdsb).PARP(dna!1,liIII) -> DNA32(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA32, PARP by freeing DNA32.site, PARP.dna at `kdPARP2`. | +| 1112 | `Unlabeled` | one-way | DNA33, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA33(site!1~cdsb).PARP(dna!1,liIII) -> DNA33(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA33, PARP by freeing DNA33.site, PARP.dna at `kdPARP2`. | +| 1113 | `Unlabeled` | one-way | DNA34, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA34(site!1~cdsb).PARP(dna!1,liIII) -> DNA34(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA34, PARP by freeing DNA34.site, PARP.dna at `kdPARP2`. | +| 1114 | `Unlabeled` | one-way | DNA35, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA35(site!1~cdsb).PARP(dna!1,liIII) -> DNA35(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA35, PARP by freeing DNA35.site, PARP.dna at `kdPARP2`. | +| 1115 | `Unlabeled` | one-way | DNA36, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA36(site!1~cdsb).PARP(dna!1,liIII) -> DNA36(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA36, PARP by freeing DNA36.site, PARP.dna at `kdPARP2`. | +| 1116 | `Unlabeled` | one-way | DNA37, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA37(site!1~cdsb).PARP(dna!1,liIII) -> DNA37(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA37, PARP by freeing DNA37.site, PARP.dna at `kdPARP2`. | +| 1117 | `Unlabeled` | one-way | DNA38, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA38(site!1~cdsb).PARP(dna!1,liIII) -> DNA38(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA38, PARP by freeing DNA38.site, PARP.dna at `kdPARP2`. | +| 1118 | `Unlabeled` | one-way | DNA39, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA39(site!1~cdsb).PARP(dna!1,liIII) -> DNA39(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA39, PARP by freeing DNA39.site, PARP.dna at `kdPARP2`. | +| 1119 | `Unlabeled` | one-way | DNA40, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA40(site!1~cdsb).PARP(dna!1,liIII) -> DNA40(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA40, PARP by freeing DNA40.site, PARP.dna at `kdPARP2`. | +| 1120 | `Unlabeled` | one-way | DNA41, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA41(site!1~cdsb).PARP(dna!1,liIII) -> DNA41(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA41, PARP by freeing DNA41.site, PARP.dna at `kdPARP2`. | +| 1121 | `Unlabeled` | one-way | DNA42, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA42(site!1~cdsb).PARP(dna!1,liIII) -> DNA42(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA42, PARP by freeing DNA42.site, PARP.dna at `kdPARP2`. | +| 1122 | `Unlabeled` | one-way | DNA43, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA43(site!1~cdsb).PARP(dna!1,liIII) -> DNA43(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA43, PARP by freeing DNA43.site, PARP.dna at `kdPARP2`. | +| 1123 | `Unlabeled` | one-way | DNA44, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA44(site!1~cdsb).PARP(dna!1,liIII) -> DNA44(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA44, PARP by freeing DNA44.site, PARP.dna at `kdPARP2`. | +| 1124 | `Unlabeled` | one-way | DNA45, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA45(site!1~cdsb).PARP(dna!1,liIII) -> DNA45(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA45, PARP by freeing DNA45.site, PARP.dna at `kdPARP2`. | +| 1125 | `Unlabeled` | one-way | DNA46, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA46(site!1~cdsb).PARP(dna!1,liIII) -> DNA46(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA46, PARP by freeing DNA46.site, PARP.dna at `kdPARP2`. | +| 1126 | `Unlabeled` | one-way | DNA47, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA47(site!1~cdsb).PARP(dna!1,liIII) -> DNA47(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA47, PARP by freeing DNA47.site, PARP.dna at `kdPARP2`. | +| 1127 | `Unlabeled` | one-way | DNA48, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA48(site!1~cdsb).PARP(dna!1,liIII) -> DNA48(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA48, PARP by freeing DNA48.site, PARP.dna at `kdPARP2`. | +| 1128 | `Unlabeled` | one-way | DNA49, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA49(site!1~cdsb).PARP(dna!1,liIII) -> DNA49(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA49, PARP by freeing DNA49.site, PARP.dna at `kdPARP2`. | +| 1129 | `Unlabeled` | one-way | DNA50, PARP | `kdPARP2` | state and binding-pattern rewrite | `DNA50(site!1~cdsb).PARP(dna!1,liIII) -> DNA50(site~cdsb) + PARP(dna,liIII)` | Releases a complex/contact among DNA50, PARP by freeing DNA50.site, PARP.dna at `kdPARP2`. | +| 1130 | `Unlabeled` | one-way | DNA1, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA1(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA1(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA1, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1131 | `Unlabeled` | one-way | DNA2, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA2(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA2(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA2, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1132 | `Unlabeled` | one-way | DNA3, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA3(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA3(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA3, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1133 | `Unlabeled` | one-way | DNA4, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA4(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA4(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA4, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1134 | `Unlabeled` | one-way | DNA5, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA5(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA5(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA5, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1135 | `Unlabeled` | one-way | DNA6, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA6(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA6(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA6, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1136 | `Unlabeled` | one-way | DNA7, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA7(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA7(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA7, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1137 | `Unlabeled` | one-way | DNA8, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA8(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA8(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA8, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1138 | `Unlabeled` | one-way | DNA9, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA9(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA9(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA9, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1139 | `Unlabeled` | one-way | DNA10, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA10(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA10(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA10, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1140 | `Unlabeled` | one-way | DNA11, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA11(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA11(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA11, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1141 | `Unlabeled` | one-way | DNA12, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA12(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA12(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA12, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1142 | `Unlabeled` | one-way | DNA13, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA13(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA13(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA13, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1143 | `Unlabeled` | one-way | DNA14, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA14(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA14(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA14, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1144 | `Unlabeled` | one-way | DNA15, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA15(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA15(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA15, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1145 | `Unlabeled` | one-way | DNA16, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA16(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA16(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA16, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1146 | `Unlabeled` | one-way | DNA17, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA17(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA17(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA17, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1147 | `Unlabeled` | one-way | DNA18, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA18(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA18(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA18, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1148 | `Unlabeled` | one-way | DNA19, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA19(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA19(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA19, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1149 | `Unlabeled` | one-way | DNA20, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA20(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA20(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA20, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1150 | `Unlabeled` | one-way | DNA21, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA21(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA21(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA21, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1151 | `Unlabeled` | one-way | DNA22, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA22(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA22(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA22, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1152 | `Unlabeled` | one-way | DNA23, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA23(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA23(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA23, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1153 | `Unlabeled` | one-way | DNA24, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA24(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA24(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA24, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1154 | `Unlabeled` | one-way | DNA25, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA25(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA25(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA25, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1155 | `Unlabeled` | one-way | DNA26, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA26(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA26(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA26, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1156 | `Unlabeled` | one-way | DNA27, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA27(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA27(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA27, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1157 | `Unlabeled` | one-way | DNA28, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA28(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA28(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA28, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1158 | `Unlabeled` | one-way | DNA29, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA29(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA29(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA29, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1159 | `Unlabeled` | one-way | DNA30, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA30(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA30(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA30, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1160 | `Unlabeled` | one-way | DNA31, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA31(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA31(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA31, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1161 | `Unlabeled` | one-way | DNA32, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA32(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA32(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA32, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1162 | `Unlabeled` | one-way | DNA33, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA33(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA33(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA33, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1163 | `Unlabeled` | one-way | DNA34, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA34(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA34(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA34, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1164 | `Unlabeled` | one-way | DNA35, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA35(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA35(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA35, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1165 | `Unlabeled` | one-way | DNA36, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA36(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA36(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA36, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1166 | `Unlabeled` | one-way | DNA37, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA37(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA37(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA37, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1167 | `Unlabeled` | one-way | DNA38, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA38(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA38(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA38, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1168 | `Unlabeled` | one-way | DNA39, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA39(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA39(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA39, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1169 | `Unlabeled` | one-way | DNA40, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA40(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA40(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA40, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1170 | `Unlabeled` | one-way | DNA41, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA41(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA41(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA41, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1171 | `Unlabeled` | one-way | DNA42, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA42(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA42(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA42, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1172 | `Unlabeled` | one-way | DNA43, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA43(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA43(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA43, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1173 | `Unlabeled` | one-way | DNA44, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA44(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA44(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA44, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1174 | `Unlabeled` | one-way | DNA45, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA45(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA45(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA45, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1175 | `Unlabeled` | one-way | DNA46, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA46(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA46(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA46, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1176 | `Unlabeled` | one-way | DNA47, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA47(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA47(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA47, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1177 | `Unlabeled` | one-way | DNA48, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA48(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA48(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA48, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1178 | `Unlabeled` | one-way | DNA49, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA49(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA49(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA49, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1179 | `Unlabeled` | one-way | DNA50, LiIII, PARP | `kliIII1` | internal-state conversion/modification | `DNA50(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA50(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA50, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII1`. | +| 1180 | `Unlabeled` | one-way | DNA1, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA1(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA1(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA1, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1181 | `Unlabeled` | one-way | DNA2, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA2(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA2(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA2, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1182 | `Unlabeled` | one-way | DNA3, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA3(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA3(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA3, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1183 | `Unlabeled` | one-way | DNA4, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA4(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA4(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA4, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1184 | `Unlabeled` | one-way | DNA5, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA5(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA5(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA5, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1185 | `Unlabeled` | one-way | DNA6, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA6(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA6(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA6, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1186 | `Unlabeled` | one-way | DNA7, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA7(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA7(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA7, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1187 | `Unlabeled` | one-way | DNA8, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA8(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA8(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA8, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1188 | `Unlabeled` | one-way | DNA9, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA9(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA9(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA9, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1189 | `Unlabeled` | one-way | DNA10, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA10(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA10(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA10, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1190 | `Unlabeled` | one-way | DNA11, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA11(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA11(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA11, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1191 | `Unlabeled` | one-way | DNA12, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA12(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA12(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA12, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1192 | `Unlabeled` | one-way | DNA13, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA13(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA13(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA13, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1193 | `Unlabeled` | one-way | DNA14, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA14(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA14(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA14, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1194 | `Unlabeled` | one-way | DNA15, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA15(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA15(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA15, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1195 | `Unlabeled` | one-way | DNA16, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA16(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA16(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA16, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1196 | `Unlabeled` | one-way | DNA17, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA17(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA17(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA17, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1197 | `Unlabeled` | one-way | DNA18, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA18(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA18(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA18, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1198 | `Unlabeled` | one-way | DNA19, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA19(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA19(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA19, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1199 | `Unlabeled` | one-way | DNA20, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA20(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA20(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA20, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1200 | `Unlabeled` | one-way | DNA21, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA21(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA21(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA21, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1201 | `Unlabeled` | one-way | DNA22, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA22(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA22(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA22, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1202 | `Unlabeled` | one-way | DNA23, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA23(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA23(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA23, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1203 | `Unlabeled` | one-way | DNA24, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA24(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA24(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA24, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1204 | `Unlabeled` | one-way | DNA25, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA25(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA25(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA25, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1205 | `Unlabeled` | one-way | DNA26, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA26(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA26(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA26, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1206 | `Unlabeled` | one-way | DNA27, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA27(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA27(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA27, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1207 | `Unlabeled` | one-way | DNA28, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA28(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA28(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA28, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1208 | `Unlabeled` | one-way | DNA29, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA29(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA29(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA29, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1209 | `Unlabeled` | one-way | DNA30, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA30(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA30(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA30, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1210 | `Unlabeled` | one-way | DNA31, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA31(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA31(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA31, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1211 | `Unlabeled` | one-way | DNA32, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA32(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA32(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA32, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1212 | `Unlabeled` | one-way | DNA33, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA33(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA33(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA33, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1213 | `Unlabeled` | one-way | DNA34, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA34(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA34(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA34, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1214 | `Unlabeled` | one-way | DNA35, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA35(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA35(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA35, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1215 | `Unlabeled` | one-way | DNA36, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA36(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA36(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA36, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1216 | `Unlabeled` | one-way | DNA37, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA37(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA37(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA37, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1217 | `Unlabeled` | one-way | DNA38, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA38(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA38(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA38, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1218 | `Unlabeled` | one-way | DNA39, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA39(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA39(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA39, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1219 | `Unlabeled` | one-way | DNA40, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA40(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA40(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA40, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1220 | `Unlabeled` | one-way | DNA41, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA41(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA41(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA41, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1221 | `Unlabeled` | one-way | DNA42, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA42(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA42(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA42, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1222 | `Unlabeled` | one-way | DNA43, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA43(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA43(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA43, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1223 | `Unlabeled` | one-way | DNA44, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA44(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA44(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA44, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1224 | `Unlabeled` | one-way | DNA45, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA45(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA45(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA45, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1225 | `Unlabeled` | one-way | DNA46, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA46(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA46(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA46, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1226 | `Unlabeled` | one-way | DNA47, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA47(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA47(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA47, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1227 | `Unlabeled` | one-way | DNA48, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA48(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA48(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA48, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1228 | `Unlabeled` | one-way | DNA49, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA49(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA49(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA49, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1229 | `Unlabeled` | one-way | DNA50, LiIII, PARP | `kliIII2` | internal-state conversion/modification | `DNA50(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP) -> DNA50(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2)` | Forms a complex/contact among DNA50, LiIII, PARP through LiIII.PARP, PARP.liIII at `kliIII2`. | +| 1230 | `Unlabeled` | one-way | DNA1, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA1(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA1(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA1, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1231 | `Unlabeled` | one-way | DNA2, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA2(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA2(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA2, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1232 | `Unlabeled` | one-way | DNA3, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA3(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA3(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA3, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1233 | `Unlabeled` | one-way | DNA4, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA4(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA4(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA4, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1234 | `Unlabeled` | one-way | DNA5, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA5(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA5(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA5, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1235 | `Unlabeled` | one-way | DNA6, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA6(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA6(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA6, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1236 | `Unlabeled` | one-way | DNA7, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA7(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA7(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA7, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1237 | `Unlabeled` | one-way | DNA8, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA8(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA8(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA8, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1238 | `Unlabeled` | one-way | DNA9, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA9(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA9(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA9, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1239 | `Unlabeled` | one-way | DNA10, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA10(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA10(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA10, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1240 | `Unlabeled` | one-way | DNA11, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA11(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA11(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA11, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1241 | `Unlabeled` | one-way | DNA12, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA12(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA12(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA12, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1242 | `Unlabeled` | one-way | DNA13, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA13(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA13(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA13, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1243 | `Unlabeled` | one-way | DNA14, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA14(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA14(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA14, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1244 | `Unlabeled` | one-way | DNA15, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA15(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA15(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA15, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1245 | `Unlabeled` | one-way | DNA16, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA16(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA16(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA16, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1246 | `Unlabeled` | one-way | DNA17, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA17(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA17(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA17, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1247 | `Unlabeled` | one-way | DNA18, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA18(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA18(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA18, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1248 | `Unlabeled` | one-way | DNA19, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA19(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA19(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA19, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1249 | `Unlabeled` | one-way | DNA20, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA20(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA20(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA20, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1250 | `Unlabeled` | one-way | DNA21, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA21(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA21(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA21, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | + +### Rules 1251-1500 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1251 | `Unlabeled` | one-way | DNA22, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA22(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA22(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA22, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1252 | `Unlabeled` | one-way | DNA23, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA23(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA23(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA23, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1253 | `Unlabeled` | one-way | DNA24, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA24(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA24(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA24, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1254 | `Unlabeled` | one-way | DNA25, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA25(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA25(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA25, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1255 | `Unlabeled` | one-way | DNA26, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA26(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA26(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA26, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1256 | `Unlabeled` | one-way | DNA27, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA27(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA27(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA27, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1257 | `Unlabeled` | one-way | DNA28, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA28(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA28(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA28, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1258 | `Unlabeled` | one-way | DNA29, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA29(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA29(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA29, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1259 | `Unlabeled` | one-way | DNA30, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA30(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA30(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA30, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1260 | `Unlabeled` | one-way | DNA31, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA31(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA31(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA31, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1261 | `Unlabeled` | one-way | DNA32, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA32(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA32(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA32, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1262 | `Unlabeled` | one-way | DNA33, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA33(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA33(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA33, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1263 | `Unlabeled` | one-way | DNA34, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA34(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA34(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA34, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1264 | `Unlabeled` | one-way | DNA35, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA35(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA35(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA35, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1265 | `Unlabeled` | one-way | DNA36, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA36(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA36(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA36, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1266 | `Unlabeled` | one-way | DNA37, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA37(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA37(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA37, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1267 | `Unlabeled` | one-way | DNA38, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA38(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA38(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA38, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1268 | `Unlabeled` | one-way | DNA39, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA39(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA39(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA39, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1269 | `Unlabeled` | one-way | DNA40, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA40(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA40(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA40, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1270 | `Unlabeled` | one-way | DNA41, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA41(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA41(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA41, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1271 | `Unlabeled` | one-way | DNA42, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA42(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA42(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA42, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1272 | `Unlabeled` | one-way | DNA43, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA43(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA43(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA43, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1273 | `Unlabeled` | one-way | DNA44, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA44(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA44(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA44, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1274 | `Unlabeled` | one-way | DNA45, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA45(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA45(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA45, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1275 | `Unlabeled` | one-way | DNA46, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA46(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA46(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA46, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1276 | `Unlabeled` | one-way | DNA47, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA47(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA47(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA47, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1277 | `Unlabeled` | one-way | DNA48, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA48(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA48(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA48, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1278 | `Unlabeled` | one-way | DNA49, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA49(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA49(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA49, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1279 | `Unlabeled` | one-way | DNA50, LiIII, PARP | `kdliIII1` | internal-state conversion/modification | `DNA50(site!1~sdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA50(site!1~sdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA50, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII1`. | +| 1280 | `Unlabeled` | one-way | DNA1, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA1(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA1(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA1, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1281 | `Unlabeled` | one-way | DNA2, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA2(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA2(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA2, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1282 | `Unlabeled` | one-way | DNA3, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA3(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA3(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA3, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1283 | `Unlabeled` | one-way | DNA4, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA4(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA4(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA4, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1284 | `Unlabeled` | one-way | DNA5, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA5(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA5(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA5, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1285 | `Unlabeled` | one-way | DNA6, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA6(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA6(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA6, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1286 | `Unlabeled` | one-way | DNA7, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA7(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA7(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA7, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1287 | `Unlabeled` | one-way | DNA8, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA8(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA8(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA8, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1288 | `Unlabeled` | one-way | DNA9, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA9(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA9(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA9, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1289 | `Unlabeled` | one-way | DNA10, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA10(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA10(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA10, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1290 | `Unlabeled` | one-way | DNA11, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA11(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA11(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA11, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1291 | `Unlabeled` | one-way | DNA12, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA12(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA12(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA12, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1292 | `Unlabeled` | one-way | DNA13, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA13(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA13(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA13, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1293 | `Unlabeled` | one-way | DNA14, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA14(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA14(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA14, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1294 | `Unlabeled` | one-way | DNA15, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA15(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA15(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA15, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1295 | `Unlabeled` | one-way | DNA16, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA16(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA16(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA16, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1296 | `Unlabeled` | one-way | DNA17, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA17(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA17(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA17, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1297 | `Unlabeled` | one-way | DNA18, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA18(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA18(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA18, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1298 | `Unlabeled` | one-way | DNA19, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA19(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA19(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA19, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1299 | `Unlabeled` | one-way | DNA20, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA20(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA20(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA20, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1300 | `Unlabeled` | one-way | DNA21, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA21(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA21(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA21, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1301 | `Unlabeled` | one-way | DNA22, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA22(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA22(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA22, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1302 | `Unlabeled` | one-way | DNA23, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA23(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA23(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA23, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1303 | `Unlabeled` | one-way | DNA24, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA24(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA24(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA24, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1304 | `Unlabeled` | one-way | DNA25, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA25(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA25(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA25, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1305 | `Unlabeled` | one-way | DNA26, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA26(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA26(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA26, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1306 | `Unlabeled` | one-way | DNA27, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA27(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA27(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA27, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1307 | `Unlabeled` | one-way | DNA28, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA28(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA28(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA28, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1308 | `Unlabeled` | one-way | DNA29, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA29(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA29(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA29, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1309 | `Unlabeled` | one-way | DNA30, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA30(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA30(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA30, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1310 | `Unlabeled` | one-way | DNA31, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA31(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA31(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA31, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1311 | `Unlabeled` | one-way | DNA32, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA32(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA32(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA32, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1312 | `Unlabeled` | one-way | DNA33, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA33(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA33(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA33, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1313 | `Unlabeled` | one-way | DNA34, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA34(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA34(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA34, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1314 | `Unlabeled` | one-way | DNA35, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA35(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA35(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA35, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1315 | `Unlabeled` | one-way | DNA36, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA36(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA36(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA36, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1316 | `Unlabeled` | one-way | DNA37, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA37(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA37(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA37, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1317 | `Unlabeled` | one-way | DNA38, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA38(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA38(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA38, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1318 | `Unlabeled` | one-way | DNA39, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA39(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA39(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA39, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1319 | `Unlabeled` | one-way | DNA40, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA40(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA40(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA40, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1320 | `Unlabeled` | one-way | DNA41, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA41(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA41(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA41, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1321 | `Unlabeled` | one-way | DNA42, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA42(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA42(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA42, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1322 | `Unlabeled` | one-way | DNA43, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA43(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA43(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA43, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1323 | `Unlabeled` | one-way | DNA44, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA44(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA44(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA44, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1324 | `Unlabeled` | one-way | DNA45, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA45(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA45(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA45, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1325 | `Unlabeled` | one-way | DNA46, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA46(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA46(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA46, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1326 | `Unlabeled` | one-way | DNA47, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA47(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA47(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA47, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1327 | `Unlabeled` | one-way | DNA48, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA48(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA48(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA48, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1328 | `Unlabeled` | one-way | DNA49, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA49(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA49(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA49, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1329 | `Unlabeled` | one-way | DNA50, LiIII, PARP | `kdliIII2` | internal-state conversion/modification | `DNA50(site!1~cdsb).PARP(dna!1,liIII!2).LiIII(PARP!2) -> DNA50(site!1~cdsb).PARP(dna!1,liIII) + LiIII(PARP)` | Releases a complex/contact among DNA50, LiIII, PARP by freeing LiIII.PARP, PARP.liIII at `kdliIII2`. | +| 1330 | `Unlabeled` | one-way | ATM, DNA1, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA1(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA1, LiIII, PARP by freeing DNA1.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1331 | `Unlabeled` | one-way | ATM, DNA2, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA2(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA2, LiIII, PARP by freeing DNA2.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1332 | `Unlabeled` | one-way | ATM, DNA3, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA3(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA3, LiIII, PARP by freeing DNA3.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1333 | `Unlabeled` | one-way | ATM, DNA4, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA4(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA4, LiIII, PARP by freeing DNA4.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1334 | `Unlabeled` | one-way | ATM, DNA5, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA5(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA5, LiIII, PARP by freeing DNA5.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1335 | `Unlabeled` | one-way | ATM, DNA6, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA6(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA6, LiIII, PARP by freeing DNA6.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1336 | `Unlabeled` | one-way | ATM, DNA7, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA7(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA7, LiIII, PARP by freeing DNA7.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1337 | `Unlabeled` | one-way | ATM, DNA8, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA8(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA8, LiIII, PARP by freeing DNA8.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1338 | `Unlabeled` | one-way | ATM, DNA9, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA9(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA9, LiIII, PARP by freeing DNA9.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1339 | `Unlabeled` | one-way | ATM, DNA10, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA10(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA10, LiIII, PARP by freeing DNA10.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1340 | `Unlabeled` | one-way | ATM, DNA11, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA11(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA11, LiIII, PARP by freeing DNA11.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1341 | `Unlabeled` | one-way | ATM, DNA12, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA12(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA12, LiIII, PARP by freeing DNA12.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1342 | `Unlabeled` | one-way | ATM, DNA13, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA13(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA13, LiIII, PARP by freeing DNA13.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1343 | `Unlabeled` | one-way | ATM, DNA14, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA14(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA14, LiIII, PARP by freeing DNA14.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1344 | `Unlabeled` | one-way | ATM, DNA15, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA15(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA15, LiIII, PARP by freeing DNA15.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1345 | `Unlabeled` | one-way | ATM, DNA16, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA16(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA16, LiIII, PARP by freeing DNA16.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1346 | `Unlabeled` | one-way | ATM, DNA17, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA17(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA17, LiIII, PARP by freeing DNA17.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1347 | `Unlabeled` | one-way | ATM, DNA18, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA18(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA18, LiIII, PARP by freeing DNA18.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1348 | `Unlabeled` | one-way | ATM, DNA19, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA19(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA19, LiIII, PARP by freeing DNA19.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1349 | `Unlabeled` | one-way | ATM, DNA20, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA20(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA20, LiIII, PARP by freeing DNA20.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1350 | `Unlabeled` | one-way | ATM, DNA21, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA21(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA21, LiIII, PARP by freeing DNA21.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1351 | `Unlabeled` | one-way | ATM, DNA22, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA22(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA22, LiIII, PARP by freeing DNA22.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1352 | `Unlabeled` | one-way | ATM, DNA23, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA23(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA23, LiIII, PARP by freeing DNA23.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1353 | `Unlabeled` | one-way | ATM, DNA24, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA24(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA24, LiIII, PARP by freeing DNA24.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1354 | `Unlabeled` | one-way | ATM, DNA25, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA25(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA25, LiIII, PARP by freeing DNA25.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1355 | `Unlabeled` | one-way | ATM, DNA26, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA26(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA26, LiIII, PARP by freeing DNA26.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1356 | `Unlabeled` | one-way | ATM, DNA27, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA27(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA27, LiIII, PARP by freeing DNA27.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1357 | `Unlabeled` | one-way | ATM, DNA28, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA28(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA28, LiIII, PARP by freeing DNA28.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1358 | `Unlabeled` | one-way | ATM, DNA29, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA29(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA29, LiIII, PARP by freeing DNA29.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1359 | `Unlabeled` | one-way | ATM, DNA30, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA30(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA30, LiIII, PARP by freeing DNA30.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1360 | `Unlabeled` | one-way | ATM, DNA31, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA31(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA31, LiIII, PARP by freeing DNA31.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1361 | `Unlabeled` | one-way | ATM, DNA32, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA32(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA32, LiIII, PARP by freeing DNA32.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1362 | `Unlabeled` | one-way | ATM, DNA33, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA33(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA33, LiIII, PARP by freeing DNA33.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1363 | `Unlabeled` | one-way | ATM, DNA34, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA34(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA34, LiIII, PARP by freeing DNA34.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1364 | `Unlabeled` | one-way | ATM, DNA35, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA35(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA35, LiIII, PARP by freeing DNA35.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1365 | `Unlabeled` | one-way | ATM, DNA36, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA36(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA36, LiIII, PARP by freeing DNA36.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1366 | `Unlabeled` | one-way | ATM, DNA37, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA37(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA37, LiIII, PARP by freeing DNA37.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1367 | `Unlabeled` | one-way | ATM, DNA38, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA38(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA38, LiIII, PARP by freeing DNA38.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1368 | `Unlabeled` | one-way | ATM, DNA39, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA39(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA39, LiIII, PARP by freeing DNA39.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1369 | `Unlabeled` | one-way | ATM, DNA40, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA40(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA40, LiIII, PARP by freeing DNA40.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1370 | `Unlabeled` | one-way | ATM, DNA41, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA41(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA41, LiIII, PARP by freeing DNA41.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1371 | `Unlabeled` | one-way | ATM, DNA42, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA42(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA42, LiIII, PARP by freeing DNA42.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1372 | `Unlabeled` | one-way | ATM, DNA43, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA43(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA43, LiIII, PARP by freeing DNA43.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1373 | `Unlabeled` | one-way | ATM, DNA44, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA44(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA44, LiIII, PARP by freeing DNA44.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1374 | `Unlabeled` | one-way | ATM, DNA45, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA45(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA45, LiIII, PARP by freeing DNA45.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1375 | `Unlabeled` | one-way | ATM, DNA46, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA46(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA46, LiIII, PARP by freeing DNA46.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1376 | `Unlabeled` | one-way | ATM, DNA47, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA47(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA47, LiIII, PARP by freeing DNA47.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1377 | `Unlabeled` | one-way | ATM, DNA48, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA48(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA48, LiIII, PARP by freeing DNA48.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1378 | `Unlabeled` | one-way | ATM, DNA49, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA49(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA49, LiIII, PARP by freeing DNA49.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1379 | `Unlabeled` | one-way | ATM, DNA50, LiIII, PARP | `kfixIII1` | internal-state conversion/modification | `DNA50(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA50, LiIII, PARP by freeing DNA50.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII1`. | +| 1380 | `Unlabeled` | one-way | ATM, DNA1, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA1(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA1, LiIII, PARP by freeing DNA1.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1381 | `Unlabeled` | one-way | ATM, DNA2, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA2(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA2, LiIII, PARP by freeing DNA2.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1382 | `Unlabeled` | one-way | ATM, DNA3, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA3(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA3, LiIII, PARP by freeing DNA3.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1383 | `Unlabeled` | one-way | ATM, DNA4, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA4(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA4, LiIII, PARP by freeing DNA4.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1384 | `Unlabeled` | one-way | ATM, DNA5, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA5(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA5, LiIII, PARP by freeing DNA5.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1385 | `Unlabeled` | one-way | ATM, DNA6, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA6(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA6, LiIII, PARP by freeing DNA6.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1386 | `Unlabeled` | one-way | ATM, DNA7, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA7(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA7, LiIII, PARP by freeing DNA7.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1387 | `Unlabeled` | one-way | ATM, DNA8, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA8(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA8, LiIII, PARP by freeing DNA8.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1388 | `Unlabeled` | one-way | ATM, DNA9, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA9(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA9, LiIII, PARP by freeing DNA9.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1389 | `Unlabeled` | one-way | ATM, DNA10, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA10(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA10, LiIII, PARP by freeing DNA10.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1390 | `Unlabeled` | one-way | ATM, DNA11, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA11(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA11, LiIII, PARP by freeing DNA11.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1391 | `Unlabeled` | one-way | ATM, DNA12, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA12(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA12, LiIII, PARP by freeing DNA12.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1392 | `Unlabeled` | one-way | ATM, DNA13, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA13(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA13, LiIII, PARP by freeing DNA13.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1393 | `Unlabeled` | one-way | ATM, DNA14, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA14(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA14, LiIII, PARP by freeing DNA14.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1394 | `Unlabeled` | one-way | ATM, DNA15, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA15(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA15, LiIII, PARP by freeing DNA15.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1395 | `Unlabeled` | one-way | ATM, DNA16, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA16(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA16, LiIII, PARP by freeing DNA16.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1396 | `Unlabeled` | one-way | ATM, DNA17, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA17(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA17, LiIII, PARP by freeing DNA17.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1397 | `Unlabeled` | one-way | ATM, DNA18, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA18(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA18, LiIII, PARP by freeing DNA18.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1398 | `Unlabeled` | one-way | ATM, DNA19, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA19(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA19, LiIII, PARP by freeing DNA19.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1399 | `Unlabeled` | one-way | ATM, DNA20, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA20(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA20, LiIII, PARP by freeing DNA20.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1400 | `Unlabeled` | one-way | ATM, DNA21, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA21(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA21, LiIII, PARP by freeing DNA21.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1401 | `Unlabeled` | one-way | ATM, DNA22, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA22(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA22, LiIII, PARP by freeing DNA22.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1402 | `Unlabeled` | one-way | ATM, DNA23, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA23(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA23, LiIII, PARP by freeing DNA23.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1403 | `Unlabeled` | one-way | ATM, DNA24, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA24(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA24, LiIII, PARP by freeing DNA24.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1404 | `Unlabeled` | one-way | ATM, DNA25, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA25(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA25, LiIII, PARP by freeing DNA25.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1405 | `Unlabeled` | one-way | ATM, DNA26, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA26(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA26, LiIII, PARP by freeing DNA26.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1406 | `Unlabeled` | one-way | ATM, DNA27, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA27(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA27, LiIII, PARP by freeing DNA27.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1407 | `Unlabeled` | one-way | ATM, DNA28, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA28(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA28, LiIII, PARP by freeing DNA28.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1408 | `Unlabeled` | one-way | ATM, DNA29, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA29(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA29, LiIII, PARP by freeing DNA29.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1409 | `Unlabeled` | one-way | ATM, DNA30, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA30(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA30, LiIII, PARP by freeing DNA30.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1410 | `Unlabeled` | one-way | ATM, DNA31, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA31(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA31, LiIII, PARP by freeing DNA31.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1411 | `Unlabeled` | one-way | ATM, DNA32, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA32(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA32, LiIII, PARP by freeing DNA32.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1412 | `Unlabeled` | one-way | ATM, DNA33, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA33(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA33, LiIII, PARP by freeing DNA33.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1413 | `Unlabeled` | one-way | ATM, DNA34, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA34(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA34, LiIII, PARP by freeing DNA34.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1414 | `Unlabeled` | one-way | ATM, DNA35, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA35(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA35, LiIII, PARP by freeing DNA35.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1415 | `Unlabeled` | one-way | ATM, DNA36, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA36(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA36, LiIII, PARP by freeing DNA36.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1416 | `Unlabeled` | one-way | ATM, DNA37, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA37(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA37, LiIII, PARP by freeing DNA37.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1417 | `Unlabeled` | one-way | ATM, DNA38, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA38(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA38, LiIII, PARP by freeing DNA38.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1418 | `Unlabeled` | one-way | ATM, DNA39, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA39(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA39, LiIII, PARP by freeing DNA39.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1419 | `Unlabeled` | one-way | ATM, DNA40, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA40(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA40, LiIII, PARP by freeing DNA40.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1420 | `Unlabeled` | one-way | ATM, DNA41, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA41(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA41, LiIII, PARP by freeing DNA41.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1421 | `Unlabeled` | one-way | ATM, DNA42, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA42(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA42, LiIII, PARP by freeing DNA42.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1422 | `Unlabeled` | one-way | ATM, DNA43, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA43(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA43, LiIII, PARP by freeing DNA43.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1423 | `Unlabeled` | one-way | ATM, DNA44, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA44(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA44, LiIII, PARP by freeing DNA44.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1424 | `Unlabeled` | one-way | ATM, DNA45, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA45(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA45, LiIII, PARP by freeing DNA45.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1425 | `Unlabeled` | one-way | ATM, DNA46, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA46(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA46, LiIII, PARP by freeing DNA46.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1426 | `Unlabeled` | one-way | ATM, DNA47, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA47(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA47, LiIII, PARP by freeing DNA47.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1427 | `Unlabeled` | one-way | ATM, DNA48, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA48(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA48, LiIII, PARP by freeing DNA48.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1428 | `Unlabeled` | one-way | ATM, DNA49, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA49(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA49, LiIII, PARP by freeing DNA49.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1429 | `Unlabeled` | one-way | ATM, DNA50, LiIII, PARP | `kfixIII2` | internal-state conversion/modification | `DNA50(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA50, LiIII, PARP by freeing DNA50.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII2`. | +| 1430 | `Unlabeled` | one-way | ATM, DNA1, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA1(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA1, LiIII, PARP by freeing DNA1.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1431 | `Unlabeled` | one-way | ATM, DNA2, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA2(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA2, LiIII, PARP by freeing DNA2.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1432 | `Unlabeled` | one-way | ATM, DNA3, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA3(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA3, LiIII, PARP by freeing DNA3.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1433 | `Unlabeled` | one-way | ATM, DNA4, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA4(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA4, LiIII, PARP by freeing DNA4.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1434 | `Unlabeled` | one-way | ATM, DNA5, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA5(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA5, LiIII, PARP by freeing DNA5.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1435 | `Unlabeled` | one-way | ATM, DNA6, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA6(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA6, LiIII, PARP by freeing DNA6.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1436 | `Unlabeled` | one-way | ATM, DNA7, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA7(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA7, LiIII, PARP by freeing DNA7.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1437 | `Unlabeled` | one-way | ATM, DNA8, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA8(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA8, LiIII, PARP by freeing DNA8.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1438 | `Unlabeled` | one-way | ATM, DNA9, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA9(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA9, LiIII, PARP by freeing DNA9.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1439 | `Unlabeled` | one-way | ATM, DNA10, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA10(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA10, LiIII, PARP by freeing DNA10.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1440 | `Unlabeled` | one-way | ATM, DNA11, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA11(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA11, LiIII, PARP by freeing DNA11.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1441 | `Unlabeled` | one-way | ATM, DNA12, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA12(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA12, LiIII, PARP by freeing DNA12.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1442 | `Unlabeled` | one-way | ATM, DNA13, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA13(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA13, LiIII, PARP by freeing DNA13.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1443 | `Unlabeled` | one-way | ATM, DNA14, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA14(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA14, LiIII, PARP by freeing DNA14.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1444 | `Unlabeled` | one-way | ATM, DNA15, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA15(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA15, LiIII, PARP by freeing DNA15.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1445 | `Unlabeled` | one-way | ATM, DNA16, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA16(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA16, LiIII, PARP by freeing DNA16.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1446 | `Unlabeled` | one-way | ATM, DNA17, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA17(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA17, LiIII, PARP by freeing DNA17.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1447 | `Unlabeled` | one-way | ATM, DNA18, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA18(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA18, LiIII, PARP by freeing DNA18.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1448 | `Unlabeled` | one-way | ATM, DNA19, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA19(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA19, LiIII, PARP by freeing DNA19.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1449 | `Unlabeled` | one-way | ATM, DNA20, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA20(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA20, LiIII, PARP by freeing DNA20.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1450 | `Unlabeled` | one-way | ATM, DNA21, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA21(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA21, LiIII, PARP by freeing DNA21.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1451 | `Unlabeled` | one-way | ATM, DNA22, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA22(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA22, LiIII, PARP by freeing DNA22.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1452 | `Unlabeled` | one-way | ATM, DNA23, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA23(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA23, LiIII, PARP by freeing DNA23.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1453 | `Unlabeled` | one-way | ATM, DNA24, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA24(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA24, LiIII, PARP by freeing DNA24.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1454 | `Unlabeled` | one-way | ATM, DNA25, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA25(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA25, LiIII, PARP by freeing DNA25.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1455 | `Unlabeled` | one-way | ATM, DNA26, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA26(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA26, LiIII, PARP by freeing DNA26.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1456 | `Unlabeled` | one-way | ATM, DNA27, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA27(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA27, LiIII, PARP by freeing DNA27.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1457 | `Unlabeled` | one-way | ATM, DNA28, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA28(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA28, LiIII, PARP by freeing DNA28.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1458 | `Unlabeled` | one-way | ATM, DNA29, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA29(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA29, LiIII, PARP by freeing DNA29.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1459 | `Unlabeled` | one-way | ATM, DNA30, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA30(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA30, LiIII, PARP by freeing DNA30.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1460 | `Unlabeled` | one-way | ATM, DNA31, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA31(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA31, LiIII, PARP by freeing DNA31.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1461 | `Unlabeled` | one-way | ATM, DNA32, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA32(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA32, LiIII, PARP by freeing DNA32.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1462 | `Unlabeled` | one-way | ATM, DNA33, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA33(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA33, LiIII, PARP by freeing DNA33.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1463 | `Unlabeled` | one-way | ATM, DNA34, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA34(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA34, LiIII, PARP by freeing DNA34.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1464 | `Unlabeled` | one-way | ATM, DNA35, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA35(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA35, LiIII, PARP by freeing DNA35.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1465 | `Unlabeled` | one-way | ATM, DNA36, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA36(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA36, LiIII, PARP by freeing DNA36.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1466 | `Unlabeled` | one-way | ATM, DNA37, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA37(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA37, LiIII, PARP by freeing DNA37.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1467 | `Unlabeled` | one-way | ATM, DNA38, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA38(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA38, LiIII, PARP by freeing DNA38.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1468 | `Unlabeled` | one-way | ATM, DNA39, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA39(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA39, LiIII, PARP by freeing DNA39.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1469 | `Unlabeled` | one-way | ATM, DNA40, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA40(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA40, LiIII, PARP by freeing DNA40.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1470 | `Unlabeled` | one-way | ATM, DNA41, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA41(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA41, LiIII, PARP by freeing DNA41.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1471 | `Unlabeled` | one-way | ATM, DNA42, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA42(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA42, LiIII, PARP by freeing DNA42.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1472 | `Unlabeled` | one-way | ATM, DNA43, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA43(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA43, LiIII, PARP by freeing DNA43.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1473 | `Unlabeled` | one-way | ATM, DNA44, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA44(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA44, LiIII, PARP by freeing DNA44.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1474 | `Unlabeled` | one-way | ATM, DNA45, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA45(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA45, LiIII, PARP by freeing DNA45.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1475 | `Unlabeled` | one-way | ATM, DNA46, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA46(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA46, LiIII, PARP by freeing DNA46.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1476 | `Unlabeled` | one-way | ATM, DNA47, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA47(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA47, LiIII, PARP by freeing DNA47.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1477 | `Unlabeled` | one-way | ATM, DNA48, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA48(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA48, LiIII, PARP by freeing DNA48.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1478 | `Unlabeled` | one-way | ATM, DNA49, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA49(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA49, LiIII, PARP by freeing DNA49.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1479 | `Unlabeled` | one-way | ATM, DNA50, LiIII, PARP | `kfixIII3` | internal-state conversion/modification | `DNA50(site!1~sdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA50, LiIII, PARP by freeing DNA50.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII3`. | +| 1480 | `Unlabeled` | one-way | ATM, DNA1, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA1(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA1(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA1, LiIII, PARP by freeing DNA1.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1481 | `Unlabeled` | one-way | ATM, DNA2, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA2(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA2(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA2, LiIII, PARP by freeing DNA2.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1482 | `Unlabeled` | one-way | ATM, DNA3, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA3(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA3(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA3, LiIII, PARP by freeing DNA3.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1483 | `Unlabeled` | one-way | ATM, DNA4, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA4(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA4(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA4, LiIII, PARP by freeing DNA4.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1484 | `Unlabeled` | one-way | ATM, DNA5, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA5(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA5(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA5, LiIII, PARP by freeing DNA5.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1485 | `Unlabeled` | one-way | ATM, DNA6, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA6(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA6(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA6, LiIII, PARP by freeing DNA6.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1486 | `Unlabeled` | one-way | ATM, DNA7, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA7(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA7(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA7, LiIII, PARP by freeing DNA7.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1487 | `Unlabeled` | one-way | ATM, DNA8, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA8(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA8(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA8, LiIII, PARP by freeing DNA8.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1488 | `Unlabeled` | one-way | ATM, DNA9, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA9(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA9(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA9, LiIII, PARP by freeing DNA9.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1489 | `Unlabeled` | one-way | ATM, DNA10, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA10(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA10(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA10, LiIII, PARP by freeing DNA10.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1490 | `Unlabeled` | one-way | ATM, DNA11, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA11(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA11(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA11, LiIII, PARP by freeing DNA11.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1491 | `Unlabeled` | one-way | ATM, DNA12, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA12(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA12(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA12, LiIII, PARP by freeing DNA12.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1492 | `Unlabeled` | one-way | ATM, DNA13, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA13(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA13(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA13, LiIII, PARP by freeing DNA13.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1493 | `Unlabeled` | one-way | ATM, DNA14, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA14(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA14(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA14, LiIII, PARP by freeing DNA14.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1494 | `Unlabeled` | one-way | ATM, DNA15, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA15(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA15(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA15, LiIII, PARP by freeing DNA15.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1495 | `Unlabeled` | one-way | ATM, DNA16, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA16(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA16(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA16, LiIII, PARP by freeing DNA16.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1496 | `Unlabeled` | one-way | ATM, DNA17, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA17(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA17(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA17, LiIII, PARP by freeing DNA17.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1497 | `Unlabeled` | one-way | ATM, DNA18, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA18(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA18(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA18, LiIII, PARP by freeing DNA18.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1498 | `Unlabeled` | one-way | ATM, DNA19, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA19(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA19(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA19, LiIII, PARP by freeing DNA19.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1499 | `Unlabeled` | one-way | ATM, DNA20, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA20(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA20(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA20, LiIII, PARP by freeing DNA20.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1500 | `Unlabeled` | one-way | ATM, DNA21, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA21(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA21(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA21, LiIII, PARP by freeing DNA21.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | + +### Rules 1501-1750 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1501 | `Unlabeled` | one-way | ATM, DNA22, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA22(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA22(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA22, LiIII, PARP by freeing DNA22.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1502 | `Unlabeled` | one-way | ATM, DNA23, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA23(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA23(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA23, LiIII, PARP by freeing DNA23.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1503 | `Unlabeled` | one-way | ATM, DNA24, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA24(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA24(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA24, LiIII, PARP by freeing DNA24.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1504 | `Unlabeled` | one-way | ATM, DNA25, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA25(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA25(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA25, LiIII, PARP by freeing DNA25.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1505 | `Unlabeled` | one-way | ATM, DNA26, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA26(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA26(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA26, LiIII, PARP by freeing DNA26.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1506 | `Unlabeled` | one-way | ATM, DNA27, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA27(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA27(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA27, LiIII, PARP by freeing DNA27.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1507 | `Unlabeled` | one-way | ATM, DNA28, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA28(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA28(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA28, LiIII, PARP by freeing DNA28.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1508 | `Unlabeled` | one-way | ATM, DNA29, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA29(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA29(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA29, LiIII, PARP by freeing DNA29.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1509 | `Unlabeled` | one-way | ATM, DNA30, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA30(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA30(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA30, LiIII, PARP by freeing DNA30.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1510 | `Unlabeled` | one-way | ATM, DNA31, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA31(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA31(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA31, LiIII, PARP by freeing DNA31.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1511 | `Unlabeled` | one-way | ATM, DNA32, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA32(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA32(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA32, LiIII, PARP by freeing DNA32.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1512 | `Unlabeled` | one-way | ATM, DNA33, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA33(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA33(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA33, LiIII, PARP by freeing DNA33.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1513 | `Unlabeled` | one-way | ATM, DNA34, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA34(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA34(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA34, LiIII, PARP by freeing DNA34.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1514 | `Unlabeled` | one-way | ATM, DNA35, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA35(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA35(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA35, LiIII, PARP by freeing DNA35.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1515 | `Unlabeled` | one-way | ATM, DNA36, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA36(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA36(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA36, LiIII, PARP by freeing DNA36.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1516 | `Unlabeled` | one-way | ATM, DNA37, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA37(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA37(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA37, LiIII, PARP by freeing DNA37.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1517 | `Unlabeled` | one-way | ATM, DNA38, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA38(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA38(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA38, LiIII, PARP by freeing DNA38.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1518 | `Unlabeled` | one-way | ATM, DNA39, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA39(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA39(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA39, LiIII, PARP by freeing DNA39.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1519 | `Unlabeled` | one-way | ATM, DNA40, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA40(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA40(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA40, LiIII, PARP by freeing DNA40.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1520 | `Unlabeled` | one-way | ATM, DNA41, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA41(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA41(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA41, LiIII, PARP by freeing DNA41.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1521 | `Unlabeled` | one-way | ATM, DNA42, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA42(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA42(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA42, LiIII, PARP by freeing DNA42.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1522 | `Unlabeled` | one-way | ATM, DNA43, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA43(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA43(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA43, LiIII, PARP by freeing DNA43.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1523 | `Unlabeled` | one-way | ATM, DNA44, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA44(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA44(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA44, LiIII, PARP by freeing DNA44.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1524 | `Unlabeled` | one-way | ATM, DNA45, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA45(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA45(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA45, LiIII, PARP by freeing DNA45.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1525 | `Unlabeled` | one-way | ATM, DNA46, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA46(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA46(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA46, LiIII, PARP by freeing DNA46.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1526 | `Unlabeled` | one-way | ATM, DNA47, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA47(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA47(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA47, LiIII, PARP by freeing DNA47.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1527 | `Unlabeled` | one-way | ATM, DNA48, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA48(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA48(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA48, LiIII, PARP by freeing DNA48.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1528 | `Unlabeled` | one-way | ATM, DNA49, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA49(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA49(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA49, LiIII, PARP by freeing DNA49.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1529 | `Unlabeled` | one-way | ATM, DNA50, LiIII, PARP | `kfixIII4` | internal-state conversion/modification | `DNA50(site!1~cdsb,h2ax!3~foc).PARP(dna!1,liIII!2).LiIII(PARP!2).ATM(h2ax!3) -> DNA50(site~ok,h2ax!1~foc).ATM(h2ax!1) + PARP(dna,liIII) + LiIII(PARP)` | Releases a complex/contact among ATM, DNA50, LiIII, PARP by freeing DNA50.site, LiIII.PARP, PARP.dna, PARP.liIII at `kfixIII4`. | +| 1530 | `Unlabeled` | one-way | ATM, DNA1 | `kATMact` | internal-state conversion/modification | `DNA1(site!?~sdsb) + ATM(state~0,h2ax) -> DNA1(site!?~sdsb) + ATM(state~1,h2ax)` | Changes internal modification/state marks on ATM, DNA1: ATM.state 0→1 at `kATMact`. | +| 1531 | `Unlabeled` | one-way | ATM, DNA2 | `kATMact` | internal-state conversion/modification | `DNA2(site!?~sdsb) + ATM(state~0,h2ax) -> DNA2(site!?~sdsb) + ATM(state~2,h2ax)` | Changes internal modification/state marks on ATM, DNA2: ATM.state 0→2 at `kATMact`. | +| 1532 | `Unlabeled` | one-way | ATM, DNA3 | `kATMact` | internal-state conversion/modification | `DNA3(site!?~sdsb) + ATM(state~0,h2ax) -> DNA3(site!?~sdsb) + ATM(state~3,h2ax)` | Changes internal modification/state marks on ATM, DNA3: ATM.state 0→3 at `kATMact`. | +| 1533 | `Unlabeled` | one-way | ATM, DNA4 | `kATMact` | internal-state conversion/modification | `DNA4(site!?~sdsb) + ATM(state~0,h2ax) -> DNA4(site!?~sdsb) + ATM(state~4,h2ax)` | Changes internal modification/state marks on ATM, DNA4: ATM.state 0→4 at `kATMact`. | +| 1534 | `Unlabeled` | one-way | ATM, DNA5 | `kATMact` | internal-state conversion/modification | `DNA5(site!?~sdsb) + ATM(state~0,h2ax) -> DNA5(site!?~sdsb) + ATM(state~5,h2ax)` | Changes internal modification/state marks on ATM, DNA5: ATM.state 0→5 at `kATMact`. | +| 1535 | `Unlabeled` | one-way | ATM, DNA6 | `kATMact` | internal-state conversion/modification | `DNA6(site!?~sdsb) + ATM(state~0,h2ax) -> DNA6(site!?~sdsb) + ATM(state~6,h2ax)` | Changes internal modification/state marks on ATM, DNA6: ATM.state 0→6 at `kATMact`. | +| 1536 | `Unlabeled` | one-way | ATM, DNA7 | `kATMact` | internal-state conversion/modification | `DNA7(site!?~sdsb) + ATM(state~0,h2ax) -> DNA7(site!?~sdsb) + ATM(state~7,h2ax)` | Changes internal modification/state marks on ATM, DNA7: ATM.state 0→7 at `kATMact`. | +| 1537 | `Unlabeled` | one-way | ATM, DNA8 | `kATMact` | internal-state conversion/modification | `DNA8(site!?~sdsb) + ATM(state~0,h2ax) -> DNA8(site!?~sdsb) + ATM(state~8,h2ax)` | Changes internal modification/state marks on ATM, DNA8: ATM.state 0→8 at `kATMact`. | +| 1538 | `Unlabeled` | one-way | ATM, DNA9 | `kATMact` | internal-state conversion/modification | `DNA9(site!?~sdsb) + ATM(state~0,h2ax) -> DNA9(site!?~sdsb) + ATM(state~9,h2ax)` | Changes internal modification/state marks on ATM, DNA9: ATM.state 0→9 at `kATMact`. | +| 1539 | `Unlabeled` | one-way | ATM, DNA10 | `kATMact` | internal-state conversion/modification | `DNA10(site!?~sdsb) + ATM(state~0,h2ax) -> DNA10(site!?~sdsb) + ATM(state~10,h2ax)` | Changes internal modification/state marks on ATM, DNA10: ATM.state 0→10 at `kATMact`. | +| 1540 | `Unlabeled` | one-way | ATM, DNA11 | `kATMact` | internal-state conversion/modification | `DNA11(site!?~sdsb) + ATM(state~0,h2ax) -> DNA11(site!?~sdsb) + ATM(state~11,h2ax)` | Changes internal modification/state marks on ATM, DNA11: ATM.state 0→11 at `kATMact`. | +| 1541 | `Unlabeled` | one-way | ATM, DNA12 | `kATMact` | internal-state conversion/modification | `DNA12(site!?~sdsb) + ATM(state~0,h2ax) -> DNA12(site!?~sdsb) + ATM(state~12,h2ax)` | Changes internal modification/state marks on ATM, DNA12: ATM.state 0→12 at `kATMact`. | +| 1542 | `Unlabeled` | one-way | ATM, DNA13 | `kATMact` | internal-state conversion/modification | `DNA13(site!?~sdsb) + ATM(state~0,h2ax) -> DNA13(site!?~sdsb) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA13: ATM.state 0→13 at `kATMact`. | +| 1543 | `Unlabeled` | one-way | ATM, DNA14 | `kATMact` | internal-state conversion/modification | `DNA14(site!?~sdsb) + ATM(state~0,h2ax) -> DNA14(site!?~sdsb) + ATM(state~14,h2ax)` | Changes internal modification/state marks on ATM, DNA14: ATM.state 0→14 at `kATMact`. | +| 1544 | `Unlabeled` | one-way | ATM, DNA15 | `kATMact` | internal-state conversion/modification | `DNA15(site!?~sdsb) + ATM(state~0,h2ax) -> DNA15(site!?~sdsb) + ATM(state~15,h2ax)` | Changes internal modification/state marks on ATM, DNA15: ATM.state 0→15 at `kATMact`. | +| 1545 | `Unlabeled` | one-way | ATM, DNA16 | `kATMact` | internal-state conversion/modification | `DNA16(site!?~sdsb) + ATM(state~0,h2ax) -> DNA16(site!?~sdsb) + ATM(state~16,h2ax)` | Changes internal modification/state marks on ATM, DNA16: ATM.state 0→16 at `kATMact`. | +| 1546 | `Unlabeled` | one-way | ATM, DNA17 | `kATMact` | internal-state conversion/modification | `DNA17(site!?~sdsb) + ATM(state~0,h2ax) -> DNA17(site!?~sdsb) + ATM(state~17,h2ax)` | Changes internal modification/state marks on ATM, DNA17: ATM.state 0→17 at `kATMact`. | +| 1547 | `Unlabeled` | one-way | ATM, DNA18 | `kATMact` | internal-state conversion/modification | `DNA18(site!?~sdsb) + ATM(state~0,h2ax) -> DNA18(site!?~sdsb) + ATM(state~18,h2ax)` | Changes internal modification/state marks on ATM, DNA18: ATM.state 0→18 at `kATMact`. | +| 1548 | `Unlabeled` | one-way | ATM, DNA19 | `kATMact` | internal-state conversion/modification | `DNA19(site!?~sdsb) + ATM(state~0,h2ax) -> DNA19(site!?~sdsb) + ATM(state~19,h2ax)` | Changes internal modification/state marks on ATM, DNA19: ATM.state 0→19 at `kATMact`. | +| 1549 | `Unlabeled` | one-way | ATM, DNA20 | `kATMact` | internal-state conversion/modification | `DNA20(site!?~sdsb) + ATM(state~0,h2ax) -> DNA20(site!?~sdsb) + ATM(state~20,h2ax)` | Changes internal modification/state marks on ATM, DNA20: ATM.state 0→20 at `kATMact`. | +| 1550 | `Unlabeled` | one-way | ATM, DNA21 | `kATMact` | internal-state conversion/modification | `DNA21(site!?~sdsb) + ATM(state~0,h2ax) -> DNA21(site!?~sdsb) + ATM(state~21,h2ax)` | Changes internal modification/state marks on ATM, DNA21: ATM.state 0→21 at `kATMact`. | +| 1551 | `Unlabeled` | one-way | ATM, DNA22 | `kATMact` | internal-state conversion/modification | `DNA22(site!?~sdsb) + ATM(state~0,h2ax) -> DNA22(site!?~sdsb) + ATM(state~22,h2ax)` | Changes internal modification/state marks on ATM, DNA22: ATM.state 0→22 at `kATMact`. | +| 1552 | `Unlabeled` | one-way | ATM, DNA23 | `kATMact` | internal-state conversion/modification | `DNA23(site!?~sdsb) + ATM(state~0,h2ax) -> DNA23(site!?~sdsb) + ATM(state~23,h2ax)` | Changes internal modification/state marks on ATM, DNA23: ATM.state 0→23 at `kATMact`. | +| 1553 | `Unlabeled` | one-way | ATM, DNA24 | `kATMact` | internal-state conversion/modification | `DNA24(site!?~sdsb) + ATM(state~0,h2ax) -> DNA24(site!?~sdsb) + ATM(state~24,h2ax)` | Changes internal modification/state marks on ATM, DNA24: ATM.state 0→24 at `kATMact`. | +| 1554 | `Unlabeled` | one-way | ATM, DNA25 | `kATMact` | internal-state conversion/modification | `DNA25(site!?~sdsb) + ATM(state~0,h2ax) -> DNA25(site!?~sdsb) + ATM(state~25,h2ax)` | Changes internal modification/state marks on ATM, DNA25: ATM.state 0→25 at `kATMact`. | +| 1555 | `Unlabeled` | one-way | ATM, DNA26 | `kATMact` | internal-state conversion/modification | `DNA26(site!?~sdsb) + ATM(state~0,h2ax) -> DNA26(site!?~sdsb) + ATM(state~26,h2ax)` | Changes internal modification/state marks on ATM, DNA26: ATM.state 0→26 at `kATMact`. | +| 1556 | `Unlabeled` | one-way | ATM, DNA27 | `kATMact` | internal-state conversion/modification | `DNA27(site!?~sdsb) + ATM(state~0,h2ax) -> DNA27(site!?~sdsb) + ATM(state~27,h2ax)` | Changes internal modification/state marks on ATM, DNA27: ATM.state 0→27 at `kATMact`. | +| 1557 | `Unlabeled` | one-way | ATM, DNA28 | `kATMact` | internal-state conversion/modification | `DNA28(site!?~sdsb) + ATM(state~0,h2ax) -> DNA28(site!?~sdsb) + ATM(state~28,h2ax)` | Changes internal modification/state marks on ATM, DNA28: ATM.state 0→28 at `kATMact`. | +| 1558 | `Unlabeled` | one-way | ATM, DNA29 | `kATMact` | internal-state conversion/modification | `DNA29(site!?~sdsb) + ATM(state~0,h2ax) -> DNA29(site!?~sdsb) + ATM(state~29,h2ax)` | Changes internal modification/state marks on ATM, DNA29: ATM.state 0→29 at `kATMact`. | +| 1559 | `Unlabeled` | one-way | ATM, DNA30 | `kATMact` | internal-state conversion/modification | `DNA30(site!?~sdsb) + ATM(state~0,h2ax) -> DNA30(site!?~sdsb) + ATM(state~30,h2ax)` | Changes internal modification/state marks on ATM, DNA30: ATM.state 0→30 at `kATMact`. | +| 1560 | `Unlabeled` | one-way | ATM, DNA31 | `kATMact` | internal-state conversion/modification | `DNA31(site!?~sdsb) + ATM(state~0,h2ax) -> DNA31(site!?~sdsb) + ATM(state~31,h2ax)` | Changes internal modification/state marks on ATM, DNA31: ATM.state 0→31 at `kATMact`. | +| 1561 | `Unlabeled` | one-way | ATM, DNA32 | `kATMact` | internal-state conversion/modification | `DNA32(site!?~sdsb) + ATM(state~0,h2ax) -> DNA32(site!?~sdsb) + ATM(state~32,h2ax)` | Changes internal modification/state marks on ATM, DNA32: ATM.state 0→32 at `kATMact`. | +| 1562 | `Unlabeled` | one-way | ATM, DNA33 | `kATMact` | internal-state conversion/modification | `DNA33(site!?~sdsb) + ATM(state~0,h2ax) -> DNA33(site!?~sdsb) + ATM(state~33,h2ax)` | Changes internal modification/state marks on ATM, DNA33: ATM.state 0→33 at `kATMact`. | +| 1563 | `Unlabeled` | one-way | ATM, DNA34 | `kATMact` | internal-state conversion/modification | `DNA34(site!?~sdsb) + ATM(state~0,h2ax) -> DNA34(site!?~sdsb) + ATM(state~34,h2ax)` | Changes internal modification/state marks on ATM, DNA34: ATM.state 0→34 at `kATMact`. | +| 1564 | `Unlabeled` | one-way | ATM, DNA35 | `kATMact` | internal-state conversion/modification | `DNA35(site!?~sdsb) + ATM(state~0,h2ax) -> DNA35(site!?~sdsb) + ATM(state~35,h2ax)` | Changes internal modification/state marks on ATM, DNA35: ATM.state 0→35 at `kATMact`. | +| 1565 | `Unlabeled` | one-way | ATM, DNA36 | `kATMact` | internal-state conversion/modification | `DNA36(site!?~sdsb) + ATM(state~0,h2ax) -> DNA36(site!?~sdsb) + ATM(state~36,h2ax)` | Changes internal modification/state marks on ATM, DNA36: ATM.state 0→36 at `kATMact`. | +| 1566 | `Unlabeled` | one-way | ATM, DNA37 | `kATMact` | internal-state conversion/modification | `DNA37(site!?~sdsb) + ATM(state~0,h2ax) -> DNA37(site!?~sdsb) + ATM(state~37,h2ax)` | Changes internal modification/state marks on ATM, DNA37: ATM.state 0→37 at `kATMact`. | +| 1567 | `Unlabeled` | one-way | ATM, DNA38 | `kATMact` | internal-state conversion/modification | `DNA38(site!?~sdsb) + ATM(state~0,h2ax) -> DNA38(site!?~sdsb) + ATM(state~38,h2ax)` | Changes internal modification/state marks on ATM, DNA38: ATM.state 0→38 at `kATMact`. | +| 1568 | `Unlabeled` | one-way | ATM, DNA39 | `kATMact` | internal-state conversion/modification | `DNA39(site!?~sdsb) + ATM(state~0,h2ax) -> DNA39(site!?~sdsb) + ATM(state~39,h2ax)` | Changes internal modification/state marks on ATM, DNA39: ATM.state 0→39 at `kATMact`. | +| 1569 | `Unlabeled` | one-way | ATM, DNA40 | `kATMact` | internal-state conversion/modification | `DNA40(site!?~sdsb) + ATM(state~0,h2ax) -> DNA40(site!?~sdsb) + ATM(state~40,h2ax)` | Changes internal modification/state marks on ATM, DNA40: ATM.state 0→40 at `kATMact`. | +| 1570 | `Unlabeled` | one-way | ATM, DNA41 | `kATMact` | internal-state conversion/modification | `DNA41(site!?~sdsb) + ATM(state~0,h2ax) -> DNA41(site!?~sdsb) + ATM(state~41,h2ax)` | Changes internal modification/state marks on ATM, DNA41: ATM.state 0→41 at `kATMact`. | +| 1571 | `Unlabeled` | one-way | ATM, DNA42 | `kATMact` | internal-state conversion/modification | `DNA42(site!?~sdsb) + ATM(state~0,h2ax) -> DNA42(site!?~sdsb) + ATM(state~42,h2ax)` | Changes internal modification/state marks on ATM, DNA42: ATM.state 0→42 at `kATMact`. | +| 1572 | `Unlabeled` | one-way | ATM, DNA43 | `kATMact` | internal-state conversion/modification | `DNA43(site!?~sdsb) + ATM(state~0,h2ax) -> DNA43(site!?~sdsb) + ATM(state~43,h2ax)` | Changes internal modification/state marks on ATM, DNA43: ATM.state 0→43 at `kATMact`. | +| 1573 | `Unlabeled` | one-way | ATM, DNA44 | `kATMact` | internal-state conversion/modification | `DNA44(site!?~sdsb) + ATM(state~0,h2ax) -> DNA44(site!?~sdsb) + ATM(state~44,h2ax)` | Changes internal modification/state marks on ATM, DNA44: ATM.state 0→44 at `kATMact`. | +| 1574 | `Unlabeled` | one-way | ATM, DNA45 | `kATMact` | internal-state conversion/modification | `DNA45(site!?~sdsb) + ATM(state~0,h2ax) -> DNA45(site!?~sdsb) + ATM(state~45,h2ax)` | Changes internal modification/state marks on ATM, DNA45: ATM.state 0→45 at `kATMact`. | +| 1575 | `Unlabeled` | one-way | ATM, DNA46 | `kATMact` | internal-state conversion/modification | `DNA46(site!?~sdsb) + ATM(state~0,h2ax) -> DNA46(site!?~sdsb) + ATM(state~46,h2ax)` | Changes internal modification/state marks on ATM, DNA46: ATM.state 0→46 at `kATMact`. | +| 1576 | `Unlabeled` | one-way | ATM, DNA47 | `kATMact` | internal-state conversion/modification | `DNA47(site!?~sdsb) + ATM(state~0,h2ax) -> DNA47(site!?~sdsb) + ATM(state~47,h2ax)` | Changes internal modification/state marks on ATM, DNA47: ATM.state 0→47 at `kATMact`. | +| 1577 | `Unlabeled` | one-way | ATM, DNA48 | `kATMact` | internal-state conversion/modification | `DNA48(site!?~sdsb) + ATM(state~0,h2ax) -> DNA48(site!?~sdsb) + ATM(state~48,h2ax)` | Changes internal modification/state marks on ATM, DNA48: ATM.state 0→48 at `kATMact`. | +| 1578 | `Unlabeled` | one-way | ATM, DNA49 | `kATMact` | internal-state conversion/modification | `DNA49(site!?~sdsb) + ATM(state~0,h2ax) -> DNA49(site!?~sdsb) + ATM(state~49,h2ax)` | Changes internal modification/state marks on ATM, DNA49: ATM.state 0→49 at `kATMact`. | +| 1579 | `Unlabeled` | one-way | ATM, DNA50 | `kATMact` | internal-state conversion/modification | `DNA50(site!?~sdsb) + ATM(state~0,h2ax) -> DNA50(site!?~sdsb) + ATM(state~50,h2ax)` | Changes internal modification/state marks on ATM, DNA50: ATM.state 0→50 at `kATMact`. | +| 1580 | `Unlabeled` | one-way | ATM, DNA1 | `kATMact` | internal-state conversion/modification | `DNA1(site!?~cdsb) + ATM(state~0,h2ax) -> DNA1(site!?~cdsb) + ATM(state~1,h2ax)` | Changes internal modification/state marks on ATM, DNA1: ATM.state 0→1 at `kATMact`. | +| 1581 | `Unlabeled` | one-way | ATM, DNA2 | `kATMact` | internal-state conversion/modification | `DNA2(site!?~cdsb) + ATM(state~0,h2ax) -> DNA2(site!?~cdsb) + ATM(state~2,h2ax)` | Changes internal modification/state marks on ATM, DNA2: ATM.state 0→2 at `kATMact`. | +| 1582 | `Unlabeled` | one-way | ATM, DNA3 | `kATMact` | internal-state conversion/modification | `DNA3(site!?~cdsb) + ATM(state~0,h2ax) -> DNA3(site!?~cdsb) + ATM(state~3,h2ax)` | Changes internal modification/state marks on ATM, DNA3: ATM.state 0→3 at `kATMact`. | +| 1583 | `Unlabeled` | one-way | ATM, DNA4 | `kATMact` | internal-state conversion/modification | `DNA4(site!?~cdsb) + ATM(state~0,h2ax) -> DNA4(site!?~cdsb) + ATM(state~4,h2ax)` | Changes internal modification/state marks on ATM, DNA4: ATM.state 0→4 at `kATMact`. | +| 1584 | `Unlabeled` | one-way | ATM, DNA5 | `kATMact` | internal-state conversion/modification | `DNA5(site!?~cdsb) + ATM(state~0,h2ax) -> DNA5(site!?~cdsb) + ATM(state~5,h2ax)` | Changes internal modification/state marks on ATM, DNA5: ATM.state 0→5 at `kATMact`. | +| 1585 | `Unlabeled` | one-way | ATM, DNA6 | `kATMact` | internal-state conversion/modification | `DNA6(site!?~cdsb) + ATM(state~0,h2ax) -> DNA6(site!?~cdsb) + ATM(state~6,h2ax)` | Changes internal modification/state marks on ATM, DNA6: ATM.state 0→6 at `kATMact`. | +| 1586 | `Unlabeled` | one-way | ATM, DNA7 | `kATMact` | internal-state conversion/modification | `DNA7(site!?~cdsb) + ATM(state~0,h2ax) -> DNA7(site!?~cdsb) + ATM(state~7,h2ax)` | Changes internal modification/state marks on ATM, DNA7: ATM.state 0→7 at `kATMact`. | +| 1587 | `Unlabeled` | one-way | ATM, DNA8 | `kATMact` | internal-state conversion/modification | `DNA8(site!?~cdsb) + ATM(state~0,h2ax) -> DNA8(site!?~cdsb) + ATM(state~8,h2ax)` | Changes internal modification/state marks on ATM, DNA8: ATM.state 0→8 at `kATMact`. | +| 1588 | `Unlabeled` | one-way | ATM, DNA9 | `kATMact` | internal-state conversion/modification | `DNA9(site!?~cdsb) + ATM(state~0,h2ax) -> DNA9(site!?~cdsb) + ATM(state~9,h2ax)` | Changes internal modification/state marks on ATM, DNA9: ATM.state 0→9 at `kATMact`. | +| 1589 | `Unlabeled` | one-way | ATM, DNA10 | `kATMact` | internal-state conversion/modification | `DNA10(site!?~cdsb) + ATM(state~0,h2ax) -> DNA10(site!?~cdsb) + ATM(state~10,h2ax)` | Changes internal modification/state marks on ATM, DNA10: ATM.state 0→10 at `kATMact`. | +| 1590 | `Unlabeled` | one-way | ATM, DNA11 | `kATMact` | internal-state conversion/modification | `DNA11(site!?~cdsb) + ATM(state~0,h2ax) -> DNA11(site!?~cdsb) + ATM(state~12,h2ax)` | Changes internal modification/state marks on ATM, DNA11: ATM.state 0→12 at `kATMact`. | +| 1591 | `Unlabeled` | one-way | ATM, DNA12 | `kATMact` | internal-state conversion/modification | `DNA12(site!?~cdsb) + ATM(state~0,h2ax) -> DNA12(site!?~cdsb) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA12: ATM.state 0→13 at `kATMact`. | +| 1592 | `Unlabeled` | one-way | ATM, DNA13 | `kATMact` | internal-state conversion/modification | `DNA13(site!?~cdsb) + ATM(state~0,h2ax) -> DNA13(site!?~cdsb) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA13: ATM.state 0→13 at `kATMact`. | +| 1593 | `Unlabeled` | one-way | ATM, DNA14 | `kATMact` | internal-state conversion/modification | `DNA14(site!?~cdsb) + ATM(state~0,h2ax) -> DNA14(site!?~cdsb) + ATM(state~14,h2ax)` | Changes internal modification/state marks on ATM, DNA14: ATM.state 0→14 at `kATMact`. | +| 1594 | `Unlabeled` | one-way | ATM, DNA15 | `kATMact` | internal-state conversion/modification | `DNA15(site!?~cdsb) + ATM(state~0,h2ax) -> DNA15(site!?~cdsb) + ATM(state~15,h2ax)` | Changes internal modification/state marks on ATM, DNA15: ATM.state 0→15 at `kATMact`. | +| 1595 | `Unlabeled` | one-way | ATM, DNA16 | `kATMact` | internal-state conversion/modification | `DNA16(site!?~cdsb) + ATM(state~0,h2ax) -> DNA16(site!?~cdsb) + ATM(state~16,h2ax)` | Changes internal modification/state marks on ATM, DNA16: ATM.state 0→16 at `kATMact`. | +| 1596 | `Unlabeled` | one-way | ATM, DNA17 | `kATMact` | internal-state conversion/modification | `DNA17(site!?~cdsb) + ATM(state~0,h2ax) -> DNA17(site!?~cdsb) + ATM(state~17,h2ax)` | Changes internal modification/state marks on ATM, DNA17: ATM.state 0→17 at `kATMact`. | +| 1597 | `Unlabeled` | one-way | ATM, DNA18 | `kATMact` | internal-state conversion/modification | `DNA18(site!?~cdsb) + ATM(state~0,h2ax) -> DNA18(site!?~cdsb) + ATM(state~18,h2ax)` | Changes internal modification/state marks on ATM, DNA18: ATM.state 0→18 at `kATMact`. | +| 1598 | `Unlabeled` | one-way | ATM, DNA19 | `kATMact` | internal-state conversion/modification | `DNA19(site!?~cdsb) + ATM(state~0,h2ax) -> DNA19(site!?~cdsb) + ATM(state~19,h2ax)` | Changes internal modification/state marks on ATM, DNA19: ATM.state 0→19 at `kATMact`. | +| 1599 | `Unlabeled` | one-way | ATM, DNA20 | `kATMact` | internal-state conversion/modification | `DNA20(site!?~cdsb) + ATM(state~0,h2ax) -> DNA20(site!?~cdsb) + ATM(state~20,h2ax)` | Changes internal modification/state marks on ATM, DNA20: ATM.state 0→20 at `kATMact`. | +| 1600 | `Unlabeled` | one-way | ATM, DNA21 | `kATMact` | internal-state conversion/modification | `DNA21(site!?~cdsb) + ATM(state~0,h2ax) -> DNA21(site!?~cdsb) + ATM(state~21,h2ax)` | Changes internal modification/state marks on ATM, DNA21: ATM.state 0→21 at `kATMact`. | +| 1601 | `Unlabeled` | one-way | ATM, DNA22 | `kATMact` | internal-state conversion/modification | `DNA22(site!?~cdsb) + ATM(state~0,h2ax) -> DNA22(site!?~cdsb) + ATM(state~22,h2ax)` | Changes internal modification/state marks on ATM, DNA22: ATM.state 0→22 at `kATMact`. | +| 1602 | `Unlabeled` | one-way | ATM, DNA23 | `kATMact` | internal-state conversion/modification | `DNA23(site!?~cdsb) + ATM(state~0,h2ax) -> DNA23(site!?~cdsb) + ATM(state~23,h2ax)` | Changes internal modification/state marks on ATM, DNA23: ATM.state 0→23 at `kATMact`. | +| 1603 | `Unlabeled` | one-way | ATM, DNA24 | `kATMact` | internal-state conversion/modification | `DNA24(site!?~cdsb) + ATM(state~0,h2ax) -> DNA24(site!?~cdsb) + ATM(state~24,h2ax)` | Changes internal modification/state marks on ATM, DNA24: ATM.state 0→24 at `kATMact`. | +| 1604 | `Unlabeled` | one-way | ATM, DNA25 | `kATMact` | internal-state conversion/modification | `DNA25(site!?~cdsb) + ATM(state~0,h2ax) -> DNA25(site!?~cdsb) + ATM(state~25,h2ax)` | Changes internal modification/state marks on ATM, DNA25: ATM.state 0→25 at `kATMact`. | +| 1605 | `Unlabeled` | one-way | ATM, DNA26 | `kATMact` | internal-state conversion/modification | `DNA26(site!?~cdsb) + ATM(state~0,h2ax) -> DNA26(site!?~cdsb) + ATM(state~26,h2ax)` | Changes internal modification/state marks on ATM, DNA26: ATM.state 0→26 at `kATMact`. | +| 1606 | `Unlabeled` | one-way | ATM, DNA27 | `kATMact` | internal-state conversion/modification | `DNA27(site!?~cdsb) + ATM(state~0,h2ax) -> DNA27(site!?~cdsb) + ATM(state~27,h2ax)` | Changes internal modification/state marks on ATM, DNA27: ATM.state 0→27 at `kATMact`. | +| 1607 | `Unlabeled` | one-way | ATM, DNA28 | `kATMact` | internal-state conversion/modification | `DNA28(site!?~cdsb) + ATM(state~0,h2ax) -> DNA28(site!?~cdsb) + ATM(state~28,h2ax)` | Changes internal modification/state marks on ATM, DNA28: ATM.state 0→28 at `kATMact`. | +| 1608 | `Unlabeled` | one-way | ATM, DNA29 | `kATMact` | internal-state conversion/modification | `DNA29(site!?~cdsb) + ATM(state~0,h2ax) -> DNA29(site!?~cdsb) + ATM(state~29,h2ax)` | Changes internal modification/state marks on ATM, DNA29: ATM.state 0→29 at `kATMact`. | +| 1609 | `Unlabeled` | one-way | ATM, DNA30 | `kATMact` | internal-state conversion/modification | `DNA30(site!?~cdsb) + ATM(state~0,h2ax) -> DNA30(site!?~cdsb) + ATM(state~30,h2ax)` | Changes internal modification/state marks on ATM, DNA30: ATM.state 0→30 at `kATMact`. | +| 1610 | `Unlabeled` | one-way | ATM, DNA31 | `kATMact` | internal-state conversion/modification | `DNA31(site!?~cdsb) + ATM(state~0,h2ax) -> DNA31(site!?~cdsb) + ATM(state~31,h2ax)` | Changes internal modification/state marks on ATM, DNA31: ATM.state 0→31 at `kATMact`. | +| 1611 | `Unlabeled` | one-way | ATM, DNA32 | `kATMact` | internal-state conversion/modification | `DNA32(site!?~cdsb) + ATM(state~0,h2ax) -> DNA32(site!?~cdsb) + ATM(state~32,h2ax)` | Changes internal modification/state marks on ATM, DNA32: ATM.state 0→32 at `kATMact`. | +| 1612 | `Unlabeled` | one-way | ATM, DNA33 | `kATMact` | internal-state conversion/modification | `DNA33(site!?~cdsb) + ATM(state~0,h2ax) -> DNA33(site!?~cdsb) + ATM(state~33,h2ax)` | Changes internal modification/state marks on ATM, DNA33: ATM.state 0→33 at `kATMact`. | +| 1613 | `Unlabeled` | one-way | ATM, DNA34 | `kATMact` | internal-state conversion/modification | `DNA34(site!?~cdsb) + ATM(state~0,h2ax) -> DNA34(site!?~cdsb) + ATM(state~34,h2ax)` | Changes internal modification/state marks on ATM, DNA34: ATM.state 0→34 at `kATMact`. | +| 1614 | `Unlabeled` | one-way | ATM, DNA35 | `kATMact` | internal-state conversion/modification | `DNA35(site!?~cdsb) + ATM(state~0,h2ax) -> DNA35(site!?~cdsb) + ATM(state~35,h2ax)` | Changes internal modification/state marks on ATM, DNA35: ATM.state 0→35 at `kATMact`. | +| 1615 | `Unlabeled` | one-way | ATM, DNA36 | `kATMact` | internal-state conversion/modification | `DNA36(site!?~cdsb) + ATM(state~0,h2ax) -> DNA36(site!?~cdsb) + ATM(state~36,h2ax)` | Changes internal modification/state marks on ATM, DNA36: ATM.state 0→36 at `kATMact`. | +| 1616 | `Unlabeled` | one-way | ATM, DNA37 | `kATMact` | internal-state conversion/modification | `DNA37(site!?~cdsb) + ATM(state~0,h2ax) -> DNA37(site!?~cdsb) + ATM(state~37,h2ax)` | Changes internal modification/state marks on ATM, DNA37: ATM.state 0→37 at `kATMact`. | +| 1617 | `Unlabeled` | one-way | ATM, DNA38 | `kATMact` | internal-state conversion/modification | `DNA38(site!?~cdsb) + ATM(state~0,h2ax) -> DNA38(site!?~cdsb) + ATM(state~38,h2ax)` | Changes internal modification/state marks on ATM, DNA38: ATM.state 0→38 at `kATMact`. | +| 1618 | `Unlabeled` | one-way | ATM, DNA39 | `kATMact` | internal-state conversion/modification | `DNA39(site!?~cdsb) + ATM(state~0,h2ax) -> DNA39(site!?~cdsb) + ATM(state~39,h2ax)` | Changes internal modification/state marks on ATM, DNA39: ATM.state 0→39 at `kATMact`. | +| 1619 | `Unlabeled` | one-way | ATM, DNA40 | `kATMact` | internal-state conversion/modification | `DNA40(site!?~cdsb) + ATM(state~0,h2ax) -> DNA40(site!?~cdsb) + ATM(state~40,h2ax)` | Changes internal modification/state marks on ATM, DNA40: ATM.state 0→40 at `kATMact`. | +| 1620 | `Unlabeled` | one-way | ATM, DNA41 | `kATMact` | internal-state conversion/modification | `DNA41(site!?~cdsb) + ATM(state~0,h2ax) -> DNA41(site!?~cdsb) + ATM(state~41,h2ax)` | Changes internal modification/state marks on ATM, DNA41: ATM.state 0→41 at `kATMact`. | +| 1621 | `Unlabeled` | one-way | ATM, DNA42 | `kATMact` | internal-state conversion/modification | `DNA42(site!?~cdsb) + ATM(state~0,h2ax) -> DNA42(site!?~cdsb) + ATM(state~42,h2ax)` | Changes internal modification/state marks on ATM, DNA42: ATM.state 0→42 at `kATMact`. | +| 1622 | `Unlabeled` | one-way | ATM, DNA43 | `kATMact` | internal-state conversion/modification | `DNA43(site!?~cdsb) + ATM(state~0,h2ax) -> DNA43(site!?~cdsb) + ATM(state~43,h2ax)` | Changes internal modification/state marks on ATM, DNA43: ATM.state 0→43 at `kATMact`. | +| 1623 | `Unlabeled` | one-way | ATM, DNA44 | `kATMact` | internal-state conversion/modification | `DNA44(site!?~cdsb) + ATM(state~0,h2ax) -> DNA44(site!?~cdsb) + ATM(state~44,h2ax)` | Changes internal modification/state marks on ATM, DNA44: ATM.state 0→44 at `kATMact`. | +| 1624 | `Unlabeled` | one-way | ATM, DNA45 | `kATMact` | internal-state conversion/modification | `DNA45(site!?~cdsb) + ATM(state~0,h2ax) -> DNA45(site!?~cdsb) + ATM(state~45,h2ax)` | Changes internal modification/state marks on ATM, DNA45: ATM.state 0→45 at `kATMact`. | +| 1625 | `Unlabeled` | one-way | ATM, DNA46 | `kATMact` | internal-state conversion/modification | `DNA46(site!?~cdsb) + ATM(state~0,h2ax) -> DNA46(site!?~cdsb) + ATM(state~46,h2ax)` | Changes internal modification/state marks on ATM, DNA46: ATM.state 0→46 at `kATMact`. | +| 1626 | `Unlabeled` | one-way | ATM, DNA47 | `kATMact` | internal-state conversion/modification | `DNA47(site!?~cdsb) + ATM(state~0,h2ax) -> DNA47(site!?~cdsb) + ATM(state~47,h2ax)` | Changes internal modification/state marks on ATM, DNA47: ATM.state 0→47 at `kATMact`. | +| 1627 | `Unlabeled` | one-way | ATM, DNA48 | `kATMact` | internal-state conversion/modification | `DNA48(site!?~cdsb) + ATM(state~0,h2ax) -> DNA48(site!?~cdsb) + ATM(state~48,h2ax)` | Changes internal modification/state marks on ATM, DNA48: ATM.state 0→48 at `kATMact`. | +| 1628 | `Unlabeled` | one-way | ATM, DNA49 | `kATMact` | internal-state conversion/modification | `DNA49(site!?~cdsb) + ATM(state~0,h2ax) -> DNA49(site!?~cdsb) + ATM(state~49,h2ax)` | Changes internal modification/state marks on ATM, DNA49: ATM.state 0→49 at `kATMact`. | +| 1629 | `Unlabeled` | one-way | ATM, DNA50 | `kATMact` | internal-state conversion/modification | `DNA50(site!?~cdsb) + ATM(state~0,h2ax) -> DNA50(site!?~cdsb) + ATM(state~50,h2ax)` | Changes internal modification/state marks on ATM, DNA50: ATM.state 0→50 at `kATMact`. | +| 1630 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~1,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 1→0 at `kATMinact`. | +| 1631 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~2,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 2→0 at `kATMinact`. | +| 1632 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~3,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 3→0 at `kATMinact`. | +| 1633 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~4,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 4→0 at `kATMinact`. | +| 1634 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~5,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 5→0 at `kATMinact`. | +| 1635 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~6,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 6→0 at `kATMinact`. | +| 1636 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~7,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 7→0 at `kATMinact`. | +| 1637 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~8,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 8→0 at `kATMinact`. | +| 1638 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~9,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 9→0 at `kATMinact`. | +| 1639 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~10,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 10→0 at `kATMinact`. | +| 1640 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~11,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 11→0 at `kATMinact`. | +| 1641 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~12,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 12→0 at `kATMinact`. | +| 1642 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~13,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 13→0 at `kATMinact`. | +| 1643 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~14,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 14→0 at `kATMinact`. | +| 1644 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~15,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 15→0 at `kATMinact`. | +| 1645 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~16,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 16→0 at `kATMinact`. | +| 1646 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~17,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 17→0 at `kATMinact`. | +| 1647 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~18,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 18→0 at `kATMinact`. | +| 1648 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~19,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 19→0 at `kATMinact`. | +| 1649 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~20,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 20→0 at `kATMinact`. | +| 1650 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~21,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 21→0 at `kATMinact`. | +| 1651 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~22,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 22→0 at `kATMinact`. | +| 1652 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~23,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 23→0 at `kATMinact`. | +| 1653 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~24,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 24→0 at `kATMinact`. | +| 1654 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~25,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 25→0 at `kATMinact`. | +| 1655 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~26,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 26→0 at `kATMinact`. | +| 1656 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~27,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 27→0 at `kATMinact`. | +| 1657 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~28,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 28→0 at `kATMinact`. | +| 1658 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~29,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 29→0 at `kATMinact`. | +| 1659 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~30,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 30→0 at `kATMinact`. | +| 1660 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~31,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 31→0 at `kATMinact`. | +| 1661 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~32,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 32→0 at `kATMinact`. | +| 1662 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~33,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 33→0 at `kATMinact`. | +| 1663 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~34,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 34→0 at `kATMinact`. | +| 1664 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~35,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 35→0 at `kATMinact`. | +| 1665 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~36,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 36→0 at `kATMinact`. | +| 1666 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~37,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 37→0 at `kATMinact`. | +| 1667 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~38,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 38→0 at `kATMinact`. | +| 1668 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~39,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 39→0 at `kATMinact`. | +| 1669 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~40,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 40→0 at `kATMinact`. | +| 1670 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~41,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 41→0 at `kATMinact`. | +| 1671 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~42,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 42→0 at `kATMinact`. | +| 1672 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~43,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 43→0 at `kATMinact`. | +| 1673 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~44,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 44→0 at `kATMinact`. | +| 1674 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~45,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 45→0 at `kATMinact`. | +| 1675 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~46,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 46→0 at `kATMinact`. | +| 1676 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~47,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 47→0 at `kATMinact`. | +| 1677 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~48,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 48→0 at `kATMinact`. | +| 1678 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~49,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 49→0 at `kATMinact`. | +| 1679 | `Unlabeled` | one-way | ATM | `kATMinact` | internal-state conversion/modification | `ATM(state~50,h2ax) -> ATM(state~0,h2ax)` | Changes internal modification/state marks on ATM: ATM.state 50→0 at `kATMinact`. | +| 1680 | `Unlabeled` | one-way | ATM, DNA1 | `kh2axp1` | internal-state conversion/modification | `DNA1(site!?~sdsb,h2ax~u) + ATM(state~1,h2ax) -> DNA1(site!?~sdsb,h2ax~p) + ATM(state~1,h2ax)` | Changes internal modification/state marks on ATM, DNA1: DNA1.h2ax u→p at `kh2axp1`. | +| 1681 | `Unlabeled` | one-way | ATM, DNA2 | `kh2axp1` | internal-state conversion/modification | `DNA2(site!?~sdsb,h2ax~u) + ATM(state~2,h2ax) -> DNA2(site!?~sdsb,h2ax~p) + ATM(state~2,h2ax)` | Changes internal modification/state marks on ATM, DNA2: DNA2.h2ax u→p at `kh2axp1`. | +| 1682 | `Unlabeled` | one-way | ATM, DNA3 | `kh2axp1` | internal-state conversion/modification | `DNA3(site!?~sdsb,h2ax~u) + ATM(state~3,h2ax) -> DNA3(site!?~sdsb,h2ax~p) + ATM(state~3,h2ax)` | Changes internal modification/state marks on ATM, DNA3: DNA3.h2ax u→p at `kh2axp1`. | +| 1683 | `Unlabeled` | one-way | ATM, DNA4 | `kh2axp1` | internal-state conversion/modification | `DNA4(site!?~sdsb,h2ax~u) + ATM(state~4,h2ax) -> DNA4(site!?~sdsb,h2ax~p) + ATM(state~4,h2ax)` | Changes internal modification/state marks on ATM, DNA4: DNA4.h2ax u→p at `kh2axp1`. | +| 1684 | `Unlabeled` | one-way | ATM, DNA5 | `kh2axp1` | internal-state conversion/modification | `DNA5(site!?~sdsb,h2ax~u) + ATM(state~5,h2ax) -> DNA5(site!?~sdsb,h2ax~p) + ATM(state~5,h2ax)` | Changes internal modification/state marks on ATM, DNA5: DNA5.h2ax u→p at `kh2axp1`. | +| 1685 | `Unlabeled` | one-way | ATM, DNA6 | `kh2axp1` | internal-state conversion/modification | `DNA6(site!?~sdsb,h2ax~u) + ATM(state~6,h2ax) -> DNA6(site!?~sdsb,h2ax~p) + ATM(state~6,h2ax)` | Changes internal modification/state marks on ATM, DNA6: DNA6.h2ax u→p at `kh2axp1`. | +| 1686 | `Unlabeled` | one-way | ATM, DNA7 | `kh2axp1` | internal-state conversion/modification | `DNA7(site!?~sdsb,h2ax~u) + ATM(state~7,h2ax) -> DNA7(site!?~sdsb,h2ax~p) + ATM(state~7,h2ax)` | Changes internal modification/state marks on ATM, DNA7: DNA7.h2ax u→p at `kh2axp1`. | +| 1687 | `Unlabeled` | one-way | ATM, DNA8 | `kh2axp1` | internal-state conversion/modification | `DNA8(site!?~sdsb,h2ax~u) + ATM(state~8,h2ax) -> DNA8(site!?~sdsb,h2ax~p) + ATM(state~8,h2ax)` | Changes internal modification/state marks on ATM, DNA8: DNA8.h2ax u→p at `kh2axp1`. | +| 1688 | `Unlabeled` | one-way | ATM, DNA9 | `kh2axp1` | internal-state conversion/modification | `DNA9(site!?~sdsb,h2ax~u) + ATM(state~9,h2ax) -> DNA9(site!?~sdsb,h2ax~p) + ATM(state~9,h2ax)` | Changes internal modification/state marks on ATM, DNA9: DNA9.h2ax u→p at `kh2axp1`. | +| 1689 | `Unlabeled` | one-way | ATM, DNA10 | `kh2axp1` | internal-state conversion/modification | `DNA10(site!?~sdsb,h2ax~u) + ATM(state~10,h2ax) -> DNA10(site!?~sdsb,h2ax~p) + ATM(state~10,h2ax)` | Changes internal modification/state marks on ATM, DNA10: DNA10.h2ax u→p at `kh2axp1`. | +| 1690 | `Unlabeled` | one-way | ATM, DNA11 | `kh2axp1` | internal-state conversion/modification | `DNA11(site!?~sdsb,h2ax~u) + ATM(state~11,h2ax) -> DNA11(site!?~sdsb,h2ax~p) + ATM(state~11,h2ax)` | Changes internal modification/state marks on ATM, DNA11: DNA11.h2ax u→p at `kh2axp1`. | +| 1691 | `Unlabeled` | one-way | ATM, DNA12 | `kh2axp1` | internal-state conversion/modification | `DNA12(site!?~sdsb,h2ax~u) + ATM(state~12,h2ax) -> DNA12(site!?~sdsb,h2ax~p) + ATM(state~12,h2ax)` | Changes internal modification/state marks on ATM, DNA12: DNA12.h2ax u→p at `kh2axp1`. | +| 1692 | `Unlabeled` | one-way | ATM, DNA13 | `kh2axp1` | internal-state conversion/modification | `DNA13(site!?~sdsb,h2ax~u) + ATM(state~13,h2ax) -> DNA13(site!?~sdsb,h2ax~p) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA13: DNA13.h2ax u→p at `kh2axp1`. | +| 1693 | `Unlabeled` | one-way | ATM, DNA14 | `kh2axp1` | internal-state conversion/modification | `DNA14(site!?~sdsb,h2ax~u) + ATM(state~14,h2ax) -> DNA14(site!?~sdsb,h2ax~p) + ATM(state~14,h2ax)` | Changes internal modification/state marks on ATM, DNA14: DNA14.h2ax u→p at `kh2axp1`. | +| 1694 | `Unlabeled` | one-way | ATM, DNA15 | `kh2axp1` | internal-state conversion/modification | `DNA15(site!?~sdsb,h2ax~u) + ATM(state~15,h2ax) -> DNA15(site!?~sdsb,h2ax~p) + ATM(state~15,h2ax)` | Changes internal modification/state marks on ATM, DNA15: DNA15.h2ax u→p at `kh2axp1`. | +| 1695 | `Unlabeled` | one-way | ATM, DNA16 | `kh2axp1` | internal-state conversion/modification | `DNA16(site!?~sdsb,h2ax~u) + ATM(state~16,h2ax) -> DNA16(site!?~sdsb,h2ax~p) + ATM(state~16,h2ax)` | Changes internal modification/state marks on ATM, DNA16: DNA16.h2ax u→p at `kh2axp1`. | +| 1696 | `Unlabeled` | one-way | ATM, DNA17 | `kh2axp1` | internal-state conversion/modification | `DNA17(site!?~sdsb,h2ax~u) + ATM(state~17,h2ax) -> DNA17(site!?~sdsb,h2ax~p) + ATM(state~17,h2ax)` | Changes internal modification/state marks on ATM, DNA17: DNA17.h2ax u→p at `kh2axp1`. | +| 1697 | `Unlabeled` | one-way | ATM, DNA18 | `kh2axp1` | internal-state conversion/modification | `DNA18(site!?~sdsb,h2ax~u) + ATM(state~18,h2ax) -> DNA18(site!?~sdsb,h2ax~p) + ATM(state~18,h2ax)` | Changes internal modification/state marks on ATM, DNA18: DNA18.h2ax u→p at `kh2axp1`. | +| 1698 | `Unlabeled` | one-way | ATM, DNA19 | `kh2axp1` | internal-state conversion/modification | `DNA19(site!?~sdsb,h2ax~u) + ATM(state~19,h2ax) -> DNA19(site!?~sdsb,h2ax~p) + ATM(state~19,h2ax)` | Changes internal modification/state marks on ATM, DNA19: DNA19.h2ax u→p at `kh2axp1`. | +| 1699 | `Unlabeled` | one-way | ATM, DNA20 | `kh2axp1` | internal-state conversion/modification | `DNA20(site!?~sdsb,h2ax~u) + ATM(state~20,h2ax) -> DNA20(site!?~sdsb,h2ax~p) + ATM(state~20,h2ax)` | Changes internal modification/state marks on ATM, DNA20: DNA20.h2ax u→p at `kh2axp1`. | +| 1700 | `Unlabeled` | one-way | ATM, DNA21 | `kh2axp1` | internal-state conversion/modification | `DNA21(site!?~sdsb,h2ax~u) + ATM(state~21,h2ax) -> DNA21(site!?~sdsb,h2ax~p) + ATM(state~21,h2ax)` | Changes internal modification/state marks on ATM, DNA21: DNA21.h2ax u→p at `kh2axp1`. | +| 1701 | `Unlabeled` | one-way | ATM, DNA22 | `kh2axp1` | internal-state conversion/modification | `DNA22(site!?~sdsb,h2ax~u) + ATM(state~22,h2ax) -> DNA22(site!?~sdsb,h2ax~p) + ATM(state~22,h2ax)` | Changes internal modification/state marks on ATM, DNA22: DNA22.h2ax u→p at `kh2axp1`. | +| 1702 | `Unlabeled` | one-way | ATM, DNA23 | `kh2axp1` | internal-state conversion/modification | `DNA23(site!?~sdsb,h2ax~u) + ATM(state~23,h2ax) -> DNA23(site!?~sdsb,h2ax~p) + ATM(state~23,h2ax)` | Changes internal modification/state marks on ATM, DNA23: DNA23.h2ax u→p at `kh2axp1`. | +| 1703 | `Unlabeled` | one-way | ATM, DNA24 | `kh2axp1` | internal-state conversion/modification | `DNA24(site!?~sdsb,h2ax~u) + ATM(state~24,h2ax) -> DNA24(site!?~sdsb,h2ax~p) + ATM(state~24,h2ax)` | Changes internal modification/state marks on ATM, DNA24: DNA24.h2ax u→p at `kh2axp1`. | +| 1704 | `Unlabeled` | one-way | ATM, DNA25 | `kh2axp1` | internal-state conversion/modification | `DNA25(site!?~sdsb,h2ax~u) + ATM(state~25,h2ax) -> DNA25(site!?~sdsb,h2ax~p) + ATM(state~25,h2ax)` | Changes internal modification/state marks on ATM, DNA25: DNA25.h2ax u→p at `kh2axp1`. | +| 1705 | `Unlabeled` | one-way | ATM, DNA26 | `kh2axp1` | internal-state conversion/modification | `DNA26(site!?~sdsb,h2ax~u) + ATM(state~26,h2ax) -> DNA26(site!?~sdsb,h2ax~p) + ATM(state~26,h2ax)` | Changes internal modification/state marks on ATM, DNA26: DNA26.h2ax u→p at `kh2axp1`. | +| 1706 | `Unlabeled` | one-way | ATM, DNA27 | `kh2axp1` | internal-state conversion/modification | `DNA27(site!?~sdsb,h2ax~u) + ATM(state~27,h2ax) -> DNA27(site!?~sdsb,h2ax~p) + ATM(state~27,h2ax)` | Changes internal modification/state marks on ATM, DNA27: DNA27.h2ax u→p at `kh2axp1`. | +| 1707 | `Unlabeled` | one-way | ATM, DNA28 | `kh2axp1` | internal-state conversion/modification | `DNA28(site!?~sdsb,h2ax~u) + ATM(state~28,h2ax) -> DNA28(site!?~sdsb,h2ax~p) + ATM(state~28,h2ax)` | Changes internal modification/state marks on ATM, DNA28: DNA28.h2ax u→p at `kh2axp1`. | +| 1708 | `Unlabeled` | one-way | ATM, DNA29 | `kh2axp1` | internal-state conversion/modification | `DNA29(site!?~sdsb,h2ax~u) + ATM(state~29,h2ax) -> DNA29(site!?~sdsb,h2ax~p) + ATM(state~29,h2ax)` | Changes internal modification/state marks on ATM, DNA29: DNA29.h2ax u→p at `kh2axp1`. | +| 1709 | `Unlabeled` | one-way | ATM, DNA30 | `kh2axp1` | internal-state conversion/modification | `DNA30(site!?~sdsb,h2ax~u) + ATM(state~30,h2ax) -> DNA30(site!?~sdsb,h2ax~p) + ATM(state~30,h2ax)` | Changes internal modification/state marks on ATM, DNA30: DNA30.h2ax u→p at `kh2axp1`. | +| 1710 | `Unlabeled` | one-way | ATM, DNA31 | `kh2axp1` | internal-state conversion/modification | `DNA31(site!?~sdsb,h2ax~u) + ATM(state~31,h2ax) -> DNA31(site!?~sdsb,h2ax~p) + ATM(state~31,h2ax)` | Changes internal modification/state marks on ATM, DNA31: DNA31.h2ax u→p at `kh2axp1`. | +| 1711 | `Unlabeled` | one-way | ATM, DNA32 | `kh2axp1` | internal-state conversion/modification | `DNA32(site!?~sdsb,h2ax~u) + ATM(state~32,h2ax) -> DNA32(site!?~sdsb,h2ax~p) + ATM(state~32,h2ax)` | Changes internal modification/state marks on ATM, DNA32: DNA32.h2ax u→p at `kh2axp1`. | +| 1712 | `Unlabeled` | one-way | ATM, DNA33 | `kh2axp1` | internal-state conversion/modification | `DNA33(site!?~sdsb,h2ax~u) + ATM(state~33,h2ax) -> DNA33(site!?~sdsb,h2ax~p) + ATM(state~33,h2ax)` | Changes internal modification/state marks on ATM, DNA33: DNA33.h2ax u→p at `kh2axp1`. | +| 1713 | `Unlabeled` | one-way | ATM, DNA34 | `kh2axp1` | internal-state conversion/modification | `DNA34(site!?~sdsb,h2ax~u) + ATM(state~34,h2ax) -> DNA34(site!?~sdsb,h2ax~p) + ATM(state~34,h2ax)` | Changes internal modification/state marks on ATM, DNA34: DNA34.h2ax u→p at `kh2axp1`. | +| 1714 | `Unlabeled` | one-way | ATM, DNA35 | `kh2axp1` | internal-state conversion/modification | `DNA35(site!?~sdsb,h2ax~u) + ATM(state~35,h2ax) -> DNA35(site!?~sdsb,h2ax~p) + ATM(state~35,h2ax)` | Changes internal modification/state marks on ATM, DNA35: DNA35.h2ax u→p at `kh2axp1`. | +| 1715 | `Unlabeled` | one-way | ATM, DNA36 | `kh2axp1` | internal-state conversion/modification | `DNA36(site!?~sdsb,h2ax~u) + ATM(state~36,h2ax) -> DNA36(site!?~sdsb,h2ax~p) + ATM(state~36,h2ax)` | Changes internal modification/state marks on ATM, DNA36: DNA36.h2ax u→p at `kh2axp1`. | +| 1716 | `Unlabeled` | one-way | ATM, DNA37 | `kh2axp1` | internal-state conversion/modification | `DNA37(site!?~sdsb,h2ax~u) + ATM(state~37,h2ax) -> DNA37(site!?~sdsb,h2ax~p) + ATM(state~37,h2ax)` | Changes internal modification/state marks on ATM, DNA37: DNA37.h2ax u→p at `kh2axp1`. | +| 1717 | `Unlabeled` | one-way | ATM, DNA38 | `kh2axp1` | internal-state conversion/modification | `DNA38(site!?~sdsb,h2ax~u) + ATM(state~38,h2ax) -> DNA38(site!?~sdsb,h2ax~p) + ATM(state~38,h2ax)` | Changes internal modification/state marks on ATM, DNA38: DNA38.h2ax u→p at `kh2axp1`. | +| 1718 | `Unlabeled` | one-way | ATM, DNA39 | `kh2axp1` | internal-state conversion/modification | `DNA39(site!?~sdsb,h2ax~u) + ATM(state~39,h2ax) -> DNA39(site!?~sdsb,h2ax~p) + ATM(state~39,h2ax)` | Changes internal modification/state marks on ATM, DNA39: DNA39.h2ax u→p at `kh2axp1`. | +| 1719 | `Unlabeled` | one-way | ATM, DNA40 | `kh2axp1` | internal-state conversion/modification | `DNA40(site!?~sdsb,h2ax~u) + ATM(state~40,h2ax) -> DNA40(site!?~sdsb,h2ax~p) + ATM(state~40,h2ax)` | Changes internal modification/state marks on ATM, DNA40: DNA40.h2ax u→p at `kh2axp1`. | +| 1720 | `Unlabeled` | one-way | ATM, DNA41 | `kh2axp1` | internal-state conversion/modification | `DNA41(site!?~sdsb,h2ax~u) + ATM(state~41,h2ax) -> DNA41(site!?~sdsb,h2ax~p) + ATM(state~41,h2ax)` | Changes internal modification/state marks on ATM, DNA41: DNA41.h2ax u→p at `kh2axp1`. | +| 1721 | `Unlabeled` | one-way | ATM, DNA42 | `kh2axp1` | internal-state conversion/modification | `DNA42(site!?~sdsb,h2ax~u) + ATM(state~42,h2ax) -> DNA42(site!?~sdsb,h2ax~p) + ATM(state~42,h2ax)` | Changes internal modification/state marks on ATM, DNA42: DNA42.h2ax u→p at `kh2axp1`. | +| 1722 | `Unlabeled` | one-way | ATM, DNA43 | `kh2axp1` | internal-state conversion/modification | `DNA43(site!?~sdsb,h2ax~u) + ATM(state~43,h2ax) -> DNA43(site!?~sdsb,h2ax~p) + ATM(state~43,h2ax)` | Changes internal modification/state marks on ATM, DNA43: DNA43.h2ax u→p at `kh2axp1`. | +| 1723 | `Unlabeled` | one-way | ATM, DNA44 | `kh2axp1` | internal-state conversion/modification | `DNA44(site!?~sdsb,h2ax~u) + ATM(state~44,h2ax) -> DNA44(site!?~sdsb,h2ax~p) + ATM(state~44,h2ax)` | Changes internal modification/state marks on ATM, DNA44: DNA44.h2ax u→p at `kh2axp1`. | +| 1724 | `Unlabeled` | one-way | ATM, DNA45 | `kh2axp1` | internal-state conversion/modification | `DNA45(site!?~sdsb,h2ax~u) + ATM(state~45,h2ax) -> DNA45(site!?~sdsb,h2ax~p) + ATM(state~45,h2ax)` | Changes internal modification/state marks on ATM, DNA45: DNA45.h2ax u→p at `kh2axp1`. | +| 1725 | `Unlabeled` | one-way | ATM, DNA46 | `kh2axp1` | internal-state conversion/modification | `DNA46(site!?~sdsb,h2ax~u) + ATM(state~46,h2ax) -> DNA46(site!?~sdsb,h2ax~p) + ATM(state~46,h2ax)` | Changes internal modification/state marks on ATM, DNA46: DNA46.h2ax u→p at `kh2axp1`. | +| 1726 | `Unlabeled` | one-way | ATM, DNA47 | `kh2axp1` | internal-state conversion/modification | `DNA47(site!?~sdsb,h2ax~u) + ATM(state~47,h2ax) -> DNA47(site!?~sdsb,h2ax~p) + ATM(state~47,h2ax)` | Changes internal modification/state marks on ATM, DNA47: DNA47.h2ax u→p at `kh2axp1`. | +| 1727 | `Unlabeled` | one-way | ATM, DNA48 | `kh2axp1` | internal-state conversion/modification | `DNA48(site!?~sdsb,h2ax~u) + ATM(state~48,h2ax) -> DNA48(site!?~sdsb,h2ax~p) + ATM(state~48,h2ax)` | Changes internal modification/state marks on ATM, DNA48: DNA48.h2ax u→p at `kh2axp1`. | +| 1728 | `Unlabeled` | one-way | ATM, DNA49 | `kh2axp1` | internal-state conversion/modification | `DNA49(site!?~sdsb,h2ax~u) + ATM(state~49,h2ax) -> DNA49(site!?~sdsb,h2ax~p) + ATM(state~49,h2ax)` | Changes internal modification/state marks on ATM, DNA49: DNA49.h2ax u→p at `kh2axp1`. | +| 1729 | `Unlabeled` | one-way | ATM, DNA50 | `kh2axp1` | internal-state conversion/modification | `DNA50(site!?~sdsb,h2ax~u) + ATM(state~50,h2ax) -> DNA50(site!?~sdsb,h2ax~p) + ATM(state~50,h2ax)` | Changes internal modification/state marks on ATM, DNA50: DNA50.h2ax u→p at `kh2axp1`. | +| 1730 | `Unlabeled` | one-way | ATM, DNA1 | `kh2axp1` | internal-state conversion/modification | `DNA1(site!?~cdsb,h2ax~u) + ATM(state~1,h2ax) -> DNA1(site!?~cdsb,h2ax~p) + ATM(state~1,h2ax)` | Changes internal modification/state marks on ATM, DNA1: DNA1.h2ax u→p at `kh2axp1`. | +| 1731 | `Unlabeled` | one-way | ATM, DNA2 | `kh2axp1` | internal-state conversion/modification | `DNA2(site!?~cdsb,h2ax~u) + ATM(state~2,h2ax) -> DNA2(site!?~cdsb,h2ax~p) + ATM(state~2,h2ax)` | Changes internal modification/state marks on ATM, DNA2: DNA2.h2ax u→p at `kh2axp1`. | +| 1732 | `Unlabeled` | one-way | ATM, DNA3 | `kh2axp1` | internal-state conversion/modification | `DNA3(site!?~cdsb,h2ax~u) + ATM(state~3,h2ax) -> DNA3(site!?~cdsb,h2ax~p) + ATM(state~3,h2ax)` | Changes internal modification/state marks on ATM, DNA3: DNA3.h2ax u→p at `kh2axp1`. | +| 1733 | `Unlabeled` | one-way | ATM, DNA4 | `kh2axp1` | internal-state conversion/modification | `DNA4(site!?~cdsb,h2ax~u) + ATM(state~4,h2ax) -> DNA4(site!?~cdsb,h2ax~p) + ATM(state~4,h2ax)` | Changes internal modification/state marks on ATM, DNA4: DNA4.h2ax u→p at `kh2axp1`. | +| 1734 | `Unlabeled` | one-way | ATM, DNA5 | `kh2axp1` | internal-state conversion/modification | `DNA5(site!?~cdsb,h2ax~u) + ATM(state~5,h2ax) -> DNA5(site!?~cdsb,h2ax~p) + ATM(state~5,h2ax)` | Changes internal modification/state marks on ATM, DNA5: DNA5.h2ax u→p at `kh2axp1`. | +| 1735 | `Unlabeled` | one-way | ATM, DNA6 | `kh2axp1` | internal-state conversion/modification | `DNA6(site!?~cdsb,h2ax~u) + ATM(state~6,h2ax) -> DNA6(site!?~cdsb,h2ax~p) + ATM(state~6,h2ax)` | Changes internal modification/state marks on ATM, DNA6: DNA6.h2ax u→p at `kh2axp1`. | +| 1736 | `Unlabeled` | one-way | ATM, DNA7 | `kh2axp1` | internal-state conversion/modification | `DNA7(site!?~cdsb,h2ax~u) + ATM(state~7,h2ax) -> DNA7(site!?~cdsb,h2ax~p) + ATM(state~7,h2ax)` | Changes internal modification/state marks on ATM, DNA7: DNA7.h2ax u→p at `kh2axp1`. | +| 1737 | `Unlabeled` | one-way | ATM, DNA8 | `kh2axp1` | internal-state conversion/modification | `DNA8(site!?~cdsb,h2ax~u) + ATM(state~8,h2ax) -> DNA8(site!?~cdsb,h2ax~p) + ATM(state~8,h2ax)` | Changes internal modification/state marks on ATM, DNA8: DNA8.h2ax u→p at `kh2axp1`. | +| 1738 | `Unlabeled` | one-way | ATM, DNA9 | `kh2axp1` | internal-state conversion/modification | `DNA9(site!?~cdsb,h2ax~u) + ATM(state~9,h2ax) -> DNA9(site!?~cdsb,h2ax~p) + ATM(state~9,h2ax)` | Changes internal modification/state marks on ATM, DNA9: DNA9.h2ax u→p at `kh2axp1`. | +| 1739 | `Unlabeled` | one-way | ATM, DNA10 | `kh2axp1` | internal-state conversion/modification | `DNA10(site!?~cdsb,h2ax~u) + ATM(state~10,h2ax) -> DNA10(site!?~cdsb,h2ax~p) + ATM(state~10,h2ax)` | Changes internal modification/state marks on ATM, DNA10: DNA10.h2ax u→p at `kh2axp1`. | +| 1740 | `Unlabeled` | one-way | ATM, DNA11 | `kh2axp1` | internal-state conversion/modification | `DNA11(site!?~cdsb,h2ax~u) + ATM(state~11,h2ax) -> DNA11(site!?~cdsb,h2ax~p) + ATM(state~11,h2ax)` | Changes internal modification/state marks on ATM, DNA11: DNA11.h2ax u→p at `kh2axp1`. | +| 1741 | `Unlabeled` | one-way | ATM, DNA12 | `kh2axp1` | internal-state conversion/modification | `DNA12(site!?~cdsb,h2ax~u) + ATM(state~12,h2ax) -> DNA12(site!?~cdsb,h2ax~p) + ATM(state~12,h2ax)` | Changes internal modification/state marks on ATM, DNA12: DNA12.h2ax u→p at `kh2axp1`. | +| 1742 | `Unlabeled` | one-way | ATM, DNA13 | `kh2axp1` | internal-state conversion/modification | `DNA13(site!?~cdsb,h2ax~u) + ATM(state~13,h2ax) -> DNA13(site!?~cdsb,h2ax~p) + ATM(state~13,h2ax)` | Changes internal modification/state marks on ATM, DNA13: DNA13.h2ax u→p at `kh2axp1`. | +| 1743 | `Unlabeled` | one-way | ATM, DNA14 | `kh2axp1` | internal-state conversion/modification | `DNA14(site!?~cdsb,h2ax~u) + ATM(state~14,h2ax) -> DNA14(site!?~cdsb,h2ax~p) + ATM(state~14,h2ax)` | Changes internal modification/state marks on ATM, DNA14: DNA14.h2ax u→p at `kh2axp1`. | +| 1744 | `Unlabeled` | one-way | ATM, DNA15 | `kh2axp1` | internal-state conversion/modification | `DNA15(site!?~cdsb,h2ax~u) + ATM(state~15,h2ax) -> DNA15(site!?~cdsb,h2ax~p) + ATM(state~15,h2ax)` | Changes internal modification/state marks on ATM, DNA15: DNA15.h2ax u→p at `kh2axp1`. | +| 1745 | `Unlabeled` | one-way | ATM, DNA16 | `kh2axp1` | internal-state conversion/modification | `DNA16(site!?~cdsb,h2ax~u) + ATM(state~16,h2ax) -> DNA16(site!?~cdsb,h2ax~p) + ATM(state~16,h2ax)` | Changes internal modification/state marks on ATM, DNA16: DNA16.h2ax u→p at `kh2axp1`. | +| 1746 | `Unlabeled` | one-way | ATM, DNA17 | `kh2axp1` | internal-state conversion/modification | `DNA17(site!?~cdsb,h2ax~u) + ATM(state~17,h2ax) -> DNA17(site!?~cdsb,h2ax~p) + ATM(state~17,h2ax)` | Changes internal modification/state marks on ATM, DNA17: DNA17.h2ax u→p at `kh2axp1`. | +| 1747 | `Unlabeled` | one-way | ATM, DNA18 | `kh2axp1` | internal-state conversion/modification | `DNA18(site!?~cdsb,h2ax~u) + ATM(state~18,h2ax) -> DNA18(site!?~cdsb,h2ax~p) + ATM(state~18,h2ax)` | Changes internal modification/state marks on ATM, DNA18: DNA18.h2ax u→p at `kh2axp1`. | +| 1748 | `Unlabeled` | one-way | ATM, DNA19 | `kh2axp1` | internal-state conversion/modification | `DNA19(site!?~cdsb,h2ax~u) + ATM(state~19,h2ax) -> DNA19(site!?~cdsb,h2ax~p) + ATM(state~19,h2ax)` | Changes internal modification/state marks on ATM, DNA19: DNA19.h2ax u→p at `kh2axp1`. | +| 1749 | `Unlabeled` | one-way | ATM, DNA20 | `kh2axp1` | internal-state conversion/modification | `DNA20(site!?~cdsb,h2ax~u) + ATM(state~20,h2ax) -> DNA20(site!?~cdsb,h2ax~p) + ATM(state~20,h2ax)` | Changes internal modification/state marks on ATM, DNA20: DNA20.h2ax u→p at `kh2axp1`. | +| 1750 | `Unlabeled` | one-way | ATM, DNA21 | `kh2axp1` | internal-state conversion/modification | `DNA21(site!?~cdsb,h2ax~u) + ATM(state~21,h2ax) -> DNA21(site!?~cdsb,h2ax~p) + ATM(state~21,h2ax)` | Changes internal modification/state marks on ATM, DNA21: DNA21.h2ax u→p at `kh2axp1`. | + +### Rules 1751-2000 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1751 | `Unlabeled` | one-way | ATM, DNA22 | `kh2axp1` | internal-state conversion/modification | `DNA22(site!?~cdsb,h2ax~u) + ATM(state~22,h2ax) -> DNA22(site!?~cdsb,h2ax~p) + ATM(state~22,h2ax)` | Changes internal modification/state marks on ATM, DNA22: DNA22.h2ax u→p at `kh2axp1`. | +| 1752 | `Unlabeled` | one-way | ATM, DNA23 | `kh2axp1` | internal-state conversion/modification | `DNA23(site!?~cdsb,h2ax~u) + ATM(state~23,h2ax) -> DNA23(site!?~cdsb,h2ax~p) + ATM(state~23,h2ax)` | Changes internal modification/state marks on ATM, DNA23: DNA23.h2ax u→p at `kh2axp1`. | +| 1753 | `Unlabeled` | one-way | ATM, DNA24 | `kh2axp1` | internal-state conversion/modification | `DNA24(site!?~cdsb,h2ax~u) + ATM(state~24,h2ax) -> DNA24(site!?~cdsb,h2ax~p) + ATM(state~24,h2ax)` | Changes internal modification/state marks on ATM, DNA24: DNA24.h2ax u→p at `kh2axp1`. | +| 1754 | `Unlabeled` | one-way | ATM, DNA25 | `kh2axp1` | internal-state conversion/modification | `DNA25(site!?~cdsb,h2ax~u) + ATM(state~25,h2ax) -> DNA25(site!?~cdsb,h2ax~p) + ATM(state~25,h2ax)` | Changes internal modification/state marks on ATM, DNA25: DNA25.h2ax u→p at `kh2axp1`. | +| 1755 | `Unlabeled` | one-way | ATM, DNA26 | `kh2axp1` | internal-state conversion/modification | `DNA26(site!?~cdsb,h2ax~u) + ATM(state~26,h2ax) -> DNA26(site!?~cdsb,h2ax~p) + ATM(state~26,h2ax)` | Changes internal modification/state marks on ATM, DNA26: DNA26.h2ax u→p at `kh2axp1`. | +| 1756 | `Unlabeled` | one-way | ATM, DNA27 | `kh2axp1` | internal-state conversion/modification | `DNA27(site!?~cdsb,h2ax~u) + ATM(state~27,h2ax) -> DNA27(site!?~cdsb,h2ax~p) + ATM(state~27,h2ax)` | Changes internal modification/state marks on ATM, DNA27: DNA27.h2ax u→p at `kh2axp1`. | +| 1757 | `Unlabeled` | one-way | ATM, DNA28 | `kh2axp1` | internal-state conversion/modification | `DNA28(site!?~cdsb,h2ax~u) + ATM(state~28,h2ax) -> DNA28(site!?~cdsb,h2ax~p) + ATM(state~28,h2ax)` | Changes internal modification/state marks on ATM, DNA28: DNA28.h2ax u→p at `kh2axp1`. | +| 1758 | `Unlabeled` | one-way | ATM, DNA29 | `kh2axp1` | internal-state conversion/modification | `DNA29(site!?~cdsb,h2ax~u) + ATM(state~29,h2ax) -> DNA29(site!?~cdsb,h2ax~p) + ATM(state~29,h2ax)` | Changes internal modification/state marks on ATM, DNA29: DNA29.h2ax u→p at `kh2axp1`. | +| 1759 | `Unlabeled` | one-way | ATM, DNA30 | `kh2axp1` | internal-state conversion/modification | `DNA30(site!?~cdsb,h2ax~u) + ATM(state~30,h2ax) -> DNA30(site!?~cdsb,h2ax~p) + ATM(state~30,h2ax)` | Changes internal modification/state marks on ATM, DNA30: DNA30.h2ax u→p at `kh2axp1`. | +| 1760 | `Unlabeled` | one-way | ATM, DNA31 | `kh2axp1` | internal-state conversion/modification | `DNA31(site!?~cdsb,h2ax~u) + ATM(state~31,h2ax) -> DNA31(site!?~cdsb,h2ax~p) + ATM(state~31,h2ax)` | Changes internal modification/state marks on ATM, DNA31: DNA31.h2ax u→p at `kh2axp1`. | +| 1761 | `Unlabeled` | one-way | ATM, DNA32 | `kh2axp1` | internal-state conversion/modification | `DNA32(site!?~cdsb,h2ax~u) + ATM(state~32,h2ax) -> DNA32(site!?~cdsb,h2ax~p) + ATM(state~32,h2ax)` | Changes internal modification/state marks on ATM, DNA32: DNA32.h2ax u→p at `kh2axp1`. | +| 1762 | `Unlabeled` | one-way | ATM, DNA33 | `kh2axp1` | internal-state conversion/modification | `DNA33(site!?~cdsb,h2ax~u) + ATM(state~33,h2ax) -> DNA33(site!?~cdsb,h2ax~p) + ATM(state~33,h2ax)` | Changes internal modification/state marks on ATM, DNA33: DNA33.h2ax u→p at `kh2axp1`. | +| 1763 | `Unlabeled` | one-way | ATM, DNA34 | `kh2axp1` | internal-state conversion/modification | `DNA34(site!?~cdsb,h2ax~u) + ATM(state~34,h2ax) -> DNA34(site!?~cdsb,h2ax~p) + ATM(state~34,h2ax)` | Changes internal modification/state marks on ATM, DNA34: DNA34.h2ax u→p at `kh2axp1`. | +| 1764 | `Unlabeled` | one-way | ATM, DNA35 | `kh2axp1` | internal-state conversion/modification | `DNA35(site!?~cdsb,h2ax~u) + ATM(state~35,h2ax) -> DNA35(site!?~cdsb,h2ax~p) + ATM(state~35,h2ax)` | Changes internal modification/state marks on ATM, DNA35: DNA35.h2ax u→p at `kh2axp1`. | +| 1765 | `Unlabeled` | one-way | ATM, DNA36 | `kh2axp1` | internal-state conversion/modification | `DNA36(site!?~cdsb,h2ax~u) + ATM(state~36,h2ax) -> DNA36(site!?~cdsb,h2ax~p) + ATM(state~36,h2ax)` | Changes internal modification/state marks on ATM, DNA36: DNA36.h2ax u→p at `kh2axp1`. | +| 1766 | `Unlabeled` | one-way | ATM, DNA37 | `kh2axp1` | internal-state conversion/modification | `DNA37(site!?~cdsb,h2ax~u) + ATM(state~37,h2ax) -> DNA37(site!?~cdsb,h2ax~p) + ATM(state~37,h2ax)` | Changes internal modification/state marks on ATM, DNA37: DNA37.h2ax u→p at `kh2axp1`. | +| 1767 | `Unlabeled` | one-way | ATM, DNA38 | `kh2axp1` | internal-state conversion/modification | `DNA38(site!?~cdsb,h2ax~u) + ATM(state~38,h2ax) -> DNA38(site!?~cdsb,h2ax~p) + ATM(state~38,h2ax)` | Changes internal modification/state marks on ATM, DNA38: DNA38.h2ax u→p at `kh2axp1`. | +| 1768 | `Unlabeled` | one-way | ATM, DNA39 | `kh2axp1` | internal-state conversion/modification | `DNA39(site!?~cdsb,h2ax~u) + ATM(state~39,h2ax) -> DNA39(site!?~cdsb,h2ax~p) + ATM(state~39,h2ax)` | Changes internal modification/state marks on ATM, DNA39: DNA39.h2ax u→p at `kh2axp1`. | +| 1769 | `Unlabeled` | one-way | ATM, DNA40 | `kh2axp1` | internal-state conversion/modification | `DNA40(site!?~cdsb,h2ax~u) + ATM(state~40,h2ax) -> DNA40(site!?~cdsb,h2ax~p) + ATM(state~40,h2ax)` | Changes internal modification/state marks on ATM, DNA40: DNA40.h2ax u→p at `kh2axp1`. | +| 1770 | `Unlabeled` | one-way | ATM, DNA41 | `kh2axp1` | internal-state conversion/modification | `DNA41(site!?~cdsb,h2ax~u) + ATM(state~41,h2ax) -> DNA41(site!?~cdsb,h2ax~p) + ATM(state~41,h2ax)` | Changes internal modification/state marks on ATM, DNA41: DNA41.h2ax u→p at `kh2axp1`. | +| 1771 | `Unlabeled` | one-way | ATM, DNA42 | `kh2axp1` | internal-state conversion/modification | `DNA42(site!?~cdsb,h2ax~u) + ATM(state~42,h2ax) -> DNA42(site!?~cdsb,h2ax~p) + ATM(state~42,h2ax)` | Changes internal modification/state marks on ATM, DNA42: DNA42.h2ax u→p at `kh2axp1`. | +| 1772 | `Unlabeled` | one-way | ATM, DNA43 | `kh2axp1` | internal-state conversion/modification | `DNA43(site!?~cdsb,h2ax~u) + ATM(state~43,h2ax) -> DNA43(site!?~cdsb,h2ax~p) + ATM(state~43,h2ax)` | Changes internal modification/state marks on ATM, DNA43: DNA43.h2ax u→p at `kh2axp1`. | +| 1773 | `Unlabeled` | one-way | ATM, DNA44 | `kh2axp1` | internal-state conversion/modification | `DNA44(site!?~cdsb,h2ax~u) + ATM(state~44,h2ax) -> DNA44(site!?~cdsb,h2ax~p) + ATM(state~44,h2ax)` | Changes internal modification/state marks on ATM, DNA44: DNA44.h2ax u→p at `kh2axp1`. | +| 1774 | `Unlabeled` | one-way | ATM, DNA45 | `kh2axp1` | internal-state conversion/modification | `DNA45(site!?~cdsb,h2ax~u) + ATM(state~45,h2ax) -> DNA45(site!?~cdsb,h2ax~p) + ATM(state~45,h2ax)` | Changes internal modification/state marks on ATM, DNA45: DNA45.h2ax u→p at `kh2axp1`. | +| 1775 | `Unlabeled` | one-way | ATM, DNA46 | `kh2axp1` | internal-state conversion/modification | `DNA46(site!?~cdsb,h2ax~u) + ATM(state~46,h2ax) -> DNA46(site!?~cdsb,h2ax~p) + ATM(state~46,h2ax)` | Changes internal modification/state marks on ATM, DNA46: DNA46.h2ax u→p at `kh2axp1`. | +| 1776 | `Unlabeled` | one-way | ATM, DNA47 | `kh2axp1` | internal-state conversion/modification | `DNA47(site!?~cdsb,h2ax~u) + ATM(state~47,h2ax) -> DNA47(site!?~cdsb,h2ax~p) + ATM(state~47,h2ax)` | Changes internal modification/state marks on ATM, DNA47: DNA47.h2ax u→p at `kh2axp1`. | +| 1777 | `Unlabeled` | one-way | ATM, DNA48 | `kh2axp1` | internal-state conversion/modification | `DNA48(site!?~cdsb,h2ax~u) + ATM(state~48,h2ax) -> DNA48(site!?~cdsb,h2ax~p) + ATM(state~48,h2ax)` | Changes internal modification/state marks on ATM, DNA48: DNA48.h2ax u→p at `kh2axp1`. | +| 1778 | `Unlabeled` | one-way | ATM, DNA49 | `kh2axp1` | internal-state conversion/modification | `DNA49(site!?~cdsb,h2ax~u) + ATM(state~49,h2ax) -> DNA49(site!?~cdsb,h2ax~p) + ATM(state~49,h2ax)` | Changes internal modification/state marks on ATM, DNA49: DNA49.h2ax u→p at `kh2axp1`. | +| 1779 | `Unlabeled` | one-way | ATM, DNA50 | `kh2axp1` | internal-state conversion/modification | `DNA50(site!?~cdsb,h2ax~u) + ATM(state~50,h2ax) -> DNA50(site!?~cdsb,h2ax~p) + ATM(state~50,h2ax)` | Changes internal modification/state marks on ATM, DNA50: DNA50.h2ax u→p at `kh2axp1`. | +| 1780 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA1(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA1(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA1, DNAPKcs, Ku: DNA1.h2ax u→p at `kh2axp2`. | +| 1781 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA2(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA2(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA2, DNAPKcs, Ku: DNA2.h2ax u→p at `kh2axp2`. | +| 1782 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA3(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA3(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA3, DNAPKcs, Ku: DNA3.h2ax u→p at `kh2axp2`. | +| 1783 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA4(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA4(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA4, DNAPKcs, Ku: DNA4.h2ax u→p at `kh2axp2`. | +| 1784 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA5(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA5(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA5, DNAPKcs, Ku: DNA5.h2ax u→p at `kh2axp2`. | +| 1785 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA6(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA6(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA6, DNAPKcs, Ku: DNA6.h2ax u→p at `kh2axp2`. | +| 1786 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA7(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA7(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA7, DNAPKcs, Ku: DNA7.h2ax u→p at `kh2axp2`. | +| 1787 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA8(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA8(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA8, DNAPKcs, Ku: DNA8.h2ax u→p at `kh2axp2`. | +| 1788 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA9(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA9(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA9, DNAPKcs, Ku: DNA9.h2ax u→p at `kh2axp2`. | +| 1789 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA10(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA10(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA10, DNAPKcs, Ku: DNA10.h2ax u→p at `kh2axp2`. | +| 1790 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA11(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA11(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA11, DNAPKcs, Ku: DNA11.h2ax u→p at `kh2axp2`. | +| 1791 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA12(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA12(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA12, DNAPKcs, Ku: DNA12.h2ax u→p at `kh2axp2`. | +| 1792 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA13(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA13(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA13, DNAPKcs, Ku: DNA13.h2ax u→p at `kh2axp2`. | +| 1793 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA14(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA14(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA14, DNAPKcs, Ku: DNA14.h2ax u→p at `kh2axp2`. | +| 1794 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA15(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA15(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA15, DNAPKcs, Ku: DNA15.h2ax u→p at `kh2axp2`. | +| 1795 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA16(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA16(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA16, DNAPKcs, Ku: DNA16.h2ax u→p at `kh2axp2`. | +| 1796 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA17(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA17(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA17, DNAPKcs, Ku: DNA17.h2ax u→p at `kh2axp2`. | +| 1797 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA18(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA18(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA18, DNAPKcs, Ku: DNA18.h2ax u→p at `kh2axp2`. | +| 1798 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA19(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA19(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA19, DNAPKcs, Ku: DNA19.h2ax u→p at `kh2axp2`. | +| 1799 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA20(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA20(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA20, DNAPKcs, Ku: DNA20.h2ax u→p at `kh2axp2`. | +| 1800 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA21(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA21(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA21, DNAPKcs, Ku: DNA21.h2ax u→p at `kh2axp2`. | +| 1801 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA22(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA22(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA22, DNAPKcs, Ku: DNA22.h2ax u→p at `kh2axp2`. | +| 1802 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA23(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA23(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA23, DNAPKcs, Ku: DNA23.h2ax u→p at `kh2axp2`. | +| 1803 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA24(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA24(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA24, DNAPKcs, Ku: DNA24.h2ax u→p at `kh2axp2`. | +| 1804 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA25(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA25(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA25, DNAPKcs, Ku: DNA25.h2ax u→p at `kh2axp2`. | +| 1805 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA26(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA26(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA26, DNAPKcs, Ku: DNA26.h2ax u→p at `kh2axp2`. | +| 1806 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA27(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA27(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA27, DNAPKcs, Ku: DNA27.h2ax u→p at `kh2axp2`. | +| 1807 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA28(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA28(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA28, DNAPKcs, Ku: DNA28.h2ax u→p at `kh2axp2`. | +| 1808 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA29(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA29(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA29, DNAPKcs, Ku: DNA29.h2ax u→p at `kh2axp2`. | +| 1809 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA30(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA30(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA30, DNAPKcs, Ku: DNA30.h2ax u→p at `kh2axp2`. | +| 1810 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA31(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA31(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA31, DNAPKcs, Ku: DNA31.h2ax u→p at `kh2axp2`. | +| 1811 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA32(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA32(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA32, DNAPKcs, Ku: DNA32.h2ax u→p at `kh2axp2`. | +| 1812 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA33(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA33(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA33, DNAPKcs, Ku: DNA33.h2ax u→p at `kh2axp2`. | +| 1813 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA34(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA34(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA34, DNAPKcs, Ku: DNA34.h2ax u→p at `kh2axp2`. | +| 1814 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA35(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA35(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA35, DNAPKcs, Ku: DNA35.h2ax u→p at `kh2axp2`. | +| 1815 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA36(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA36(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA36, DNAPKcs, Ku: DNA36.h2ax u→p at `kh2axp2`. | +| 1816 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA37(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA37(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA37, DNAPKcs, Ku: DNA37.h2ax u→p at `kh2axp2`. | +| 1817 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA38(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA38(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA38, DNAPKcs, Ku: DNA38.h2ax u→p at `kh2axp2`. | +| 1818 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA39(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA39(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA39, DNAPKcs, Ku: DNA39.h2ax u→p at `kh2axp2`. | +| 1819 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA40(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA40(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA40, DNAPKcs, Ku: DNA40.h2ax u→p at `kh2axp2`. | +| 1820 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA41(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA41(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA41, DNAPKcs, Ku: DNA41.h2ax u→p at `kh2axp2`. | +| 1821 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA42(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA42(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA42, DNAPKcs, Ku: DNA42.h2ax u→p at `kh2axp2`. | +| 1822 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA43(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA43(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA43, DNAPKcs, Ku: DNA43.h2ax u→p at `kh2axp2`. | +| 1823 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA44(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA44(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA44, DNAPKcs, Ku: DNA44.h2ax u→p at `kh2axp2`. | +| 1824 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA45(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA45(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA45, DNAPKcs, Ku: DNA45.h2ax u→p at `kh2axp2`. | +| 1825 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA46(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA46(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA46, DNAPKcs, Ku: DNA46.h2ax u→p at `kh2axp2`. | +| 1826 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA47(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA47(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA47, DNAPKcs, Ku: DNA47.h2ax u→p at `kh2axp2`. | +| 1827 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA48(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA48(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA48, DNAPKcs, Ku: DNA48.h2ax u→p at `kh2axp2`. | +| 1828 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA49(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA49(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA49, DNAPKcs, Ku: DNA49.h2ax u→p at `kh2axp2`. | +| 1829 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA50(site!1~sdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA50(site!1~sdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA50, DNAPKcs, Ku: DNA50.h2ax u→p at `kh2axp2`. | +| 1830 | `Unlabeled` | one-way | DNA1, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA1(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA1(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA1, DNAPKcs, Ku: DNA1.h2ax u→p at `kh2axp2`. | +| 1831 | `Unlabeled` | one-way | DNA2, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA2(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA2(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA2, DNAPKcs, Ku: DNA2.h2ax u→p at `kh2axp2`. | +| 1832 | `Unlabeled` | one-way | DNA3, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA3(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA3(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA3, DNAPKcs, Ku: DNA3.h2ax u→p at `kh2axp2`. | +| 1833 | `Unlabeled` | one-way | DNA4, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA4(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA4(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA4, DNAPKcs, Ku: DNA4.h2ax u→p at `kh2axp2`. | +| 1834 | `Unlabeled` | one-way | DNA5, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA5(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA5(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA5, DNAPKcs, Ku: DNA5.h2ax u→p at `kh2axp2`. | +| 1835 | `Unlabeled` | one-way | DNA6, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA6(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA6(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA6, DNAPKcs, Ku: DNA6.h2ax u→p at `kh2axp2`. | +| 1836 | `Unlabeled` | one-way | DNA7, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA7(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA7(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA7, DNAPKcs, Ku: DNA7.h2ax u→p at `kh2axp2`. | +| 1837 | `Unlabeled` | one-way | DNA8, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA8(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA8(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA8, DNAPKcs, Ku: DNA8.h2ax u→p at `kh2axp2`. | +| 1838 | `Unlabeled` | one-way | DNA9, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA9(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA9(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA9, DNAPKcs, Ku: DNA9.h2ax u→p at `kh2axp2`. | +| 1839 | `Unlabeled` | one-way | DNA10, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA10(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA10(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA10, DNAPKcs, Ku: DNA10.h2ax u→p at `kh2axp2`. | +| 1840 | `Unlabeled` | one-way | DNA11, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA11(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA11(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA11, DNAPKcs, Ku: DNA11.h2ax u→p at `kh2axp2`. | +| 1841 | `Unlabeled` | one-way | DNA12, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA12(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA12(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA12, DNAPKcs, Ku: DNA12.h2ax u→p at `kh2axp2`. | +| 1842 | `Unlabeled` | one-way | DNA13, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA13(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA13(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA13, DNAPKcs, Ku: DNA13.h2ax u→p at `kh2axp2`. | +| 1843 | `Unlabeled` | one-way | DNA14, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA14(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA14(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA14, DNAPKcs, Ku: DNA14.h2ax u→p at `kh2axp2`. | +| 1844 | `Unlabeled` | one-way | DNA15, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA15(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA15(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA15, DNAPKcs, Ku: DNA15.h2ax u→p at `kh2axp2`. | +| 1845 | `Unlabeled` | one-way | DNA16, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA16(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA16(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA16, DNAPKcs, Ku: DNA16.h2ax u→p at `kh2axp2`. | +| 1846 | `Unlabeled` | one-way | DNA17, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA17(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA17(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA17, DNAPKcs, Ku: DNA17.h2ax u→p at `kh2axp2`. | +| 1847 | `Unlabeled` | one-way | DNA18, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA18(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA18(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA18, DNAPKcs, Ku: DNA18.h2ax u→p at `kh2axp2`. | +| 1848 | `Unlabeled` | one-way | DNA19, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA19(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA19(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA19, DNAPKcs, Ku: DNA19.h2ax u→p at `kh2axp2`. | +| 1849 | `Unlabeled` | one-way | DNA20, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA20(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA20(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA20, DNAPKcs, Ku: DNA20.h2ax u→p at `kh2axp2`. | +| 1850 | `Unlabeled` | one-way | DNA21, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA21(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA21(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA21, DNAPKcs, Ku: DNA21.h2ax u→p at `kh2axp2`. | +| 1851 | `Unlabeled` | one-way | DNA22, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA22(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA22(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA22, DNAPKcs, Ku: DNA22.h2ax u→p at `kh2axp2`. | +| 1852 | `Unlabeled` | one-way | DNA23, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA23(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA23(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA23, DNAPKcs, Ku: DNA23.h2ax u→p at `kh2axp2`. | +| 1853 | `Unlabeled` | one-way | DNA24, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA24(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA24(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA24, DNAPKcs, Ku: DNA24.h2ax u→p at `kh2axp2`. | +| 1854 | `Unlabeled` | one-way | DNA25, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA25(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA25(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA25, DNAPKcs, Ku: DNA25.h2ax u→p at `kh2axp2`. | +| 1855 | `Unlabeled` | one-way | DNA26, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA26(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA26(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA26, DNAPKcs, Ku: DNA26.h2ax u→p at `kh2axp2`. | +| 1856 | `Unlabeled` | one-way | DNA27, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA27(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA27(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA27, DNAPKcs, Ku: DNA27.h2ax u→p at `kh2axp2`. | +| 1857 | `Unlabeled` | one-way | DNA28, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA28(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA28(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA28, DNAPKcs, Ku: DNA28.h2ax u→p at `kh2axp2`. | +| 1858 | `Unlabeled` | one-way | DNA29, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA29(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA29(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA29, DNAPKcs, Ku: DNA29.h2ax u→p at `kh2axp2`. | +| 1859 | `Unlabeled` | one-way | DNA30, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA30(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA30(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA30, DNAPKcs, Ku: DNA30.h2ax u→p at `kh2axp2`. | +| 1860 | `Unlabeled` | one-way | DNA31, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA31(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA31(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA31, DNAPKcs, Ku: DNA31.h2ax u→p at `kh2axp2`. | +| 1861 | `Unlabeled` | one-way | DNA32, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA32(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA32(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA32, DNAPKcs, Ku: DNA32.h2ax u→p at `kh2axp2`. | +| 1862 | `Unlabeled` | one-way | DNA33, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA33(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA33(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA33, DNAPKcs, Ku: DNA33.h2ax u→p at `kh2axp2`. | +| 1863 | `Unlabeled` | one-way | DNA34, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA34(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA34(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA34, DNAPKcs, Ku: DNA34.h2ax u→p at `kh2axp2`. | +| 1864 | `Unlabeled` | one-way | DNA35, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA35(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA35(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA35, DNAPKcs, Ku: DNA35.h2ax u→p at `kh2axp2`. | +| 1865 | `Unlabeled` | one-way | DNA36, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA36(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA36(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA36, DNAPKcs, Ku: DNA36.h2ax u→p at `kh2axp2`. | +| 1866 | `Unlabeled` | one-way | DNA37, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA37(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA37(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA37, DNAPKcs, Ku: DNA37.h2ax u→p at `kh2axp2`. | +| 1867 | `Unlabeled` | one-way | DNA38, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA38(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA38(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA38, DNAPKcs, Ku: DNA38.h2ax u→p at `kh2axp2`. | +| 1868 | `Unlabeled` | one-way | DNA39, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA39(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA39(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA39, DNAPKcs, Ku: DNA39.h2ax u→p at `kh2axp2`. | +| 1869 | `Unlabeled` | one-way | DNA40, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA40(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA40(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA40, DNAPKcs, Ku: DNA40.h2ax u→p at `kh2axp2`. | +| 1870 | `Unlabeled` | one-way | DNA41, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA41(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA41(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA41, DNAPKcs, Ku: DNA41.h2ax u→p at `kh2axp2`. | +| 1871 | `Unlabeled` | one-way | DNA42, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA42(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA42(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA42, DNAPKcs, Ku: DNA42.h2ax u→p at `kh2axp2`. | +| 1872 | `Unlabeled` | one-way | DNA43, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA43(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA43(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA43, DNAPKcs, Ku: DNA43.h2ax u→p at `kh2axp2`. | +| 1873 | `Unlabeled` | one-way | DNA44, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA44(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA44(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA44, DNAPKcs, Ku: DNA44.h2ax u→p at `kh2axp2`. | +| 1874 | `Unlabeled` | one-way | DNA45, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA45(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA45(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA45, DNAPKcs, Ku: DNA45.h2ax u→p at `kh2axp2`. | +| 1875 | `Unlabeled` | one-way | DNA46, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA46(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA46(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA46, DNAPKcs, Ku: DNA46.h2ax u→p at `kh2axp2`. | +| 1876 | `Unlabeled` | one-way | DNA47, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA47(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA47(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA47, DNAPKcs, Ku: DNA47.h2ax u→p at `kh2axp2`. | +| 1877 | `Unlabeled` | one-way | DNA48, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA48(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA48(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA48, DNAPKcs, Ku: DNA48.h2ax u→p at `kh2axp2`. | +| 1878 | `Unlabeled` | one-way | DNA49, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA49(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA49(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA49, DNAPKcs, Ku: DNA49.h2ax u→p at `kh2axp2`. | +| 1879 | `Unlabeled` | one-way | DNA50, DNAPKcs, Ku | `kh2axp2` | internal-state conversion/modification | `DNA50(site!1~cdsb,h2ax~u).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p) -> DNA50(site!1~cdsb,h2ax~p).Ku(dna!1,cs!2).DNAPKcs(ku!2,liIV,psite~p)` | Changes internal modification/state marks on DNA50, DNAPKcs, Ku: DNA50.h2ax u→p at `kh2axp2`. | +| 1880 | `Unlabeled` | one-way | DNA1 | `kh2axu` | internal-state conversion/modification | `DNA1(h2ax~p) -> DNA1(h2ax~u)` | Changes internal modification/state marks on DNA1: DNA1.h2ax p→u at `kh2axu`. | +| 1881 | `Unlabeled` | one-way | DNA2 | `kh2axu` | internal-state conversion/modification | `DNA2(h2ax~p) -> DNA2(h2ax~u)` | Changes internal modification/state marks on DNA2: DNA2.h2ax p→u at `kh2axu`. | +| 1882 | `Unlabeled` | one-way | DNA3 | `kh2axu` | internal-state conversion/modification | `DNA3(h2ax~p) -> DNA3(h2ax~u)` | Changes internal modification/state marks on DNA3: DNA3.h2ax p→u at `kh2axu`. | +| 1883 | `Unlabeled` | one-way | DNA4 | `kh2axu` | internal-state conversion/modification | `DNA4(h2ax~p) -> DNA4(h2ax~u)` | Changes internal modification/state marks on DNA4: DNA4.h2ax p→u at `kh2axu`. | +| 1884 | `Unlabeled` | one-way | DNA5 | `kh2axu` | internal-state conversion/modification | `DNA5(h2ax~p) -> DNA5(h2ax~u)` | Changes internal modification/state marks on DNA5: DNA5.h2ax p→u at `kh2axu`. | +| 1885 | `Unlabeled` | one-way | DNA6 | `kh2axu` | internal-state conversion/modification | `DNA6(h2ax~p) -> DNA6(h2ax~u)` | Changes internal modification/state marks on DNA6: DNA6.h2ax p→u at `kh2axu`. | +| 1886 | `Unlabeled` | one-way | DNA7 | `kh2axu` | internal-state conversion/modification | `DNA7(h2ax~p) -> DNA7(h2ax~u)` | Changes internal modification/state marks on DNA7: DNA7.h2ax p→u at `kh2axu`. | +| 1887 | `Unlabeled` | one-way | DNA8 | `kh2axu` | internal-state conversion/modification | `DNA8(h2ax~p) -> DNA8(h2ax~u)` | Changes internal modification/state marks on DNA8: DNA8.h2ax p→u at `kh2axu`. | +| 1888 | `Unlabeled` | one-way | DNA9 | `kh2axu` | internal-state conversion/modification | `DNA9(h2ax~p) -> DNA9(h2ax~u)` | Changes internal modification/state marks on DNA9: DNA9.h2ax p→u at `kh2axu`. | +| 1889 | `Unlabeled` | one-way | DNA10 | `kh2axu` | internal-state conversion/modification | `DNA10(h2ax~p) -> DNA10(h2ax~u)` | Changes internal modification/state marks on DNA10: DNA10.h2ax p→u at `kh2axu`. | +| 1890 | `Unlabeled` | one-way | DNA11 | `kh2axu` | internal-state conversion/modification | `DNA11(h2ax~p) -> DNA11(h2ax~u)` | Changes internal modification/state marks on DNA11: DNA11.h2ax p→u at `kh2axu`. | +| 1891 | `Unlabeled` | one-way | DNA12 | `kh2axu` | internal-state conversion/modification | `DNA12(h2ax~p) -> DNA12(h2ax~u)` | Changes internal modification/state marks on DNA12: DNA12.h2ax p→u at `kh2axu`. | +| 1892 | `Unlabeled` | one-way | DNA13 | `kh2axu` | internal-state conversion/modification | `DNA13(h2ax~p) -> DNA13(h2ax~u)` | Changes internal modification/state marks on DNA13: DNA13.h2ax p→u at `kh2axu`. | +| 1893 | `Unlabeled` | one-way | DNA14 | `kh2axu` | internal-state conversion/modification | `DNA14(h2ax~p) -> DNA14(h2ax~u)` | Changes internal modification/state marks on DNA14: DNA14.h2ax p→u at `kh2axu`. | +| 1894 | `Unlabeled` | one-way | DNA15 | `kh2axu` | internal-state conversion/modification | `DNA15(h2ax~p) -> DNA15(h2ax~u)` | Changes internal modification/state marks on DNA15: DNA15.h2ax p→u at `kh2axu`. | +| 1895 | `Unlabeled` | one-way | DNA16 | `kh2axu` | internal-state conversion/modification | `DNA16(h2ax~p) -> DNA16(h2ax~u)` | Changes internal modification/state marks on DNA16: DNA16.h2ax p→u at `kh2axu`. | +| 1896 | `Unlabeled` | one-way | DNA17 | `kh2axu` | internal-state conversion/modification | `DNA17(h2ax~p) -> DNA17(h2ax~u)` | Changes internal modification/state marks on DNA17: DNA17.h2ax p→u at `kh2axu`. | +| 1897 | `Unlabeled` | one-way | DNA18 | `kh2axu` | internal-state conversion/modification | `DNA18(h2ax~p) -> DNA18(h2ax~u)` | Changes internal modification/state marks on DNA18: DNA18.h2ax p→u at `kh2axu`. | +| 1898 | `Unlabeled` | one-way | DNA19 | `kh2axu` | internal-state conversion/modification | `DNA19(h2ax~p) -> DNA19(h2ax~u)` | Changes internal modification/state marks on DNA19: DNA19.h2ax p→u at `kh2axu`. | +| 1899 | `Unlabeled` | one-way | DNA20 | `kh2axu` | internal-state conversion/modification | `DNA20(h2ax~p) -> DNA20(h2ax~u)` | Changes internal modification/state marks on DNA20: DNA20.h2ax p→u at `kh2axu`. | +| 1900 | `Unlabeled` | one-way | DNA21 | `kh2axu` | internal-state conversion/modification | `DNA21(h2ax~p) -> DNA21(h2ax~u)` | Changes internal modification/state marks on DNA21: DNA21.h2ax p→u at `kh2axu`. | +| 1901 | `Unlabeled` | one-way | DNA22 | `kh2axu` | internal-state conversion/modification | `DNA22(h2ax~p) -> DNA22(h2ax~u)` | Changes internal modification/state marks on DNA22: DNA22.h2ax p→u at `kh2axu`. | +| 1902 | `Unlabeled` | one-way | DNA23 | `kh2axu` | internal-state conversion/modification | `DNA23(h2ax~p) -> DNA23(h2ax~u)` | Changes internal modification/state marks on DNA23: DNA23.h2ax p→u at `kh2axu`. | +| 1903 | `Unlabeled` | one-way | DNA24 | `kh2axu` | internal-state conversion/modification | `DNA24(h2ax~p) -> DNA24(h2ax~u)` | Changes internal modification/state marks on DNA24: DNA24.h2ax p→u at `kh2axu`. | +| 1904 | `Unlabeled` | one-way | DNA25 | `kh2axu` | internal-state conversion/modification | `DNA25(h2ax~p) -> DNA25(h2ax~u)` | Changes internal modification/state marks on DNA25: DNA25.h2ax p→u at `kh2axu`. | +| 1905 | `Unlabeled` | one-way | DNA26 | `kh2axu` | internal-state conversion/modification | `DNA26(h2ax~p) -> DNA26(h2ax~u)` | Changes internal modification/state marks on DNA26: DNA26.h2ax p→u at `kh2axu`. | +| 1906 | `Unlabeled` | one-way | DNA27 | `kh2axu` | internal-state conversion/modification | `DNA27(h2ax~p) -> DNA27(h2ax~u)` | Changes internal modification/state marks on DNA27: DNA27.h2ax p→u at `kh2axu`. | +| 1907 | `Unlabeled` | one-way | DNA28 | `kh2axu` | internal-state conversion/modification | `DNA28(h2ax~p) -> DNA28(h2ax~u)` | Changes internal modification/state marks on DNA28: DNA28.h2ax p→u at `kh2axu`. | +| 1908 | `Unlabeled` | one-way | DNA29 | `kh2axu` | internal-state conversion/modification | `DNA29(h2ax~p) -> DNA29(h2ax~u)` | Changes internal modification/state marks on DNA29: DNA29.h2ax p→u at `kh2axu`. | +| 1909 | `Unlabeled` | one-way | DNA30 | `kh2axu` | internal-state conversion/modification | `DNA30(h2ax~p) -> DNA30(h2ax~u)` | Changes internal modification/state marks on DNA30: DNA30.h2ax p→u at `kh2axu`. | +| 1910 | `Unlabeled` | one-way | DNA31 | `kh2axu` | internal-state conversion/modification | `DNA31(h2ax~p) -> DNA31(h2ax~u)` | Changes internal modification/state marks on DNA31: DNA31.h2ax p→u at `kh2axu`. | +| 1911 | `Unlabeled` | one-way | DNA32 | `kh2axu` | internal-state conversion/modification | `DNA32(h2ax~p) -> DNA32(h2ax~u)` | Changes internal modification/state marks on DNA32: DNA32.h2ax p→u at `kh2axu`. | +| 1912 | `Unlabeled` | one-way | DNA33 | `kh2axu` | internal-state conversion/modification | `DNA33(h2ax~p) -> DNA33(h2ax~u)` | Changes internal modification/state marks on DNA33: DNA33.h2ax p→u at `kh2axu`. | +| 1913 | `Unlabeled` | one-way | DNA34 | `kh2axu` | internal-state conversion/modification | `DNA34(h2ax~p) -> DNA34(h2ax~u)` | Changes internal modification/state marks on DNA34: DNA34.h2ax p→u at `kh2axu`. | +| 1914 | `Unlabeled` | one-way | DNA35 | `kh2axu` | internal-state conversion/modification | `DNA35(h2ax~p) -> DNA35(h2ax~u)` | Changes internal modification/state marks on DNA35: DNA35.h2ax p→u at `kh2axu`. | +| 1915 | `Unlabeled` | one-way | DNA36 | `kh2axu` | internal-state conversion/modification | `DNA36(h2ax~p) -> DNA36(h2ax~u)` | Changes internal modification/state marks on DNA36: DNA36.h2ax p→u at `kh2axu`. | +| 1916 | `Unlabeled` | one-way | DNA37 | `kh2axu` | internal-state conversion/modification | `DNA37(h2ax~p) -> DNA37(h2ax~u)` | Changes internal modification/state marks on DNA37: DNA37.h2ax p→u at `kh2axu`. | +| 1917 | `Unlabeled` | one-way | DNA38 | `kh2axu` | internal-state conversion/modification | `DNA38(h2ax~p) -> DNA38(h2ax~u)` | Changes internal modification/state marks on DNA38: DNA38.h2ax p→u at `kh2axu`. | +| 1918 | `Unlabeled` | one-way | DNA39 | `kh2axu` | internal-state conversion/modification | `DNA39(h2ax~p) -> DNA39(h2ax~u)` | Changes internal modification/state marks on DNA39: DNA39.h2ax p→u at `kh2axu`. | +| 1919 | `Unlabeled` | one-way | DNA40 | `kh2axu` | internal-state conversion/modification | `DNA40(h2ax~p) -> DNA40(h2ax~u)` | Changes internal modification/state marks on DNA40: DNA40.h2ax p→u at `kh2axu`. | +| 1920 | `Unlabeled` | one-way | DNA41 | `kh2axu` | internal-state conversion/modification | `DNA41(h2ax~p) -> DNA41(h2ax~u)` | Changes internal modification/state marks on DNA41: DNA41.h2ax p→u at `kh2axu`. | +| 1921 | `Unlabeled` | one-way | DNA42 | `kh2axu` | internal-state conversion/modification | `DNA42(h2ax~p) -> DNA42(h2ax~u)` | Changes internal modification/state marks on DNA42: DNA42.h2ax p→u at `kh2axu`. | +| 1922 | `Unlabeled` | one-way | DNA43 | `kh2axu` | internal-state conversion/modification | `DNA43(h2ax~p) -> DNA43(h2ax~u)` | Changes internal modification/state marks on DNA43: DNA43.h2ax p→u at `kh2axu`. | +| 1923 | `Unlabeled` | one-way | DNA44 | `kh2axu` | internal-state conversion/modification | `DNA44(h2ax~p) -> DNA44(h2ax~u)` | Changes internal modification/state marks on DNA44: DNA44.h2ax p→u at `kh2axu`. | +| 1924 | `Unlabeled` | one-way | DNA45 | `kh2axu` | internal-state conversion/modification | `DNA45(h2ax~p) -> DNA45(h2ax~u)` | Changes internal modification/state marks on DNA45: DNA45.h2ax p→u at `kh2axu`. | +| 1925 | `Unlabeled` | one-way | DNA46 | `kh2axu` | internal-state conversion/modification | `DNA46(h2ax~p) -> DNA46(h2ax~u)` | Changes internal modification/state marks on DNA46: DNA46.h2ax p→u at `kh2axu`. | +| 1926 | `Unlabeled` | one-way | DNA47 | `kh2axu` | internal-state conversion/modification | `DNA47(h2ax~p) -> DNA47(h2ax~u)` | Changes internal modification/state marks on DNA47: DNA47.h2ax p→u at `kh2axu`. | +| 1927 | `Unlabeled` | one-way | DNA48 | `kh2axu` | internal-state conversion/modification | `DNA48(h2ax~p) -> DNA48(h2ax~u)` | Changes internal modification/state marks on DNA48: DNA48.h2ax p→u at `kh2axu`. | +| 1928 | `Unlabeled` | one-way | DNA49 | `kh2axu` | internal-state conversion/modification | `DNA49(h2ax~p) -> DNA49(h2ax~u)` | Changes internal modification/state marks on DNA49: DNA49.h2ax p→u at `kh2axu`. | +| 1929 | `Unlabeled` | one-way | DNA50 | `kh2axu` | internal-state conversion/modification | `DNA50(h2ax~p) -> DNA50(h2ax~u)` | Changes internal modification/state marks on DNA50: DNA50.h2ax p→u at `kh2axu`. | +| 1930 | `Unlabeled` | one-way | DNA1 | `kh2axfoc` | internal-state conversion/modification | `DNA1(h2ax~p) -> DNA1(h2ax~foc)` | Changes internal modification/state marks on DNA1: DNA1.h2ax p→foc at `kh2axfoc`. | +| 1931 | `Unlabeled` | one-way | DNA2 | `kh2axfoc` | internal-state conversion/modification | `DNA2(h2ax~p) -> DNA2(h2ax~foc)` | Changes internal modification/state marks on DNA2: DNA2.h2ax p→foc at `kh2axfoc`. | +| 1932 | `Unlabeled` | one-way | DNA3 | `kh2axfoc` | internal-state conversion/modification | `DNA3(h2ax~p) -> DNA3(h2ax~foc)` | Changes internal modification/state marks on DNA3: DNA3.h2ax p→foc at `kh2axfoc`. | +| 1933 | `Unlabeled` | one-way | DNA4 | `kh2axfoc` | internal-state conversion/modification | `DNA4(h2ax~p) -> DNA4(h2ax~foc)` | Changes internal modification/state marks on DNA4: DNA4.h2ax p→foc at `kh2axfoc`. | +| 1934 | `Unlabeled` | one-way | DNA5 | `kh2axfoc` | internal-state conversion/modification | `DNA5(h2ax~p) -> DNA5(h2ax~foc)` | Changes internal modification/state marks on DNA5: DNA5.h2ax p→foc at `kh2axfoc`. | +| 1935 | `Unlabeled` | one-way | DNA6 | `kh2axfoc` | internal-state conversion/modification | `DNA6(h2ax~p) -> DNA6(h2ax~foc)` | Changes internal modification/state marks on DNA6: DNA6.h2ax p→foc at `kh2axfoc`. | +| 1936 | `Unlabeled` | one-way | DNA7 | `kh2axfoc` | internal-state conversion/modification | `DNA7(h2ax~p) -> DNA7(h2ax~foc)` | Changes internal modification/state marks on DNA7: DNA7.h2ax p→foc at `kh2axfoc`. | +| 1937 | `Unlabeled` | one-way | DNA8 | `kh2axfoc` | internal-state conversion/modification | `DNA8(h2ax~p) -> DNA8(h2ax~foc)` | Changes internal modification/state marks on DNA8: DNA8.h2ax p→foc at `kh2axfoc`. | +| 1938 | `Unlabeled` | one-way | DNA9 | `kh2axfoc` | internal-state conversion/modification | `DNA9(h2ax~p) -> DNA9(h2ax~foc)` | Changes internal modification/state marks on DNA9: DNA9.h2ax p→foc at `kh2axfoc`. | +| 1939 | `Unlabeled` | one-way | DNA10 | `kh2axfoc` | internal-state conversion/modification | `DNA10(h2ax~p) -> DNA10(h2ax~foc)` | Changes internal modification/state marks on DNA10: DNA10.h2ax p→foc at `kh2axfoc`. | +| 1940 | `Unlabeled` | one-way | DNA11 | `kh2axfoc` | internal-state conversion/modification | `DNA11(h2ax~p) -> DNA11(h2ax~foc)` | Changes internal modification/state marks on DNA11: DNA11.h2ax p→foc at `kh2axfoc`. | +| 1941 | `Unlabeled` | one-way | DNA12 | `kh2axfoc` | internal-state conversion/modification | `DNA12(h2ax~p) -> DNA12(h2ax~foc)` | Changes internal modification/state marks on DNA12: DNA12.h2ax p→foc at `kh2axfoc`. | +| 1942 | `Unlabeled` | one-way | DNA13 | `kh2axfoc` | internal-state conversion/modification | `DNA13(h2ax~p) -> DNA13(h2ax~foc)` | Changes internal modification/state marks on DNA13: DNA13.h2ax p→foc at `kh2axfoc`. | +| 1943 | `Unlabeled` | one-way | DNA14 | `kh2axfoc` | internal-state conversion/modification | `DNA14(h2ax~p) -> DNA14(h2ax~foc)` | Changes internal modification/state marks on DNA14: DNA14.h2ax p→foc at `kh2axfoc`. | +| 1944 | `Unlabeled` | one-way | DNA15 | `kh2axfoc` | internal-state conversion/modification | `DNA15(h2ax~p) -> DNA15(h2ax~foc)` | Changes internal modification/state marks on DNA15: DNA15.h2ax p→foc at `kh2axfoc`. | +| 1945 | `Unlabeled` | one-way | DNA16 | `kh2axfoc` | internal-state conversion/modification | `DNA16(h2ax~p) -> DNA16(h2ax~foc)` | Changes internal modification/state marks on DNA16: DNA16.h2ax p→foc at `kh2axfoc`. | +| 1946 | `Unlabeled` | one-way | DNA17 | `kh2axfoc` | internal-state conversion/modification | `DNA17(h2ax~p) -> DNA17(h2ax~foc)` | Changes internal modification/state marks on DNA17: DNA17.h2ax p→foc at `kh2axfoc`. | +| 1947 | `Unlabeled` | one-way | DNA18 | `kh2axfoc` | internal-state conversion/modification | `DNA18(h2ax~p) -> DNA18(h2ax~foc)` | Changes internal modification/state marks on DNA18: DNA18.h2ax p→foc at `kh2axfoc`. | +| 1948 | `Unlabeled` | one-way | DNA19 | `kh2axfoc` | internal-state conversion/modification | `DNA19(h2ax~p) -> DNA19(h2ax~foc)` | Changes internal modification/state marks on DNA19: DNA19.h2ax p→foc at `kh2axfoc`. | +| 1949 | `Unlabeled` | one-way | DNA20 | `kh2axfoc` | internal-state conversion/modification | `DNA20(h2ax~p) -> DNA20(h2ax~foc)` | Changes internal modification/state marks on DNA20: DNA20.h2ax p→foc at `kh2axfoc`. | +| 1950 | `Unlabeled` | one-way | DNA21 | `kh2axfoc` | internal-state conversion/modification | `DNA21(h2ax~p) -> DNA21(h2ax~foc)` | Changes internal modification/state marks on DNA21: DNA21.h2ax p→foc at `kh2axfoc`. | +| 1951 | `Unlabeled` | one-way | DNA22 | `kh2axfoc` | internal-state conversion/modification | `DNA22(h2ax~p) -> DNA22(h2ax~foc)` | Changes internal modification/state marks on DNA22: DNA22.h2ax p→foc at `kh2axfoc`. | +| 1952 | `Unlabeled` | one-way | DNA23 | `kh2axfoc` | internal-state conversion/modification | `DNA23(h2ax~p) -> DNA23(h2ax~foc)` | Changes internal modification/state marks on DNA23: DNA23.h2ax p→foc at `kh2axfoc`. | +| 1953 | `Unlabeled` | one-way | DNA24 | `kh2axfoc` | internal-state conversion/modification | `DNA24(h2ax~p) -> DNA24(h2ax~foc)` | Changes internal modification/state marks on DNA24: DNA24.h2ax p→foc at `kh2axfoc`. | +| 1954 | `Unlabeled` | one-way | DNA25 | `kh2axfoc` | internal-state conversion/modification | `DNA25(h2ax~p) -> DNA25(h2ax~foc)` | Changes internal modification/state marks on DNA25: DNA25.h2ax p→foc at `kh2axfoc`. | +| 1955 | `Unlabeled` | one-way | DNA26 | `kh2axfoc` | internal-state conversion/modification | `DNA26(h2ax~p) -> DNA26(h2ax~foc)` | Changes internal modification/state marks on DNA26: DNA26.h2ax p→foc at `kh2axfoc`. | +| 1956 | `Unlabeled` | one-way | DNA27 | `kh2axfoc` | internal-state conversion/modification | `DNA27(h2ax~p) -> DNA27(h2ax~foc)` | Changes internal modification/state marks on DNA27: DNA27.h2ax p→foc at `kh2axfoc`. | +| 1957 | `Unlabeled` | one-way | DNA28 | `kh2axfoc` | internal-state conversion/modification | `DNA28(h2ax~p) -> DNA28(h2ax~foc)` | Changes internal modification/state marks on DNA28: DNA28.h2ax p→foc at `kh2axfoc`. | +| 1958 | `Unlabeled` | one-way | DNA29 | `kh2axfoc` | internal-state conversion/modification | `DNA29(h2ax~p) -> DNA29(h2ax~foc)` | Changes internal modification/state marks on DNA29: DNA29.h2ax p→foc at `kh2axfoc`. | +| 1959 | `Unlabeled` | one-way | DNA30 | `kh2axfoc` | internal-state conversion/modification | `DNA30(h2ax~p) -> DNA30(h2ax~foc)` | Changes internal modification/state marks on DNA30: DNA30.h2ax p→foc at `kh2axfoc`. | +| 1960 | `Unlabeled` | one-way | DNA31 | `kh2axfoc` | internal-state conversion/modification | `DNA31(h2ax~p) -> DNA31(h2ax~foc)` | Changes internal modification/state marks on DNA31: DNA31.h2ax p→foc at `kh2axfoc`. | +| 1961 | `Unlabeled` | one-way | DNA32 | `kh2axfoc` | internal-state conversion/modification | `DNA32(h2ax~p) -> DNA32(h2ax~foc)` | Changes internal modification/state marks on DNA32: DNA32.h2ax p→foc at `kh2axfoc`. | +| 1962 | `Unlabeled` | one-way | DNA33 | `kh2axfoc` | internal-state conversion/modification | `DNA33(h2ax~p) -> DNA33(h2ax~foc)` | Changes internal modification/state marks on DNA33: DNA33.h2ax p→foc at `kh2axfoc`. | +| 1963 | `Unlabeled` | one-way | DNA34 | `kh2axfoc` | internal-state conversion/modification | `DNA34(h2ax~p) -> DNA34(h2ax~foc)` | Changes internal modification/state marks on DNA34: DNA34.h2ax p→foc at `kh2axfoc`. | +| 1964 | `Unlabeled` | one-way | DNA35 | `kh2axfoc` | internal-state conversion/modification | `DNA35(h2ax~p) -> DNA35(h2ax~foc)` | Changes internal modification/state marks on DNA35: DNA35.h2ax p→foc at `kh2axfoc`. | +| 1965 | `Unlabeled` | one-way | DNA36 | `kh2axfoc` | internal-state conversion/modification | `DNA36(h2ax~p) -> DNA36(h2ax~foc)` | Changes internal modification/state marks on DNA36: DNA36.h2ax p→foc at `kh2axfoc`. | +| 1966 | `Unlabeled` | one-way | DNA37 | `kh2axfoc` | internal-state conversion/modification | `DNA37(h2ax~p) -> DNA37(h2ax~foc)` | Changes internal modification/state marks on DNA37: DNA37.h2ax p→foc at `kh2axfoc`. | +| 1967 | `Unlabeled` | one-way | DNA38 | `kh2axfoc` | internal-state conversion/modification | `DNA38(h2ax~p) -> DNA38(h2ax~foc)` | Changes internal modification/state marks on DNA38: DNA38.h2ax p→foc at `kh2axfoc`. | +| 1968 | `Unlabeled` | one-way | DNA39 | `kh2axfoc` | internal-state conversion/modification | `DNA39(h2ax~p) -> DNA39(h2ax~foc)` | Changes internal modification/state marks on DNA39: DNA39.h2ax p→foc at `kh2axfoc`. | +| 1969 | `Unlabeled` | one-way | DNA40 | `kh2axfoc` | internal-state conversion/modification | `DNA40(h2ax~p) -> DNA40(h2ax~foc)` | Changes internal modification/state marks on DNA40: DNA40.h2ax p→foc at `kh2axfoc`. | +| 1970 | `Unlabeled` | one-way | DNA41 | `kh2axfoc` | internal-state conversion/modification | `DNA41(h2ax~p) -> DNA41(h2ax~foc)` | Changes internal modification/state marks on DNA41: DNA41.h2ax p→foc at `kh2axfoc`. | +| 1971 | `Unlabeled` | one-way | DNA42 | `kh2axfoc` | internal-state conversion/modification | `DNA42(h2ax~p) -> DNA42(h2ax~foc)` | Changes internal modification/state marks on DNA42: DNA42.h2ax p→foc at `kh2axfoc`. | +| 1972 | `Unlabeled` | one-way | DNA43 | `kh2axfoc` | internal-state conversion/modification | `DNA43(h2ax~p) -> DNA43(h2ax~foc)` | Changes internal modification/state marks on DNA43: DNA43.h2ax p→foc at `kh2axfoc`. | +| 1973 | `Unlabeled` | one-way | DNA44 | `kh2axfoc` | internal-state conversion/modification | `DNA44(h2ax~p) -> DNA44(h2ax~foc)` | Changes internal modification/state marks on DNA44: DNA44.h2ax p→foc at `kh2axfoc`. | +| 1974 | `Unlabeled` | one-way | DNA45 | `kh2axfoc` | internal-state conversion/modification | `DNA45(h2ax~p) -> DNA45(h2ax~foc)` | Changes internal modification/state marks on DNA45: DNA45.h2ax p→foc at `kh2axfoc`. | +| 1975 | `Unlabeled` | one-way | DNA46 | `kh2axfoc` | internal-state conversion/modification | `DNA46(h2ax~p) -> DNA46(h2ax~foc)` | Changes internal modification/state marks on DNA46: DNA46.h2ax p→foc at `kh2axfoc`. | +| 1976 | `Unlabeled` | one-way | DNA47 | `kh2axfoc` | internal-state conversion/modification | `DNA47(h2ax~p) -> DNA47(h2ax~foc)` | Changes internal modification/state marks on DNA47: DNA47.h2ax p→foc at `kh2axfoc`. | +| 1977 | `Unlabeled` | one-way | DNA48 | `kh2axfoc` | internal-state conversion/modification | `DNA48(h2ax~p) -> DNA48(h2ax~foc)` | Changes internal modification/state marks on DNA48: DNA48.h2ax p→foc at `kh2axfoc`. | +| 1978 | `Unlabeled` | one-way | DNA49 | `kh2axfoc` | internal-state conversion/modification | `DNA49(h2ax~p) -> DNA49(h2ax~foc)` | Changes internal modification/state marks on DNA49: DNA49.h2ax p→foc at `kh2axfoc`. | +| 1979 | `Unlabeled` | one-way | DNA50 | `kh2axfoc` | internal-state conversion/modification | `DNA50(h2ax~p) -> DNA50(h2ax~foc)` | Changes internal modification/state marks on DNA50: DNA50.h2ax p→foc at `kh2axfoc`. | +| 1980 | `Unlabeled` | one-way | DNA1 | `kfocback` | internal-state conversion/modification | `DNA1(h2ax~foc) -> DNA1(h2ax~u)` | Changes internal modification/state marks on DNA1: DNA1.h2ax foc→u at `kfocback`. | +| 1981 | `Unlabeled` | one-way | DNA2 | `kfocback` | internal-state conversion/modification | `DNA2(h2ax~foc) -> DNA2(h2ax~u)` | Changes internal modification/state marks on DNA2: DNA2.h2ax foc→u at `kfocback`. | +| 1982 | `Unlabeled` | one-way | DNA3 | `kfocback` | internal-state conversion/modification | `DNA3(h2ax~foc) -> DNA3(h2ax~u)` | Changes internal modification/state marks on DNA3: DNA3.h2ax foc→u at `kfocback`. | +| 1983 | `Unlabeled` | one-way | DNA4 | `kfocback` | internal-state conversion/modification | `DNA4(h2ax~foc) -> DNA4(h2ax~u)` | Changes internal modification/state marks on DNA4: DNA4.h2ax foc→u at `kfocback`. | +| 1984 | `Unlabeled` | one-way | DNA5 | `kfocback` | internal-state conversion/modification | `DNA5(h2ax~foc) -> DNA5(h2ax~u)` | Changes internal modification/state marks on DNA5: DNA5.h2ax foc→u at `kfocback`. | +| 1985 | `Unlabeled` | one-way | DNA6 | `kfocback` | internal-state conversion/modification | `DNA6(h2ax~foc) -> DNA6(h2ax~u)` | Changes internal modification/state marks on DNA6: DNA6.h2ax foc→u at `kfocback`. | +| 1986 | `Unlabeled` | one-way | DNA7 | `kfocback` | internal-state conversion/modification | `DNA7(h2ax~foc) -> DNA7(h2ax~u)` | Changes internal modification/state marks on DNA7: DNA7.h2ax foc→u at `kfocback`. | +| 1987 | `Unlabeled` | one-way | DNA8 | `kfocback` | internal-state conversion/modification | `DNA8(h2ax~foc) -> DNA8(h2ax~u)` | Changes internal modification/state marks on DNA8: DNA8.h2ax foc→u at `kfocback`. | +| 1988 | `Unlabeled` | one-way | DNA9 | `kfocback` | internal-state conversion/modification | `DNA9(h2ax~foc) -> DNA9(h2ax~u)` | Changes internal modification/state marks on DNA9: DNA9.h2ax foc→u at `kfocback`. | +| 1989 | `Unlabeled` | one-way | DNA10 | `kfocback` | internal-state conversion/modification | `DNA10(h2ax~foc) -> DNA10(h2ax~u)` | Changes internal modification/state marks on DNA10: DNA10.h2ax foc→u at `kfocback`. | +| 1990 | `Unlabeled` | one-way | DNA11 | `kfocback` | internal-state conversion/modification | `DNA11(h2ax~foc) -> DNA11(h2ax~u)` | Changes internal modification/state marks on DNA11: DNA11.h2ax foc→u at `kfocback`. | +| 1991 | `Unlabeled` | one-way | DNA12 | `kfocback` | internal-state conversion/modification | `DNA12(h2ax~foc) -> DNA12(h2ax~u)` | Changes internal modification/state marks on DNA12: DNA12.h2ax foc→u at `kfocback`. | +| 1992 | `Unlabeled` | one-way | DNA13 | `kfocback` | internal-state conversion/modification | `DNA13(h2ax~foc) -> DNA13(h2ax~u)` | Changes internal modification/state marks on DNA13: DNA13.h2ax foc→u at `kfocback`. | +| 1993 | `Unlabeled` | one-way | DNA14 | `kfocback` | internal-state conversion/modification | `DNA14(h2ax~foc) -> DNA14(h2ax~u)` | Changes internal modification/state marks on DNA14: DNA14.h2ax foc→u at `kfocback`. | +| 1994 | `Unlabeled` | one-way | DNA15 | `kfocback` | internal-state conversion/modification | `DNA15(h2ax~foc) -> DNA15(h2ax~u)` | Changes internal modification/state marks on DNA15: DNA15.h2ax foc→u at `kfocback`. | +| 1995 | `Unlabeled` | one-way | DNA16 | `kfocback` | internal-state conversion/modification | `DNA16(h2ax~foc) -> DNA16(h2ax~u)` | Changes internal modification/state marks on DNA16: DNA16.h2ax foc→u at `kfocback`. | +| 1996 | `Unlabeled` | one-way | DNA17 | `kfocback` | internal-state conversion/modification | `DNA17(h2ax~foc) -> DNA17(h2ax~u)` | Changes internal modification/state marks on DNA17: DNA17.h2ax foc→u at `kfocback`. | +| 1997 | `Unlabeled` | one-way | DNA18 | `kfocback` | internal-state conversion/modification | `DNA18(h2ax~foc) -> DNA18(h2ax~u)` | Changes internal modification/state marks on DNA18: DNA18.h2ax foc→u at `kfocback`. | +| 1998 | `Unlabeled` | one-way | DNA19 | `kfocback` | internal-state conversion/modification | `DNA19(h2ax~foc) -> DNA19(h2ax~u)` | Changes internal modification/state marks on DNA19: DNA19.h2ax foc→u at `kfocback`. | +| 1999 | `Unlabeled` | one-way | DNA20 | `kfocback` | internal-state conversion/modification | `DNA20(h2ax~foc) -> DNA20(h2ax~u)` | Changes internal modification/state marks on DNA20: DNA20.h2ax foc→u at `kfocback`. | +| 2000 | `Unlabeled` | one-way | DNA21 | `kfocback` | internal-state conversion/modification | `DNA21(h2ax~foc) -> DNA21(h2ax~u)` | Changes internal modification/state marks on DNA21: DNA21.h2ax foc→u at `kfocback`. | + +### Rules 2001-2250 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 2001 | `Unlabeled` | one-way | DNA22 | `kfocback` | internal-state conversion/modification | `DNA22(h2ax~foc) -> DNA22(h2ax~u)` | Changes internal modification/state marks on DNA22: DNA22.h2ax foc→u at `kfocback`. | +| 2002 | `Unlabeled` | one-way | DNA23 | `kfocback` | internal-state conversion/modification | `DNA23(h2ax~foc) -> DNA23(h2ax~u)` | Changes internal modification/state marks on DNA23: DNA23.h2ax foc→u at `kfocback`. | +| 2003 | `Unlabeled` | one-way | DNA24 | `kfocback` | internal-state conversion/modification | `DNA24(h2ax~foc) -> DNA24(h2ax~u)` | Changes internal modification/state marks on DNA24: DNA24.h2ax foc→u at `kfocback`. | +| 2004 | `Unlabeled` | one-way | DNA25 | `kfocback` | internal-state conversion/modification | `DNA25(h2ax~foc) -> DNA25(h2ax~u)` | Changes internal modification/state marks on DNA25: DNA25.h2ax foc→u at `kfocback`. | +| 2005 | `Unlabeled` | one-way | DNA26 | `kfocback` | internal-state conversion/modification | `DNA26(h2ax~foc) -> DNA26(h2ax~u)` | Changes internal modification/state marks on DNA26: DNA26.h2ax foc→u at `kfocback`. | +| 2006 | `Unlabeled` | one-way | DNA27 | `kfocback` | internal-state conversion/modification | `DNA27(h2ax~foc) -> DNA27(h2ax~u)` | Changes internal modification/state marks on DNA27: DNA27.h2ax foc→u at `kfocback`. | +| 2007 | `Unlabeled` | one-way | DNA28 | `kfocback` | internal-state conversion/modification | `DNA28(h2ax~foc) -> DNA28(h2ax~u)` | Changes internal modification/state marks on DNA28: DNA28.h2ax foc→u at `kfocback`. | +| 2008 | `Unlabeled` | one-way | DNA29 | `kfocback` | internal-state conversion/modification | `DNA29(h2ax~foc) -> DNA29(h2ax~u)` | Changes internal modification/state marks on DNA29: DNA29.h2ax foc→u at `kfocback`. | +| 2009 | `Unlabeled` | one-way | DNA30 | `kfocback` | internal-state conversion/modification | `DNA30(h2ax~foc) -> DNA30(h2ax~u)` | Changes internal modification/state marks on DNA30: DNA30.h2ax foc→u at `kfocback`. | +| 2010 | `Unlabeled` | one-way | DNA31 | `kfocback` | internal-state conversion/modification | `DNA31(h2ax~foc) -> DNA31(h2ax~u)` | Changes internal modification/state marks on DNA31: DNA31.h2ax foc→u at `kfocback`. | +| 2011 | `Unlabeled` | one-way | DNA32 | `kfocback` | internal-state conversion/modification | `DNA32(h2ax~foc) -> DNA32(h2ax~u)` | Changes internal modification/state marks on DNA32: DNA32.h2ax foc→u at `kfocback`. | +| 2012 | `Unlabeled` | one-way | DNA33 | `kfocback` | internal-state conversion/modification | `DNA33(h2ax~foc) -> DNA33(h2ax~u)` | Changes internal modification/state marks on DNA33: DNA33.h2ax foc→u at `kfocback`. | +| 2013 | `Unlabeled` | one-way | DNA34 | `kfocback` | internal-state conversion/modification | `DNA34(h2ax~foc) -> DNA34(h2ax~u)` | Changes internal modification/state marks on DNA34: DNA34.h2ax foc→u at `kfocback`. | +| 2014 | `Unlabeled` | one-way | DNA35 | `kfocback` | internal-state conversion/modification | `DNA35(h2ax~foc) -> DNA35(h2ax~u)` | Changes internal modification/state marks on DNA35: DNA35.h2ax foc→u at `kfocback`. | +| 2015 | `Unlabeled` | one-way | DNA36 | `kfocback` | internal-state conversion/modification | `DNA36(h2ax~foc) -> DNA36(h2ax~u)` | Changes internal modification/state marks on DNA36: DNA36.h2ax foc→u at `kfocback`. | +| 2016 | `Unlabeled` | one-way | DNA37 | `kfocback` | internal-state conversion/modification | `DNA37(h2ax~foc) -> DNA37(h2ax~u)` | Changes internal modification/state marks on DNA37: DNA37.h2ax foc→u at `kfocback`. | +| 2017 | `Unlabeled` | one-way | DNA38 | `kfocback` | internal-state conversion/modification | `DNA38(h2ax~foc) -> DNA38(h2ax~u)` | Changes internal modification/state marks on DNA38: DNA38.h2ax foc→u at `kfocback`. | +| 2018 | `Unlabeled` | one-way | DNA39 | `kfocback` | internal-state conversion/modification | `DNA39(h2ax~foc) -> DNA39(h2ax~u)` | Changes internal modification/state marks on DNA39: DNA39.h2ax foc→u at `kfocback`. | +| 2019 | `Unlabeled` | one-way | DNA40 | `kfocback` | internal-state conversion/modification | `DNA40(h2ax~foc) -> DNA40(h2ax~u)` | Changes internal modification/state marks on DNA40: DNA40.h2ax foc→u at `kfocback`. | +| 2020 | `Unlabeled` | one-way | DNA41 | `kfocback` | internal-state conversion/modification | `DNA41(h2ax~foc) -> DNA41(h2ax~u)` | Changes internal modification/state marks on DNA41: DNA41.h2ax foc→u at `kfocback`. | +| 2021 | `Unlabeled` | one-way | DNA42 | `kfocback` | internal-state conversion/modification | `DNA42(h2ax~foc) -> DNA42(h2ax~u)` | Changes internal modification/state marks on DNA42: DNA42.h2ax foc→u at `kfocback`. | +| 2022 | `Unlabeled` | one-way | DNA43 | `kfocback` | internal-state conversion/modification | `DNA43(h2ax~foc) -> DNA43(h2ax~u)` | Changes internal modification/state marks on DNA43: DNA43.h2ax foc→u at `kfocback`. | +| 2023 | `Unlabeled` | one-way | DNA44 | `kfocback` | internal-state conversion/modification | `DNA44(h2ax~foc) -> DNA44(h2ax~u)` | Changes internal modification/state marks on DNA44: DNA44.h2ax foc→u at `kfocback`. | +| 2024 | `Unlabeled` | one-way | DNA45 | `kfocback` | internal-state conversion/modification | `DNA45(h2ax~foc) -> DNA45(h2ax~u)` | Changes internal modification/state marks on DNA45: DNA45.h2ax foc→u at `kfocback`. | +| 2025 | `Unlabeled` | one-way | DNA46 | `kfocback` | internal-state conversion/modification | `DNA46(h2ax~foc) -> DNA46(h2ax~u)` | Changes internal modification/state marks on DNA46: DNA46.h2ax foc→u at `kfocback`. | +| 2026 | `Unlabeled` | one-way | DNA47 | `kfocback` | internal-state conversion/modification | `DNA47(h2ax~foc) -> DNA47(h2ax~u)` | Changes internal modification/state marks on DNA47: DNA47.h2ax foc→u at `kfocback`. | +| 2027 | `Unlabeled` | one-way | DNA48 | `kfocback` | internal-state conversion/modification | `DNA48(h2ax~foc) -> DNA48(h2ax~u)` | Changes internal modification/state marks on DNA48: DNA48.h2ax foc→u at `kfocback`. | +| 2028 | `Unlabeled` | one-way | DNA49 | `kfocback` | internal-state conversion/modification | `DNA49(h2ax~foc) -> DNA49(h2ax~u)` | Changes internal modification/state marks on DNA49: DNA49.h2ax foc→u at `kfocback`. | +| 2029 | `Unlabeled` | one-way | DNA50 | `kfocback` | internal-state conversion/modification | `DNA50(h2ax~foc) -> DNA50(h2ax~u)` | Changes internal modification/state marks on DNA50: DNA50.h2ax foc→u at `kfocback`. | +| 2030 | `Unlabeled` | one-way | ATM, DNA1 | `kh2axfull` | state and binding-pattern rewrite | `DNA1(h2ax~foc) + ATM(state~1,h2ax) -> DNA1(h2ax!1~foc).ATM(state~1,h2ax!1)` | Forms a complex/contact among ATM, DNA1 through ATM.h2ax, DNA1.h2ax at `kh2axfull`. | +| 2031 | `Unlabeled` | one-way | ATM, DNA2 | `kh2axfull` | state and binding-pattern rewrite | `DNA2(h2ax~foc) + ATM(state~2,h2ax) -> DNA2(h2ax!1~foc).ATM(state~2,h2ax!1)` | Forms a complex/contact among ATM, DNA2 through ATM.h2ax, DNA2.h2ax at `kh2axfull`. | +| 2032 | `Unlabeled` | one-way | ATM, DNA3 | `kh2axfull` | state and binding-pattern rewrite | `DNA3(h2ax~foc) + ATM(state~3,h2ax) -> DNA3(h2ax!1~foc).ATM(state~3,h2ax!1)` | Forms a complex/contact among ATM, DNA3 through ATM.h2ax, DNA3.h2ax at `kh2axfull`. | +| 2033 | `Unlabeled` | one-way | ATM, DNA4 | `kh2axfull` | state and binding-pattern rewrite | `DNA4(h2ax~foc) + ATM(state~4,h2ax) -> DNA4(h2ax!1~foc).ATM(state~4,h2ax!1)` | Forms a complex/contact among ATM, DNA4 through ATM.h2ax, DNA4.h2ax at `kh2axfull`. | +| 2034 | `Unlabeled` | one-way | ATM, DNA5 | `kh2axfull` | state and binding-pattern rewrite | `DNA5(h2ax~foc) + ATM(state~5,h2ax) -> DNA5(h2ax!1~foc).ATM(state~5,h2ax!1)` | Forms a complex/contact among ATM, DNA5 through ATM.h2ax, DNA5.h2ax at `kh2axfull`. | +| 2035 | `Unlabeled` | one-way | ATM, DNA6 | `kh2axfull` | state and binding-pattern rewrite | `DNA6(h2ax~foc) + ATM(state~6,h2ax) -> DNA6(h2ax!1~foc).ATM(state~6,h2ax!1)` | Forms a complex/contact among ATM, DNA6 through ATM.h2ax, DNA6.h2ax at `kh2axfull`. | +| 2036 | `Unlabeled` | one-way | ATM, DNA7 | `kh2axfull` | state and binding-pattern rewrite | `DNA7(h2ax~foc) + ATM(state~7,h2ax) -> DNA7(h2ax!1~foc).ATM(state~7,h2ax!1)` | Forms a complex/contact among ATM, DNA7 through ATM.h2ax, DNA7.h2ax at `kh2axfull`. | +| 2037 | `Unlabeled` | one-way | ATM, DNA8 | `kh2axfull` | state and binding-pattern rewrite | `DNA8(h2ax~foc) + ATM(state~8,h2ax) -> DNA8(h2ax!1~foc).ATM(state~8,h2ax!1)` | Forms a complex/contact among ATM, DNA8 through ATM.h2ax, DNA8.h2ax at `kh2axfull`. | +| 2038 | `Unlabeled` | one-way | ATM, DNA9 | `kh2axfull` | state and binding-pattern rewrite | `DNA9(h2ax~foc) + ATM(state~9,h2ax) -> DNA9(h2ax!1~foc).ATM(state~9,h2ax!1)` | Forms a complex/contact among ATM, DNA9 through ATM.h2ax, DNA9.h2ax at `kh2axfull`. | +| 2039 | `Unlabeled` | one-way | ATM, DNA10 | `kh2axfull` | state and binding-pattern rewrite | `DNA10(h2ax~foc) + ATM(state~10,h2ax) -> DNA10(h2ax!1~foc).ATM(state~10,h2ax!1)` | Forms a complex/contact among ATM, DNA10 through ATM.h2ax, DNA10.h2ax at `kh2axfull`. | +| 2040 | `Unlabeled` | one-way | ATM, DNA11 | `kh2axfull` | state and binding-pattern rewrite | `DNA11(h2ax~foc) + ATM(state~11,h2ax) -> DNA11(h2ax!1~foc).ATM(state~11,h2ax!1)` | Forms a complex/contact among ATM, DNA11 through ATM.h2ax, DNA11.h2ax at `kh2axfull`. | +| 2041 | `Unlabeled` | one-way | ATM, DNA12 | `kh2axfull` | state and binding-pattern rewrite | `DNA12(h2ax~foc) + ATM(state~12,h2ax) -> DNA12(h2ax!1~foc).ATM(state~12,h2ax!1)` | Forms a complex/contact among ATM, DNA12 through ATM.h2ax, DNA12.h2ax at `kh2axfull`. | +| 2042 | `Unlabeled` | one-way | ATM, DNA13 | `kh2axfull` | state and binding-pattern rewrite | `DNA13(h2ax~foc) + ATM(state~13,h2ax) -> DNA13(h2ax!1~foc).ATM(state~13,h2ax!1)` | Forms a complex/contact among ATM, DNA13 through ATM.h2ax, DNA13.h2ax at `kh2axfull`. | +| 2043 | `Unlabeled` | one-way | ATM, DNA14 | `kh2axfull` | state and binding-pattern rewrite | `DNA14(h2ax~foc) + ATM(state~14,h2ax) -> DNA14(h2ax!1~foc).ATM(state~14,h2ax!1)` | Forms a complex/contact among ATM, DNA14 through ATM.h2ax, DNA14.h2ax at `kh2axfull`. | +| 2044 | `Unlabeled` | one-way | ATM, DNA15 | `kh2axfull` | state and binding-pattern rewrite | `DNA15(h2ax~foc) + ATM(state~15,h2ax) -> DNA15(h2ax!1~foc).ATM(state~15,h2ax!1)` | Forms a complex/contact among ATM, DNA15 through ATM.h2ax, DNA15.h2ax at `kh2axfull`. | +| 2045 | `Unlabeled` | one-way | ATM, DNA16 | `kh2axfull` | state and binding-pattern rewrite | `DNA16(h2ax~foc) + ATM(state~16,h2ax) -> DNA16(h2ax!1~foc).ATM(state~16,h2ax!1)` | Forms a complex/contact among ATM, DNA16 through ATM.h2ax, DNA16.h2ax at `kh2axfull`. | +| 2046 | `Unlabeled` | one-way | ATM, DNA17 | `kh2axfull` | state and binding-pattern rewrite | `DNA17(h2ax~foc) + ATM(state~17,h2ax) -> DNA17(h2ax!1~foc).ATM(state~17,h2ax!1)` | Forms a complex/contact among ATM, DNA17 through ATM.h2ax, DNA17.h2ax at `kh2axfull`. | +| 2047 | `Unlabeled` | one-way | ATM, DNA18 | `kh2axfull` | state and binding-pattern rewrite | `DNA18(h2ax~foc) + ATM(state~18,h2ax) -> DNA18(h2ax!1~foc).ATM(state~18,h2ax!1)` | Forms a complex/contact among ATM, DNA18 through ATM.h2ax, DNA18.h2ax at `kh2axfull`. | +| 2048 | `Unlabeled` | one-way | ATM, DNA19 | `kh2axfull` | state and binding-pattern rewrite | `DNA19(h2ax~foc) + ATM(state~19,h2ax) -> DNA19(h2ax!1~foc).ATM(state~19,h2ax!1)` | Forms a complex/contact among ATM, DNA19 through ATM.h2ax, DNA19.h2ax at `kh2axfull`. | +| 2049 | `Unlabeled` | one-way | ATM, DNA20 | `kh2axfull` | state and binding-pattern rewrite | `DNA20(h2ax~foc) + ATM(state~20,h2ax) -> DNA20(h2ax!1~foc).ATM(state~20,h2ax!1)` | Forms a complex/contact among ATM, DNA20 through ATM.h2ax, DNA20.h2ax at `kh2axfull`. | +| 2050 | `Unlabeled` | one-way | ATM, DNA21 | `kh2axfull` | state and binding-pattern rewrite | `DNA21(h2ax~foc) + ATM(state~21,h2ax) -> DNA21(h2ax!1~foc).ATM(state~21,h2ax!1)` | Forms a complex/contact among ATM, DNA21 through ATM.h2ax, DNA21.h2ax at `kh2axfull`. | +| 2051 | `Unlabeled` | one-way | ATM, DNA22 | `kh2axfull` | state and binding-pattern rewrite | `DNA22(h2ax~foc) + ATM(state~22,h2ax) -> DNA22(h2ax!1~foc).ATM(state~22,h2ax!1)` | Forms a complex/contact among ATM, DNA22 through ATM.h2ax, DNA22.h2ax at `kh2axfull`. | +| 2052 | `Unlabeled` | one-way | ATM, DNA23 | `kh2axfull` | state and binding-pattern rewrite | `DNA23(h2ax~foc) + ATM(state~23,h2ax) -> DNA23(h2ax!1~foc).ATM(state~23,h2ax!1)` | Forms a complex/contact among ATM, DNA23 through ATM.h2ax, DNA23.h2ax at `kh2axfull`. | +| 2053 | `Unlabeled` | one-way | ATM, DNA24 | `kh2axfull` | state and binding-pattern rewrite | `DNA24(h2ax~foc) + ATM(state~24,h2ax) -> DNA24(h2ax!1~foc).ATM(state~24,h2ax!1)` | Forms a complex/contact among ATM, DNA24 through ATM.h2ax, DNA24.h2ax at `kh2axfull`. | +| 2054 | `Unlabeled` | one-way | ATM, DNA25 | `kh2axfull` | state and binding-pattern rewrite | `DNA25(h2ax~foc) + ATM(state~25,h2ax) -> DNA25(h2ax!1~foc).ATM(state~25,h2ax!1)` | Forms a complex/contact among ATM, DNA25 through ATM.h2ax, DNA25.h2ax at `kh2axfull`. | +| 2055 | `Unlabeled` | one-way | ATM, DNA26 | `kh2axfull` | state and binding-pattern rewrite | `DNA26(h2ax~foc) + ATM(state~26,h2ax) -> DNA26(h2ax!1~foc).ATM(state~26,h2ax!1)` | Forms a complex/contact among ATM, DNA26 through ATM.h2ax, DNA26.h2ax at `kh2axfull`. | +| 2056 | `Unlabeled` | one-way | ATM, DNA27 | `kh2axfull` | state and binding-pattern rewrite | `DNA27(h2ax~foc) + ATM(state~27,h2ax) -> DNA27(h2ax!1~foc).ATM(state~27,h2ax!1)` | Forms a complex/contact among ATM, DNA27 through ATM.h2ax, DNA27.h2ax at `kh2axfull`. | +| 2057 | `Unlabeled` | one-way | ATM, DNA28 | `kh2axfull` | state and binding-pattern rewrite | `DNA28(h2ax~foc) + ATM(state~28,h2ax) -> DNA28(h2ax!1~foc).ATM(state~28,h2ax!1)` | Forms a complex/contact among ATM, DNA28 through ATM.h2ax, DNA28.h2ax at `kh2axfull`. | +| 2058 | `Unlabeled` | one-way | ATM, DNA29 | `kh2axfull` | state and binding-pattern rewrite | `DNA29(h2ax~foc) + ATM(state~29,h2ax) -> DNA29(h2ax!1~foc).ATM(state~29,h2ax!1)` | Forms a complex/contact among ATM, DNA29 through ATM.h2ax, DNA29.h2ax at `kh2axfull`. | +| 2059 | `Unlabeled` | one-way | ATM, DNA30 | `kh2axfull` | state and binding-pattern rewrite | `DNA30(h2ax~foc) + ATM(state~30,h2ax) -> DNA30(h2ax!1~foc).ATM(state~30,h2ax!1)` | Forms a complex/contact among ATM, DNA30 through ATM.h2ax, DNA30.h2ax at `kh2axfull`. | +| 2060 | `Unlabeled` | one-way | ATM, DNA31 | `kh2axfull` | state and binding-pattern rewrite | `DNA31(h2ax~foc) + ATM(state~31,h2ax) -> DNA31(h2ax!1~foc).ATM(state~31,h2ax!1)` | Forms a complex/contact among ATM, DNA31 through ATM.h2ax, DNA31.h2ax at `kh2axfull`. | +| 2061 | `Unlabeled` | one-way | ATM, DNA32 | `kh2axfull` | state and binding-pattern rewrite | `DNA32(h2ax~foc) + ATM(state~32,h2ax) -> DNA32(h2ax!1~foc).ATM(state~32,h2ax!1)` | Forms a complex/contact among ATM, DNA32 through ATM.h2ax, DNA32.h2ax at `kh2axfull`. | +| 2062 | `Unlabeled` | one-way | ATM, DNA33 | `kh2axfull` | state and binding-pattern rewrite | `DNA33(h2ax~foc) + ATM(state~33,h2ax) -> DNA33(h2ax!1~foc).ATM(state~33,h2ax!1)` | Forms a complex/contact among ATM, DNA33 through ATM.h2ax, DNA33.h2ax at `kh2axfull`. | +| 2063 | `Unlabeled` | one-way | ATM, DNA34 | `kh2axfull` | state and binding-pattern rewrite | `DNA34(h2ax~foc) + ATM(state~34,h2ax) -> DNA34(h2ax!1~foc).ATM(state~34,h2ax!1)` | Forms a complex/contact among ATM, DNA34 through ATM.h2ax, DNA34.h2ax at `kh2axfull`. | +| 2064 | `Unlabeled` | one-way | ATM, DNA35 | `kh2axfull` | state and binding-pattern rewrite | `DNA35(h2ax~foc) + ATM(state~35,h2ax) -> DNA35(h2ax!1~foc).ATM(state~35,h2ax!1)` | Forms a complex/contact among ATM, DNA35 through ATM.h2ax, DNA35.h2ax at `kh2axfull`. | +| 2065 | `Unlabeled` | one-way | ATM, DNA36 | `kh2axfull` | state and binding-pattern rewrite | `DNA36(h2ax~foc) + ATM(state~36,h2ax) -> DNA36(h2ax!1~foc).ATM(state~36,h2ax!1)` | Forms a complex/contact among ATM, DNA36 through ATM.h2ax, DNA36.h2ax at `kh2axfull`. | +| 2066 | `Unlabeled` | one-way | ATM, DNA37 | `kh2axfull` | state and binding-pattern rewrite | `DNA37(h2ax~foc) + ATM(state~37,h2ax) -> DNA37(h2ax!1~foc).ATM(state~37,h2ax!1)` | Forms a complex/contact among ATM, DNA37 through ATM.h2ax, DNA37.h2ax at `kh2axfull`. | +| 2067 | `Unlabeled` | one-way | ATM, DNA38 | `kh2axfull` | state and binding-pattern rewrite | `DNA38(h2ax~foc) + ATM(state~38,h2ax) -> DNA38(h2ax!1~foc).ATM(state~38,h2ax!1)` | Forms a complex/contact among ATM, DNA38 through ATM.h2ax, DNA38.h2ax at `kh2axfull`. | +| 2068 | `Unlabeled` | one-way | ATM, DNA39 | `kh2axfull` | state and binding-pattern rewrite | `DNA39(h2ax~foc) + ATM(state~39,h2ax) -> DNA39(h2ax!1~foc).ATM(state~39,h2ax!1)` | Forms a complex/contact among ATM, DNA39 through ATM.h2ax, DNA39.h2ax at `kh2axfull`. | +| 2069 | `Unlabeled` | one-way | ATM, DNA40 | `kh2axfull` | state and binding-pattern rewrite | `DNA40(h2ax~foc) + ATM(state~40,h2ax) -> DNA40(h2ax!1~foc).ATM(state~40,h2ax!1)` | Forms a complex/contact among ATM, DNA40 through ATM.h2ax, DNA40.h2ax at `kh2axfull`. | +| 2070 | `Unlabeled` | one-way | ATM, DNA41 | `kh2axfull` | state and binding-pattern rewrite | `DNA41(h2ax~foc) + ATM(state~41,h2ax) -> DNA41(h2ax!1~foc).ATM(state~41,h2ax!1)` | Forms a complex/contact among ATM, DNA41 through ATM.h2ax, DNA41.h2ax at `kh2axfull`. | +| 2071 | `Unlabeled` | one-way | ATM, DNA42 | `kh2axfull` | state and binding-pattern rewrite | `DNA42(h2ax~foc) + ATM(state~42,h2ax) -> DNA42(h2ax!1~foc).ATM(state~42,h2ax!1)` | Forms a complex/contact among ATM, DNA42 through ATM.h2ax, DNA42.h2ax at `kh2axfull`. | +| 2072 | `Unlabeled` | one-way | ATM, DNA43 | `kh2axfull` | state and binding-pattern rewrite | `DNA43(h2ax~foc) + ATM(state~43,h2ax) -> DNA43(h2ax!1~foc).ATM(state~43,h2ax!1)` | Forms a complex/contact among ATM, DNA43 through ATM.h2ax, DNA43.h2ax at `kh2axfull`. | +| 2073 | `Unlabeled` | one-way | ATM, DNA44 | `kh2axfull` | state and binding-pattern rewrite | `DNA44(h2ax~foc) + ATM(state~44,h2ax) -> DNA44(h2ax!1~foc).ATM(state~44,h2ax!1)` | Forms a complex/contact among ATM, DNA44 through ATM.h2ax, DNA44.h2ax at `kh2axfull`. | +| 2074 | `Unlabeled` | one-way | ATM, DNA45 | `kh2axfull` | state and binding-pattern rewrite | `DNA45(h2ax~foc) + ATM(state~45,h2ax) -> DNA45(h2ax!1~foc).ATM(state~45,h2ax!1)` | Forms a complex/contact among ATM, DNA45 through ATM.h2ax, DNA45.h2ax at `kh2axfull`. | +| 2075 | `Unlabeled` | one-way | ATM, DNA46 | `kh2axfull` | state and binding-pattern rewrite | `DNA46(h2ax~foc) + ATM(state~46,h2ax) -> DNA46(h2ax!1~foc).ATM(state~46,h2ax!1)` | Forms a complex/contact among ATM, DNA46 through ATM.h2ax, DNA46.h2ax at `kh2axfull`. | +| 2076 | `Unlabeled` | one-way | ATM, DNA47 | `kh2axfull` | state and binding-pattern rewrite | `DNA47(h2ax~foc) + ATM(state~47,h2ax) -> DNA47(h2ax!1~foc).ATM(state~47,h2ax!1)` | Forms a complex/contact among ATM, DNA47 through ATM.h2ax, DNA47.h2ax at `kh2axfull`. | +| 2077 | `Unlabeled` | one-way | ATM, DNA48 | `kh2axfull` | state and binding-pattern rewrite | `DNA48(h2ax~foc) + ATM(state~48,h2ax) -> DNA48(h2ax!1~foc).ATM(state~48,h2ax!1)` | Forms a complex/contact among ATM, DNA48 through ATM.h2ax, DNA48.h2ax at `kh2axfull`. | +| 2078 | `Unlabeled` | one-way | ATM, DNA49 | `kh2axfull` | state and binding-pattern rewrite | `DNA49(h2ax~foc) + ATM(state~49,h2ax) -> DNA49(h2ax!1~foc).ATM(state~49,h2ax!1)` | Forms a complex/contact among ATM, DNA49 through ATM.h2ax, DNA49.h2ax at `kh2axfull`. | +| 2079 | `Unlabeled` | one-way | ATM, DNA50 | `kh2axfull` | state and binding-pattern rewrite | `DNA50(h2ax~foc) + ATM(state~50,h2ax) -> DNA50(h2ax!1~foc).ATM(state~50,h2ax!1)` | Forms a complex/contact among ATM, DNA50 through ATM.h2ax, DNA50.h2ax at `kh2axfull`. | +| 2080 | `Unlabeled` | one-way | ATM, DNA1 | `kfocfin` | state and binding-pattern rewrite | `DNA1(h2ax!1~foc).ATM(state~1,h2ax!1) -> DNA1(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 1→0) with binding-site changes (removes ATM.h2ax, DNA1.h2ax) at `kfocfin`. | +| 2081 | `Unlabeled` | one-way | ATM, DNA2 | `kfocfin` | state and binding-pattern rewrite | `DNA2(h2ax!1~foc).ATM(state~2,h2ax!1) -> DNA2(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 2→0) with binding-site changes (removes ATM.h2ax, DNA2.h2ax) at `kfocfin`. | +| 2082 | `Unlabeled` | one-way | ATM, DNA3 | `kfocfin` | state and binding-pattern rewrite | `DNA3(h2ax!1~foc).ATM(state~3,h2ax!1) -> DNA3(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 3→0) with binding-site changes (removes ATM.h2ax, DNA3.h2ax) at `kfocfin`. | +| 2083 | `Unlabeled` | one-way | ATM, DNA4 | `kfocfin` | state and binding-pattern rewrite | `DNA4(h2ax!1~foc).ATM(state~4,h2ax!1) -> DNA4(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 4→0) with binding-site changes (removes ATM.h2ax, DNA4.h2ax) at `kfocfin`. | +| 2084 | `Unlabeled` | one-way | ATM, DNA5 | `kfocfin` | state and binding-pattern rewrite | `DNA5(h2ax!1~foc).ATM(state~5,h2ax!1) -> DNA5(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 5→0) with binding-site changes (removes ATM.h2ax, DNA5.h2ax) at `kfocfin`. | +| 2085 | `Unlabeled` | one-way | ATM, DNA6 | `kfocfin` | state and binding-pattern rewrite | `DNA6(h2ax!1~foc).ATM(state~6,h2ax!1) -> DNA6(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 6→0) with binding-site changes (removes ATM.h2ax, DNA6.h2ax) at `kfocfin`. | +| 2086 | `Unlabeled` | one-way | ATM, DNA7 | `kfocfin` | state and binding-pattern rewrite | `DNA7(h2ax!1~foc).ATM(state~7,h2ax!1) -> DNA7(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 7→0) with binding-site changes (removes ATM.h2ax, DNA7.h2ax) at `kfocfin`. | +| 2087 | `Unlabeled` | one-way | ATM, DNA8 | `kfocfin` | state and binding-pattern rewrite | `DNA8(h2ax!1~foc).ATM(state~8,h2ax!1) -> DNA8(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 8→0) with binding-site changes (removes ATM.h2ax, DNA8.h2ax) at `kfocfin`. | +| 2088 | `Unlabeled` | one-way | ATM, DNA9 | `kfocfin` | state and binding-pattern rewrite | `DNA9(h2ax!1~foc).ATM(state~9,h2ax!1) -> DNA9(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 9→0) with binding-site changes (removes ATM.h2ax, DNA9.h2ax) at `kfocfin`. | +| 2089 | `Unlabeled` | one-way | ATM, DNA10 | `kfocfin` | state and binding-pattern rewrite | `DNA10(h2ax!1~foc).ATM(state~10,h2ax!1) -> DNA10(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 10→0) with binding-site changes (removes ATM.h2ax, DNA10.h2ax) at `kfocfin`. | +| 2090 | `Unlabeled` | one-way | ATM, DNA11 | `kfocfin` | state and binding-pattern rewrite | `DNA11(h2ax!1~foc).ATM(state~11,h2ax!1) -> DNA11(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 11→0) with binding-site changes (removes ATM.h2ax, DNA11.h2ax) at `kfocfin`. | +| 2091 | `Unlabeled` | one-way | ATM, DNA12 | `kfocfin` | state and binding-pattern rewrite | `DNA12(h2ax!1~foc).ATM(state~12,h2ax!1) -> DNA12(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 12→0) with binding-site changes (removes ATM.h2ax, DNA12.h2ax) at `kfocfin`. | +| 2092 | `Unlabeled` | one-way | ATM, DNA13 | `kfocfin` | state and binding-pattern rewrite | `DNA13(h2ax!1~foc).ATM(state~13,h2ax!1) -> DNA13(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 13→0) with binding-site changes (removes ATM.h2ax, DNA13.h2ax) at `kfocfin`. | +| 2093 | `Unlabeled` | one-way | ATM, DNA14 | `kfocfin` | state and binding-pattern rewrite | `DNA14(h2ax!1~foc).ATM(state~14,h2ax!1) -> DNA14(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 14→0) with binding-site changes (removes ATM.h2ax, DNA14.h2ax) at `kfocfin`. | +| 2094 | `Unlabeled` | one-way | ATM, DNA15 | `kfocfin` | state and binding-pattern rewrite | `DNA15(h2ax!1~foc).ATM(state~15,h2ax!1) -> DNA15(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 15→0) with binding-site changes (removes ATM.h2ax, DNA15.h2ax) at `kfocfin`. | +| 2095 | `Unlabeled` | one-way | ATM, DNA16 | `kfocfin` | state and binding-pattern rewrite | `DNA16(h2ax!1~foc).ATM(state~16,h2ax!1) -> DNA16(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 16→0) with binding-site changes (removes ATM.h2ax, DNA16.h2ax) at `kfocfin`. | +| 2096 | `Unlabeled` | one-way | ATM, DNA17 | `kfocfin` | state and binding-pattern rewrite | `DNA17(h2ax!1~foc).ATM(state~17,h2ax!1) -> DNA17(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 17→0) with binding-site changes (removes ATM.h2ax, DNA17.h2ax) at `kfocfin`. | +| 2097 | `Unlabeled` | one-way | ATM, DNA18 | `kfocfin` | state and binding-pattern rewrite | `DNA18(h2ax!1~foc).ATM(state~18,h2ax!1) -> DNA18(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 18→0) with binding-site changes (removes ATM.h2ax, DNA18.h2ax) at `kfocfin`. | +| 2098 | `Unlabeled` | one-way | ATM, DNA19 | `kfocfin` | state and binding-pattern rewrite | `DNA19(h2ax!1~foc).ATM(state~19,h2ax!1) -> DNA19(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 19→0) with binding-site changes (removes ATM.h2ax, DNA19.h2ax) at `kfocfin`. | +| 2099 | `Unlabeled` | one-way | ATM, DNA20 | `kfocfin` | state and binding-pattern rewrite | `DNA20(h2ax!1~foc).ATM(state~20,h2ax!1) -> DNA20(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 20→0) with binding-site changes (removes ATM.h2ax, DNA20.h2ax) at `kfocfin`. | +| 2100 | `Unlabeled` | one-way | ATM, DNA21 | `kfocfin` | state and binding-pattern rewrite | `DNA21(h2ax!1~foc).ATM(state~21,h2ax!1) -> DNA21(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 21→0) with binding-site changes (removes ATM.h2ax, DNA21.h2ax) at `kfocfin`. | +| 2101 | `Unlabeled` | one-way | ATM, DNA22 | `kfocfin` | state and binding-pattern rewrite | `DNA22(h2ax!1~foc).ATM(state~22,h2ax!1) -> DNA22(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 22→0) with binding-site changes (removes ATM.h2ax, DNA22.h2ax) at `kfocfin`. | +| 2102 | `Unlabeled` | one-way | ATM, DNA23 | `kfocfin` | state and binding-pattern rewrite | `DNA23(h2ax!1~foc).ATM(state~23,h2ax!1) -> DNA23(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 23→0) with binding-site changes (removes ATM.h2ax, DNA23.h2ax) at `kfocfin`. | +| 2103 | `Unlabeled` | one-way | ATM, DNA24 | `kfocfin` | state and binding-pattern rewrite | `DNA24(h2ax!1~foc).ATM(state~24,h2ax!1) -> DNA24(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 24→0) with binding-site changes (removes ATM.h2ax, DNA24.h2ax) at `kfocfin`. | +| 2104 | `Unlabeled` | one-way | ATM, DNA25 | `kfocfin` | state and binding-pattern rewrite | `DNA25(h2ax!1~foc).ATM(state~25,h2ax!1) -> DNA25(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 25→0) with binding-site changes (removes ATM.h2ax, DNA25.h2ax) at `kfocfin`. | +| 2105 | `Unlabeled` | one-way | ATM, DNA26 | `kfocfin` | state and binding-pattern rewrite | `DNA26(h2ax!1~foc).ATM(state~26,h2ax!1) -> DNA26(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 26→0) with binding-site changes (removes ATM.h2ax, DNA26.h2ax) at `kfocfin`. | +| 2106 | `Unlabeled` | one-way | ATM, DNA27 | `kfocfin` | state and binding-pattern rewrite | `DNA27(h2ax!1~foc).ATM(state~27,h2ax!1) -> DNA27(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 27→0) with binding-site changes (removes ATM.h2ax, DNA27.h2ax) at `kfocfin`. | +| 2107 | `Unlabeled` | one-way | ATM, DNA28 | `kfocfin` | state and binding-pattern rewrite | `DNA28(h2ax!1~foc).ATM(state~28,h2ax!1) -> DNA28(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 28→0) with binding-site changes (removes ATM.h2ax, DNA28.h2ax) at `kfocfin`. | +| 2108 | `Unlabeled` | one-way | ATM, DNA29 | `kfocfin` | state and binding-pattern rewrite | `DNA29(h2ax!1~foc).ATM(state~29,h2ax!1) -> DNA29(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 29→0) with binding-site changes (removes ATM.h2ax, DNA29.h2ax) at `kfocfin`. | +| 2109 | `Unlabeled` | one-way | ATM, DNA30 | `kfocfin` | state and binding-pattern rewrite | `DNA30(h2ax!1~foc).ATM(state~30,h2ax!1) -> DNA30(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 30→0) with binding-site changes (removes ATM.h2ax, DNA30.h2ax) at `kfocfin`. | +| 2110 | `Unlabeled` | one-way | ATM, DNA31 | `kfocfin` | state and binding-pattern rewrite | `DNA31(h2ax!1~foc).ATM(state~31,h2ax!1) -> DNA31(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 31→0) with binding-site changes (removes ATM.h2ax, DNA31.h2ax) at `kfocfin`. | +| 2111 | `Unlabeled` | one-way | ATM, DNA32 | `kfocfin` | state and binding-pattern rewrite | `DNA32(h2ax!1~foc).ATM(state~32,h2ax!1) -> DNA32(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 32→0) with binding-site changes (removes ATM.h2ax, DNA32.h2ax) at `kfocfin`. | +| 2112 | `Unlabeled` | one-way | ATM, DNA33 | `kfocfin` | state and binding-pattern rewrite | `DNA33(h2ax!1~foc).ATM(state~33,h2ax!1) -> DNA33(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 33→0) with binding-site changes (removes ATM.h2ax, DNA33.h2ax) at `kfocfin`. | +| 2113 | `Unlabeled` | one-way | ATM, DNA34 | `kfocfin` | state and binding-pattern rewrite | `DNA34(h2ax!1~foc).ATM(state~34,h2ax!1) -> DNA34(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 34→0) with binding-site changes (removes ATM.h2ax, DNA34.h2ax) at `kfocfin`. | +| 2114 | `Unlabeled` | one-way | ATM, DNA35 | `kfocfin` | state and binding-pattern rewrite | `DNA35(h2ax!1~foc).ATM(state~35,h2ax!1) -> DNA35(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 35→0) with binding-site changes (removes ATM.h2ax, DNA35.h2ax) at `kfocfin`. | +| 2115 | `Unlabeled` | one-way | ATM, DNA36 | `kfocfin` | state and binding-pattern rewrite | `DNA36(h2ax!1~foc).ATM(state~36,h2ax!1) -> DNA36(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 36→0) with binding-site changes (removes ATM.h2ax, DNA36.h2ax) at `kfocfin`. | +| 2116 | `Unlabeled` | one-way | ATM, DNA37 | `kfocfin` | state and binding-pattern rewrite | `DNA37(h2ax!1~foc).ATM(state~37,h2ax!1) -> DNA37(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 37→0) with binding-site changes (removes ATM.h2ax, DNA37.h2ax) at `kfocfin`. | +| 2117 | `Unlabeled` | one-way | ATM, DNA38 | `kfocfin` | state and binding-pattern rewrite | `DNA38(h2ax!1~foc).ATM(state~38,h2ax!1) -> DNA38(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 38→0) with binding-site changes (removes ATM.h2ax, DNA38.h2ax) at `kfocfin`. | +| 2118 | `Unlabeled` | one-way | ATM, DNA39 | `kfocfin` | state and binding-pattern rewrite | `DNA39(h2ax!1~foc).ATM(state~39,h2ax!1) -> DNA39(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 39→0) with binding-site changes (removes ATM.h2ax, DNA39.h2ax) at `kfocfin`. | +| 2119 | `Unlabeled` | one-way | ATM, DNA40 | `kfocfin` | state and binding-pattern rewrite | `DNA40(h2ax!1~foc).ATM(state~40,h2ax!1) -> DNA40(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 40→0) with binding-site changes (removes ATM.h2ax, DNA40.h2ax) at `kfocfin`. | +| 2120 | `Unlabeled` | one-way | ATM, DNA41 | `kfocfin` | state and binding-pattern rewrite | `DNA41(h2ax!1~foc).ATM(state~41,h2ax!1) -> DNA41(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 41→0) with binding-site changes (removes ATM.h2ax, DNA41.h2ax) at `kfocfin`. | +| 2121 | `Unlabeled` | one-way | ATM, DNA42 | `kfocfin` | state and binding-pattern rewrite | `DNA42(h2ax!1~foc).ATM(state~42,h2ax!1) -> DNA42(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 42→0) with binding-site changes (removes ATM.h2ax, DNA42.h2ax) at `kfocfin`. | +| 2122 | `Unlabeled` | one-way | ATM, DNA43 | `kfocfin` | state and binding-pattern rewrite | `DNA43(h2ax!1~foc).ATM(state~43,h2ax!1) -> DNA43(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 43→0) with binding-site changes (removes ATM.h2ax, DNA43.h2ax) at `kfocfin`. | +| 2123 | `Unlabeled` | one-way | ATM, DNA44 | `kfocfin` | state and binding-pattern rewrite | `DNA44(h2ax!1~foc).ATM(state~44,h2ax!1) -> DNA44(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 44→0) with binding-site changes (removes ATM.h2ax, DNA44.h2ax) at `kfocfin`. | +| 2124 | `Unlabeled` | one-way | ATM, DNA45 | `kfocfin` | state and binding-pattern rewrite | `DNA45(h2ax!1~foc).ATM(state~45,h2ax!1) -> DNA45(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 45→0) with binding-site changes (removes ATM.h2ax, DNA45.h2ax) at `kfocfin`. | +| 2125 | `Unlabeled` | one-way | ATM, DNA46 | `kfocfin` | state and binding-pattern rewrite | `DNA46(h2ax!1~foc).ATM(state~46,h2ax!1) -> DNA46(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 46→0) with binding-site changes (removes ATM.h2ax, DNA46.h2ax) at `kfocfin`. | +| 2126 | `Unlabeled` | one-way | ATM, DNA47 | `kfocfin` | state and binding-pattern rewrite | `DNA47(h2ax!1~foc).ATM(state~47,h2ax!1) -> DNA47(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 47→0) with binding-site changes (removes ATM.h2ax, DNA47.h2ax) at `kfocfin`. | +| 2127 | `Unlabeled` | one-way | ATM, DNA48 | `kfocfin` | state and binding-pattern rewrite | `DNA48(h2ax!1~foc).ATM(state~48,h2ax!1) -> DNA48(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 48→0) with binding-site changes (removes ATM.h2ax, DNA48.h2ax) at `kfocfin`. | +| 2128 | `Unlabeled` | one-way | ATM, DNA49 | `kfocfin` | state and binding-pattern rewrite | `DNA49(h2ax!1~foc).ATM(state~49,h2ax!1) -> DNA49(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 49→0) with binding-site changes (removes ATM.h2ax, DNA49.h2ax) at `kfocfin`. | +| 2129 | `Unlabeled` | one-way | ATM, DNA50 | `kfocfin` | state and binding-pattern rewrite | `DNA50(h2ax!1~foc).ATM(state~50,h2ax!1) -> DNA50(h2ax~u) + ATM(state~0,h2ax)` | Couples site-state changes (ATM.state 50→0) with binding-site changes (removes ATM.h2ax, DNA50.h2ax) at `kfocfin`. | +| 2130 | `Unlabeled` | one-way | I, ROS | `kROS` | source/synthesis or algebraic source term | `I() -> I() + ROS()` | Produces ROS while retaining or consuming I at `kROS`. | +| 2131 | `Unlabeled` | one-way | ROS, Sink | `kdROS` | sink/degradation/removal | `ROS() -> Sink()` | Degrades or diverts ROS into the model sink at `kdROS`, reducing that active species pool. | +| 2132 | `Unlabeled` | one-way | IR, ROS | `kIR` | stoichiometric pattern rewrite | `IR() -> IR() + ROS()` | Produces ROS while retaining or consuming IR at `kIR`. | +| 2133 | `Unlabeled` | one-way | DNA1, ROS | `kdam1` | internal-state conversion/modification | `DNA1(site~ok) + ROS() -> DNA1(site~sdsb)` | Changes internal modification/state marks on DNA1, ROS: DNA1.site ok→sdsb at `kdam1`. | +| 2134 | `Unlabeled` | one-way | DNA2, ROS | `kdam1` | internal-state conversion/modification | `DNA2(site~ok) + ROS() -> DNA2(site~sdsb)` | Changes internal modification/state marks on DNA2, ROS: DNA2.site ok→sdsb at `kdam1`. | +| 2135 | `Unlabeled` | one-way | DNA3, ROS | `kdam1` | internal-state conversion/modification | `DNA3(site~ok) + ROS() -> DNA3(site~sdsb)` | Changes internal modification/state marks on DNA3, ROS: DNA3.site ok→sdsb at `kdam1`. | +| 2136 | `Unlabeled` | one-way | DNA4, ROS | `kdam1` | internal-state conversion/modification | `DNA4(site~ok) + ROS() -> DNA4(site~sdsb)` | Changes internal modification/state marks on DNA4, ROS: DNA4.site ok→sdsb at `kdam1`. | +| 2137 | `Unlabeled` | one-way | DNA5, ROS | `kdam1` | internal-state conversion/modification | `DNA5(site~ok) + ROS() -> DNA5(site~sdsb)` | Changes internal modification/state marks on DNA5, ROS: DNA5.site ok→sdsb at `kdam1`. | +| 2138 | `Unlabeled` | one-way | DNA6, ROS | `kdam1` | internal-state conversion/modification | `DNA6(site~ok) + ROS() -> DNA6(site~sdsb)` | Changes internal modification/state marks on DNA6, ROS: DNA6.site ok→sdsb at `kdam1`. | +| 2139 | `Unlabeled` | one-way | DNA7, ROS | `kdam1` | internal-state conversion/modification | `DNA7(site~ok) + ROS() -> DNA7(site~sdsb)` | Changes internal modification/state marks on DNA7, ROS: DNA7.site ok→sdsb at `kdam1`. | +| 2140 | `Unlabeled` | one-way | DNA8, ROS | `kdam1` | internal-state conversion/modification | `DNA8(site~ok) + ROS() -> DNA8(site~sdsb)` | Changes internal modification/state marks on DNA8, ROS: DNA8.site ok→sdsb at `kdam1`. | +| 2141 | `Unlabeled` | one-way | DNA9, ROS | `kdam1` | internal-state conversion/modification | `DNA9(site~ok) + ROS() -> DNA9(site~sdsb)` | Changes internal modification/state marks on DNA9, ROS: DNA9.site ok→sdsb at `kdam1`. | +| 2142 | `Unlabeled` | one-way | DNA10, ROS | `kdam1` | internal-state conversion/modification | `DNA10(site~ok) + ROS() -> DNA10(site~sdsb)` | Changes internal modification/state marks on DNA10, ROS: DNA10.site ok→sdsb at `kdam1`. | +| 2143 | `Unlabeled` | one-way | DNA11, ROS | `kdam1` | internal-state conversion/modification | `DNA11(site~ok) + ROS() -> DNA11(site~sdsb)` | Changes internal modification/state marks on DNA11, ROS: DNA11.site ok→sdsb at `kdam1`. | +| 2144 | `Unlabeled` | one-way | DNA12, ROS | `kdam1` | internal-state conversion/modification | `DNA12(site~ok) + ROS() -> DNA12(site~sdsb)` | Changes internal modification/state marks on DNA12, ROS: DNA12.site ok→sdsb at `kdam1`. | +| 2145 | `Unlabeled` | one-way | DNA13, ROS | `kdam1` | internal-state conversion/modification | `DNA13(site~ok) + ROS() -> DNA13(site~sdsb)` | Changes internal modification/state marks on DNA13, ROS: DNA13.site ok→sdsb at `kdam1`. | +| 2146 | `Unlabeled` | one-way | DNA14, ROS | `kdam1` | internal-state conversion/modification | `DNA14(site~ok) + ROS() -> DNA14(site~sdsb)` | Changes internal modification/state marks on DNA14, ROS: DNA14.site ok→sdsb at `kdam1`. | +| 2147 | `Unlabeled` | one-way | DNA15, ROS | `kdam1` | internal-state conversion/modification | `DNA15(site~ok) + ROS() -> DNA15(site~sdsb)` | Changes internal modification/state marks on DNA15, ROS: DNA15.site ok→sdsb at `kdam1`. | +| 2148 | `Unlabeled` | one-way | DNA16, ROS | `kdam1` | internal-state conversion/modification | `DNA16(site~ok) + ROS() -> DNA16(site~sdsb)` | Changes internal modification/state marks on DNA16, ROS: DNA16.site ok→sdsb at `kdam1`. | +| 2149 | `Unlabeled` | one-way | DNA17, ROS | `kdam1` | internal-state conversion/modification | `DNA17(site~ok) + ROS() -> DNA17(site~sdsb)` | Changes internal modification/state marks on DNA17, ROS: DNA17.site ok→sdsb at `kdam1`. | +| 2150 | `Unlabeled` | one-way | DNA18, ROS | `kdam1` | internal-state conversion/modification | `DNA18(site~ok) + ROS() -> DNA18(site~sdsb)` | Changes internal modification/state marks on DNA18, ROS: DNA18.site ok→sdsb at `kdam1`. | +| 2151 | `Unlabeled` | one-way | DNA19, ROS | `kdam1` | internal-state conversion/modification | `DNA19(site~ok) + ROS() -> DNA19(site~sdsb)` | Changes internal modification/state marks on DNA19, ROS: DNA19.site ok→sdsb at `kdam1`. | +| 2152 | `Unlabeled` | one-way | DNA20, ROS | `kdam1` | internal-state conversion/modification | `DNA20(site~ok) + ROS() -> DNA20(site~sdsb)` | Changes internal modification/state marks on DNA20, ROS: DNA20.site ok→sdsb at `kdam1`. | +| 2153 | `Unlabeled` | one-way | DNA21, ROS | `kdam1` | internal-state conversion/modification | `DNA21(site~ok) + ROS() -> DNA21(site~sdsb)` | Changes internal modification/state marks on DNA21, ROS: DNA21.site ok→sdsb at `kdam1`. | +| 2154 | `Unlabeled` | one-way | DNA22, ROS | `kdam1` | internal-state conversion/modification | `DNA22(site~ok) + ROS() -> DNA22(site~sdsb)` | Changes internal modification/state marks on DNA22, ROS: DNA22.site ok→sdsb at `kdam1`. | +| 2155 | `Unlabeled` | one-way | DNA23, ROS | `kdam1` | internal-state conversion/modification | `DNA23(site~ok) + ROS() -> DNA23(site~sdsb)` | Changes internal modification/state marks on DNA23, ROS: DNA23.site ok→sdsb at `kdam1`. | +| 2156 | `Unlabeled` | one-way | DNA24, ROS | `kdam1` | internal-state conversion/modification | `DNA24(site~ok) + ROS() -> DNA24(site~sdsb)` | Changes internal modification/state marks on DNA24, ROS: DNA24.site ok→sdsb at `kdam1`. | +| 2157 | `Unlabeled` | one-way | DNA25, ROS | `kdam1` | internal-state conversion/modification | `DNA25(site~ok) + ROS() -> DNA25(site~sdsb)` | Changes internal modification/state marks on DNA25, ROS: DNA25.site ok→sdsb at `kdam1`. | +| 2158 | `Unlabeled` | one-way | DNA26, ROS | `kdam1` | internal-state conversion/modification | `DNA26(site~ok) + ROS() -> DNA26(site~sdsb)` | Changes internal modification/state marks on DNA26, ROS: DNA26.site ok→sdsb at `kdam1`. | +| 2159 | `Unlabeled` | one-way | DNA27, ROS | `kdam1` | internal-state conversion/modification | `DNA27(site~ok) + ROS() -> DNA27(site~sdsb)` | Changes internal modification/state marks on DNA27, ROS: DNA27.site ok→sdsb at `kdam1`. | +| 2160 | `Unlabeled` | one-way | DNA28, ROS | `kdam1` | internal-state conversion/modification | `DNA28(site~ok) + ROS() -> DNA28(site~sdsb)` | Changes internal modification/state marks on DNA28, ROS: DNA28.site ok→sdsb at `kdam1`. | +| 2161 | `Unlabeled` | one-way | DNA29, ROS | `kdam1` | internal-state conversion/modification | `DNA29(site~ok) + ROS() -> DNA29(site~sdsb)` | Changes internal modification/state marks on DNA29, ROS: DNA29.site ok→sdsb at `kdam1`. | +| 2162 | `Unlabeled` | one-way | DNA30, ROS | `kdam1` | internal-state conversion/modification | `DNA30(site~ok) + ROS() -> DNA30(site~sdsb)` | Changes internal modification/state marks on DNA30, ROS: DNA30.site ok→sdsb at `kdam1`. | +| 2163 | `Unlabeled` | one-way | DNA31, ROS | `kdam1` | internal-state conversion/modification | `DNA31(site~ok) + ROS() -> DNA31(site~sdsb)` | Changes internal modification/state marks on DNA31, ROS: DNA31.site ok→sdsb at `kdam1`. | +| 2164 | `Unlabeled` | one-way | DNA32, ROS | `kdam1` | internal-state conversion/modification | `DNA32(site~ok) + ROS() -> DNA32(site~sdsb)` | Changes internal modification/state marks on DNA32, ROS: DNA32.site ok→sdsb at `kdam1`. | +| 2165 | `Unlabeled` | one-way | DNA33, ROS | `kdam1` | internal-state conversion/modification | `DNA33(site~ok) + ROS() -> DNA33(site~sdsb)` | Changes internal modification/state marks on DNA33, ROS: DNA33.site ok→sdsb at `kdam1`. | +| 2166 | `Unlabeled` | one-way | DNA34, ROS | `kdam1` | internal-state conversion/modification | `DNA34(site~ok) + ROS() -> DNA34(site~sdsb)` | Changes internal modification/state marks on DNA34, ROS: DNA34.site ok→sdsb at `kdam1`. | +| 2167 | `Unlabeled` | one-way | DNA35, ROS | `kdam1` | internal-state conversion/modification | `DNA35(site~ok) + ROS() -> DNA35(site~sdsb)` | Changes internal modification/state marks on DNA35, ROS: DNA35.site ok→sdsb at `kdam1`. | +| 2168 | `Unlabeled` | one-way | DNA36, ROS | `kdam1` | internal-state conversion/modification | `DNA36(site~ok) + ROS() -> DNA36(site~sdsb)` | Changes internal modification/state marks on DNA36, ROS: DNA36.site ok→sdsb at `kdam1`. | +| 2169 | `Unlabeled` | one-way | DNA37, ROS | `kdam1` | internal-state conversion/modification | `DNA37(site~ok) + ROS() -> DNA37(site~sdsb)` | Changes internal modification/state marks on DNA37, ROS: DNA37.site ok→sdsb at `kdam1`. | +| 2170 | `Unlabeled` | one-way | DNA38, ROS | `kdam1` | internal-state conversion/modification | `DNA38(site~ok) + ROS() -> DNA38(site~sdsb)` | Changes internal modification/state marks on DNA38, ROS: DNA38.site ok→sdsb at `kdam1`. | +| 2171 | `Unlabeled` | one-way | DNA39, ROS | `kdam1` | internal-state conversion/modification | `DNA39(site~ok) + ROS() -> DNA39(site~sdsb)` | Changes internal modification/state marks on DNA39, ROS: DNA39.site ok→sdsb at `kdam1`. | +| 2172 | `Unlabeled` | one-way | DNA40, ROS | `kdam1` | internal-state conversion/modification | `DNA40(site~ok) + ROS() -> DNA40(site~sdsb)` | Changes internal modification/state marks on DNA40, ROS: DNA40.site ok→sdsb at `kdam1`. | +| 2173 | `Unlabeled` | one-way | DNA41, ROS | `kdam1` | internal-state conversion/modification | `DNA41(site~ok) + ROS() -> DNA41(site~sdsb)` | Changes internal modification/state marks on DNA41, ROS: DNA41.site ok→sdsb at `kdam1`. | +| 2174 | `Unlabeled` | one-way | DNA42, ROS | `kdam1` | internal-state conversion/modification | `DNA42(site~ok) + ROS() -> DNA42(site~sdsb)` | Changes internal modification/state marks on DNA42, ROS: DNA42.site ok→sdsb at `kdam1`. | +| 2175 | `Unlabeled` | one-way | DNA43, ROS | `kdam1` | internal-state conversion/modification | `DNA43(site~ok) + ROS() -> DNA43(site~sdsb)` | Changes internal modification/state marks on DNA43, ROS: DNA43.site ok→sdsb at `kdam1`. | +| 2176 | `Unlabeled` | one-way | DNA44, ROS | `kdam1` | internal-state conversion/modification | `DNA44(site~ok) + ROS() -> DNA44(site~sdsb)` | Changes internal modification/state marks on DNA44, ROS: DNA44.site ok→sdsb at `kdam1`. | +| 2177 | `Unlabeled` | one-way | DNA45, ROS | `kdam1` | internal-state conversion/modification | `DNA45(site~ok) + ROS() -> DNA45(site~sdsb)` | Changes internal modification/state marks on DNA45, ROS: DNA45.site ok→sdsb at `kdam1`. | +| 2178 | `Unlabeled` | one-way | DNA46, ROS | `kdam1` | internal-state conversion/modification | `DNA46(site~ok) + ROS() -> DNA46(site~sdsb)` | Changes internal modification/state marks on DNA46, ROS: DNA46.site ok→sdsb at `kdam1`. | +| 2179 | `Unlabeled` | one-way | DNA47, ROS | `kdam1` | internal-state conversion/modification | `DNA47(site~ok) + ROS() -> DNA47(site~sdsb)` | Changes internal modification/state marks on DNA47, ROS: DNA47.site ok→sdsb at `kdam1`. | +| 2180 | `Unlabeled` | one-way | DNA48, ROS | `kdam1` | internal-state conversion/modification | `DNA48(site~ok) + ROS() -> DNA48(site~sdsb)` | Changes internal modification/state marks on DNA48, ROS: DNA48.site ok→sdsb at `kdam1`. | +| 2181 | `Unlabeled` | one-way | DNA49, ROS | `kdam1` | internal-state conversion/modification | `DNA49(site~ok) + ROS() -> DNA49(site~sdsb)` | Changes internal modification/state marks on DNA49, ROS: DNA49.site ok→sdsb at `kdam1`. | +| 2182 | `Unlabeled` | one-way | DNA50, ROS | `kdam1` | internal-state conversion/modification | `DNA50(site~ok) + ROS() -> DNA50(site~sdsb)` | Changes internal modification/state marks on DNA50, ROS: DNA50.site ok→sdsb at `kdam1`. | +| 2183 | `Unlabeled` | one-way | DNA1, ROS | `kdam2` | internal-state conversion/modification | `DNA1(site~ok) + ROS() -> DNA1(site~cdsb)` | Changes internal modification/state marks on DNA1, ROS: DNA1.site ok→cdsb at `kdam2`. | +| 2184 | `Unlabeled` | one-way | DNA2, ROS | `kdam2` | internal-state conversion/modification | `DNA2(site~ok) + ROS() -> DNA2(site~cdsb)` | Changes internal modification/state marks on DNA2, ROS: DNA2.site ok→cdsb at `kdam2`. | +| 2185 | `Unlabeled` | one-way | DNA3, ROS | `kdam2` | internal-state conversion/modification | `DNA3(site~ok) + ROS() -> DNA3(site~cdsb)` | Changes internal modification/state marks on DNA3, ROS: DNA3.site ok→cdsb at `kdam2`. | +| 2186 | `Unlabeled` | one-way | DNA4, ROS | `kdam2` | internal-state conversion/modification | `DNA4(site~ok) + ROS() -> DNA4(site~cdsb)` | Changes internal modification/state marks on DNA4, ROS: DNA4.site ok→cdsb at `kdam2`. | +| 2187 | `Unlabeled` | one-way | DNA5, ROS | `kdam2` | internal-state conversion/modification | `DNA5(site~ok) + ROS() -> DNA5(site~cdsb)` | Changes internal modification/state marks on DNA5, ROS: DNA5.site ok→cdsb at `kdam2`. | +| 2188 | `Unlabeled` | one-way | DNA6, ROS | `kdam2` | internal-state conversion/modification | `DNA6(site~ok) + ROS() -> DNA6(site~cdsb)` | Changes internal modification/state marks on DNA6, ROS: DNA6.site ok→cdsb at `kdam2`. | +| 2189 | `Unlabeled` | one-way | DNA7, ROS | `kdam2` | internal-state conversion/modification | `DNA7(site~ok) + ROS() -> DNA7(site~cdsb)` | Changes internal modification/state marks on DNA7, ROS: DNA7.site ok→cdsb at `kdam2`. | +| 2190 | `Unlabeled` | one-way | DNA8, ROS | `kdam2` | internal-state conversion/modification | `DNA8(site~ok) + ROS() -> DNA8(site~cdsb)` | Changes internal modification/state marks on DNA8, ROS: DNA8.site ok→cdsb at `kdam2`. | +| 2191 | `Unlabeled` | one-way | DNA9, ROS | `kdam2` | internal-state conversion/modification | `DNA9(site~ok) + ROS() -> DNA9(site~cdsb)` | Changes internal modification/state marks on DNA9, ROS: DNA9.site ok→cdsb at `kdam2`. | +| 2192 | `Unlabeled` | one-way | DNA10, ROS | `kdam2` | internal-state conversion/modification | `DNA10(site~ok) + ROS() -> DNA10(site~cdsb)` | Changes internal modification/state marks on DNA10, ROS: DNA10.site ok→cdsb at `kdam2`. | +| 2193 | `Unlabeled` | one-way | DNA11, ROS | `kdam2` | internal-state conversion/modification | `DNA11(site~ok) + ROS() -> DNA11(site~cdsb)` | Changes internal modification/state marks on DNA11, ROS: DNA11.site ok→cdsb at `kdam2`. | +| 2194 | `Unlabeled` | one-way | DNA12, ROS | `kdam2` | internal-state conversion/modification | `DNA12(site~ok) + ROS() -> DNA12(site~cdsb)` | Changes internal modification/state marks on DNA12, ROS: DNA12.site ok→cdsb at `kdam2`. | +| 2195 | `Unlabeled` | one-way | DNA13, ROS | `kdam2` | internal-state conversion/modification | `DNA13(site~ok) + ROS() -> DNA13(site~cdsb)` | Changes internal modification/state marks on DNA13, ROS: DNA13.site ok→cdsb at `kdam2`. | +| 2196 | `Unlabeled` | one-way | DNA14, ROS | `kdam2` | internal-state conversion/modification | `DNA14(site~ok) + ROS() -> DNA14(site~cdsb)` | Changes internal modification/state marks on DNA14, ROS: DNA14.site ok→cdsb at `kdam2`. | +| 2197 | `Unlabeled` | one-way | DNA15, ROS | `kdam2` | internal-state conversion/modification | `DNA15(site~ok) + ROS() -> DNA15(site~cdsb)` | Changes internal modification/state marks on DNA15, ROS: DNA15.site ok→cdsb at `kdam2`. | +| 2198 | `Unlabeled` | one-way | DNA16, ROS | `kdam2` | internal-state conversion/modification | `DNA16(site~ok) + ROS() -> DNA16(site~cdsb)` | Changes internal modification/state marks on DNA16, ROS: DNA16.site ok→cdsb at `kdam2`. | +| 2199 | `Unlabeled` | one-way | DNA17, ROS | `kdam2` | internal-state conversion/modification | `DNA17(site~ok) + ROS() -> DNA17(site~cdsb)` | Changes internal modification/state marks on DNA17, ROS: DNA17.site ok→cdsb at `kdam2`. | +| 2200 | `Unlabeled` | one-way | DNA18, ROS | `kdam2` | internal-state conversion/modification | `DNA18(site~ok) + ROS() -> DNA18(site~cdsb)` | Changes internal modification/state marks on DNA18, ROS: DNA18.site ok→cdsb at `kdam2`. | +| 2201 | `Unlabeled` | one-way | DNA19, ROS | `kdam2` | internal-state conversion/modification | `DNA19(site~ok) + ROS() -> DNA19(site~cdsb)` | Changes internal modification/state marks on DNA19, ROS: DNA19.site ok→cdsb at `kdam2`. | +| 2202 | `Unlabeled` | one-way | DNA20, ROS | `kdam2` | internal-state conversion/modification | `DNA20(site~ok) + ROS() -> DNA20(site~cdsb)` | Changes internal modification/state marks on DNA20, ROS: DNA20.site ok→cdsb at `kdam2`. | +| 2203 | `Unlabeled` | one-way | DNA21, ROS | `kdam2` | internal-state conversion/modification | `DNA21(site~ok) + ROS() -> DNA21(site~cdsb)` | Changes internal modification/state marks on DNA21, ROS: DNA21.site ok→cdsb at `kdam2`. | +| 2204 | `Unlabeled` | one-way | DNA22, ROS | `kdam2` | internal-state conversion/modification | `DNA22(site~ok) + ROS() -> DNA22(site~cdsb)` | Changes internal modification/state marks on DNA22, ROS: DNA22.site ok→cdsb at `kdam2`. | +| 2205 | `Unlabeled` | one-way | DNA23, ROS | `kdam2` | internal-state conversion/modification | `DNA23(site~ok) + ROS() -> DNA23(site~cdsb)` | Changes internal modification/state marks on DNA23, ROS: DNA23.site ok→cdsb at `kdam2`. | +| 2206 | `Unlabeled` | one-way | DNA24, ROS | `kdam2` | internal-state conversion/modification | `DNA24(site~ok) + ROS() -> DNA24(site~cdsb)` | Changes internal modification/state marks on DNA24, ROS: DNA24.site ok→cdsb at `kdam2`. | +| 2207 | `Unlabeled` | one-way | DNA25, ROS | `kdam2` | internal-state conversion/modification | `DNA25(site~ok) + ROS() -> DNA25(site~cdsb)` | Changes internal modification/state marks on DNA25, ROS: DNA25.site ok→cdsb at `kdam2`. | +| 2208 | `Unlabeled` | one-way | DNA26, ROS | `kdam2` | internal-state conversion/modification | `DNA26(site~ok) + ROS() -> DNA26(site~cdsb)` | Changes internal modification/state marks on DNA26, ROS: DNA26.site ok→cdsb at `kdam2`. | +| 2209 | `Unlabeled` | one-way | DNA27, ROS | `kdam2` | internal-state conversion/modification | `DNA27(site~ok) + ROS() -> DNA27(site~cdsb)` | Changes internal modification/state marks on DNA27, ROS: DNA27.site ok→cdsb at `kdam2`. | +| 2210 | `Unlabeled` | one-way | DNA28, ROS | `kdam2` | internal-state conversion/modification | `DNA28(site~ok) + ROS() -> DNA28(site~cdsb)` | Changes internal modification/state marks on DNA28, ROS: DNA28.site ok→cdsb at `kdam2`. | +| 2211 | `Unlabeled` | one-way | DNA29, ROS | `kdam2` | internal-state conversion/modification | `DNA29(site~ok) + ROS() -> DNA29(site~cdsb)` | Changes internal modification/state marks on DNA29, ROS: DNA29.site ok→cdsb at `kdam2`. | +| 2212 | `Unlabeled` | one-way | DNA30, ROS | `kdam2` | internal-state conversion/modification | `DNA30(site~ok) + ROS() -> DNA30(site~cdsb)` | Changes internal modification/state marks on DNA30, ROS: DNA30.site ok→cdsb at `kdam2`. | +| 2213 | `Unlabeled` | one-way | DNA31, ROS | `kdam2` | internal-state conversion/modification | `DNA31(site~ok) + ROS() -> DNA31(site~cdsb)` | Changes internal modification/state marks on DNA31, ROS: DNA31.site ok→cdsb at `kdam2`. | +| 2214 | `Unlabeled` | one-way | DNA32, ROS | `kdam2` | internal-state conversion/modification | `DNA32(site~ok) + ROS() -> DNA32(site~cdsb)` | Changes internal modification/state marks on DNA32, ROS: DNA32.site ok→cdsb at `kdam2`. | +| 2215 | `Unlabeled` | one-way | DNA33, ROS | `kdam2` | internal-state conversion/modification | `DNA33(site~ok) + ROS() -> DNA33(site~cdsb)` | Changes internal modification/state marks on DNA33, ROS: DNA33.site ok→cdsb at `kdam2`. | +| 2216 | `Unlabeled` | one-way | DNA34, ROS | `kdam2` | internal-state conversion/modification | `DNA34(site~ok) + ROS() -> DNA34(site~cdsb)` | Changes internal modification/state marks on DNA34, ROS: DNA34.site ok→cdsb at `kdam2`. | +| 2217 | `Unlabeled` | one-way | DNA35, ROS | `kdam2` | internal-state conversion/modification | `DNA35(site~ok) + ROS() -> DNA35(site~cdsb)` | Changes internal modification/state marks on DNA35, ROS: DNA35.site ok→cdsb at `kdam2`. | +| 2218 | `Unlabeled` | one-way | DNA36, ROS | `kdam2` | internal-state conversion/modification | `DNA36(site~ok) + ROS() -> DNA36(site~cdsb)` | Changes internal modification/state marks on DNA36, ROS: DNA36.site ok→cdsb at `kdam2`. | +| 2219 | `Unlabeled` | one-way | DNA37, ROS | `kdam2` | internal-state conversion/modification | `DNA37(site~ok) + ROS() -> DNA37(site~cdsb)` | Changes internal modification/state marks on DNA37, ROS: DNA37.site ok→cdsb at `kdam2`. | +| 2220 | `Unlabeled` | one-way | DNA38, ROS | `kdam2` | internal-state conversion/modification | `DNA38(site~ok) + ROS() -> DNA38(site~cdsb)` | Changes internal modification/state marks on DNA38, ROS: DNA38.site ok→cdsb at `kdam2`. | +| 2221 | `Unlabeled` | one-way | DNA39, ROS | `kdam2` | internal-state conversion/modification | `DNA39(site~ok) + ROS() -> DNA39(site~cdsb)` | Changes internal modification/state marks on DNA39, ROS: DNA39.site ok→cdsb at `kdam2`. | +| 2222 | `Unlabeled` | one-way | DNA40, ROS | `kdam2` | internal-state conversion/modification | `DNA40(site~ok) + ROS() -> DNA40(site~cdsb)` | Changes internal modification/state marks on DNA40, ROS: DNA40.site ok→cdsb at `kdam2`. | +| 2223 | `Unlabeled` | one-way | DNA41, ROS | `kdam2` | internal-state conversion/modification | `DNA41(site~ok) + ROS() -> DNA41(site~cdsb)` | Changes internal modification/state marks on DNA41, ROS: DNA41.site ok→cdsb at `kdam2`. | +| 2224 | `Unlabeled` | one-way | DNA42, ROS | `kdam2` | internal-state conversion/modification | `DNA42(site~ok) + ROS() -> DNA42(site~cdsb)` | Changes internal modification/state marks on DNA42, ROS: DNA42.site ok→cdsb at `kdam2`. | +| 2225 | `Unlabeled` | one-way | DNA43, ROS | `kdam2` | internal-state conversion/modification | `DNA43(site~ok) + ROS() -> DNA43(site~cdsb)` | Changes internal modification/state marks on DNA43, ROS: DNA43.site ok→cdsb at `kdam2`. | +| 2226 | `Unlabeled` | one-way | DNA44, ROS | `kdam2` | internal-state conversion/modification | `DNA44(site~ok) + ROS() -> DNA44(site~cdsb)` | Changes internal modification/state marks on DNA44, ROS: DNA44.site ok→cdsb at `kdam2`. | +| 2227 | `Unlabeled` | one-way | DNA45, ROS | `kdam2` | internal-state conversion/modification | `DNA45(site~ok) + ROS() -> DNA45(site~cdsb)` | Changes internal modification/state marks on DNA45, ROS: DNA45.site ok→cdsb at `kdam2`. | +| 2228 | `Unlabeled` | one-way | DNA46, ROS | `kdam2` | internal-state conversion/modification | `DNA46(site~ok) + ROS() -> DNA46(site~cdsb)` | Changes internal modification/state marks on DNA46, ROS: DNA46.site ok→cdsb at `kdam2`. | +| 2229 | `Unlabeled` | one-way | DNA47, ROS | `kdam2` | internal-state conversion/modification | `DNA47(site~ok) + ROS() -> DNA47(site~cdsb)` | Changes internal modification/state marks on DNA47, ROS: DNA47.site ok→cdsb at `kdam2`. | +| 2230 | `Unlabeled` | one-way | DNA48, ROS | `kdam2` | internal-state conversion/modification | `DNA48(site~ok) + ROS() -> DNA48(site~cdsb)` | Changes internal modification/state marks on DNA48, ROS: DNA48.site ok→cdsb at `kdam2`. | +| 2231 | `Unlabeled` | one-way | DNA49, ROS | `kdam2` | internal-state conversion/modification | `DNA49(site~ok) + ROS() -> DNA49(site~cdsb)` | Changes internal modification/state marks on DNA49, ROS: DNA49.site ok→cdsb at `kdam2`. | +| 2232 | `Unlabeled` | one-way | DNA50, ROS | `kdam2` | internal-state conversion/modification | `DNA50(site~ok) + ROS() -> DNA50(site~cdsb)` | Changes internal modification/state marks on DNA50, ROS: DNA50.site ok→cdsb at `kdam2`. | +| 2233 | `Unlabeled` | one-way | Ku, ROS | `kox` | internal-state conversion/modification | `Ku(dna,cs,cys~red) + ROS() -> Ku(dna,cs,cys~ox) + ROS()` | Changes internal modification/state marks on Ku, ROS: Ku.cys red→ox at `kox`. | +| 2234 | `Unlabeled` | one-way | Ku | `kred` | internal-state conversion/modification | `Ku(dna,cs,cys~ox) -> Ku(dna,cs,cys~red)` | Changes internal modification/state marks on Ku: Ku.cys ox→red at `kred`. | +| 2235 | `Unlabeled` | one-way | DNA1, Ku | `kdku3` | state and binding-pattern rewrite | `DNA1(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA1(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA1, Ku by freeing DNA1.site, Ku.dna at `kdku3`. | +| 2236 | `Unlabeled` | one-way | DNA2, Ku | `kdku3` | state and binding-pattern rewrite | `DNA2(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA2(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA2, Ku by freeing DNA2.site, Ku.dna at `kdku3`. | +| 2237 | `Unlabeled` | one-way | DNA3, Ku | `kdku3` | state and binding-pattern rewrite | `DNA3(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA3(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA3, Ku by freeing DNA3.site, Ku.dna at `kdku3`. | +| 2238 | `Unlabeled` | one-way | DNA4, Ku | `kdku3` | state and binding-pattern rewrite | `DNA4(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA4(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA4, Ku by freeing DNA4.site, Ku.dna at `kdku3`. | +| 2239 | `Unlabeled` | one-way | DNA5, Ku | `kdku3` | state and binding-pattern rewrite | `DNA5(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA5(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA5, Ku by freeing DNA5.site, Ku.dna at `kdku3`. | +| 2240 | `Unlabeled` | one-way | DNA6, Ku | `kdku3` | state and binding-pattern rewrite | `DNA6(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA6(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA6, Ku by freeing DNA6.site, Ku.dna at `kdku3`. | +| 2241 | `Unlabeled` | one-way | DNA7, Ku | `kdku3` | state and binding-pattern rewrite | `DNA7(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA7(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA7, Ku by freeing DNA7.site, Ku.dna at `kdku3`. | +| 2242 | `Unlabeled` | one-way | DNA8, Ku | `kdku3` | state and binding-pattern rewrite | `DNA8(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA8(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA8, Ku by freeing DNA8.site, Ku.dna at `kdku3`. | +| 2243 | `Unlabeled` | one-way | DNA9, Ku | `kdku3` | state and binding-pattern rewrite | `DNA9(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA9(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA9, Ku by freeing DNA9.site, Ku.dna at `kdku3`. | +| 2244 | `Unlabeled` | one-way | DNA10, Ku | `kdku3` | state and binding-pattern rewrite | `DNA10(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA10(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA10, Ku by freeing DNA10.site, Ku.dna at `kdku3`. | +| 2245 | `Unlabeled` | one-way | DNA11, Ku | `kdku3` | state and binding-pattern rewrite | `DNA11(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA11(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA11, Ku by freeing DNA11.site, Ku.dna at `kdku3`. | +| 2246 | `Unlabeled` | one-way | DNA12, Ku | `kdku3` | state and binding-pattern rewrite | `DNA12(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA12(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA12, Ku by freeing DNA12.site, Ku.dna at `kdku3`. | +| 2247 | `Unlabeled` | one-way | DNA13, Ku | `kdku3` | state and binding-pattern rewrite | `DNA13(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA13(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA13, Ku by freeing DNA13.site, Ku.dna at `kdku3`. | +| 2248 | `Unlabeled` | one-way | DNA14, Ku | `kdku3` | state and binding-pattern rewrite | `DNA14(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA14(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA14, Ku by freeing DNA14.site, Ku.dna at `kdku3`. | +| 2249 | `Unlabeled` | one-way | DNA15, Ku | `kdku3` | state and binding-pattern rewrite | `DNA15(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA15(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA15, Ku by freeing DNA15.site, Ku.dna at `kdku3`. | +| 2250 | `Unlabeled` | one-way | DNA16, Ku | `kdku3` | state and binding-pattern rewrite | `DNA16(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA16(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA16, Ku by freeing DNA16.site, Ku.dna at `kdku3`. | + +### Rules 2251-2339 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 2251 | `Unlabeled` | one-way | DNA17, Ku | `kdku3` | state and binding-pattern rewrite | `DNA17(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA17(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA17, Ku by freeing DNA17.site, Ku.dna at `kdku3`. | +| 2252 | `Unlabeled` | one-way | DNA18, Ku | `kdku3` | state and binding-pattern rewrite | `DNA18(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA18(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA18, Ku by freeing DNA18.site, Ku.dna at `kdku3`. | +| 2253 | `Unlabeled` | one-way | DNA19, Ku | `kdku3` | state and binding-pattern rewrite | `DNA19(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA19(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA19, Ku by freeing DNA19.site, Ku.dna at `kdku3`. | +| 2254 | `Unlabeled` | one-way | DNA20, Ku | `kdku3` | state and binding-pattern rewrite | `DNA20(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA20(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA20, Ku by freeing DNA20.site, Ku.dna at `kdku3`. | +| 2255 | `Unlabeled` | one-way | DNA21, Ku | `kdku3` | state and binding-pattern rewrite | `DNA21(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA21(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA21, Ku by freeing DNA21.site, Ku.dna at `kdku3`. | +| 2256 | `Unlabeled` | one-way | DNA22, Ku | `kdku3` | state and binding-pattern rewrite | `DNA22(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA22(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA22, Ku by freeing DNA22.site, Ku.dna at `kdku3`. | +| 2257 | `Unlabeled` | one-way | DNA23, Ku | `kdku3` | state and binding-pattern rewrite | `DNA23(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA23(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA23, Ku by freeing DNA23.site, Ku.dna at `kdku3`. | +| 2258 | `Unlabeled` | one-way | DNA24, Ku | `kdku3` | state and binding-pattern rewrite | `DNA24(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA24(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA24, Ku by freeing DNA24.site, Ku.dna at `kdku3`. | +| 2259 | `Unlabeled` | one-way | DNA25, Ku | `kdku3` | state and binding-pattern rewrite | `DNA25(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA25(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA25, Ku by freeing DNA25.site, Ku.dna at `kdku3`. | +| 2260 | `Unlabeled` | one-way | DNA26, Ku | `kdku3` | state and binding-pattern rewrite | `DNA26(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA26(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA26, Ku by freeing DNA26.site, Ku.dna at `kdku3`. | +| 2261 | `Unlabeled` | one-way | DNA27, Ku | `kdku3` | state and binding-pattern rewrite | `DNA27(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA27(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA27, Ku by freeing DNA27.site, Ku.dna at `kdku3`. | +| 2262 | `Unlabeled` | one-way | DNA28, Ku | `kdku3` | state and binding-pattern rewrite | `DNA28(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA28(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA28, Ku by freeing DNA28.site, Ku.dna at `kdku3`. | +| 2263 | `Unlabeled` | one-way | DNA29, Ku | `kdku3` | state and binding-pattern rewrite | `DNA29(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA29(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA29, Ku by freeing DNA29.site, Ku.dna at `kdku3`. | +| 2264 | `Unlabeled` | one-way | DNA30, Ku | `kdku3` | state and binding-pattern rewrite | `DNA30(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA30(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA30, Ku by freeing DNA30.site, Ku.dna at `kdku3`. | +| 2265 | `Unlabeled` | one-way | DNA31, Ku | `kdku3` | state and binding-pattern rewrite | `DNA31(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA31(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA31, Ku by freeing DNA31.site, Ku.dna at `kdku3`. | +| 2266 | `Unlabeled` | one-way | DNA32, Ku | `kdku3` | state and binding-pattern rewrite | `DNA32(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA32(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA32, Ku by freeing DNA32.site, Ku.dna at `kdku3`. | +| 2267 | `Unlabeled` | one-way | DNA33, Ku | `kdku3` | state and binding-pattern rewrite | `DNA33(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA33(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA33, Ku by freeing DNA33.site, Ku.dna at `kdku3`. | +| 2268 | `Unlabeled` | one-way | DNA34, Ku | `kdku3` | state and binding-pattern rewrite | `DNA34(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA34(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA34, Ku by freeing DNA34.site, Ku.dna at `kdku3`. | +| 2269 | `Unlabeled` | one-way | DNA35, Ku | `kdku3` | state and binding-pattern rewrite | `DNA35(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA35(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA35, Ku by freeing DNA35.site, Ku.dna at `kdku3`. | +| 2270 | `Unlabeled` | one-way | DNA36, Ku | `kdku3` | state and binding-pattern rewrite | `DNA36(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA36(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA36, Ku by freeing DNA36.site, Ku.dna at `kdku3`. | +| 2271 | `Unlabeled` | one-way | DNA37, Ku | `kdku3` | state and binding-pattern rewrite | `DNA37(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA37(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA37, Ku by freeing DNA37.site, Ku.dna at `kdku3`. | +| 2272 | `Unlabeled` | one-way | DNA38, Ku | `kdku3` | state and binding-pattern rewrite | `DNA38(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA38(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA38, Ku by freeing DNA38.site, Ku.dna at `kdku3`. | +| 2273 | `Unlabeled` | one-way | DNA39, Ku | `kdku3` | state and binding-pattern rewrite | `DNA39(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA39(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA39, Ku by freeing DNA39.site, Ku.dna at `kdku3`. | +| 2274 | `Unlabeled` | one-way | DNA40, Ku | `kdku3` | state and binding-pattern rewrite | `DNA40(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA40(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA40, Ku by freeing DNA40.site, Ku.dna at `kdku3`. | +| 2275 | `Unlabeled` | one-way | DNA41, Ku | `kdku3` | state and binding-pattern rewrite | `DNA41(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA41(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA41, Ku by freeing DNA41.site, Ku.dna at `kdku3`. | +| 2276 | `Unlabeled` | one-way | DNA42, Ku | `kdku3` | state and binding-pattern rewrite | `DNA42(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA42(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA42, Ku by freeing DNA42.site, Ku.dna at `kdku3`. | +| 2277 | `Unlabeled` | one-way | DNA43, Ku | `kdku3` | state and binding-pattern rewrite | `DNA43(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA43(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA43, Ku by freeing DNA43.site, Ku.dna at `kdku3`. | +| 2278 | `Unlabeled` | one-way | DNA44, Ku | `kdku3` | state and binding-pattern rewrite | `DNA44(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA44(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA44, Ku by freeing DNA44.site, Ku.dna at `kdku3`. | +| 2279 | `Unlabeled` | one-way | DNA45, Ku | `kdku3` | state and binding-pattern rewrite | `DNA45(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA45(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA45, Ku by freeing DNA45.site, Ku.dna at `kdku3`. | +| 2280 | `Unlabeled` | one-way | DNA46, Ku | `kdku3` | state and binding-pattern rewrite | `DNA46(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA46(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA46, Ku by freeing DNA46.site, Ku.dna at `kdku3`. | +| 2281 | `Unlabeled` | one-way | DNA47, Ku | `kdku3` | state and binding-pattern rewrite | `DNA47(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA47(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA47, Ku by freeing DNA47.site, Ku.dna at `kdku3`. | +| 2282 | `Unlabeled` | one-way | DNA48, Ku | `kdku3` | state and binding-pattern rewrite | `DNA48(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA48(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA48, Ku by freeing DNA48.site, Ku.dna at `kdku3`. | +| 2283 | `Unlabeled` | one-way | DNA49, Ku | `kdku3` | state and binding-pattern rewrite | `DNA49(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA49(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA49, Ku by freeing DNA49.site, Ku.dna at `kdku3`. | +| 2284 | `Unlabeled` | one-way | DNA50, Ku | `kdku3` | state and binding-pattern rewrite | `DNA50(site!1~sdsb).Ku(dna!1,cs,cys~ox) -> DNA50(site~sdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA50, Ku by freeing DNA50.site, Ku.dna at `kdku3`. | +| 2285 | `Unlabeled` | one-way | DNA1, Ku | `kdku4` | state and binding-pattern rewrite | `DNA1(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA1(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA1, Ku by freeing DNA1.site, Ku.dna at `kdku4`. | +| 2286 | `Unlabeled` | one-way | DNA2, Ku | `kdku4` | state and binding-pattern rewrite | `DNA2(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA2(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA2, Ku by freeing DNA2.site, Ku.dna at `kdku4`. | +| 2287 | `Unlabeled` | one-way | DNA3, Ku | `kdku4` | state and binding-pattern rewrite | `DNA3(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA3(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA3, Ku by freeing DNA3.site, Ku.dna at `kdku4`. | +| 2288 | `Unlabeled` | one-way | DNA4, Ku | `kdku4` | state and binding-pattern rewrite | `DNA4(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA4(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA4, Ku by freeing DNA4.site, Ku.dna at `kdku4`. | +| 2289 | `Unlabeled` | one-way | DNA5, Ku | `kdku4` | state and binding-pattern rewrite | `DNA5(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA5(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA5, Ku by freeing DNA5.site, Ku.dna at `kdku4`. | +| 2290 | `Unlabeled` | one-way | DNA6, Ku | `kdku4` | state and binding-pattern rewrite | `DNA6(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA6(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA6, Ku by freeing DNA6.site, Ku.dna at `kdku4`. | +| 2291 | `Unlabeled` | one-way | DNA7, Ku | `kdku4` | state and binding-pattern rewrite | `DNA7(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA7(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA7, Ku by freeing DNA7.site, Ku.dna at `kdku4`. | +| 2292 | `Unlabeled` | one-way | DNA8, Ku | `kdku4` | state and binding-pattern rewrite | `DNA8(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA8(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA8, Ku by freeing DNA8.site, Ku.dna at `kdku4`. | +| 2293 | `Unlabeled` | one-way | DNA9, Ku | `kdku4` | state and binding-pattern rewrite | `DNA9(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA9(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA9, Ku by freeing DNA9.site, Ku.dna at `kdku4`. | +| 2294 | `Unlabeled` | one-way | DNA10, Ku | `kdku4` | state and binding-pattern rewrite | `DNA10(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA10(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA10, Ku by freeing DNA10.site, Ku.dna at `kdku4`. | +| 2295 | `Unlabeled` | one-way | DNA11, Ku | `kdku4` | state and binding-pattern rewrite | `DNA11(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA11(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA11, Ku by freeing DNA11.site, Ku.dna at `kdku4`. | +| 2296 | `Unlabeled` | one-way | DNA12, Ku | `kdku4` | state and binding-pattern rewrite | `DNA12(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA12(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA12, Ku by freeing DNA12.site, Ku.dna at `kdku4`. | +| 2297 | `Unlabeled` | one-way | DNA13, Ku | `kdku4` | state and binding-pattern rewrite | `DNA13(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA13(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA13, Ku by freeing DNA13.site, Ku.dna at `kdku4`. | +| 2298 | `Unlabeled` | one-way | DNA14, Ku | `kdku4` | state and binding-pattern rewrite | `DNA14(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA14(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA14, Ku by freeing DNA14.site, Ku.dna at `kdku4`. | +| 2299 | `Unlabeled` | one-way | DNA15, Ku | `kdku4` | state and binding-pattern rewrite | `DNA15(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA15(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA15, Ku by freeing DNA15.site, Ku.dna at `kdku4`. | +| 2300 | `Unlabeled` | one-way | DNA16, Ku | `kdku4` | state and binding-pattern rewrite | `DNA16(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA16(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA16, Ku by freeing DNA16.site, Ku.dna at `kdku4`. | +| 2301 | `Unlabeled` | one-way | DNA17, Ku | `kdku4` | state and binding-pattern rewrite | `DNA17(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA17(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA17, Ku by freeing DNA17.site, Ku.dna at `kdku4`. | +| 2302 | `Unlabeled` | one-way | DNA18, Ku | `kdku4` | state and binding-pattern rewrite | `DNA18(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA18(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA18, Ku by freeing DNA18.site, Ku.dna at `kdku4`. | +| 2303 | `Unlabeled` | one-way | DNA19, Ku | `kdku4` | state and binding-pattern rewrite | `DNA19(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA19(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA19, Ku by freeing DNA19.site, Ku.dna at `kdku4`. | +| 2304 | `Unlabeled` | one-way | DNA20, Ku | `kdku4` | state and binding-pattern rewrite | `DNA20(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA20(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA20, Ku by freeing DNA20.site, Ku.dna at `kdku4`. | +| 2305 | `Unlabeled` | one-way | DNA21, Ku | `kdku4` | state and binding-pattern rewrite | `DNA21(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA21(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA21, Ku by freeing DNA21.site, Ku.dna at `kdku4`. | +| 2306 | `Unlabeled` | one-way | DNA22, Ku | `kdku4` | state and binding-pattern rewrite | `DNA22(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA22(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA22, Ku by freeing DNA22.site, Ku.dna at `kdku4`. | +| 2307 | `Unlabeled` | one-way | DNA23, Ku | `kdku4` | state and binding-pattern rewrite | `DNA23(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA23(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA23, Ku by freeing DNA23.site, Ku.dna at `kdku4`. | +| 2308 | `Unlabeled` | one-way | DNA24, Ku | `kdku4` | state and binding-pattern rewrite | `DNA24(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA24(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA24, Ku by freeing DNA24.site, Ku.dna at `kdku4`. | +| 2309 | `Unlabeled` | one-way | DNA25, Ku | `kdku4` | state and binding-pattern rewrite | `DNA25(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA25(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA25, Ku by freeing DNA25.site, Ku.dna at `kdku4`. | +| 2310 | `Unlabeled` | one-way | DNA26, Ku | `kdku4` | state and binding-pattern rewrite | `DNA26(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA26(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA26, Ku by freeing DNA26.site, Ku.dna at `kdku4`. | +| 2311 | `Unlabeled` | one-way | DNA27, Ku | `kdku4` | state and binding-pattern rewrite | `DNA27(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA27(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA27, Ku by freeing DNA27.site, Ku.dna at `kdku4`. | +| 2312 | `Unlabeled` | one-way | DNA28, Ku | `kdku4` | state and binding-pattern rewrite | `DNA28(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA28(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA28, Ku by freeing DNA28.site, Ku.dna at `kdku4`. | +| 2313 | `Unlabeled` | one-way | DNA29, Ku | `kdku4` | state and binding-pattern rewrite | `DNA29(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA29(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA29, Ku by freeing DNA29.site, Ku.dna at `kdku4`. | +| 2314 | `Unlabeled` | one-way | DNA30, Ku | `kdku4` | state and binding-pattern rewrite | `DNA30(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA30(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA30, Ku by freeing DNA30.site, Ku.dna at `kdku4`. | +| 2315 | `Unlabeled` | one-way | DNA31, Ku | `kdku4` | state and binding-pattern rewrite | `DNA31(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA31(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA31, Ku by freeing DNA31.site, Ku.dna at `kdku4`. | +| 2316 | `Unlabeled` | one-way | DNA32, Ku | `kdku4` | state and binding-pattern rewrite | `DNA32(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA32(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA32, Ku by freeing DNA32.site, Ku.dna at `kdku4`. | +| 2317 | `Unlabeled` | one-way | DNA33, Ku | `kdku4` | state and binding-pattern rewrite | `DNA33(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA33(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA33, Ku by freeing DNA33.site, Ku.dna at `kdku4`. | +| 2318 | `Unlabeled` | one-way | DNA34, Ku | `kdku4` | state and binding-pattern rewrite | `DNA34(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA34(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA34, Ku by freeing DNA34.site, Ku.dna at `kdku4`. | +| 2319 | `Unlabeled` | one-way | DNA35, Ku | `kdku4` | state and binding-pattern rewrite | `DNA35(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA35(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA35, Ku by freeing DNA35.site, Ku.dna at `kdku4`. | +| 2320 | `Unlabeled` | one-way | DNA36, Ku | `kdku4` | state and binding-pattern rewrite | `DNA36(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA36(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA36, Ku by freeing DNA36.site, Ku.dna at `kdku4`. | +| 2321 | `Unlabeled` | one-way | DNA37, Ku | `kdku4` | state and binding-pattern rewrite | `DNA37(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA37(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA37, Ku by freeing DNA37.site, Ku.dna at `kdku4`. | +| 2322 | `Unlabeled` | one-way | DNA38, Ku | `kdku4` | state and binding-pattern rewrite | `DNA38(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA38(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA38, Ku by freeing DNA38.site, Ku.dna at `kdku4`. | +| 2323 | `Unlabeled` | one-way | DNA39, Ku | `kdku4` | state and binding-pattern rewrite | `DNA39(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA39(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA39, Ku by freeing DNA39.site, Ku.dna at `kdku4`. | +| 2324 | `Unlabeled` | one-way | DNA40, Ku | `kdku4` | state and binding-pattern rewrite | `DNA40(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA40(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA40, Ku by freeing DNA40.site, Ku.dna at `kdku4`. | +| 2325 | `Unlabeled` | one-way | DNA41, Ku | `kdku4` | state and binding-pattern rewrite | `DNA41(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA41(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA41, Ku by freeing DNA41.site, Ku.dna at `kdku4`. | +| 2326 | `Unlabeled` | one-way | DNA42, Ku | `kdku4` | state and binding-pattern rewrite | `DNA42(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA42(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA42, Ku by freeing DNA42.site, Ku.dna at `kdku4`. | +| 2327 | `Unlabeled` | one-way | DNA43, Ku | `kdku4` | state and binding-pattern rewrite | `DNA43(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA43(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA43, Ku by freeing DNA43.site, Ku.dna at `kdku4`. | +| 2328 | `Unlabeled` | one-way | DNA44, Ku | `kdku4` | state and binding-pattern rewrite | `DNA44(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA44(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA44, Ku by freeing DNA44.site, Ku.dna at `kdku4`. | +| 2329 | `Unlabeled` | one-way | DNA45, Ku | `kdku4` | state and binding-pattern rewrite | `DNA45(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA45(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA45, Ku by freeing DNA45.site, Ku.dna at `kdku4`. | +| 2330 | `Unlabeled` | one-way | DNA46, Ku | `kdku4` | state and binding-pattern rewrite | `DNA46(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA46(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA46, Ku by freeing DNA46.site, Ku.dna at `kdku4`. | +| 2331 | `Unlabeled` | one-way | DNA47, Ku | `kdku4` | state and binding-pattern rewrite | `DNA47(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA47(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA47, Ku by freeing DNA47.site, Ku.dna at `kdku4`. | +| 2332 | `Unlabeled` | one-way | DNA48, Ku | `kdku4` | state and binding-pattern rewrite | `DNA48(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA48(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA48, Ku by freeing DNA48.site, Ku.dna at `kdku4`. | +| 2333 | `Unlabeled` | one-way | DNA49, Ku | `kdku4` | state and binding-pattern rewrite | `DNA49(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA49(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA49, Ku by freeing DNA49.site, Ku.dna at `kdku4`. | +| 2334 | `Unlabeled` | one-way | DNA50, Ku | `kdku4` | state and binding-pattern rewrite | `DNA50(site!1~cdsb).Ku(dna!1,cs,cys~ox) -> DNA50(site~cdsb) + Ku(dna,cs,cys~ox)` | Releases a complex/contact among DNA50, Ku by freeing DNA50.site, Ku.dna at `kdku4`. | +| 2335 | `Unlabeled` | one-way | Sen | `kplus()` | internal-state conversion/modification | `Sen(int~?,State~normal) -> Sen(int~PLUS,State~normal)` | Rewrites the matched Sen pattern without an obvious state or bond-count change at `kplus()`; the table row preserves the exact implementation pattern. | +| 2336 | `Unlabeled` | one-way | Sen | `kminus()` | internal-state conversion/modification | `Sen(int~?,State~normal) -> Sen(int~MINUS,State~normal)` | Rewrites the matched Sen pattern without an obvious state or bond-count change at `kminus()`; the table row preserves the exact implementation pattern. | +| 2337 | `Unlabeled` | one-way | Sen | `ksen` | internal-state conversion/modification | `Sen(int~10,State~normal) -> Sen(int~10,State~sen)` | Changes internal modification/state marks on Sen: Sen.State normal→sen at `ksen`. | +| 2338 | `Unlabeled` | one-way | Ku, Sink, kKuDown | `kKustop()` | sink/degradation/removal | `Ku(dna,cs,cys~?) -> Sink() kKuDown() *` | Degrades or diverts Ku into the model sink at `kKustop()`, reducing that active species pool. | +| 2339 | `Unlabeled` | one-way | PARP, Sink, kParpDown | `kParpstop()` | sink/degradation/removal | `PARP(dna,liIII) -> Sink() kParpDown() *` | Degrades or diverts PARP into the model sink at `kParpstop()`, reducing that active species pool. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Time` | `Molecules` | `Time()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p53` | `Molecules` | `p53()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p53_Bound` | `Molecules` | `p53(Site1!1~u).MDM2(Site1!1~u)` | Reports bound or complexed species matching the pattern. | +| `p53_Phos` | `Molecules` | `p53(Site1~p)` | Reports phosphorylated or modified species matching the pattern. | +| `p53_Unphos` | `Molecules` | `p53(Site1~u)` | Reports phosphorylated or modified species matching the pattern. | +| `p21` | `Molecules` | `p21(step~3)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p38p` | `Molecules` | `p38(Site1~p)` | Reports phosphorylated or modified species matching the pattern. | +| `p38u` | `Molecules` | `p38(Site1~u)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ROS` | `Molecules` | `ROS()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p53_mRNA` | `Molecules` | `p53_mRNA()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `MDM2_Phos` | `Molecules` | `MDM2(Site1~p)` | Reports phosphorylated or modified species matching the pattern. | +| `MDM2_Unphos` | `Molecules` | `MDM2(Site1~u)` | Reports phosphorylated or modified species matching the pattern. | +| `MDM2_mRNA` | `Molecules` | `MDM2_mRNA()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `p21_mRNA` | `Molecules` | `p21_mRNA()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `GADD45` | `Molecules` | `GADD45()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM0` | `Molecules` | `ATM(state~0)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM1` | `Molecules` | `ATM(state~1)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM2` | `Molecules` | `ATM(state~2)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM3` | `Molecules` | `ATM(state~3)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM4` | `Molecules` | `ATM(state~4)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM5` | `Molecules` | `ATM(state~5)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM6` | `Molecules` | `ATM(state~6)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM7` | `Molecules` | `ATM(state~7)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM8` | `Molecules` | `ATM(state~8)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM9` | `Molecules` | `ATM(state~9)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM10` | `Molecules` | `ATM(state~10)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM11` | `Molecules` | `ATM(state~11)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM12` | `Molecules` | `ATM(state~12)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM13` | `Molecules` | `ATM(state~13)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM14` | `Molecules` | `ATM(state~14)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM15` | `Molecules` | `ATM(state~15)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM16` | `Molecules` | `ATM(state~16)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM17` | `Molecules` | `ATM(state~17)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM18` | `Molecules` | `ATM(state~18)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM19` | `Molecules` | `ATM(state~19)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM20` | `Molecules` | `ATM(state~20)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM21` | `Molecules` | `ATM(state~21)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM22` | `Molecules` | `ATM(state~22)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM23` | `Molecules` | `ATM(state~23)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM24` | `Molecules` | `ATM(state~24)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM25` | `Molecules` | `ATM(state~25)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM26` | `Molecules` | `ATM(state~26)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM27` | `Molecules` | `ATM(state~27)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM28` | `Molecules` | `ATM(state~28)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM29` | `Molecules` | `ATM(state~29)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM30` | `Molecules` | `ATM(state~30)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM31` | `Molecules` | `ATM(state~31)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM32` | `Molecules` | `ATM(state~32)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM33` | `Molecules` | `ATM(state~33)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM34` | `Molecules` | `ATM(state~34)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM35` | `Molecules` | `ATM(state~35)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM36` | `Molecules` | `ATM(state~36)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM37` | `Molecules` | `ATM(state~37)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM38` | `Molecules` | `ATM(state~38)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM39` | `Molecules` | `ATM(state~39)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM40` | `Molecules` | `ATM(state~40)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM41` | `Molecules` | `ATM(state~41)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM42` | `Molecules` | `ATM(state~42)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM43` | `Molecules` | `ATM(state~43)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM44` | `Molecules` | `ATM(state~44)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM45` | `Molecules` | `ATM(state~45)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM46` | `Molecules` | `ATM(state~46)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM47` | `Molecules` | `ATM(state~47)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM48` | `Molecules` | `ATM(state~48)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM49` | `Molecules` | `ATM(state~49)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `ATM50` | `Molecules` | `ATM(state~50)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Damage_Foci_1` | `Molecules` | `DNA1(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_1` | `Molecules` | `DNA1(h2ax!1~foc).ATM(state~1,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_2` | `Molecules` | `DNA2(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_2` | `Molecules` | `DNA2(h2ax!1~foc).ATM(state~2,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_3` | `Molecules` | `DNA3(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_3` | `Molecules` | `DNA3(h2ax!1~foc).ATM(state~3,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_4` | `Molecules` | `DNA4(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_4` | `Molecules` | `DNA4(h2ax!1~foc).ATM(state~4,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_5` | `Molecules` | `DNA5(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_5` | `Molecules` | `DNA5(h2ax!1~foc).ATM(state~5,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_6` | `Molecules` | `DNA6(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_6` | `Molecules` | `DNA6(h2ax!1~foc).ATM(state~6,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_7` | `Molecules` | `DNA7(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_7` | `Molecules` | `DNA7(h2ax!1~foc).ATM(state~7,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_8` | `Molecules` | `DNA8(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_8` | `Molecules` | `DNA8(h2ax!1~foc).ATM(state~8,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_9` | `Molecules` | `DNA9(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_9` | `Molecules` | `DNA9(h2ax!1~foc).ATM(state~9,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_10` | `Molecules` | `DNA10(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_10` | `Molecules` | `DNA10(h2ax!1~foc).ATM(state~10,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_11` | `Molecules` | `DNA11(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_11` | `Molecules` | `DNA11(h2ax!1~foc).ATM(state~11,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_12` | `Molecules` | `DNA12(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_12` | `Molecules` | `DNA12(h2ax!1~foc).ATM(state~12,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_13` | `Molecules` | `DNA13(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_13` | `Molecules` | `DNA13(h2ax!1~foc).ATM(state~13,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_14` | `Molecules` | `DNA14(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_14` | `Molecules` | `DNA14(h2ax!1~foc).ATM(state~14,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_15` | `Molecules` | `DNA15(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_15` | `Molecules` | `DNA15(h2ax!1~foc).ATM(state~15,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_16` | `Molecules` | `DNA16(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_16` | `Molecules` | `DNA16(h2ax!1~foc).ATM(state~16,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_17` | `Molecules` | `DNA17(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_17` | `Molecules` | `DNA17(h2ax!1~foc).ATM(state~17,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_18` | `Molecules` | `DNA18(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_18` | `Molecules` | `DNA18(h2ax!1~foc).ATM(state~18,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_19` | `Molecules` | `DNA19(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_19` | `Molecules` | `DNA19(h2ax!1~foc).ATM(state~19,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_20` | `Molecules` | `DNA20(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_20` | `Molecules` | `DNA20(h2ax!1~foc).ATM(state~20,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_21` | `Molecules` | `DNA21(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_21` | `Molecules` | `DNA21(h2ax!1~foc).ATM(state~21,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_22` | `Molecules` | `DNA22(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_22` | `Molecules` | `DNA22(h2ax!1~foc).ATM(state~22,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_23` | `Molecules` | `DNA23(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_23` | `Molecules` | `DNA23(h2ax!1~foc).ATM(state~23,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_24` | `Molecules` | `DNA24(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_24` | `Molecules` | `DNA24(h2ax!1~foc).ATM(state~24,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_25` | `Molecules` | `DNA25(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_25` | `Molecules` | `DNA25(h2ax!1~foc).ATM(state~25,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_26` | `Molecules` | `DNA26(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_26` | `Molecules` | `DNA26(h2ax!1~foc).ATM(state~26,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_27` | `Molecules` | `DNA27(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_27` | `Molecules` | `DNA27(h2ax!1~foc).ATM(state~27,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_28` | `Molecules` | `DNA28(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_28` | `Molecules` | `DNA28(h2ax!1~foc).ATM(state~28,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_29` | `Molecules` | `DNA29(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_29` | `Molecules` | `DNA29(h2ax!1~foc).ATM(state~29,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_30` | `Molecules` | `DNA30(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_30` | `Molecules` | `DNA30(h2ax!1~foc).ATM(state~30,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_31` | `Molecules` | `DNA31(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_31` | `Molecules` | `DNA31(h2ax!1~foc).ATM(state~31,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_32` | `Molecules` | `DNA32(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_32` | `Molecules` | `DNA32(h2ax!1~foc).ATM(state~32,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_33` | `Molecules` | `DNA33(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_33` | `Molecules` | `DNA33(h2ax!1~foc).ATM(state~33,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_34` | `Molecules` | `DNA34(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_34` | `Molecules` | `DNA34(h2ax!1~foc).ATM(state~34,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_35` | `Molecules` | `DNA35(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_35` | `Molecules` | `DNA35(h2ax!1~foc).ATM(state~35,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_36` | `Molecules` | `DNA36(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_36` | `Molecules` | `DNA36(h2ax!1~foc).ATM(state~36,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_37` | `Molecules` | `DNA37(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_37` | `Molecules` | `DNA37(h2ax!1~foc).ATM(state~37,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_38` | `Molecules` | `DNA38(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_38` | `Molecules` | `DNA38(h2ax!1~foc).ATM(state~38,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_39` | `Molecules` | `DNA39(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_39` | `Molecules` | `DNA39(h2ax!1~foc).ATM(state~39,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_40` | `Molecules` | `DNA40(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_40` | `Molecules` | `DNA40(h2ax!1~foc).ATM(state~40,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_41` | `Molecules` | `DNA41(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_41` | `Molecules` | `DNA41(h2ax!1~foc).ATM(state~41,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_42` | `Molecules` | `DNA42(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_42` | `Molecules` | `DNA42(h2ax!1~foc).ATM(state~42,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_43` | `Molecules` | `DNA43(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_43` | `Molecules` | `DNA43(h2ax!1~foc).ATM(state~43,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_44` | `Molecules` | `DNA44(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_44` | `Molecules` | `DNA44(h2ax!1~foc).ATM(state~44,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_45` | `Molecules` | `DNA45(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_45` | `Molecules` | `DNA45(h2ax!1~foc).ATM(state~45,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_46` | `Molecules` | `DNA46(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_46` | `Molecules` | `DNA46(h2ax!1~foc).ATM(state~46,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_47` | `Molecules` | `DNA47(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_47` | `Molecules` | `DNA47(h2ax!1~foc).ATM(state~47,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_48` | `Molecules` | `DNA48(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_48` | `Molecules` | `DNA48(h2ax!1~foc).ATM(state~48,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_49` | `Molecules` | `DNA49(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_49` | `Molecules` | `DNA49(h2ax!1~foc).ATM(state~49,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Damage_Foci_50` | `Molecules` | `DNA50(site!?~?,h2ax~foc)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Complete_Damage_Foci_50` | `Molecules` | `DNA50(h2ax!1~foc).ATM(state~50,h2ax!1)` | Reports bound or complexed species matching the pattern. | +| `Ku` | `Molecules` | `Ku(dna,cs,cys~?)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `PARP` | `Molecules` | `PARP(dna,liIII)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Ku_Red` | `Molecules` | `Ku(dna,cs,cys~red)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Ku_Ox` | `Molecules` | `Ku(dna,cs,cys~ox)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `DNA_PKcs` | `Molecules` | `DNAPKcs(ku,liIV,psite~u)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `LiIII` | `Molecules` | `LiIII(PARP)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `LiIV` | `Molecules` | `LiIV(cs)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Senescent_Counter` | `Molecules` | `Sen(int~?,State~sen)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Sen_Min` | `Molecules` | `Sen(int~1,State~?)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Sink` | `Molecules` | `Sink()` | Reports the BNGL pattern for downstream plotting or rate expressions. | + +## 8. Actions and simulation workflow + +1. `simulate_nf({suffix=>"nf_run1",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +2. `simulate_nf({suffix=>"nf_run2",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +3. `simulate_nf({suffix=>"nf_run3",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +4. `simulate_nf({suffix=>"nf_run4",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +5. `simulate_nf({suffix=>"nf_run5",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +6. `simulate_nf({suffix=>"nf_run6",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +7. `simulate_nf({suffix=>"nf_run7",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +8. `simulate_nf({suffix=>"nf_run8",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +9. `simulate_nf({suffix=>"nf_run9",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +10. `simulate_nf({suffix=>"nf_run10",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +11. `simulate_nf({suffix=>"nf_run11",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +12. `simulate_nf({suffix=>"nf_run12",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +13. `simulate_nf({suffix=>"nf_run13",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +14. `simulate_nf({suffix=>"nf_run14",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +15. `simulate_nf({suffix=>"nf_run15",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +16. `simulate_nf({suffix=>"nf_run16",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +17. `simulate_nf({suffix=>"nf_run17",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +18. `simulate_nf({suffix=>"nf_run18",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +19. `simulate_nf({suffix=>"nf_run19",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +20. `simulate_nf({suffix=>"nf_run20",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +21. `simulate_nf({suffix=>"nf_run21",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +22. `simulate_nf({suffix=>"nf_run22",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +23. `simulate_nf({suffix=>"nf_run23",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +24. `simulate_nf({suffix=>"nf_run24",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +25. `simulate_nf({suffix=>"nf_run25",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +26. `simulate_nf({suffix=>"nf_run26",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +27. `simulate_nf({suffix=>"nf_run27",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +28. `simulate_nf({suffix=>"nf_run28",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +29. `simulate_nf({suffix=>"nf_run29",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +30. `simulate_nf({suffix=>"nf_run30",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +31. `simulate_nf({suffix=>"nf_run31",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +32. `simulate_nf({suffix=>"nf_run32",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +33. `simulate_nf({suffix=>"nf_run33",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +34. `simulate_nf({suffix=>"nf_run34",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +35. `simulate_nf({suffix=>"nf_run35",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +36. `simulate_nf({suffix=>"nf_run36",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +37. `simulate_nf({suffix=>"nf_run37",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +38. `simulate_nf({suffix=>"nf_run38",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +39. `simulate_nf({suffix=>"nf_run39",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +40. `simulate_nf({suffix=>"nf_run40",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +41. `simulate_nf({suffix=>"nf_run41",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +42. `simulate_nf({suffix=>"nf_run42",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +43. `simulate_nf({suffix=>"nf_run43",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +44. `simulate_nf({suffix=>"nf_run44",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +45. `simulate_nf({suffix=>"nf_run45",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +46. `simulate_nf({suffix=>"nf_run46",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +47. `simulate_nf({suffix=>"nf_run47",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +48. `simulate_nf({suffix=>"nf_run48",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +49. `simulate_nf({suffix=>"nf_run49",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +50. `simulate_nf({suffix=>"nf_run50",t_end=>2400,n_steps=>2400,param=> "-v -gml 1000000000"})` — execution command affecting network generation, simulation, scanning, or output. + +## 9. Technical caveats and ambiguities + +- No compartments or anchors are declared; all spatial interpretation is abstract. + +- The 50 DNA molecule types are explicit copies, so many rule families repeat once per DNA locus rather than using a single generic DNA molecule. + +- The reaction-rule inventory is intentionally very large because the source file literally enumerates each locus-specific rule. + +- The complete rule inventory has 2339 rows; downstream review should compare this count with the `begin reaction rules` block after any source edits. + +- The summary keeps raw molecule, site, state, and parameter names because this is the coder-facing version and those identifiers are necessary for implementation review. diff --git a/data/summaries_detailed/Dreisigmeyer2008_lac_operon_ai_coder.md b/data/summaries_detailed/Dreisigmeyer2008_lac_operon_ai_coder.md new file mode 100644 index 00000000..6466b19a --- /dev/null +++ b/data/summaries_detailed/Dreisigmeyer2008_lac_operon_ai_coder.md @@ -0,0 +1,116 @@ +# Coder Model Explanation: Dreisigmeyer 2008 + +## 1. Model identity and scope + +- **Model id:** `Dreisigmeyer_2008` +- **Title:** Dreisigmeyer 2008 +- **BNGL path:** `Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl` +- **YAML path:** `Published/Dreisigmeyer2008/metadata.yaml` +- **Metadata description:** Lac operon +- **Scope:** This is a concentration-based ODE implementation of lac operon lactose induction. It has three explicit dynamic species: internal lactose `L`, allolactose `A`, and beta-galactosidase `Z`. The BNGL rules are intentionally site-free source/sink rules; the biological specificity lives in the algebraic functions that compute lactose import, lactose/allolactose metabolism, allolactose-driven beta-gal expression, and growth dilution. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 18 parameters covering units/conversion constants, external lactose, growth dilution, transport constants, metabolism constants, and Hill-expression constants. | +| Compartments | No | No BNGL compartment block; concentrations are implicit ODE state variables. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 3 site-free molecule types: `L`, `A`, `Z`. | +| Seed/species | Yes | 3 initial concentration-like species: `L=0`, `A=0`, `Z=c_basal`. | +| Observables | Yes | 3 concentration readouts: `Obs_Tot_L`, `Obs_Tot_A`, `Obs_Tot_Z`. | +| Functions | Yes | 5 functions; these are the actual mechanistic rate laws. | +| Reaction rules | Yes | 8 source/sink ODE rules. | +| Actions | Yes | Network generation, concentration saving, time-course ODE simulation, and lactose-scan ODE simulation. | + +## 3. Parameters, functions, and rate laws + +The model uses BNGL rules as ODE terms. There are no molecule sites, bonds, or internal states, so rate-law interpretation depends on the functions and observables. + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `NA` | `6.02214076e23` | Avogadro constant kept for possible population conversion; not used by the active concentration ODE rules. | +| `V_ref` | `1e-15` | Reference E. coli volume for possible concentration/population conversion. | +| `f` | `1.0` | Subvolume scale factor; present but not used in active rules. | +| `l_ext` | `1000.0` | Constant extracellular lactose concentration used by `transport_L()`. | +| `growth_rate` | `0.0231` | First-order dilution rate applied separately to `L`, `A`, and `Z`; also scales `syn_Z()`. | +| `alpha` | `600.0` | Import turnover factor in the permease-dependent lactose transport function. | +| `phi` | `0.5` | Export/import asymmetry factor in `transport_L()`. | +| `rho` | `0.1` | Michaelis asymmetry factor in `transport_L()`. | +| `K_i` | `500.0` | Permease Michaelis constant in the transport denominator. | +| `beta` | `2.85e4` | Lactose metabolism turnover constant in `metab_L()` and `prod_A()`. | +| `nu` | `0.468` | Branching fraction from lactose metabolism into allolactose production. | +| `K_m_l` | `2530.0` | Lactose Michaelis constant in the shared competitive-inhibition denominator. | +| `delta` | `2.30e4` | Allolactose metabolism turnover constant in `metab_A()`. | +| `K_m_a` | `1200.0` | Allolactose Michaelis constant in the shared competitive-inhibition denominator. | +| `eps` | `34.285` | Fully induced beta-gal level in `syn_Z()`. | +| `c_basal` | `0.0343` | Initial and basal beta-gal level. | +| `K_z` | `105.0` | Half-maximal allolactose level in the Hill induction term. | +| `n_Hill` | `2.0` | Hill coefficient for allolactose-dependent beta-gal induction. | + +**Functions and derived rates** + +| Function | Inputs used | Technical interpretation | +| --- | --- | --- | +| `transport_L()` | `Obs_Tot_Z`, `l_ext`, `Obs_Tot_L`, `alpha`, `phi`, `rho`, `K_i` | Net lactose import source term. It increases `L` and is proportional to beta-gal/permease proxy `Z`; the numerator subtracts an export-like term from external lactose. | +| `metab_L()` | `Obs_Tot_Z`, `Obs_Tot_A`, `Obs_Tot_L`, `beta`, `K_m_l`, `K_m_a` | Effective first-order lactose-removal coefficient. BNGL multiplies this function by the matched `L()` amount in rule 2. | +| `prod_A()` | `Obs_Tot_Z`, `Obs_Tot_L`, `Obs_Tot_A`, `nu`, `beta`, `K_m_l`, `K_m_a` | Allolactose source term produced from lactose metabolism; unlike `metab_L()`, it already includes `Obs_Tot_L` in the expression because the rule source is `0`. | +| `metab_A()` | `Obs_Tot_Z`, `Obs_Tot_A`, `Obs_Tot_L`, `delta`, `K_m_a`, `K_m_l` | Effective first-order allolactose-removal coefficient. BNGL multiplies it by matched `A()`. | +| `syn_Z()` | `Obs_Tot_A`, `growth_rate`, `c_basal`, `eps`, `K_z`, `n_Hill` | Beta-gal synthesis source term: basal expression plus Hill induction by allolactose, scaled by growth/dilution rate. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `L` | 0 | none | none | none | Whole-species ODE state for intracellular lactose. | No site-level interactions; all regulation is in rate functions. | +| `A` | 0 | none | none | none | Whole-species ODE state for allolactose. | Drives `syn_Z()` through `Obs_Tot_A`. | +| `Z` | 0 | none | none | none | Whole-species ODE state for beta-galactosidase/permease proxy. | Appears in transport and metabolism functions through `Obs_Tot_Z`. | + +## 5. Compartments, anchors, initial species, and setup + +- Compartments: none declared. +- Anchors: none declared. +- Initial setup: `L()` and `A()` start at zero, while `Z()` starts at `c_basal`, allowing lactose import and allolactose feedback to develop from an initially basal induced state. + +| Initial species/pattern | Initial amount | Setup role | +| --- | --- | --- | +| `L()` | `0` | No internal lactose initially. | +| `A()` | `0` | No allolactose initially. | +| `Z()` | `c_basal` | Basal beta-gal/permease proxy level. | + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** This model has no binding sites or internal states. Every rule is a source/sink ODE term for one of the three concentration variables. The site-level statement for each rule is therefore explicitly “none”; the meaningful implementation detail is whether the rule is a source term, a first-order sink term, or growth dilution. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | Product: `L`; no sites/components | `transport_L()` | Source `0 → L()`; no sites or states. | Adds internal lactose according to the permease-dependent transport function. The term depends on `Z`, external lactose, and current internal lactose. | +| 2 | `Unlabeled` | one-way | Reactant: `L`; no sites/components | `metab_L()` | Sink `L() → 0`; no sites or states. | Removes internal lactose by beta-gal-catalyzed metabolism. Because the rule matches `L()`, the function acts as an effective first-order coefficient for lactose. | +| 3 | `Unlabeled` | one-way | Reactant: `L`; no sites/components | `growth_rate` | Sink `L() → 0`; no sites or states. | Dilutes internal lactose by cell growth independently of enzymatic metabolism. | +| 4 | `Unlabeled` | one-way | Product: `A`; no sites/components | `prod_A()` | Source `0 → A()`; no sites or states. | Produces allolactose from lactose metabolism; the lactose dependence is inside `prod_A()` rather than in the reactant pattern. | +| 5 | `Unlabeled` | one-way | Reactant: `A`; no sites/components | `metab_A()` | Sink `A() → 0`; no sites or states. | Removes allolactose by beta-gal-catalyzed metabolism with competitive inhibition by lactose/allolactose encoded in the function. | +| 6 | `Unlabeled` | one-way | Reactant: `A`; no sites/components | `growth_rate` | Sink `A() → 0`; no sites or states. | Dilutes allolactose through growth. | +| 7 | `Unlabeled` | one-way | Product: `Z`; no sites/components | `syn_Z()` | Source `0 → Z()`; no sites or states. | Synthesizes beta-galactosidase/permease proxy from a basal-plus-Hill function of allolactose. | +| 8 | `Unlabeled` | one-way | Reactant: `Z`; no sites/components | `growth_rate` | Sink `Z() → 0`; no sites or states. | Dilutes beta-galactosidase by growth, balancing the allolactose-induced synthesis term. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Tot_L` | `Molecules` | `L()` | Current intracellular lactose concentration-like state; used by `transport_L()`, `metab_L()`, and `prod_A()`. | +| `Obs_Tot_A` | `Molecules` | `A()` | Current allolactose state; used in competitive metabolism and the Hill expression for `Z` synthesis. | +| `Obs_Tot_Z` | `Molecules` | `Z()` | Current beta-gal/permease proxy; controls lactose import and metabolism rates. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1})` creates the three-species/eight-reaction ODE network. +2. `saveConcentrations()` requests concentration-style output. +3. `resetConcentrations()` restores the basal initial condition before simulation. +4. `simulate({method=>"ode", suffix=>"ode", t_start=>0, t_end=>500, n_steps=>500})` integrates the lactose induction time course. +5. `parameter_scan({method=>"ode", parameter=>"l_ext", ...})` scans external lactose over a log range to produce an induction curve. + +## 9. Technical caveats and ambiguities + +- The source comments explicitly state that these are concentration-based ODE rate expressions; SSA/NFsim would require population-based conversion. +- The BNGL molecule declarations are site-free, so a coder should not look for binding-site or phosphorylation-site mechanisms here. +- `Z` is named beta-galactosidase in comments, but it also functions as the transport/metabolism activity proxy in the equations. diff --git a/data/summaries_detailed/Dreisigmeyer2008_lac_operon_coder.md b/data/summaries_detailed/Dreisigmeyer2008_lac_operon_coder.md new file mode 100644 index 00000000..6466b19a --- /dev/null +++ b/data/summaries_detailed/Dreisigmeyer2008_lac_operon_coder.md @@ -0,0 +1,116 @@ +# Coder Model Explanation: Dreisigmeyer 2008 + +## 1. Model identity and scope + +- **Model id:** `Dreisigmeyer_2008` +- **Title:** Dreisigmeyer 2008 +- **BNGL path:** `Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl` +- **YAML path:** `Published/Dreisigmeyer2008/metadata.yaml` +- **Metadata description:** Lac operon +- **Scope:** This is a concentration-based ODE implementation of lac operon lactose induction. It has three explicit dynamic species: internal lactose `L`, allolactose `A`, and beta-galactosidase `Z`. The BNGL rules are intentionally site-free source/sink rules; the biological specificity lives in the algebraic functions that compute lactose import, lactose/allolactose metabolism, allolactose-driven beta-gal expression, and growth dilution. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 18 parameters covering units/conversion constants, external lactose, growth dilution, transport constants, metabolism constants, and Hill-expression constants. | +| Compartments | No | No BNGL compartment block; concentrations are implicit ODE state variables. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 3 site-free molecule types: `L`, `A`, `Z`. | +| Seed/species | Yes | 3 initial concentration-like species: `L=0`, `A=0`, `Z=c_basal`. | +| Observables | Yes | 3 concentration readouts: `Obs_Tot_L`, `Obs_Tot_A`, `Obs_Tot_Z`. | +| Functions | Yes | 5 functions; these are the actual mechanistic rate laws. | +| Reaction rules | Yes | 8 source/sink ODE rules. | +| Actions | Yes | Network generation, concentration saving, time-course ODE simulation, and lactose-scan ODE simulation. | + +## 3. Parameters, functions, and rate laws + +The model uses BNGL rules as ODE terms. There are no molecule sites, bonds, or internal states, so rate-law interpretation depends on the functions and observables. + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `NA` | `6.02214076e23` | Avogadro constant kept for possible population conversion; not used by the active concentration ODE rules. | +| `V_ref` | `1e-15` | Reference E. coli volume for possible concentration/population conversion. | +| `f` | `1.0` | Subvolume scale factor; present but not used in active rules. | +| `l_ext` | `1000.0` | Constant extracellular lactose concentration used by `transport_L()`. | +| `growth_rate` | `0.0231` | First-order dilution rate applied separately to `L`, `A`, and `Z`; also scales `syn_Z()`. | +| `alpha` | `600.0` | Import turnover factor in the permease-dependent lactose transport function. | +| `phi` | `0.5` | Export/import asymmetry factor in `transport_L()`. | +| `rho` | `0.1` | Michaelis asymmetry factor in `transport_L()`. | +| `K_i` | `500.0` | Permease Michaelis constant in the transport denominator. | +| `beta` | `2.85e4` | Lactose metabolism turnover constant in `metab_L()` and `prod_A()`. | +| `nu` | `0.468` | Branching fraction from lactose metabolism into allolactose production. | +| `K_m_l` | `2530.0` | Lactose Michaelis constant in the shared competitive-inhibition denominator. | +| `delta` | `2.30e4` | Allolactose metabolism turnover constant in `metab_A()`. | +| `K_m_a` | `1200.0` | Allolactose Michaelis constant in the shared competitive-inhibition denominator. | +| `eps` | `34.285` | Fully induced beta-gal level in `syn_Z()`. | +| `c_basal` | `0.0343` | Initial and basal beta-gal level. | +| `K_z` | `105.0` | Half-maximal allolactose level in the Hill induction term. | +| `n_Hill` | `2.0` | Hill coefficient for allolactose-dependent beta-gal induction. | + +**Functions and derived rates** + +| Function | Inputs used | Technical interpretation | +| --- | --- | --- | +| `transport_L()` | `Obs_Tot_Z`, `l_ext`, `Obs_Tot_L`, `alpha`, `phi`, `rho`, `K_i` | Net lactose import source term. It increases `L` and is proportional to beta-gal/permease proxy `Z`; the numerator subtracts an export-like term from external lactose. | +| `metab_L()` | `Obs_Tot_Z`, `Obs_Tot_A`, `Obs_Tot_L`, `beta`, `K_m_l`, `K_m_a` | Effective first-order lactose-removal coefficient. BNGL multiplies this function by the matched `L()` amount in rule 2. | +| `prod_A()` | `Obs_Tot_Z`, `Obs_Tot_L`, `Obs_Tot_A`, `nu`, `beta`, `K_m_l`, `K_m_a` | Allolactose source term produced from lactose metabolism; unlike `metab_L()`, it already includes `Obs_Tot_L` in the expression because the rule source is `0`. | +| `metab_A()` | `Obs_Tot_Z`, `Obs_Tot_A`, `Obs_Tot_L`, `delta`, `K_m_a`, `K_m_l` | Effective first-order allolactose-removal coefficient. BNGL multiplies it by matched `A()`. | +| `syn_Z()` | `Obs_Tot_A`, `growth_rate`, `c_basal`, `eps`, `K_z`, `n_Hill` | Beta-gal synthesis source term: basal expression plus Hill induction by allolactose, scaled by growth/dilution rate. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `L` | 0 | none | none | none | Whole-species ODE state for intracellular lactose. | No site-level interactions; all regulation is in rate functions. | +| `A` | 0 | none | none | none | Whole-species ODE state for allolactose. | Drives `syn_Z()` through `Obs_Tot_A`. | +| `Z` | 0 | none | none | none | Whole-species ODE state for beta-galactosidase/permease proxy. | Appears in transport and metabolism functions through `Obs_Tot_Z`. | + +## 5. Compartments, anchors, initial species, and setup + +- Compartments: none declared. +- Anchors: none declared. +- Initial setup: `L()` and `A()` start at zero, while `Z()` starts at `c_basal`, allowing lactose import and allolactose feedback to develop from an initially basal induced state. + +| Initial species/pattern | Initial amount | Setup role | +| --- | --- | --- | +| `L()` | `0` | No internal lactose initially. | +| `A()` | `0` | No allolactose initially. | +| `Z()` | `c_basal` | Basal beta-gal/permease proxy level. | + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** This model has no binding sites or internal states. Every rule is a source/sink ODE term for one of the three concentration variables. The site-level statement for each rule is therefore explicitly “none”; the meaningful implementation detail is whether the rule is a source term, a first-order sink term, or growth dilution. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | Product: `L`; no sites/components | `transport_L()` | Source `0 → L()`; no sites or states. | Adds internal lactose according to the permease-dependent transport function. The term depends on `Z`, external lactose, and current internal lactose. | +| 2 | `Unlabeled` | one-way | Reactant: `L`; no sites/components | `metab_L()` | Sink `L() → 0`; no sites or states. | Removes internal lactose by beta-gal-catalyzed metabolism. Because the rule matches `L()`, the function acts as an effective first-order coefficient for lactose. | +| 3 | `Unlabeled` | one-way | Reactant: `L`; no sites/components | `growth_rate` | Sink `L() → 0`; no sites or states. | Dilutes internal lactose by cell growth independently of enzymatic metabolism. | +| 4 | `Unlabeled` | one-way | Product: `A`; no sites/components | `prod_A()` | Source `0 → A()`; no sites or states. | Produces allolactose from lactose metabolism; the lactose dependence is inside `prod_A()` rather than in the reactant pattern. | +| 5 | `Unlabeled` | one-way | Reactant: `A`; no sites/components | `metab_A()` | Sink `A() → 0`; no sites or states. | Removes allolactose by beta-gal-catalyzed metabolism with competitive inhibition by lactose/allolactose encoded in the function. | +| 6 | `Unlabeled` | one-way | Reactant: `A`; no sites/components | `growth_rate` | Sink `A() → 0`; no sites or states. | Dilutes allolactose through growth. | +| 7 | `Unlabeled` | one-way | Product: `Z`; no sites/components | `syn_Z()` | Source `0 → Z()`; no sites or states. | Synthesizes beta-galactosidase/permease proxy from a basal-plus-Hill function of allolactose. | +| 8 | `Unlabeled` | one-way | Reactant: `Z`; no sites/components | `growth_rate` | Sink `Z() → 0`; no sites or states. | Dilutes beta-galactosidase by growth, balancing the allolactose-induced synthesis term. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Tot_L` | `Molecules` | `L()` | Current intracellular lactose concentration-like state; used by `transport_L()`, `metab_L()`, and `prod_A()`. | +| `Obs_Tot_A` | `Molecules` | `A()` | Current allolactose state; used in competitive metabolism and the Hill expression for `Z` synthesis. | +| `Obs_Tot_Z` | `Molecules` | `Z()` | Current beta-gal/permease proxy; controls lactose import and metabolism rates. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1})` creates the three-species/eight-reaction ODE network. +2. `saveConcentrations()` requests concentration-style output. +3. `resetConcentrations()` restores the basal initial condition before simulation. +4. `simulate({method=>"ode", suffix=>"ode", t_start=>0, t_end=>500, n_steps=>500})` integrates the lactose induction time course. +5. `parameter_scan({method=>"ode", parameter=>"l_ext", ...})` scans external lactose over a log range to produce an induction curve. + +## 9. Technical caveats and ambiguities + +- The source comments explicitly state that these are concentration-based ODE rate expressions; SSA/NFsim would require population-based conversion. +- The BNGL molecule declarations are site-free, so a coder should not look for binding-site or phosphorylation-site mechanisms here. +- `Z` is named beta-galactosidase in comments, but it also functions as the transport/metabolism activity proxy in the equations. diff --git a/data/summaries_detailed/Gardner2000_ai_coder.md b/data/summaries_detailed/Gardner2000_ai_coder.md new file mode 100644 index 00000000..30fbbd24 --- /dev/null +++ b/data/summaries_detailed/Gardner2000_ai_coder.md @@ -0,0 +1,77 @@ +# Coder Model Explanation: Gardner 2000 + +## 1. Model identity and scope + +- **Model id:** `Gardner_2000` +- **Title:** Gardner 2000 +- **BNGL path:** `Published/Gardner2000/genetic_switch_gardner2000.bngl` +- **YAML path:** `Published/Gardner2000/metadata.yaml` +- **Scope:** This is a dimensionless ODE implementation of the Gardner-Cantor-Collins genetic toggle switch. It represents two mutually repressing gene products, not explicit promoter binding. The comments map the model to the two ODEs from Gardner et al. 2000. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 5 dimensionless parameters. | +| Compartments | No | No compartments. | +| Molecule types | Yes | 2 zero-site molecule types: `R1` and `R2`. | +| Seed species | Yes | 2 initial species, both initialized to 0. | +| Observables | Yes | 2 molecule-count readouts for total repressor levels. | +| Functions | Yes | 2 Hill-repressed synthesis functions. | +| Reaction rules | Yes | 4 rules: two synthesis and two degradation rules. | +| Actions | Yes | Network generation, sequential ODE simulations, parameter changes, and a parameter scan. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value | Role | +| --- | ---: | --- | +| `alpha_1` | 156.25 | Maximum dimensionless synthesis rate for `R1`. | +| `alpha_2` | 15.6 | Maximum dimensionless synthesis rate for `R2`; later temporarily changed to 600 by an action. | +| `beta` | 2.5 | Hill coefficient for repression of `R1` synthesis by `R2`. | +| `gamma` | 1.0 | Hill coefficient for repression of `R2` synthesis by `R1`. | +| `k_deg` | 1.0 | First-order degradation rate for both repressors, fixed by nondimensionalization. | + +`Obs_Tot_R1` and `Obs_Tot_R2` feed the functions. `syn_R1()` computes `alpha_1 / (1 + Obs_Tot_R2^beta)`, so high `R2` suppresses `R1` synthesis. `syn_R2()` computes `alpha_2 / (1 + Obs_Tot_R1^gamma)`, so high `R1` suppresses `R2` synthesis. The rule rates therefore encode mutual repression through functions rather than through explicit promoter-bound species. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `R1` | 0 | None | None | None | Represents the first normalized repressor concentration, called `u` in the comments. | +| `R2` | 0 | None | None | None | Represents the second normalized repressor concentration, called `v` in the comments. | + +## 5. Initial species, compartments, and setup + +Both repressors start at zero. There are no compartments, complexes, binding sites, or explicit gene states. The ODE behavior is controlled by synthesis from the null source, degradation to the null sink, and Hill functions that use current total repressor levels. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | Synthesis of `R1` | One-way source | No reactant; product `R1` has no sites | `syn_R1()` | Creates `R1` | Produces repressor 1 at a rate suppressed by the current `R2` level. | +| 2 | Synthesis of `R2` | One-way source | No reactant; product `R2` has no sites | `syn_R2()` | Creates `R2` | Produces repressor 2 at a rate suppressed by the current `R1` level. | +| 3 | Degradation of `R1` | One-way sink | `R1` with no sites | `k_deg` | Removes `R1` | Implements first-order loss of repressor 1 in dimensionless time. | +| 4 | Degradation of `R2` | One-way sink | `R2` with no sites | `k_deg` | Removes `R2` | Implements first-order loss of repressor 2 in dimensionless time. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Tot_R1` | `Molecules` | `R1()` | Dimensionless total level of the first repressor; also the feedback variable used in `syn_R2()`. | +| `Obs_Tot_R2` | `Molecules` | `R2()` | Dimensionless total level of the second repressor; also the feedback variable used in `syn_R1()`. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1})` creates a two-species, four-reaction ODE network. +2. First ODE simulation runs from 0 to 8 to relax from the origin toward the `R1`-dominant steady state. +3. `setParameter("alpha_2",600.0)` temporarily raises `R2` production, modeling induction that can push the system across the separatrix. +4. A continued ODE simulation runs from 8 to 12 under high `alpha_2`. +5. `setParameter("alpha_2",15.6)` restores the default `R2` synthesis strength. +6. A continued ODE simulation runs from 12 to 20, testing whether the model remains in the `R2`-dominant basin. +7. `parameter_scan` scans `alpha_2` from 1 to 500 at fixed `alpha_1` to explore the bistable-to-monostable boundary. + +## 9. Technical caveats and ambiguities + +- This model is intentionally nondimensional; molecule counts should not be interpreted as stochastic copy numbers. +- Mutual repression is encoded through algebraic functions of observables, not explicit promoter occupancy rules. +- The comments explicitly mark ODE as the appropriate method; stochastic simulation would not match the dimensionless formulation. diff --git a/data/summaries_detailed/Gardner2000_coder.md b/data/summaries_detailed/Gardner2000_coder.md new file mode 100644 index 00000000..30fbbd24 --- /dev/null +++ b/data/summaries_detailed/Gardner2000_coder.md @@ -0,0 +1,77 @@ +# Coder Model Explanation: Gardner 2000 + +## 1. Model identity and scope + +- **Model id:** `Gardner_2000` +- **Title:** Gardner 2000 +- **BNGL path:** `Published/Gardner2000/genetic_switch_gardner2000.bngl` +- **YAML path:** `Published/Gardner2000/metadata.yaml` +- **Scope:** This is a dimensionless ODE implementation of the Gardner-Cantor-Collins genetic toggle switch. It represents two mutually repressing gene products, not explicit promoter binding. The comments map the model to the two ODEs from Gardner et al. 2000. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 5 dimensionless parameters. | +| Compartments | No | No compartments. | +| Molecule types | Yes | 2 zero-site molecule types: `R1` and `R2`. | +| Seed species | Yes | 2 initial species, both initialized to 0. | +| Observables | Yes | 2 molecule-count readouts for total repressor levels. | +| Functions | Yes | 2 Hill-repressed synthesis functions. | +| Reaction rules | Yes | 4 rules: two synthesis and two degradation rules. | +| Actions | Yes | Network generation, sequential ODE simulations, parameter changes, and a parameter scan. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value | Role | +| --- | ---: | --- | +| `alpha_1` | 156.25 | Maximum dimensionless synthesis rate for `R1`. | +| `alpha_2` | 15.6 | Maximum dimensionless synthesis rate for `R2`; later temporarily changed to 600 by an action. | +| `beta` | 2.5 | Hill coefficient for repression of `R1` synthesis by `R2`. | +| `gamma` | 1.0 | Hill coefficient for repression of `R2` synthesis by `R1`. | +| `k_deg` | 1.0 | First-order degradation rate for both repressors, fixed by nondimensionalization. | + +`Obs_Tot_R1` and `Obs_Tot_R2` feed the functions. `syn_R1()` computes `alpha_1 / (1 + Obs_Tot_R2^beta)`, so high `R2` suppresses `R1` synthesis. `syn_R2()` computes `alpha_2 / (1 + Obs_Tot_R1^gamma)`, so high `R1` suppresses `R2` synthesis. The rule rates therefore encode mutual repression through functions rather than through explicit promoter-bound species. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `R1` | 0 | None | None | None | Represents the first normalized repressor concentration, called `u` in the comments. | +| `R2` | 0 | None | None | None | Represents the second normalized repressor concentration, called `v` in the comments. | + +## 5. Initial species, compartments, and setup + +Both repressors start at zero. There are no compartments, complexes, binding sites, or explicit gene states. The ODE behavior is controlled by synthesis from the null source, degradation to the null sink, and Hill functions that use current total repressor levels. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | Synthesis of `R1` | One-way source | No reactant; product `R1` has no sites | `syn_R1()` | Creates `R1` | Produces repressor 1 at a rate suppressed by the current `R2` level. | +| 2 | Synthesis of `R2` | One-way source | No reactant; product `R2` has no sites | `syn_R2()` | Creates `R2` | Produces repressor 2 at a rate suppressed by the current `R1` level. | +| 3 | Degradation of `R1` | One-way sink | `R1` with no sites | `k_deg` | Removes `R1` | Implements first-order loss of repressor 1 in dimensionless time. | +| 4 | Degradation of `R2` | One-way sink | `R2` with no sites | `k_deg` | Removes `R2` | Implements first-order loss of repressor 2 in dimensionless time. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Tot_R1` | `Molecules` | `R1()` | Dimensionless total level of the first repressor; also the feedback variable used in `syn_R2()`. | +| `Obs_Tot_R2` | `Molecules` | `R2()` | Dimensionless total level of the second repressor; also the feedback variable used in `syn_R1()`. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1})` creates a two-species, four-reaction ODE network. +2. First ODE simulation runs from 0 to 8 to relax from the origin toward the `R1`-dominant steady state. +3. `setParameter("alpha_2",600.0)` temporarily raises `R2` production, modeling induction that can push the system across the separatrix. +4. A continued ODE simulation runs from 8 to 12 under high `alpha_2`. +5. `setParameter("alpha_2",15.6)` restores the default `R2` synthesis strength. +6. A continued ODE simulation runs from 12 to 20, testing whether the model remains in the `R2`-dominant basin. +7. `parameter_scan` scans `alpha_2` from 1 to 500 at fixed `alpha_1` to explore the bistable-to-monostable boundary. + +## 9. Technical caveats and ambiguities + +- This model is intentionally nondimensional; molecule counts should not be interpreted as stochastic copy numbers. +- Mutual repression is encoded through algebraic functions of observables, not explicit promoter occupancy rules. +- The comments explicitly mark ODE as the appropriate method; stochastic simulation would not match the dimensionless formulation. diff --git a/data/summaries_detailed/Hlavacek2001_kinetic_proofreading_ai_coder.md b/data/summaries_detailed/Hlavacek2001_kinetic_proofreading_ai_coder.md new file mode 100644 index 00000000..d1648da0 --- /dev/null +++ b/data/summaries_detailed/Hlavacek2001_kinetic_proofreading_ai_coder.md @@ -0,0 +1,114 @@ +# Coder Model Explanation: Hlavacek 2001 + +## 1. Model identity and scope + +- **Model id:** `Hlavacek_2001` +- **Title:** Hlavacek 2001 +- **BNGL path:** `Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl` +- **YAML path:** `Published/Hlavacek2001/metadata.yaml` +- **Metadata description:** Kinetic proofreading +- **Scope:** This is a compact kinetic-proofreading model for receptor signaling. A bivalent ligand `L` uses two equivalent `r` sites to bind receptor `R(l)`, forming singly bound ligand and then receptor dimers. The ligand carries a `mod` state counter (`0` through `5`) that advances only while both ligand sites are receptor-bound. Any ligand-receptor bond dissociation resets `L.mod` to `0`. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 8 parameters for copy-number conversion, ligand/receptor totals, binding, unbinding, and proofreading modification. | +| Compartments | No | No explicit compartments. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 2 molecule types: bivalent ligand `L` and receptor `R`. | +| Seed/species | Yes | 2 initial species: free ligand and free receptor. | +| Observables | Yes | 10 species observables for free pools, singly bound ligand, total dimers, and dimer modification states. | +| Functions | Yes | 4 derived readouts: `alpha`, dimer fraction, terminal fraction, receptor-terminal fraction. | +| Reaction rules | Yes | 13 concrete rules. | +| Actions | Yes | Network generation, concentration saving, ODE time course, and `koff` scan. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `NA` | `6.02214076e23` | Avogadro constant used in concentration-to-population conversion comments. | +| `V_ref` | `1e-9` | Extracellular volume per cell. | +| `NR` | `300000` | Total receptor copy number. | +| `NL` | `602` | Total ligand copy number at the modeled concentration. | +| `kon1` | `1.661e-8` | First ligand-site receptor-capture rate; BNGL symmetry handles two equivalent `L.r` sites. | +| `kon2` | `3.333e-6` | Crosslinking rate for the second receptor binding event. | +| `koff` | `0.1` | Per-bond ligand-receptor dissociation rate. | +| `kp` | `0.4` | Unidirectional modification-step rate for fully receptor-crosslinked ligand. | + +**Functions and derived readouts** + +| Function | Technical interpretation | +| --- | --- | +| `alpha() = kp / (kp + 2 * koff)` | Probability-like proofreading factor: modification competes against two possible dimer bond breaks. | +| `frac_dimers() = 2 * Obs_Tot_Dimers / NR` | Fraction of receptors present in dimers. | +| `frac_term() = Obs_D5 / (Obs_Tot_Dimers + 1e-30)` | Fraction of dimers that reached terminal modification state `mod~5`; small denominator offset prevents division by zero. | +| `frac_R_term() = 2 * Obs_D5 / NR` | Fraction of all receptors in terminal dimers. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `L` | 3 | `r`, `r`, `mod` | `mod~0~1~2~3~4~5` | none | The two repeated `r` components are equivalent receptor-binding sites; `mod` is the proofreading counter. | `L.mod` is the implementation state for dimer progress, even though the biological interpretation is receptor modification. | +| `R` | 1 | `l` | none | none | `R.l` binds ligand site `L.r`. | Receptor has no explicit modification state; reset behavior is represented by `L.mod`. | + +## 5. Compartments, anchors, initial species, and setup + +- Compartments: none declared. +- Anchors: none declared. +- Initial setup: all ligand starts unbound with `mod~0`; all receptor starts free. + +| Initial species/pattern | Initial amount | Setup role | +| --- | --- | --- | +| `L(r,r,mod~0)` | `NL` | Free bivalent ligand with both `r` sites open and proofreading counter at zero. | +| `R(l)` | `NR` | Free monovalent receptor with ligand-binding site `l` open. | + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 1-2 build ligand-receptor complexes through `L.r`/`R.l` bonds. Rules 3-8 are dissociation/reset rules: breaking `L.r!1`/`R.l!1` releases receptor and sets `L.mod` to `0`. Rules 9-13 advance `L.mod` from `0` to `5`, but only for ligands with both repeated `r` sites bound (`L(r!+,r!+)`). + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | `L.r` + `R.l` | `kon1` | Forms one `L.r!1`–`R.l!1` bond while `L.mod` remains `0`; the second `L.r` stays free. | Ligand capture: free bivalent ligand binds one receptor. Because `L` has two equivalent `r` sites, BioNetGen applies the symmetry factor for either site being used. | +| 2 | `Unlabeled` | one-way | free `L.r` on singly bound ligand + `R.l` | `kon2` | Forms an additional `L.r!1`–`R.l!1` bond on a ligand already carrying one receptor; `L.mod` remains `0`. | Receptor crosslinking: singly bound ligand recruits a second receptor to form a dimer scaffold capable of proofreading modification. | +| 3 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~0` | `koff` | Releases the ligand-receptor bond; `L.mod` stays `0`. | Dissociation of an unmodified singly/doubly bound ligand-receptor contact. No reset is visible because the counter is already zero. | +| 4 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~1` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 1→0`. | A dimer that completed one proofreading step loses a receptor bond and immediately returns to basal ligand state. | +| 5 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~2` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 2→0`. | Encodes proofreading loss after two completed modification steps. | +| 6 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~3` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 3→0`. | Encodes proofreading loss after three completed modification steps. | +| 7 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~4` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 4→0`. | Encodes proofreading loss after four completed modification steps. | +| 8 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~5` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 5→0`. | Even terminally modified dimers lose the proofreading state when a ligand-receptor bond breaks. | +| 9 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~0` | `kp` | Changes `L.mod 0→1`; both `L.r` sites must be bound. | First proofreading modification step on a receptor dimer. | +| 10 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~1` | `kp` | Changes `L.mod 1→2`; both `L.r` sites remain bound. | Second proofreading modification step. | +| 11 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~2` | `kp` | Changes `L.mod 2→3`; both `L.r` sites remain bound. | Third proofreading modification step. | +| 12 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~3` | `kp` | Changes `L.mod 3→4`; both `L.r` sites remain bound. | Fourth proofreading modification step. | +| 13 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~4` | `kp` | Changes `L.mod 4→5`; both `L.r` sites remain bound. | Terminal proofreading step producing the `Obs_D5` signaling readout. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Free_L` | `Species` | `L(r,r,mod~0)` | Free ligand with both `r` sites unbound and counter zero. | +| `Obs_Free_R` | `Species` | `R(l)` | Free receptor with open `l` site. | +| `Obs_Singly_Bound` | `Species` | `L(r!+,r,mod~0)` | Ligand with one receptor bound and one `r` site free. | +| `Obs_Tot_Dimers` | `Species` | `L(r!+,r!+)` | Ligand with both `r` sites bound, regardless of modification state. | +| `Obs_D0` | `Species` | `L(r!+,r!+,mod~0)` | Dimer before any proofreading modification. | +| `Obs_D1` | `Species` | `L(r!+,r!+,mod~1)` | Dimer after one modification. | +| `Obs_D2` | `Species` | `L(r!+,r!+,mod~2)` | Dimer after two modifications. | +| `Obs_D3` | `Species` | `L(r!+,r!+,mod~3)` | Dimer after three modifications. | +| `Obs_D4` | `Species` | `L(r!+,r!+,mod~4)` | Dimer after four modifications. | +| `Obs_D5` | `Species` | `L(r!+,r!+,mod~5)` | Terminally modified dimer. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1})` builds the small reaction network. +2. `saveConcentrations()` requests output. +3. `resetConcentrations()` restores all-free ligand/receptor initial conditions. +4. `simulate({method=>"ode", suffix=>"ode", t_start=>0, t_end=>600, n_steps=>300})` runs the proofreading time course. +5. A second `resetConcentrations()` prepares the `koff` scan. +6. `parameter_scan({method=>"ode", parameter=>"koff", ...})` scans dissociation rate to show proofreading sensitivity. + +## 9. Technical caveats and ambiguities + +- The model stores modification progress on ligand `L.mod`, not on receptor `R`; this is an implementation choice for dimer state. +- The repeated `L.r` components are equivalent, so symmetry factors are part of the intended kinetics. +- There are no compartments; receptor surface context is encoded by rates and molecule naming rather than explicit membrane localization. diff --git a/data/summaries_detailed/Hlavacek2001_kinetic_proofreading_coder.md b/data/summaries_detailed/Hlavacek2001_kinetic_proofreading_coder.md new file mode 100644 index 00000000..d1648da0 --- /dev/null +++ b/data/summaries_detailed/Hlavacek2001_kinetic_proofreading_coder.md @@ -0,0 +1,114 @@ +# Coder Model Explanation: Hlavacek 2001 + +## 1. Model identity and scope + +- **Model id:** `Hlavacek_2001` +- **Title:** Hlavacek 2001 +- **BNGL path:** `Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl` +- **YAML path:** `Published/Hlavacek2001/metadata.yaml` +- **Metadata description:** Kinetic proofreading +- **Scope:** This is a compact kinetic-proofreading model for receptor signaling. A bivalent ligand `L` uses two equivalent `r` sites to bind receptor `R(l)`, forming singly bound ligand and then receptor dimers. The ligand carries a `mod` state counter (`0` through `5`) that advances only while both ligand sites are receptor-bound. Any ligand-receptor bond dissociation resets `L.mod` to `0`. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 8 parameters for copy-number conversion, ligand/receptor totals, binding, unbinding, and proofreading modification. | +| Compartments | No | No explicit compartments. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 2 molecule types: bivalent ligand `L` and receptor `R`. | +| Seed/species | Yes | 2 initial species: free ligand and free receptor. | +| Observables | Yes | 10 species observables for free pools, singly bound ligand, total dimers, and dimer modification states. | +| Functions | Yes | 4 derived readouts: `alpha`, dimer fraction, terminal fraction, receptor-terminal fraction. | +| Reaction rules | Yes | 13 concrete rules. | +| Actions | Yes | Network generation, concentration saving, ODE time course, and `koff` scan. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `NA` | `6.02214076e23` | Avogadro constant used in concentration-to-population conversion comments. | +| `V_ref` | `1e-9` | Extracellular volume per cell. | +| `NR` | `300000` | Total receptor copy number. | +| `NL` | `602` | Total ligand copy number at the modeled concentration. | +| `kon1` | `1.661e-8` | First ligand-site receptor-capture rate; BNGL symmetry handles two equivalent `L.r` sites. | +| `kon2` | `3.333e-6` | Crosslinking rate for the second receptor binding event. | +| `koff` | `0.1` | Per-bond ligand-receptor dissociation rate. | +| `kp` | `0.4` | Unidirectional modification-step rate for fully receptor-crosslinked ligand. | + +**Functions and derived readouts** + +| Function | Technical interpretation | +| --- | --- | +| `alpha() = kp / (kp + 2 * koff)` | Probability-like proofreading factor: modification competes against two possible dimer bond breaks. | +| `frac_dimers() = 2 * Obs_Tot_Dimers / NR` | Fraction of receptors present in dimers. | +| `frac_term() = Obs_D5 / (Obs_Tot_Dimers + 1e-30)` | Fraction of dimers that reached terminal modification state `mod~5`; small denominator offset prevents division by zero. | +| `frac_R_term() = 2 * Obs_D5 / NR` | Fraction of all receptors in terminal dimers. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `L` | 3 | `r`, `r`, `mod` | `mod~0~1~2~3~4~5` | none | The two repeated `r` components are equivalent receptor-binding sites; `mod` is the proofreading counter. | `L.mod` is the implementation state for dimer progress, even though the biological interpretation is receptor modification. | +| `R` | 1 | `l` | none | none | `R.l` binds ligand site `L.r`. | Receptor has no explicit modification state; reset behavior is represented by `L.mod`. | + +## 5. Compartments, anchors, initial species, and setup + +- Compartments: none declared. +- Anchors: none declared. +- Initial setup: all ligand starts unbound with `mod~0`; all receptor starts free. + +| Initial species/pattern | Initial amount | Setup role | +| --- | --- | --- | +| `L(r,r,mod~0)` | `NL` | Free bivalent ligand with both `r` sites open and proofreading counter at zero. | +| `R(l)` | `NR` | Free monovalent receptor with ligand-binding site `l` open. | + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 1-2 build ligand-receptor complexes through `L.r`/`R.l` bonds. Rules 3-8 are dissociation/reset rules: breaking `L.r!1`/`R.l!1` releases receptor and sets `L.mod` to `0`. Rules 9-13 advance `L.mod` from `0` to `5`, but only for ligands with both repeated `r` sites bound (`L(r!+,r!+)`). + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | `L.r` + `R.l` | `kon1` | Forms one `L.r!1`–`R.l!1` bond while `L.mod` remains `0`; the second `L.r` stays free. | Ligand capture: free bivalent ligand binds one receptor. Because `L` has two equivalent `r` sites, BioNetGen applies the symmetry factor for either site being used. | +| 2 | `Unlabeled` | one-way | free `L.r` on singly bound ligand + `R.l` | `kon2` | Forms an additional `L.r!1`–`R.l!1` bond on a ligand already carrying one receptor; `L.mod` remains `0`. | Receptor crosslinking: singly bound ligand recruits a second receptor to form a dimer scaffold capable of proofreading modification. | +| 3 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~0` | `koff` | Releases the ligand-receptor bond; `L.mod` stays `0`. | Dissociation of an unmodified singly/doubly bound ligand-receptor contact. No reset is visible because the counter is already zero. | +| 4 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~1` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 1→0`. | A dimer that completed one proofreading step loses a receptor bond and immediately returns to basal ligand state. | +| 5 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~2` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 2→0`. | Encodes proofreading loss after two completed modification steps. | +| 6 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~3` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 3→0`. | Encodes proofreading loss after three completed modification steps. | +| 7 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~4` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 4→0`. | Encodes proofreading loss after four completed modification steps. | +| 8 | `Unlabeled` | one-way | `L.r!1`, `R.l!1`, `L.mod~5` | `koff` | Releases `L.r!1`–`R.l!1` and resets `L.mod 5→0`. | Even terminally modified dimers lose the proofreading state when a ligand-receptor bond breaks. | +| 9 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~0` | `kp` | Changes `L.mod 0→1`; both `L.r` sites must be bound. | First proofreading modification step on a receptor dimer. | +| 10 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~1` | `kp` | Changes `L.mod 1→2`; both `L.r` sites remain bound. | Second proofreading modification step. | +| 11 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~2` | `kp` | Changes `L.mod 2→3`; both `L.r` sites remain bound. | Third proofreading modification step. | +| 12 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~3` | `kp` | Changes `L.mod 3→4`; both `L.r` sites remain bound. | Fourth proofreading modification step. | +| 13 | `Unlabeled` | one-way | `L(r!+,r!+)`, `L.mod~4` | `kp` | Changes `L.mod 4→5`; both `L.r` sites remain bound. | Terminal proofreading step producing the `Obs_D5` signaling readout. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Obs_Free_L` | `Species` | `L(r,r,mod~0)` | Free ligand with both `r` sites unbound and counter zero. | +| `Obs_Free_R` | `Species` | `R(l)` | Free receptor with open `l` site. | +| `Obs_Singly_Bound` | `Species` | `L(r!+,r,mod~0)` | Ligand with one receptor bound and one `r` site free. | +| `Obs_Tot_Dimers` | `Species` | `L(r!+,r!+)` | Ligand with both `r` sites bound, regardless of modification state. | +| `Obs_D0` | `Species` | `L(r!+,r!+,mod~0)` | Dimer before any proofreading modification. | +| `Obs_D1` | `Species` | `L(r!+,r!+,mod~1)` | Dimer after one modification. | +| `Obs_D2` | `Species` | `L(r!+,r!+,mod~2)` | Dimer after two modifications. | +| `Obs_D3` | `Species` | `L(r!+,r!+,mod~3)` | Dimer after three modifications. | +| `Obs_D4` | `Species` | `L(r!+,r!+,mod~4)` | Dimer after four modifications. | +| `Obs_D5` | `Species` | `L(r!+,r!+,mod~5)` | Terminally modified dimer. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1})` builds the small reaction network. +2. `saveConcentrations()` requests output. +3. `resetConcentrations()` restores all-free ligand/receptor initial conditions. +4. `simulate({method=>"ode", suffix=>"ode", t_start=>0, t_end=>600, n_steps=>300})` runs the proofreading time course. +5. A second `resetConcentrations()` prepares the `koff` scan. +6. `parameter_scan({method=>"ode", parameter=>"koff", ...})` scans dissociation rate to show proofreading sensitivity. + +## 9. Technical caveats and ambiguities + +- The model stores modification progress on ligand `L.mod`, not on receptor `R`; this is an implementation choice for dimer state. +- The repeated `L.r` components are equivalent, so symmetry factors are part of the intended kinetics. +- There are no compartments; receptor surface context is encoded by rates and molecule naming rather than explicit membrane localization. diff --git a/data/summaries_detailed/Hlavacek2018Egg_ai_coder.md b/data/summaries_detailed/Hlavacek2018Egg_ai_coder.md new file mode 100644 index 00000000..7d349eb8 --- /dev/null +++ b/data/summaries_detailed/Hlavacek2018Egg_ai_coder.md @@ -0,0 +1,74 @@ +# Coder Model Explanation: Hlavacek2018Egg + +## 1. Model identity and scope + +- **Model id:** `Hlavacek2018Egg_egg` +- **Title:** Hlavacek2018Egg +- **BNGL path:** `Published/Hlavacek2018Egg/egg.bngl` +- **YAML path:** `Published/Hlavacek2018Egg/metadata.yaml` +- **Scope:** This is a compact published/example model whose metadata describes it as the "End of permute change log." The BNGL is not a named biological pathway; it is an ODE example that advances one abstract species and prints two fitted/trigonometric functions of that species over one period. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 23 parameter definitions: 10 fitted `__FREE` values, 10 aliases, `pi`, `period`, and `m`. | +| Compartments | No | No compartment declarations. | +| Molecule types | Yes | 1 molecule type: `t`. | +| Seed species | Yes | 1 initial species, `t`, initialized to 0. | +| Observables | Yes | 1 species-count observable for `t`. | +| Functions | Yes | 2 functions, `X()` and `Y()`, both Fourier-like expressions of `t`. | +| Reaction rules | Yes | 1 rule that creates `t` at a constant rate. | +| Actions | Yes | Network generation plus one ODE simulation with function printing. | + +## 3. Parameters, functions, and rate laws + +The parameter set is almost entirely numerical coefficients for the two output functions. The `a*` and `b*` values feed `X()`, while the `c*` and `d*` values feed `Y()`. Each `__FREE` value is copied into a shorter alias, so the function definitions use `a0`, `a1`, `a2`, `b1`, `b2`, `c0`, `c1`, `c2`, `d1`, and `d2` rather than the raw fitted names. + +| Parameter | Value / expression | Role | +| --- | ---: | --- | +| `a0__FREE`, `a1__FREE`, `a2__FREE` | 99.9318747, 1.00606018, -0.752962956 | Fitted cosine/offset coefficients for `X()`. | +| `b1__FREE`, `b2__FREE` | -30.8973913, 1.26208508 | Fitted sine coefficients for `X()`. | +| `c0__FREE`, `c1__FREE`, `c2__FREE` | 139.738978, -39.1791542, -1.56811184 | Fitted cosine/offset coefficients for `Y()`. | +| `d1__FREE`, `d2__FREE` | -1.21914775, 1.28080122 | Fitted sine coefficients for `Y()`. | +| `a0`-`d2` aliases | Each aliases the corresponding `__FREE` value | Short names used inside functions. | +| `pi` | `2*asin(1)` | Computes pi for angular frequency. | +| `period` | 180 | Period used for the trigonometric waveforms. | +| `m` | `2*pi/period` | Fundamental angular frequency. | + +`X()` computes an offset plus first- and second-harmonic sine/cosine terms using the `a*` and `b*` coefficients. `Y()` uses the same harmonic structure with `c*` and `d*` coefficients. The only reaction-rate expression is the constant `1`, so `t` increases linearly under ODE simulation. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `t` | 0 | None | None | None | This is an abstract scalar species used as the independent variable for the printed functions, not a biological molecule. | + +## 5. Initial species, compartments, and setup + +The model starts with `t` at zero. There are no compartments, no complexes, no binding sites, and no molecular states. Because the single rule continuously creates `t`, the ODE trajectory effectively turns `t` into a time-like ramp from 0 over the simulation interval. `X()` and `Y()` are then printed as functions of this ramp. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | Unlabeled `0 -> t` | One-way synthesis/source | No reactant; product is the zero-site species `t` | `1` | Constant creation of `t` | Drives `t` upward at unit rate so the functions `X()` and `Y()` can be evaluated over a 180-step period. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `t` | `Species` | The zero-site species `t` | Reports the amount of the abstract species being accumulated by the source rule. | + +`X()` and `Y()` are not observables but are printed functions requested by the simulation action. They are the main numerical outputs of interest. + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1})` builds the one-species, one-reaction network. +2. `simulate({suffix=>"egg", method=>"ode", t_start=>0, t_end=>180, n_steps=>180, print_functions=>1})` integrates the constant source rule over one 180-unit period and prints `X()` and `Y()` alongside the species trajectory. + +## 9. Technical caveats and ambiguities + +- The molecule name `t` is abstract; the current files do not support interpreting it as a biological species. +- The useful outputs are the printed functions, not a mechanistic pathway trajectory. +- The comments identify fitted or permuted parameter values but do not explain the biological origin of the coefficients. diff --git a/data/summaries_detailed/Hlavacek2018Egg_coder.md b/data/summaries_detailed/Hlavacek2018Egg_coder.md new file mode 100644 index 00000000..7d349eb8 --- /dev/null +++ b/data/summaries_detailed/Hlavacek2018Egg_coder.md @@ -0,0 +1,74 @@ +# Coder Model Explanation: Hlavacek2018Egg + +## 1. Model identity and scope + +- **Model id:** `Hlavacek2018Egg_egg` +- **Title:** Hlavacek2018Egg +- **BNGL path:** `Published/Hlavacek2018Egg/egg.bngl` +- **YAML path:** `Published/Hlavacek2018Egg/metadata.yaml` +- **Scope:** This is a compact published/example model whose metadata describes it as the "End of permute change log." The BNGL is not a named biological pathway; it is an ODE example that advances one abstract species and prints two fitted/trigonometric functions of that species over one period. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 23 parameter definitions: 10 fitted `__FREE` values, 10 aliases, `pi`, `period`, and `m`. | +| Compartments | No | No compartment declarations. | +| Molecule types | Yes | 1 molecule type: `t`. | +| Seed species | Yes | 1 initial species, `t`, initialized to 0. | +| Observables | Yes | 1 species-count observable for `t`. | +| Functions | Yes | 2 functions, `X()` and `Y()`, both Fourier-like expressions of `t`. | +| Reaction rules | Yes | 1 rule that creates `t` at a constant rate. | +| Actions | Yes | Network generation plus one ODE simulation with function printing. | + +## 3. Parameters, functions, and rate laws + +The parameter set is almost entirely numerical coefficients for the two output functions. The `a*` and `b*` values feed `X()`, while the `c*` and `d*` values feed `Y()`. Each `__FREE` value is copied into a shorter alias, so the function definitions use `a0`, `a1`, `a2`, `b1`, `b2`, `c0`, `c1`, `c2`, `d1`, and `d2` rather than the raw fitted names. + +| Parameter | Value / expression | Role | +| --- | ---: | --- | +| `a0__FREE`, `a1__FREE`, `a2__FREE` | 99.9318747, 1.00606018, -0.752962956 | Fitted cosine/offset coefficients for `X()`. | +| `b1__FREE`, `b2__FREE` | -30.8973913, 1.26208508 | Fitted sine coefficients for `X()`. | +| `c0__FREE`, `c1__FREE`, `c2__FREE` | 139.738978, -39.1791542, -1.56811184 | Fitted cosine/offset coefficients for `Y()`. | +| `d1__FREE`, `d2__FREE` | -1.21914775, 1.28080122 | Fitted sine coefficients for `Y()`. | +| `a0`-`d2` aliases | Each aliases the corresponding `__FREE` value | Short names used inside functions. | +| `pi` | `2*asin(1)` | Computes pi for angular frequency. | +| `period` | 180 | Period used for the trigonometric waveforms. | +| `m` | `2*pi/period` | Fundamental angular frequency. | + +`X()` computes an offset plus first- and second-harmonic sine/cosine terms using the `a*` and `b*` coefficients. `Y()` uses the same harmonic structure with `c*` and `d*` coefficients. The only reaction-rate expression is the constant `1`, so `t` increases linearly under ODE simulation. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | +| `t` | 0 | None | None | None | This is an abstract scalar species used as the independent variable for the printed functions, not a biological molecule. | + +## 5. Initial species, compartments, and setup + +The model starts with `t` at zero. There are no compartments, no complexes, no binding sites, and no molecular states. Because the single rule continuously creates `t`, the ODE trajectory effectively turns `t` into a time-like ramp from 0 over the simulation interval. `X()` and `Y()` are then printed as functions of this ramp. + +## 6. Complete reaction-rule inventory + +| # | Rule label/name | Direction | Participants and sites | Rate | Modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | Unlabeled `0 -> t` | One-way synthesis/source | No reactant; product is the zero-site species `t` | `1` | Constant creation of `t` | Drives `t` upward at unit rate so the functions `X()` and `Y()` can be evaluated over a 180-step period. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `t` | `Species` | The zero-site species `t` | Reports the amount of the abstract species being accumulated by the source rule. | + +`X()` and `Y()` are not observables but are printed functions requested by the simulation action. They are the main numerical outputs of interest. + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1})` builds the one-species, one-reaction network. +2. `simulate({suffix=>"egg", method=>"ode", t_start=>0, t_end=>180, n_steps=>180, print_functions=>1})` integrates the constant source rule over one 180-unit period and prints `X()` and `Y()` alongside the species trajectory. + +## 9. Technical caveats and ambiguities + +- The molecule name `t` is abstract; the current files do not support interpreting it as a biological species. +- The useful outputs are the printed functions, not a mechanistic pathway trajectory. +- The comments identify fitted or permuted parameter values but do not explain the biological origin of the coefficients. diff --git a/data/summaries_detailed/JaruszewiczBlonska2023_NFkB_ai_coder.md b/data/summaries_detailed/JaruszewiczBlonska2023_NFkB_ai_coder.md new file mode 100644 index 00000000..0288c619 --- /dev/null +++ b/data/summaries_detailed/JaruszewiczBlonska2023_NFkB_ai_coder.md @@ -0,0 +1,117 @@ +# Coder Model Explanation: Jaruszewicz 2023 + +## 1. Model identity and scope + +- **Model id:** `Jaruszewicz-Blonska_2023` +- **Title:** Jaruszewicz 2023 +- **BNGL path:** `Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023.bngl` +- **YAML path:** `Published/JaruszewiczBlonska2023/metadata.yaml` +- **Metadata description:** T-cell discrimination +- **Scope:** The BNGL file implements a compact canonical NF-kappaB ODE model. `IKK` has a real internal state site `st~n~a`; the other species (`IkBa`, `IkBa_mRNA`, `A20`, `NFkB`) are site-free pools. TNF input is represented by parameter `TR`, which gates IKK activation and A20-mediated IKK removal. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 14 fitted/control parameters, including `TR` as TNF off/on switch. | +| Compartments | No | No formal BNGL compartments. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 5 molecule types; only `IKK` has a site/state. | +| Seed/species | Yes | 6 initial species: neutral IKK starts at 1; all other pools start at 0. | +| Observables | Yes | 6 species observables for active/neutral IKK, IkBa mRNA/protein, A20, and NFkB. | +| Functions | Yes | 3 rate functions for NFkB import/export and IkBa transport/removal. | +| Reaction rules | Yes | 14 ODE-style rules. | +| Actions | Yes | Network generation, `TR=0`, long steady-state ODE run, and concentration saving. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `k_1` | `0.00195` | TNF-gated activation rate for `IKK.st n→a`. | +| `k_deg` | `0.000107` | Basal IKK production/degradation rate. | +| `k_3` | `0.00145` | Extra loss term for active IKK. | +| `k_2` | `0.0357` | TNF-gated A20-mediated removal rate for active IKK. | +| `c_deg` | `0.000106` | A20 synthesis/degradation rate in this implementation. | +| `c_3a` | `0.000372` | IkBa mRNA transcription/degradation rate. | +| `c_4a` | `0.00313` | IkBa protein translation rate from IkBa mRNA. | +| `c_5a` | `0.0000578` | IkBa degradation rate. | +| `a_3`, `delta`, `epsilon`, `i_1a`, `a_2` | fitted values | Parameters used inside NFkB import/export and IkBa transport functions. | +| `TR` | `0` | TNF input switch; active actions set it to 0 before steady-state simulation. | + +**Functions and derived rates** + +| Function | Technical interpretation | +| --- | --- | +| `k_NFkBimport() = a_3*delta*(1-NFkB_n)/(IkBa+delta)` | Produces/imports `NFkB()` from active IKK; decreases as observable `NFkB_n` approaches 1 and depends inversely on `IkBa`. | +| `k_NFkBexport() = i_1a/(NFkB_n+epsilon)` | Removes the `NFkB()+IkBa()` pair; depends on current nuclear NFkB observable. | +| `k_IkBatransport() = a_2+(a_3*(1-NFkB_n))/(IkBa+delta)` | Removes `IkBa()` in the presence of active IKK; combines basal and NFkB/IkBa-dependent terms. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `IKK` | 1 | `st` | `st~n~a` | none | `st` is the neutral/active switch. | This is the only declared site/state in the model. | +| `IkBa` | 0 | none | none | none | Whole-pool inhibitor species. | Comments label it cytoplasmic, but no compartment syntax is used. | +| `IkBa_mRNA` | 0 | none | none | none | Whole-pool transcript species. | Produced by NFkB and translated to IkBa. | +| `A20` | 0 | none | none | none | Whole-pool feedback species. | Removes active IKK in rule 11 while being preserved. | +| `NFkB` | 0 | none | none | none | Whole-pool nuclear NFkB readout. | Comments call it nuclear, but this is not a BNGL compartment. | + +## 5. Compartments, anchors, initial species, and setup + +- Compartments: none declared. +- Anchors: none declared. +- Initial setup: neutral IKK starts present; active IKK, IkBa, IkBa mRNA, A20, and NFkB start at zero. + +| Initial species/pattern | Initial amount | Setup role | +| --- | --- | --- | +| `IKK(st~n)` | `1` | Initial neutral IKK pool. | +| `IKK(st~a)` | `0` | No active IKK initially. | +| `IkBa()` | `0` | No inhibitor protein initially. | +| `IkBa_mRNA()` | `0` | No transcript initially. | +| `A20()` | `0` | No feedback species initially. | +| `NFkB()` | `0` | No nuclear NFkB pool initially. | + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rule 1 is the only site-state conversion (`IKK.st n→a`). The remaining rules are source/sink or catalytic carry-through ODE terms for site-free pools. Rules with a species on both sides, such as `NFkB() -> NFkB() + A20()`, preserve the catalyst/readout species while producing another pool. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | `IKK.st` | `k_1*TR` | `IKK.st n→a`. | TNF-gated IKK activation; if `TR=0`, this activation term is zero. | +| 2 | `Unlabeled` | one-way | product `IKK.st~n` | `k_deg` | Source `0 → IKK(st~n)`. | Basal replenishment of neutral IKK. | +| 3 | `Unlabeled` | one-way | `IKK.st~a` | `k_deg+k_3` | Sink `IKK(st~a) → 0`. | Removes active IKK by basal plus active-specific degradation. | +| 4 | `Unlabeled` | one-way | `IKK.st~n` | `k_deg` | Sink `IKK(st~n) → 0`. | Basal neutral IKK degradation. | +| 5 | `Unlabeled` | one-way | `NFkB` preserved, `A20` produced | `c_deg` | `NFkB() → NFkB() + A20()`. | NFkB-driven A20 synthesis; `NFkB` is catalytic/preserved in the rule pattern. | +| 6 | `Unlabeled` | one-way | `A20` | `c_deg` | Sink `A20() → 0`. | A20 degradation. | +| 7 | `Unlabeled` | one-way | `NFkB` preserved, `IkBa_mRNA` produced | `c_3a` | `NFkB() → NFkB() + IkBa_mRNA()`. | NFkB-driven IkBa transcript production. | +| 8 | `Unlabeled` | one-way | `IkBa_mRNA` | `c_3a` | Sink `IkBa_mRNA() → 0`. | IkBa transcript degradation. | +| 9 | `Unlabeled` | one-way | `IkBa_mRNA` preserved, `IkBa` produced | `c_4a` | `IkBa_mRNA() → IkBa_mRNA() + IkBa()`. | Translation of IkBa protein from its mRNA. | +| 10 | `Unlabeled` | one-way | `IkBa` | `c_5a` | Sink `IkBa() → 0`. | IkBa protein degradation. | +| 11 | `Unlabeled` | one-way | `A20` preserved, `IKK.st~a` consumed | `k_2*TR` | `A20() + IKK(st~a) → A20()`. | A20-mediated active IKK removal; gated by TNF switch `TR`. | +| 12 | `Unlabeled` | one-way | `IKK.st~a` preserved, `NFkB` produced | `k_NFkBimport()` | `IKK(st~a) → IKK(st~a) + NFkB()`. | Active IKK drives NFkB production/import using a rate dependent on `NFkB_n` and `IkBa`. | +| 13 | `Unlabeled` | one-way | `NFkB` + `IkBa` | `k_NFkBexport()` | Sink `NFkB() + IkBa() → 0`. | IkBa-associated NFkB export/removal; both pools are removed by this pattern. | +| 14 | `Unlabeled` | one-way | `IKK.st~a` preserved, `IkBa` consumed | `k_IkBatransport()` | `IKK(st~a)+IkBa() → IKK(st~a)`. | Active IKK-associated IkBa removal/transport using the model’s combined basal/NFkB-dependent function. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `IKK_a` | `Species` | `IKK(st~a)` | Active IKK pool. | +| `tIkBa` | `Species` | `IkBa_mRNA()` | IkBa transcript pool. | +| `A20` | `Species` | `A20()` | A20 feedback species. | +| `NFkB_n` | `Species` | `NFkB()` | Nuclear NFkB pool used by functions. | +| `IkBa` | `Species` | `IkBa()` | IkBa inhibitor protein pool used by functions. | +| `IKK_n` | `Species` | `IKK(st~n)` | Neutral IKK pool. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1});` builds the reaction network. +2. `setParameter("TR",0);` explicitly keeps TNF input off for the active simulation. +3. `simulate_ode({suffix=>"continuous", t_end=>30*24*3600, ... steady_state=>1});` runs a long ODE simulation to steady state. +4. `saveConcentrations()` writes concentration outputs. + +## 9. Technical caveats and ambiguities + +- The YAML description says T-cell discrimination, but the BNGL file text describes canonical NF-kappaB signaling; this summary follows the BNGL file. +- Comments label NFkB as nuclear and IkBa/A20 as cytoplasmic, but there are no BNGL compartments or anchors. +- Many pulse protocols are commented/auto-disabled; the active workflow is the continuous steady-state run with `TR=0`. diff --git a/data/summaries_detailed/JaruszewiczBlonska2023_NFkB_coder.md b/data/summaries_detailed/JaruszewiczBlonska2023_NFkB_coder.md new file mode 100644 index 00000000..0288c619 --- /dev/null +++ b/data/summaries_detailed/JaruszewiczBlonska2023_NFkB_coder.md @@ -0,0 +1,117 @@ +# Coder Model Explanation: Jaruszewicz 2023 + +## 1. Model identity and scope + +- **Model id:** `Jaruszewicz-Blonska_2023` +- **Title:** Jaruszewicz 2023 +- **BNGL path:** `Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023.bngl` +- **YAML path:** `Published/JaruszewiczBlonska2023/metadata.yaml` +- **Metadata description:** T-cell discrimination +- **Scope:** The BNGL file implements a compact canonical NF-kappaB ODE model. `IKK` has a real internal state site `st~n~a`; the other species (`IkBa`, `IkBa_mRNA`, `A20`, `NFkB`) are site-free pools. TNF input is represented by parameter `TR`, which gates IKK activation and A20-mediated IKK removal. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 14 fitted/control parameters, including `TR` as TNF off/on switch. | +| Compartments | No | No formal BNGL compartments. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 5 molecule types; only `IKK` has a site/state. | +| Seed/species | Yes | 6 initial species: neutral IKK starts at 1; all other pools start at 0. | +| Observables | Yes | 6 species observables for active/neutral IKK, IkBa mRNA/protein, A20, and NFkB. | +| Functions | Yes | 3 rate functions for NFkB import/export and IkBa transport/removal. | +| Reaction rules | Yes | 14 ODE-style rules. | +| Actions | Yes | Network generation, `TR=0`, long steady-state ODE run, and concentration saving. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `k_1` | `0.00195` | TNF-gated activation rate for `IKK.st n→a`. | +| `k_deg` | `0.000107` | Basal IKK production/degradation rate. | +| `k_3` | `0.00145` | Extra loss term for active IKK. | +| `k_2` | `0.0357` | TNF-gated A20-mediated removal rate for active IKK. | +| `c_deg` | `0.000106` | A20 synthesis/degradation rate in this implementation. | +| `c_3a` | `0.000372` | IkBa mRNA transcription/degradation rate. | +| `c_4a` | `0.00313` | IkBa protein translation rate from IkBa mRNA. | +| `c_5a` | `0.0000578` | IkBa degradation rate. | +| `a_3`, `delta`, `epsilon`, `i_1a`, `a_2` | fitted values | Parameters used inside NFkB import/export and IkBa transport functions. | +| `TR` | `0` | TNF input switch; active actions set it to 0 before steady-state simulation. | + +**Functions and derived rates** + +| Function | Technical interpretation | +| --- | --- | +| `k_NFkBimport() = a_3*delta*(1-NFkB_n)/(IkBa+delta)` | Produces/imports `NFkB()` from active IKK; decreases as observable `NFkB_n` approaches 1 and depends inversely on `IkBa`. | +| `k_NFkBexport() = i_1a/(NFkB_n+epsilon)` | Removes the `NFkB()+IkBa()` pair; depends on current nuclear NFkB observable. | +| `k_IkBatransport() = a_2+(a_3*(1-NFkB_n))/(IkBa+delta)` | Removes `IkBa()` in the presence of active IKK; combines basal and NFkB/IkBa-dependent terms. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `IKK` | 1 | `st` | `st~n~a` | none | `st` is the neutral/active switch. | This is the only declared site/state in the model. | +| `IkBa` | 0 | none | none | none | Whole-pool inhibitor species. | Comments label it cytoplasmic, but no compartment syntax is used. | +| `IkBa_mRNA` | 0 | none | none | none | Whole-pool transcript species. | Produced by NFkB and translated to IkBa. | +| `A20` | 0 | none | none | none | Whole-pool feedback species. | Removes active IKK in rule 11 while being preserved. | +| `NFkB` | 0 | none | none | none | Whole-pool nuclear NFkB readout. | Comments call it nuclear, but this is not a BNGL compartment. | + +## 5. Compartments, anchors, initial species, and setup + +- Compartments: none declared. +- Anchors: none declared. +- Initial setup: neutral IKK starts present; active IKK, IkBa, IkBa mRNA, A20, and NFkB start at zero. + +| Initial species/pattern | Initial amount | Setup role | +| --- | --- | --- | +| `IKK(st~n)` | `1` | Initial neutral IKK pool. | +| `IKK(st~a)` | `0` | No active IKK initially. | +| `IkBa()` | `0` | No inhibitor protein initially. | +| `IkBa_mRNA()` | `0` | No transcript initially. | +| `A20()` | `0` | No feedback species initially. | +| `NFkB()` | `0` | No nuclear NFkB pool initially. | + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rule 1 is the only site-state conversion (`IKK.st n→a`). The remaining rules are source/sink or catalytic carry-through ODE terms for site-free pools. Rules with a species on both sides, such as `NFkB() -> NFkB() + A20()`, preserve the catalyst/readout species while producing another pool. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | `IKK.st` | `k_1*TR` | `IKK.st n→a`. | TNF-gated IKK activation; if `TR=0`, this activation term is zero. | +| 2 | `Unlabeled` | one-way | product `IKK.st~n` | `k_deg` | Source `0 → IKK(st~n)`. | Basal replenishment of neutral IKK. | +| 3 | `Unlabeled` | one-way | `IKK.st~a` | `k_deg+k_3` | Sink `IKK(st~a) → 0`. | Removes active IKK by basal plus active-specific degradation. | +| 4 | `Unlabeled` | one-way | `IKK.st~n` | `k_deg` | Sink `IKK(st~n) → 0`. | Basal neutral IKK degradation. | +| 5 | `Unlabeled` | one-way | `NFkB` preserved, `A20` produced | `c_deg` | `NFkB() → NFkB() + A20()`. | NFkB-driven A20 synthesis; `NFkB` is catalytic/preserved in the rule pattern. | +| 6 | `Unlabeled` | one-way | `A20` | `c_deg` | Sink `A20() → 0`. | A20 degradation. | +| 7 | `Unlabeled` | one-way | `NFkB` preserved, `IkBa_mRNA` produced | `c_3a` | `NFkB() → NFkB() + IkBa_mRNA()`. | NFkB-driven IkBa transcript production. | +| 8 | `Unlabeled` | one-way | `IkBa_mRNA` | `c_3a` | Sink `IkBa_mRNA() → 0`. | IkBa transcript degradation. | +| 9 | `Unlabeled` | one-way | `IkBa_mRNA` preserved, `IkBa` produced | `c_4a` | `IkBa_mRNA() → IkBa_mRNA() + IkBa()`. | Translation of IkBa protein from its mRNA. | +| 10 | `Unlabeled` | one-way | `IkBa` | `c_5a` | Sink `IkBa() → 0`. | IkBa protein degradation. | +| 11 | `Unlabeled` | one-way | `A20` preserved, `IKK.st~a` consumed | `k_2*TR` | `A20() + IKK(st~a) → A20()`. | A20-mediated active IKK removal; gated by TNF switch `TR`. | +| 12 | `Unlabeled` | one-way | `IKK.st~a` preserved, `NFkB` produced | `k_NFkBimport()` | `IKK(st~a) → IKK(st~a) + NFkB()`. | Active IKK drives NFkB production/import using a rate dependent on `NFkB_n` and `IkBa`. | +| 13 | `Unlabeled` | one-way | `NFkB` + `IkBa` | `k_NFkBexport()` | Sink `NFkB() + IkBa() → 0`. | IkBa-associated NFkB export/removal; both pools are removed by this pattern. | +| 14 | `Unlabeled` | one-way | `IKK.st~a` preserved, `IkBa` consumed | `k_IkBatransport()` | `IKK(st~a)+IkBa() → IKK(st~a)`. | Active IKK-associated IkBa removal/transport using the model’s combined basal/NFkB-dependent function. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `IKK_a` | `Species` | `IKK(st~a)` | Active IKK pool. | +| `tIkBa` | `Species` | `IkBa_mRNA()` | IkBa transcript pool. | +| `A20` | `Species` | `A20()` | A20 feedback species. | +| `NFkB_n` | `Species` | `NFkB()` | Nuclear NFkB pool used by functions. | +| `IkBa` | `Species` | `IkBa()` | IkBa inhibitor protein pool used by functions. | +| `IKK_n` | `Species` | `IKK(st~n)` | Neutral IKK pool. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1});` builds the reaction network. +2. `setParameter("TR",0);` explicitly keeps TNF input off for the active simulation. +3. `simulate_ode({suffix=>"continuous", t_end=>30*24*3600, ... steady_state=>1});` runs a long ODE simulation to steady state. +4. `saveConcentrations()` writes concentration outputs. + +## 9. Technical caveats and ambiguities + +- The YAML description says T-cell discrimination, but the BNGL file text describes canonical NF-kappaB signaling; this summary follows the BNGL file. +- Comments label NFkB as nuclear and IkBa/A20 as cytoplasmic, but there are no BNGL compartments or anchors. +- Many pulse protocols are commented/auto-disabled; the active workflow is the continuous steady-state run with `TR=0`. diff --git a/data/summaries_detailed/Jung2017_M1R_signaling_ai_coder.md b/data/summaries_detailed/Jung2017_M1R_signaling_ai_coder.md new file mode 100644 index 00000000..af9932ca --- /dev/null +++ b/data/summaries_detailed/Jung2017_M1R_signaling_ai_coder.md @@ -0,0 +1,105 @@ +# Coder Model Explanation: Jung 2017 + +## 1. Model identity and scope + +- **Model id:** `Jung_2017` +- **Title:** Jung 2017 +- **BNGL path:** `Published/Jung2017/Jung_2017.bngl` +- **YAML path:** `Published/Jung2017/metadata.yaml` +- **Metadata description:** M1 receptor signaling +- **Scope:** This compartmental BNGL model connects extracellular agonist conversion/binding to plasma-membrane M1R, receptor phosphorylation at `S228` and `S273`, arrestin recruitment through `M1R.Arr`/`Arrestin.RLP`, MEK/ERK scaffold assembly on arrestin, PP2A-mediated pERK dephosphorylation, GRK- and CK2-mediated M1R phosphorylation, and a probe/phospho-probe reporter. There are no anchors; localization is expressed directly with `@EC`, `@PM`, and `@cytoplasm` prefixes. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 6 declared parameters for timing/control factors; many rule-rate multipliers are referenced but not declared in this file. | +| Compartments | Yes | 3 compartments: `cytoplasm`, `EC`, and `PM`. | +| Anchors | No | No anchors block; compartment constraints appear directly in patterns. | +| Molecule types | Yes | 13 molecule types. | +| Seed/species | Yes | 27 seed species, many zero-initialized complexes. | +| Observables | Yes | 20 molecule observables. | +| Functions | Yes | 2 time-gating functions: `washing_agonist()` and `off_set()`. | +| Reaction rules | Yes | 19 active rules. | +| Actions | Yes | One `generate_network` command after the model. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `start` | `60.0` | Timing parameter, not directly referenced by an active rule. | +| `end` | `540.0` | Timing parameter, not directly referenced by an active rule. | +| `time` | `60.0` | Timing parameter, not directly referenced by an active rule. | +| `on_set` | `1.0` | Control parameter, not directly referenced by an active rule. | +| `converting_factor` | `0.0` | Control parameter, not directly referenced by an active rule. | +| `Dephos_factor` | `0.1` | Control parameter; note the rules reference lowercase `dephosphorylation_factor`, not this exact name. | + +| Function | Technical interpretation | +| --- | --- | +| `washing_agonist() = (1.0 * (t > 60.0)) && (t < 540.0)` | Time window that gates agonist/M1R binding in rule `R_L_PM`; nonzero only after 60 and before 540. | +| `off_set() = 0.0 * (t > 480.0)` | Always evaluates to zero because of the leading `0.0`; it is not used by an active rule. | + +Several rule rates include undeclared names (`RLpp_arrestin_binding_factor`, `negative_arrestin_binding`, `dephosphorylation_factor`, `phos_factor_PP`, `PP2A_dephos_factor`, `MEK_effect`, `GRK_binding_factor`, `RLGRK_pp_dissociation`). Those names must be supplied externally or corrected before standalone execution. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `M1R` | 7 | `L`, `S228`, `S273`, `Arr`, `GRK`, `PP1`, `CK2` | `S228`: `u`, `p`; `S273`: `u`, `p` | Directly used at `@PM` | `L` binds `Oxo.R`; `Arr` binds `Arrestin.RLP`; `GRK`, `PP1`, `CK2` bind corresponding kinase/phosphatase `RL` sites; `S228/S273` are receptor state sites. | `PP1` site is seeded but not used by active rules. | +| `Oxo` | 1 | `R` | none | Produced at `@EC`, binds at `@PM` complex product | Binds `M1R.L`. | Agonist ligand represented separately from precursor `Oxo_EC`. | +| `Arrestin` | 3 | `RLP`, `MEK`, `PP2A` | none | Seeded at `@cytoplasm`; complexes appear at `@PM` | `RLP` binds `M1R.Arr`; `MEK` binds `MEK.Arr`; `PP2A` binds `PP2A.Arrestin`. | Acts as scaffold between receptor, MEK, and PP2A. | +| `MEK` | 2 | `Arr`, `ERK` | none | Seeded at `@cytoplasm`; scaffolded complexes at `@PM` | `Arr` binds arrestin; `ERK` binds ERK/pERK `MEK`. | Catalytic role is represented by ERK→pERK conversion in bound complex. | +| `ERK` | 4 | `MEK`, `s`, `PP2A`, `PP1` | `s`: `u` | Primarily `@cytoplasm`, also recruited to `@PM` scaffold | `MEK` binds `MEK.ERK`; `s~u` is unphosphorylated state in the ERK molecule type. | `ERK` and `pERK` are separate molecule types despite state-like names. | +| `pERK` | 4 | `MEK`, `s`, `PP2A`, `PP1` | `s`: `p` | Primarily `@cytoplasm`, also scaffolded at `@PM` | `MEK` binds scaffolded MEK; `PP2A` can bind through `PP2A.ERK`; `s~p` marks phosphorylated ERK type. | Dephosphorylation converts `pERK` molecule type to `ERK`. | +| `Oxo_EC` | 0 | none | none | `@EC` seed; one observable appears with `@cytoplasm`, likely inconsistent | Precursor/source species for `Oxo`. | Rule 8 converts it to `Oxo(R)`. | +| `PP2A` | 2 | `Arrestin`, `ERK` | none | Seeded at `@cytoplasm`; can be scaffolded at `@PM` | `Arrestin` binds arrestin; `ERK` appears bound to ERK/pERK in seed species. | Dephosphorylates pERK in rule 10. | +| `probe` | 1 | `site` | `site`: `u` | `@cytoplasm` | Reporter substrate in rule 16. | Converted to separate `phos_probe` type. | +| `phos_probe` | 1 | `Site0` | `Site0`: `p` | `@cytoplasm` | Reporter product in rule 16. | Separate molecule type rather than state transition on `probe`. | +| `GRK` | 1 | `RL` | none | `@PM` in seed/rules | `RL` binds `M1R.GRK`. | Catalyzes/marks receptor phosphorylation in rule 5. | +| `PP1` | 1 | `RL` | none | Seeded at `@cytoplasm`; one zero seed at `@PM` complex | `RL` can bind `M1R.PP1` in seed species, but no active rule uses it. | Declared/seeded but not active in rules. | +| `CK2` | 1 | `RL` | none | Seeded `@cytoplasm`; complex product at `@PM` | `RL` binds `M1R.CK2`. | Phosphorylates receptor in rule 18. | + +## 5. Compartments, anchors, initial species, and setup + +Compartments are `cytoplasm` (3D), `EC` (3D), and `PM` (2D). No anchors constrain molecule localization, so each rule’s `@compartment` prefixes define where reactants/products are matched. Initial species include large free `@PM:M1R`, `@EC:Oxo_EC`, cytoplasmic arrestin/MEK/ERK/PP2A/pERK/probe pools, PM-localized GRK, cytoplasmic PP1/CK2, and many zero-initialized receptor/arrestin/MEK/ERK/PP2A/GRK/CK2 complexes used as named starting states. + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** The model uses explicit compartment prefixes and mixed molecule-type conversion. Rules 1-3 and 6-7 build ligand/receptor/arrestin/MEK/ERK complexes by forming named site bonds. Rules 4-5 and 18 modify M1R `S228/S273`. Rules 10-12 and 15-16 convert ERK/probe molecule types while preserving catalytic/scaffold molecules on both sides. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `R_L_PM` | reversible | `@EC:Oxo.R` + `@PM:M1R.L`; requires `M1R.S228~u,S273~u` | `20.0 * washing_agonist, 4.0` | Forms/releases `Oxo.R!1`–`M1R.L!1`; product complex is at `@PM`. | Moves agonist binding into a PM receptor complex only during the `washing_agonist()` time window. | +| 2 | `RLppA` | reversible | phosphorylated ligand-bound `M1R.Arr` + `Arrestin.RLP` | `1.0 * RLpp_arrestin_binding_factor, 10.0 * RLpp_arrestin_binding_factor` | Forms/releases `M1R.Arr!2`–`Arrestin.RLP!2`; `M1R.S228/S273` remain `p`. | Arrestin binds phosphorylated agonist-bound receptor. | +| 3 | `RLA` | reversible | unphosphorylated ligand-bound `M1R.Arr` + `Arrestin.RLP` | `0.24 * negative_arrestin_binding, 2.8 * negative_arrestin_binding` | Forms/releases `M1R.Arr!2`–`Arrestin.RLP!2`; `M1R.S228/S273` remain `u`. | Allows weaker/differently scaled arrestin binding to unphosphorylated receptor. | +| 4 | `DeP_RLGRK_pp` | one-way | ligand-bound `M1R.S228~p,S273~p` | `0.5 * dephosphorylation_factor` | `M1R.S228 p→u` and `M1R.S273 p→u`; `Oxo.R!1`–`M1R.L!1` remains. | Dephosphorylates both receptor sites without requiring a bound phosphatase molecule. | +| 5 | `RLGRK_pp` | one-way | `M1R.GRK!2`–`GRK.RL!2` with ligand-bound unphosphorylated receptor | `0.9 * phos_factor_PP` | `M1R.S228 u→p` and `M1R.S273 u→p`; GRK bond remains. | GRK-bound receptor is phosphorylated at both modeled receptor sites. | +| 6 | `RLppAM` | reversible | phosphorylated receptor/arrestin complex, `Arrestin.MEK` + `MEK.Arr` | `0.1, 5.0E-5` | Forms/releases `Arrestin.MEK!3`–`MEK.Arr!3`. | Recruits MEK to phosphorylated receptor-bound arrestin scaffold. | +| 7 | `RLppAME` | reversible | scaffolded `MEK.ERK` + cytoplasmic `ERK.MEK`, `ERK.s~u` | `2.0, 2.5` | Forms/releases `MEK.ERK!4`–`ERK.MEK!4`. | Adds unphosphorylated ERK to the receptor/arrestin/MEK scaffold. | +| 8 | `Oxo_conversion` | one-way | `@EC:Oxo_EC` | `50.0` | Converts `Oxo_EC()` to `Oxo(R)` at `@EC`. | Generates receptor-binding agonist from precursor/source species. | +| 9 | `RLAPP2A` | reversible | unphosphorylated receptor/arrestin complex, `Arrestin.PP2A` + `PP2A.Arrestin` | `3.0E-5, 6.0E-5` | Forms/releases `Arrestin.PP2A!3`–`PP2A.Arrestin!3`. | Recruits PP2A to an arrestin-bound unphosphorylated receptor complex. | +| 10 | `DeP_pERK_PP2A` | reversible with zero reverse | scaffolded PP2A complex + cytoplasmic `pERK.s~p` | `9.0 * PP2A_dephos_factor, 0.0` | Converts free `pERK(MEK,s~p,PP2A,PP1)` to free `ERK(MEK,s~u,PP2A,PP1)`; PP2A scaffold is unchanged. | PP2A-containing receptor/arrestin complex catalytically dephosphorylates cytoplasmic pERK. | +| 11 | `RLppAMpE` | reversible | scaffolded `MEK.ERK!4`–`ERK.MEK!4`; `ERK.s~u` | `9.0 * MEK_effect, 0.36 * MEK_effect` | Converts bound `ERK(s~u)` molecule type to bound `pERK(s~p)` while preserving `MEK.ERK!4`–`pERK.MEK!4`. | MEK scaffold phosphorylates ERK while it remains bound to the MEK site. | +| 12 | `RLppAMpE_dissociation` | reversible with zero reverse | bound `MEK.ERK!4`–`pERK.MEK!4` | `2.0, 0.0` | Releases `pERK` from `MEK.ERK`; `MEK.ERK` becomes free and pERK moves to cytoplasm. | Irreversible-in-practice release of phosphorylated ERK from scaffold because reverse rate is zero. | +| 13 | `RL_GRK` | reversible | ligand-bound unphosphorylated `M1R.GRK` + `GRK.RL` at `@PM` | `4.0 * GRK_binding_factor, 4.0` | Forms/releases `M1R.GRK!2`–`GRK.RL!2`. | Recruits GRK to ligand-bound receptor before phosphorylation. | +| 14 | `RLGRK_pp_dissociation` | reversible | phosphorylated `M1R.GRK!2`–`GRK.RL!2` | `2.0 * RLGRK_pp_dissociation, 2.0 * RLGRK_pp_dissociation` | Releases/forms `M1R.GRK!2`–`GRK.RL!2`; receptor stays phosphorylated. | Lets GRK detach after receptor phosphorylation. | +| 15 | `ERK_balancing` | reversible | cytoplasmic `ERK.s~u` and `pERK.s~p` | `0.1, 1.0` | Converts free `ERK` molecule type to free `pERK`, and reverse converts `pERK` to `ERK`. | Background ERK phosphorylation/dephosphorylation balance independent of scaffold. | +| 16 | `P_probe` | reversible | cytoplasmic `pERK.s~p`, `probe.site~u`, `phos_probe.Site0~p` | `2.0, 2.0` | Forward converts `probe(site~u)` to `phos_probe(Site0~p)` while pERK is preserved; reverse converts reporter product back. | Reporter phosphorylation/dephosphorylation proxy driven by pERK presence. | +| 17 | `RL_CK2_binding` | reversible | ligand-bound unphosphorylated `M1R.CK2` + `CK2.RL` | `5.0E-5, 1.0` | Forms/releases `M1R.CK2!2`–`CK2.RL!2`; product complex is at `@PM`. | Recruits CK2 to ligand-bound receptor. | +| 18 | `RL_CK2_phos` | one-way | `M1R.CK2!2`–`CK2.RL!2` complex | `0.01` | `M1R.S228 u→p` and `M1R.S273 u→p`; CK2 bond remains. | CK2-bound receptor is phosphorylated at both modeled receptor sites. | +| 19 | `RL_CK2_phos_dissociation` | reversible | phosphorylated `M1R.CK2!2`–`CK2.RL!2` | `10.0, 10.0` | Releases/forms `M1R.CK2!2`–`CK2.RL!2`; receptor stays phosphorylated. | CK2 can detach from phosphorylated receptor or rebind it at the same rate. | + +## 7. Observables and technical readouts + +The 20 `Molecules` observables report compartment-specific pools or complexes: total PM M1R, EC agonist, cytoplasmic arrestin/MEK/ERK/pERK/PP2A/PP1/CK2, receptor-arrestin states (`O0_RLPPA`, `O0_RLA`), receptor phosphorylation (`O0_RLPP`), MEK/ERK scaffolded complexes (`O0_RLPPA_M`, `O0_RLppAME`, `O0_RLppAMpE`), PP2A scaffold recruitment (`O0_RLAPP2A`), and probe/phospho-probe totals. Note that `O0_Oxo_EC_tot` targets `@cytoplasm:Oxo_EC()` even though the seed and conversion rule place `Oxo_EC` at `@EC`; that observable may be inconsistent with the intended pool. + +## 8. Actions and simulation workflow + +The file calls `generate_network({max_iter=>6,max_agg=>10,max_stoich=>{...},overwrite=>1})`. This generates a bounded reaction network with high stoichiometry caps for all declared molecule types. No simulation command is included. + +## 9. Technical caveats and ambiguities + +- Several rate-factor identifiers are undeclared locally; this is the major execution caveat. +- The model has compartments but no anchors, so compartment correctness depends entirely on each pattern’s `@` prefix. +- `ERK` and `pERK` are separate molecule types, not one molecule type with `s~u~p`; conversion rules therefore change molecule identity as well as the apparent phosphorylation state. +- `PP1` is declared and seeded but does not participate in active reaction rules. diff --git a/data/summaries_detailed/Jung2017_M1R_signaling_coder.md b/data/summaries_detailed/Jung2017_M1R_signaling_coder.md new file mode 100644 index 00000000..af9932ca --- /dev/null +++ b/data/summaries_detailed/Jung2017_M1R_signaling_coder.md @@ -0,0 +1,105 @@ +# Coder Model Explanation: Jung 2017 + +## 1. Model identity and scope + +- **Model id:** `Jung_2017` +- **Title:** Jung 2017 +- **BNGL path:** `Published/Jung2017/Jung_2017.bngl` +- **YAML path:** `Published/Jung2017/metadata.yaml` +- **Metadata description:** M1 receptor signaling +- **Scope:** This compartmental BNGL model connects extracellular agonist conversion/binding to plasma-membrane M1R, receptor phosphorylation at `S228` and `S273`, arrestin recruitment through `M1R.Arr`/`Arrestin.RLP`, MEK/ERK scaffold assembly on arrestin, PP2A-mediated pERK dephosphorylation, GRK- and CK2-mediated M1R phosphorylation, and a probe/phospho-probe reporter. There are no anchors; localization is expressed directly with `@EC`, `@PM`, and `@cytoplasm` prefixes. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 6 declared parameters for timing/control factors; many rule-rate multipliers are referenced but not declared in this file. | +| Compartments | Yes | 3 compartments: `cytoplasm`, `EC`, and `PM`. | +| Anchors | No | No anchors block; compartment constraints appear directly in patterns. | +| Molecule types | Yes | 13 molecule types. | +| Seed/species | Yes | 27 seed species, many zero-initialized complexes. | +| Observables | Yes | 20 molecule observables. | +| Functions | Yes | 2 time-gating functions: `washing_agonist()` and `off_set()`. | +| Reaction rules | Yes | 19 active rules. | +| Actions | Yes | One `generate_network` command after the model. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `start` | `60.0` | Timing parameter, not directly referenced by an active rule. | +| `end` | `540.0` | Timing parameter, not directly referenced by an active rule. | +| `time` | `60.0` | Timing parameter, not directly referenced by an active rule. | +| `on_set` | `1.0` | Control parameter, not directly referenced by an active rule. | +| `converting_factor` | `0.0` | Control parameter, not directly referenced by an active rule. | +| `Dephos_factor` | `0.1` | Control parameter; note the rules reference lowercase `dephosphorylation_factor`, not this exact name. | + +| Function | Technical interpretation | +| --- | --- | +| `washing_agonist() = (1.0 * (t > 60.0)) && (t < 540.0)` | Time window that gates agonist/M1R binding in rule `R_L_PM`; nonzero only after 60 and before 540. | +| `off_set() = 0.0 * (t > 480.0)` | Always evaluates to zero because of the leading `0.0`; it is not used by an active rule. | + +Several rule rates include undeclared names (`RLpp_arrestin_binding_factor`, `negative_arrestin_binding`, `dephosphorylation_factor`, `phos_factor_PP`, `PP2A_dephos_factor`, `MEK_effect`, `GRK_binding_factor`, `RLGRK_pp_dissociation`). Those names must be supplied externally or corrected before standalone execution. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `M1R` | 7 | `L`, `S228`, `S273`, `Arr`, `GRK`, `PP1`, `CK2` | `S228`: `u`, `p`; `S273`: `u`, `p` | Directly used at `@PM` | `L` binds `Oxo.R`; `Arr` binds `Arrestin.RLP`; `GRK`, `PP1`, `CK2` bind corresponding kinase/phosphatase `RL` sites; `S228/S273` are receptor state sites. | `PP1` site is seeded but not used by active rules. | +| `Oxo` | 1 | `R` | none | Produced at `@EC`, binds at `@PM` complex product | Binds `M1R.L`. | Agonist ligand represented separately from precursor `Oxo_EC`. | +| `Arrestin` | 3 | `RLP`, `MEK`, `PP2A` | none | Seeded at `@cytoplasm`; complexes appear at `@PM` | `RLP` binds `M1R.Arr`; `MEK` binds `MEK.Arr`; `PP2A` binds `PP2A.Arrestin`. | Acts as scaffold between receptor, MEK, and PP2A. | +| `MEK` | 2 | `Arr`, `ERK` | none | Seeded at `@cytoplasm`; scaffolded complexes at `@PM` | `Arr` binds arrestin; `ERK` binds ERK/pERK `MEK`. | Catalytic role is represented by ERK→pERK conversion in bound complex. | +| `ERK` | 4 | `MEK`, `s`, `PP2A`, `PP1` | `s`: `u` | Primarily `@cytoplasm`, also recruited to `@PM` scaffold | `MEK` binds `MEK.ERK`; `s~u` is unphosphorylated state in the ERK molecule type. | `ERK` and `pERK` are separate molecule types despite state-like names. | +| `pERK` | 4 | `MEK`, `s`, `PP2A`, `PP1` | `s`: `p` | Primarily `@cytoplasm`, also scaffolded at `@PM` | `MEK` binds scaffolded MEK; `PP2A` can bind through `PP2A.ERK`; `s~p` marks phosphorylated ERK type. | Dephosphorylation converts `pERK` molecule type to `ERK`. | +| `Oxo_EC` | 0 | none | none | `@EC` seed; one observable appears with `@cytoplasm`, likely inconsistent | Precursor/source species for `Oxo`. | Rule 8 converts it to `Oxo(R)`. | +| `PP2A` | 2 | `Arrestin`, `ERK` | none | Seeded at `@cytoplasm`; can be scaffolded at `@PM` | `Arrestin` binds arrestin; `ERK` appears bound to ERK/pERK in seed species. | Dephosphorylates pERK in rule 10. | +| `probe` | 1 | `site` | `site`: `u` | `@cytoplasm` | Reporter substrate in rule 16. | Converted to separate `phos_probe` type. | +| `phos_probe` | 1 | `Site0` | `Site0`: `p` | `@cytoplasm` | Reporter product in rule 16. | Separate molecule type rather than state transition on `probe`. | +| `GRK` | 1 | `RL` | none | `@PM` in seed/rules | `RL` binds `M1R.GRK`. | Catalyzes/marks receptor phosphorylation in rule 5. | +| `PP1` | 1 | `RL` | none | Seeded at `@cytoplasm`; one zero seed at `@PM` complex | `RL` can bind `M1R.PP1` in seed species, but no active rule uses it. | Declared/seeded but not active in rules. | +| `CK2` | 1 | `RL` | none | Seeded `@cytoplasm`; complex product at `@PM` | `RL` binds `M1R.CK2`. | Phosphorylates receptor in rule 18. | + +## 5. Compartments, anchors, initial species, and setup + +Compartments are `cytoplasm` (3D), `EC` (3D), and `PM` (2D). No anchors constrain molecule localization, so each rule’s `@compartment` prefixes define where reactants/products are matched. Initial species include large free `@PM:M1R`, `@EC:Oxo_EC`, cytoplasmic arrestin/MEK/ERK/PP2A/pERK/probe pools, PM-localized GRK, cytoplasmic PP1/CK2, and many zero-initialized receptor/arrestin/MEK/ERK/PP2A/GRK/CK2 complexes used as named starting states. + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** The model uses explicit compartment prefixes and mixed molecule-type conversion. Rules 1-3 and 6-7 build ligand/receptor/arrestin/MEK/ERK complexes by forming named site bonds. Rules 4-5 and 18 modify M1R `S228/S273`. Rules 10-12 and 15-16 convert ERK/probe molecule types while preserving catalytic/scaffold molecules on both sides. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `R_L_PM` | reversible | `@EC:Oxo.R` + `@PM:M1R.L`; requires `M1R.S228~u,S273~u` | `20.0 * washing_agonist, 4.0` | Forms/releases `Oxo.R!1`–`M1R.L!1`; product complex is at `@PM`. | Moves agonist binding into a PM receptor complex only during the `washing_agonist()` time window. | +| 2 | `RLppA` | reversible | phosphorylated ligand-bound `M1R.Arr` + `Arrestin.RLP` | `1.0 * RLpp_arrestin_binding_factor, 10.0 * RLpp_arrestin_binding_factor` | Forms/releases `M1R.Arr!2`–`Arrestin.RLP!2`; `M1R.S228/S273` remain `p`. | Arrestin binds phosphorylated agonist-bound receptor. | +| 3 | `RLA` | reversible | unphosphorylated ligand-bound `M1R.Arr` + `Arrestin.RLP` | `0.24 * negative_arrestin_binding, 2.8 * negative_arrestin_binding` | Forms/releases `M1R.Arr!2`–`Arrestin.RLP!2`; `M1R.S228/S273` remain `u`. | Allows weaker/differently scaled arrestin binding to unphosphorylated receptor. | +| 4 | `DeP_RLGRK_pp` | one-way | ligand-bound `M1R.S228~p,S273~p` | `0.5 * dephosphorylation_factor` | `M1R.S228 p→u` and `M1R.S273 p→u`; `Oxo.R!1`–`M1R.L!1` remains. | Dephosphorylates both receptor sites without requiring a bound phosphatase molecule. | +| 5 | `RLGRK_pp` | one-way | `M1R.GRK!2`–`GRK.RL!2` with ligand-bound unphosphorylated receptor | `0.9 * phos_factor_PP` | `M1R.S228 u→p` and `M1R.S273 u→p`; GRK bond remains. | GRK-bound receptor is phosphorylated at both modeled receptor sites. | +| 6 | `RLppAM` | reversible | phosphorylated receptor/arrestin complex, `Arrestin.MEK` + `MEK.Arr` | `0.1, 5.0E-5` | Forms/releases `Arrestin.MEK!3`–`MEK.Arr!3`. | Recruits MEK to phosphorylated receptor-bound arrestin scaffold. | +| 7 | `RLppAME` | reversible | scaffolded `MEK.ERK` + cytoplasmic `ERK.MEK`, `ERK.s~u` | `2.0, 2.5` | Forms/releases `MEK.ERK!4`–`ERK.MEK!4`. | Adds unphosphorylated ERK to the receptor/arrestin/MEK scaffold. | +| 8 | `Oxo_conversion` | one-way | `@EC:Oxo_EC` | `50.0` | Converts `Oxo_EC()` to `Oxo(R)` at `@EC`. | Generates receptor-binding agonist from precursor/source species. | +| 9 | `RLAPP2A` | reversible | unphosphorylated receptor/arrestin complex, `Arrestin.PP2A` + `PP2A.Arrestin` | `3.0E-5, 6.0E-5` | Forms/releases `Arrestin.PP2A!3`–`PP2A.Arrestin!3`. | Recruits PP2A to an arrestin-bound unphosphorylated receptor complex. | +| 10 | `DeP_pERK_PP2A` | reversible with zero reverse | scaffolded PP2A complex + cytoplasmic `pERK.s~p` | `9.0 * PP2A_dephos_factor, 0.0` | Converts free `pERK(MEK,s~p,PP2A,PP1)` to free `ERK(MEK,s~u,PP2A,PP1)`; PP2A scaffold is unchanged. | PP2A-containing receptor/arrestin complex catalytically dephosphorylates cytoplasmic pERK. | +| 11 | `RLppAMpE` | reversible | scaffolded `MEK.ERK!4`–`ERK.MEK!4`; `ERK.s~u` | `9.0 * MEK_effect, 0.36 * MEK_effect` | Converts bound `ERK(s~u)` molecule type to bound `pERK(s~p)` while preserving `MEK.ERK!4`–`pERK.MEK!4`. | MEK scaffold phosphorylates ERK while it remains bound to the MEK site. | +| 12 | `RLppAMpE_dissociation` | reversible with zero reverse | bound `MEK.ERK!4`–`pERK.MEK!4` | `2.0, 0.0` | Releases `pERK` from `MEK.ERK`; `MEK.ERK` becomes free and pERK moves to cytoplasm. | Irreversible-in-practice release of phosphorylated ERK from scaffold because reverse rate is zero. | +| 13 | `RL_GRK` | reversible | ligand-bound unphosphorylated `M1R.GRK` + `GRK.RL` at `@PM` | `4.0 * GRK_binding_factor, 4.0` | Forms/releases `M1R.GRK!2`–`GRK.RL!2`. | Recruits GRK to ligand-bound receptor before phosphorylation. | +| 14 | `RLGRK_pp_dissociation` | reversible | phosphorylated `M1R.GRK!2`–`GRK.RL!2` | `2.0 * RLGRK_pp_dissociation, 2.0 * RLGRK_pp_dissociation` | Releases/forms `M1R.GRK!2`–`GRK.RL!2`; receptor stays phosphorylated. | Lets GRK detach after receptor phosphorylation. | +| 15 | `ERK_balancing` | reversible | cytoplasmic `ERK.s~u` and `pERK.s~p` | `0.1, 1.0` | Converts free `ERK` molecule type to free `pERK`, and reverse converts `pERK` to `ERK`. | Background ERK phosphorylation/dephosphorylation balance independent of scaffold. | +| 16 | `P_probe` | reversible | cytoplasmic `pERK.s~p`, `probe.site~u`, `phos_probe.Site0~p` | `2.0, 2.0` | Forward converts `probe(site~u)` to `phos_probe(Site0~p)` while pERK is preserved; reverse converts reporter product back. | Reporter phosphorylation/dephosphorylation proxy driven by pERK presence. | +| 17 | `RL_CK2_binding` | reversible | ligand-bound unphosphorylated `M1R.CK2` + `CK2.RL` | `5.0E-5, 1.0` | Forms/releases `M1R.CK2!2`–`CK2.RL!2`; product complex is at `@PM`. | Recruits CK2 to ligand-bound receptor. | +| 18 | `RL_CK2_phos` | one-way | `M1R.CK2!2`–`CK2.RL!2` complex | `0.01` | `M1R.S228 u→p` and `M1R.S273 u→p`; CK2 bond remains. | CK2-bound receptor is phosphorylated at both modeled receptor sites. | +| 19 | `RL_CK2_phos_dissociation` | reversible | phosphorylated `M1R.CK2!2`–`CK2.RL!2` | `10.0, 10.0` | Releases/forms `M1R.CK2!2`–`CK2.RL!2`; receptor stays phosphorylated. | CK2 can detach from phosphorylated receptor or rebind it at the same rate. | + +## 7. Observables and technical readouts + +The 20 `Molecules` observables report compartment-specific pools or complexes: total PM M1R, EC agonist, cytoplasmic arrestin/MEK/ERK/pERK/PP2A/PP1/CK2, receptor-arrestin states (`O0_RLPPA`, `O0_RLA`), receptor phosphorylation (`O0_RLPP`), MEK/ERK scaffolded complexes (`O0_RLPPA_M`, `O0_RLppAME`, `O0_RLppAMpE`), PP2A scaffold recruitment (`O0_RLAPP2A`), and probe/phospho-probe totals. Note that `O0_Oxo_EC_tot` targets `@cytoplasm:Oxo_EC()` even though the seed and conversion rule place `Oxo_EC` at `@EC`; that observable may be inconsistent with the intended pool. + +## 8. Actions and simulation workflow + +The file calls `generate_network({max_iter=>6,max_agg=>10,max_stoich=>{...},overwrite=>1})`. This generates a bounded reaction network with high stoichiometry caps for all declared molecule types. No simulation command is included. + +## 9. Technical caveats and ambiguities + +- Several rate-factor identifiers are undeclared locally; this is the major execution caveat. +- The model has compartments but no anchors, so compartment correctness depends entirely on each pattern’s `@` prefix. +- `ERK` and `pERK` are separate molecule types, not one molecule type with `s~u~p`; conversion rules therefore change molecule identity as well as the apparent phosphorylation state. +- `PP1` is declared and seeded but does not participate in active reaction rules. diff --git a/data/summaries_detailed/Kocieniewski2012_MAPK_scaffold_ai_coder.md b/data/summaries_detailed/Kocieniewski2012_MAPK_scaffold_ai_coder.md new file mode 100644 index 00000000..d10981e6 --- /dev/null +++ b/data/summaries_detailed/Kocieniewski2012_MAPK_scaffold_ai_coder.md @@ -0,0 +1,98 @@ +# Coder Model Explanation: Kocieniewski 2012 + +## 1. Model identity and scope + +- **Model id:** `Kocieniewski_2012` +- **Title:** Kocieniewski 2012 +- **BNGL path:** `Published/Kocieniewski2012/Kocieniewski_2012.bngl` +- **YAML path:** `Published/Kocieniewski2012/metadata.yaml` +- **Metadata description:** The YAML says “Actin dynamics,” but the BNGL file is a scaffolded MAPK cascade. +- **Scope:** This model encodes a minimal MAP3K/MAP2K/MAPK cascade organized by a scaffold. `Scaff` has three independent docking sites (`map3k`, `map2k`, `mapk`). The kinases bind through their `s` docking sites. `MAP3K.S` switches between inactive `I` and active `A`; `MAP2K.R1/R2` and `MAPK.R1/R2` switch between unphosphorylated `Y` and phosphorylated `Yp`. Scaffold-bound active MAP3K phosphorylates scaffold-bound MAP2K, and fully phosphorylated scaffold-bound MAP2K phosphorylates scaffold-bound MAPK. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 10 parameters: four initial totals and six kinetic/control rates. | +| Compartments | No | No compartment block. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 4 molecule types: `MAP3K`, `MAP2K`, `MAPK`, `Scaff`. | +| Seed/species | Yes | 4 initial free species. | +| Observables | Yes | 2 scaffold-complex observables. | +| Functions | No | No functions block. | +| Reaction rules | Yes | 20 rules. | +| Actions | No | No action block or inline simulation command. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `Atot` | `1e5` | Initial MAP3K count. | +| `Btot` | `1e5` | Initial MAP2K count. | +| `Ctot` | `5e5` | Initial MAPK count. | +| `Stot` | `1e5` | Initial scaffold count. | +| `a` | `1e-6` | Forward scaffold docking rate for MAP3K, MAP2K, and MAPK binding rules. | +| `d1` | `0.1` | Reverse rate for reversible scaffold docking. | +| `d2` | `100` | One-way scaffold release for inactive MAP3K and doubly phosphorylated MAPK. | +| `pscaff` | `100` | Scaffold-local phosphorylation rate. | +| `u` | `0.1` | Global deactivation/dephosphorylation rate. | +| `S` | `1` | Basal MAP3K activation rate. | + +No functions are declared; all rule rates are direct parameters. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `MAP3K` | 2 | `s`, `S` | `S`: `I`, `A` | none | `s` docks to `Scaff.map3k`; `S` is activation state. | Only active `S~A` drives MAP2K phosphorylation on scaffold. | +| `MAP2K` | 3 | `s`, `R1`, `R2` | `R1`: `Y`, `Yp`; `R2`: `Y`, `Yp` | none | `s` docks to `Scaff.map2k`; `R1/R2` are phosphorylation sites. | Must have both `R1~Yp` and `R2~Yp` to phosphorylate MAPK in this file. | +| `MAPK` | 3 | `s`, `R1`, `R2` | `R1`: `Y`, `Yp`; `R2`: `Y`, `Yp` | none | `s` docks to `Scaff.mapk`; `R1/R2` are phosphorylation sites. | Doubly phosphorylated scaffold-bound MAPK has a special one-way release rule. | +| `Scaff` | 3 | `map3k`, `map2k`, `mapk` | none | none | Docking platform for one MAP3K, one MAP2K, and one MAPK. | Sites are distinct and typed by kinase layer. | + +## 5. Compartments, anchors, initial species, and setup + +No compartments or anchors are present. Initial species are all free: inactive `MAP3K(s,S~I)` at `Atot`, unphosphorylated `MAP2K(s,R1~Y,R2~Y)` at `Btot`, unphosphorylated `MAPK(s,R1~Y,R2~Y)` at `Ctot`, and empty `Scaff(map3k,map2k,mapk)` at `Stot`. + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 2-11 are scaffold docking/release rules using kinase `s` sites and matching scaffold sites. Rules 12-15 are scaffold-local phosphorylation rules where an upstream active kinase remains scaffold-bound while the downstream kinase’s `R1` or `R2` state changes. Rules 16-20 globally reverse activation/phosphorylation without requiring scaffold binding. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | `MAP3K.S` | `S` | `MAP3K.S I→A`; `MAP3K.s` remains free. | Basally activates MAP3K before or independent of scaffold docking. | +| 2 | `Unlabeled` | reversible | `MAP3K.s` + `Scaff.map3k` | `a, d1` | Forms/releases `MAP3K.s!1`–`Scaff.map3k!1` for active `MAP3K.S~A`. | Docks active MAP3K onto the scaffold’s MAP3K slot. | +| 3 | `Unlabeled` | one-way | `MAP3K.s!1` + `Scaff.map3k!1` | `d2` | Releases `MAP3K.s!1`–`Scaff.map3k!1` for inactive `MAP3K.S~I`. | Forces inactive scaffold-bound MAP3K off the scaffold. | +| 4 | `Unlabeled` | reversible | `MAP2K.s` + `Scaff.map2k`; `MAP2K.R1~Y,R2~Y` | `a, d1` | Forms/releases `MAP2K.s!1`–`Scaff.map2k!1`. | Docks completely unphosphorylated MAP2K. | +| 5 | `Unlabeled` | reversible | `MAP2K.s` + `Scaff.map2k`; `MAP2K.R1~Yp,R2~Y` | `a, d1` | Forms/releases `MAP2K.s!1`–`Scaff.map2k!1`. | Docks MAP2K already phosphorylated at `R1` only. | +| 6 | `Unlabeled` | reversible | `MAP2K.s` + `Scaff.map2k`; `MAP2K.R1~Y,R2~Yp` | `a, d1` | Forms/releases `MAP2K.s!1`–`Scaff.map2k!1`. | Docks MAP2K already phosphorylated at `R2` only. | +| 7 | `Unlabeled` | reversible | `MAP2K.s` + `Scaff.map2k`; `MAP2K.R1~Yp,R2~Yp` | `a, d1` | Forms/releases `MAP2K.s!1`–`Scaff.map2k!1`. | Docks doubly phosphorylated MAP2K, which can support MAPK phosphorylation in rules 14-15. | +| 8 | `Unlabeled` | reversible | `MAPK.s` + `Scaff.mapk`; `MAPK.R1~Y,R2~Y` | `a, d1` | Forms/releases `MAPK.s!1`–`Scaff.mapk!1`. | Docks unphosphorylated MAPK. | +| 9 | `Unlabeled` | reversible | `MAPK.s` + `Scaff.mapk`; `MAPK.R1~Yp,R2~Y` | `a, d1` | Forms/releases `MAPK.s!1`–`Scaff.mapk!1`. | Docks MAPK phosphorylated at `R1` only. | +| 10 | `Unlabeled` | reversible | `MAPK.s` + `Scaff.mapk`; `MAPK.R1~Y,R2~Yp` | `a, d1` | Forms/releases `MAPK.s!1`–`Scaff.mapk!1`. | Docks MAPK phosphorylated at `R2` only. | +| 11 | `Unlabeled` | one-way | `MAPK.s!1` + `Scaff.mapk!1`; `MAPK.R1~Yp,R2~Yp` | `d2` | Releases doubly phosphorylated `MAPK.s!1`–`Scaff.mapk!1`. | Removes fully phosphorylated MAPK from the scaffold after signal completion. | +| 12 | `Unlabeled` | one-way | `MAP3K.S~A`, `MAP3K.s!1`–`Scaff.map3k!1`, `MAP2K.s!2`–`Scaff.map2k!2`, `MAP2K.R1~Y` | `pscaff` | `MAP2K.R1 Y→Yp`; all scaffold bonds remain. | Active scaffold-bound MAP3K phosphorylates scaffold-bound MAP2K site `R1`. | +| 13 | `Unlabeled` | one-way | Same scaffolded MAP3K/MAP2K complex, `MAP2K.R2~Y` | `pscaff` | `MAP2K.R2 Y→Yp`; all scaffold bonds remain. | Active scaffold-bound MAP3K phosphorylates MAP2K site `R2`. | +| 14 | `Unlabeled` | one-way | `MAP2K.R1~Yp,R2~Yp`, `MAP2K.s!2`–`Scaff.map2k!2`, `MAPK.s!1`–`Scaff.mapk!1`, `MAPK.R1~Y` | `pscaff` | `MAPK.R1 Y→Yp`; scaffold bonds remain. | Fully phosphorylated scaffold-bound MAP2K phosphorylates scaffold-bound MAPK site `R1`. | +| 15 | `Unlabeled` | one-way | Same scaffolded MAP2K/MAPK complex, `MAPK.R2~Y` | `pscaff` | `MAPK.R2 Y→Yp`; scaffold bonds remain. | Fully phosphorylated scaffold-bound MAP2K phosphorylates MAPK site `R2`. | +| 16 | `Unlabeled` | one-way | `MAP3K.S~A` | `u` | `MAP3K.S A→I`. | Global MAP3K deactivation; pattern does not require a scaffold bond. | +| 17 | `Unlabeled` | one-way | `MAP2K.R1~Yp` | `u` | `MAP2K.R1 Yp→Y`. | Global dephosphorylation of MAP2K site `R1`. | +| 18 | `Unlabeled` | one-way | `MAP2K.R2~Yp` | `u` | `MAP2K.R2 Yp→Y`. | Global dephosphorylation of MAP2K site `R2`. | +| 19 | `Unlabeled` | one-way | `MAPK.R1~Yp` | `u` | `MAPK.R1 Yp→Y`. | Global dephosphorylation of MAPK site `R1`. | +| 20 | `Unlabeled` | one-way | `MAPK.R2~Yp` | `u` | `MAPK.R2 Yp→Y`. | Global dephosphorylation of MAPK site `R2`. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `MAPKchainone` | `Molecules` | `MAPK(s!1,R1~Yp).Scaff(mapk!1,map2k!2).MAP2K(s!2,R1~Yp,R2~Yp)` | Counts scaffold complexes containing scaffold-bound MAPK phosphorylated at `R1` and scaffold-bound doubly phosphorylated MAP2K. | +| `MAPKchaintwo` | `Molecules` | `MAP3K(s!1,S~A).Scaff(map3k!1,map2k!2).MAP2K(s!2,R1~Yp,R2~Yp)` | Counts scaffold complexes containing active scaffold-bound MAP3K and scaffold-bound doubly phosphorylated MAP2K. | + +## 8. Actions and simulation workflow + +No action block or inline simulation command is declared. The BNGL file defines the network logic; the caller must choose generation and simulation settings externally. + +## 9. Technical caveats and ambiguities + +- The YAML description does not match the BNGL cascade; this summary follows the BNGL file. +- Rules 12-15 require scaffold colocalization through explicit bonds; they are not free-solution phosphorylation rules. +- Rules 16-20 use partial patterns, so they can dephosphorylate matching molecules whether free or scaffold-bound unless other generated-context constraints apply. diff --git a/data/summaries_detailed/Kocieniewski2012_MAPK_scaffold_coder.md b/data/summaries_detailed/Kocieniewski2012_MAPK_scaffold_coder.md new file mode 100644 index 00000000..d10981e6 --- /dev/null +++ b/data/summaries_detailed/Kocieniewski2012_MAPK_scaffold_coder.md @@ -0,0 +1,98 @@ +# Coder Model Explanation: Kocieniewski 2012 + +## 1. Model identity and scope + +- **Model id:** `Kocieniewski_2012` +- **Title:** Kocieniewski 2012 +- **BNGL path:** `Published/Kocieniewski2012/Kocieniewski_2012.bngl` +- **YAML path:** `Published/Kocieniewski2012/metadata.yaml` +- **Metadata description:** The YAML says “Actin dynamics,” but the BNGL file is a scaffolded MAPK cascade. +- **Scope:** This model encodes a minimal MAP3K/MAP2K/MAPK cascade organized by a scaffold. `Scaff` has three independent docking sites (`map3k`, `map2k`, `mapk`). The kinases bind through their `s` docking sites. `MAP3K.S` switches between inactive `I` and active `A`; `MAP2K.R1/R2` and `MAPK.R1/R2` switch between unphosphorylated `Y` and phosphorylated `Yp`. Scaffold-bound active MAP3K phosphorylates scaffold-bound MAP2K, and fully phosphorylated scaffold-bound MAP2K phosphorylates scaffold-bound MAPK. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 10 parameters: four initial totals and six kinetic/control rates. | +| Compartments | No | No compartment block. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 4 molecule types: `MAP3K`, `MAP2K`, `MAPK`, `Scaff`. | +| Seed/species | Yes | 4 initial free species. | +| Observables | Yes | 2 scaffold-complex observables. | +| Functions | No | No functions block. | +| Reaction rules | Yes | 20 rules. | +| Actions | No | No action block or inline simulation command. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `Atot` | `1e5` | Initial MAP3K count. | +| `Btot` | `1e5` | Initial MAP2K count. | +| `Ctot` | `5e5` | Initial MAPK count. | +| `Stot` | `1e5` | Initial scaffold count. | +| `a` | `1e-6` | Forward scaffold docking rate for MAP3K, MAP2K, and MAPK binding rules. | +| `d1` | `0.1` | Reverse rate for reversible scaffold docking. | +| `d2` | `100` | One-way scaffold release for inactive MAP3K and doubly phosphorylated MAPK. | +| `pscaff` | `100` | Scaffold-local phosphorylation rate. | +| `u` | `0.1` | Global deactivation/dephosphorylation rate. | +| `S` | `1` | Basal MAP3K activation rate. | + +No functions are declared; all rule rates are direct parameters. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `MAP3K` | 2 | `s`, `S` | `S`: `I`, `A` | none | `s` docks to `Scaff.map3k`; `S` is activation state. | Only active `S~A` drives MAP2K phosphorylation on scaffold. | +| `MAP2K` | 3 | `s`, `R1`, `R2` | `R1`: `Y`, `Yp`; `R2`: `Y`, `Yp` | none | `s` docks to `Scaff.map2k`; `R1/R2` are phosphorylation sites. | Must have both `R1~Yp` and `R2~Yp` to phosphorylate MAPK in this file. | +| `MAPK` | 3 | `s`, `R1`, `R2` | `R1`: `Y`, `Yp`; `R2`: `Y`, `Yp` | none | `s` docks to `Scaff.mapk`; `R1/R2` are phosphorylation sites. | Doubly phosphorylated scaffold-bound MAPK has a special one-way release rule. | +| `Scaff` | 3 | `map3k`, `map2k`, `mapk` | none | none | Docking platform for one MAP3K, one MAP2K, and one MAPK. | Sites are distinct and typed by kinase layer. | + +## 5. Compartments, anchors, initial species, and setup + +No compartments or anchors are present. Initial species are all free: inactive `MAP3K(s,S~I)` at `Atot`, unphosphorylated `MAP2K(s,R1~Y,R2~Y)` at `Btot`, unphosphorylated `MAPK(s,R1~Y,R2~Y)` at `Ctot`, and empty `Scaff(map3k,map2k,mapk)` at `Stot`. + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 2-11 are scaffold docking/release rules using kinase `s` sites and matching scaffold sites. Rules 12-15 are scaffold-local phosphorylation rules where an upstream active kinase remains scaffold-bound while the downstream kinase’s `R1` or `R2` state changes. Rules 16-20 globally reverse activation/phosphorylation without requiring scaffold binding. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | `MAP3K.S` | `S` | `MAP3K.S I→A`; `MAP3K.s` remains free. | Basally activates MAP3K before or independent of scaffold docking. | +| 2 | `Unlabeled` | reversible | `MAP3K.s` + `Scaff.map3k` | `a, d1` | Forms/releases `MAP3K.s!1`–`Scaff.map3k!1` for active `MAP3K.S~A`. | Docks active MAP3K onto the scaffold’s MAP3K slot. | +| 3 | `Unlabeled` | one-way | `MAP3K.s!1` + `Scaff.map3k!1` | `d2` | Releases `MAP3K.s!1`–`Scaff.map3k!1` for inactive `MAP3K.S~I`. | Forces inactive scaffold-bound MAP3K off the scaffold. | +| 4 | `Unlabeled` | reversible | `MAP2K.s` + `Scaff.map2k`; `MAP2K.R1~Y,R2~Y` | `a, d1` | Forms/releases `MAP2K.s!1`–`Scaff.map2k!1`. | Docks completely unphosphorylated MAP2K. | +| 5 | `Unlabeled` | reversible | `MAP2K.s` + `Scaff.map2k`; `MAP2K.R1~Yp,R2~Y` | `a, d1` | Forms/releases `MAP2K.s!1`–`Scaff.map2k!1`. | Docks MAP2K already phosphorylated at `R1` only. | +| 6 | `Unlabeled` | reversible | `MAP2K.s` + `Scaff.map2k`; `MAP2K.R1~Y,R2~Yp` | `a, d1` | Forms/releases `MAP2K.s!1`–`Scaff.map2k!1`. | Docks MAP2K already phosphorylated at `R2` only. | +| 7 | `Unlabeled` | reversible | `MAP2K.s` + `Scaff.map2k`; `MAP2K.R1~Yp,R2~Yp` | `a, d1` | Forms/releases `MAP2K.s!1`–`Scaff.map2k!1`. | Docks doubly phosphorylated MAP2K, which can support MAPK phosphorylation in rules 14-15. | +| 8 | `Unlabeled` | reversible | `MAPK.s` + `Scaff.mapk`; `MAPK.R1~Y,R2~Y` | `a, d1` | Forms/releases `MAPK.s!1`–`Scaff.mapk!1`. | Docks unphosphorylated MAPK. | +| 9 | `Unlabeled` | reversible | `MAPK.s` + `Scaff.mapk`; `MAPK.R1~Yp,R2~Y` | `a, d1` | Forms/releases `MAPK.s!1`–`Scaff.mapk!1`. | Docks MAPK phosphorylated at `R1` only. | +| 10 | `Unlabeled` | reversible | `MAPK.s` + `Scaff.mapk`; `MAPK.R1~Y,R2~Yp` | `a, d1` | Forms/releases `MAPK.s!1`–`Scaff.mapk!1`. | Docks MAPK phosphorylated at `R2` only. | +| 11 | `Unlabeled` | one-way | `MAPK.s!1` + `Scaff.mapk!1`; `MAPK.R1~Yp,R2~Yp` | `d2` | Releases doubly phosphorylated `MAPK.s!1`–`Scaff.mapk!1`. | Removes fully phosphorylated MAPK from the scaffold after signal completion. | +| 12 | `Unlabeled` | one-way | `MAP3K.S~A`, `MAP3K.s!1`–`Scaff.map3k!1`, `MAP2K.s!2`–`Scaff.map2k!2`, `MAP2K.R1~Y` | `pscaff` | `MAP2K.R1 Y→Yp`; all scaffold bonds remain. | Active scaffold-bound MAP3K phosphorylates scaffold-bound MAP2K site `R1`. | +| 13 | `Unlabeled` | one-way | Same scaffolded MAP3K/MAP2K complex, `MAP2K.R2~Y` | `pscaff` | `MAP2K.R2 Y→Yp`; all scaffold bonds remain. | Active scaffold-bound MAP3K phosphorylates MAP2K site `R2`. | +| 14 | `Unlabeled` | one-way | `MAP2K.R1~Yp,R2~Yp`, `MAP2K.s!2`–`Scaff.map2k!2`, `MAPK.s!1`–`Scaff.mapk!1`, `MAPK.R1~Y` | `pscaff` | `MAPK.R1 Y→Yp`; scaffold bonds remain. | Fully phosphorylated scaffold-bound MAP2K phosphorylates scaffold-bound MAPK site `R1`. | +| 15 | `Unlabeled` | one-way | Same scaffolded MAP2K/MAPK complex, `MAPK.R2~Y` | `pscaff` | `MAPK.R2 Y→Yp`; scaffold bonds remain. | Fully phosphorylated scaffold-bound MAP2K phosphorylates MAPK site `R2`. | +| 16 | `Unlabeled` | one-way | `MAP3K.S~A` | `u` | `MAP3K.S A→I`. | Global MAP3K deactivation; pattern does not require a scaffold bond. | +| 17 | `Unlabeled` | one-way | `MAP2K.R1~Yp` | `u` | `MAP2K.R1 Yp→Y`. | Global dephosphorylation of MAP2K site `R1`. | +| 18 | `Unlabeled` | one-way | `MAP2K.R2~Yp` | `u` | `MAP2K.R2 Yp→Y`. | Global dephosphorylation of MAP2K site `R2`. | +| 19 | `Unlabeled` | one-way | `MAPK.R1~Yp` | `u` | `MAPK.R1 Yp→Y`. | Global dephosphorylation of MAPK site `R1`. | +| 20 | `Unlabeled` | one-way | `MAPK.R2~Yp` | `u` | `MAPK.R2 Yp→Y`. | Global dephosphorylation of MAPK site `R2`. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `MAPKchainone` | `Molecules` | `MAPK(s!1,R1~Yp).Scaff(mapk!1,map2k!2).MAP2K(s!2,R1~Yp,R2~Yp)` | Counts scaffold complexes containing scaffold-bound MAPK phosphorylated at `R1` and scaffold-bound doubly phosphorylated MAP2K. | +| `MAPKchaintwo` | `Molecules` | `MAP3K(s!1,S~A).Scaff(map3k!1,map2k!2).MAP2K(s!2,R1~Yp,R2~Yp)` | Counts scaffold complexes containing active scaffold-bound MAP3K and scaffold-bound doubly phosphorylated MAP2K. | + +## 8. Actions and simulation workflow + +No action block or inline simulation command is declared. The BNGL file defines the network logic; the caller must choose generation and simulation settings externally. + +## 9. Technical caveats and ambiguities + +- The YAML description does not match the BNGL cascade; this summary follows the BNGL file. +- Rules 12-15 require scaffold colocalization through explicit bonds; they are not free-solution phosphorylation rules. +- Rules 16-20 use partial patterns, so they can dephosphorylate matching molecules whether free or scaffold-bound unless other generated-context constraints apply. diff --git a/data/summaries_detailed/Ligon2014_lipoplex_delivery_ai_coder.md b/data/summaries_detailed/Ligon2014_lipoplex_delivery_ai_coder.md new file mode 100644 index 00000000..fd60d042 --- /dev/null +++ b/data/summaries_detailed/Ligon2014_lipoplex_delivery_ai_coder.md @@ -0,0 +1,124 @@ +# Coder Model Explanation: Ligon 2014 + +## 1. Model identity and scope + +- **Model id:** `Ligon_2014` +- **Title:** Ligon 2014 +- **BNGL path:** `Published/Ligon2014/Ligon_2014.bngl` +- **YAML path:** `Published/Ligon2014/metadata.yaml` +- **Metadata description:** Lipoplex delivery +- **Scope:** This NFsim-oriented model tracks external lipoplexes (`Lext`) attaching to pit/endosome carrier sites (`Pit.l1` through `Pit.l10`), pit-to-endosome conversion through `Pit.s p→e`, lysis into internal lipoplexes (`Lint`) with cargo-number state `n`, unpacking into population `mRNA`, translation to population `GFP`, degradation into `Trash`, and a `Timer` population that switches on washout through the `wash` function. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 11 kinetic/control parameters for attachment, endocytosis, lysis, unpacking, translation, wash/degradation, and fast cleanup. | +| Compartments | No | No BNGL compartment block; external/internal/endosome distinctions are encoded as molecule names and `Pit.s` states. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 8 molecule types, including population types for `mRNA`, `GFP`, `I`, and `Timer`. | +| Seed/species | Yes | 16 seed species: 11 `Lext` cargo-number states, one pit, and population/readout species. | +| Observables | Yes | 7 active observables. | +| Functions | Yes | 1 function, `wash`, controlled by `TimerCount`. | +| Reaction rules | Yes | 33 active rules; many higher-occupancy expansions are commented out and excluded. | +| Actions | Yes | One `simulate_nf` command. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `kFast` | `1e20` | Declared but not used by active rules. | +| `kA` | `0.016*3600` | Lipoplex attachment rate to pit slots `l1`-`l7`. | +| `kE` | `0.45*3600` | Pit-to-endosome conversion rate for occupied pits; rules use `DeleteMolecules`. | +| `kL` | `0.4*3600` | Endosome lysis rate converting bound external lipoplex cargo to internal `Lint`. | +| `kU` | `0.4*3600` | Unpacking rate converting `Lint(n~345/346)` to five `mRNA` population increments. | +| `kTL` | `100.0*3600` | Translation rate: `mRNA -> mRNA + GFP`. | +| `dW` | `0` | Wash parameter declared but not used; active wash uses function `wash`. | +| `dM` | `0.051*3600` | mRNA degradation to `Trash`. | +| `dG` | `0.056*3600` | GFP degradation to `Trash`. | +| `dL` | `0.01*3600` | Internal lipoplex degradation to `Trash`. | +| `dE` | `1.0*3600` | Empty endosome degradation to `Trash`. | + +| Function | Technical interpretation | +| --- | --- | +| `wash = if(TimerCount>3600,1e20,0)` | Wash rate is zero until the `TimerCount` observable exceeds 3600, then external `Lext` is sent to `Trash` at a very large rate. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Lext` | 2 | `p`, `n` | `n`: `345`-`355` | none | `p` binds a pit slot; `n` stores cargo-number state. | External lipoplex. Active rules use `n~345`-`355` for lysis and `p` bonds to pit slots. | +| `Pit` | 11 | `s`, `l1`-`l10` | `s`: `p`, `e` | none | `s` distinguishes pit/endosome; `l1`-`l10` are lipoplex attachment slots. | Active attachment rules fill `l1` through `l7`; active endocytosis rules cover one through five occupied slots. | +| `Lint` | 1 | `n` | `n`: `345`-`355` | none | Internal cargo state; no binding site. | Product of endosome lysis. | +| `mRNA` | 0 | population molecule | none | none | Population count species. | Produced by unpacking and preserved during translation. | +| `GFP` | 0 | population molecule | none | none | Population count species. | Produced from mRNA and degraded to Trash. | +| `Trash` | 0 | none | none | none | Sink species. | Receives washed/degraded material. | +| `I` | 0 | population molecule | none | none | Timer catalyst/source. | Preserved while producing `Timer`. | +| `Timer` | 0 | population molecule | none | none | Timer count for wash function. | Drives `wash` indirectly through observable `TimerCount`. | + +## 5. Compartments, anchors, initial species, and setup + +No compartments or anchors are declared. Initial `Lext` is distributed across cargo states `n~345` through `n~355` with counts `1,2,6,12,18,20,18,12,6,3,1`. One empty pit starts in state `Pit.s~p` with all ten `l` slots free. `mRNA`, `GFP`, and `Timer` start at zero; `I` starts at one and catalytically produces timer population. + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 2-8 sequentially add external lipoplexes to pit slots `l1`-`l7`; each new `Lext.p` site bonds to the next open `Pit.l*` site. Rules 9-13 convert occupied pits to endosomes by changing `Pit.s p→e` while preserving existing `Lext.p`/`Pit.l*` bonds and using `DeleteMolecules`. Rules 15-26 lyse endosomes and discard the pit/bonds while creating internal `Lint` cargo states. Rules 28-29 unpack only `Lint.n~345` and `Lint.n~346` in the active source. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | `Lext.p`, `Lext.n` | `wash` | `Lext(p,n) → Trash`; no pit bond required. | Removes any external lipoplex after the timer-gated wash turns on. | +| 2 | `Unlabeled` | one-way | free `Lext.p` + free `Pit.l1`, `Pit.s~p` | `kA` | Forms `Lext.p!1`–`Pit.l1!1`; also creates a new free `Pit(s~p,...)` product. | First lipoplex attaches to slot `l1`; the extra free pit product in the rule is a source-like amplification term in the active BNGL. | +| 3 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l2` on a pit already carrying `l1!1` | `kA` | Forms `Lext.p!2`–`Pit.l2!2`; preserves the existing `l1!1` bond. | Adds a second lipoplex to slot `l2`. | +| 4 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l3` on a two-lipoplex pit | `kA` | Forms `Lext.p!3`–`Pit.l3!3`; preserves `l1!1,l2!2`. | Adds a third lipoplex to slot `l3`. | +| 5 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l4` | `kA` | Forms `Lext.p!4`–`Pit.l4!4`; preserves earlier slot bonds. | Adds a fourth lipoplex to slot `l4`. | +| 6 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l5` | `kA` | Forms `Lext.p!5`–`Pit.l5!5`. | Adds a fifth lipoplex to slot `l5`. | +| 7 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l6` | `kA` | Forms `Lext.p!6`–`Pit.l6!6`. | Adds a sixth lipoplex to slot `l6`. | +| 8 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l7` | `kA` | Forms `Lext.p!7`–`Pit.l7!7`. | Adds a seventh lipoplex to slot `l7`; higher slot rules are commented out. | +| 9 | `Unlabeled` | one-way | one-lipoplex pit: `Lext.p!1`–`Pit.l1!1`, `Pit.s~p` | `kE DeleteMolecules` | `Pit.s p→e`; preserves `l1!1`; deletes unmatched molecules from the reactant complex context. | Converts a one-lipoplex pit into an endosome. | +| 10 | `Unlabeled` | one-way | two-lipoplex pit: bonds at `l1!1,l2!2`, `Pit.s~p` | `kE DeleteMolecules` | `Pit.s p→e`; preserves bonds at `l1,l2`. | Converts a two-lipoplex pit into an endosome. | +| 11 | `Unlabeled` | one-way | three-lipoplex pit: bonds at `l1!1,l2!2,l3!3` | `kE DeleteMolecules` | `Pit.s p→e`; preserves bonds at `l1`-`l3`. | Converts a three-lipoplex pit into an endosome. | +| 12 | `Unlabeled` | one-way | four-lipoplex pit: bonds at `l1!1`-`l4!4` | `kE DeleteMolecules` | `Pit.s p→e`; preserves bonds at `l1`-`l4`. | Converts a four-lipoplex pit into an endosome. | +| 13 | `Unlabeled` | one-way | five-lipoplex pit: bonds at `l1!1`-`l5!5` | `kE DeleteMolecules` | `Pit.s p→e`; preserves bonds at `l1`-`l5`. | Converts a five-lipoplex pit into an endosome; the source comments say five more endocytosis rules would be needed. | +| 14 | `Unlabeled` | one-way | empty `Pit.s~e` with all `l1`-`l10` free | `dE` | `Pit(s~e, free slots) → Trash`. | Degrades an empty endosome. | +| 15 | `Unlabeled` | one-way | `Lext.p!1,n~345` bound to `Pit.s~e,l1!1` | `kL` | Releases/deletes the endosome complex and creates `Lint(n~345)`. | Lyses a one-lipoplex endosome carrying `n~345`. | +| 16 | `Unlabeled` | one-way | `Lext.p!1,n~346` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~346)`. | Lyses a one-lipoplex endosome carrying `n~346`. | +| 17 | `Unlabeled` | one-way | `Lext.p!1,n~347` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~347)`. | Lyses a one-lipoplex endosome carrying `n~347`. | +| 18 | `Unlabeled` | one-way | `Lext.p!1,n~348` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~348)`. | Lyses a one-lipoplex endosome carrying `n~348`. | +| 19 | `Unlabeled` | one-way | `Lext.p!1,n~349` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~349)`. | Lyses a one-lipoplex endosome carrying `n~349`. | +| 20 | `Unlabeled` | one-way | `Lext.p!1,n~350` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~350)`. | Lyses a one-lipoplex endosome carrying `n~350`. | +| 21 | `Unlabeled` | one-way | `Lext.p!1,n~351` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~351)`. | Lyses a one-lipoplex endosome carrying `n~351`. | +| 22 | `Unlabeled` | one-way | `Lext.p!1,n~352` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~352)`. | Lyses a one-lipoplex endosome carrying `n~352`. | +| 23 | `Unlabeled` | one-way | `Lext.p!1,n~353` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~353)`. | Lyses a one-lipoplex endosome carrying `n~353`. | +| 24 | `Unlabeled` | one-way | `Lext.p!1,n~354` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~354)`. | Lyses a one-lipoplex endosome carrying `n~354`. | +| 25 | `Unlabeled` | one-way | `Lext.p!1,n~355` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~355)`. | Lyses a one-lipoplex endosome carrying `n~355`. | +| 26 | `Unlabeled` | one-way | two `Lext` molecules both `n~345`, bound at `Pit.l1!1` and `Pit.l2!2` in an endosome | `kL` | Creates two `Lint(n~345)` products; pit/endosome complex is consumed. | Special two-lipoplex lysis case for the `345/345` cargo-state pair only. | +| 27 | `Unlabeled` | one-way | `Lint` any `n` state | `dL` | `Lint → Trash`. | Degrades internal lipoplex cargo regardless of `n` state. | +| 28 | `Unlabeled` | one-way | `Lint.n~345` | `kU` | `Lint(n~345) → 5 mRNA`. | Unpacks an internal `n~345` lipoplex into five population mRNA increments, not 345 mRNA. | +| 29 | `Unlabeled` | one-way | `Lint.n~346` | `kU` | `Lint(n~346) → 5 mRNA`. | Unpacks an internal `n~346` lipoplex into five mRNA increments; other `n` states have no active unpacking rule. | +| 30 | `Unlabeled` | one-way | population `mRNA` | `dM` | `mRNA → Trash`. | Degrades one mRNA population unit. | +| 31 | `Unlabeled` | one-way | population `mRNA` | `kTL` | `mRNA → mRNA + GFP`. | Translates GFP while preserving the mRNA population unit. | +| 32 | `Unlabeled` | one-way | population `GFP` | `dG` | `GFP → Trash`. | Degrades GFP. | +| 33 | `Unlabeled` | one-way | population `I` | `1` | `I → I + Timer`. | Preserves timer source `I` and increments `Timer`, which eventually activates `wash`. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Lext` | `Molecules` | `Lext(p,n)` | Counts external lipoplex molecules with unbound `p` and any declared `n` state. Bound `Lext(p!*,n)` is not matched by this exact free-site pattern. | +| `Pit` | `Molecules` | `Pit(s~p)` | Counts pit-state `Pit` molecules regardless of slot occupancy. | +| `Endo` | `Molecules` | `Pit(s~e)` | Counts endosome-state `Pit` molecules. | +| `Lint` | `Molecules` | `Lint()` | Counts internal lipoplex molecules across all `n` states. | +| `mRNA` | `Molecules` | `mRNA` | Counts mRNA population units. | +| `GFP` | `Molecules` | `GFP` | Counts GFP population units. | +| `TimerCount` | `Molecules` | `Timer` | Counts timer population units and feeds the `wash` function. | + +## 8. Actions and simulation workflow + +`simulate_nf({suffix=>nf,t_end=>30*3600,n_steps=>300});` runs an NFsim simulation for 30 hours of model time with 300 output steps. The commented `writeXML()` is inactive. + +## 9. Technical caveats and ambiguities + +- The active rule set is deliberately incomplete relative to the comments: higher pit occupancies, many lysis combinations, and most unpacking states are commented out or summarized by comments rather than active BNGL rules. +- Rule 2 creates an additional free `Pit` product while binding the first lipoplex; this is unusual and should be verified against the intended delivery model. +- Population declarations make this NFsim-oriented; some standalone deterministic workflows may not treat population species the same way. +- `dW` and `kFast` are declared but not used by active rules. diff --git a/data/summaries_detailed/Ligon2014_lipoplex_delivery_coder.md b/data/summaries_detailed/Ligon2014_lipoplex_delivery_coder.md new file mode 100644 index 00000000..fd60d042 --- /dev/null +++ b/data/summaries_detailed/Ligon2014_lipoplex_delivery_coder.md @@ -0,0 +1,124 @@ +# Coder Model Explanation: Ligon 2014 + +## 1. Model identity and scope + +- **Model id:** `Ligon_2014` +- **Title:** Ligon 2014 +- **BNGL path:** `Published/Ligon2014/Ligon_2014.bngl` +- **YAML path:** `Published/Ligon2014/metadata.yaml` +- **Metadata description:** Lipoplex delivery +- **Scope:** This NFsim-oriented model tracks external lipoplexes (`Lext`) attaching to pit/endosome carrier sites (`Pit.l1` through `Pit.l10`), pit-to-endosome conversion through `Pit.s p→e`, lysis into internal lipoplexes (`Lint`) with cargo-number state `n`, unpacking into population `mRNA`, translation to population `GFP`, degradation into `Trash`, and a `Timer` population that switches on washout through the `wash` function. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 11 kinetic/control parameters for attachment, endocytosis, lysis, unpacking, translation, wash/degradation, and fast cleanup. | +| Compartments | No | No BNGL compartment block; external/internal/endosome distinctions are encoded as molecule names and `Pit.s` states. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 8 molecule types, including population types for `mRNA`, `GFP`, `I`, and `Timer`. | +| Seed/species | Yes | 16 seed species: 11 `Lext` cargo-number states, one pit, and population/readout species. | +| Observables | Yes | 7 active observables. | +| Functions | Yes | 1 function, `wash`, controlled by `TimerCount`. | +| Reaction rules | Yes | 33 active rules; many higher-occupancy expansions are commented out and excluded. | +| Actions | Yes | One `simulate_nf` command. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `kFast` | `1e20` | Declared but not used by active rules. | +| `kA` | `0.016*3600` | Lipoplex attachment rate to pit slots `l1`-`l7`. | +| `kE` | `0.45*3600` | Pit-to-endosome conversion rate for occupied pits; rules use `DeleteMolecules`. | +| `kL` | `0.4*3600` | Endosome lysis rate converting bound external lipoplex cargo to internal `Lint`. | +| `kU` | `0.4*3600` | Unpacking rate converting `Lint(n~345/346)` to five `mRNA` population increments. | +| `kTL` | `100.0*3600` | Translation rate: `mRNA -> mRNA + GFP`. | +| `dW` | `0` | Wash parameter declared but not used; active wash uses function `wash`. | +| `dM` | `0.051*3600` | mRNA degradation to `Trash`. | +| `dG` | `0.056*3600` | GFP degradation to `Trash`. | +| `dL` | `0.01*3600` | Internal lipoplex degradation to `Trash`. | +| `dE` | `1.0*3600` | Empty endosome degradation to `Trash`. | + +| Function | Technical interpretation | +| --- | --- | +| `wash = if(TimerCount>3600,1e20,0)` | Wash rate is zero until the `TimerCount` observable exceeds 3600, then external `Lext` is sent to `Trash` at a very large rate. | + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `Lext` | 2 | `p`, `n` | `n`: `345`-`355` | none | `p` binds a pit slot; `n` stores cargo-number state. | External lipoplex. Active rules use `n~345`-`355` for lysis and `p` bonds to pit slots. | +| `Pit` | 11 | `s`, `l1`-`l10` | `s`: `p`, `e` | none | `s` distinguishes pit/endosome; `l1`-`l10` are lipoplex attachment slots. | Active attachment rules fill `l1` through `l7`; active endocytosis rules cover one through five occupied slots. | +| `Lint` | 1 | `n` | `n`: `345`-`355` | none | Internal cargo state; no binding site. | Product of endosome lysis. | +| `mRNA` | 0 | population molecule | none | none | Population count species. | Produced by unpacking and preserved during translation. | +| `GFP` | 0 | population molecule | none | none | Population count species. | Produced from mRNA and degraded to Trash. | +| `Trash` | 0 | none | none | none | Sink species. | Receives washed/degraded material. | +| `I` | 0 | population molecule | none | none | Timer catalyst/source. | Preserved while producing `Timer`. | +| `Timer` | 0 | population molecule | none | none | Timer count for wash function. | Drives `wash` indirectly through observable `TimerCount`. | + +## 5. Compartments, anchors, initial species, and setup + +No compartments or anchors are declared. Initial `Lext` is distributed across cargo states `n~345` through `n~355` with counts `1,2,6,12,18,20,18,12,6,3,1`. One empty pit starts in state `Pit.s~p` with all ten `l` slots free. `mRNA`, `GFP`, and `Timer` start at zero; `I` starts at one and catalytically produces timer population. + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 2-8 sequentially add external lipoplexes to pit slots `l1`-`l7`; each new `Lext.p` site bonds to the next open `Pit.l*` site. Rules 9-13 convert occupied pits to endosomes by changing `Pit.s p→e` while preserving existing `Lext.p`/`Pit.l*` bonds and using `DeleteMolecules`. Rules 15-26 lyse endosomes and discard the pit/bonds while creating internal `Lint` cargo states. Rules 28-29 unpack only `Lint.n~345` and `Lint.n~346` in the active source. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | one-way | `Lext.p`, `Lext.n` | `wash` | `Lext(p,n) → Trash`; no pit bond required. | Removes any external lipoplex after the timer-gated wash turns on. | +| 2 | `Unlabeled` | one-way | free `Lext.p` + free `Pit.l1`, `Pit.s~p` | `kA` | Forms `Lext.p!1`–`Pit.l1!1`; also creates a new free `Pit(s~p,...)` product. | First lipoplex attaches to slot `l1`; the extra free pit product in the rule is a source-like amplification term in the active BNGL. | +| 3 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l2` on a pit already carrying `l1!1` | `kA` | Forms `Lext.p!2`–`Pit.l2!2`; preserves the existing `l1!1` bond. | Adds a second lipoplex to slot `l2`. | +| 4 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l3` on a two-lipoplex pit | `kA` | Forms `Lext.p!3`–`Pit.l3!3`; preserves `l1!1,l2!2`. | Adds a third lipoplex to slot `l3`. | +| 5 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l4` | `kA` | Forms `Lext.p!4`–`Pit.l4!4`; preserves earlier slot bonds. | Adds a fourth lipoplex to slot `l4`. | +| 6 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l5` | `kA` | Forms `Lext.p!5`–`Pit.l5!5`. | Adds a fifth lipoplex to slot `l5`. | +| 7 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l6` | `kA` | Forms `Lext.p!6`–`Pit.l6!6`. | Adds a sixth lipoplex to slot `l6`. | +| 8 | `Unlabeled` | one-way | free `Lext.p` + open `Pit.l7` | `kA` | Forms `Lext.p!7`–`Pit.l7!7`. | Adds a seventh lipoplex to slot `l7`; higher slot rules are commented out. | +| 9 | `Unlabeled` | one-way | one-lipoplex pit: `Lext.p!1`–`Pit.l1!1`, `Pit.s~p` | `kE DeleteMolecules` | `Pit.s p→e`; preserves `l1!1`; deletes unmatched molecules from the reactant complex context. | Converts a one-lipoplex pit into an endosome. | +| 10 | `Unlabeled` | one-way | two-lipoplex pit: bonds at `l1!1,l2!2`, `Pit.s~p` | `kE DeleteMolecules` | `Pit.s p→e`; preserves bonds at `l1,l2`. | Converts a two-lipoplex pit into an endosome. | +| 11 | `Unlabeled` | one-way | three-lipoplex pit: bonds at `l1!1,l2!2,l3!3` | `kE DeleteMolecules` | `Pit.s p→e`; preserves bonds at `l1`-`l3`. | Converts a three-lipoplex pit into an endosome. | +| 12 | `Unlabeled` | one-way | four-lipoplex pit: bonds at `l1!1`-`l4!4` | `kE DeleteMolecules` | `Pit.s p→e`; preserves bonds at `l1`-`l4`. | Converts a four-lipoplex pit into an endosome. | +| 13 | `Unlabeled` | one-way | five-lipoplex pit: bonds at `l1!1`-`l5!5` | `kE DeleteMolecules` | `Pit.s p→e`; preserves bonds at `l1`-`l5`. | Converts a five-lipoplex pit into an endosome; the source comments say five more endocytosis rules would be needed. | +| 14 | `Unlabeled` | one-way | empty `Pit.s~e` with all `l1`-`l10` free | `dE` | `Pit(s~e, free slots) → Trash`. | Degrades an empty endosome. | +| 15 | `Unlabeled` | one-way | `Lext.p!1,n~345` bound to `Pit.s~e,l1!1` | `kL` | Releases/deletes the endosome complex and creates `Lint(n~345)`. | Lyses a one-lipoplex endosome carrying `n~345`. | +| 16 | `Unlabeled` | one-way | `Lext.p!1,n~346` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~346)`. | Lyses a one-lipoplex endosome carrying `n~346`. | +| 17 | `Unlabeled` | one-way | `Lext.p!1,n~347` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~347)`. | Lyses a one-lipoplex endosome carrying `n~347`. | +| 18 | `Unlabeled` | one-way | `Lext.p!1,n~348` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~348)`. | Lyses a one-lipoplex endosome carrying `n~348`. | +| 19 | `Unlabeled` | one-way | `Lext.p!1,n~349` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~349)`. | Lyses a one-lipoplex endosome carrying `n~349`. | +| 20 | `Unlabeled` | one-way | `Lext.p!1,n~350` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~350)`. | Lyses a one-lipoplex endosome carrying `n~350`. | +| 21 | `Unlabeled` | one-way | `Lext.p!1,n~351` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~351)`. | Lyses a one-lipoplex endosome carrying `n~351`. | +| 22 | `Unlabeled` | one-way | `Lext.p!1,n~352` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~352)`. | Lyses a one-lipoplex endosome carrying `n~352`. | +| 23 | `Unlabeled` | one-way | `Lext.p!1,n~353` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~353)`. | Lyses a one-lipoplex endosome carrying `n~353`. | +| 24 | `Unlabeled` | one-way | `Lext.p!1,n~354` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~354)`. | Lyses a one-lipoplex endosome carrying `n~354`. | +| 25 | `Unlabeled` | one-way | `Lext.p!1,n~355` bound to `Pit.s~e,l1!1` | `kL` | Creates `Lint(n~355)`. | Lyses a one-lipoplex endosome carrying `n~355`. | +| 26 | `Unlabeled` | one-way | two `Lext` molecules both `n~345`, bound at `Pit.l1!1` and `Pit.l2!2` in an endosome | `kL` | Creates two `Lint(n~345)` products; pit/endosome complex is consumed. | Special two-lipoplex lysis case for the `345/345` cargo-state pair only. | +| 27 | `Unlabeled` | one-way | `Lint` any `n` state | `dL` | `Lint → Trash`. | Degrades internal lipoplex cargo regardless of `n` state. | +| 28 | `Unlabeled` | one-way | `Lint.n~345` | `kU` | `Lint(n~345) → 5 mRNA`. | Unpacks an internal `n~345` lipoplex into five population mRNA increments, not 345 mRNA. | +| 29 | `Unlabeled` | one-way | `Lint.n~346` | `kU` | `Lint(n~346) → 5 mRNA`. | Unpacks an internal `n~346` lipoplex into five mRNA increments; other `n` states have no active unpacking rule. | +| 30 | `Unlabeled` | one-way | population `mRNA` | `dM` | `mRNA → Trash`. | Degrades one mRNA population unit. | +| 31 | `Unlabeled` | one-way | population `mRNA` | `kTL` | `mRNA → mRNA + GFP`. | Translates GFP while preserving the mRNA population unit. | +| 32 | `Unlabeled` | one-way | population `GFP` | `dG` | `GFP → Trash`. | Degrades GFP. | +| 33 | `Unlabeled` | one-way | population `I` | `1` | `I → I + Timer`. | Preserves timer source `I` and increments `Timer`, which eventually activates `wash`. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `Lext` | `Molecules` | `Lext(p,n)` | Counts external lipoplex molecules with unbound `p` and any declared `n` state. Bound `Lext(p!*,n)` is not matched by this exact free-site pattern. | +| `Pit` | `Molecules` | `Pit(s~p)` | Counts pit-state `Pit` molecules regardless of slot occupancy. | +| `Endo` | `Molecules` | `Pit(s~e)` | Counts endosome-state `Pit` molecules. | +| `Lint` | `Molecules` | `Lint()` | Counts internal lipoplex molecules across all `n` states. | +| `mRNA` | `Molecules` | `mRNA` | Counts mRNA population units. | +| `GFP` | `Molecules` | `GFP` | Counts GFP population units. | +| `TimerCount` | `Molecules` | `Timer` | Counts timer population units and feeds the `wash` function. | + +## 8. Actions and simulation workflow + +`simulate_nf({suffix=>nf,t_end=>30*3600,n_steps=>300});` runs an NFsim simulation for 30 hours of model time with 300 output steps. The commented `writeXML()` is inactive. + +## 9. Technical caveats and ambiguities + +- The active rule set is deliberately incomplete relative to the comments: higher pit occupancies, many lysis combinations, and most unpacking states are commented out or summarized by comments rather than active BNGL rules. +- Rule 2 creates an additional free `Pit` product while binding the first lipoplex; this is unusual and should be verified against the intended delivery model. +- Population declarations make this NFsim-oriented; some standalone deterministic workflows may not treat population species the same way. +- `dW` and `kFast` are declared but not used by active rules. diff --git a/data/summaries_detailed/McMillan2021_TNF_ai_coder.md b/data/summaries_detailed/McMillan2021_TNF_ai_coder.md new file mode 100644 index 00000000..fafebcbc --- /dev/null +++ b/data/summaries_detailed/McMillan2021_TNF_ai_coder.md @@ -0,0 +1,100 @@ +# Coder Model Explanation: McMillan 2021 + +## 1. Model identity and scope + +- **Model id:** `McMillan_2021` +- **Title:** McMillan 2021 +- **BNGL path:** `Published/McMillan2021/McMillan_2021.bngl` +- **YAML path:** `Published/McMillan2021/metadata.yaml` +- **Metadata description:** TNF signaling +- **Scope:** This model enumerates trivalent TNF binding to receptor through the receptor `R.a` site. TNF molecule `T` has three sites, `1`, `2`, and `3`; the active rules explicitly list every first, second, and third receptor-binding event. Receptor site `R.p` is declared but not used by active rules. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 17 parameters for Avogadro/volume conversion, initial concentrations, dissociation, affinity constants, and microscopic rates. | +| Compartments | No | No compartments. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 2 molecule types: receptor `R(p,a)` and TNF `T(1,2,3)`. | +| Seed/species | Yes | 2 initial species: free receptor and free trivalent TNF. | +| Observables | Yes | 5 active observables for free receptor/TNF and TNF bound by 1, 2, or 3 receptors. | +| Functions | No | No functions block. | +| Reaction rules | Yes | 12 active reversible TNF-receptor binding rules. | +| Actions | Yes | Inline `generate_network` and `simulate_ode` commands after the commented `#actions` marker. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `Na` | `6.02e23` | Avogadro conversion. | +| `Vol` | `1e-15` | Volume used for concentration-to-molecule conversion. | +| `R0_conc` | `20000` | Receptor concentration in nM. | +| `T0_conc` | `6250` | TNF concentration in nM. | +| `R0_tot` | `(R0_conc)*(1e-9)*Na*Vol` | Initial receptor molecule count. | +| `T0_tot` | `(T0_conc)*(1e-9)*Na*Vol` | Initial TNF molecule count. | +| `koff` | `0.01` | Reverse rate shared by all TNF-receptor binding rules. | +| `Kp`, `Ka` | `200`, `200` | Affinity constants for commented receptor dimerization rules; not used by active rules. | +| `K1`, `K2`, `K3` | `10`, `100`, `1000` | Macroscopic affinity constants for first, second, third TNF binding classes. | +| `kp`, `ka` | `koff/(Kp...)`, `koff/(Ka...)` | Microscopic rates for commented receptor dimerization; not used by active rules. | +| `k1`, `k2`, `k3` | `koff/(K1...)`, `koff/(K2...)`, `koff/(K3...)` | Microscopic forward rates for first, second, third receptor-binding events. | + +No separate functions block is declared. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `R` | 2 | `p`, `a` | none | none | `a` is the active TNF-binding site; `p` is unused by active rules. | Commented rules suggest `p`/`a` could have represented receptor dimerization, but those rules are inactive. | +| `T` | 3 | `1`, `2`, `3` | none | none | `1`, `2`, and `3` are equivalent-looking TNF receptor-binding sites, but the file enumerates them explicitly. | The occupancy of these sites determines whether observables count TNF1R, TNF2R, or TNF3R. | + +## 5. Compartments, anchors, initial species, and setup + +- Compartments: none declared. +- Anchors: none declared. +- Initial setup: all receptors start as `R(p,a)` and all TNF starts as `T(1,2,3)`. + +| Initial species/pattern | Initial amount | Setup role | +| --- | --- | --- | +| `R(p,a)` | `R0_tot` | Free receptor with both declared sites unbound; only `a` participates in active rules. | +| `T(1,2,3)` | `T0_tot` | Free trivalent TNF with all three binding sites open. | + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 1-3 are first receptor-binding events at TNF sites `1`, `2`, and `3` using `k1`. Rules 4-9 add a second receptor to whichever TNF site remains open, using `k2`. Rules 10-12 add the third receptor, using `k3`. Every rule forms or breaks one specific `T.`–`R.a` bond and uses `koff` as the reverse rate. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `3` | reversible | `T.1` + `R.a` | `k1, koff` | Forms/releases `T.1!1`–`R.a!1`. | First receptor binds TNF site `1`; reverse unbinds that receptor. | +| 2 | `4` | reversible | `T.2` + `R.a` | `k1, koff` | Forms/releases `T.2!1`–`R.a!1`. | First receptor binds TNF site `2`. | +| 3 | `5` | reversible | `T.3` + `R.a` | `k1, koff` | Forms/releases `T.3!1`–`R.a!1`. | First receptor binds TNF site `3`. | +| 4 | `6` | reversible | open `T.2` on a `T.1`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.2!1`–`R.a!1` bond while `T.1` remains occupied. | Second receptor binds site `2` after site `1` is already occupied. | +| 5 | `7` | reversible | open `T.3` on a `T.1`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.3!1`–`R.a!1` bond while `T.1` remains occupied. | Second receptor binds site `3` after site `1` is already occupied. | +| 6 | `8` | reversible | open `T.1` on a `T.2`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.1!1`–`R.a!1` bond while `T.2` remains occupied. | Second receptor binds site `1` after site `2` is already occupied. | +| 7 | `9` | reversible | open `T.3` on a `T.2`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.3!1`–`R.a!1` bond while `T.2` remains occupied. | Second receptor binds site `3` after site `2` is already occupied. | +| 8 | `10` | reversible | open `T.1` on a `T.3`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.1!1`–`R.a!1` bond while `T.3` remains occupied. | Second receptor binds site `1` after site `3` is already occupied. | +| 9 | `11` | reversible | open `T.2` on a `T.3`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.2!1`–`R.a!1` bond while `T.3` remains occupied. | Second receptor binds site `2` after site `3` is already occupied. | +| 10 | `12` | reversible | open `T.3` on a `T.1,T.2`-bound TNF + `R.a` | `k3, koff` | Adds/removes the third bond at `T.3!1`–`R.a!1`. | Completes trivalent occupancy for the `T.1/T.2` partial complex. | +| 11 | `13` | reversible | open `T.2` on a `T.1,T.3`-bound TNF + `R.a` | `k3, koff` | Adds/removes the third bond at `T.2!1`–`R.a!1`. | Completes trivalent occupancy for the `T.1/T.3` partial complex. | +| 12 | `14` | reversible | open `T.1` on a `T.2,T.3`-bound TNF + `R.a` | `k3, koff` | Adds/removes the third bond at `T.1!1`–`R.a!1`. | Completes trivalent occupancy for the `T.2/T.3` partial complex. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `MonomerReceptor` | `Molecules` | `R(p,a)` | Free receptor with unbound `a` site. | +| `freeTNF` | `Molecules` | `T(1,2,3)` | TNF with all three sites open. | +| `TNF1R` | `Molecules` | `T(1!+,2,3)`, `T(1,2!+,3)`, `T(1,2,3!+)` | TNF bound by exactly one receptor at any one of the three sites. | +| `TNF2R` | `Molecules` | two occupied TNF sites | TNF bound by exactly two receptors. | +| `TNF3R` | `Molecules` | `T(1!+,2!+,3!+)` | Fully occupied trivalent TNF. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1});` builds the finite network for the trivalent binding system. +2. `simulate_ode({suffix=>ode,n_steps=>5,t_end=>10000});` runs a coarse ODE simulation. + +## 9. Technical caveats and ambiguities + +- `R.p` is declared and initialized but not used by active rules. +- Receptor dimerization rules are present only as comments; they should not be counted as active model behavior. +- The metadata says simulation method `nf`, but the active command in this file is `simulate_ode`. diff --git a/data/summaries_detailed/McMillan2021_TNF_coder.md b/data/summaries_detailed/McMillan2021_TNF_coder.md new file mode 100644 index 00000000..fafebcbc --- /dev/null +++ b/data/summaries_detailed/McMillan2021_TNF_coder.md @@ -0,0 +1,100 @@ +# Coder Model Explanation: McMillan 2021 + +## 1. Model identity and scope + +- **Model id:** `McMillan_2021` +- **Title:** McMillan 2021 +- **BNGL path:** `Published/McMillan2021/McMillan_2021.bngl` +- **YAML path:** `Published/McMillan2021/metadata.yaml` +- **Metadata description:** TNF signaling +- **Scope:** This model enumerates trivalent TNF binding to receptor through the receptor `R.a` site. TNF molecule `T` has three sites, `1`, `2`, and `3`; the active rules explicitly list every first, second, and third receptor-binding event. Receptor site `R.p` is declared but not used by active rules. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 17 parameters for Avogadro/volume conversion, initial concentrations, dissociation, affinity constants, and microscopic rates. | +| Compartments | No | No compartments. | +| Anchors | No | No anchors. | +| Molecule types | Yes | 2 molecule types: receptor `R(p,a)` and TNF `T(1,2,3)`. | +| Seed/species | Yes | 2 initial species: free receptor and free trivalent TNF. | +| Observables | Yes | 5 active observables for free receptor/TNF and TNF bound by 1, 2, or 3 receptors. | +| Functions | No | No functions block. | +| Reaction rules | Yes | 12 active reversible TNF-receptor binding rules. | +| Actions | Yes | Inline `generate_network` and `simulate_ode` commands after the commented `#actions` marker. | + +## 3. Parameters, functions, and rate laws + +| Parameter | Value/expression | Technical role | +| --- | --- | --- | +| `Na` | `6.02e23` | Avogadro conversion. | +| `Vol` | `1e-15` | Volume used for concentration-to-molecule conversion. | +| `R0_conc` | `20000` | Receptor concentration in nM. | +| `T0_conc` | `6250` | TNF concentration in nM. | +| `R0_tot` | `(R0_conc)*(1e-9)*Na*Vol` | Initial receptor molecule count. | +| `T0_tot` | `(T0_conc)*(1e-9)*Na*Vol` | Initial TNF molecule count. | +| `koff` | `0.01` | Reverse rate shared by all TNF-receptor binding rules. | +| `Kp`, `Ka` | `200`, `200` | Affinity constants for commented receptor dimerization rules; not used by active rules. | +| `K1`, `K2`, `K3` | `10`, `100`, `1000` | Macroscopic affinity constants for first, second, third TNF binding classes. | +| `kp`, `ka` | `koff/(Kp...)`, `koff/(Ka...)` | Microscopic rates for commented receptor dimerization; not used by active rules. | +| `k1`, `k2`, `k3` | `koff/(K1...)`, `koff/(K2...)`, `koff/(K3...)` | Microscopic forward rates for first, second, third receptor-binding events. | + +No separate functions block is declared. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `R` | 2 | `p`, `a` | none | none | `a` is the active TNF-binding site; `p` is unused by active rules. | Commented rules suggest `p`/`a` could have represented receptor dimerization, but those rules are inactive. | +| `T` | 3 | `1`, `2`, `3` | none | none | `1`, `2`, and `3` are equivalent-looking TNF receptor-binding sites, but the file enumerates them explicitly. | The occupancy of these sites determines whether observables count TNF1R, TNF2R, or TNF3R. | + +## 5. Compartments, anchors, initial species, and setup + +- Compartments: none declared. +- Anchors: none declared. +- Initial setup: all receptors start as `R(p,a)` and all TNF starts as `T(1,2,3)`. + +| Initial species/pattern | Initial amount | Setup role | +| --- | --- | --- | +| `R(p,a)` | `R0_tot` | Free receptor with both declared sites unbound; only `a` participates in active rules. | +| `T(1,2,3)` | `T0_tot` | Free trivalent TNF with all three binding sites open. | + +## 6. Complete reaction-rule inventory + +**Rule-family orientation:** Rules 1-3 are first receptor-binding events at TNF sites `1`, `2`, and `3` using `k1`. Rules 4-9 add a second receptor to whichever TNF site remains open, using `k2`. Rules 10-12 add the third receptor, using `k3`. Every rule forms or breaks one specific `T.`–`R.a` bond and uses `koff` as the reverse rate. + +| # | Rule label/name | Direction | Participants and sites/components | Rate/expression | Exact modeled change | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | +| 1 | `3` | reversible | `T.1` + `R.a` | `k1, koff` | Forms/releases `T.1!1`–`R.a!1`. | First receptor binds TNF site `1`; reverse unbinds that receptor. | +| 2 | `4` | reversible | `T.2` + `R.a` | `k1, koff` | Forms/releases `T.2!1`–`R.a!1`. | First receptor binds TNF site `2`. | +| 3 | `5` | reversible | `T.3` + `R.a` | `k1, koff` | Forms/releases `T.3!1`–`R.a!1`. | First receptor binds TNF site `3`. | +| 4 | `6` | reversible | open `T.2` on a `T.1`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.2!1`–`R.a!1` bond while `T.1` remains occupied. | Second receptor binds site `2` after site `1` is already occupied. | +| 5 | `7` | reversible | open `T.3` on a `T.1`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.3!1`–`R.a!1` bond while `T.1` remains occupied. | Second receptor binds site `3` after site `1` is already occupied. | +| 6 | `8` | reversible | open `T.1` on a `T.2`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.1!1`–`R.a!1` bond while `T.2` remains occupied. | Second receptor binds site `1` after site `2` is already occupied. | +| 7 | `9` | reversible | open `T.3` on a `T.2`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.3!1`–`R.a!1` bond while `T.2` remains occupied. | Second receptor binds site `3` after site `2` is already occupied. | +| 8 | `10` | reversible | open `T.1` on a `T.3`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.1!1`–`R.a!1` bond while `T.3` remains occupied. | Second receptor binds site `1` after site `3` is already occupied. | +| 9 | `11` | reversible | open `T.2` on a `T.3`-bound TNF + `R.a` | `k2, koff` | Adds/removes a `T.2!1`–`R.a!1` bond while `T.3` remains occupied. | Second receptor binds site `2` after site `3` is already occupied. | +| 10 | `12` | reversible | open `T.3` on a `T.1,T.2`-bound TNF + `R.a` | `k3, koff` | Adds/removes the third bond at `T.3!1`–`R.a!1`. | Completes trivalent occupancy for the `T.1/T.2` partial complex. | +| 11 | `13` | reversible | open `T.2` on a `T.1,T.3`-bound TNF + `R.a` | `k3, koff` | Adds/removes the third bond at `T.2!1`–`R.a!1`. | Completes trivalent occupancy for the `T.1/T.3` partial complex. | +| 12 | `14` | reversible | open `T.1` on a `T.2,T.3`-bound TNF + `R.a` | `k3, koff` | Adds/removes the third bond at `T.1!1`–`R.a!1`. | Completes trivalent occupancy for the `T.2/T.3` partial complex. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `MonomerReceptor` | `Molecules` | `R(p,a)` | Free receptor with unbound `a` site. | +| `freeTNF` | `Molecules` | `T(1,2,3)` | TNF with all three sites open. | +| `TNF1R` | `Molecules` | `T(1!+,2,3)`, `T(1,2!+,3)`, `T(1,2,3!+)` | TNF bound by exactly one receptor at any one of the three sites. | +| `TNF2R` | `Molecules` | two occupied TNF sites | TNF bound by exactly two receptors. | +| `TNF3R` | `Molecules` | `T(1!+,2!+,3!+)` | Fully occupied trivalent TNF. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1});` builds the finite network for the trivalent binding system. +2. `simulate_ode({suffix=>ode,n_steps=>5,t_end=>10000});` runs a coarse ODE simulation. + +## 9. Technical caveats and ambiguities + +- `R.p` is declared and initialized but not used by active rules. +- Receptor dimerization rules are present only as comments; they should not be counted as active model behavior. +- The metadata says simulation method `nf`, but the active command in this file is `simulate_ode`. diff --git a/data/summaries_detailed/Zhang2023_ai_coder.md b/data/summaries_detailed/Zhang2023_ai_coder.md new file mode 100644 index 00000000..9c36790e --- /dev/null +++ b/data/summaries_detailed/Zhang2023_ai_coder.md @@ -0,0 +1,692 @@ +# Coder Model Explanation: Zhang 2023 + +## 1. Model identity and scope + +- **Model id:** `Zhang_2023` +- **Title:** Zhang 2023 +- **BNGL path:** `Published/Zhang2023/Zhang_2023.bngl` +- **YAML path:** `Published/Zhang2023/metadata.yaml` +- **Metadata description:** VEGF signaling +- **Scope:** A large VEGF signaling model centered on VEGF165a, VEGFR2, VEGFR1, NRP1, CD47/TSP1, PI3K/AKT, PLCγ/IP3/DAG/calcium, eNOS, PKC/CIB1/SphK/S1P, Ras/Raf/MEK/ERK, and Axl/Src cross-talk. It is long but still smaller than Dolan2015, with hundreds of explicit rules and no declared compartments or anchors. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 180 parameter entries. | +| Compartments | No | 0 compartment entries. | +| Anchors | No | 0 anchor entries. | +| Molecule types | Yes | 38 molecule type entries. | +| Seed/species | Yes | 34 initial species entries. | +| Observables | Yes | 129 observable entries. | +| Functions | No | 0 function entries. | +| Reaction rules | Yes | 232 reaction rules. | +| Actions | Yes | 1 action or inline execution commands. | + +## 3. Parameters, functions, and rate laws + +The model uses the following parameter entries. Comment text is preserved when the source provides it; otherwise the role is inferred from the parameter name and where it is used. + +| Parameter | Value/expression | Role / source comment | +| --- | --- | --- | +| `Volcyto` | `9.12E-13` | Geometry/scaling parameter. | +| `VolER` | `3.35E-13` | Geometry/scaling parameter. | +| `fextmolar` | `1.205E+15` | Model parameter used by rules, functions, species, or observables. | +| `cellarea` | `1400` | Geometry/scaling parameter. | +| `VEGF165a_0` | `0.0012` | Initial amount or baseline condition parameter. | +| `VEGFR2_0` | `4.29E+00` | Initial amount or baseline condition parameter. | +| `VEGFR1_0` | `1.43` | Initial amount or baseline condition parameter. | +| `NRP1_0` | `2.86E+01` | Initial amount or baseline condition parameter. | +| `TSP1_0` | `0.00E+00` | Initial amount or baseline condition parameter. | +| `Calcium_0` | `0.05` | Initial amount or baseline condition parameter. | +| `CaM_0` | `1` | Initial amount or baseline condition parameter. | +| `eNOS_0` | `0.1` | Initial amount or baseline condition parameter. | +| `kvron` | `10.3` | Kinetic rate or kinetic expression parameter. | +| `kvroff` | `2.36E-01` | Kinetic rate or kinetic expression parameter. | +| `kcVR` | `0.0045` | Kinetic rate or kinetic expression parameter. | +| `kcRR` | `1.11` | Kinetic rate or kinetic expression parameter. | +| `kdRR` | `0.78` | Kinetic rate or kinetic expression parameter. | +| `kvr1on` | `22` | Kinetic rate or kinetic expression parameter. | +| `kvr1off` | `0.026` | Kinetic rate or kinetic expression parameter. | +| `kdeltaRR` | `2.5` | Kinetic rate or kinetic expression parameter. | +| `kdeltaVR` | `2.05` | Kinetic rate or kinetic expression parameter. | +| `kpr2` | `30` | Kinetic rate or kinetic expression parameter. | +| `kdps` | `640` | Kinetic rate or kinetic expression parameter. | +| `kdpi` | `0.72` | Kinetic rate or kinetic expression parameter. | +| `kdpr` | `1.00E+01` | Kinetic rate or kinetic expression parameter. | +| `kcd47free_on` | `100` | Kinetic rate or kinetic expression parameter. | +| `kr2si` | `0.031` | Kinetic rate or kinetic expression parameter. | +| `kr2rs` | `17.18` | Kinetic rate or kinetic expression parameter. | +| `kr2NRP1si` | `0.0014` | Kinetic rate or kinetic expression parameter. | +| `kr2NRP1i2r` | `48` | Kinetic rate or kinetic expression parameter. | +| `kVEGFNRP1on` | `2.48` | Kinetic rate or kinetic expression parameter. | +| `kVEGFNRP1off` | `0.0008` | Kinetic rate or kinetic expression parameter. | +| `kNRP1VEGFR2on` | `0.15` | Kinetic rate or kinetic expression parameter. | +| `kNRP1VEGFR2off` | `0.045` | Kinetic rate or kinetic expression parameter. | +| `kNRP1VEGFR1on` | `5.07` | Kinetic rate or kinetic expression parameter. | +| `kNRP1VEGFR1off` | `0.016` | Kinetic rate or kinetic expression parameter. | +| `kVEGFR2NRP1on` | `0.0022` | Kinetic rate or kinetic expression parameter. | +| `kVEGFR2NRP1off` | `0.014` | Kinetic rate or kinetic expression parameter. | +| `kVEGFR1NRP1on` | `0.004` | Kinetic rate or kinetic expression parameter. | +| `kVEGFR1NRP1off` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `PI3K_0` | `0.1` | Initial amount or baseline condition parameter. | +| `PIP2_0` | `10` | Initial amount or baseline condition parameter. | +| `kPIP2gen` | `0.000048` | Kinetic rate or kinetic expression parameter. | +| `kmPIP2PI3K` | `309.9` | Kinetic rate or kinetic expression parameter. | +| `kcatPI3KPIP2` | `1764.48` | Kinetic rate or kinetic expression parameter. | +| `PTEN_0` | `0.1` | Initial amount or baseline condition parameter. | +| `kmPIP3PTEN` | `6.27` | Kinetic rate or kinetic expression parameter. | +| `kcatPTENPIP3` | `4767.44` | Kinetic rate or kinetic expression parameter. | +| `konPDK1PIP3` | `5828.07` | Kinetic rate or kinetic expression parameter. | +| `koffPDK1PIP3` | `0.64` | Kinetic rate or kinetic expression parameter. | +| `konAKTPIP3` | `12.48` | Kinetic rate or kinetic expression parameter. | +| `koffAKTPIP3` | `0.032` | Kinetic rate or kinetic expression parameter. | +| `AKT_0` | `0.1` | Initial amount or baseline condition parameter. | +| `PDK1_0` | `0.1` | Initial amount or baseline condition parameter. | +| `kpAKTPDK1` | `2` | Kinetic rate or kinetic expression parameter. | +| `mTOR_0` | `0.1` | Initial amount or baseline condition parameter. | +| `kpmTORAKT` | `2` | Kinetic rate or kinetic expression parameter. | +| `kdp473AKTPPase` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `kdp308AKTPPase` | `0.038` | Kinetic rate or kinetic expression parameter. | +| `kpPLCgamma` | `0.045` | Kinetic rate or kinetic expression parameter. | +| `kdpPLCgamma` | `0.014` | Kinetic rate or kinetic expression parameter. | +| `PLCgamma_0` | `0.2` | Initial amount or baseline condition parameter. | +| `kmPIP2PLCgamma` | `4.34` | Kinetic rate or kinetic expression parameter. | +| `nDAG` | `2.6` | Model parameter used by rules, functions, species, or observables. | +| `kcatPLCgammaDAG` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `kdeg_ip3` | `0.47` | Kinetic rate or kinetic expression parameter. | +| `kdeg_DAG` | `0.11` | Kinetic rate or kinetic expression parameter. | +| `CaER_0` | `2.00E+03` | Initial amount or baseline condition parameter. | +| `Iip3Ramp` | `1.31E+05` | Model parameter used by rules, functions, species, or observables. | +| `KmIP3R` | `1.6` | Kinetic rate or kinetic expression parameter. | +| `I_PMCAbar` | `2.02` | Model parameter used by rules, functions, species, or observables. | +| `KmPMCA` | `0.26` | Kinetic rate or kinetic expression parameter. | +| `vSERCA` | `0.39` | Model parameter used by rules, functions, species, or observables. | +| `KleakER` | `1.00E-08` | Kinetic rate or kinetic expression parameter. | +| `KmSERCA` | `0.15` | Kinetic rate or kinetic expression parameter. | +| `KiCa` | `1` | Kinetic rate or kinetic expression parameter. | +| `KBon` | `100` | Kinetic rate or kinetic expression parameter. | +| `KBoff` | `300` | Kinetic rate or kinetic expression parameter. | +| `CaF_0` | `118` | Initial amount or baseline condition parameter. | +| `CaFbound_0` | `2` | Initial amount or baseline condition parameter. | +| `koffCaNCaM1` | `500` | Kinetic rate or kinetic expression parameter. | +| `kdCaNCaM` | `24` | Kinetic rate or kinetic expression parameter. | +| `koffCaCCaM1` | `10` | Kinetic rate or kinetic expression parameter. | +| `kdCaCCaM` | `3.1` | Kinetic rate or kinetic expression parameter. | +| `CSQN_total` | `15000` | Model parameter used by rules, functions, species, or observables. | +| `KCSQN` | `800` | Kinetic rate or kinetic expression parameter. | +| `kdegi0` | `2.02E-03` | Initial amount or baseline condition parameter. | +| `kdegr2NRP1i0` | `7.91E-03` | Initial amount or baseline condition parameter. | +| `kdegi0noP` | `2.85E+00` | Kinetic rate or kinetic expression parameter. | +| `kdegr2NRP1i0noP` | `2.22E-04` | Kinetic rate or kinetic expression parameter. | +| `kr2ii2` | `4.30E-03` | Kinetic rate or kinetic expression parameter. | +| `kr2NRP1ii2` | `4.80E+00` | Kinetic rate or kinetic expression parameter. | +| `kr2i2i` | `3.23E-02` | Kinetic rate or kinetic expression parameter. | +| `kr2NRP1i2i` | `1.00E-03` | Kinetic rate or kinetic expression parameter. | +| `kdegi20` | `2.43E+02` | Initial amount or baseline condition parameter. | +| `kdegr2NRP1i20` | `3.76E-02` | Initial amount or baseline condition parameter. | +| `kdegi20noP` | `4.16E-01` | Kinetic rate or kinetic expression parameter. | +| `kdegr2NRP1i20noP` | `7.56E+02` | Kinetic rate or kinetic expression parameter. | +| `ksingleR2syn` | `1.40E-04` | Kinetic rate or kinetic expression parameter. | +| `ksingleR2deg` | `5.88E-04` | Kinetic rate or kinetic expression parameter. | +| `ksingleR2si` | `7.56E-04` | Kinetic rate or kinetic expression parameter. | +| `ksingleR2is` | `8.66E-04` | Kinetic rate or kinetic expression parameter. | +| `ICracamp` | `5.86E+03` | Model parameter used by rules, functions, species, or observables. | +| `Kcrac` | `169` | Kinetic rate or kinetic expression parameter. | +| `Istim0` | `0.18` | Initial amount or baseline condition parameter. | +| `tau_stim` | `4` | Model parameter used by rules, functions, species, or observables. | +| `ncrac` | `4.2` | Model parameter used by rules, functions, species, or observables. | +| `Src_0` | `0.1` | Initial amount or baseline condition parameter. | +| `Axl_0` | `7.14` | Initial amount or baseline condition parameter. | +| `kpSrc` | `0.61` | Kinetic rate or kinetic expression parameter. | +| `kdpSrc` | `136.5` | Kinetic rate or kinetic expression parameter. | +| `kpSrcAxl` | `3.92` | Kinetic rate or kinetic expression parameter. | +| `kpAxlauto` | `0.12` | Kinetic rate or kinetic expression parameter. | +| `kdpautoAxl` | `1291.1` | Kinetic rate or kinetic expression parameter. | +| `kdpSrcAxl` | `1.79E-03` | Kinetic rate or kinetic expression parameter. | +| `konPI3KAxl` | `55.91688952` | Kinetic rate or kinetic expression parameter. | +| `koffPI3KAxl` | `0.6` | Kinetic rate or kinetic expression parameter. | +| `kDCD47TSP1` | `1.00E-05` | Kinetic rate or kinetic expression parameter. | +| `koffCD47TSP1` | `0.001` | Kinetic rate or kinetic expression parameter. | +| `CD47free_0` | `7.14E+00` | Initial amount or baseline condition parameter. | +| `kdpeNOS` | `5.17E-02` | Kinetic rate or kinetic expression parameter. | +| `konCaMeNOS` | `9.80E+02` | Kinetic rate or kinetic expression parameter. | +| `koffCaMeNOS` | `9.73E+00` | Kinetic rate or kinetic expression parameter. | +| `koffeNOScav1` | `6.875` | Kinetic rate or kinetic expression parameter. | +| `koncaveNOS` | `81.9375` | Kinetic rate or kinetic expression parameter. | +| `kcateNOSAKT` | `1000` | Kinetic rate or kinetic expression parameter. | +| `kr2CD47off` | `1.00E+00` | Kinetic rate or kinetic expression parameter. | +| `f_TSP1deg` | `1.00E+00` | Model parameter used by rules, functions, species, or observables. | +| `fTSP1dp` | `1.00E+00` | Model parameter used by rules, functions, species, or observables. | +| `fTSP1i2r` | `1.00E+00` | Model parameter used by rules, functions, species, or observables. | +| `PKC_0` | `0.1` | Initial amount or baseline condition parameter. | +| `konCaPKC` | `0.3` | Kinetic rate or kinetic expression parameter. | +| `koffCaPKC` | `0.01` | Kinetic rate or kinetic expression parameter. | +| `konDAGPKC` | `0.029957319` | Kinetic rate or kinetic expression parameter. | +| `koffDAGPKC` | `0.124096212` | Kinetic rate or kinetic expression parameter. | +| `kon1CaCIB1` | `0.052631579` | Kinetic rate or kinetic expression parameter. | +| `koff1CaCIB1` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `kon2CaCIB1` | `0.185185185` | Kinetic rate or kinetic expression parameter. | +| `koff2CaCIB1` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `CIB1_0` | `0.5` | Initial amount or baseline condition parameter. | +| `konCIB1SphK1` | `17.6028519` | Kinetic rate or kinetic expression parameter. | +| `koffCIB1SphK1` | `4.403956392` | Kinetic rate or kinetic expression parameter. | +| `SphK_0` | `0.1` | Initial amount or baseline condition parameter. | +| `Sph_0` | `10` | Initial amount or baseline condition parameter. | +| `S1P_0` | `0` | Initial amount or baseline condition parameter. | +| `kcatERK` | `7.882741692` | Kinetic rate or kinetic expression parameter. | +| `kmERKSK1` | `1.198236617` | Kinetic rate or kinetic expression parameter. | +| `ktSK1` | `1` | Kinetic rate or kinetic expression parameter. | +| `koffSK1` | `1.04E-01` | Kinetic rate or kinetic expression parameter. | +| `ktoffSK1` | `6.97E-04` | Kinetic rate or kinetic expression parameter. | +| `kcatPKC` | `10.20798409` | Kinetic rate or kinetic expression parameter. | +| `kmPKCRaf` | `0.313875333` | Kinetic rate or kinetic expression parameter. | +| `RasGTP_0` | `0` | Initial amount or baseline condition parameter. | +| `RasGDP_0` | `0.1` | Initial amount or baseline condition parameter. | +| `Raf_0` | `0.355471965` | Initial amount or baseline condition parameter. | +| `MEK12_0` | `0.288919159` | Initial amount or baseline condition parameter. | +| `ERK12_0` | `0.382329627` | Initial amount or baseline condition parameter. | +| `kdpSK1` | `0.02182773` | Kinetic rate or kinetic expression parameter. | +| `kdpPKCRaf` | `0.720296112` | Kinetic rate or kinetic expression parameter. | +| `kSphgen` | `0.000048` | Kinetic rate or kinetic expression parameter. | +| `kcatSK1Sph` | `37.23820691` | Kinetic rate or kinetic expression parameter. | +| `KmSK1Sph` | `0.029430478` | Kinetic rate or kinetic expression parameter. | +| `kdpS1P` | `1.188017664` | Kinetic rate or kinetic expression parameter. | +| `kS1PRas` | `1.556423632` | Kinetic rate or kinetic expression parameter. | +| `KmS1PRas` | `5.899306591` | Kinetic rate or kinetic expression parameter. | +| `kRasGAP` | `2.941097467` | Kinetic rate or kinetic expression parameter. | +| `konRasRaf` | `13.10183719` | Kinetic rate or kinetic expression parameter. | +| `koffRasRaf` | `0.151878139` | Kinetic rate or kinetic expression parameter. | +| `kpRaf` | `1.67558904` | Kinetic rate or kinetic expression parameter. | +| `kdpRaf` | `0.894826206` | Kinetic rate or kinetic expression parameter. | +| `kpMEK12Raf1` | `1.801786102` | Kinetic rate or kinetic expression parameter. | +| `kpMEK12Raf2` | `1.204676328` | Kinetic rate or kinetic expression parameter. | +| `KmMEK12Raf` | `0.807388937` | Kinetic rate or kinetic expression parameter. | +| `kdpMEK12_1` | `0.111827134` | Kinetic rate or kinetic expression parameter. | +| `kdpMEK12_2` | `0.139705453` | Kinetic rate or kinetic expression parameter. | +| `kpMEK12ERK12_1` | `12.14930177` | Kinetic rate or kinetic expression parameter. | +| `kmMEKERK12` | `0.25546079` | Kinetic rate or kinetic expression parameter. | +| `kpMEK12ERK12_2` | `0.516270813` | Kinetic rate or kinetic expression parameter. | +| `kdpERK12_1` | `6.06E+00` | Kinetic rate or kinetic expression parameter. | +| `kdpERK12_2` | `1.053392443` | Kinetic rate or kinetic expression parameter. | + +No separate BNGL functions are declared; rule rates are direct parameters or algebraic expressions embedded in the rule inventory. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `vegf` | 4 | `r`, `r`, `nrp1bd`, `c` | c: s, i, i2, r | None | r is used as a binding/matching component; r is used as a binding/matching component; nrp1bd is used as a binding/matching component; c is an internal state/modification coordinate | vegf165a | +| `vegfr2` | 5 | `l1`, `Y1175`, `CD47bd`, `dimer`, `c` | Y1175: Y, pY; c: s, i, i2, r | None | l1 is used as a binding/matching component; Y1175 is an internal state/modification coordinate; CD47bd is used as a binding/matching component; dimer is used as a binding/matching component; c is an internal state/modification coordinate | Declared in molecule types block. | +| `vegfr1` | 4 | `l2`, `dimer`, `nrp1bd`, `c` | c: s | None | l2 is used as a binding/matching component; dimer is used as a binding/matching component; nrp1bd is used as a binding/matching component; c is an internal state/modification coordinate | Declared in molecule types block. | +| `NRP1` | 2 | `vegfabd`, `c` | c: s, i, i2, r | None | vegfabd is used as a binding/matching component; c is an internal state/modification coordinate | Declared in molecule types block. | +| `PI` | 1 | `PIsite` | PIsite: 3P, 4P | None | PIsite is an internal state/modification coordinate | Declared in molecule types block. | +| `PLCgamma` | 1 | `Yplc` | Yplc: Y, pY | None | Yplc is an internal state/modification coordinate | Declared in molecule types block. | +| `DAG` | 1 | `pkcbd` | None | None | pkcbd is used as a binding/matching component | Declared in molecule types block. | +| `IP3_cyto` | 1 | `ip3rbd` | None | None | ip3rbd is used as a binding/matching component | Declared in molecule types block. | +| `Calcium_cyto` | 1 | `bd` | None | None | bd is used as a binding/matching component | Declared in molecule types block. | +| `Trash` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `CaER` | 1 | `bd` | None | None | bd is used as a binding/matching component | Declared in molecule types block. | +| `CaF` | 1 | `cabd` | None | None | cabd is used as a binding/matching component | Declared in molecule types block. | +| `CSQNF` | 1 | `cabd` | None | None | cabd is used as a binding/matching component | Declared in molecule types block. | +| `CaM` | 5 | `NCaM`, `NCaM`, `CCaM`, `CCaM`, `CaMtargetbd` | None | None | CaMtargetbd is used as a binding/matching component | Declared in molecule types block. | +| `I` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `Istim` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `PTEN` | 1 | `PIP3docking` | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `TSADSrc` | 1 | `Y1` | Y1: Y, pY | None | Y1 is an internal state/modification coordinate | Declared in molecule types block. | +| `Axl` | 2 | `Ysrc`, `Yaxl` | Ysrc: Y, pY; Yaxl: Y, pY | None | Ysrc is an internal state/modification coordinate; Yaxl is an internal state/modification coordinate | Declared in molecule types block. | +| `PI3K` | 1 | `state` | state: active, inactive | None | state is an internal state/modification coordinate | Declared in molecule types block. | +| `AKT` | 3 | `PHakt`, `T308`, `S473` | T308: S, pS; S473: S, pS | None | T308 is an internal state/modification coordinate; S473 is an internal state/modification coordinate | Declared in molecule types block. | +| `PDK1` | 2 | `PHpdk1`, `aktbd` | None | None | aktbd is used as a binding/matching component | Declared in molecule types block. | +| `mTOR` | 1 | `aktbd` | None | None | aktbd is used as a binding/matching component | Declared in molecule types block. | +| `CD47SIRPa` | 4 | `VEGFR2bd`, `TSP1bd`, `Y1`, `c` | Y1: Y, pY; c: s, i, i2, r | None | VEGFR2bd is used as a binding/matching component; TSP1bd is used as a binding/matching component; Y1 is an internal state/modification coordinate; c is an internal state/modification coordinate | Declared in molecule types block. | +| `TSP1` | 1 | `CD47bd` | None | None | CD47bd is used as a binding/matching component | Declared in molecule types block. | +| `eNOS` | 3 | `CaMBD`, `S1177`, `cav1BD` | S1177: S, pS | None | CaMBD is used as a binding/matching component; S1177 is an internal state/modification coordinate; cav1BD is used as a binding/matching component | Declared in molecule types block. | +| `caveolin1` | 1 | `eNOSbd` | None | None | eNOSbd is used as a binding/matching component | Declared in molecule types block. | +| `PKC` | 2 | `CalciumBD`, `DAGBD` | None | None | CalciumBD is used as a binding/matching component; DAGBD is used as a binding/matching component | Declared in molecule types block. | +| `CIB1` | 4 | `EF1`, `EF2`, `sk1bd`, `location` | location: cytosol, membrane | None | sk1bd is used as a binding/matching component; location is an internal state/modification coordinate | Declared in molecule types block. | +| `SphK` | 2 | `CIB1bd`, `Serk` | Serk: S, pS | None | CIB1bd is used as a binding/matching component; Serk is an internal state/modification coordinate | Declared in molecule types block. | +| `Sph` | 1 | `skbd` | None | None | skbd is used as a binding/matching component | Declared in molecule types block. | +| `S1P` | 1 | `bd` | None | None | bd is used as a binding/matching component | Declared in molecule types block. | +| `RasGDP` | 1 | `rafbd` | None | None | rafbd is used as a binding/matching component | Declared in molecule types block. | +| `RasGTP` | 1 | `rafbd` | None | None | rafbd is used as a binding/matching component | Declared in molecule types block. | +| `Raf` | 4 | `mekbd`, `rasbd`, `Y1Y2`, `Spkc` | Y1Y2: Y, pY; Spkc: S, pS | None | mekbd is used as a binding/matching component; rasbd is used as a binding/matching component; Y1Y2 is an internal state/modification coordinate; Spkc is an internal state/modification coordinate | Declared in molecule types block. | +| `MEK12` | 3 | `bd`, `S1`, `S2` | S1: S, pS; S2: S, pS | None | bd is used as a binding/matching component; S1 is an internal state/modification coordinate; S2 is an internal state/modification coordinate | Declared in molecule types block. | +| `ERK1` | 2 | `MEK12bd`, `S1` | S1: S, pS | None | MEK12bd is used as a binding/matching component; S1 is an internal state/modification coordinate | Declared in molecule types block. | +| `ERK2` | 2 | `MEK12bd`, `S2` | S2: S, pS | None | MEK12bd is used as a binding/matching component; S2 is an internal state/modification coordinate | Declared in molecule types block. | + +## 5. Compartments, anchors, initial species, and setup + +No BNGL compartment block is declared. + +No anchors block is declared. + +VEGF/NRP1/receptor assemblies control VEGFR2 phosphorylation and trafficking, then branch into PI3K/AKT, PLCγ-calcium, eNOS, and MAPK/S1P pathways. TSP1/CD47 and Axl/Src modules provide additional regulation around receptor state, PI3K recruitment, and downstream kinase activity. + +| Initial species entry | Initial amount/expression | Technical setup meaning | +| --- | --- | --- | +| `vegf(r,r,nrp1bd,c~s)` | `VEGF165a_0` | Initial population or concentration for this exact pattern. | +| `vegfr1(l2,dimer,nrp1bd,c~s)` | `VEGFR1_0` | Initial population or concentration for this exact pattern. | +| `vegfr2(l1,Y1175~Y,CD47bd,dimer,c~s)` | `VEGFR2_0` | Initial population or concentration for this exact pattern. | +| `NRP1(vegfabd,c~s)` | `NRP1_0` | Initial population or concentration for this exact pattern. | +| `PI(PIsite~3P)` | `PIP2_0` | Initial population or concentration for this exact pattern. | +| `PLCgamma(Yplc~Y)` | `PLCgamma_0` | Initial population or concentration for this exact pattern. | +| `CaER(bd)` | `CaER_0` | Initial population or concentration for this exact pattern. | +| `Calcium_cyto(bd)` | `Calcium_0` | Initial population or concentration for this exact pattern. | +| `CaF(cabd)` | `CaF_0` | Initial population or concentration for this exact pattern. | +| `Calcium_cyto(bd!1).CaF(cabd!1)` | `CaFbound_0` | Initial population or concentration for this exact pattern. | +| `CaM(NCaM,NCaM,CCaM,CCaM,CaMtargetbd)` | `CaM_0` | Initial population or concentration for this exact pattern. | +| `I()` | `1` | Initial population or concentration for this exact pattern. | +| `Istim()` | `Istim0` | Initial population or concentration for this exact pattern. | +| `PTEN(PIP3docking)` | `PTEN_0` | Initial population or concentration for this exact pattern. | +| `TSADSrc(Y1~Y)` | `Src_0` | Initial population or concentration for this exact pattern. | +| `Axl(Ysrc~Y,Yaxl~Y)` | `Axl_0` | Initial population or concentration for this exact pattern. | +| `PI3K(state~inactive)` | `PI3K_0` | Initial population or concentration for this exact pattern. | +| `AKT(PHakt,T308~S,S473~S)` | `AKT_0` | Initial population or concentration for this exact pattern. | +| `PDK1(PHpdk1,aktbd)` | `PDK1_0` | Initial population or concentration for this exact pattern. | +| `mTOR(aktbd)` | `mTOR_0` | Initial population or concentration for this exact pattern. | +| `TSP1(CD47bd)` | `TSP1_0` | Initial population or concentration for this exact pattern. | +| `CD47SIRPa(VEGFR2bd,TSP1bd,Y1~Y,c~s)` | `CD47free_0` | Initial population or concentration for this exact pattern. | +| `eNOS(CaMBD,S1177~S,cav1BD!1).caveolin1(eNOSbd!1)` | `eNOS_0` | Initial population or concentration for this exact pattern. | +| `PKC(CalciumBD,DAGBD)` | `PKC_0` | Initial population or concentration for this exact pattern. | +| `CIB1(EF1,EF2,sk1bd,location~cytosol)` | `CIB1_0` | Initial population or concentration for this exact pattern. | +| `SphK(CIB1bd,Serk~S)` | `SphK_0` | Initial population or concentration for this exact pattern. | +| `Sph(skbd)` | `Sph_0` | Initial population or concentration for this exact pattern. | +| `S1P(bd)` | `S1P_0` | Initial population or concentration for this exact pattern. | +| `RasGDP(rafbd)` | `RasGDP_0` | Initial population or concentration for this exact pattern. | +| `RasGTP(rafbd)` | `RasGTP_0` | Initial population or concentration for this exact pattern. | +| `Raf(mekbd,rasbd,Y1Y2~Y,Spkc~S)` | `Raf_0` | Initial population or concentration for this exact pattern. | +| `MEK12(bd,S1~S,S2~S)` | `MEK12_0` | Initial population or concentration for this exact pattern. | +| `ERK1(MEK12bd,S1~S)` | `ERK12_0` | Initial population or concentration for this exact pattern. | +| `ERK2(MEK12bd,S2~S)` | `ERK12_0` | Initial population or concentration for this exact pattern. | + +## 6. Complete reaction-rule inventory + +The source contains **232** reaction rules. The inventory below preserves one row per source rule, grouped only for readability. + +### Rules 1-232 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | reversible | vegfr2 | `kcRR, kdRR` | state and binding-pattern rewrite | `vegfr2(l1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegfr2(l1,dimer!1,c~s).vegfr2(l1,dimer!1,c~s)` | Reversibly forms a complex/contact among vegfr2 through vegfr2.dimer at `kcRR, kdRR`. | +| 2 | `Unlabeled` | reversible | vegfr1, vegfr2 | `kcRR, kdRR` | state and binding-pattern rewrite | `vegfr2(l1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegfr2(l1,dimer!1,c~s).vegfr1(l2,dimer!1,c~s)` | Reversibly forms a complex/contact among vegfr1, vegfr2 through vegfr1.dimer, vegfr2.dimer at `kcRR, kdRR`. | +| 3 | `Unlabeled` | reversible | vegfr1 | `kcRR, kdRR` | state and binding-pattern rewrite | `vegfr1(l2,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegfr1(l2,dimer!1,c~s).vegfr1(l2,dimer!1,c~s)` | Reversibly forms a complex/contact among vegfr1 through vegfr1.dimer at `kcRR, kdRR`. | +| 4 | `Unlabeled` | reversible | vegf, vegfr2 | `kdeltaRR, kdRR` | internal-state conversion/modification | `vegf(r!1,r!2,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr2 through vegfr2.dimer at `kdeltaRR, kdRR`. | +| 5 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaRR, kdRR` | internal-state conversion/modification | `vegf(r!1,r!2,c~s).vegfr2(l1!1,dimer,c~s).vegfr1(l2!2,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.dimer, vegfr2.dimer at `kdeltaRR, kdRR`. | +| 6 | `Unlabeled` | reversible | vegf, vegfr1 | `kdeltaRR, kdRR` | internal-state conversion/modification | `vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer,c~s).vegfr1(l2!2,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1 through vegfr1.dimer at `kdeltaRR, kdRR`. | +| 7 | `Unlabeled` | reversible | NRP1, vegfr1 | `kNRP1VEGFR1on, kNRP1VEGFR1off` | state and binding-pattern rewrite | `vegfr1(nrp1bd,c~s) + NRP1(vegfabd,c~s) <-> vegfr1(nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Reversibly forms a complex/contact among NRP1, vegfr1 through NRP1.vegfabd, vegfr1.nrp1bd at `kNRP1VEGFR1on, kNRP1VEGFR1off`. | +| 8 | `Unlabeled` | one-way | I, vegf | `-(kVEGFNRP1on*cellarea/fextmolar)*vegffrees*nrp1s+(kVEGFNRP1off*cellarea/fextmolar)*vegfnrp1s` | source/synthesis or algebraic source term | `I() -> I() + vegf(r,r,nrp1bd,c~s)` | Produces vegf while retaining or consuming I at `-(kVEGFNRP1on*cellarea/fextmolar)*vegffrees*nrp1s+(kVEGFNRP1off*cellarea/fextmolar)*vegfnrp1s`. | +| 9 | `Unlabeled` | one-way | NRP1, vegf | `kVEGFNRP1on` | state and binding-pattern rewrite | `vegf(r,r,nrp1bd,c~s) + NRP1(vegfabd,c~s) -> vegf(r,r,nrp1bd,c~s) + vegf(r,r,nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Forms a complex/contact among NRP1, vegf through NRP1.vegfabd, vegf.nrp1bd at `kVEGFNRP1on`. | +| 10 | `Unlabeled` | one-way | NRP1, vegf | `kVEGFNRP1off` | state and binding-pattern rewrite | `vegf(r,r,nrp1bd!1,c~s).NRP1(vegfabd!1,c~s) -> NRP1(vegfabd,c~s)` | Releases a complex/contact among NRP1, vegf by freeing NRP1.vegfabd, vegf.nrp1bd at `kVEGFNRP1off`. | +| 11 | `Unlabeled` | reversible | vegf, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr2(l1!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr2 through vegf.r, vegfr2.l1 at `kNRP1VEGFR2on, kNRP1VEGFR2off`. | +| 12 | `Unlabeled` | reversible | vegf, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr2(l1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr2(l1!2,dimer!3,c~s).vegfr2(l1,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr2 through vegf.r, vegfr2.l1 at `kNRP1VEGFR2on, kNRP1VEGFR2off`. | +| 13 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr2(l1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr2(l1!2,dimer!3,c~s).vegfr1(l2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegf.r, vegfr2.l1 at `kNRP1VEGFR2on, kNRP1VEGFR2off`. | +| 14 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr1(l2!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1 through vegf.r, vegfr1.l2 at `kcVR, kvr1off`. | +| 15 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr1(l2,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr1(l2!2,dimer!3,c~s).vegfr1(l2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1 through vegf.r, vegfr1.l2 at `kcVR, kvr1off`. | +| 16 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr1(l2,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr1(l2!2,dimer!3,c~s).vegfr2(l1,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegf.r, vegfr1.l2 at `kcVR, kvr1off`. | +| 17 | `Unlabeled` | one-way | I, vegf | `-(kvron*cellarea/fextmolar)*vegffrees*vr2s+(kvroff*cellarea/fextmolar)*vegfr2s` | source/synthesis or algebraic source term | `I() -> I() + vegf(r,r,nrp1bd,c~s)` | Produces vegf while retaining or consuming I at `-(kvron*cellarea/fextmolar)*vegffrees*vr2s+(kvroff*cellarea/fextmolar)*vegfr2s`. | +| 18 | `Unlabeled` | one-way | vegf, vegfr2 | `kvron` | state and binding-pattern rewrite | `vegf(r,r,nrp1bd,c~s) + vegfr2(l1,c~s) -> vegf(r,r,nrp1bd,c~s) + vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,c~s)` | Forms a complex/contact among vegf, vegfr2 through vegf.r, vegfr2.l1 at `kvron`. | +| 19 | `Unlabeled` | one-way | vegf, vegfr2 | `kvroff` | state and binding-pattern rewrite | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,c~s) -> vegfr2(l1,c~s)` | Releases a complex/contact among vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kvroff`. | +| 20 | `Unlabeled` | reversible | vegf, vegfr2 | `kcVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Rewrites the matched vegf, vegfr2 pattern without an obvious state or bond-count change at `kcVR, kvroff`; the table row preserves the exact implementation pattern. | +| 21 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.l2 at `kcVR, kvr1off`. | +| 22 | `Unlabeled` | reversible | vegf, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr2 pattern without an obvious state or bond-count change at `kdeltaVR, kvroff`; the table row preserves the exact implementation pattern. | +| 23 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.l2 at `kdeltaVR, kvr1off`. | +| 24 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kcVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 25 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kcVR, kvroff`. | +| 26 | `Unlabeled` | reversible | vegf, vegfr1 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kdeltaVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 27 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kdeltaVR, kvroff`. | +| 28 | `Unlabeled` | reversible | vegf, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr2(l1!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Rewrites the matched vegf, vegfr2 pattern without an obvious state or bond-count change at `kNRP1VEGFR2on, kNRP1VEGFR2off`; the table row preserves the exact implementation pattern. | +| 29 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr2(l1!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.l2 at `kcVR, kvr1off`. | +| 30 | `Unlabeled` | reversible | vegf, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr2 pattern without an obvious state or bond-count change at `kdeltaVR, kvroff`; the table row preserves the exact implementation pattern. | +| 31 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.l2 at `kdeltaVR, kvr1off`. | +| 32 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr1(l2!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr1(l2!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kcVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 33 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr1(l2!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr1(l2!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kNRP1VEGFR2on, kNRP1VEGFR2off`. | +| 34 | `Unlabeled` | reversible | vegf, vegfr1 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kdeltaVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 35 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kdeltaVR, kvroff`. | +| 36 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r!2,nrp1bd!4,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s).NRP1(vegfabd!4,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr2 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 37 | `Unlabeled` | reversible | NRP1, vegf, vegfr1 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r!2,nrp1bd!4,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s).NRP1(vegfabd!4,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr1 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 38 | `Unlabeled` | reversible | NRP1, vegf, vegfr1, vegfr2 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r!2,nrp1bd!4,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s).NRP1(vegfabd!4,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr1, vegfr2 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 39 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r!2,nrp1bd!4,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s).NRP1(vegfabd!4,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr2 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 40 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r,nrp1bd!2,c~s).vegfr2(l1!1,c~s).NRP1(vegfabd!2,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr2 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 41 | `Unlabeled` | reversible | NRP1, vegf, vegfr1 | `kVEGFR1NRP1on, kVEGFR1NRP1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r,nrp1bd!2,c~s).vegfr1(l2!1,c~s).NRP1(vegfabd!2,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr1 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR1NRP1on, kVEGFR1NRP1off`. | +| 42 | `Unlabeled` | one-way | I, vegf | `-kvr1on*cellarea/fextmolar*vegffrees*vr1s+kvr1off*vegfr1s*(cellarea/fextmolar)` | source/synthesis or algebraic source term | `I() -> I() + vegf(r,r,nrp1bd,c~s)` | Produces vegf while retaining or consuming I at `-kvr1on*cellarea/fextmolar*vegffrees*vr1s+kvr1off*vegfr1s*(cellarea/fextmolar)`. | +| 43 | `Unlabeled` | one-way | vegf, vegfr1 | `kvr1on` | state and binding-pattern rewrite | `vegf(r,r,nrp1bd,c~s) + vegfr1(l2,c~s) -> vegf(r,r,nrp1bd,c~s) + vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,c~s)` | Forms a complex/contact among vegf, vegfr1 through vegf.r, vegfr1.l2 at `kvr1on`. | +| 44 | `Unlabeled` | one-way | vegf, vegfr1 | `kvr1off` | state and binding-pattern rewrite | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,c~s) -> vegfr1(l2,c~s)` | Releases a complex/contact among vegf, vegfr1 by freeing vegf.r, vegfr1.l2 at `kvr1off`. | +| 45 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,c~s).vegfr1(l2!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kcVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 46 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,c~s).vegfr1(l2!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kcVR, kvroff`. | +| 47 | `Unlabeled` | reversible | vegf, vegfr1 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kdeltaVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 48 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kdeltaVR, kvroff`. | +| 49 | `Unlabeled` | one-way | vegf, vegfr2 | `kpr2` | internal-state conversion/modification | `vegf(r!1,r!2,c~s).vegfr2(l1!1,c~s).vegfr2(l1!2,Y1175~Y,c~s) -> vegf(r!1,r!2,c~s).vegfr2(l1!1,c~s).vegfr2(l1!2,Y1175~pY,c~s)` | Changes internal modification/state marks on vegf, vegfr2: vegfr2.Y1175 Y→pY at `kpr2`. | +| 50 | `Unlabeled` | one-way | vegf, vegfr2 | `kpr2` | internal-state conversion/modification | `vegf(r!1,r!2,c~i).vegfr2(l1!1,c~i).vegfr2(l1!2,Y1175~Y,c~i) -> vegf(r!1,r!2,c~i).vegfr2(l1!1,c~i).vegfr2(l1!2,Y1175~pY,c~i)` | Changes internal modification/state marks on vegf, vegfr2: vegfr2.Y1175 Y→pY at `kpr2`. | +| 51 | `Unlabeled` | one-way | vegf, vegfr2 | `kpr2` | internal-state conversion/modification | `vegf(r!1,r!2,c~i2).vegfr2(l1!1,c~i2).vegfr2(l1!2,Y1175~Y,c~i2) -> vegf(r!1,r!2,c~i2).vegfr2(l1!1,c~i2).vegfr2(l1!2,Y1175~pY,c~i2)` | Changes internal modification/state marks on vegf, vegfr2: vegfr2.Y1175 Y→pY at `kpr2`. | +| 52 | `Unlabeled` | one-way | vegf, vegfr2 | `kpr2` | internal-state conversion/modification | `vegf(r!1,r!2,c~r).vegfr2(l1!1,c~r).vegfr2(l1!2,Y1175~Y,c~r) -> vegf(r!1,r!2,c~r).vegfr2(l1!1,c~r).vegfr2(l1!2,Y1175~pY,c~r)` | Changes internal modification/state marks on vegf, vegfr2: vegfr2.Y1175 Y→pY at `kpr2`. | +| 53 | `Unlabeled` | one-way | vegfr2 | `kdps` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd,c~s) -> vegfr2(Y1175~Y,CD47bd,c~s)` | Changes internal modification/state marks on vegfr2: vegfr2.Y1175 pY→Y at `kdps`. | +| 54 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdps` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~s).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~s) -> vegfr2(Y1175~Y,CD47bd!3,c~s).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~s)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdps`. | +| 55 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdps*fTSP1dp` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~s).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~s) -> vegfr2(Y1175~Y,CD47bd!3,c~s).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~s)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdps*fTSP1dp`. | +| 56 | `Unlabeled` | one-way | vegfr2 | `kdpi` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd,c~i) -> vegfr2(Y1175~Y,CD47bd,c~i)` | Changes internal modification/state marks on vegfr2: vegfr2.Y1175 pY→Y at `kdpi`. | +| 57 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdpi` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i) -> vegfr2(Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdpi`. | +| 58 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdpi*fTSP1dp` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i) -> vegfr2(Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdpi*fTSP1dp`. | +| 59 | `Unlabeled` | one-way | vegfr2 | `kdpi` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd,c~i2) -> vegfr2(Y1175~Y,CD47bd,c~i2)` | Changes internal modification/state marks on vegfr2: vegfr2.Y1175 pY→Y at `kdpi`. | +| 60 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdpi` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2) -> vegfr2(Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdpi`. | +| 61 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdpi*fTSP1dp` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2) -> vegfr2(Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdpi*fTSP1dp`. | +| 62 | `Unlabeled` | one-way | vegfr2 | `kdpr` | internal-state conversion/modification | `vegfr2(Y1175~pY,c~r) -> vegfr2(Y1175~Y,c~r)` | Changes internal modification/state marks on vegfr2: vegfr2.Y1175 pY→Y at `kdpr`. | +| 63 | `Unlabeled` | one-way | vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd,dimer,c~s).vegfr2(l1!2,CD47bd,dimer,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd,dimer,c~i).vegfr2(l1!2,CD47bd,dimer,c~i)` | Changes internal modification/state marks on vegf, vegfr2: vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 64 | `Unlabeled` | one-way | vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd,dimer!6,c~s).vegfr2(l1!2,CD47bd,dimer!6,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd,dimer!6,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i)` | Changes internal modification/state marks on vegf, vegfr2: vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 65 | `Unlabeled` | one-way | CD47SIRPa, vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd!3,dimer,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd,dimer,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 66 | `Unlabeled` | one-way | CD47SIRPa, vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd!3,dimer!6,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd,dimer!6,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 67 | `Unlabeled` | one-way | CD47SIRPa, vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd!3,dimer,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd!4,dimer,c~s).CD47SIRPa(VEGFR2bd!4,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer,c~i).CD47SIRPa(VEGFR2bd!4,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 68 | `Unlabeled` | one-way | CD47SIRPa, vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd!3,dimer!6,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd!4,dimer!6,c~s).CD47SIRPa(VEGFR2bd!4,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer!6,c~i).CD47SIRPa(VEGFR2bd!4,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 69 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd,dimer,c~s).vegfr2(l1!2,CD47bd,dimer,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd,dimer,c~i).vegfr2(l1!2,CD47bd,dimer,c~i)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 70 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd!3,dimer,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd,dimer,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer,c~i)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c s→i, NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 71 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd!3,dimer,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd!4,dimer,c~s).CD47SIRPa(VEGFR2bd!4,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer,c~i).CD47SIRPa(VEGFR2bd!4,c~i)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c s→i, NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 72 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd,dimer!6,c~s).vegfr2(l1!2,CD47bd,dimer!6,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd,dimer!6,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 73 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd!3,dimer!6,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd,dimer!6,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c s→i, NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 74 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd!3,dimer!6,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd!4,dimer!6,c~s).CD47SIRPa(VEGFR2bd!4,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer!6,c~i).CD47SIRPa(VEGFR2bd!4,c~i)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c s→i, NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 75 | `Unlabeled` | reversible | vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd,dimer,c~i).vegfr2(l1!2,CD47bd,dimer,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd,dimer,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2)` | Changes internal modification/state marks on vegf, vegfr2: vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 76 | `Unlabeled` | reversible | vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd,dimer!6,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd,dimer!6,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2)` | Changes internal modification/state marks on vegf, vegfr2: vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 77 | `Unlabeled` | reversible | CD47SIRPa, vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 78 | `Unlabeled` | reversible | CD47SIRPa, vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer!4,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer!4,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd!3,dimer!4,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 79 | `Unlabeled` | reversible | CD47SIRPa, vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer,c~i).CD47SIRPa(VEGFR2bd!4,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 80 | `Unlabeled` | reversible | CD47SIRPa, vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer!6,c~i).CD47SIRPa(VEGFR2bd!4,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 81 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd,dimer,c~i).vegfr2(l1!2,CD47bd,dimer,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd,dimer,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 82 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd,dimer!6,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd,dimer!6,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 83 | `Unlabeled` | reversible | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i→i2, NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 84 | `Unlabeled` | reversible | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i→i2, NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 85 | `Unlabeled` | reversible | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer,c~i).CD47SIRPa(VEGFR2bd!4,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i→i2, NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 86 | `Unlabeled` | reversible | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer!6,c~i).CD47SIRPa(VEGFR2bd!4,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i→i2, NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 87 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd,dimer,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd,dimer,c~r).vegfr2(l1!2,CD47bd,dimer,c~r)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 88 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd,dimer!6,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd,dimer!6,c~r).vegfr2(l1!2,CD47bd,dimer!6,c~r)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 89 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd,dimer,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 90 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer!6,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd,dimer!6,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 91 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd!4,dimer,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 92 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer!6,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer!6,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd!4,dimer!6,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 93 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r*fTSP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer,c~r).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd,dimer,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r*fTSP1i2r`. | +| 94 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r*fTSP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer!6,c~r).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd,dimer!6,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r*fTSP1i2r`. | +| 95 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r*fTSP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer,c~r).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd!4,dimer,c~r).CD47SIRPa(VEGFR2bd!4,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r*fTSP1i2r`. | +| 96 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r*fTSP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer!6,c~r).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd!4,dimer!6,c~r).CD47SIRPa(VEGFR2bd!4,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r*fTSP1i2r`. | +| 97 | `Unlabeled` | one-way | vegfr2 | `kr2rs` | internal-state conversion/modification | `vegfr2(l1,Y1175~Y,CD47bd,dimer,c~r) -> vegfr2(l1,Y1175~Y,CD47bd,dimer,c~s)` | Changes internal modification/state marks on vegfr2: vegfr2.c r→s at `kr2rs`. | +| 98 | `Unlabeled` | one-way | NRP1 | `kr2rs` | internal-state conversion/modification | `NRP1(vegfabd,c~r) -> NRP1(vegfabd,c~s)` | Changes internal modification/state marks on NRP1: NRP1.c r→s at `kr2rs`. | +| 99 | `Unlabeled` | one-way | CD47SIRPa | `kr2rs` | internal-state conversion/modification | `CD47SIRPa(TSP1bd,VEGFR2bd,c~r) -> CD47SIRPa(TSP1bd,VEGFR2bd,c~s)` | Changes internal modification/state marks on CD47SIRPa: CD47SIRPa.c r→s at `kr2rs`. | +| 100 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kvroff` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,dimer,c~r).vegfr2(l1!2,dimer,c~r) -> NRP1(vegfabd,c~r) + vegfr2(l1,dimer,c~r) + vegfr2(l1,dimer,c~r)` | Releases a complex/contact among NRP1, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kvroff`. | +| 101 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kvroff` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,dimer!6,c~r).vegfr2(l1!2,dimer!6,c~r) -> NRP1(vegfabd,c~r) + vegfr2(l1,dimer!6,c~r).vegfr2(l1,dimer!6,c~r)` | Releases a complex/contact among NRP1, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kvroff`. | +| 102 | `Unlabeled` | one-way | vegfr2 | `kdRR` | state and binding-pattern rewrite | `vegfr2(dimer!6,c~r).vegfr2(dimer!6,c~r) -> vegfr2(dimer,c~r) + vegfr2(dimer,c~r)` | Releases a complex/contact among vegfr2 by freeing vegfr2.dimer at `kdRR`. | +| 103 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kr2CD47off` | state and binding-pattern rewrite | `vegfr2(CD47bd!3,c~r).CD47SIRPa(VEGFR2bd!3,c~r) -> vegfr2(CD47bd,c~r) + CD47SIRPa(VEGFR2bd,c~r)` | Releases a complex/contact among CD47SIRPa, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegfr2.CD47bd at `kr2CD47off`. | +| 104 | `Unlabeled` | one-way | CD47SIRPa, TSP1 | `koffCD47TSP1` | state and binding-pattern rewrite | `CD47SIRPa(TSP1bd!1,c~r).TSP1(CD47bd!1) -> CD47SIRPa(TSP1bd,c~r)` | Releases a complex/contact among CD47SIRPa, TSP1 by freeing CD47SIRPa.TSP1bd, TSP1.CD47bd at `koffCD47TSP1`. | +| 105 | `Unlabeled` | one-way | Trash, vegf, vegfr2 | `kdegi0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among Trash, vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kdegi0`. | +| 106 | `Unlabeled` | one-way | Trash, vegf, vegfr2 | `kdegi0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among Trash, vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kdegi0noP`. | +| 107 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0`. | +| 108 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0noP`. | +| 109 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0`. | +| 110 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0noP`. | +| 111 | `Unlabeled` | one-way | Trash, vegf, vegfr2 | `kdegi20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among Trash, vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kdegi20`. | +| 112 | `Unlabeled` | one-way | Trash, vegf, vegfr2 | `kdegi20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among Trash, vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kdegi20noP`. | +| 113 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20`. | +| 114 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20noP`. | +| 115 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20`. | +| 116 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20noP`. | +| 117 | `Unlabeled` | one-way | NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among NRP1, Trash, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kdegr2NRP1i0`. | +| 118 | `Unlabeled` | one-way | NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among NRP1, Trash, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kdegr2NRP1i0noP`. | +| 119 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0`. | +| 120 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0noP`. | +| 121 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0`. | +| 122 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0noP`. | +| 123 | `Unlabeled` | one-way | NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among NRP1, Trash, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kdegr2NRP1i20`. | +| 124 | `Unlabeled` | one-way | NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among NRP1, Trash, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kdegr2NRP1i20noP`. | +| 125 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20`. | +| 126 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20noP`. | +| 127 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20`. | +| 128 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20noP`. | +| 129 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0*f_TSP1deg`. | +| 130 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0noP*f_TSP1deg`. | +| 131 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,c~i).CD47SIRPa(VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0*f_TSP1deg`. | +| 132 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i).CD47SIRPa(VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0noP*f_TSP1deg`. | +| 133 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20*f_TSP1deg`. | +| 134 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20noP*f_TSP1deg`. | +| 135 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20*f_TSP1deg`. | +| 136 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20noP*f_TSP1deg`. | +| 137 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0*f_TSP1deg`. | +| 138 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0noP*f_TSP1deg`. | +| 139 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,c~i).CD47SIRPa(VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0*f_TSP1deg`. | +| 140 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i).CD47SIRPa(VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0noP*f_TSP1deg`. | +| 141 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20*f_TSP1deg`. | +| 142 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20noP*f_TSP1deg`. | +| 143 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20*f_TSP1deg`. | +| 144 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20noP*f_TSP1deg`. | +| 145 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegfr2 | `ksingleR2deg` | state and binding-pattern rewrite | `vegfr2(l1,CD47bd!1,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!1,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegfr2.CD47bd at `ksingleR2deg`. | +| 146 | `Unlabeled` | one-way | Trash, vegfr2 | `ksingleR2deg` | internal-state conversion/modification | `vegfr2(l1,CD47bd,c~i) -> Trash()` | Produces Trash while retaining or consuming vegfr2 at `ksingleR2deg`. | +| 147 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegfr2 | `ksingleR2deg*f_TSP1deg` | state and binding-pattern rewrite | `vegfr2(l1,CD47bd!1,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!1,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegfr2.CD47bd at `ksingleR2deg*f_TSP1deg`. | +| 148 | `Unlabeled` | one-way | I, vegfr2 | `ksingleR2syn*VEGFR2total` | source/synthesis or algebraic source term | `I() -> I() + vegfr2(l1,Y1175~Y,CD47bd,dimer,c~s)` | Produces vegfr2 while retaining or consuming I at `ksingleR2syn*VEGFR2total`. | +| 149 | `Unlabeled` | reversible | vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd,dimer,c~s) <-> vegfr2(l1,CD47bd,dimer,c~i)` | Changes internal modification/state marks on vegfr2: vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 150 | `Unlabeled` | reversible | CD47SIRPa, vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd!1,dimer,c~s).CD47SIRPa(VEGFR2bd!1,c~s) <-> vegfr2(l1,CD47bd!1,dimer,c~i).CD47SIRPa(VEGFR2bd!1,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: CD47SIRPa.c s→i, vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 151 | `Unlabeled` | reversible | vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd,dimer!3,c~s).vegfr2(l1,CD47bd,dimer!3,c~s) <-> vegfr2(l1,CD47bd,dimer!3,c~i).vegfr2(l1,CD47bd,dimer!3,c~i)` | Changes internal modification/state marks on vegfr2: vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 152 | `Unlabeled` | reversible | CD47SIRPa, vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd!1,dimer!3,c~s).CD47SIRPa(VEGFR2bd!1,c~s).vegfr2(l1,CD47bd,dimer!3,c~s) <-> vegfr2(l1,CD47bd!1,dimer!3,c~i).CD47SIRPa(VEGFR2bd!1,c~i).vegfr2(l1,CD47bd,dimer!3,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: CD47SIRPa.c s→i, vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 153 | `Unlabeled` | reversible | CD47SIRPa, vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd!1,dimer!3,c~s).CD47SIRPa(VEGFR2bd!1,c~s).vegfr2(l1,CD47bd!2,dimer!3,c~s).CD47SIRPa(VEGFR2bd!2,c~s) <-> vegfr2(l1,CD47bd!1,dimer!3,c~i).CD47SIRPa(VEGFR2bd!1,c~i).vegfr2(l1,CD47bd!2,dimer!3,c~i).CD47SIRPa(VEGFR2bd!2,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: CD47SIRPa.c s→i, vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 154 | `Unlabeled` | one-way | PLCgamma, vegfr2 | `kpPLCgamma` | internal-state conversion/modification | `PLCgamma(Yplc~Y) + vegfr2(Y1175~pY,c~s) -> PLCgamma(Yplc~pY) + vegfr2(Y1175~pY,c~s)` | Changes internal modification/state marks on PLCgamma, vegfr2: PLCgamma.Yplc Y→pY at `kpPLCgamma`. | +| 155 | `Unlabeled` | one-way | PLCgamma, vegfr2 | `kpPLCgamma` | internal-state conversion/modification | `PLCgamma(Yplc~Y) + vegfr2(Y1175~pY,c~i) -> PLCgamma(Yplc~pY) + vegfr2(Y1175~pY,c~i)` | Changes internal modification/state marks on PLCgamma, vegfr2: PLCgamma.Yplc Y→pY at `kpPLCgamma`. | +| 156 | `Unlabeled` | one-way | PLCgamma, vegfr2 | `kpPLCgamma` | internal-state conversion/modification | `PLCgamma(Yplc~Y) + vegfr2(Y1175~pY,c~i2) -> PLCgamma(Yplc~pY) + vegfr2(Y1175~pY,c~i2)` | Changes internal modification/state marks on PLCgamma, vegfr2: PLCgamma.Yplc Y→pY at `kpPLCgamma`. | +| 157 | `Unlabeled` | one-way | PLCgamma | `kdpPLCgamma` | internal-state conversion/modification | `PLCgamma(Yplc~pY) -> PLCgamma(Yplc~Y)` | Changes internal modification/state marks on PLCgamma: PLCgamma.Yplc pY→Y at `kdpPLCgamma`. | +| 158 | `Unlabeled` | one-way | IP3_cyto, PI, PLCgamma | `kcatPLCgammaDAG*freepip2^(nDAG-1)/(kmPIP2PLCgamma^nDAG+freepip2^nDAG)` | internal-state conversion/modification | `PLCgamma(Yplc~pY) + PI(PIsite~3P) -> IP3_cyto(ip3rbd) + PLCgamma(Yplc~pY)` | Produces IP3_cyto while retaining or consuming PI, PLCgamma at `kcatPLCgammaDAG*freepip2^(nDAG-1)/(kmPIP2PLCgamma^nDAG+freepip2^nDAG)`. | +| 159 | `Unlabeled` | one-way | DAG, PI, PLCgamma | `kcatPLCgammaDAG*freepip2^(nDAG-1)/(kmPIP2PLCgamma^nDAG+freepip2^nDAG)` | internal-state conversion/modification | `PLCgamma(Yplc~pY) + PI(PIsite~3P) -> DAG(pkcbd) + PLCgamma(Yplc~pY)` | Produces DAG while retaining or consuming PI, PLCgamma at `kcatPLCgammaDAG*freepip2^(nDAG-1)/(kmPIP2PLCgamma^nDAG+freepip2^nDAG)`. | +| 160 | `Unlabeled` | one-way | I, PI | `kPIP2gen` | source/synthesis or algebraic source term | `I() -> I() + PI(PIsite~3P)` | Produces PI while retaining or consuming I at `kPIP2gen`. | +| 161 | `Unlabeled` | one-way | IP3_cyto, Trash | `kdeg_ip3` | pattern rewrite | `IP3_cyto(ip3rbd) -> Trash()` | Produces Trash while retaining or consuming IP3_cyto at `kdeg_ip3`. | +| 162 | `Unlabeled` | one-way | DAG, Trash | `kdeg_DAG` | pattern rewrite | `DAG(pkcbd) -> Trash()` | Produces Trash while retaining or consuming DAG at `kdeg_DAG`. | +| 163 | `Unlabeled` | reversible | CaF, Calcium_cyto | `KBon, KBoff` | binding/complex formation | `Calcium_cyto(bd) + CaF(cabd) <-> Calcium_cyto(bd!1).CaF(cabd!1)` | Reversibly forms a complex/contact among CaF, Calcium_cyto through CaF.cabd, Calcium_cyto.bd at `KBon, KBoff`. | +| 164 | `Unlabeled` | one-way | I, Istim | `ICracamp*(Kcrac^ncrac/(Kcrac^ncrac+Caer^ncrac))/tau_stim-Iopenstim/tau_stim` | source/synthesis or algebraic source term | `I() -> I() + Istim()` | Produces Istim while retaining or consuming I at `ICracamp*(Kcrac^ncrac/(Kcrac^ncrac+Caer^ncrac))/tau_stim-Iopenstim/tau_stim`. | +| 165 | `Unlabeled` | one-way | Calcium_cyto, I | `(VolER/Volcyto)*Iip3Ramp*(Caer-Cac)*(freeip3cyto^3.8/(freeip3cyto^3.8+KmIP3R^3.8))*(KiCa^3.8/(KiCa^3.8+Cac^3.8))` | source/synthesis or algebraic source term | `I() -> I() + Calcium_cyto(bd)` | Produces Calcium_cyto while retaining or consuming I at `(VolER/Volcyto)*Iip3Ramp*(Caer-Cac)*(freeip3cyto^3.8/(freeip3cyto^3.8+KmIP3R^3.8))*(KiCa^3.8/(KiCa^3.8+Cac^3.8))`. | +| 166 | `Unlabeled` | one-way | CaER, I | `)` | source/synthesis or algebraic source term | `I() -> I() + CaER(bd) -Iip3Ramp*(Caer-Cac)*(freeip3cyto^3.8/(freeip3cyto^3.8+KmIP3R^3.8))*(KiCa^3.8/(KiCa^3.8+Cac^3.8))*( 1/(1+CSQN_total/(KCSQN+Caer)^2)` | Produces CaER while retaining or consuming I at `)`. | +| 167 | `Unlabeled` | one-way | Calcium_cyto, I | `Iopenstim` | source/synthesis or algebraic source term | `I() -> I() + Calcium_cyto(bd) -I_PMCAbar*Cac^1.4/(KmPMCA^1.4+Cac^1.4) +` | Produces Calcium_cyto while retaining or consuming I at `Iopenstim`. | +| 168 | `Unlabeled` | one-way | Calcium_cyto, I | `KleakER*(Caer-Cac)^2` | source/synthesis or algebraic source term | `I() -> I() + Calcium_cyto(bd) -vSERCA*(Cac/(KmSERCA+Cac))^2 +` | Produces Calcium_cyto while retaining or consuming I at `KleakER*(Caer-Cac)^2`. | +| 169 | `Unlabeled` | one-way | CaER, I | `vSERCA*(Cac/(KmSERCA+Cac))^2*(Volcyto/VolER)*(1/(1+CSQN_total/(KCSQN+Caer)^2))` | source/synthesis or algebraic source term | `I() -> I() + CaER(bd)` | Produces CaER while retaining or consuming I at `vSERCA*(Cac/(KmSERCA+Cac))^2*(Volcyto/VolER)*(1/(1+CSQN_total/(KCSQN+Caer)^2))`. | +| 170 | `Unlabeled` | one-way | CaER, I | `-KleakER*(Volcyto/VolER)*((Caer-Cac)^2)*(1/(1+CSQN_total/(KCSQN+Caer)^2))` | source/synthesis or algebraic source term | `I() -> I() + CaER(bd)` | Produces CaER while retaining or consuming I at `-KleakER*(Volcyto/VolER)*((Caer-Cac)^2)*(1/(1+CSQN_total/(KCSQN+Caer)^2))`. | +| 171 | `Unlabeled` | one-way | CaM, Calcium_cyto | `(koffCaNCaM1/kdCaNCaM)` | binding/complex formation | `CaM(NCaM) + Calcium_cyto(bd) -> CaM(NCaM!1).Calcium_cyto(bd!1) + Calcium_cyto(bd)` | Forms a complex/contact among CaM, Calcium_cyto through CaM.NCaM, Calcium_cyto.bd at `(koffCaNCaM1/kdCaNCaM)`. | +| 172 | `Unlabeled` | one-way | CaM, Calcium_cyto | `koffCaNCaM1` | unbinding/complex dissociation | `CaM(NCaM!1).Calcium_cyto(bd!1) -> CaM(NCaM)` | Releases a complex/contact among CaM, Calcium_cyto by freeing CaM.NCaM, Calcium_cyto.bd at `koffCaNCaM1`. | +| 173 | `Unlabeled` | one-way | CaM, Calcium_cyto | `(koffCaCCaM1/kdCaCCaM)` | binding/complex formation | `CaM(CCaM) + Calcium_cyto(bd) -> CaM(CCaM!1).Calcium_cyto(bd!1) + Calcium_cyto(bd)` | Forms a complex/contact among CaM, Calcium_cyto through CaM.CCaM, Calcium_cyto.bd at `(koffCaCCaM1/kdCaCCaM)`. | +| 174 | `Unlabeled` | one-way | CaM, Calcium_cyto | `koffCaCCaM1` | unbinding/complex dissociation | `CaM(CCaM!1).Calcium_cyto(bd!1) -> CaM(CCaM)` | Releases a complex/contact among CaM, Calcium_cyto by freeing CaM.CCaM, Calcium_cyto.bd at `koffCaCCaM1`. | +| 175 | `Unlabeled` | one-way | TSADSrc, vegfr2 | `kpSrc` | internal-state conversion/modification | `TSADSrc(Y1~Y) + vegfr2(Y1175~pY!?,c~s) -> TSADSrc(Y1~pY) + vegfr2(Y1175~pY!?,c~s)` | Changes internal modification/state marks on TSADSrc, vegfr2: TSADSrc.Y1 Y→pY at `kpSrc`. | +| 176 | `Unlabeled` | one-way | TSADSrc, vegfr2 | `kpSrc` | internal-state conversion/modification | `TSADSrc(Y1~Y) + vegfr2(Y1175~pY!?,c~i) -> TSADSrc(Y1~pY) + vegfr2(Y1175~pY!?,c~i)` | Changes internal modification/state marks on TSADSrc, vegfr2: TSADSrc.Y1 Y→pY at `kpSrc`. | +| 177 | `Unlabeled` | one-way | TSADSrc, vegfr2 | `kpSrc` | internal-state conversion/modification | `TSADSrc(Y1~Y) + vegfr2(Y1175~pY!?,c~i2) -> TSADSrc(Y1~pY) + vegfr2(Y1175~pY!?,c~i2)` | Changes internal modification/state marks on TSADSrc, vegfr2: TSADSrc.Y1 Y→pY at `kpSrc`. | +| 178 | `Unlabeled` | one-way | TSADSrc | `kdpSrc` | internal-state conversion/modification | `TSADSrc(Y1~pY) -> TSADSrc(Y1~Y)` | Changes internal modification/state marks on TSADSrc: TSADSrc.Y1 pY→Y at `kdpSrc`. | +| 179 | `Unlabeled` | one-way | Axl, TSADSrc | `kpSrcAxl` | internal-state conversion/modification | `TSADSrc(Y1~pY) + Axl(Ysrc~Y) -> TSADSrc(Y1~pY) + Axl(Ysrc~pY)` | Changes internal modification/state marks on Axl, TSADSrc: Axl.Ysrc Y→pY at `kpSrcAxl`. | +| 180 | `Unlabeled` | one-way | Axl | `kpAxlauto` | internal-state conversion/modification | `Axl(Ysrc~pY,Yaxl~Y) -> Axl(Ysrc~pY,Yaxl~pY)` | Changes internal modification/state marks on Axl: Axl.Yaxl Y→pY at `kpAxlauto`. | +| 181 | `Unlabeled` | one-way | Axl | `kdpautoAxl` | internal-state conversion/modification | `Axl(Yaxl~pY) -> Axl(Yaxl~Y)` | Changes internal modification/state marks on Axl: Axl.Yaxl pY→Y at `kdpautoAxl`. | +| 182 | `Unlabeled` | one-way | Axl | `kdpSrcAxl` | internal-state conversion/modification | `Axl(Ysrc~pY) -> Axl(Ysrc~Y)` | Changes internal modification/state marks on Axl: Axl.Ysrc pY→Y at `kdpSrcAxl`. | +| 183 | `Unlabeled` | one-way | Axl, PI3K | `konPI3KAxl` | internal-state conversion/modification | `PI3K(state~inactive) + Axl(Yaxl~pY) -> PI3K(state~active) + Axl(Yaxl~pY)` | Changes internal modification/state marks on Axl, PI3K: PI3K.state inactive→active at `konPI3KAxl`. | +| 184 | `Unlabeled` | one-way | PI3K | `koffPI3KAxl` | internal-state conversion/modification | `PI3K(state~active) -> PI3K(state~inactive)` | Changes internal modification/state marks on PI3K: PI3K.state active→inactive at `koffPI3KAxl`. | +| 185 | `Unlabeled` | one-way | PI, PI3K | `kcatPI3KPIP2/(kmPIP2PI3K+freepip2)` | internal-state conversion/modification | `PI3K(state~active) + PI(PIsite~3P) -> PI3K(state~active) + PI(PIsite~4P)` | Changes internal modification/state marks on PI, PI3K: PI.PIsite 3P→4P at `kcatPI3KPIP2/(kmPIP2PI3K+freepip2)`. | +| 186 | `Unlabeled` | one-way | PI, PTEN | `kcatPTENPIP3/(kmPIP3PTEN+freepip3)` | internal-state conversion/modification | `PTEN(PIP3docking) + PI(PIsite~4P) -> PTEN(PIP3docking) + PI(PIsite~3P)` | Changes internal modification/state marks on PI, PTEN: PI.PIsite 4P→3P at `kcatPTENPIP3/(kmPIP3PTEN+freepip3)`. | +| 187 | `Unlabeled` | reversible | PDK1, PI | `konPDK1PIP3, koffPDK1PIP3` | state and binding-pattern rewrite | `PDK1(PHpdk1) + PI(PIsite~4P) <-> PDK1(PHpdk1!1).PI(PIsite~4P!1)` | Reversibly forms a complex/contact among PDK1, PI through PDK1.PHpdk1, PI.P at `konPDK1PIP3, koffPDK1PIP3`. | +| 188 | `Unlabeled` | reversible | AKT, PI | `konAKTPIP3, koffAKTPIP3` | state and binding-pattern rewrite | `AKT(PHakt) + PI(PIsite~4P) <-> AKT(PHakt!1).PI(PIsite~4P!1)` | Reversibly forms a complex/contact among AKT, PI through AKT.PHakt, PI.P at `konAKTPIP3, koffAKTPIP3`. | +| 189 | `Unlabeled` | one-way | AKT | `kpmTORAKT` | internal-state conversion/modification | `AKT(PHakt!+,S473~S) -> AKT(PHakt!+,S473~pS)` | Changes internal modification/state marks on AKT: AKT.S473 S→pS at `kpmTORAKT`. | +| 190 | `Unlabeled` | one-way | AKT, PDK1 | `kpAKTPDK1` | internal-state conversion/modification | `AKT(PHakt!+,S473~pS,T308~S) + PDK1(PHpdk1!+) -> PDK1(PHpdk1!+) + AKT(PHakt!+,S473~pS,T308~pS)` | Changes internal modification/state marks on AKT, PDK1: AKT.T308 S→pS at `kpAKTPDK1`. | +| 191 | `Unlabeled` | one-way | AKT | `kdp473AKTPPase` | internal-state conversion/modification | `AKT(S473~pS) -> AKT(S473~S)` | Changes internal modification/state marks on AKT: AKT.S473 pS→S at `kdp473AKTPPase`. | +| 192 | `Unlabeled` | one-way | AKT | `kdp308AKTPPase` | internal-state conversion/modification | `AKT(T308~pS) -> AKT(T308~S)` | Changes internal modification/state marks on AKT: AKT.T308 pS→S at `kdp308AKTPPase`. | +| 193 | `Unlabeled` | reversible | CaM, eNOS | `konCaMeNOS, koffCaMeNOS` | stoichiometric pattern rewrite | `CaM(NCaM!+,NCaM!+,CCaM!+,CCaM!+,CaMtargetbd) + eNOS(CaMBD) <-> CaM(NCaM!+,NCaM!+,CCaM!+,CCaM!+,CaMtargetbd!1).eNOS(CaMBD!1)` | Reversibly forms a complex/contact among CaM, eNOS through CaM.CaMtargetbd, eNOS.CaMBD at `konCaMeNOS, koffCaMeNOS`. | +| 194 | `Unlabeled` | one-way | caveolin1, eNOS | `koffeNOScav1` | stoichiometric pattern rewrite | `eNOS(CaMBD!+,cav1BD!1).caveolin1(eNOSbd!1) -> eNOS(CaMBD!+,cav1BD) + caveolin1(eNOSbd)` | Releases a complex/contact among caveolin1, eNOS by freeing caveolin1.eNOSbd, eNOS.cav1BD at `koffeNOScav1`. | +| 195 | `Unlabeled` | one-way | caveolin1, eNOS | `koffeNOScav1` | state and binding-pattern rewrite | `eNOS(cav1BD!1,S1177~pS).caveolin1(eNOSbd!1) -> eNOS(cav1BD,S1177~pS) + caveolin1(eNOSbd)` | Releases a complex/contact among caveolin1, eNOS by freeing caveolin1.eNOSbd, eNOS.cav1BD at `koffeNOScav1`. | +| 196 | `Unlabeled` | one-way | caveolin1, eNOS | `koncaveNOS` | state and binding-pattern rewrite | `eNOS(CaMBD,cav1BD,S1177~S) + caveolin1(eNOSbd) -> eNOS(CaMBD,cav1BD!1,S1177~S).caveolin1(eNOSbd!1)` | Forms a complex/contact among caveolin1, eNOS through caveolin1.eNOSbd, eNOS.cav1BD at `koncaveNOS`. | +| 197 | `Unlabeled` | one-way | AKT, eNOS | `kcateNOSAKT` | internal-state conversion/modification | `eNOS(CaMBD!+,S1177~S) + AKT(T308~pS,S473~pS) -> eNOS(CaMBD!+,S1177~pS) + AKT(T308~pS,S473~pS)` | Changes internal modification/state marks on AKT, eNOS: eNOS.S1177 S→pS at `kcateNOSAKT`. | +| 198 | `Unlabeled` | one-way | eNOS | `kdpeNOS` | internal-state conversion/modification | `eNOS(S1177~pS) -> eNOS(S1177~S)` | Changes internal modification/state marks on eNOS: eNOS.S1177 pS→S at `kdpeNOS`. | +| 199 | `Unlabeled` | one-way | I, TSP1 | `-(koffCD47TSP1/kDCD47TSP1)/fextmolar*tsp1frees*cellarea*cd47s+koffCD47TSP1*cd47tsp1s*cellarea*(1/fextmolar)` | source/synthesis or algebraic source term | `I() -> I() + TSP1(CD47bd)` | Produces TSP1 while retaining or consuming I at `-(koffCD47TSP1/kDCD47TSP1)/fextmolar*tsp1frees*cellarea*cd47s+koffCD47TSP1*cd47tsp1s*cellarea*(1/fextmolar)`. | +| 200 | `Unlabeled` | one-way | CD47SIRPa, TSP1 | `(koffCD47TSP1/kDCD47TSP1)` | state and binding-pattern rewrite | `TSP1(CD47bd) + CD47SIRPa(TSP1bd,c~s) -> TSP1(CD47bd) + TSP1(CD47bd!1).CD47SIRPa(TSP1bd!1,c~s)` | Forms a complex/contact among CD47SIRPa, TSP1 through CD47SIRPa.TSP1bd, TSP1.CD47bd at `(koffCD47TSP1/kDCD47TSP1)`. | +| 201 | `Unlabeled` | one-way | CD47SIRPa, TSP1 | `koffCD47TSP1` | state and binding-pattern rewrite | `TSP1(CD47bd!1).CD47SIRPa(TSP1bd!1,c~s) -> CD47SIRPa(TSP1bd,c~s)` | Releases a complex/contact among CD47SIRPa, TSP1 by freeing CD47SIRPa.TSP1bd, TSP1.CD47bd at `koffCD47TSP1`. | +| 202 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kcd47free_on` | state and binding-pattern rewrite | `vegfr2(CD47bd,c~s) + CD47SIRPa(VEGFR2bd,c~s) -> vegfr2(CD47bd!1,c~s).CD47SIRPa(VEGFR2bd!1,c~s)` | Forms a complex/contact among CD47SIRPa, vegfr2 through CD47SIRPa.VEGFR2bd, vegfr2.CD47bd at `kcd47free_on`. | +| 203 | `Unlabeled` | reversible | Calcium_cyto, PKC | `konCaPKC, koffCaPKC` | binding/complex formation | `PKC(CalciumBD) + Calcium_cyto(bd) <-> PKC(CalciumBD!1).Calcium_cyto(bd!1)` | Reversibly forms a complex/contact among Calcium_cyto, PKC through Calcium_cyto.bd, PKC.CalciumBD at `konCaPKC, koffCaPKC`. | +| 204 | `Unlabeled` | reversible | DAG, PKC | `konDAGPKC, koffDAGPKC` | binding/complex formation | `PKC(DAGBD) + DAG(pkcbd) <-> PKC(DAGBD!1).DAG(pkcbd!1)` | Reversibly forms a complex/contact among DAG, PKC through DAG.pkcbd, PKC.DAGBD at `konDAGPKC, koffDAGPKC`. | +| 205 | `Unlabeled` | reversible | CIB1, Calcium_cyto | `kon1CaCIB1, koff1CaCIB1` | binding/complex formation | `CIB1(EF1) + Calcium_cyto(bd) <-> CIB1(EF1!1).Calcium_cyto(bd!1)` | Reversibly forms a complex/contact among CIB1, Calcium_cyto through CIB1.EF1, Calcium_cyto.bd at `kon1CaCIB1, koff1CaCIB1`. | +| 206 | `Unlabeled` | reversible | CIB1, Calcium_cyto | `kon2CaCIB1, koff2CaCIB1` | binding/complex formation | `CIB1(EF2) + Calcium_cyto(bd) <-> CIB1(EF2!1).Calcium_cyto(bd!1)` | Reversibly forms a complex/contact among CIB1, Calcium_cyto through CIB1.EF2, Calcium_cyto.bd at `kon2CaCIB1, koff2CaCIB1`. | +| 207 | `Unlabeled` | reversible | CIB1, SphK | `konCIB1SphK1, koffCIB1SphK1` | internal-state conversion/modification | `CIB1(EF1!+,EF2!+,sk1bd,location~cytosol) + SphK(CIB1bd,Serk~pS) <-> CIB1(EF1!+,EF2!+,sk1bd!1,location~cytosol).SphK(CIB1bd!1,Serk~pS)` | Reversibly forms a complex/contact among CIB1, SphK through CIB1.sk1bd, SphK.CIB1bd at `konCIB1SphK1, koffCIB1SphK1`. | +| 208 | `Unlabeled` | one-way | ERK2, SphK | `kcatERK/(freeSphK1+kmERKSK1)` | internal-state conversion/modification | `ERK2(S2~pS) + SphK(Serk~S) -> ERK2(S2~pS) + SphK(Serk~pS)` | Changes internal modification/state marks on ERK2, SphK: SphK.Serk S→pS at `kcatERK/(freeSphK1+kmERKSK1)`. | +| 209 | `Unlabeled` | reversible | CIB1 | `ktSK1, ktoffSK1` | internal-state conversion/modification | `CIB1(EF1!+,EF2!+,sk1bd!+,location~cytosol) <-> CIB1(EF1!+,EF2!+,sk1bd!+,location~membrane)` | Changes internal modification/state marks on CIB1: CIB1.location cytosol→membrane at `ktSK1, ktoffSK1`. | +| 210 | `Unlabeled` | one-way | CIB1 | `koffSK1` | internal-state conversion/modification | `CIB1(EF1,EF2,location~membrane) -> CIB1(EF1,EF2,location~cytosol)` | Changes internal modification/state marks on CIB1: CIB1.location membrane→cytosol at `koffSK1`. | +| 211 | `Unlabeled` | one-way | DAG, PKC, Raf | `kcatPKC/(freeraf+kmPKCRaf)` | internal-state conversion/modification | `PKC(CalciumBD!+,DAGBD!1).DAG(pkcbd!1) + Raf(Spkc~S) -> PKC(CalciumBD!+,DAGBD!1).DAG(pkcbd!1) + Raf(Spkc~pS)` | Changes internal modification/state marks on DAG, PKC, Raf: Raf.Spkc S→pS at `kcatPKC/(freeraf+kmPKCRaf)`. | +| 212 | `Unlabeled` | one-way | SphK | `kdpSK1` | internal-state conversion/modification | `SphK(Serk~pS) -> SphK(Serk~S)` | Changes internal modification/state marks on SphK: SphK.Serk pS→S at `kdpSK1`. | +| 213 | `Unlabeled` | one-way | Raf | `kdpPKCRaf` | internal-state conversion/modification | `Raf(Spkc~pS) -> Raf(Spkc~S)` | Changes internal modification/state marks on Raf: Raf.Spkc pS→S at `kdpPKCRaf`. | +| 214 | `Unlabeled` | one-way | I, Sph | `kSphgen` | source/synthesis or algebraic source term | `I() -> I() + Sph(skbd)` | Produces Sph while retaining or consuming I at `kSphgen`. | +| 215 | `Unlabeled` | one-way | CIB1, S1P, Sph, SphK | `kcatSK1Sph/(KmSK1Sph+freesphingosin)` | internal-state conversion/modification | `CIB1(sk1bd!1,location~membrane).SphK(CIB1bd!1,Serk~pS) + Sph(skbd) -> S1P(bd) + CIB1(sk1bd!1,location~membrane).SphK(CIB1bd!1,Serk~pS)` | Produces S1P while retaining or consuming CIB1, Sph, SphK at `kcatSK1Sph/(KmSK1Sph+freesphingosin)`. | +| 216 | `Unlabeled` | one-way | S1P, Sph | `kdpS1P` | pattern rewrite | `S1P(bd) -> Sph(skbd)` | Produces Sph while retaining or consuming S1P at `kdpS1P`. | +| 217 | `Unlabeled` | one-way | I, RasGTP | `kS1PRas*frees1p/(KmS1PRas+frees1p)-kRasGAP*gtpfreeras` | source/synthesis or algebraic source term | `I() -> I() + RasGTP(rafbd)` | Produces RasGTP while retaining or consuming I at `kS1PRas*frees1p/(KmS1PRas+frees1p)-kRasGAP*gtpfreeras`. | +| 218 | `Unlabeled` | reversible | Raf, RasGTP | `konRasRaf, koffRasRaf` | binding/complex formation | `Raf(rasbd) + RasGTP(rafbd) <-> Raf(rasbd!1).RasGTP(rafbd!1)` | Reversibly forms a complex/contact among Raf, RasGTP through Raf.rasbd, RasGTP.rafbd at `konRasRaf, koffRasRaf`. | +| 219 | `Unlabeled` | one-way | Raf, RasGTP | `kpRaf` | internal-state conversion/modification | `Raf(rasbd!1,Y1Y2~Y).RasGTP(rafbd!1) -> Raf(rasbd!1,Y1Y2~pY).RasGTP(rafbd!1)` | Changes internal modification/state marks on Raf, RasGTP: Raf.Y1Y2 Y→pY at `kpRaf`. | +| 220 | `Unlabeled` | one-way | Raf | `kdpRaf` | internal-state conversion/modification | `Raf(Y1Y2~pY) -> Raf(Y1Y2~Y)` | Changes internal modification/state marks on Raf: Raf.Y1Y2 pY→Y at `kdpRaf`. | +| 221 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf1/(KmMEK12Raf+mek12s1)` | internal-state conversion/modification | `MEK12(S1~S) + Raf(Y1Y2~pY,Spkc~S) -> Raf(Y1Y2~pY,Spkc~S) + MEK12(S1~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S1 S→pS at `kpMEK12Raf1/(KmMEK12Raf+mek12s1)`. | +| 222 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf2/(KmMEK12Raf+mek12s2)` | internal-state conversion/modification | `MEK12(S2~S) + Raf(Y1Y2~pY,Spkc~S) -> Raf(Y1Y2~pY,Spkc~S) + MEK12(S2~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S2 S→pS at `kpMEK12Raf2/(KmMEK12Raf+mek12s2)`. | +| 223 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf1/(KmMEK12Raf+mek12s2)` | internal-state conversion/modification | `MEK12(S1~S) + Raf(Y1Y2~pY,Spkc~pS) -> Raf(Y1Y2~pY,Spkc~pS) + MEK12(S1~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S1 S→pS at `kpMEK12Raf1/(KmMEK12Raf+mek12s2)`. | +| 224 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf2/(KmMEK12Raf+mek12s2)` | internal-state conversion/modification | `MEK12(S2~S) + Raf(Y1Y2~pY,Spkc~pS) -> Raf(Y1Y2~pY,Spkc~pS) + MEK12(S2~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S2 S→pS at `kpMEK12Raf2/(KmMEK12Raf+mek12s2)`. | +| 225 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf1/(KmMEK12Raf+mek12s1)` | internal-state conversion/modification | `MEK12(S1~S) + Raf(Y1Y2~Y,Spkc~pS) -> Raf(Y1Y2~Y,Spkc~pS) + MEK12(S1~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S1 S→pS at `kpMEK12Raf1/(KmMEK12Raf+mek12s1)`. | +| 226 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf2/(KmMEK12Raf+mek12s2)` | internal-state conversion/modification | `MEK12(S2~S) + Raf(Y1Y2~Y,Spkc~pS) -> Raf(Y1Y2~Y,Spkc~pS) + MEK12(S2~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S2 S→pS at `kpMEK12Raf2/(KmMEK12Raf+mek12s2)`. | +| 227 | `Unlabeled` | one-way | MEK12 | `kdpMEK12_1` | internal-state conversion/modification | `MEK12(S1~pS) -> MEK12(S1~S)` | Changes internal modification/state marks on MEK12: MEK12.S1 pS→S at `kdpMEK12_1`. | +| 228 | `Unlabeled` | one-way | MEK12 | `kdpMEK12_2` | internal-state conversion/modification | `MEK12(S2~pS) -> MEK12(S2~S)` | Changes internal modification/state marks on MEK12: MEK12.S2 pS→S at `kdpMEK12_2`. | +| 229 | `Unlabeled` | one-way | ERK1, MEK12 | `(kpMEK12ERK12_1/(kmMEKERK12+erk12s1))` | internal-state conversion/modification | `MEK12(S1~pS,S2~pS) + ERK1(S1~S) -> MEK12(S1~pS,S2~pS) + ERK1(S1~pS)` | Changes internal modification/state marks on ERK1, MEK12: ERK1.S1 S→pS at `(kpMEK12ERK12_1/(kmMEKERK12+erk12s1))`. | +| 230 | `Unlabeled` | one-way | ERK2, MEK12 | `(kpMEK12ERK12_2/(kmMEKERK12+erk12s2))` | internal-state conversion/modification | `MEK12(S1~pS,S2~pS) + ERK2(S2~S) -> MEK12(S1~pS,S2~pS) + ERK2(S2~pS)` | Changes internal modification/state marks on ERK2, MEK12: ERK2.S2 S→pS at `(kpMEK12ERK12_2/(kmMEKERK12+erk12s2))`. | +| 231 | `Unlabeled` | one-way | ERK1 | `kdpERK12_1` | internal-state conversion/modification | `ERK1(S1~pS) -> ERK1(S1~S)` | Changes internal modification/state marks on ERK1: ERK1.S1 pS→S at `kdpERK12_1`. | +| 232 | `Unlabeled` | one-way | ERK2 | `kdpERK12_2` | internal-state conversion/modification | `ERK2(S2~pS) -> ERK2(S2~S)` | Changes internal modification/state marks on ERK2: ERK2.S2 pS→S at `kdpERK12_2`. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `vegffrees` | `Molecules` | `vegf(r,r,nrp1bd,c~s)` | Reports free/unbound species matching the pattern. | +| `VEGFR2total` | `Molecules` | `vegfr2()` | Reports total pool matching the pattern. | +| `tsp1frees` | `Molecules` | `TSP1(CD47bd)` | Reports free/unbound species matching the pattern. | +| `cd47tsp1s` | `Molecules` | `TSP1(CD47bd!1).CD47SIRPa(TSP1bd!1,Y1~Y,c~s)` | Reports bound or complexed species matching the pattern. | +| `cd47s` | `Molecules` | `CD47SIRPa(TSP1bd,Y1~Y,c~s)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `VEGFR2tots` | `Molecules` | `vegfr2(c~s)` | Reports total pool matching the pattern. | +| `VEGFR2toti` | `Molecules` | `vegfr2(c~i)` | Reports total pool matching the pattern. | +| `vr2s` | `Molecules` | `vegfr2(l1,c~s)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `vr2i` | `Molecules` | `vegfr2(l1,c~i)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `vr1s` | `Molecules` | `vegfr1(l2,nrp1bd,c~s)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `vegfr2Y1175ps` | `Molecules` | `vegfr2(Y1175~pY!?,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `vegfr2Y1175pi` | `Molecules` | `vegfr2(Y1175~pY!?,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `pr2Y1175total` | `Molecules` | `vegfr2(Y1175~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `vegfr1tots` | `Molecules` | `vegfr1(c~s)` | Reports total pool matching the pattern. | +| `NRP1VEGFR2s` | `Molecules` | `vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,c~s).vegfr2(l1!2,c~s)` | Reports bound or complexed species matching the pattern. | +| `NRP1VEGFR2i` | `Molecules` | `vegf(r!1,r!2,nrp1bd!+,c~i).vegfr2(l1!1,c~i).vegfr2(l1!2,c~i)` | Reports bound or complexed species matching the pattern. | +| `freeDAGs` | `Molecules` | `DAG(pkcbd!?)` | Reports free/unbound species matching the pattern. | +| `activePLCgamma` | `Molecules` | `PLCgamma(Yplc~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `PIP2` | `Molecules` | `PI(PIsite~3P)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `PIP3` | `Molecules` | `PI(PIsite~4P)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `freeip3cyto` | `Molecules` | `IP3_cyto(ip3rbd)` | Reports free/unbound species matching the pattern. | +| `Cac` | `Molecules` | `Calcium_cyto(bd)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Caer` | `Molecules` | `CaER(bd)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `CaBuf_fer` | `Molecules` | `CaF(cabd!+)` | Reports bound or complexed species matching the pattern. | +| `activePKCs` | `Molecules` | `PKC(CalciumBD!+,DAGBD!1).DAG(pkcbd!1)` | Reports bound or complexed species matching the pattern. | +| `activePKCtot` | `Molecules` | `PKC(CalciumBD!+,DAGBD!+)` | Reports total pool matching the pattern. | +| `SphKpkc` | `Molecules` | `SphK(Serk~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `S1phosphate` | `Molecules` | `S1P(bd)` | Reports phosphorylated or modified species matching the pattern. | +| `NRP1frees` | `Molecules` | `NRP1(vegfabd,c~s)` | Reports free/unbound species matching the pattern. | +| `NRP1freei` | `Molecules` | `NRP1(vegfabd,c~i)` | Reports free/unbound species matching the pattern. | +| `NRP1bounds` | `Molecules` | `NRP1(vegfabd!+,c~s)` | Reports bound or complexed species matching the pattern. | +| `NRP1boundi` | `Molecules` | `NRP1(vegfabd!+,c~i)` | Reports bound or complexed species matching the pattern. | +| `vr2dimers` | `Molecules` | `vegfr2(l1,dimer!1,c~s).vegfr2(l1,dimer!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `vr2dimeri` | `Molecules` | `vegfr2(l1,dimer!1,c~i).vegfr2(l1,dimer!1,c~i)` | Reports bound or complexed species matching the pattern. | +| `NRP1totals` | `Molecules` | `NRP1(c~s)` | Reports total pool matching the pattern. | +| `NRP1totali` | `Molecules` | `NRP1(c~i)` | Reports total pool matching the pattern. | +| `singleNRP1totals` | `Molecules` | `NRP1(vegfabd,c~s)` | Reports total pool matching the pattern. | +| `singleNRP1totali` | `Molecules` | `NRP1(vegfabd,c~i)` | Reports total pool matching the pattern. | +| `vegfr2total` | `Molecules` | `vegf(r!1).vegfr2(l1!1)` | Reports total pool matching the pattern. | +| `vr2Y1175s` | `Molecules` | `vegfr2(Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2Y1175i` | `Molecules` | `vegfr2(Y1175~pY,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `plcgammafree` | `Molecules` | `PLCgamma(Yplc~Y)` | Reports free/unbound species matching the pattern. | +| `rasgdpfree` | `Molecules` | `RasGDP(rafbd!?)` | Reports free/unbound species matching the pattern. | +| `rasgtpfree` | `Molecules` | `RasGTP(rafbd!?)` | Reports free/unbound species matching the pattern. | +| `activeRafbyrastot` | `Molecules` | `Raf(Y1Y2~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoMEK12tot` | `Molecules` | `MEK12(S1~pS!?,S2~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoERK1tot` | `Molecules` | `ERK1(S1~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoERK2tot` | `Molecules` | `ERK2(S2~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `SphK1` | `Molecules` | `SphK(CIB1bd!+,Serk~S).CIB1(sk1bd!1,location~membrane)` | Reports bound or complexed species matching the pattern. | +| `SphK1mempS` | `Molecules` | `SphK(CIB1bd!+,Serk~pS).CIB1(sk1bd!1,location~membrane)` | Reports phosphorylated or modified species matching the pattern. | +| `SphK1cytosol` | `Molecules` | `SphK(CIB1bd!+,Serk~S).CIB1(sk1bd!1,location~cytosol)` | Reports bound or complexed species matching the pattern. | +| `activeSphK1` | `Molecules` | `SphK(Serk~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `freeSK1` | `Molecules` | `SphK(CIB1bd,Serk~S)` | Reports free/unbound species matching the pattern. | +| `freeSK1mem` | `Molecules` | `SphK(CIB1bd!1,Serk~S).CIB1(sk1bd!1,location~membrane)` | Reports free/unbound species matching the pattern. | +| `freecib1` | `Molecules` | `CIB1(EF1,EF2,sk1bd)` | Reports free/unbound species matching the pattern. | +| `calciumcib1` | `Molecules` | `CIB1(EF1!+,EF2!+,sk1bd)` | Reports bound or complexed species matching the pattern. | +| `sk1bcib1` | `Molecules` | `CIB1(EF1!+,EF2!+,sk1bd!+)` | Reports bound or complexed species matching the pattern. | +| `nrp1s` | `Molecules` | `NRP1(vegfabd,c~s)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `vegfnrp1s` | `Molecules` | `vegf(r,r,nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfr1s` | `Molecules` | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfr2s` | `Molecules` | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s)` | Reports bound or complexed species matching the pattern. | +| `freepip2` | `Molecules` | `PI(PIsite~3P)` | Reports free/unbound species matching the pattern. | +| `freesphingosin` | `Molecules` | `Sph(skbd)` | Reports free/unbound species matching the pattern. | +| `freeraf` | `Molecules` | `Raf(Spkc~S)` | Reports free/unbound species matching the pattern. | +| `activeRafPKC` | `Molecules` | `Raf(Spkc~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `activeRafPKCERK1` | `Molecules` | `Raf(Spkc~pS!?,Y1Y2~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `activeRafPKCERK2` | `Molecules` | `Raf(Spkc~pS!?,Y1Y2~Y!?)` | Reports phosphorylated or modified species matching the pattern. | +| `activeRafPKCERK3` | `Molecules` | `Raf(Spkc~S!?,Y1Y2~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `rafY1Y2pY` | `Molecules` | `Raf(Y1Y2~pY,Spkc~S)` | Reports phosphorylated or modified species matching the pattern. | +| `rafY1Y2pYpS` | `Molecules` | `Raf(Y1Y2~pY,Spkc~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `rafpS` | `Molecules` | `Raf(Y1Y2~Y,Spkc~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `erk1s` | `Molecules` | `ERK1(S1~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `mek12s` | `Molecules` | `MEK12(S1~S,S2~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `R2singlei` | `Molecules` | `vegfr2(l1,Y1175~Y,dimer,c~i)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `pERK1s` | `Molecules` | `ERK1(S1~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `mek12ps` | `Molecules` | `MEK12(S1~pS,S2~S)` | Reports phosphorylated or modified species matching the pattern. | +| `pERK2s` | `Molecules` | `ERK2(S2~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `mek12ps1` | `Molecules` | `MEK12(S1~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `mek12ps2` | `Molecules` | `MEK12(S2~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `erk1ps` | `Molecules` | `ERK1(S1~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `erk2ps` | `Molecules` | `ERK2(S2~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2r2py1175s` | `Molecules` | `vegfr2(Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2r2py1175i` | `Molecules` | `vegfr2(Y1175~pY,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2py1175s` | `Species` | `vegf(r!1,r,c~s).vegfr2(l1!1,Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2py1175i` | `Species` | `vegf(r!1,r,c~i).vegfr2(l1!1,Y1175~pY,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `r2singlepy1175s` | `Molecules` | `vegfr2(l1,Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `r2singlepy1175i` | `Molecules` | `vegfr2(l1,Y1175~pY,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `vr1r2pY1165s` | `Molecules` | `vegf(r!1,r!2,c~s).vegfr1(l2!1,c~s).vegfr2(l1!2,Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `pSK1` | `Molecules` | `SphK(Serk~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `frees1p` | `Molecules` | `S1P(bd)` | Reports free/unbound species matching the pattern. | +| `py1y2rafs` | `Molecules` | `Raf(Y1Y2~pY)` | Reports phosphorylated or modified species matching the pattern. | +| `vegfnrp1i` | `Molecules` | `vegf(r,r,nrp1bd!1,c~i).NRP1(vegfabd!1,c~i)` | Reports bound or complexed species matching the pattern. | +| `vegfr2i` | `Species` | `vegf(r!1,r,nrp1bd,c~i).vegfr2(l1!1,c~i)` | Reports bound or complexed species matching the pattern. | +| `totalnrp1` | `Molecules` | `NRP1(vegfabd)` | Reports total pool matching the pattern. | +| `pplcgamma` | `Molecules` | `PLCgamma(Yplc~pY)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoERKpS1` | `Molecules` | `ERK1(S1~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoERKpS2` | `Molecules` | `ERK2(S2~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoMEKpS1` | `Molecules` | `MEK12(S1~pS!?,S2~S)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoMEKpS2` | `Molecules` | `MEK12(S1~S,S2~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `freeSphK1` | `Molecules` | `SphK(CIB1bd,Serk~S)` | Reports free/unbound species matching the pattern. | +| `rafpkc` | `Molecules` | `Raf(Spkc~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `mek12s1` | `Molecules` | `MEK12(S1~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `mek12s2` | `Molecules` | `MEK12(S2~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `erk12s1` | `Molecules` | `ERK1(S1~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `erk12s2` | `Molecules` | `ERK2(S2~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `yplcgamma` | `Molecules` | `PLCgamma(Yplc~Y)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `gtpfreeras` | `Molecules` | `RasGTP(rafbd)` | Reports free/unbound species matching the pattern. | +| `bvegfr2` | `Molecules` | `vegf(r!1,nrp1bd,c~s).vegfr2(l1!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `bnrp1` | `Molecules` | `vegf(nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `bvegfr1` | `Molecules` | `vegf(r!1,nrp1bd,c~s).vegfr1(l2!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `bvegfr1dimer` | `Molecules` | `vegf(r!1,r!2,c~s).vegfr1(l2!1,c~s).vegfr1(l2!2,c~s)` | Reports bound or complexed species matching the pattern. | +| `bvegfr2_2` | `Molecules` | `vegf(r!1,c~s).vegfr2(l1!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `bvegfr1_2` | `Molecules` | `vegf(r!1,c~s).vegfr1(l2!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfbound_1` | `Molecules` | `vegf(r!+,nrp1bd,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfbound_2` | `Species` | `vegf(r,nrp1bd!+,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfbound_3` | `Molecules` | `vegf(r!+,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfbound_4` | `Species` | `vegf(r,r,nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `Iopenstim` | `Molecules` | `Istim()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `nrp1r1s` | `Molecules` | `NRP1(vegfabd!1,c~s).vegfr1(nrp1bd!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `CIB1mem` | `Molecules` | `CIB1(location~membrane)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `freepip3` | `Molecules` | `PI(PIsite~4P)` | Reports free/unbound species matching the pattern. | +| `ps473akt` | `Molecules` | `AKT(S473~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `ps308akt` | `Molecules` | `AKT(T308~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoAxltotal` | `Molecules` | `Axl(Ysrc~pY!?,Yaxl~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoAxlpSrc` | `Molecules` | `Axl(Ysrc~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoAxlpauto` | `Molecules` | `Axl(Yaxl~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `activeSrc` | `Molecules` | `TSADSrc(Y1~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoeNOS` | `Molecules` | `eNOS(S1177~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `ppAkt` | `Molecules` | `AKT(S473~pS,T308~pS)` | Reports phosphorylated or modified species matching the pattern. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1,max_agg=>10})` — execution command affecting network generation, simulation, scanning, or output. + +## 9. Technical caveats and ambiguities + +- No compartments or anchors are declared despite many molecule states named like surface/internal/recycling states (`s`, `i`, `i2`, `r`). Those are internal states, not BNGL compartments. + +- The model uses many algebraic rate expressions directly in reaction rules rather than a separate functions block. + +- Several receptor-state transitions are encoded as explicit rules over the `c` internal state. + +- The complete rule inventory has 232 rows; downstream review should compare this count with the `begin reaction rules` block after any source edits. + +- The summary keeps raw molecule, site, state, and parameter names because this is the coder-facing version and those identifiers are necessary for implementation review. diff --git a/data/summaries_detailed/Zhang2023_coder.md b/data/summaries_detailed/Zhang2023_coder.md new file mode 100644 index 00000000..9c36790e --- /dev/null +++ b/data/summaries_detailed/Zhang2023_coder.md @@ -0,0 +1,692 @@ +# Coder Model Explanation: Zhang 2023 + +## 1. Model identity and scope + +- **Model id:** `Zhang_2023` +- **Title:** Zhang 2023 +- **BNGL path:** `Published/Zhang2023/Zhang_2023.bngl` +- **YAML path:** `Published/Zhang2023/metadata.yaml` +- **Metadata description:** VEGF signaling +- **Scope:** A large VEGF signaling model centered on VEGF165a, VEGFR2, VEGFR1, NRP1, CD47/TSP1, PI3K/AKT, PLCγ/IP3/DAG/calcium, eNOS, PKC/CIB1/SphK/S1P, Ras/Raf/MEK/ERK, and Axl/Src cross-talk. It is long but still smaller than Dolan2015, with hundreds of explicit rules and no declared compartments or anchors. + +## 2. BNGL block inventory + +| Block | Present? | Count / role | +| --- | --- | --- | +| Parameters | Yes | 180 parameter entries. | +| Compartments | No | 0 compartment entries. | +| Anchors | No | 0 anchor entries. | +| Molecule types | Yes | 38 molecule type entries. | +| Seed/species | Yes | 34 initial species entries. | +| Observables | Yes | 129 observable entries. | +| Functions | No | 0 function entries. | +| Reaction rules | Yes | 232 reaction rules. | +| Actions | Yes | 1 action or inline execution commands. | + +## 3. Parameters, functions, and rate laws + +The model uses the following parameter entries. Comment text is preserved when the source provides it; otherwise the role is inferred from the parameter name and where it is used. + +| Parameter | Value/expression | Role / source comment | +| --- | --- | --- | +| `Volcyto` | `9.12E-13` | Geometry/scaling parameter. | +| `VolER` | `3.35E-13` | Geometry/scaling parameter. | +| `fextmolar` | `1.205E+15` | Model parameter used by rules, functions, species, or observables. | +| `cellarea` | `1400` | Geometry/scaling parameter. | +| `VEGF165a_0` | `0.0012` | Initial amount or baseline condition parameter. | +| `VEGFR2_0` | `4.29E+00` | Initial amount or baseline condition parameter. | +| `VEGFR1_0` | `1.43` | Initial amount or baseline condition parameter. | +| `NRP1_0` | `2.86E+01` | Initial amount or baseline condition parameter. | +| `TSP1_0` | `0.00E+00` | Initial amount or baseline condition parameter. | +| `Calcium_0` | `0.05` | Initial amount or baseline condition parameter. | +| `CaM_0` | `1` | Initial amount or baseline condition parameter. | +| `eNOS_0` | `0.1` | Initial amount or baseline condition parameter. | +| `kvron` | `10.3` | Kinetic rate or kinetic expression parameter. | +| `kvroff` | `2.36E-01` | Kinetic rate or kinetic expression parameter. | +| `kcVR` | `0.0045` | Kinetic rate or kinetic expression parameter. | +| `kcRR` | `1.11` | Kinetic rate or kinetic expression parameter. | +| `kdRR` | `0.78` | Kinetic rate or kinetic expression parameter. | +| `kvr1on` | `22` | Kinetic rate or kinetic expression parameter. | +| `kvr1off` | `0.026` | Kinetic rate or kinetic expression parameter. | +| `kdeltaRR` | `2.5` | Kinetic rate or kinetic expression parameter. | +| `kdeltaVR` | `2.05` | Kinetic rate or kinetic expression parameter. | +| `kpr2` | `30` | Kinetic rate or kinetic expression parameter. | +| `kdps` | `640` | Kinetic rate or kinetic expression parameter. | +| `kdpi` | `0.72` | Kinetic rate or kinetic expression parameter. | +| `kdpr` | `1.00E+01` | Kinetic rate or kinetic expression parameter. | +| `kcd47free_on` | `100` | Kinetic rate or kinetic expression parameter. | +| `kr2si` | `0.031` | Kinetic rate or kinetic expression parameter. | +| `kr2rs` | `17.18` | Kinetic rate or kinetic expression parameter. | +| `kr2NRP1si` | `0.0014` | Kinetic rate or kinetic expression parameter. | +| `kr2NRP1i2r` | `48` | Kinetic rate or kinetic expression parameter. | +| `kVEGFNRP1on` | `2.48` | Kinetic rate or kinetic expression parameter. | +| `kVEGFNRP1off` | `0.0008` | Kinetic rate or kinetic expression parameter. | +| `kNRP1VEGFR2on` | `0.15` | Kinetic rate or kinetic expression parameter. | +| `kNRP1VEGFR2off` | `0.045` | Kinetic rate or kinetic expression parameter. | +| `kNRP1VEGFR1on` | `5.07` | Kinetic rate or kinetic expression parameter. | +| `kNRP1VEGFR1off` | `0.016` | Kinetic rate or kinetic expression parameter. | +| `kVEGFR2NRP1on` | `0.0022` | Kinetic rate or kinetic expression parameter. | +| `kVEGFR2NRP1off` | `0.014` | Kinetic rate or kinetic expression parameter. | +| `kVEGFR1NRP1on` | `0.004` | Kinetic rate or kinetic expression parameter. | +| `kVEGFR1NRP1off` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `PI3K_0` | `0.1` | Initial amount or baseline condition parameter. | +| `PIP2_0` | `10` | Initial amount or baseline condition parameter. | +| `kPIP2gen` | `0.000048` | Kinetic rate or kinetic expression parameter. | +| `kmPIP2PI3K` | `309.9` | Kinetic rate or kinetic expression parameter. | +| `kcatPI3KPIP2` | `1764.48` | Kinetic rate or kinetic expression parameter. | +| `PTEN_0` | `0.1` | Initial amount or baseline condition parameter. | +| `kmPIP3PTEN` | `6.27` | Kinetic rate or kinetic expression parameter. | +| `kcatPTENPIP3` | `4767.44` | Kinetic rate or kinetic expression parameter. | +| `konPDK1PIP3` | `5828.07` | Kinetic rate or kinetic expression parameter. | +| `koffPDK1PIP3` | `0.64` | Kinetic rate or kinetic expression parameter. | +| `konAKTPIP3` | `12.48` | Kinetic rate or kinetic expression parameter. | +| `koffAKTPIP3` | `0.032` | Kinetic rate or kinetic expression parameter. | +| `AKT_0` | `0.1` | Initial amount or baseline condition parameter. | +| `PDK1_0` | `0.1` | Initial amount or baseline condition parameter. | +| `kpAKTPDK1` | `2` | Kinetic rate or kinetic expression parameter. | +| `mTOR_0` | `0.1` | Initial amount or baseline condition parameter. | +| `kpmTORAKT` | `2` | Kinetic rate or kinetic expression parameter. | +| `kdp473AKTPPase` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `kdp308AKTPPase` | `0.038` | Kinetic rate or kinetic expression parameter. | +| `kpPLCgamma` | `0.045` | Kinetic rate or kinetic expression parameter. | +| `kdpPLCgamma` | `0.014` | Kinetic rate or kinetic expression parameter. | +| `PLCgamma_0` | `0.2` | Initial amount or baseline condition parameter. | +| `kmPIP2PLCgamma` | `4.34` | Kinetic rate or kinetic expression parameter. | +| `nDAG` | `2.6` | Model parameter used by rules, functions, species, or observables. | +| `kcatPLCgammaDAG` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `kdeg_ip3` | `0.47` | Kinetic rate or kinetic expression parameter. | +| `kdeg_DAG` | `0.11` | Kinetic rate or kinetic expression parameter. | +| `CaER_0` | `2.00E+03` | Initial amount or baseline condition parameter. | +| `Iip3Ramp` | `1.31E+05` | Model parameter used by rules, functions, species, or observables. | +| `KmIP3R` | `1.6` | Kinetic rate or kinetic expression parameter. | +| `I_PMCAbar` | `2.02` | Model parameter used by rules, functions, species, or observables. | +| `KmPMCA` | `0.26` | Kinetic rate or kinetic expression parameter. | +| `vSERCA` | `0.39` | Model parameter used by rules, functions, species, or observables. | +| `KleakER` | `1.00E-08` | Kinetic rate or kinetic expression parameter. | +| `KmSERCA` | `0.15` | Kinetic rate or kinetic expression parameter. | +| `KiCa` | `1` | Kinetic rate or kinetic expression parameter. | +| `KBon` | `100` | Kinetic rate or kinetic expression parameter. | +| `KBoff` | `300` | Kinetic rate or kinetic expression parameter. | +| `CaF_0` | `118` | Initial amount or baseline condition parameter. | +| `CaFbound_0` | `2` | Initial amount or baseline condition parameter. | +| `koffCaNCaM1` | `500` | Kinetic rate or kinetic expression parameter. | +| `kdCaNCaM` | `24` | Kinetic rate or kinetic expression parameter. | +| `koffCaCCaM1` | `10` | Kinetic rate or kinetic expression parameter. | +| `kdCaCCaM` | `3.1` | Kinetic rate or kinetic expression parameter. | +| `CSQN_total` | `15000` | Model parameter used by rules, functions, species, or observables. | +| `KCSQN` | `800` | Kinetic rate or kinetic expression parameter. | +| `kdegi0` | `2.02E-03` | Initial amount or baseline condition parameter. | +| `kdegr2NRP1i0` | `7.91E-03` | Initial amount or baseline condition parameter. | +| `kdegi0noP` | `2.85E+00` | Kinetic rate or kinetic expression parameter. | +| `kdegr2NRP1i0noP` | `2.22E-04` | Kinetic rate or kinetic expression parameter. | +| `kr2ii2` | `4.30E-03` | Kinetic rate or kinetic expression parameter. | +| `kr2NRP1ii2` | `4.80E+00` | Kinetic rate or kinetic expression parameter. | +| `kr2i2i` | `3.23E-02` | Kinetic rate or kinetic expression parameter. | +| `kr2NRP1i2i` | `1.00E-03` | Kinetic rate or kinetic expression parameter. | +| `kdegi20` | `2.43E+02` | Initial amount or baseline condition parameter. | +| `kdegr2NRP1i20` | `3.76E-02` | Initial amount or baseline condition parameter. | +| `kdegi20noP` | `4.16E-01` | Kinetic rate or kinetic expression parameter. | +| `kdegr2NRP1i20noP` | `7.56E+02` | Kinetic rate or kinetic expression parameter. | +| `ksingleR2syn` | `1.40E-04` | Kinetic rate or kinetic expression parameter. | +| `ksingleR2deg` | `5.88E-04` | Kinetic rate or kinetic expression parameter. | +| `ksingleR2si` | `7.56E-04` | Kinetic rate or kinetic expression parameter. | +| `ksingleR2is` | `8.66E-04` | Kinetic rate or kinetic expression parameter. | +| `ICracamp` | `5.86E+03` | Model parameter used by rules, functions, species, or observables. | +| `Kcrac` | `169` | Kinetic rate or kinetic expression parameter. | +| `Istim0` | `0.18` | Initial amount or baseline condition parameter. | +| `tau_stim` | `4` | Model parameter used by rules, functions, species, or observables. | +| `ncrac` | `4.2` | Model parameter used by rules, functions, species, or observables. | +| `Src_0` | `0.1` | Initial amount or baseline condition parameter. | +| `Axl_0` | `7.14` | Initial amount or baseline condition parameter. | +| `kpSrc` | `0.61` | Kinetic rate or kinetic expression parameter. | +| `kdpSrc` | `136.5` | Kinetic rate or kinetic expression parameter. | +| `kpSrcAxl` | `3.92` | Kinetic rate or kinetic expression parameter. | +| `kpAxlauto` | `0.12` | Kinetic rate or kinetic expression parameter. | +| `kdpautoAxl` | `1291.1` | Kinetic rate or kinetic expression parameter. | +| `kdpSrcAxl` | `1.79E-03` | Kinetic rate or kinetic expression parameter. | +| `konPI3KAxl` | `55.91688952` | Kinetic rate or kinetic expression parameter. | +| `koffPI3KAxl` | `0.6` | Kinetic rate or kinetic expression parameter. | +| `kDCD47TSP1` | `1.00E-05` | Kinetic rate or kinetic expression parameter. | +| `koffCD47TSP1` | `0.001` | Kinetic rate or kinetic expression parameter. | +| `CD47free_0` | `7.14E+00` | Initial amount or baseline condition parameter. | +| `kdpeNOS` | `5.17E-02` | Kinetic rate or kinetic expression parameter. | +| `konCaMeNOS` | `9.80E+02` | Kinetic rate or kinetic expression parameter. | +| `koffCaMeNOS` | `9.73E+00` | Kinetic rate or kinetic expression parameter. | +| `koffeNOScav1` | `6.875` | Kinetic rate or kinetic expression parameter. | +| `koncaveNOS` | `81.9375` | Kinetic rate or kinetic expression parameter. | +| `kcateNOSAKT` | `1000` | Kinetic rate or kinetic expression parameter. | +| `kr2CD47off` | `1.00E+00` | Kinetic rate or kinetic expression parameter. | +| `f_TSP1deg` | `1.00E+00` | Model parameter used by rules, functions, species, or observables. | +| `fTSP1dp` | `1.00E+00` | Model parameter used by rules, functions, species, or observables. | +| `fTSP1i2r` | `1.00E+00` | Model parameter used by rules, functions, species, or observables. | +| `PKC_0` | `0.1` | Initial amount or baseline condition parameter. | +| `konCaPKC` | `0.3` | Kinetic rate or kinetic expression parameter. | +| `koffCaPKC` | `0.01` | Kinetic rate or kinetic expression parameter. | +| `konDAGPKC` | `0.029957319` | Kinetic rate or kinetic expression parameter. | +| `koffDAGPKC` | `0.124096212` | Kinetic rate or kinetic expression parameter. | +| `kon1CaCIB1` | `0.052631579` | Kinetic rate or kinetic expression parameter. | +| `koff1CaCIB1` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `kon2CaCIB1` | `0.185185185` | Kinetic rate or kinetic expression parameter. | +| `koff2CaCIB1` | `0.1` | Kinetic rate or kinetic expression parameter. | +| `CIB1_0` | `0.5` | Initial amount or baseline condition parameter. | +| `konCIB1SphK1` | `17.6028519` | Kinetic rate or kinetic expression parameter. | +| `koffCIB1SphK1` | `4.403956392` | Kinetic rate or kinetic expression parameter. | +| `SphK_0` | `0.1` | Initial amount or baseline condition parameter. | +| `Sph_0` | `10` | Initial amount or baseline condition parameter. | +| `S1P_0` | `0` | Initial amount or baseline condition parameter. | +| `kcatERK` | `7.882741692` | Kinetic rate or kinetic expression parameter. | +| `kmERKSK1` | `1.198236617` | Kinetic rate or kinetic expression parameter. | +| `ktSK1` | `1` | Kinetic rate or kinetic expression parameter. | +| `koffSK1` | `1.04E-01` | Kinetic rate or kinetic expression parameter. | +| `ktoffSK1` | `6.97E-04` | Kinetic rate or kinetic expression parameter. | +| `kcatPKC` | `10.20798409` | Kinetic rate or kinetic expression parameter. | +| `kmPKCRaf` | `0.313875333` | Kinetic rate or kinetic expression parameter. | +| `RasGTP_0` | `0` | Initial amount or baseline condition parameter. | +| `RasGDP_0` | `0.1` | Initial amount or baseline condition parameter. | +| `Raf_0` | `0.355471965` | Initial amount or baseline condition parameter. | +| `MEK12_0` | `0.288919159` | Initial amount or baseline condition parameter. | +| `ERK12_0` | `0.382329627` | Initial amount or baseline condition parameter. | +| `kdpSK1` | `0.02182773` | Kinetic rate or kinetic expression parameter. | +| `kdpPKCRaf` | `0.720296112` | Kinetic rate or kinetic expression parameter. | +| `kSphgen` | `0.000048` | Kinetic rate or kinetic expression parameter. | +| `kcatSK1Sph` | `37.23820691` | Kinetic rate or kinetic expression parameter. | +| `KmSK1Sph` | `0.029430478` | Kinetic rate or kinetic expression parameter. | +| `kdpS1P` | `1.188017664` | Kinetic rate or kinetic expression parameter. | +| `kS1PRas` | `1.556423632` | Kinetic rate or kinetic expression parameter. | +| `KmS1PRas` | `5.899306591` | Kinetic rate or kinetic expression parameter. | +| `kRasGAP` | `2.941097467` | Kinetic rate or kinetic expression parameter. | +| `konRasRaf` | `13.10183719` | Kinetic rate or kinetic expression parameter. | +| `koffRasRaf` | `0.151878139` | Kinetic rate or kinetic expression parameter. | +| `kpRaf` | `1.67558904` | Kinetic rate or kinetic expression parameter. | +| `kdpRaf` | `0.894826206` | Kinetic rate or kinetic expression parameter. | +| `kpMEK12Raf1` | `1.801786102` | Kinetic rate or kinetic expression parameter. | +| `kpMEK12Raf2` | `1.204676328` | Kinetic rate or kinetic expression parameter. | +| `KmMEK12Raf` | `0.807388937` | Kinetic rate or kinetic expression parameter. | +| `kdpMEK12_1` | `0.111827134` | Kinetic rate or kinetic expression parameter. | +| `kdpMEK12_2` | `0.139705453` | Kinetic rate or kinetic expression parameter. | +| `kpMEK12ERK12_1` | `12.14930177` | Kinetic rate or kinetic expression parameter. | +| `kmMEKERK12` | `0.25546079` | Kinetic rate or kinetic expression parameter. | +| `kpMEK12ERK12_2` | `0.516270813` | Kinetic rate or kinetic expression parameter. | +| `kdpERK12_1` | `6.06E+00` | Kinetic rate or kinetic expression parameter. | +| `kdpERK12_2` | `1.053392443` | Kinetic rate or kinetic expression parameter. | + +No separate BNGL functions are declared; rule rates are direct parameters or algebraic expressions embedded in the rule inventory. + +## 4. Molecule types, sites, and states + +| Molecule type | Site count | Sites/components | Internal states | Anchor/allowed compartments | Binding/modification roles | Notes | +| --- | ---: | --- | --- | --- | --- | --- | +| `vegf` | 4 | `r`, `r`, `nrp1bd`, `c` | c: s, i, i2, r | None | r is used as a binding/matching component; r is used as a binding/matching component; nrp1bd is used as a binding/matching component; c is an internal state/modification coordinate | vegf165a | +| `vegfr2` | 5 | `l1`, `Y1175`, `CD47bd`, `dimer`, `c` | Y1175: Y, pY; c: s, i, i2, r | None | l1 is used as a binding/matching component; Y1175 is an internal state/modification coordinate; CD47bd is used as a binding/matching component; dimer is used as a binding/matching component; c is an internal state/modification coordinate | Declared in molecule types block. | +| `vegfr1` | 4 | `l2`, `dimer`, `nrp1bd`, `c` | c: s | None | l2 is used as a binding/matching component; dimer is used as a binding/matching component; nrp1bd is used as a binding/matching component; c is an internal state/modification coordinate | Declared in molecule types block. | +| `NRP1` | 2 | `vegfabd`, `c` | c: s, i, i2, r | None | vegfabd is used as a binding/matching component; c is an internal state/modification coordinate | Declared in molecule types block. | +| `PI` | 1 | `PIsite` | PIsite: 3P, 4P | None | PIsite is an internal state/modification coordinate | Declared in molecule types block. | +| `PLCgamma` | 1 | `Yplc` | Yplc: Y, pY | None | Yplc is an internal state/modification coordinate | Declared in molecule types block. | +| `DAG` | 1 | `pkcbd` | None | None | pkcbd is used as a binding/matching component | Declared in molecule types block. | +| `IP3_cyto` | 1 | `ip3rbd` | None | None | ip3rbd is used as a binding/matching component | Declared in molecule types block. | +| `Calcium_cyto` | 1 | `bd` | None | None | bd is used as a binding/matching component | Declared in molecule types block. | +| `Trash` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `CaER` | 1 | `bd` | None | None | bd is used as a binding/matching component | Declared in molecule types block. | +| `CaF` | 1 | `cabd` | None | None | cabd is used as a binding/matching component | Declared in molecule types block. | +| `CSQNF` | 1 | `cabd` | None | None | cabd is used as a binding/matching component | Declared in molecule types block. | +| `CaM` | 5 | `NCaM`, `NCaM`, `CCaM`, `CCaM`, `CaMtargetbd` | None | None | CaMtargetbd is used as a binding/matching component | Declared in molecule types block. | +| `I` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `Istim` | 0 | None | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `PTEN` | 1 | `PIP3docking` | None | None | No specific role inferred beyond molecule identity. | Declared in molecule types block. | +| `TSADSrc` | 1 | `Y1` | Y1: Y, pY | None | Y1 is an internal state/modification coordinate | Declared in molecule types block. | +| `Axl` | 2 | `Ysrc`, `Yaxl` | Ysrc: Y, pY; Yaxl: Y, pY | None | Ysrc is an internal state/modification coordinate; Yaxl is an internal state/modification coordinate | Declared in molecule types block. | +| `PI3K` | 1 | `state` | state: active, inactive | None | state is an internal state/modification coordinate | Declared in molecule types block. | +| `AKT` | 3 | `PHakt`, `T308`, `S473` | T308: S, pS; S473: S, pS | None | T308 is an internal state/modification coordinate; S473 is an internal state/modification coordinate | Declared in molecule types block. | +| `PDK1` | 2 | `PHpdk1`, `aktbd` | None | None | aktbd is used as a binding/matching component | Declared in molecule types block. | +| `mTOR` | 1 | `aktbd` | None | None | aktbd is used as a binding/matching component | Declared in molecule types block. | +| `CD47SIRPa` | 4 | `VEGFR2bd`, `TSP1bd`, `Y1`, `c` | Y1: Y, pY; c: s, i, i2, r | None | VEGFR2bd is used as a binding/matching component; TSP1bd is used as a binding/matching component; Y1 is an internal state/modification coordinate; c is an internal state/modification coordinate | Declared in molecule types block. | +| `TSP1` | 1 | `CD47bd` | None | None | CD47bd is used as a binding/matching component | Declared in molecule types block. | +| `eNOS` | 3 | `CaMBD`, `S1177`, `cav1BD` | S1177: S, pS | None | CaMBD is used as a binding/matching component; S1177 is an internal state/modification coordinate; cav1BD is used as a binding/matching component | Declared in molecule types block. | +| `caveolin1` | 1 | `eNOSbd` | None | None | eNOSbd is used as a binding/matching component | Declared in molecule types block. | +| `PKC` | 2 | `CalciumBD`, `DAGBD` | None | None | CalciumBD is used as a binding/matching component; DAGBD is used as a binding/matching component | Declared in molecule types block. | +| `CIB1` | 4 | `EF1`, `EF2`, `sk1bd`, `location` | location: cytosol, membrane | None | sk1bd is used as a binding/matching component; location is an internal state/modification coordinate | Declared in molecule types block. | +| `SphK` | 2 | `CIB1bd`, `Serk` | Serk: S, pS | None | CIB1bd is used as a binding/matching component; Serk is an internal state/modification coordinate | Declared in molecule types block. | +| `Sph` | 1 | `skbd` | None | None | skbd is used as a binding/matching component | Declared in molecule types block. | +| `S1P` | 1 | `bd` | None | None | bd is used as a binding/matching component | Declared in molecule types block. | +| `RasGDP` | 1 | `rafbd` | None | None | rafbd is used as a binding/matching component | Declared in molecule types block. | +| `RasGTP` | 1 | `rafbd` | None | None | rafbd is used as a binding/matching component | Declared in molecule types block. | +| `Raf` | 4 | `mekbd`, `rasbd`, `Y1Y2`, `Spkc` | Y1Y2: Y, pY; Spkc: S, pS | None | mekbd is used as a binding/matching component; rasbd is used as a binding/matching component; Y1Y2 is an internal state/modification coordinate; Spkc is an internal state/modification coordinate | Declared in molecule types block. | +| `MEK12` | 3 | `bd`, `S1`, `S2` | S1: S, pS; S2: S, pS | None | bd is used as a binding/matching component; S1 is an internal state/modification coordinate; S2 is an internal state/modification coordinate | Declared in molecule types block. | +| `ERK1` | 2 | `MEK12bd`, `S1` | S1: S, pS | None | MEK12bd is used as a binding/matching component; S1 is an internal state/modification coordinate | Declared in molecule types block. | +| `ERK2` | 2 | `MEK12bd`, `S2` | S2: S, pS | None | MEK12bd is used as a binding/matching component; S2 is an internal state/modification coordinate | Declared in molecule types block. | + +## 5. Compartments, anchors, initial species, and setup + +No BNGL compartment block is declared. + +No anchors block is declared. + +VEGF/NRP1/receptor assemblies control VEGFR2 phosphorylation and trafficking, then branch into PI3K/AKT, PLCγ-calcium, eNOS, and MAPK/S1P pathways. TSP1/CD47 and Axl/Src modules provide additional regulation around receptor state, PI3K recruitment, and downstream kinase activity. + +| Initial species entry | Initial amount/expression | Technical setup meaning | +| --- | --- | --- | +| `vegf(r,r,nrp1bd,c~s)` | `VEGF165a_0` | Initial population or concentration for this exact pattern. | +| `vegfr1(l2,dimer,nrp1bd,c~s)` | `VEGFR1_0` | Initial population or concentration for this exact pattern. | +| `vegfr2(l1,Y1175~Y,CD47bd,dimer,c~s)` | `VEGFR2_0` | Initial population or concentration for this exact pattern. | +| `NRP1(vegfabd,c~s)` | `NRP1_0` | Initial population or concentration for this exact pattern. | +| `PI(PIsite~3P)` | `PIP2_0` | Initial population or concentration for this exact pattern. | +| `PLCgamma(Yplc~Y)` | `PLCgamma_0` | Initial population or concentration for this exact pattern. | +| `CaER(bd)` | `CaER_0` | Initial population or concentration for this exact pattern. | +| `Calcium_cyto(bd)` | `Calcium_0` | Initial population or concentration for this exact pattern. | +| `CaF(cabd)` | `CaF_0` | Initial population or concentration for this exact pattern. | +| `Calcium_cyto(bd!1).CaF(cabd!1)` | `CaFbound_0` | Initial population or concentration for this exact pattern. | +| `CaM(NCaM,NCaM,CCaM,CCaM,CaMtargetbd)` | `CaM_0` | Initial population or concentration for this exact pattern. | +| `I()` | `1` | Initial population or concentration for this exact pattern. | +| `Istim()` | `Istim0` | Initial population or concentration for this exact pattern. | +| `PTEN(PIP3docking)` | `PTEN_0` | Initial population or concentration for this exact pattern. | +| `TSADSrc(Y1~Y)` | `Src_0` | Initial population or concentration for this exact pattern. | +| `Axl(Ysrc~Y,Yaxl~Y)` | `Axl_0` | Initial population or concentration for this exact pattern. | +| `PI3K(state~inactive)` | `PI3K_0` | Initial population or concentration for this exact pattern. | +| `AKT(PHakt,T308~S,S473~S)` | `AKT_0` | Initial population or concentration for this exact pattern. | +| `PDK1(PHpdk1,aktbd)` | `PDK1_0` | Initial population or concentration for this exact pattern. | +| `mTOR(aktbd)` | `mTOR_0` | Initial population or concentration for this exact pattern. | +| `TSP1(CD47bd)` | `TSP1_0` | Initial population or concentration for this exact pattern. | +| `CD47SIRPa(VEGFR2bd,TSP1bd,Y1~Y,c~s)` | `CD47free_0` | Initial population or concentration for this exact pattern. | +| `eNOS(CaMBD,S1177~S,cav1BD!1).caveolin1(eNOSbd!1)` | `eNOS_0` | Initial population or concentration for this exact pattern. | +| `PKC(CalciumBD,DAGBD)` | `PKC_0` | Initial population or concentration for this exact pattern. | +| `CIB1(EF1,EF2,sk1bd,location~cytosol)` | `CIB1_0` | Initial population or concentration for this exact pattern. | +| `SphK(CIB1bd,Serk~S)` | `SphK_0` | Initial population or concentration for this exact pattern. | +| `Sph(skbd)` | `Sph_0` | Initial population or concentration for this exact pattern. | +| `S1P(bd)` | `S1P_0` | Initial population or concentration for this exact pattern. | +| `RasGDP(rafbd)` | `RasGDP_0` | Initial population or concentration for this exact pattern. | +| `RasGTP(rafbd)` | `RasGTP_0` | Initial population or concentration for this exact pattern. | +| `Raf(mekbd,rasbd,Y1Y2~Y,Spkc~S)` | `Raf_0` | Initial population or concentration for this exact pattern. | +| `MEK12(bd,S1~S,S2~S)` | `MEK12_0` | Initial population or concentration for this exact pattern. | +| `ERK1(MEK12bd,S1~S)` | `ERK12_0` | Initial population or concentration for this exact pattern. | +| `ERK2(MEK12bd,S2~S)` | `ERK12_0` | Initial population or concentration for this exact pattern. | + +## 6. Complete reaction-rule inventory + +The source contains **232** reaction rules. The inventory below preserves one row per source rule, grouped only for readability. + +### Rules 1-232 + +| # | Rule label/name | Direction | Participants | Rate/expression | Modeled change | Rule pattern | Technical meaning | +| ---: | --- | --- | --- | --- | --- | --- | --- | +| 1 | `Unlabeled` | reversible | vegfr2 | `kcRR, kdRR` | state and binding-pattern rewrite | `vegfr2(l1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegfr2(l1,dimer!1,c~s).vegfr2(l1,dimer!1,c~s)` | Reversibly forms a complex/contact among vegfr2 through vegfr2.dimer at `kcRR, kdRR`. | +| 2 | `Unlabeled` | reversible | vegfr1, vegfr2 | `kcRR, kdRR` | state and binding-pattern rewrite | `vegfr2(l1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegfr2(l1,dimer!1,c~s).vegfr1(l2,dimer!1,c~s)` | Reversibly forms a complex/contact among vegfr1, vegfr2 through vegfr1.dimer, vegfr2.dimer at `kcRR, kdRR`. | +| 3 | `Unlabeled` | reversible | vegfr1 | `kcRR, kdRR` | state and binding-pattern rewrite | `vegfr1(l2,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegfr1(l2,dimer!1,c~s).vegfr1(l2,dimer!1,c~s)` | Reversibly forms a complex/contact among vegfr1 through vegfr1.dimer at `kcRR, kdRR`. | +| 4 | `Unlabeled` | reversible | vegf, vegfr2 | `kdeltaRR, kdRR` | internal-state conversion/modification | `vegf(r!1,r!2,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr2 through vegfr2.dimer at `kdeltaRR, kdRR`. | +| 5 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaRR, kdRR` | internal-state conversion/modification | `vegf(r!1,r!2,c~s).vegfr2(l1!1,dimer,c~s).vegfr1(l2!2,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.dimer, vegfr2.dimer at `kdeltaRR, kdRR`. | +| 6 | `Unlabeled` | reversible | vegf, vegfr1 | `kdeltaRR, kdRR` | internal-state conversion/modification | `vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer,c~s).vegfr1(l2!2,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1 through vegfr1.dimer at `kdeltaRR, kdRR`. | +| 7 | `Unlabeled` | reversible | NRP1, vegfr1 | `kNRP1VEGFR1on, kNRP1VEGFR1off` | state and binding-pattern rewrite | `vegfr1(nrp1bd,c~s) + NRP1(vegfabd,c~s) <-> vegfr1(nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Reversibly forms a complex/contact among NRP1, vegfr1 through NRP1.vegfabd, vegfr1.nrp1bd at `kNRP1VEGFR1on, kNRP1VEGFR1off`. | +| 8 | `Unlabeled` | one-way | I, vegf | `-(kVEGFNRP1on*cellarea/fextmolar)*vegffrees*nrp1s+(kVEGFNRP1off*cellarea/fextmolar)*vegfnrp1s` | source/synthesis or algebraic source term | `I() -> I() + vegf(r,r,nrp1bd,c~s)` | Produces vegf while retaining or consuming I at `-(kVEGFNRP1on*cellarea/fextmolar)*vegffrees*nrp1s+(kVEGFNRP1off*cellarea/fextmolar)*vegfnrp1s`. | +| 9 | `Unlabeled` | one-way | NRP1, vegf | `kVEGFNRP1on` | state and binding-pattern rewrite | `vegf(r,r,nrp1bd,c~s) + NRP1(vegfabd,c~s) -> vegf(r,r,nrp1bd,c~s) + vegf(r,r,nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Forms a complex/contact among NRP1, vegf through NRP1.vegfabd, vegf.nrp1bd at `kVEGFNRP1on`. | +| 10 | `Unlabeled` | one-way | NRP1, vegf | `kVEGFNRP1off` | state and binding-pattern rewrite | `vegf(r,r,nrp1bd!1,c~s).NRP1(vegfabd!1,c~s) -> NRP1(vegfabd,c~s)` | Releases a complex/contact among NRP1, vegf by freeing NRP1.vegfabd, vegf.nrp1bd at `kVEGFNRP1off`. | +| 11 | `Unlabeled` | reversible | vegf, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr2(l1!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr2 through vegf.r, vegfr2.l1 at `kNRP1VEGFR2on, kNRP1VEGFR2off`. | +| 12 | `Unlabeled` | reversible | vegf, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr2(l1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr2(l1!2,dimer!3,c~s).vegfr2(l1,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr2 through vegf.r, vegfr2.l1 at `kNRP1VEGFR2on, kNRP1VEGFR2off`. | +| 13 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr2(l1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr2(l1!2,dimer!3,c~s).vegfr1(l2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegf.r, vegfr2.l1 at `kNRP1VEGFR2on, kNRP1VEGFR2off`. | +| 14 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr1(l2!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1 through vegf.r, vegfr1.l2 at `kcVR, kvr1off`. | +| 15 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr1(l2,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr1(l2!2,dimer!3,c~s).vegfr1(l2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1 through vegf.r, vegfr1.l2 at `kcVR, kvr1off`. | +| 16 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r,r,nrp1bd!+,c~s) + vegfr1(l2,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!2,r,nrp1bd!+,c~s).vegfr1(l2!2,dimer!3,c~s).vegfr2(l1,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegf.r, vegfr1.l2 at `kcVR, kvr1off`. | +| 17 | `Unlabeled` | one-way | I, vegf | `-(kvron*cellarea/fextmolar)*vegffrees*vr2s+(kvroff*cellarea/fextmolar)*vegfr2s` | source/synthesis or algebraic source term | `I() -> I() + vegf(r,r,nrp1bd,c~s)` | Produces vegf while retaining or consuming I at `-(kvron*cellarea/fextmolar)*vegffrees*vr2s+(kvroff*cellarea/fextmolar)*vegfr2s`. | +| 18 | `Unlabeled` | one-way | vegf, vegfr2 | `kvron` | state and binding-pattern rewrite | `vegf(r,r,nrp1bd,c~s) + vegfr2(l1,c~s) -> vegf(r,r,nrp1bd,c~s) + vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,c~s)` | Forms a complex/contact among vegf, vegfr2 through vegf.r, vegfr2.l1 at `kvron`. | +| 19 | `Unlabeled` | one-way | vegf, vegfr2 | `kvroff` | state and binding-pattern rewrite | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,c~s) -> vegfr2(l1,c~s)` | Releases a complex/contact among vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kvroff`. | +| 20 | `Unlabeled` | reversible | vegf, vegfr2 | `kcVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Rewrites the matched vegf, vegfr2 pattern without an obvious state or bond-count change at `kcVR, kvroff`; the table row preserves the exact implementation pattern. | +| 21 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.l2 at `kcVR, kvr1off`. | +| 22 | `Unlabeled` | reversible | vegf, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr2 pattern without an obvious state or bond-count change at `kdeltaVR, kvroff`; the table row preserves the exact implementation pattern. | +| 23 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.l2 at `kdeltaVR, kvr1off`. | +| 24 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kcVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 25 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kcVR, kvroff`. | +| 26 | `Unlabeled` | reversible | vegf, vegfr1 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kdeltaVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 27 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kdeltaVR, kvroff`. | +| 28 | `Unlabeled` | reversible | vegf, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr2(l1!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Rewrites the matched vegf, vegfr2 pattern without an obvious state or bond-count change at `kNRP1VEGFR2on, kNRP1VEGFR2off`; the table row preserves the exact implementation pattern. | +| 29 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr2(l1!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.l2 at `kcVR, kvr1off`. | +| 30 | `Unlabeled` | reversible | vegf, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr2 pattern without an obvious state or bond-count change at `kdeltaVR, kvroff`; the table row preserves the exact implementation pattern. | +| 31 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr1.l2 at `kdeltaVR, kvr1off`. | +| 32 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr1(l2!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr1(l2!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kcVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 33 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kNRP1VEGFR2on, kNRP1VEGFR2off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr1(l2!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr1(l2!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kNRP1VEGFR2on, kNRP1VEGFR2off`. | +| 34 | `Unlabeled` | reversible | vegf, vegfr1 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kdeltaVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 35 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd!+,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,nrp1bd!+,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kdeltaVR, kvroff`. | +| 36 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r!2,nrp1bd!4,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s).NRP1(vegfabd!4,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr2 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 37 | `Unlabeled` | reversible | NRP1, vegf, vegfr1 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r!2,nrp1bd!4,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s).NRP1(vegfabd!4,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr1 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 38 | `Unlabeled` | reversible | NRP1, vegf, vegfr1, vegfr2 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r!2,nrp1bd!4,c~s).vegfr2(l1!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s).NRP1(vegfabd!4,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr1, vegfr2 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 39 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r!2,nrp1bd!4,c~s).vegfr2(l1!1,dimer,c~s).vegfr2(l1!2,dimer,c~s).NRP1(vegfabd!4,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr2 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 40 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kVEGFR2NRP1on, kVEGFR2NRP1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r,nrp1bd!2,c~s).vegfr2(l1!1,c~s).NRP1(vegfabd!2,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr2 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR2NRP1on, kVEGFR2NRP1off`. | +| 41 | `Unlabeled` | reversible | NRP1, vegf, vegfr1 | `kVEGFR1NRP1on, kVEGFR1NRP1off` | internal-state conversion/modification | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,c~s) + NRP1(vegfabd,c~s) <-> vegf(r!1,r,nrp1bd!2,c~s).vegfr1(l2!1,c~s).NRP1(vegfabd!2,c~s)` | Reversibly forms a complex/contact among NRP1, vegf, vegfr1 through NRP1.vegfabd, vegf.nrp1bd at `kVEGFR1NRP1on, kVEGFR1NRP1off`. | +| 42 | `Unlabeled` | one-way | I, vegf | `-kvr1on*cellarea/fextmolar*vegffrees*vr1s+kvr1off*vegfr1s*(cellarea/fextmolar)` | source/synthesis or algebraic source term | `I() -> I() + vegf(r,r,nrp1bd,c~s)` | Produces vegf while retaining or consuming I at `-kvr1on*cellarea/fextmolar*vegffrees*vr1s+kvr1off*vegfr1s*(cellarea/fextmolar)`. | +| 43 | `Unlabeled` | one-way | vegf, vegfr1 | `kvr1on` | state and binding-pattern rewrite | `vegf(r,r,nrp1bd,c~s) + vegfr1(l2,c~s) -> vegf(r,r,nrp1bd,c~s) + vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,c~s)` | Forms a complex/contact among vegf, vegfr1 through vegf.r, vegfr1.l2 at `kvr1on`. | +| 44 | `Unlabeled` | one-way | vegf, vegfr1 | `kvr1off` | state and binding-pattern rewrite | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,c~s) -> vegfr1(l2,c~s)` | Releases a complex/contact among vegf, vegfr1 by freeing vegf.r, vegfr1.l2 at `kvr1off`. | +| 45 | `Unlabeled` | reversible | vegf, vegfr1 | `kcVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,c~s).vegfr1(l2!1,dimer,c~s) + vegfr1(l2,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer,c~s).vegfr1(l2!2,dimer,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kcVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 46 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kcVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,c~s).vegfr1(l2!1,dimer,c~s) + vegfr2(l1,dimer,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer,c~s).vegfr2(l1!2,dimer,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kcVR, kvroff`. | +| 47 | `Unlabeled` | reversible | vegf, vegfr1 | `kdeltaVR, kvr1off` | internal-state conversion/modification | `vegf(r!1,r,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2,dimer!3,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr1(l2!2,dimer!3,c~s)` | Rewrites the matched vegf, vegfr1 pattern without an obvious state or bond-count change at `kdeltaVR, kvr1off`; the table row preserves the exact implementation pattern. | +| 48 | `Unlabeled` | reversible | vegf, vegfr1, vegfr2 | `kdeltaVR, kvroff` | internal-state conversion/modification | `vegf(r!1,r,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1,dimer!3,c~s) <-> vegf(r!1,r!2,c~s).vegfr1(l2!1,dimer!3,c~s).vegfr2(l1!2,dimer!3,c~s)` | Reversibly forms a complex/contact among vegf, vegfr1, vegfr2 through vegfr2.l1 at `kdeltaVR, kvroff`. | +| 49 | `Unlabeled` | one-way | vegf, vegfr2 | `kpr2` | internal-state conversion/modification | `vegf(r!1,r!2,c~s).vegfr2(l1!1,c~s).vegfr2(l1!2,Y1175~Y,c~s) -> vegf(r!1,r!2,c~s).vegfr2(l1!1,c~s).vegfr2(l1!2,Y1175~pY,c~s)` | Changes internal modification/state marks on vegf, vegfr2: vegfr2.Y1175 Y→pY at `kpr2`. | +| 50 | `Unlabeled` | one-way | vegf, vegfr2 | `kpr2` | internal-state conversion/modification | `vegf(r!1,r!2,c~i).vegfr2(l1!1,c~i).vegfr2(l1!2,Y1175~Y,c~i) -> vegf(r!1,r!2,c~i).vegfr2(l1!1,c~i).vegfr2(l1!2,Y1175~pY,c~i)` | Changes internal modification/state marks on vegf, vegfr2: vegfr2.Y1175 Y→pY at `kpr2`. | +| 51 | `Unlabeled` | one-way | vegf, vegfr2 | `kpr2` | internal-state conversion/modification | `vegf(r!1,r!2,c~i2).vegfr2(l1!1,c~i2).vegfr2(l1!2,Y1175~Y,c~i2) -> vegf(r!1,r!2,c~i2).vegfr2(l1!1,c~i2).vegfr2(l1!2,Y1175~pY,c~i2)` | Changes internal modification/state marks on vegf, vegfr2: vegfr2.Y1175 Y→pY at `kpr2`. | +| 52 | `Unlabeled` | one-way | vegf, vegfr2 | `kpr2` | internal-state conversion/modification | `vegf(r!1,r!2,c~r).vegfr2(l1!1,c~r).vegfr2(l1!2,Y1175~Y,c~r) -> vegf(r!1,r!2,c~r).vegfr2(l1!1,c~r).vegfr2(l1!2,Y1175~pY,c~r)` | Changes internal modification/state marks on vegf, vegfr2: vegfr2.Y1175 Y→pY at `kpr2`. | +| 53 | `Unlabeled` | one-way | vegfr2 | `kdps` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd,c~s) -> vegfr2(Y1175~Y,CD47bd,c~s)` | Changes internal modification/state marks on vegfr2: vegfr2.Y1175 pY→Y at `kdps`. | +| 54 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdps` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~s).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~s) -> vegfr2(Y1175~Y,CD47bd!3,c~s).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~s)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdps`. | +| 55 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdps*fTSP1dp` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~s).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~s) -> vegfr2(Y1175~Y,CD47bd!3,c~s).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~s)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdps*fTSP1dp`. | +| 56 | `Unlabeled` | one-way | vegfr2 | `kdpi` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd,c~i) -> vegfr2(Y1175~Y,CD47bd,c~i)` | Changes internal modification/state marks on vegfr2: vegfr2.Y1175 pY→Y at `kdpi`. | +| 57 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdpi` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i) -> vegfr2(Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdpi`. | +| 58 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdpi*fTSP1dp` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i) -> vegfr2(Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdpi*fTSP1dp`. | +| 59 | `Unlabeled` | one-way | vegfr2 | `kdpi` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd,c~i2) -> vegfr2(Y1175~Y,CD47bd,c~i2)` | Changes internal modification/state marks on vegfr2: vegfr2.Y1175 pY→Y at `kdpi`. | +| 60 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdpi` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2) -> vegfr2(Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdpi`. | +| 61 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kdpi*fTSP1dp` | internal-state conversion/modification | `vegfr2(Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2) -> vegfr2(Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: vegfr2.Y1175 pY→Y at `kdpi*fTSP1dp`. | +| 62 | `Unlabeled` | one-way | vegfr2 | `kdpr` | internal-state conversion/modification | `vegfr2(Y1175~pY,c~r) -> vegfr2(Y1175~Y,c~r)` | Changes internal modification/state marks on vegfr2: vegfr2.Y1175 pY→Y at `kdpr`. | +| 63 | `Unlabeled` | one-way | vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd,dimer,c~s).vegfr2(l1!2,CD47bd,dimer,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd,dimer,c~i).vegfr2(l1!2,CD47bd,dimer,c~i)` | Changes internal modification/state marks on vegf, vegfr2: vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 64 | `Unlabeled` | one-way | vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd,dimer!6,c~s).vegfr2(l1!2,CD47bd,dimer!6,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd,dimer!6,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i)` | Changes internal modification/state marks on vegf, vegfr2: vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 65 | `Unlabeled` | one-way | CD47SIRPa, vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd!3,dimer,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd,dimer,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 66 | `Unlabeled` | one-way | CD47SIRPa, vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd!3,dimer!6,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd,dimer!6,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 67 | `Unlabeled` | one-way | CD47SIRPa, vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd!3,dimer,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd!4,dimer,c~s).CD47SIRPa(VEGFR2bd!4,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer,c~i).CD47SIRPa(VEGFR2bd!4,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 68 | `Unlabeled` | one-way | CD47SIRPa, vegf, vegfr2 | `kr2si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~s).vegfr2(l1!1,CD47bd!3,dimer!6,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd!4,dimer!6,c~s).CD47SIRPa(VEGFR2bd!4,c~s) -> vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer!6,c~i).CD47SIRPa(VEGFR2bd!4,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2si`. | +| 69 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd,dimer,c~s).vegfr2(l1!2,CD47bd,dimer,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd,dimer,c~i).vegfr2(l1!2,CD47bd,dimer,c~i)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 70 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd!3,dimer,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd,dimer,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer,c~i)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c s→i, NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 71 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd!3,dimer,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd!4,dimer,c~s).CD47SIRPa(VEGFR2bd!4,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer,c~i).CD47SIRPa(VEGFR2bd!4,c~i)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c s→i, NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 72 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd,dimer!6,c~s).vegfr2(l1!2,CD47bd,dimer!6,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd,dimer!6,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 73 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd!3,dimer!6,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd,dimer!6,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c s→i, NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 74 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1si` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~s).NRP1(vegfabd!9,c~s).vegfr2(l1!1,CD47bd!3,dimer!6,c~s).CD47SIRPa(VEGFR2bd!3,c~s).vegfr2(l1!2,CD47bd!4,dimer!6,c~s).CD47SIRPa(VEGFR2bd!4,c~s) -> vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer!6,c~i).CD47SIRPa(VEGFR2bd!4,c~i)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c s→i, NRP1.c s→i, vegf.c s→i, vegfr2.c s→i at `kr2NRP1si`. | +| 75 | `Unlabeled` | reversible | vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd,dimer,c~i).vegfr2(l1!2,CD47bd,dimer,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd,dimer,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2)` | Changes internal modification/state marks on vegf, vegfr2: vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 76 | `Unlabeled` | reversible | vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd,dimer!6,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd,dimer!6,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2)` | Changes internal modification/state marks on vegf, vegfr2: vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 77 | `Unlabeled` | reversible | CD47SIRPa, vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 78 | `Unlabeled` | reversible | CD47SIRPa, vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer!4,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer!4,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd!3,dimer!4,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 79 | `Unlabeled` | reversible | CD47SIRPa, vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer,c~i).CD47SIRPa(VEGFR2bd!4,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 80 | `Unlabeled` | reversible | CD47SIRPa, vegf, vegfr2 | `kr2ii2, kr2i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer!6,c~i).CD47SIRPa(VEGFR2bd!4,c~i) <-> vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, vegf, vegfr2: CD47SIRPa.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2ii2, kr2i2i`. | +| 81 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd,dimer,c~i).vegfr2(l1!2,CD47bd,dimer,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd,dimer,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 82 | `Unlabeled` | reversible | NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd,dimer!6,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd,dimer!6,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 83 | `Unlabeled` | reversible | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i→i2, NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 84 | `Unlabeled` | reversible | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,dimer!6,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i→i2, NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 85 | `Unlabeled` | reversible | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer,c~i).CD47SIRPa(VEGFR2bd!4,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i→i2, NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 86 | `Unlabeled` | reversible | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1ii2, kr2NRP1i2i` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,CD47bd!3,dimer!6,c~i).CD47SIRPa(VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,dimer!6,c~i).CD47SIRPa(VEGFR2bd!4,c~i) <-> vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i→i2, NRP1.c i→i2, vegf.c i→i2, vegfr2.c i→i2 at `kr2NRP1ii2, kr2NRP1i2i`. | +| 87 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd,dimer,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd,dimer,c~r).vegfr2(l1!2,CD47bd,dimer,c~r)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 88 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd,dimer!6,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd,dimer!6,c~r).vegfr2(l1!2,CD47bd,dimer!6,c~r)` | Changes internal modification/state marks on NRP1, vegf, vegfr2: NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 89 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd,dimer,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 90 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer!6,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd,dimer!6,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 91 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd!4,dimer,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 92 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer!6,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer!6,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd!4,dimer!6,c~r).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r`. | +| 93 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r*fTSP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer,c~r).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd,dimer,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r*fTSP1i2r`. | +| 94 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r*fTSP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,dimer!6,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer!6,c~r).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd,dimer!6,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r*fTSP1i2r`. | +| 95 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r*fTSP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer,c~r).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd!4,dimer,c~r).CD47SIRPa(VEGFR2bd!4,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r*fTSP1i2r`. | +| 96 | `Unlabeled` | one-way | CD47SIRPa, NRP1, vegf, vegfr2 | `kr2NRP1i2r*fTSP1i2r` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,CD47bd!3,dimer!6,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,dimer!6,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,CD47bd!3,dimer!6,c~r).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~r).vegfr2(l1!2,CD47bd!4,dimer!6,c~r).CD47SIRPa(VEGFR2bd!4,c~r)` | Changes internal modification/state marks on CD47SIRPa, NRP1, vegf, vegfr2: CD47SIRPa.c i2→r, NRP1.c i2→r, vegf.c i2→r, vegfr2.c i2→r at `kr2NRP1i2r*fTSP1i2r`. | +| 97 | `Unlabeled` | one-way | vegfr2 | `kr2rs` | internal-state conversion/modification | `vegfr2(l1,Y1175~Y,CD47bd,dimer,c~r) -> vegfr2(l1,Y1175~Y,CD47bd,dimer,c~s)` | Changes internal modification/state marks on vegfr2: vegfr2.c r→s at `kr2rs`. | +| 98 | `Unlabeled` | one-way | NRP1 | `kr2rs` | internal-state conversion/modification | `NRP1(vegfabd,c~r) -> NRP1(vegfabd,c~s)` | Changes internal modification/state marks on NRP1: NRP1.c r→s at `kr2rs`. | +| 99 | `Unlabeled` | one-way | CD47SIRPa | `kr2rs` | internal-state conversion/modification | `CD47SIRPa(TSP1bd,VEGFR2bd,c~r) -> CD47SIRPa(TSP1bd,VEGFR2bd,c~s)` | Changes internal modification/state marks on CD47SIRPa: CD47SIRPa.c r→s at `kr2rs`. | +| 100 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kvroff` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,dimer,c~r).vegfr2(l1!2,dimer,c~r) -> NRP1(vegfabd,c~r) + vegfr2(l1,dimer,c~r) + vegfr2(l1,dimer,c~r)` | Releases a complex/contact among NRP1, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kvroff`. | +| 101 | `Unlabeled` | one-way | NRP1, vegf, vegfr2 | `kvroff` | internal-state conversion/modification | `vegf(r!1,r!2,nrp1bd!9,c~r).NRP1(vegfabd!9,c~r).vegfr2(l1!1,dimer!6,c~r).vegfr2(l1!2,dimer!6,c~r) -> NRP1(vegfabd,c~r) + vegfr2(l1,dimer!6,c~r).vegfr2(l1,dimer!6,c~r)` | Releases a complex/contact among NRP1, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kvroff`. | +| 102 | `Unlabeled` | one-way | vegfr2 | `kdRR` | state and binding-pattern rewrite | `vegfr2(dimer!6,c~r).vegfr2(dimer!6,c~r) -> vegfr2(dimer,c~r) + vegfr2(dimer,c~r)` | Releases a complex/contact among vegfr2 by freeing vegfr2.dimer at `kdRR`. | +| 103 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kr2CD47off` | state and binding-pattern rewrite | `vegfr2(CD47bd!3,c~r).CD47SIRPa(VEGFR2bd!3,c~r) -> vegfr2(CD47bd,c~r) + CD47SIRPa(VEGFR2bd,c~r)` | Releases a complex/contact among CD47SIRPa, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegfr2.CD47bd at `kr2CD47off`. | +| 104 | `Unlabeled` | one-way | CD47SIRPa, TSP1 | `koffCD47TSP1` | state and binding-pattern rewrite | `CD47SIRPa(TSP1bd!1,c~r).TSP1(CD47bd!1) -> CD47SIRPa(TSP1bd,c~r)` | Releases a complex/contact among CD47SIRPa, TSP1 by freeing CD47SIRPa.TSP1bd, TSP1.CD47bd at `koffCD47TSP1`. | +| 105 | `Unlabeled` | one-way | Trash, vegf, vegfr2 | `kdegi0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among Trash, vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kdegi0`. | +| 106 | `Unlabeled` | one-way | Trash, vegf, vegfr2 | `kdegi0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among Trash, vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kdegi0noP`. | +| 107 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0`. | +| 108 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0noP`. | +| 109 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0`. | +| 110 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0noP`. | +| 111 | `Unlabeled` | one-way | Trash, vegf, vegfr2 | `kdegi20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among Trash, vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kdegi20`. | +| 112 | `Unlabeled` | one-way | Trash, vegf, vegfr2 | `kdegi20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among Trash, vegf, vegfr2 by freeing vegf.r, vegfr2.l1 at `kdegi20noP`. | +| 113 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20`. | +| 114 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20noP`. | +| 115 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20`. | +| 116 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20noP`. | +| 117 | `Unlabeled` | one-way | NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among NRP1, Trash, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kdegr2NRP1i0`. | +| 118 | `Unlabeled` | one-way | NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among NRP1, Trash, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kdegr2NRP1i0noP`. | +| 119 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0`. | +| 120 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0noP`. | +| 121 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0`. | +| 122 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0noP`. | +| 123 | `Unlabeled` | one-way | NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among NRP1, Trash, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kdegr2NRP1i20`. | +| 124 | `Unlabeled` | one-way | NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among NRP1, Trash, vegf, vegfr2 by freeing NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.l1 at `kdegr2NRP1i20noP`. | +| 125 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20`. | +| 126 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20noP`. | +| 127 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20`. | +| 128 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i2).CD47SIRPa(TSP1bd,VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20noP`. | +| 129 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0*f_TSP1deg`. | +| 130 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0noP*f_TSP1deg`. | +| 131 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,c~i).CD47SIRPa(VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0*f_TSP1deg`. | +| 132 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi0noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i).CD47SIRPa(VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi0noP*f_TSP1deg`. | +| 133 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20*f_TSP1deg`. | +| 134 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20noP*f_TSP1deg`. | +| 135 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20*f_TSP1deg`. | +| 136 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegf, vegfr2 | `kdegi20noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegi20noP*f_TSP1deg`. | +| 137 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0*f_TSP1deg`. | +| 138 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0noP*f_TSP1deg`. | +| 139 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,CD47bd!4,c~i).CD47SIRPa(VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0*f_TSP1deg`. | +| 140 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i0noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i).NRP1(vegfabd!9,c~i).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i).CD47SIRPa(VEGFR2bd!4,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i0noP*f_TSP1deg`. | +| 141 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20*f_TSP1deg`. | +| 142 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20noP*f_TSP1deg`. | +| 143 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~pY,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,CD47bd!4,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20*f_TSP1deg`. | +| 144 | `Unlabeled` | one-way | CD47SIRPa, NRP1, Trash, vegf, vegfr2 | `kdegr2NRP1i20noP*f_TSP1deg` | state and binding-pattern rewrite | `vegf(r!1,r!2,nrp1bd!9,c~i2).NRP1(vegfabd!9,c~i2).vegfr2(l1!1,Y1175~Y,CD47bd!3,c~i2).CD47SIRPa(TSP1bd!+,VEGFR2bd!3,c~i2).vegfr2(l1!2,Y1175~Y,CD47bd!4,c~i2).CD47SIRPa(VEGFR2bd!4,c~i2) -> Trash()` | Releases a complex/contact among CD47SIRPa, NRP1, Trash, vegf, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, NRP1.vegfabd, vegf.nrp1bd, vegf.r, vegfr2.CD47bd, vegfr2.l1 at `kdegr2NRP1i20noP*f_TSP1deg`. | +| 145 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegfr2 | `ksingleR2deg` | state and binding-pattern rewrite | `vegfr2(l1,CD47bd!1,c~i).CD47SIRPa(TSP1bd,VEGFR2bd!1,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegfr2 by freeing CD47SIRPa.VEGFR2bd, vegfr2.CD47bd at `ksingleR2deg`. | +| 146 | `Unlabeled` | one-way | Trash, vegfr2 | `ksingleR2deg` | internal-state conversion/modification | `vegfr2(l1,CD47bd,c~i) -> Trash()` | Produces Trash while retaining or consuming vegfr2 at `ksingleR2deg`. | +| 147 | `Unlabeled` | one-way | CD47SIRPa, Trash, vegfr2 | `ksingleR2deg*f_TSP1deg` | state and binding-pattern rewrite | `vegfr2(l1,CD47bd!1,c~i).CD47SIRPa(TSP1bd!+,VEGFR2bd!1,c~i) -> Trash()` | Releases a complex/contact among CD47SIRPa, Trash, vegfr2 by freeing CD47SIRPa.TSP1bd, CD47SIRPa.VEGFR2bd, vegfr2.CD47bd at `ksingleR2deg*f_TSP1deg`. | +| 148 | `Unlabeled` | one-way | I, vegfr2 | `ksingleR2syn*VEGFR2total` | source/synthesis or algebraic source term | `I() -> I() + vegfr2(l1,Y1175~Y,CD47bd,dimer,c~s)` | Produces vegfr2 while retaining or consuming I at `ksingleR2syn*VEGFR2total`. | +| 149 | `Unlabeled` | reversible | vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd,dimer,c~s) <-> vegfr2(l1,CD47bd,dimer,c~i)` | Changes internal modification/state marks on vegfr2: vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 150 | `Unlabeled` | reversible | CD47SIRPa, vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd!1,dimer,c~s).CD47SIRPa(VEGFR2bd!1,c~s) <-> vegfr2(l1,CD47bd!1,dimer,c~i).CD47SIRPa(VEGFR2bd!1,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: CD47SIRPa.c s→i, vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 151 | `Unlabeled` | reversible | vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd,dimer!3,c~s).vegfr2(l1,CD47bd,dimer!3,c~s) <-> vegfr2(l1,CD47bd,dimer!3,c~i).vegfr2(l1,CD47bd,dimer!3,c~i)` | Changes internal modification/state marks on vegfr2: vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 152 | `Unlabeled` | reversible | CD47SIRPa, vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd!1,dimer!3,c~s).CD47SIRPa(VEGFR2bd!1,c~s).vegfr2(l1,CD47bd,dimer!3,c~s) <-> vegfr2(l1,CD47bd!1,dimer!3,c~i).CD47SIRPa(VEGFR2bd!1,c~i).vegfr2(l1,CD47bd,dimer!3,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: CD47SIRPa.c s→i, vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 153 | `Unlabeled` | reversible | CD47SIRPa, vegfr2 | `ksingleR2si, ksingleR2is` | internal-state conversion/modification | `vegfr2(l1,CD47bd!1,dimer!3,c~s).CD47SIRPa(VEGFR2bd!1,c~s).vegfr2(l1,CD47bd!2,dimer!3,c~s).CD47SIRPa(VEGFR2bd!2,c~s) <-> vegfr2(l1,CD47bd!1,dimer!3,c~i).CD47SIRPa(VEGFR2bd!1,c~i).vegfr2(l1,CD47bd!2,dimer!3,c~i).CD47SIRPa(VEGFR2bd!2,c~i)` | Changes internal modification/state marks on CD47SIRPa, vegfr2: CD47SIRPa.c s→i, vegfr2.c s→i at `ksingleR2si, ksingleR2is`. | +| 154 | `Unlabeled` | one-way | PLCgamma, vegfr2 | `kpPLCgamma` | internal-state conversion/modification | `PLCgamma(Yplc~Y) + vegfr2(Y1175~pY,c~s) -> PLCgamma(Yplc~pY) + vegfr2(Y1175~pY,c~s)` | Changes internal modification/state marks on PLCgamma, vegfr2: PLCgamma.Yplc Y→pY at `kpPLCgamma`. | +| 155 | `Unlabeled` | one-way | PLCgamma, vegfr2 | `kpPLCgamma` | internal-state conversion/modification | `PLCgamma(Yplc~Y) + vegfr2(Y1175~pY,c~i) -> PLCgamma(Yplc~pY) + vegfr2(Y1175~pY,c~i)` | Changes internal modification/state marks on PLCgamma, vegfr2: PLCgamma.Yplc Y→pY at `kpPLCgamma`. | +| 156 | `Unlabeled` | one-way | PLCgamma, vegfr2 | `kpPLCgamma` | internal-state conversion/modification | `PLCgamma(Yplc~Y) + vegfr2(Y1175~pY,c~i2) -> PLCgamma(Yplc~pY) + vegfr2(Y1175~pY,c~i2)` | Changes internal modification/state marks on PLCgamma, vegfr2: PLCgamma.Yplc Y→pY at `kpPLCgamma`. | +| 157 | `Unlabeled` | one-way | PLCgamma | `kdpPLCgamma` | internal-state conversion/modification | `PLCgamma(Yplc~pY) -> PLCgamma(Yplc~Y)` | Changes internal modification/state marks on PLCgamma: PLCgamma.Yplc pY→Y at `kdpPLCgamma`. | +| 158 | `Unlabeled` | one-way | IP3_cyto, PI, PLCgamma | `kcatPLCgammaDAG*freepip2^(nDAG-1)/(kmPIP2PLCgamma^nDAG+freepip2^nDAG)` | internal-state conversion/modification | `PLCgamma(Yplc~pY) + PI(PIsite~3P) -> IP3_cyto(ip3rbd) + PLCgamma(Yplc~pY)` | Produces IP3_cyto while retaining or consuming PI, PLCgamma at `kcatPLCgammaDAG*freepip2^(nDAG-1)/(kmPIP2PLCgamma^nDAG+freepip2^nDAG)`. | +| 159 | `Unlabeled` | one-way | DAG, PI, PLCgamma | `kcatPLCgammaDAG*freepip2^(nDAG-1)/(kmPIP2PLCgamma^nDAG+freepip2^nDAG)` | internal-state conversion/modification | `PLCgamma(Yplc~pY) + PI(PIsite~3P) -> DAG(pkcbd) + PLCgamma(Yplc~pY)` | Produces DAG while retaining or consuming PI, PLCgamma at `kcatPLCgammaDAG*freepip2^(nDAG-1)/(kmPIP2PLCgamma^nDAG+freepip2^nDAG)`. | +| 160 | `Unlabeled` | one-way | I, PI | `kPIP2gen` | source/synthesis or algebraic source term | `I() -> I() + PI(PIsite~3P)` | Produces PI while retaining or consuming I at `kPIP2gen`. | +| 161 | `Unlabeled` | one-way | IP3_cyto, Trash | `kdeg_ip3` | pattern rewrite | `IP3_cyto(ip3rbd) -> Trash()` | Produces Trash while retaining or consuming IP3_cyto at `kdeg_ip3`. | +| 162 | `Unlabeled` | one-way | DAG, Trash | `kdeg_DAG` | pattern rewrite | `DAG(pkcbd) -> Trash()` | Produces Trash while retaining or consuming DAG at `kdeg_DAG`. | +| 163 | `Unlabeled` | reversible | CaF, Calcium_cyto | `KBon, KBoff` | binding/complex formation | `Calcium_cyto(bd) + CaF(cabd) <-> Calcium_cyto(bd!1).CaF(cabd!1)` | Reversibly forms a complex/contact among CaF, Calcium_cyto through CaF.cabd, Calcium_cyto.bd at `KBon, KBoff`. | +| 164 | `Unlabeled` | one-way | I, Istim | `ICracamp*(Kcrac^ncrac/(Kcrac^ncrac+Caer^ncrac))/tau_stim-Iopenstim/tau_stim` | source/synthesis or algebraic source term | `I() -> I() + Istim()` | Produces Istim while retaining or consuming I at `ICracamp*(Kcrac^ncrac/(Kcrac^ncrac+Caer^ncrac))/tau_stim-Iopenstim/tau_stim`. | +| 165 | `Unlabeled` | one-way | Calcium_cyto, I | `(VolER/Volcyto)*Iip3Ramp*(Caer-Cac)*(freeip3cyto^3.8/(freeip3cyto^3.8+KmIP3R^3.8))*(KiCa^3.8/(KiCa^3.8+Cac^3.8))` | source/synthesis or algebraic source term | `I() -> I() + Calcium_cyto(bd)` | Produces Calcium_cyto while retaining or consuming I at `(VolER/Volcyto)*Iip3Ramp*(Caer-Cac)*(freeip3cyto^3.8/(freeip3cyto^3.8+KmIP3R^3.8))*(KiCa^3.8/(KiCa^3.8+Cac^3.8))`. | +| 166 | `Unlabeled` | one-way | CaER, I | `)` | source/synthesis or algebraic source term | `I() -> I() + CaER(bd) -Iip3Ramp*(Caer-Cac)*(freeip3cyto^3.8/(freeip3cyto^3.8+KmIP3R^3.8))*(KiCa^3.8/(KiCa^3.8+Cac^3.8))*( 1/(1+CSQN_total/(KCSQN+Caer)^2)` | Produces CaER while retaining or consuming I at `)`. | +| 167 | `Unlabeled` | one-way | Calcium_cyto, I | `Iopenstim` | source/synthesis or algebraic source term | `I() -> I() + Calcium_cyto(bd) -I_PMCAbar*Cac^1.4/(KmPMCA^1.4+Cac^1.4) +` | Produces Calcium_cyto while retaining or consuming I at `Iopenstim`. | +| 168 | `Unlabeled` | one-way | Calcium_cyto, I | `KleakER*(Caer-Cac)^2` | source/synthesis or algebraic source term | `I() -> I() + Calcium_cyto(bd) -vSERCA*(Cac/(KmSERCA+Cac))^2 +` | Produces Calcium_cyto while retaining or consuming I at `KleakER*(Caer-Cac)^2`. | +| 169 | `Unlabeled` | one-way | CaER, I | `vSERCA*(Cac/(KmSERCA+Cac))^2*(Volcyto/VolER)*(1/(1+CSQN_total/(KCSQN+Caer)^2))` | source/synthesis or algebraic source term | `I() -> I() + CaER(bd)` | Produces CaER while retaining or consuming I at `vSERCA*(Cac/(KmSERCA+Cac))^2*(Volcyto/VolER)*(1/(1+CSQN_total/(KCSQN+Caer)^2))`. | +| 170 | `Unlabeled` | one-way | CaER, I | `-KleakER*(Volcyto/VolER)*((Caer-Cac)^2)*(1/(1+CSQN_total/(KCSQN+Caer)^2))` | source/synthesis or algebraic source term | `I() -> I() + CaER(bd)` | Produces CaER while retaining or consuming I at `-KleakER*(Volcyto/VolER)*((Caer-Cac)^2)*(1/(1+CSQN_total/(KCSQN+Caer)^2))`. | +| 171 | `Unlabeled` | one-way | CaM, Calcium_cyto | `(koffCaNCaM1/kdCaNCaM)` | binding/complex formation | `CaM(NCaM) + Calcium_cyto(bd) -> CaM(NCaM!1).Calcium_cyto(bd!1) + Calcium_cyto(bd)` | Forms a complex/contact among CaM, Calcium_cyto through CaM.NCaM, Calcium_cyto.bd at `(koffCaNCaM1/kdCaNCaM)`. | +| 172 | `Unlabeled` | one-way | CaM, Calcium_cyto | `koffCaNCaM1` | unbinding/complex dissociation | `CaM(NCaM!1).Calcium_cyto(bd!1) -> CaM(NCaM)` | Releases a complex/contact among CaM, Calcium_cyto by freeing CaM.NCaM, Calcium_cyto.bd at `koffCaNCaM1`. | +| 173 | `Unlabeled` | one-way | CaM, Calcium_cyto | `(koffCaCCaM1/kdCaCCaM)` | binding/complex formation | `CaM(CCaM) + Calcium_cyto(bd) -> CaM(CCaM!1).Calcium_cyto(bd!1) + Calcium_cyto(bd)` | Forms a complex/contact among CaM, Calcium_cyto through CaM.CCaM, Calcium_cyto.bd at `(koffCaCCaM1/kdCaCCaM)`. | +| 174 | `Unlabeled` | one-way | CaM, Calcium_cyto | `koffCaCCaM1` | unbinding/complex dissociation | `CaM(CCaM!1).Calcium_cyto(bd!1) -> CaM(CCaM)` | Releases a complex/contact among CaM, Calcium_cyto by freeing CaM.CCaM, Calcium_cyto.bd at `koffCaCCaM1`. | +| 175 | `Unlabeled` | one-way | TSADSrc, vegfr2 | `kpSrc` | internal-state conversion/modification | `TSADSrc(Y1~Y) + vegfr2(Y1175~pY!?,c~s) -> TSADSrc(Y1~pY) + vegfr2(Y1175~pY!?,c~s)` | Changes internal modification/state marks on TSADSrc, vegfr2: TSADSrc.Y1 Y→pY at `kpSrc`. | +| 176 | `Unlabeled` | one-way | TSADSrc, vegfr2 | `kpSrc` | internal-state conversion/modification | `TSADSrc(Y1~Y) + vegfr2(Y1175~pY!?,c~i) -> TSADSrc(Y1~pY) + vegfr2(Y1175~pY!?,c~i)` | Changes internal modification/state marks on TSADSrc, vegfr2: TSADSrc.Y1 Y→pY at `kpSrc`. | +| 177 | `Unlabeled` | one-way | TSADSrc, vegfr2 | `kpSrc` | internal-state conversion/modification | `TSADSrc(Y1~Y) + vegfr2(Y1175~pY!?,c~i2) -> TSADSrc(Y1~pY) + vegfr2(Y1175~pY!?,c~i2)` | Changes internal modification/state marks on TSADSrc, vegfr2: TSADSrc.Y1 Y→pY at `kpSrc`. | +| 178 | `Unlabeled` | one-way | TSADSrc | `kdpSrc` | internal-state conversion/modification | `TSADSrc(Y1~pY) -> TSADSrc(Y1~Y)` | Changes internal modification/state marks on TSADSrc: TSADSrc.Y1 pY→Y at `kdpSrc`. | +| 179 | `Unlabeled` | one-way | Axl, TSADSrc | `kpSrcAxl` | internal-state conversion/modification | `TSADSrc(Y1~pY) + Axl(Ysrc~Y) -> TSADSrc(Y1~pY) + Axl(Ysrc~pY)` | Changes internal modification/state marks on Axl, TSADSrc: Axl.Ysrc Y→pY at `kpSrcAxl`. | +| 180 | `Unlabeled` | one-way | Axl | `kpAxlauto` | internal-state conversion/modification | `Axl(Ysrc~pY,Yaxl~Y) -> Axl(Ysrc~pY,Yaxl~pY)` | Changes internal modification/state marks on Axl: Axl.Yaxl Y→pY at `kpAxlauto`. | +| 181 | `Unlabeled` | one-way | Axl | `kdpautoAxl` | internal-state conversion/modification | `Axl(Yaxl~pY) -> Axl(Yaxl~Y)` | Changes internal modification/state marks on Axl: Axl.Yaxl pY→Y at `kdpautoAxl`. | +| 182 | `Unlabeled` | one-way | Axl | `kdpSrcAxl` | internal-state conversion/modification | `Axl(Ysrc~pY) -> Axl(Ysrc~Y)` | Changes internal modification/state marks on Axl: Axl.Ysrc pY→Y at `kdpSrcAxl`. | +| 183 | `Unlabeled` | one-way | Axl, PI3K | `konPI3KAxl` | internal-state conversion/modification | `PI3K(state~inactive) + Axl(Yaxl~pY) -> PI3K(state~active) + Axl(Yaxl~pY)` | Changes internal modification/state marks on Axl, PI3K: PI3K.state inactive→active at `konPI3KAxl`. | +| 184 | `Unlabeled` | one-way | PI3K | `koffPI3KAxl` | internal-state conversion/modification | `PI3K(state~active) -> PI3K(state~inactive)` | Changes internal modification/state marks on PI3K: PI3K.state active→inactive at `koffPI3KAxl`. | +| 185 | `Unlabeled` | one-way | PI, PI3K | `kcatPI3KPIP2/(kmPIP2PI3K+freepip2)` | internal-state conversion/modification | `PI3K(state~active) + PI(PIsite~3P) -> PI3K(state~active) + PI(PIsite~4P)` | Changes internal modification/state marks on PI, PI3K: PI.PIsite 3P→4P at `kcatPI3KPIP2/(kmPIP2PI3K+freepip2)`. | +| 186 | `Unlabeled` | one-way | PI, PTEN | `kcatPTENPIP3/(kmPIP3PTEN+freepip3)` | internal-state conversion/modification | `PTEN(PIP3docking) + PI(PIsite~4P) -> PTEN(PIP3docking) + PI(PIsite~3P)` | Changes internal modification/state marks on PI, PTEN: PI.PIsite 4P→3P at `kcatPTENPIP3/(kmPIP3PTEN+freepip3)`. | +| 187 | `Unlabeled` | reversible | PDK1, PI | `konPDK1PIP3, koffPDK1PIP3` | state and binding-pattern rewrite | `PDK1(PHpdk1) + PI(PIsite~4P) <-> PDK1(PHpdk1!1).PI(PIsite~4P!1)` | Reversibly forms a complex/contact among PDK1, PI through PDK1.PHpdk1, PI.P at `konPDK1PIP3, koffPDK1PIP3`. | +| 188 | `Unlabeled` | reversible | AKT, PI | `konAKTPIP3, koffAKTPIP3` | state and binding-pattern rewrite | `AKT(PHakt) + PI(PIsite~4P) <-> AKT(PHakt!1).PI(PIsite~4P!1)` | Reversibly forms a complex/contact among AKT, PI through AKT.PHakt, PI.P at `konAKTPIP3, koffAKTPIP3`. | +| 189 | `Unlabeled` | one-way | AKT | `kpmTORAKT` | internal-state conversion/modification | `AKT(PHakt!+,S473~S) -> AKT(PHakt!+,S473~pS)` | Changes internal modification/state marks on AKT: AKT.S473 S→pS at `kpmTORAKT`. | +| 190 | `Unlabeled` | one-way | AKT, PDK1 | `kpAKTPDK1` | internal-state conversion/modification | `AKT(PHakt!+,S473~pS,T308~S) + PDK1(PHpdk1!+) -> PDK1(PHpdk1!+) + AKT(PHakt!+,S473~pS,T308~pS)` | Changes internal modification/state marks on AKT, PDK1: AKT.T308 S→pS at `kpAKTPDK1`. | +| 191 | `Unlabeled` | one-way | AKT | `kdp473AKTPPase` | internal-state conversion/modification | `AKT(S473~pS) -> AKT(S473~S)` | Changes internal modification/state marks on AKT: AKT.S473 pS→S at `kdp473AKTPPase`. | +| 192 | `Unlabeled` | one-way | AKT | `kdp308AKTPPase` | internal-state conversion/modification | `AKT(T308~pS) -> AKT(T308~S)` | Changes internal modification/state marks on AKT: AKT.T308 pS→S at `kdp308AKTPPase`. | +| 193 | `Unlabeled` | reversible | CaM, eNOS | `konCaMeNOS, koffCaMeNOS` | stoichiometric pattern rewrite | `CaM(NCaM!+,NCaM!+,CCaM!+,CCaM!+,CaMtargetbd) + eNOS(CaMBD) <-> CaM(NCaM!+,NCaM!+,CCaM!+,CCaM!+,CaMtargetbd!1).eNOS(CaMBD!1)` | Reversibly forms a complex/contact among CaM, eNOS through CaM.CaMtargetbd, eNOS.CaMBD at `konCaMeNOS, koffCaMeNOS`. | +| 194 | `Unlabeled` | one-way | caveolin1, eNOS | `koffeNOScav1` | stoichiometric pattern rewrite | `eNOS(CaMBD!+,cav1BD!1).caveolin1(eNOSbd!1) -> eNOS(CaMBD!+,cav1BD) + caveolin1(eNOSbd)` | Releases a complex/contact among caveolin1, eNOS by freeing caveolin1.eNOSbd, eNOS.cav1BD at `koffeNOScav1`. | +| 195 | `Unlabeled` | one-way | caveolin1, eNOS | `koffeNOScav1` | state and binding-pattern rewrite | `eNOS(cav1BD!1,S1177~pS).caveolin1(eNOSbd!1) -> eNOS(cav1BD,S1177~pS) + caveolin1(eNOSbd)` | Releases a complex/contact among caveolin1, eNOS by freeing caveolin1.eNOSbd, eNOS.cav1BD at `koffeNOScav1`. | +| 196 | `Unlabeled` | one-way | caveolin1, eNOS | `koncaveNOS` | state and binding-pattern rewrite | `eNOS(CaMBD,cav1BD,S1177~S) + caveolin1(eNOSbd) -> eNOS(CaMBD,cav1BD!1,S1177~S).caveolin1(eNOSbd!1)` | Forms a complex/contact among caveolin1, eNOS through caveolin1.eNOSbd, eNOS.cav1BD at `koncaveNOS`. | +| 197 | `Unlabeled` | one-way | AKT, eNOS | `kcateNOSAKT` | internal-state conversion/modification | `eNOS(CaMBD!+,S1177~S) + AKT(T308~pS,S473~pS) -> eNOS(CaMBD!+,S1177~pS) + AKT(T308~pS,S473~pS)` | Changes internal modification/state marks on AKT, eNOS: eNOS.S1177 S→pS at `kcateNOSAKT`. | +| 198 | `Unlabeled` | one-way | eNOS | `kdpeNOS` | internal-state conversion/modification | `eNOS(S1177~pS) -> eNOS(S1177~S)` | Changes internal modification/state marks on eNOS: eNOS.S1177 pS→S at `kdpeNOS`. | +| 199 | `Unlabeled` | one-way | I, TSP1 | `-(koffCD47TSP1/kDCD47TSP1)/fextmolar*tsp1frees*cellarea*cd47s+koffCD47TSP1*cd47tsp1s*cellarea*(1/fextmolar)` | source/synthesis or algebraic source term | `I() -> I() + TSP1(CD47bd)` | Produces TSP1 while retaining or consuming I at `-(koffCD47TSP1/kDCD47TSP1)/fextmolar*tsp1frees*cellarea*cd47s+koffCD47TSP1*cd47tsp1s*cellarea*(1/fextmolar)`. | +| 200 | `Unlabeled` | one-way | CD47SIRPa, TSP1 | `(koffCD47TSP1/kDCD47TSP1)` | state and binding-pattern rewrite | `TSP1(CD47bd) + CD47SIRPa(TSP1bd,c~s) -> TSP1(CD47bd) + TSP1(CD47bd!1).CD47SIRPa(TSP1bd!1,c~s)` | Forms a complex/contact among CD47SIRPa, TSP1 through CD47SIRPa.TSP1bd, TSP1.CD47bd at `(koffCD47TSP1/kDCD47TSP1)`. | +| 201 | `Unlabeled` | one-way | CD47SIRPa, TSP1 | `koffCD47TSP1` | state and binding-pattern rewrite | `TSP1(CD47bd!1).CD47SIRPa(TSP1bd!1,c~s) -> CD47SIRPa(TSP1bd,c~s)` | Releases a complex/contact among CD47SIRPa, TSP1 by freeing CD47SIRPa.TSP1bd, TSP1.CD47bd at `koffCD47TSP1`. | +| 202 | `Unlabeled` | one-way | CD47SIRPa, vegfr2 | `kcd47free_on` | state and binding-pattern rewrite | `vegfr2(CD47bd,c~s) + CD47SIRPa(VEGFR2bd,c~s) -> vegfr2(CD47bd!1,c~s).CD47SIRPa(VEGFR2bd!1,c~s)` | Forms a complex/contact among CD47SIRPa, vegfr2 through CD47SIRPa.VEGFR2bd, vegfr2.CD47bd at `kcd47free_on`. | +| 203 | `Unlabeled` | reversible | Calcium_cyto, PKC | `konCaPKC, koffCaPKC` | binding/complex formation | `PKC(CalciumBD) + Calcium_cyto(bd) <-> PKC(CalciumBD!1).Calcium_cyto(bd!1)` | Reversibly forms a complex/contact among Calcium_cyto, PKC through Calcium_cyto.bd, PKC.CalciumBD at `konCaPKC, koffCaPKC`. | +| 204 | `Unlabeled` | reversible | DAG, PKC | `konDAGPKC, koffDAGPKC` | binding/complex formation | `PKC(DAGBD) + DAG(pkcbd) <-> PKC(DAGBD!1).DAG(pkcbd!1)` | Reversibly forms a complex/contact among DAG, PKC through DAG.pkcbd, PKC.DAGBD at `konDAGPKC, koffDAGPKC`. | +| 205 | `Unlabeled` | reversible | CIB1, Calcium_cyto | `kon1CaCIB1, koff1CaCIB1` | binding/complex formation | `CIB1(EF1) + Calcium_cyto(bd) <-> CIB1(EF1!1).Calcium_cyto(bd!1)` | Reversibly forms a complex/contact among CIB1, Calcium_cyto through CIB1.EF1, Calcium_cyto.bd at `kon1CaCIB1, koff1CaCIB1`. | +| 206 | `Unlabeled` | reversible | CIB1, Calcium_cyto | `kon2CaCIB1, koff2CaCIB1` | binding/complex formation | `CIB1(EF2) + Calcium_cyto(bd) <-> CIB1(EF2!1).Calcium_cyto(bd!1)` | Reversibly forms a complex/contact among CIB1, Calcium_cyto through CIB1.EF2, Calcium_cyto.bd at `kon2CaCIB1, koff2CaCIB1`. | +| 207 | `Unlabeled` | reversible | CIB1, SphK | `konCIB1SphK1, koffCIB1SphK1` | internal-state conversion/modification | `CIB1(EF1!+,EF2!+,sk1bd,location~cytosol) + SphK(CIB1bd,Serk~pS) <-> CIB1(EF1!+,EF2!+,sk1bd!1,location~cytosol).SphK(CIB1bd!1,Serk~pS)` | Reversibly forms a complex/contact among CIB1, SphK through CIB1.sk1bd, SphK.CIB1bd at `konCIB1SphK1, koffCIB1SphK1`. | +| 208 | `Unlabeled` | one-way | ERK2, SphK | `kcatERK/(freeSphK1+kmERKSK1)` | internal-state conversion/modification | `ERK2(S2~pS) + SphK(Serk~S) -> ERK2(S2~pS) + SphK(Serk~pS)` | Changes internal modification/state marks on ERK2, SphK: SphK.Serk S→pS at `kcatERK/(freeSphK1+kmERKSK1)`. | +| 209 | `Unlabeled` | reversible | CIB1 | `ktSK1, ktoffSK1` | internal-state conversion/modification | `CIB1(EF1!+,EF2!+,sk1bd!+,location~cytosol) <-> CIB1(EF1!+,EF2!+,sk1bd!+,location~membrane)` | Changes internal modification/state marks on CIB1: CIB1.location cytosol→membrane at `ktSK1, ktoffSK1`. | +| 210 | `Unlabeled` | one-way | CIB1 | `koffSK1` | internal-state conversion/modification | `CIB1(EF1,EF2,location~membrane) -> CIB1(EF1,EF2,location~cytosol)` | Changes internal modification/state marks on CIB1: CIB1.location membrane→cytosol at `koffSK1`. | +| 211 | `Unlabeled` | one-way | DAG, PKC, Raf | `kcatPKC/(freeraf+kmPKCRaf)` | internal-state conversion/modification | `PKC(CalciumBD!+,DAGBD!1).DAG(pkcbd!1) + Raf(Spkc~S) -> PKC(CalciumBD!+,DAGBD!1).DAG(pkcbd!1) + Raf(Spkc~pS)` | Changes internal modification/state marks on DAG, PKC, Raf: Raf.Spkc S→pS at `kcatPKC/(freeraf+kmPKCRaf)`. | +| 212 | `Unlabeled` | one-way | SphK | `kdpSK1` | internal-state conversion/modification | `SphK(Serk~pS) -> SphK(Serk~S)` | Changes internal modification/state marks on SphK: SphK.Serk pS→S at `kdpSK1`. | +| 213 | `Unlabeled` | one-way | Raf | `kdpPKCRaf` | internal-state conversion/modification | `Raf(Spkc~pS) -> Raf(Spkc~S)` | Changes internal modification/state marks on Raf: Raf.Spkc pS→S at `kdpPKCRaf`. | +| 214 | `Unlabeled` | one-way | I, Sph | `kSphgen` | source/synthesis or algebraic source term | `I() -> I() + Sph(skbd)` | Produces Sph while retaining or consuming I at `kSphgen`. | +| 215 | `Unlabeled` | one-way | CIB1, S1P, Sph, SphK | `kcatSK1Sph/(KmSK1Sph+freesphingosin)` | internal-state conversion/modification | `CIB1(sk1bd!1,location~membrane).SphK(CIB1bd!1,Serk~pS) + Sph(skbd) -> S1P(bd) + CIB1(sk1bd!1,location~membrane).SphK(CIB1bd!1,Serk~pS)` | Produces S1P while retaining or consuming CIB1, Sph, SphK at `kcatSK1Sph/(KmSK1Sph+freesphingosin)`. | +| 216 | `Unlabeled` | one-way | S1P, Sph | `kdpS1P` | pattern rewrite | `S1P(bd) -> Sph(skbd)` | Produces Sph while retaining or consuming S1P at `kdpS1P`. | +| 217 | `Unlabeled` | one-way | I, RasGTP | `kS1PRas*frees1p/(KmS1PRas+frees1p)-kRasGAP*gtpfreeras` | source/synthesis or algebraic source term | `I() -> I() + RasGTP(rafbd)` | Produces RasGTP while retaining or consuming I at `kS1PRas*frees1p/(KmS1PRas+frees1p)-kRasGAP*gtpfreeras`. | +| 218 | `Unlabeled` | reversible | Raf, RasGTP | `konRasRaf, koffRasRaf` | binding/complex formation | `Raf(rasbd) + RasGTP(rafbd) <-> Raf(rasbd!1).RasGTP(rafbd!1)` | Reversibly forms a complex/contact among Raf, RasGTP through Raf.rasbd, RasGTP.rafbd at `konRasRaf, koffRasRaf`. | +| 219 | `Unlabeled` | one-way | Raf, RasGTP | `kpRaf` | internal-state conversion/modification | `Raf(rasbd!1,Y1Y2~Y).RasGTP(rafbd!1) -> Raf(rasbd!1,Y1Y2~pY).RasGTP(rafbd!1)` | Changes internal modification/state marks on Raf, RasGTP: Raf.Y1Y2 Y→pY at `kpRaf`. | +| 220 | `Unlabeled` | one-way | Raf | `kdpRaf` | internal-state conversion/modification | `Raf(Y1Y2~pY) -> Raf(Y1Y2~Y)` | Changes internal modification/state marks on Raf: Raf.Y1Y2 pY→Y at `kdpRaf`. | +| 221 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf1/(KmMEK12Raf+mek12s1)` | internal-state conversion/modification | `MEK12(S1~S) + Raf(Y1Y2~pY,Spkc~S) -> Raf(Y1Y2~pY,Spkc~S) + MEK12(S1~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S1 S→pS at `kpMEK12Raf1/(KmMEK12Raf+mek12s1)`. | +| 222 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf2/(KmMEK12Raf+mek12s2)` | internal-state conversion/modification | `MEK12(S2~S) + Raf(Y1Y2~pY,Spkc~S) -> Raf(Y1Y2~pY,Spkc~S) + MEK12(S2~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S2 S→pS at `kpMEK12Raf2/(KmMEK12Raf+mek12s2)`. | +| 223 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf1/(KmMEK12Raf+mek12s2)` | internal-state conversion/modification | `MEK12(S1~S) + Raf(Y1Y2~pY,Spkc~pS) -> Raf(Y1Y2~pY,Spkc~pS) + MEK12(S1~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S1 S→pS at `kpMEK12Raf1/(KmMEK12Raf+mek12s2)`. | +| 224 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf2/(KmMEK12Raf+mek12s2)` | internal-state conversion/modification | `MEK12(S2~S) + Raf(Y1Y2~pY,Spkc~pS) -> Raf(Y1Y2~pY,Spkc~pS) + MEK12(S2~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S2 S→pS at `kpMEK12Raf2/(KmMEK12Raf+mek12s2)`. | +| 225 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf1/(KmMEK12Raf+mek12s1)` | internal-state conversion/modification | `MEK12(S1~S) + Raf(Y1Y2~Y,Spkc~pS) -> Raf(Y1Y2~Y,Spkc~pS) + MEK12(S1~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S1 S→pS at `kpMEK12Raf1/(KmMEK12Raf+mek12s1)`. | +| 226 | `Unlabeled` | one-way | MEK12, Raf | `kpMEK12Raf2/(KmMEK12Raf+mek12s2)` | internal-state conversion/modification | `MEK12(S2~S) + Raf(Y1Y2~Y,Spkc~pS) -> Raf(Y1Y2~Y,Spkc~pS) + MEK12(S2~pS)` | Changes internal modification/state marks on MEK12, Raf: MEK12.S2 S→pS at `kpMEK12Raf2/(KmMEK12Raf+mek12s2)`. | +| 227 | `Unlabeled` | one-way | MEK12 | `kdpMEK12_1` | internal-state conversion/modification | `MEK12(S1~pS) -> MEK12(S1~S)` | Changes internal modification/state marks on MEK12: MEK12.S1 pS→S at `kdpMEK12_1`. | +| 228 | `Unlabeled` | one-way | MEK12 | `kdpMEK12_2` | internal-state conversion/modification | `MEK12(S2~pS) -> MEK12(S2~S)` | Changes internal modification/state marks on MEK12: MEK12.S2 pS→S at `kdpMEK12_2`. | +| 229 | `Unlabeled` | one-way | ERK1, MEK12 | `(kpMEK12ERK12_1/(kmMEKERK12+erk12s1))` | internal-state conversion/modification | `MEK12(S1~pS,S2~pS) + ERK1(S1~S) -> MEK12(S1~pS,S2~pS) + ERK1(S1~pS)` | Changes internal modification/state marks on ERK1, MEK12: ERK1.S1 S→pS at `(kpMEK12ERK12_1/(kmMEKERK12+erk12s1))`. | +| 230 | `Unlabeled` | one-way | ERK2, MEK12 | `(kpMEK12ERK12_2/(kmMEKERK12+erk12s2))` | internal-state conversion/modification | `MEK12(S1~pS,S2~pS) + ERK2(S2~S) -> MEK12(S1~pS,S2~pS) + ERK2(S2~pS)` | Changes internal modification/state marks on ERK2, MEK12: ERK2.S2 S→pS at `(kpMEK12ERK12_2/(kmMEKERK12+erk12s2))`. | +| 231 | `Unlabeled` | one-way | ERK1 | `kdpERK12_1` | internal-state conversion/modification | `ERK1(S1~pS) -> ERK1(S1~S)` | Changes internal modification/state marks on ERK1: ERK1.S1 pS→S at `kdpERK12_1`. | +| 232 | `Unlabeled` | one-way | ERK2 | `kdpERK12_2` | internal-state conversion/modification | `ERK2(S2~pS) -> ERK2(S2~S)` | Changes internal modification/state marks on ERK2: ERK2.S2 pS→S at `kdpERK12_2`. | + +## 7. Observables and technical readouts + +| Observable | Type | Pattern / target | Technical interpretation | +| --- | --- | --- | --- | +| `vegffrees` | `Molecules` | `vegf(r,r,nrp1bd,c~s)` | Reports free/unbound species matching the pattern. | +| `VEGFR2total` | `Molecules` | `vegfr2()` | Reports total pool matching the pattern. | +| `tsp1frees` | `Molecules` | `TSP1(CD47bd)` | Reports free/unbound species matching the pattern. | +| `cd47tsp1s` | `Molecules` | `TSP1(CD47bd!1).CD47SIRPa(TSP1bd!1,Y1~Y,c~s)` | Reports bound or complexed species matching the pattern. | +| `cd47s` | `Molecules` | `CD47SIRPa(TSP1bd,Y1~Y,c~s)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `VEGFR2tots` | `Molecules` | `vegfr2(c~s)` | Reports total pool matching the pattern. | +| `VEGFR2toti` | `Molecules` | `vegfr2(c~i)` | Reports total pool matching the pattern. | +| `vr2s` | `Molecules` | `vegfr2(l1,c~s)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `vr2i` | `Molecules` | `vegfr2(l1,c~i)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `vr1s` | `Molecules` | `vegfr1(l2,nrp1bd,c~s)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `vegfr2Y1175ps` | `Molecules` | `vegfr2(Y1175~pY!?,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `vegfr2Y1175pi` | `Molecules` | `vegfr2(Y1175~pY!?,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `pr2Y1175total` | `Molecules` | `vegfr2(Y1175~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `vegfr1tots` | `Molecules` | `vegfr1(c~s)` | Reports total pool matching the pattern. | +| `NRP1VEGFR2s` | `Molecules` | `vegf(r!1,r!2,nrp1bd!+,c~s).vegfr2(l1!1,c~s).vegfr2(l1!2,c~s)` | Reports bound or complexed species matching the pattern. | +| `NRP1VEGFR2i` | `Molecules` | `vegf(r!1,r!2,nrp1bd!+,c~i).vegfr2(l1!1,c~i).vegfr2(l1!2,c~i)` | Reports bound or complexed species matching the pattern. | +| `freeDAGs` | `Molecules` | `DAG(pkcbd!?)` | Reports free/unbound species matching the pattern. | +| `activePLCgamma` | `Molecules` | `PLCgamma(Yplc~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `PIP2` | `Molecules` | `PI(PIsite~3P)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `PIP3` | `Molecules` | `PI(PIsite~4P)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `freeip3cyto` | `Molecules` | `IP3_cyto(ip3rbd)` | Reports free/unbound species matching the pattern. | +| `Cac` | `Molecules` | `Calcium_cyto(bd)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `Caer` | `Molecules` | `CaER(bd)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `CaBuf_fer` | `Molecules` | `CaF(cabd!+)` | Reports bound or complexed species matching the pattern. | +| `activePKCs` | `Molecules` | `PKC(CalciumBD!+,DAGBD!1).DAG(pkcbd!1)` | Reports bound or complexed species matching the pattern. | +| `activePKCtot` | `Molecules` | `PKC(CalciumBD!+,DAGBD!+)` | Reports total pool matching the pattern. | +| `SphKpkc` | `Molecules` | `SphK(Serk~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `S1phosphate` | `Molecules` | `S1P(bd)` | Reports phosphorylated or modified species matching the pattern. | +| `NRP1frees` | `Molecules` | `NRP1(vegfabd,c~s)` | Reports free/unbound species matching the pattern. | +| `NRP1freei` | `Molecules` | `NRP1(vegfabd,c~i)` | Reports free/unbound species matching the pattern. | +| `NRP1bounds` | `Molecules` | `NRP1(vegfabd!+,c~s)` | Reports bound or complexed species matching the pattern. | +| `NRP1boundi` | `Molecules` | `NRP1(vegfabd!+,c~i)` | Reports bound or complexed species matching the pattern. | +| `vr2dimers` | `Molecules` | `vegfr2(l1,dimer!1,c~s).vegfr2(l1,dimer!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `vr2dimeri` | `Molecules` | `vegfr2(l1,dimer!1,c~i).vegfr2(l1,dimer!1,c~i)` | Reports bound or complexed species matching the pattern. | +| `NRP1totals` | `Molecules` | `NRP1(c~s)` | Reports total pool matching the pattern. | +| `NRP1totali` | `Molecules` | `NRP1(c~i)` | Reports total pool matching the pattern. | +| `singleNRP1totals` | `Molecules` | `NRP1(vegfabd,c~s)` | Reports total pool matching the pattern. | +| `singleNRP1totali` | `Molecules` | `NRP1(vegfabd,c~i)` | Reports total pool matching the pattern. | +| `vegfr2total` | `Molecules` | `vegf(r!1).vegfr2(l1!1)` | Reports total pool matching the pattern. | +| `vr2Y1175s` | `Molecules` | `vegfr2(Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2Y1175i` | `Molecules` | `vegfr2(Y1175~pY,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `plcgammafree` | `Molecules` | `PLCgamma(Yplc~Y)` | Reports free/unbound species matching the pattern. | +| `rasgdpfree` | `Molecules` | `RasGDP(rafbd!?)` | Reports free/unbound species matching the pattern. | +| `rasgtpfree` | `Molecules` | `RasGTP(rafbd!?)` | Reports free/unbound species matching the pattern. | +| `activeRafbyrastot` | `Molecules` | `Raf(Y1Y2~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoMEK12tot` | `Molecules` | `MEK12(S1~pS!?,S2~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoERK1tot` | `Molecules` | `ERK1(S1~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoERK2tot` | `Molecules` | `ERK2(S2~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `SphK1` | `Molecules` | `SphK(CIB1bd!+,Serk~S).CIB1(sk1bd!1,location~membrane)` | Reports bound or complexed species matching the pattern. | +| `SphK1mempS` | `Molecules` | `SphK(CIB1bd!+,Serk~pS).CIB1(sk1bd!1,location~membrane)` | Reports phosphorylated or modified species matching the pattern. | +| `SphK1cytosol` | `Molecules` | `SphK(CIB1bd!+,Serk~S).CIB1(sk1bd!1,location~cytosol)` | Reports bound or complexed species matching the pattern. | +| `activeSphK1` | `Molecules` | `SphK(Serk~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `freeSK1` | `Molecules` | `SphK(CIB1bd,Serk~S)` | Reports free/unbound species matching the pattern. | +| `freeSK1mem` | `Molecules` | `SphK(CIB1bd!1,Serk~S).CIB1(sk1bd!1,location~membrane)` | Reports free/unbound species matching the pattern. | +| `freecib1` | `Molecules` | `CIB1(EF1,EF2,sk1bd)` | Reports free/unbound species matching the pattern. | +| `calciumcib1` | `Molecules` | `CIB1(EF1!+,EF2!+,sk1bd)` | Reports bound or complexed species matching the pattern. | +| `sk1bcib1` | `Molecules` | `CIB1(EF1!+,EF2!+,sk1bd!+)` | Reports bound or complexed species matching the pattern. | +| `nrp1s` | `Molecules` | `NRP1(vegfabd,c~s)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `vegfnrp1s` | `Molecules` | `vegf(r,r,nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfr1s` | `Molecules` | `vegf(r!1,r,nrp1bd,c~s).vegfr1(l2!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfr2s` | `Molecules` | `vegf(r!1,r,nrp1bd,c~s).vegfr2(l1!1,dimer,c~s)` | Reports bound or complexed species matching the pattern. | +| `freepip2` | `Molecules` | `PI(PIsite~3P)` | Reports free/unbound species matching the pattern. | +| `freesphingosin` | `Molecules` | `Sph(skbd)` | Reports free/unbound species matching the pattern. | +| `freeraf` | `Molecules` | `Raf(Spkc~S)` | Reports free/unbound species matching the pattern. | +| `activeRafPKC` | `Molecules` | `Raf(Spkc~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `activeRafPKCERK1` | `Molecules` | `Raf(Spkc~pS!?,Y1Y2~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `activeRafPKCERK2` | `Molecules` | `Raf(Spkc~pS!?,Y1Y2~Y!?)` | Reports phosphorylated or modified species matching the pattern. | +| `activeRafPKCERK3` | `Molecules` | `Raf(Spkc~S!?,Y1Y2~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `rafY1Y2pY` | `Molecules` | `Raf(Y1Y2~pY,Spkc~S)` | Reports phosphorylated or modified species matching the pattern. | +| `rafY1Y2pYpS` | `Molecules` | `Raf(Y1Y2~pY,Spkc~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `rafpS` | `Molecules` | `Raf(Y1Y2~Y,Spkc~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `erk1s` | `Molecules` | `ERK1(S1~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `mek12s` | `Molecules` | `MEK12(S1~S,S2~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `R2singlei` | `Molecules` | `vegfr2(l1,Y1175~Y,dimer,c~i)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `pERK1s` | `Molecules` | `ERK1(S1~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `mek12ps` | `Molecules` | `MEK12(S1~pS,S2~S)` | Reports phosphorylated or modified species matching the pattern. | +| `pERK2s` | `Molecules` | `ERK2(S2~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `mek12ps1` | `Molecules` | `MEK12(S1~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `mek12ps2` | `Molecules` | `MEK12(S2~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `erk1ps` | `Molecules` | `ERK1(S1~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `erk2ps` | `Molecules` | `ERK2(S2~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2r2py1175s` | `Molecules` | `vegfr2(Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2r2py1175i` | `Molecules` | `vegfr2(Y1175~pY,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2py1175s` | `Species` | `vegf(r!1,r,c~s).vegfr2(l1!1,Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `vr2py1175i` | `Species` | `vegf(r!1,r,c~i).vegfr2(l1!1,Y1175~pY,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `r2singlepy1175s` | `Molecules` | `vegfr2(l1,Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `r2singlepy1175i` | `Molecules` | `vegfr2(l1,Y1175~pY,c~i)` | Reports phosphorylated or modified species matching the pattern. | +| `vr1r2pY1165s` | `Molecules` | `vegf(r!1,r!2,c~s).vegfr1(l2!1,c~s).vegfr2(l1!2,Y1175~pY,c~s)` | Reports phosphorylated or modified species matching the pattern. | +| `pSK1` | `Molecules` | `SphK(Serk~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `frees1p` | `Molecules` | `S1P(bd)` | Reports free/unbound species matching the pattern. | +| `py1y2rafs` | `Molecules` | `Raf(Y1Y2~pY)` | Reports phosphorylated or modified species matching the pattern. | +| `vegfnrp1i` | `Molecules` | `vegf(r,r,nrp1bd!1,c~i).NRP1(vegfabd!1,c~i)` | Reports bound or complexed species matching the pattern. | +| `vegfr2i` | `Species` | `vegf(r!1,r,nrp1bd,c~i).vegfr2(l1!1,c~i)` | Reports bound or complexed species matching the pattern. | +| `totalnrp1` | `Molecules` | `NRP1(vegfabd)` | Reports total pool matching the pattern. | +| `pplcgamma` | `Molecules` | `PLCgamma(Yplc~pY)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoERKpS1` | `Molecules` | `ERK1(S1~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoERKpS2` | `Molecules` | `ERK2(S2~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoMEKpS1` | `Molecules` | `MEK12(S1~pS!?,S2~S)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoMEKpS2` | `Molecules` | `MEK12(S1~S,S2~pS!?)` | Reports phosphorylated or modified species matching the pattern. | +| `freeSphK1` | `Molecules` | `SphK(CIB1bd,Serk~S)` | Reports free/unbound species matching the pattern. | +| `rafpkc` | `Molecules` | `Raf(Spkc~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `mek12s1` | `Molecules` | `MEK12(S1~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `mek12s2` | `Molecules` | `MEK12(S2~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `erk12s1` | `Molecules` | `ERK1(S1~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `erk12s2` | `Molecules` | `ERK2(S2~S)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `yplcgamma` | `Molecules` | `PLCgamma(Yplc~Y)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `gtpfreeras` | `Molecules` | `RasGTP(rafbd)` | Reports free/unbound species matching the pattern. | +| `bvegfr2` | `Molecules` | `vegf(r!1,nrp1bd,c~s).vegfr2(l1!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `bnrp1` | `Molecules` | `vegf(nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `bvegfr1` | `Molecules` | `vegf(r!1,nrp1bd,c~s).vegfr1(l2!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `bvegfr1dimer` | `Molecules` | `vegf(r!1,r!2,c~s).vegfr1(l2!1,c~s).vegfr1(l2!2,c~s)` | Reports bound or complexed species matching the pattern. | +| `bvegfr2_2` | `Molecules` | `vegf(r!1,c~s).vegfr2(l1!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `bvegfr1_2` | `Molecules` | `vegf(r!1,c~s).vegfr1(l2!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfbound_1` | `Molecules` | `vegf(r!+,nrp1bd,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfbound_2` | `Species` | `vegf(r,nrp1bd!+,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfbound_3` | `Molecules` | `vegf(r!+,c~s)` | Reports bound or complexed species matching the pattern. | +| `vegfbound_4` | `Species` | `vegf(r,r,nrp1bd!1,c~s).NRP1(vegfabd!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `Iopenstim` | `Molecules` | `Istim()` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `nrp1r1s` | `Molecules` | `NRP1(vegfabd!1,c~s).vegfr1(nrp1bd!1,c~s)` | Reports bound or complexed species matching the pattern. | +| `CIB1mem` | `Molecules` | `CIB1(location~membrane)` | Reports the BNGL pattern for downstream plotting or rate expressions. | +| `freepip3` | `Molecules` | `PI(PIsite~4P)` | Reports free/unbound species matching the pattern. | +| `ps473akt` | `Molecules` | `AKT(S473~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `ps308akt` | `Molecules` | `AKT(T308~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoAxltotal` | `Molecules` | `Axl(Ysrc~pY!?,Yaxl~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoAxlpSrc` | `Molecules` | `Axl(Ysrc~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoAxlpauto` | `Molecules` | `Axl(Yaxl~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `activeSrc` | `Molecules` | `TSADSrc(Y1~pY!?)` | Reports phosphorylated or modified species matching the pattern. | +| `phosphoeNOS` | `Molecules` | `eNOS(S1177~pS)` | Reports phosphorylated or modified species matching the pattern. | +| `ppAkt` | `Molecules` | `AKT(S473~pS,T308~pS)` | Reports phosphorylated or modified species matching the pattern. | + +## 8. Actions and simulation workflow + +1. `generate_network({overwrite=>1,max_agg=>10})` — execution command affecting network generation, simulation, scanning, or output. + +## 9. Technical caveats and ambiguities + +- No compartments or anchors are declared despite many molecule states named like surface/internal/recycling states (`s`, `i`, `i2`, `r`). Those are internal states, not BNGL compartments. + +- The model uses many algebraic rate expressions directly in reaction rules rather than a separate functions block. + +- Several receptor-state transitions are encoded as explicit rules over the `c` internal state. + +- The complete rule inventory has 232 rows; downstream review should compare this count with the `begin reaction rules` block after any source edits. + +- The summary keeps raw molecule, site, state, and parameter names because this is the coder-facing version and those identifiers are necessary for implementation review. diff --git a/data/yaml_feature_audit.md b/data/yaml_feature_audit.md new file mode 100644 index 00000000..fc0ba545 --- /dev/null +++ b/data/yaml_feature_audit.md @@ -0,0 +1,804 @@ +# Published YAML Feature Audit — Pilot Batch + +This report audits 20 same-directory `Published/` BNGL/YAML pairs without editing any YAML files. It compares static BNGL feature detection against the currently present YAML values and lists proposed insertions or changes for the requested metadata fields. + +## Scope and pairing rule + +- Root inspected: `Published/` +- Pairing rule: only `.bngl` files whose `metadata.yaml` is in the same directory are eligible. +- Pilot size: 20 BNGL/YAML pairs. +- YAML edit policy for this pass: no YAML files were modified; this Markdown file records proposed insertions/changes only. + +## Detection definitions + +- `uses_cbngl_compartments`: `true` when an uncommented `begin compartments` block or compartment-prefixed pattern such as `@cyt:A()` is detected. +- `uses_vcell_compartments`: `true` when VCell-style anchor semantics are detected through an uncommented `begin anchors` block. +- `uses_energy`: `true` when an uncommented energy-pattern block is detected. +- `uses_functions`: `true` when an uncommented `begin functions` block contains entries. +- `uses_moveconnected`: `true` when an uncommented `moveConnected` call is detected. +- `uses_trash_molecules`: `true` when the BNGL uses a `Trash(...)` molecule/pattern as an explicit sink species. +- `uses_anchors`: `true` when an uncommented `begin anchors` block is detected. +- `uses_multiple_identical_sites`: `true` when a declared molecule type repeats the same component/site name within one molecule type. +- `uses_deletes_molecules`: `true` when an uncommented `DeleteMolecules` modifier/action is detected. +- `uses_exclude_include_reactants`: `true` when an uncommented `exclude_reactants` or `include_reactants` modifier is detected. +- `uses_generate_network`: `true` when an uncommented `generate_network(...)` action is detected. +- `default_sim_command`: First uncommented simulation command found in priority order: `simulate_ode`, `simulate_ssa`, `simulate_nf`, `simulate`. + +## Batch summary + +| Field | Detected true | Detected false | Detected null | Current YAML missing | Proposed insertions/changes | +|---|---:|---:|---:|---:|---:| +| `uses_cbngl_compartments` | 9 | 11 | 0 | 20 | 20 | +| `uses_vcell_compartments` | 5 | 15 | 0 | 20 | 20 | +| `uses_energy` | 0 | 20 | 0 | 0 | 0 | +| `uses_functions` | 6 | 14 | 0 | 0 | 7 | +| `uses_moveconnected` | 0 | 20 | 0 | 20 | 20 | +| `uses_trash_molecules` | 2 | 18 | 0 | 20 | 20 | +| `uses_anchors` | 5 | 15 | 0 | 20 | 20 | +| `uses_multiple_identical_sites` | 5 | 15 | 0 | 20 | 20 | +| `uses_deletes_molecules` | 4 | 16 | 0 | 20 | 20 | +| `uses_exclude_include_reactants` | 2 | 18 | 0 | 20 | 20 | +| `uses_generate_network` | 14 | 6 | 0 | 20 | 20 | +| `default_sim_command` | 0 | 0 | 1 | 20 | 20 | + +## Audited pairs + +| # | BNGL path | YAML path | Proposed updates | +|---:|---|---|---:| +| 1 | `Published/Blinovegfr/Blinov_egfr.bngl` | `Published/Blinovegfr/metadata.yaml` | 11 | +| 2 | `Published/Blinovran/Blinov_ran.bngl` | `Published/Blinovran/metadata.yaml` | 11 | +| 3 | `Published/RulebasedRantransport/Rule_based_Ran_transport.bngl` | `Published/RulebasedRantransport/metadata.yaml` | 11 | +| 4 | `Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl` | `Published/RulebasedRantransportdraft/metadata.yaml` | 11 | +| 5 | `Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl` | `Published/Rulebasedegfrcompart/metadata.yaml` | 11 | +| 6 | `Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl` | `Published/Rulebasedegfrtutorial/metadata.yaml` | 11 | +| 7 | `Published/Jung2017/Jung_2017.bngl` | `Published/Jung2017/metadata.yaml` | 10 | +| 8 | `Published/Lang2024/Lang_2024.bngl` | `Published/Lang2024/metadata.yaml` | 10 | +| 9 | `Published/Nosbisch2022/Nosbisch_2022.bngl` | `Published/Nosbisch2022/metadata.yaml` | 11 | +| 10 | `Published/Barua2007/Barua_2007.bngl` | `Published/Barua2007/metadata.yaml` | 10 | +| 11 | `Published/An2009/An_2009.bngl` | `Published/An2009/metadata.yaml` | 10 | +| 12 | `Published/Ligon2014/Ligon_2014.bngl` | `Published/Ligon2014/metadata.yaml` | 10 | +| 13 | `Published/Zhang2023/Zhang_2023.bngl` | `Published/Zhang2023/metadata.yaml` | 10 | +| 14 | `Published/ChylekFceRI2014/ChylekFceRI_2014.bngl` | `Published/ChylekFceRI2014/metadata.yaml` | 10 | +| 15 | `Published/Dolan2015/Dolan_2015.bngl` | `Published/Dolan2015/metadata.yaml` | 10 | +| 16 | `Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl` | `Published/Hlavacek2001/metadata.yaml` | 10 | +| 17 | `Published/Dembo1978/blbr_dembo1978.bngl` | `Published/Dembo1978/metadata.yaml` | 10 | +| 18 | `Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl` | `Published/Dreisigmeyer2008/metadata.yaml` | 10 | +| 19 | `Published/Gardner2000/genetic_switch_gardner2000.bngl` | `Published/Gardner2000/metadata.yaml` | 10 | +| 20 | `Published/Barua2009/Barua_2009.bngl` | `Published/Barua2009/metadata.yaml` | 10 | + +## Per-model findings + +### 1. `Published/Blinovegfr` / `Blinov_egfr.bngl` + +- BNGL: `Published/Blinovegfr/Blinov_egfr.bngl` +- YAML: `Published/Blinovegfr/metadata.yaml` +- Un-commented action commands detected: `simulate_nf` +- Compartments block entries detected: `3` +- Anchor entries detected: `2` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `true` | change from True | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `true` | `missing` | insert | `true` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `false` | `missing` | insert | `false` | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `true`. +- `uses_functions`: change from True; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `true`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `false`. +- `default_sim_command`: insert; proposed value `simulate_nf`. + +### 2. `Published/Blinovran` / `Blinov_ran.bngl` + +- BNGL: `Published/Blinovran/Blinov_ran.bngl` +- YAML: `Published/Blinovran/metadata.yaml` +- Un-commented action commands detected: `simulate_nf` +- Compartments block entries detected: `5` +- Anchor entries detected: `1` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `true` | change from True | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `true` | `missing` | insert | `true` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `false` | `missing` | insert | `false` | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `true`. +- `uses_functions`: change from True; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `true`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `false`. +- `default_sim_command`: insert; proposed value `simulate_nf`. + +### 3. `Published/RulebasedRantransport` / `Rule_based_Ran_transport.bngl` + +- BNGL: `Published/RulebasedRantransport/Rule_based_Ran_transport.bngl` +- YAML: `Published/RulebasedRantransport/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Compartments block entries detected: `5` +- Anchor entries detected: `1` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `true` | change from True | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `true` | `missing` | insert | `true` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `true`. +- `uses_functions`: change from True; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `true`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `generate_network`. + +### 4. `Published/RulebasedRantransportdraft` / `Rule_based_Ran_transport_draft.bngl` + +- BNGL: `Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl` +- YAML: `Published/RulebasedRantransportdraft/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Compartments block entries detected: `5` +- Anchor entries detected: `1` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `true` | change from True | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `true` | `missing` | insert | `true` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `true`. +- `uses_functions`: change from True; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `true`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `generate_network`. + +### 5. `Published/Rulebasedegfrcompart` / `Rule_based_egfr_compart.bngl` + +- BNGL: `Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl` +- YAML: `Published/Rulebasedegfrcompart/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Compartments block entries detected: `3` +- Anchor entries detected: `2` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `true` | change from True | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `true` | `missing` | insert | `true` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `true`. +- `uses_functions`: change from True; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `true`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `generate_network`. + +### 6. `Published/Rulebasedegfrtutorial` / `Rule_based_egfr_tutorial.bngl` + +- BNGL: `Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl` +- YAML: `Published/Rulebasedegfrtutorial/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Compartments block entries detected: `1` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `true` | change from True | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_functions`: change from True; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `generate_network`. + +### 7. `Published/Jung2017` / `Jung_2017.bngl` + +- BNGL: `Published/Jung2017/Jung_2017.bngl` +- YAML: `Published/Jung2017/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Compartments block entries detected: `3` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `true` | `true` | keep | `true` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `generate_network`. + +### 8. `Published/Lang2024` / `Lang_2024.bngl` + +- BNGL: `Published/Lang2024/Lang_2024.bngl` +- YAML: `Published/Lang2024/metadata.yaml` +- Un-commented action commands detected: `simulate`, `generate_network` +- Compartments block entries detected: `1` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `false` | keep | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | +| `uses_exclude_include_reactants` | `true` | `missing` | insert | `true` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `true`. +- `uses_exclude_include_reactants`: insert; proposed value `true`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `simulate`. + +### 9. `Published/Nosbisch2022` / `Nosbisch_2022.bngl` + +- BNGL: `Published/Nosbisch2022/Nosbisch_2022.bngl` +- YAML: `Published/Nosbisch2022/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Compartments block entries detected: `1` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `true` | `missing` | insert | `true` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `true` | change from True | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `true`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_functions`: change from True; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `generate_network`. + +### 10. `Published/Barua2007` / `Barua_2007.bngl` + +- BNGL: `Published/Barua2007/Barua_2007.bngl` +- YAML: `Published/Barua2007/metadata.yaml` +- Un-commented action commands detected: `simulate_ode`, `generate_network` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `false` | keep | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `true` | `missing` | insert | `true` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `true`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `simulate_ode`. + +### 11. `Published/An2009` / `An_2009.bngl` + +- BNGL: `Published/An2009/An_2009.bngl` +- YAML: `Published/An2009/metadata.yaml` +- Un-commented action commands detected: `simulate_ode`, `generate_network` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: + - DNA: repeated c in `DNA(A20,TNF,iNOS,IL10,IkB,c,c)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `false` | keep | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `true` | `missing` | insert | `true` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `true`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `true`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `simulate_ode`. + +### 12. `Published/Ligon2014` / `Ligon_2014.bngl` + +- BNGL: `Published/Ligon2014/Ligon_2014.bngl` +- YAML: `Published/Ligon2014/metadata.yaml` +- Un-commented action commands detected: `simulate_nf` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `true` | `true` | keep | `true` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `false` | `missing` | insert | `false` | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `true`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `false`. +- `default_sim_command`: insert; proposed value `simulate_nf`. + +### 13. `Published/Zhang2023` / `Zhang_2023.bngl` + +- BNGL: `Published/Zhang2023/Zhang_2023.bngl` +- YAML: `Published/Zhang2023/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: + - vegf: repeated r in `vegf(r,r,nrp1bd,c~s~i~i2~r)` + - CaM: repeated CCaM, NCaM in `CaM(NCaM,NCaM,CCaM,CCaM,CaMtargetbd)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `false` | keep | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `true` | `missing` | insert | `true` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `true`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `true`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `generate_network`. + +### 14. `Published/ChylekFceRI2014` / `ChylekFceRI_2014.bngl` + +- BNGL: `Published/ChylekFceRI2014/ChylekFceRI_2014.bngl` +- YAML: `Published/ChylekFceRI2014/metadata.yaml` +- Un-commented action commands detected: `writeXML` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: + - Lig: repeated hap in `Lig(hap~b~e,hap~b~e)` + - Rec: repeated fab in `Rec(fab,fab,b_Y218~0~P,b_Y224~0~P,g_Y65_Y76~0~P)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `false` | keep | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `false` | `missing` | insert | `false` | +| `default_sim_command` | `null` | `missing` | insert | `null` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `true`. +- `uses_deletes_molecules`: insert; proposed value `true`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `false`. +- `default_sim_command`: insert; proposed value `null`. + +### 15. `Published/Dolan2015` / `Dolan_2015.bngl` + +- BNGL: `Published/Dolan2015/Dolan_2015.bngl` +- YAML: `Published/Dolan2015/metadata.yaml` +- Un-commented action commands detected: `simulate_nf` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `true` | `true` | keep | `true` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `false` | `missing` | insert | `false` | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `true`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `false`. +- `default_sim_command`: insert; proposed value `simulate_nf`. + +### 16. `Published/Hlavacek2001` / `kinetic_proofreading_hlavacek2001.bngl` + +- BNGL: `Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl` +- YAML: `Published/Hlavacek2001/metadata.yaml` +- Un-commented action commands detected: `simulate`, `generate_network` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: + - L: repeated r in `L(r,r,mod~0~1~2~3~4~5)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `true` | `true` | keep | `true` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `true`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `simulate`. + +### 17. `Published/Dembo1978` / `blbr_dembo1978.bngl` + +- BNGL: `Published/Dembo1978/blbr_dembo1978.bngl` +- YAML: `Published/Dembo1978/metadata.yaml` +- Un-commented action commands detected: `simulate` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: + - L: repeated r in `L(r,r)` + - R: repeated l in `R(l,l)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `false` | keep | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `false` | `missing` | insert | `false` | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `true`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `false`. +- `default_sim_command`: insert; proposed value `simulate`. + +### 18. `Published/Dreisigmeyer2008` / `lac_operon_dreisigmeyer2008.bngl` + +- BNGL: `Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl` +- YAML: `Published/Dreisigmeyer2008/metadata.yaml` +- Un-commented action commands detected: `simulate`, `generate_network` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `true` | `true` | keep | `true` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `simulate`. + +### 19. `Published/Gardner2000` / `genetic_switch_gardner2000.bngl` + +- BNGL: `Published/Gardner2000/genetic_switch_gardner2000.bngl` +- YAML: `Published/Gardner2000/metadata.yaml` +- Un-commented action commands detected: `simulate`, `generate_network` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `true` | `true` | keep | `true` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `simulate`. + +### 20. `Published/Barua2009` / `Barua_2009.bngl` + +- BNGL: `Published/Barua2009/Barua_2009.bngl` +- YAML: `Published/Barua2009/metadata.yaml` +- Un-commented action commands detected: `simulate_ode`, `generate_network` +- Compartments block entries detected: `0` +- Anchor entries detected: `0` +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | +|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | +| `uses_energy` | `false` | `false` | keep | `false` | +| `uses_functions` | `false` | `false` | keep | `false` | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | +| `uses_anchors` | `false` | `missing` | insert | `false` | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | +| `uses_generate_network` | `true` | `missing` | insert | `true` | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. +- `uses_vcell_compartments`: insert; proposed value `false`. +- `uses_moveconnected`: insert; proposed value `false`. +- `uses_trash_molecules`: insert; proposed value `false`. +- `uses_anchors`: insert; proposed value `false`. +- `uses_multiple_identical_sites`: insert; proposed value `false`. +- `uses_deletes_molecules`: insert; proposed value `false`. +- `uses_exclude_include_reactants`: insert; proposed value `false`. +- `uses_generate_network`: insert; proposed value `true`. +- `default_sim_command`: insert; proposed value `simulate_ode`. diff --git a/data/yaml_feature_audit_2.md b/data/yaml_feature_audit_2.md new file mode 100644 index 00000000..7e492e01 --- /dev/null +++ b/data/yaml_feature_audit_2.md @@ -0,0 +1,955 @@ +# Published YAML Feature Audit 2 — Updated Definitions + +This report re-audits the same 20 same-directory `Published/` BNGL/YAML pairs from `data/yaml_feature_audit.md` using the updated block and compartment-grammar definitions. It does not modify any YAML files; proposed insertions/changes are recorded here only. + +## Scope and pairing rule + +- Root inspected: `Published/` +- Pairing rule: only `.bngl` files whose `metadata.yaml` is in the same directory are eligible. +- Pilot size: 20 BNGL/YAML pairs, matching the first audit. +- YAML edit policy for this pass: no YAML files were modified; this Markdown file records proposed insertions/changes only. + +## Updated detection policy + +### Block presence versus active block contents + +- For block-based BNGL constructs, a `uses_*` boolean records whether the relevant block/construct is present, even if the block is empty. +- Active block contents are counted separately. An active entry is an uncommented, nonempty line between the `begin ...` and `end ...` delimiters. +- Example: `begin functions` followed immediately by `end functions` still proposes `uses_functions: true`, but the report records `active function entries: 0`. + +### Compartment grammar definitions + +- A `begin compartments` block is reported as block evidence, but it does not by itself determine either compartment-grammar boolean. +- A model may be marked true for both compartment booleans if both syntax forms are actively present. + +## Field definitions + +- `uses_cbngl_compartments`: `true` when uncommented CBNGL-style `Molecule(...)@Compartment` syntax is detected. This grammar places the whole molecule pattern in the named compartment. +- `uses_vcell_compartments`: `true` when uncommented VCell-style `@Compartment:Molecule(...)` syntax is detected. This grammar attaches the compartment after the molecule pattern and can appear on individual molecule patterns inside a complex. +- `uses_energy`: `true` when an energy-pattern block is present, even if empty; active entries are counted separately. +- `uses_functions`: `true` when a `begin functions` block is present and there are uncommented lines within this block; active entries are counted separately. +- `uses_moveconnected`: `true` when an uncommented `moveConnected` call is detected. +- `uses_trash_molecules`: `true` when the BNGL uses a `Trash(...)` molecule/pattern as an explicit sink species. +- `uses_anchors`: `true` when a `begin anchors` block is present, even if empty; active entries are counted separately. +- `uses_multiple_identical_sites`: `true` when a declared molecule type repeats the same component/site name within one molecule type. +- `uses_deletes_molecules`: `true` when an uncommented `DeleteMolecules` modifier/action is detected. +- `uses_exclude_include_reactants`: `true` when an uncommented `exclude_reactants` or `include_reactants` modifier is detected. +- `uses_generate_network`: `true` when an uncommented `generate_network(...)` action is detected. +- `default_sim_command`: First uncommented simulation command found in priority order: `simulate_ode`, `simulate_ssa`, `simulate_nf`, `simulate`. + +## Batch summary + +| Field | Detected true | Detected false | Detected null | Current YAML missing | Proposed insertions/changes | +|---|---:|---:|---:|---:|---:| +| `uses_cbngl_compartments` | 0 | 20 | 0 | 20 | 20 | +| `uses_vcell_compartments` | 9 | 11 | 0 | 20 | 20 | +| `uses_energy` | 0 | 20 | 0 | 0 | 0 | +| `uses_functions` | 13 | 7 | 0 | 0 | 0 | +| `uses_moveconnected` | 0 | 20 | 0 | 20 | 20 | +| `uses_trash_molecules` | 2 | 18 | 0 | 20 | 20 | +| `uses_anchors` | 5 | 15 | 0 | 20 | 20 | +| `uses_multiple_identical_sites` | 5 | 15 | 0 | 20 | 20 | +| `uses_deletes_molecules` | 4 | 16 | 0 | 20 | 20 | +| `uses_exclude_include_reactants` | 2 | 18 | 0 | 20 | 20 | +| `uses_generate_network` | 14 | 6 | 0 | 20 | 20 | +| `default_sim_command` | 0 | 0 | 1 | 20 | 20 | + +## Audited pairs + +| # | BNGL path | YAML path | Proposed updates | +|---:|---|---|---:| +| 1 | `Published/Blinovegfr/Blinov_egfr.bngl` | `Published/Blinovegfr/metadata.yaml` | 10 | +| 2 | `Published/Blinovran/Blinov_ran.bngl` | `Published/Blinovran/metadata.yaml` | 10 | +| 3 | `Published/RulebasedRantransport/Rule_based_Ran_transport.bngl` | `Published/RulebasedRantransport/metadata.yaml` | 10 | +| 4 | `Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl` | `Published/RulebasedRantransportdraft/metadata.yaml` | 10 | +| 5 | `Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl` | `Published/Rulebasedegfrcompart/metadata.yaml` | 10 | +| 6 | `Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl` | `Published/Rulebasedegfrtutorial/metadata.yaml` | 10 | +| 7 | `Published/Jung2017/Jung_2017.bngl` | `Published/Jung2017/metadata.yaml` | 10 | +| 8 | `Published/Lang2024/Lang_2024.bngl` | `Published/Lang2024/metadata.yaml` | 10 | +| 9 | `Published/Nosbisch2022/Nosbisch_2022.bngl` | `Published/Nosbisch2022/metadata.yaml` | 10 | +| 10 | `Published/Barua2007/Barua_2007.bngl` | `Published/Barua2007/metadata.yaml` | 10 | +| 11 | `Published/An2009/An_2009.bngl` | `Published/An2009/metadata.yaml` | 10 | +| 12 | `Published/Ligon2014/Ligon_2014.bngl` | `Published/Ligon2014/metadata.yaml` | 10 | +| 13 | `Published/Zhang2023/Zhang_2023.bngl` | `Published/Zhang2023/metadata.yaml` | 10 | +| 14 | `Published/ChylekFceRI2014/ChylekFceRI_2014.bngl` | `Published/ChylekFceRI2014/metadata.yaml` | 10 | +| 15 | `Published/Dolan2015/Dolan_2015.bngl` | `Published/Dolan2015/metadata.yaml` | 10 | +| 16 | `Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl` | `Published/Hlavacek2001/metadata.yaml` | 10 | +| 17 | `Published/Dembo1978/blbr_dembo1978.bngl` | `Published/Dembo1978/metadata.yaml` | 10 | +| 18 | `Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl` | `Published/Dreisigmeyer2008/metadata.yaml` | 10 | +| 19 | `Published/Gardner2000/genetic_switch_gardner2000.bngl` | `Published/Gardner2000/metadata.yaml` | 10 | +| 20 | `Published/Barua2009/Barua_2009.bngl` | `Published/Barua2009/metadata.yaml` | 10 | + +## Per-model findings + +### 1. `Published/Blinovegfr` / `Blinov_egfr.bngl` + +- BNGL: `Published/Blinovegfr/Blinov_egfr.bngl` +- YAML: `Published/Blinovegfr/metadata.yaml` +- Un-commented action commands detected: `simulate_nf` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `3` + - `anchors` block present: `true`; active entries: `2` + - `functions` block present: `true`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@EC:EGF(rb)` + - `@M:EGFR(ecd,tmd,y1068~u,y1173~u)` + - `@Cyt:Shc(sh3,Y773~u)` + - `@M:EGFR()` + - `@EC:EGF()` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `true` | `missing` | insert | `true` | `begin anchors` block is present; active entries: 2. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No uncommented `generate_network(...)` action detected. | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | Default command chosen from uncommented actions: simulate_nf. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `true`. Rationale: `begin anchors` block is present; active entries: 2. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `false`. Rationale: No uncommented `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate_nf`. Rationale: Default command chosen from uncommented actions: simulate_nf. + +### 2. `Published/Blinovran` / `Blinov_ran.bngl` + +- BNGL: `Published/Blinovran/Blinov_ran.bngl` +- YAML: `Published/Blinovran/metadata.yaml` +- Un-commented action commands detected: `simulate_nf` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `5` + - `anchors` block present: `true`; active entries: `1` + - `functions` block present: `true`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@nuc:Ran(cargo!1)` + - `@nuc:RCC1(site)` + - `@cyt:Ran()` + - `@cyt:C()` + - `@nuc:RCC1()` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `true` | `missing` | insert | `true` | `begin anchors` block is present; active entries: 1. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No uncommented `generate_network(...)` action detected. | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | Default command chosen from uncommented actions: simulate_nf. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `true`. Rationale: `begin anchors` block is present; active entries: 1. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `false`. Rationale: No uncommented `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate_nf`. Rationale: Default command chosen from uncommented actions: simulate_nf. + +### 3. `Published/RulebasedRantransport` / `Rule_based_Ran_transport.bngl` + +- BNGL: `Published/RulebasedRantransport/Rule_based_Ran_transport.bngl` +- YAML: `Published/RulebasedRantransport/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `5` + - `anchors` block present: `true`; active entries: `1` + - `functions` block present: `true`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@nuc:Ran(cargo!1)` + - `@nuc:RCC1(site)` + - `@cyt:Ran()` + - `@cyt:C()` + - `@nuc:RCC1()` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `true` | `missing` | insert | `true` | `begin anchors` block is present; active entries: 1. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | Default command chosen from uncommented actions: generate_network. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `true`. Rationale: `begin anchors` block is present; active entries: 1. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `generate_network`. Rationale: Default command chosen from uncommented actions: generate_network. + +### 4. `Published/RulebasedRantransportdraft` / `Rule_based_Ran_transport_draft.bngl` + +- BNGL: `Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl` +- YAML: `Published/RulebasedRantransportdraft/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `5` + - `anchors` block present: `true`; active entries: `1` + - `functions` block present: `true`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@nuc:Ran(cargo!1)` + - `@nuc:RCC1(site)` + - `@cyt:Ran()` + - `@cyt:C()` + - `@nuc:RCC1()` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `true` | `missing` | insert | `true` | `begin anchors` block is present; active entries: 1. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | Default command chosen from uncommented actions: generate_network. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `true`. Rationale: `begin anchors` block is present; active entries: 1. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `generate_network`. Rationale: Default command chosen from uncommented actions: generate_network. + +### 5. `Published/Rulebasedegfrcompart` / `Rule_based_egfr_compart.bngl` + +- BNGL: `Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl` +- YAML: `Published/Rulebasedegfrcompart/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `3` + - `anchors` block present: `true`; active entries: `2` + - `functions` block present: `true`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@EC:EGF(rb)` + - `@M:EGFR(ecd,tmd,y1068~u,y1173~u)` + - `@Cyt:Shc(sh3,Y773~u)` + - `@M:EGFR()` + - `@EC:EGF()` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `true` | `missing` | insert | `true` | `begin anchors` block is present; active entries: 2. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | Default command chosen from uncommented actions: generate_network. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `true`. Rationale: `begin anchors` block is present; active entries: 2. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `generate_network`. Rationale: Default command chosen from uncommented actions: generate_network. + +### 6. `Published/Rulebasedegfrtutorial` / `Rule_based_egfr_tutorial.bngl` + +- BNGL: `Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl` +- YAML: `Published/Rulebasedegfrtutorial/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `1` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `true`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@c0:EGFR(ecd,tmd,Y1~u,Y2~u)` + - `@c0:EGF(Site)` + - `@c0:Grb2(sh2)` + - `@c0:Shc(sh3,Y~p)` + - `@c0:Shc(sh3,Y~u)` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | Default command chosen from uncommented actions: generate_network. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `generate_network`. Rationale: Default command chosen from uncommented actions: generate_network. + +### 7. `Published/Jung2017` / `Jung_2017.bngl` + +- BNGL: `Published/Jung2017/Jung_2017.bngl` +- YAML: `Published/Jung2017/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `3` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `true`; active entries: `2` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@EC:Oxo_EC()` + - `@PM:M1R(L,S228~u,S273~u,Arr,GRK,PP1,CK2)` + - `@PM:Oxo(R!1)` + - `@cytoplasm:Arrestin(RLP,MEK,PP2A)` + - `@cytoplasm:ERK(MEK,s~u,PP2A,PP1)` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 2. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | Default command chosen from uncommented actions: generate_network. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `generate_network`. Rationale: Default command chosen from uncommented actions: generate_network. + +### 8. `Published/Lang2024` / `Lang_2024.bngl` + +- BNGL: `Published/Lang2024/Lang_2024.bngl` +- YAML: `Published/Lang2024/metadata.yaml` +- Un-commented action commands detected: `simulate`, `generate_network` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `1` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `false`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@cell:CCND()` + - `@cell:CCNE(CDKN1A)` + - `@cell:E2F(DBD,RB1,Ser332~u)` + - `@cell:E2F(DBD,RB1,Ser332~p)` + - `@cell:CCNA(CDKN1A)` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `false` | `false` | keep | `false` | `begin functions` block is absent; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `true` | `missing` | insert | `true` | `include_reactants`/`exclude_reactants` modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | Default command chosen from uncommented actions: simulate. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `true`. Rationale: `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `true`. Rationale: `include_reactants`/`exclude_reactants` modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate`. Rationale: Default command chosen from uncommented actions: simulate. + +### 9. `Published/Nosbisch2022` / `Nosbisch_2022.bngl` + +- BNGL: `Published/Nosbisch2022/Nosbisch_2022.bngl` +- YAML: `Published/Nosbisch2022/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Block diagnostics: + - `compartments` block present: `true`; active entries: `1` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `true`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: + - `@cell:RTK(pY)` + - `@cell:PLCgamma1(nSH2,Tyr783~u,cSH2!1,core~inactive!1)` + - `@cell:RTK()` + - `@cell:PLCgamma1()` + - `@cell:PLCgamma1(core~active!?)` +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell-style `@Compartment:Molecule(...)` examples detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | Default command chosen from uncommented actions: generate_network. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `true`. Rationale: VCell-style `@Compartment:Molecule(...)` examples detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `generate_network`. Rationale: Default command chosen from uncommented actions: generate_network. + +### 10. `Published/Barua2007` / `Barua_2007.bngl` + +- BNGL: `Published/Barua2007/Barua_2007.bngl` +- YAML: `Published/Barua2007/metadata.yaml` +- Un-commented action commands detected: `simulate_ode`, `generate_network` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `false`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `false` | `false` | keep | `false` | `begin functions` block is absent; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `true` | `missing` | insert | `true` | `include_reactants`/`exclude_reactants` modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | Default command chosen from uncommented actions: simulate_ode. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `true`. Rationale: `include_reactants`/`exclude_reactants` modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate_ode`. Rationale: Default command chosen from uncommented actions: simulate_ode. + +### 11. `Published/An2009` / `An_2009.bngl` + +- BNGL: `Published/An2009/An_2009.bngl` +- YAML: `Published/An2009/metadata.yaml` +- Un-commented action commands detected: `simulate_ode`, `generate_network` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `false`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: + - DNA: repeated c in `DNA(A20,TNF,iNOS,IL10,IkB,c,c)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `false` | `false` | keep | `false` | `begin functions` block is absent; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `true` | `missing` | insert | `true` | `Trash(...)` sink molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | At least one molecule type declares a repeated site name. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | Default command chosen from uncommented actions: simulate_ode. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `true`. Rationale: `Trash(...)` sink molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `true`. Rationale: At least one molecule type declares a repeated site name. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate_ode`. Rationale: Default command chosen from uncommented actions: simulate_ode. + +### 12. `Published/Ligon2014` / `Ligon_2014.bngl` + +- BNGL: `Published/Ligon2014/Ligon_2014.bngl` +- YAML: `Published/Ligon2014/metadata.yaml` +- Un-commented action commands detected: `simulate_nf` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `true`; active entries: `1` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 1. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No uncommented `generate_network(...)` action detected. | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | Default command chosen from uncommented actions: simulate_nf. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `true`. Rationale: `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `false`. Rationale: No uncommented `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate_nf`. Rationale: Default command chosen from uncommented actions: simulate_nf. + +### 13. `Published/Zhang2023` / `Zhang_2023.bngl` + +- BNGL: `Published/Zhang2023/Zhang_2023.bngl` +- YAML: `Published/Zhang2023/metadata.yaml` +- Un-commented action commands detected: `generate_network` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `false`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: + - vegf: repeated r in `vegf(r,r,nrp1bd,c~s~i~i2~r)` + - CaM: repeated CCaM, NCaM in `CaM(NCaM,NCaM,CCaM,CCaM,CaMtargetbd)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `false` | `false` | keep | `false` | `begin functions` block is absent; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `true` | `missing` | insert | `true` | `Trash(...)` sink molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | At least one molecule type declares a repeated site name. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `generate_network` | `missing` | insert | `generate_network` | Default command chosen from uncommented actions: generate_network. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `true`. Rationale: `Trash(...)` sink molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `true`. Rationale: At least one molecule type declares a repeated site name. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `generate_network`. Rationale: Default command chosen from uncommented actions: generate_network. + +### 14. `Published/ChylekFceRI2014` / `ChylekFceRI_2014.bngl` + +- BNGL: `Published/ChylekFceRI2014/ChylekFceRI_2014.bngl` +- YAML: `Published/ChylekFceRI2014/metadata.yaml` +- Un-commented action commands detected: `writeXML` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `false`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: + - Lig: repeated hap in `Lig(hap~b~e,hap~b~e)` + - Rec: repeated fab in `Rec(fab,fab,b_Y218~0~P,b_Y224~0~P,g_Y65_Y76~0~P)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `false` | `false` | keep | `false` | `begin functions` block is absent; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | At least one molecule type declares a repeated site name. | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No uncommented `generate_network(...)` action detected. | +| `default_sim_command` | `null` | `missing` | insert | `null` | Default command chosen from uncommented actions: none. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `true`. Rationale: At least one molecule type declares a repeated site name. +- `uses_deletes_molecules`: insert; proposed value `true`. Rationale: `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `false`. Rationale: No uncommented `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `null`. Rationale: Default command chosen from uncommented actions: none. + +### 15. `Published/Dolan2015` / `Dolan_2015.bngl` + +- BNGL: `Published/Dolan2015/Dolan_2015.bngl` +- YAML: `Published/Dolan2015/metadata.yaml` +- Un-commented action commands detected: `simulate_nf` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `true`; active entries: `9` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 9. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No uncommented `generate_network(...)` action detected. | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | Default command chosen from uncommented actions: simulate_nf. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `true`. Rationale: `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `false`. Rationale: No uncommented `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate_nf`. Rationale: Default command chosen from uncommented actions: simulate_nf. + +### 16. `Published/Hlavacek2001` / `kinetic_proofreading_hlavacek2001.bngl` + +- BNGL: `Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl` +- YAML: `Published/Hlavacek2001/metadata.yaml` +- Un-commented action commands detected: `simulate`, `generate_network` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `true`; active entries: `4` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: + - L: repeated r in `L(r,r,mod~0~1~2~3~4~5)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 4. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | At least one molecule type declares a repeated site name. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | Default command chosen from uncommented actions: simulate. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `true`. Rationale: At least one molecule type declares a repeated site name. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate`. Rationale: Default command chosen from uncommented actions: simulate. + +### 17. `Published/Dembo1978` / `blbr_dembo1978.bngl` + +- BNGL: `Published/Dembo1978/blbr_dembo1978.bngl` +- YAML: `Published/Dembo1978/metadata.yaml` +- Un-commented action commands detected: `simulate` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `false`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: + - L: repeated r in `L(r,r)` + - R: repeated l in `R(l,l)` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `false` | `false` | keep | `false` | `begin functions` block is absent; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | At least one molecule type declares a repeated site name. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No uncommented `generate_network(...)` action detected. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | Default command chosen from uncommented actions: simulate. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `true`. Rationale: At least one molecule type declares a repeated site name. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `false`. Rationale: No uncommented `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate`. Rationale: Default command chosen from uncommented actions: simulate. + +### 18. `Published/Dreisigmeyer2008` / `lac_operon_dreisigmeyer2008.bngl` + +- BNGL: `Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl` +- YAML: `Published/Dreisigmeyer2008/metadata.yaml` +- Un-commented action commands detected: `simulate`, `generate_network` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `true`; active entries: `12` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 12. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | Default command chosen from uncommented actions: simulate. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate`. Rationale: Default command chosen from uncommented actions: simulate. + +### 19. `Published/Gardner2000` / `genetic_switch_gardner2000.bngl` + +- BNGL: `Published/Gardner2000/genetic_switch_gardner2000.bngl` +- YAML: `Published/Gardner2000/metadata.yaml` +- Un-commented action commands detected: `simulate`, `generate_network` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `true`; active entries: `2` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `true` | `true` | keep | `true` | `begin functions` block is present; active entries: 2. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | Default command chosen from uncommented actions: simulate. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate`. Rationale: Default command chosen from uncommented actions: simulate. + +### 20. `Published/Barua2009` / `Barua_2009.bngl` + +- BNGL: `Published/Barua2009/Barua_2009.bngl` +- YAML: `Published/Barua2009/metadata.yaml` +- Un-commented action commands detected: `simulate_ode`, `generate_network` +- Block diagnostics: + - `compartments` block present: `false`; active entries: `0` + - `anchors` block present: `false`; active entries: `0` + - `functions` block present: `false`; active entries: `0` + - `energy_patterns` block present: `false`; active entries: `0` +- VCell-style compartment examples: none detected. +- CBNGL-style compartment examples: none detected. +- Multiple-identical-site evidence: none detected in molecule-type declarations. + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +|---|---|---|---|---|---| +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL-style `Molecule(...)@Compartment` patterns detected. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell-style `@Compartment:Molecule(...)` patterns detected. | +| `uses_energy` | `false` | `false` | keep | `false` | energy-pattern block is absent; active entries: 0. | +| `uses_functions` | `false` | `false` | keep | `false` | `begin functions` block is absent; active entries: 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No `moveConnected` call detected. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No `Trash(...)` molecule/pattern detected. | +| `uses_anchors` | `false` | `missing` | insert | `false` | `begin anchors` block is absent; active entries: 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated site names found in molecule-type declarations. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No `DeleteMolecules` modifier/action detected. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier detected. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | `generate_network(...)` action detected. | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | Default command chosen from uncommented actions: simulate_ode. | + +Proposed YAML updates: +- `uses_cbngl_compartments`: insert; proposed value `false`. Rationale: No CBNGL-style `Molecule(...)@Compartment` patterns detected. +- `uses_vcell_compartments`: insert; proposed value `false`. Rationale: No VCell-style `@Compartment:Molecule(...)` patterns detected. +- `uses_moveconnected`: insert; proposed value `false`. Rationale: No `moveConnected` call detected. +- `uses_trash_molecules`: insert; proposed value `false`. Rationale: No `Trash(...)` molecule/pattern detected. +- `uses_anchors`: insert; proposed value `false`. Rationale: `begin anchors` block is absent; active entries: 0. +- `uses_multiple_identical_sites`: insert; proposed value `false`. Rationale: No repeated site names found in molecule-type declarations. +- `uses_deletes_molecules`: insert; proposed value `false`. Rationale: No `DeleteMolecules` modifier/action detected. +- `uses_exclude_include_reactants`: insert; proposed value `false`. Rationale: No include/exclude reactants modifier detected. +- `uses_generate_network`: insert; proposed value `true`. Rationale: `generate_network(...)` action detected. +- `default_sim_command`: insert; proposed value `simulate_ode`. Rationale: Default command chosen from uncommented actions: simulate_ode. diff --git a/data/yaml_feature_audit_3.md b/data/yaml_feature_audit_3.md new file mode 100644 index 00000000..5d086a5a --- /dev/null +++ b/data/yaml_feature_audit_3.md @@ -0,0 +1,558 @@ +# Published YAML Feature Audit 3 + +## Introduction + +This audit checks the same 20 same-directory `Published/` BNGL/YAML pairs used in the earlier reports, using the finalized `metadata_auditing` skill. Each selected BNGL file was compared against its same-directory target YAML. Audited YAML copies were created inside the corresponding model folders using `_audited.yaml`; original YAML files were not overwritten. + +## Detection definitions + +- VCell compartments are detected only from active `@Compartment:Molecule(...)` syntax. +- CBNGL compartments are detected only from active `Molecule(...)@Compartment` syntax. +- A `begin compartments` block is reported in diagnostics but does not directly set either compartment field. +- Empty blocks have active entries `0` and do not make block-based fields true. +- `uses_functions`, `uses_anchors`, and `uses_energy` require at least one uncommented, nonempty active entry inside the corresponding block. +- `default_sim_command` is the first active command among `simulate_ode`, `simulate_ssa`, `simulate_nf`, and `simulate`; if none are active, it is `null`. + +## Batch summary + +| Field | Detected true | Detected false | Detected null | Current YAML missing | Proposed insertions | Proposed changes | Manual review | +| --- | ---: | ---: | ---: | ---: | ---: | ---: | ---: | +| `uses_cbngl_compartments` | 0 | 20 | 0 | 20 | 20 | 0 | 0 | +| `uses_vcell_compartments` | 9 | 11 | 0 | 20 | 20 | 0 | 0 | +| `uses_energy` | 0 | 20 | 0 | 0 | 0 | 0 | 0 | +| `uses_functions` | 6 | 14 | 0 | 0 | 0 | 7 | 0 | +| `uses_moveconnected` | 0 | 20 | 0 | 20 | 20 | 0 | 0 | +| `uses_trash_molecules` | 2 | 18 | 0 | 20 | 20 | 0 | 0 | +| `uses_anchors` | 5 | 15 | 0 | 20 | 20 | 0 | 0 | +| `uses_multiple_identical_sites` | 5 | 15 | 0 | 20 | 20 | 0 | 0 | +| `uses_deletes_molecules` | 4 | 16 | 0 | 20 | 20 | 0 | 0 | +| `uses_exclude_include_reactants` | 2 | 18 | 0 | 20 | 20 | 0 | 0 | +| `uses_generate_network` | 14 | 6 | 0 | 20 | 20 | 0 | 0 | +| `default_sim_command` | 12 | 0 | 8 | 20 | 20 | 0 | 0 | + +## Audited pairs + +| # | BNGL path | YAML audited | Audited YAML output | Proposed updates | Manual review? | +| ---: | --- | --- | --- | ---: | --- | +| 1 | `Published/Blinovegfr/Blinov_egfr.bngl` | `Published/Blinovegfr/metadata.yaml` | `Published/Blinovegfr/metadata_audited.yaml` | 11 | no | +| 2 | `Published/Blinovran/Blinov_ran.bngl` | `Published/Blinovran/metadata.yaml` | `Published/Blinovran/metadata_audited.yaml` | 11 | no | +| 3 | `Published/RulebasedRantransport/Rule_based_Ran_transport.bngl` | `Published/RulebasedRantransport/metadata.yaml` | `Published/RulebasedRantransport/metadata_audited.yaml` | 11 | no | +| 4 | `Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl` | `Published/RulebasedRantransportdraft/metadata.yaml` | `Published/RulebasedRantransportdraft/metadata_audited.yaml` | 11 | no | +| 5 | `Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl` | `Published/Rulebasedegfrcompart/metadata.yaml` | `Published/Rulebasedegfrcompart/metadata_audited.yaml` | 11 | no | +| 6 | `Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl` | `Published/Rulebasedegfrtutorial/metadata.yaml` | `Published/Rulebasedegfrtutorial/metadata_audited.yaml` | 11 | no | +| 7 | `Published/Jung2017/Jung_2017.bngl` | `Published/Jung2017/metadata.yaml` | `Published/Jung2017/metadata_audited.yaml` | 10 | no | +| 8 | `Published/Lang2024/Lang_2024.bngl` | `Published/Lang2024/metadata.yaml` | `Published/Lang2024/metadata_audited.yaml` | 10 | no | +| 9 | `Published/Nosbisch2022/Nosbisch_2022.bngl` | `Published/Nosbisch2022/metadata.yaml` | `Published/Nosbisch2022/metadata_audited.yaml` | 11 | no | +| 10 | `Published/Barua2007/Barua_2007.bngl` | `Published/Barua2007/metadata.yaml` | `Published/Barua2007/metadata_audited.yaml` | 10 | no | +| 11 | `Published/An2009/An_2009.bngl` | `Published/An2009/metadata.yaml` | `Published/An2009/metadata_audited.yaml` | 10 | no | +| 12 | `Published/Ligon2014/Ligon_2014.bngl` | `Published/Ligon2014/metadata.yaml` | `Published/Ligon2014/metadata_audited.yaml` | 10 | no | +| 13 | `Published/Zhang2023/Zhang_2023.bngl` | `Published/Zhang2023/metadata.yaml` | `Published/Zhang2023/metadata_audited.yaml` | 10 | no | +| 14 | `Published/ChylekFceRI2014/ChylekFceRI_2014.bngl` | `Published/ChylekFceRI2014/metadata.yaml` | `Published/ChylekFceRI2014/metadata_audited.yaml` | 10 | no | +| 15 | `Published/Dolan2015/Dolan_2015.bngl` | `Published/Dolan2015/metadata.yaml` | `Published/Dolan2015/metadata_audited.yaml` | 10 | no | +| 16 | `Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl` | `Published/Hlavacek2001/metadata.yaml` | `Published/Hlavacek2001/metadata_audited.yaml` | 10 | no | +| 17 | `Published/Dembo1978/blbr_dembo1978.bngl` | `Published/Dembo1978/metadata.yaml` | `Published/Dembo1978/metadata_audited.yaml` | 10 | no | +| 18 | `Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl` | `Published/Dreisigmeyer2008/metadata.yaml` | `Published/Dreisigmeyer2008/metadata_audited.yaml` | 10 | no | +| 19 | `Published/Gardner2000/genetic_switch_gardner2000.bngl` | `Published/Gardner2000/metadata.yaml` | `Published/Gardner2000/metadata_audited.yaml` | 10 | no | +| 20 | `Published/Barua2009/Barua_2009.bngl` | `Published/Barua2009/metadata.yaml` | `Published/Barua2009/metadata_audited.yaml` | 10 | no | + +## Per-model findings + +### 1. `Blinovegfr` + +- Block diagnostics: + - `compartments`: present `true`; active entries `3` + - `anchors`: present `true`; active entries `2` + - `functions`: present `true`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@EC:EGF(rb)` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `true` | change | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `true` | `missing` | insert | `true` | anchors active entries = 2. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No active generate_network action found. | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | First active simulation command is simulate_nf. | + +### 2. `Blinovran` + +- Block diagnostics: + - `compartments`: present `true`; active entries `5` + - `anchors`: present `true`; active entries `1` + - `functions`: present `true`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@nuc:Ran(cargo!1)` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `true` | change | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `true` | `missing` | insert | `true` | anchors active entries = 1. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No active generate_network action found. | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | First active simulation command is simulate_nf. | + +### 3. `RulebasedRantransport` + +- Block diagnostics: + - `compartments`: present `true`; active entries `5` + - `anchors`: present `true`; active entries `1` + - `functions`: present `true`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@nuc:Ran(cargo!1)` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `true` | change | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `true` | `missing` | insert | `true` | anchors active entries = 1. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `null` | `missing` | insert | `null` | No active simulation command found. | + +### 4. `RulebasedRantransportdraft` + +- Block diagnostics: + - `compartments`: present `true`; active entries `5` + - `anchors`: present `true`; active entries `1` + - `functions`: present `true`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@nuc:Ran(cargo!1)` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `true` | change | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `true` | `missing` | insert | `true` | anchors active entries = 1. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `null` | `missing` | insert | `null` | No active simulation command found. | + +### 5. `Rulebasedegfrcompart` + +- Block diagnostics: + - `compartments`: present `true`; active entries `3` + - `anchors`: present `true`; active entries `2` + - `functions`: present `true`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@EC:EGF(rb)` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `true` | change | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `true` | `missing` | insert | `true` | anchors active entries = 2. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `null` | `missing` | insert | `null` | No active simulation command found. | + +### 6. `Rulebasedegfrtutorial` + +- Block diagnostics: + - `compartments`: present `true`; active entries `1` + - `anchors`: present `false`; active entries `0` + - `functions`: present `true`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@c0:EGFR(ecd,tmd,Y1~u,Y2~u)` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `true` | change | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `null` | `missing` | insert | `null` | No active simulation command found. | + +### 7. `Jung2017` + +- Block diagnostics: + - `compartments`: present `true`; active entries `3` + - `anchors`: present `false`; active entries `0` + - `functions`: present `true`; active entries `2` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@EC:Oxo_EC()` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `true` | `true` | keep | `true` | functions active entries = 2. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `null` | `missing` | insert | `null` | No active simulation command found. | + +### 8. `Lang2024` + +- Block diagnostics: + - `compartments`: present `true`; active entries `1` + - `anchors`: present `false`; active entries `0` + - `functions`: present `false`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@cell:CCND()` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `false` | keep | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | Active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `true` | `missing` | insert | `true` | Active include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | First active simulation command is simulate. | + +### 9. `Nosbisch2022` + +- Block diagnostics: + - `compartments`: present `true`; active entries `1` + - `anchors`: present `false`; active entries `0` + - `functions`: present `true`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `@cell:RTK(pY)` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `true` | `missing` | insert | `true` | VCell syntax example found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `true` | change | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `null` | `missing` | insert | `null` | No active simulation command found. | + +### 10. `Barua2007` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `false`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `false` | keep | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `true` | `missing` | insert | `true` | Active include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | First active simulation command is simulate_ode. | + +### 11. `An2009` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `false`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `false` | keep | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `true` | `missing` | insert | `true` | Active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | Repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | First active simulation command is simulate_ode. | + +### 12. `Ligon2014` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `true`; active entries `1` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `true` | `true` | keep | `true` | functions active entries = 1. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | Active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No active generate_network action found. | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | First active simulation command is simulate_nf. | + +### 13. `Zhang2023` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `false`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `false` | keep | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `true` | `missing` | insert | `true` | Active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | Repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `null` | `missing` | insert | `null` | No active simulation command found. | + +### 14. `ChylekFceRI2014` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `false`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `false` | keep | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | Repeated molecule-type site detected. | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | Active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No active generate_network action found. | +| `default_sim_command` | `null` | `missing` | insert | `null` | No active simulation command found. | + +### 15. `Dolan2015` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `true`; active entries `9` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `true` | `true` | keep | `true` | functions active entries = 9. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `true` | `missing` | insert | `true` | Active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No active generate_network action found. | +| `default_sim_command` | `simulate_nf` | `missing` | insert | `simulate_nf` | First active simulation command is simulate_nf. | + +### 16. `Hlavacek2001` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `true`; active entries `4` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `true` | `true` | keep | `true` | functions active entries = 4. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | Repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | First active simulation command is simulate. | + +### 17. `Dembo1978` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `false`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `false` | keep | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `true` | `missing` | insert | `true` | Repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `false` | `missing` | insert | `false` | No active generate_network action found. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | First active simulation command is simulate. | + +### 18. `Dreisigmeyer2008` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `true`; active entries `12` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `true` | `true` | keep | `true` | functions active entries = 12. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | First active simulation command is simulate. | + +### 19. `Gardner2000` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `true`; active entries `2` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `true` | `true` | keep | `true` | functions active entries = 2. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `simulate` | `missing` | insert | `simulate` | First active simulation command is simulate. | + +### 20. `Barua2009` + +- Block diagnostics: + - `compartments`: present `false`; active entries `0` + - `anchors`: present `false`; active entries `0` + - `functions`: present `false`; active entries `0` + - `energy patterns`: present `false`; active entries `0` +- VCell-style compartment example: `none detected` +- CBNGL-style compartment example: `none detected` + +| Field | Detected from BNGL | Current YAML value | Proposed action | Proposed value | Short rationale | +| --- | --- | --- | --- | --- | --- | +| `uses_cbngl_compartments` | `false` | `missing` | insert | `false` | No CBNGL suffix syntax found. | +| `uses_vcell_compartments` | `false` | `missing` | insert | `false` | No VCell prefix syntax found. | +| `uses_energy` | `false` | `false` | keep | `false` | energy active entries = 0. | +| `uses_functions` | `false` | `false` | keep | `false` | functions active entries = 0. | +| `uses_moveconnected` | `false` | `missing` | insert | `false` | No active moveConnected call found. | +| `uses_trash_molecules` | `false` | `missing` | insert | `false` | No active Trash pattern found. | +| `uses_anchors` | `false` | `missing` | insert | `false` | anchors active entries = 0. | +| `uses_multiple_identical_sites` | `false` | `missing` | insert | `false` | No repeated molecule-type site detected. | +| `uses_deletes_molecules` | `false` | `missing` | insert | `false` | No active DeleteMolecules found. | +| `uses_exclude_include_reactants` | `false` | `missing` | insert | `false` | No include/exclude reactants modifier found. | +| `uses_generate_network` | `true` | `missing` | insert | `true` | Active generate_network action found. | +| `default_sim_command` | `simulate_ode` | `missing` | insert | `simulate_ode` | First active simulation command is simulate_ode. | diff --git a/data/yaml_feature_audit_4.md b/data/yaml_feature_audit_4.md new file mode 100644 index 00000000..555e92cb --- /dev/null +++ b/data/yaml_feature_audit_4.md @@ -0,0 +1,150 @@ +# Published YAML Feature Audit — New 30-Model Batch + +Audited 30 models and created 30 `metadata_aigenerated.yaml` files. Inserted 239 missing values; 27 items require review. + +## Barua2013 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`. +- Review change: `default_sim_command: ode` → `simulate_ode` — active `simulate_ode(...)` action. + +## BaruaBCR2012 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`. + +## BaruaFceRI2012 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_multiple_identical_sites: true` — repeated `l` site in `L(l,l)`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Blinov2006 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`. +- Review change: `default_sim_command: ode` → `simulate_ode` — active `simulate_ode(...)` action. + +## Chattaraj2021 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`, `uses_generate_network`. + +## CheemalavaguJAKSTAT + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## ChylekTCR2014 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_deletes_molecules`, `uses_exclude_include_reactants`, `uses_generate_network`. +- Review insertion: `uses_multiple_identical_sites: true` — repeated `aCD28` site in `Lig1(aCD28,aCD28)`. + +## Dushek2011 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Dushek2014 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`. +- Review change: `uses_generate_network: true` → `false` — no active `generate_network(...)` action. + +## Erdem2021 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Goldstein1980 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_exclude_include_reactants`, `uses_generate_network`. +- Review insertion: `uses_deletes_molecules: true` — active `DeleteMolecules` construct. + +## Harmon2017 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Hat2016 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`. +- Review change: `default_sim_command: ode` → `simulate` — active `simulate(...)` action. + +## Hlavacek1999 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Hlavacek2018Egg + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## JaruszewiczBlonska2023 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Kesseler2013 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`, `uses_generate_network`. + +## Kocieniewski2012 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`. +- Review change: `uses_generate_network: true` → `false` — no active `generate_network(...)` action. + +## Korwek2023 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Kozer2013 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Kozer2014 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`. +- Review change: `default_sim_command: ode` → `simulate_ode` — active `simulate_ode(...)` action. + +## LinERK2019 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## LinPrion2019 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## LinTCR2019 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Macken1982 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_deletes_molecules`, `uses_exclude_include_reactants`, `uses_generate_network`. +- Review insertion: `uses_multiple_identical_sites: true` — repeated `r` site in `L(r,r,r)`. + +## Alabama + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Massole2023 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_deletes_molecules`, `uses_exclude_include_reactants`, `uses_generate_network`. +- Review insertion: `uses_multiple_identical_sites: true` — repeated `oh` site in `_EG_(oh~p,oh~p)`. + +## McMillan2021 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. + +## Mertins2023 + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`, `uses_generate_network`. + +## InputFiles + +- Inserted false: `uses_cbngl_compartments`, `uses_vcell_compartments`, `uses_moveconnected`, `uses_trash_molecules`, `uses_anchors`, `uses_multiple_identical_sites`, `uses_deletes_molecules`, `uses_exclude_include_reactants`. +- Review insertion: `uses_generate_network: true` — active `generate_network(...)` action. diff --git a/metadata-schema.yaml b/metadata-schema.yaml index 26ae87db..cad220b2 100644 --- a/metadata-schema.yaml +++ b/metadata-schema.yaml @@ -16,7 +16,7 @@ citation: doi: string # DOI only, no link pmid: string # PubMed ID only, no link url: string # either journal link or preprint link or website link - reference: string # regular citation string, e.g. "Author et al., Journal, Year, Volume, Pages" + reference: string # website or a regular citation string, e.g. "Author, Year" (for 1 author); "Author & Author, Year" (for 2 authors); "Author et al., Year" (for 3+ authors) date: created: YYYY-MM-DD @@ -33,6 +33,8 @@ comp_categories: - enum(tutorial, validation, showcase, computer-science, other, compartments, energy, feature-demos, nfsim, processes, wacky, cs, ml, other) compatibility: + database_visible: boolean + bngp_compatible: boolean bng2_compatible: boolean min_bng_version: string rr_compatible: boolean @@ -43,6 +45,7 @@ compatibility: simulation_methods: - enum(ode, ssa, nf, pla, hybrid, molclustpy, vcell) nfsim_compatible: boolean + mpd_compatible: boolean excluded: boolean features: diff --git a/skills/database-visibility/SKILL.md b/skills/database-visibility/SKILL.md new file mode 100644 index 00000000..80180549 --- /dev/null +++ b/skills/database-visibility/SKILL.md @@ -0,0 +1,152 @@ +# RuleHub Database Visibility Metadata + +## Purpose + +Set `compatibility.database_visible: false` for RuleHub model folders that +use only a generic `metadata.yaml` and do not have a model-specific +`NAME_metadata.yaml`. + +These models are displayed by the RuleHub website with the `NO YAML!` +indicator because they do not have a model-specific metadata file. These models should have `compatibility.database_visible: false` so that they are excluded from the database-visible results while retaining their generic `metadata.yaml` for other RuleHub purposes. + +## When to use this skill + +Use this workflow when working on RuleHub model metadata and a model folder +contains: + +- one or more `.bngl` files; +- a generic `metadata.yaml`; and +- no model-specific `NAME_metadata.yaml`. + +The absence of a model-specific metadata file is the criterion for this +workflow. Do not use the number of BNGL files alone as the criterion. + +For example: + + Published/ExampleModel/ + ├── model_a.bngl + ├── model_b.bngl + └── metadata.yaml + +should be treated as a database-invisible model. + +In contrast: + + Published/ExampleModel/ + ├── model_a.bngl + ├── model_b.bngl + └── ExampleModel_metadata.yaml + +has model-specific metadata and should not be modified by this workflow +merely because it contains multiple BNGL files. + +## Required change + +For every qualifying `metadata.yaml`, ensure that it contains: + + compatibility: + database_visible: false + +If `compatibility.database_visible` already exists and is `true`, change it +to `false`. + +If `compatibility.database_visible` is missing, add it with the value `false`. + +If `compatibility` does not exist, create the `compatibility` mapping and add: + + compatibility: + database_visible: false + +Preserve all other metadata fields and values. + +## Do not + +- Do not delete `metadata.yaml`. +- Do not create a `NAME_metadata.yaml` merely to make the model database-visible. +- Do not modify BNGL files. +- Do not change the model's `id`, `name`, `description`, `tags`, `citation`, or any other metadata fields. The only permitted metadata change is adding or updating `compatibility.database_visible`. +- Do not change `database_visible` for a folder that has an appropriate + model-specific `NAME_metadata.yaml`. +- Do not assume that having multiple BNGL files alone means that + `database_visible` must be false. +- Do not modify `_aigenerated.yaml` files as part of this workflow. +- Do not remove or overwrite existing metadata unnecessarily. + +## Identifying model-specific metadata + +A model-specific metadata file is a `NAME_metadata.yaml` file located in the same model folder as the BNGL file(s), where `NAME` is something other than the literal `metadata`. + +For example: + + Hlavacek2018Elephant_metadata.yaml + 28-mapk_metadata.yaml + +are model-specific metadata files. + +The generic fallback file is: + + metadata.yaml + +## Relationship to RuleHub's website + +RuleHub's website currently handles metadata sources approximately as follows: + +1. Prefer `NAME_metadata.yaml`. +2. Otherwise fall back to `metadata.yaml`. +3. Otherwise keep the model without YAML metadata. + +When only `metadata.yaml` is available, the website indicates that there is +no model-specific YAML link by displaying `NO YAML!`. + +The purpose of `compatibility.database_visible: false` is separate from the +website's `NO YAML!` display. It prevents the corresponding metadata row from +being included in the database-visible results. + +Do not change the website's `NO YAML!` behavior as part of this skill unless +the task explicitly requests a change to the website code. + +## Validation + +After making changes: + +1. Confirm that every qualifying model has: + + compatibility: + database_visible: false + +2. Confirm that models with model-specific `NAME_metadata.yaml` files were + not modified by this workflow. + +3. Confirm that no BNGL files were modified. + +4. Confirm that all other metadata fields in modified files remain unchanged. + +5. If possible, verify that the RuleHub website's database visibility filter + excludes the affected model rows. + +## Example + +Before: + + id: example_model + name: Example Model + description: Example BNGL model + + compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + +After: + + id: example_model + name: Example Model + description: Example BNGL model + + compatibility: + database_visible: false + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + +Only `compatibility.database_visible` should be added or changed. diff --git a/skills/explain-model-brief/SKILL.md b/skills/explain-model-brief/SKILL.md new file mode 100644 index 00000000..335121e1 --- /dev/null +++ b/skills/explain-model-brief/SKILL.md @@ -0,0 +1,213 @@ +# Explain Model (Brief) + +## Purpose + +Use this skill to write a polished, biologist-facing Markdown explanation of an existing RuleHub model. The reader is a biologist, curator, student, or domain scientist who wants to understand what the model *shows biologically*, not how BNGL syntax works. + +The output must be a readable explanatory article. It should explain the biological story, the major players, the key modeled events, what the model measures, and the expected behavior of this specific model in plots. It must avoid exposing the reader to implementation details unless those details are needed for website integration outside the prose. + +## Required Inputs + +Before writing, read the model files in this order: + +1. The model `metadata.yaml` or `.yaml` file. +2. The model `.bngl` file. +3. Any nearby `README.md` or other local documentation. +4. Comments inside the BNGL file, especially title, description, reference, pathway notes, reaction-family comments, localization/anchor notes, and observable/readout comments. + +Use local repository files only. Do not rely on raw GitHub URLs. + +If more than one BNGL file is present for a model, choose the file that metadata identifies when possible. If the choice is ambiguous, resolve it before writing or record the chosen file only in machine-readable JSON, not in the biologist-facing prose. + +## Core Writing Principle + +Write what the model shows, not what the code says. + +Good summary prose sounds like: + +> This model shows how LPS is assembled with CD14 and MD2 before activating TLR4, how adaptor arms route the signal to TAK1 and IKK, and how A20 and IkB feedback restrain NF-kB-driven inflammatory output. + +Bad summary prose sounds like: + +> The local BNGL file has seed species, observables, and reaction rules where `TLR4(TRAM)` binds `TRIF`. + +Never make the biologist wade through raw BNGL syntax, file logistics, implementation notes, or long rule lists. + +## Strict Prohibitions for Markdown Summaries + +Do **not** include any of the following in the Markdown prose: + +- Raw BNGL patterns, such as molecule-site syntax, bond labels, state syntax, arrows, or rate expressions. +- Code fences containing model code. +- Long lists of every reaction rule. +- Phrases such as “local model,” “local metadata,” “BNGL file,” “YAML file,” “seed species,” “observables,” or “reaction rules.” +- File paths, unless the user explicitly asks for file-path documentation inside the Markdown. Paths belong in JSON, not the reader-facing summary. +- Generic filler such as “the model encodes molecular species, initial conditions, observables, and rules.” +- Unsupported biological claims, organisms, cell types, or experimental conclusions not implied by metadata, comments, molecule names, or local documentation. + +The Markdown may use important molecule names, pathway names, protein names, ligand names, and biological state names. These names should be plain text, not raw syntax dumps. + +## Required Markdown Structure + +Use this structure exactly for each generated Markdown summary: + +```markdown +# Model Explanation: + +## One-sentence summary + +## What the model shows + +## Biological story + +## Main biological players + +## Mechanism in plain English + +## Key modeled events + +## What the model measures + +## Expected behavior in plots + +## Caveats +``` + +### Section-by-section requirements + +#### `# Model Explanation: <title>` + +Use the clean model title from metadata when available. If metadata is sparse, use a readable title inferred from the directory or BNGL title comment. + +#### `## One-sentence summary` + +Write one specific sentence naming the biological process and the central modeled behavior. Avoid “uses BNGL,” “encodes,” or “contains.” + +Good: + +> Beta-catenin control by the Axin/APC/GSK3/CK1 destruction complex. + +Bad: + +> This model represents beta-catenin using BNGL rules. + +#### `## What the model shows` + +Write one paragraph explaining the model’s biological purpose. State the central mechanism and why the model is useful. This should be specific enough that a biologist can tell this model apart from another model in the same pathway. + +#### `## Biological story` + +Write a short conceptual paragraph that connects the model to a biological narrative: stimulus, assembly, modification, feedback, degradation, transport, gene expression, phenotype, or other response. Avoid implementation details. + +#### `## Main biological players` + +List the major molecules, complexes, variables, or pathway modules in readable biological language. Do not list every minor species. Do not include sites in BNGL syntax. It is acceptable to name important domains or residues in prose when biologically meaningful, such as SH2 domains, ITAMs, phosphorylation sites, or receptor arms. + +#### `## Mechanism in plain English` + +Explain the causal mechanism in one detailed paragraph. Use concrete verbs: binds, recruits, phosphorylates, dephosphorylates, activates, inhibits, releases, degrades, imports, exports, transcribes, translates, recycles, or dilutes. + +This section should say what happens and why it matters. It must not be a raw rule translation. + +#### `## Key modeled events` + +Include exactly three to five bullets. Each bullet should describe one important modeled event or event family in plain English. + +Rules for these bullets: + +- Select only the most biologically important events. +- Prefer event families over exhaustive lists. +- Mention direction and consequence when clear. +- Mention important molecules by name. +- Do not include raw syntax, arrows, rate constants, or parameter names unless the parameter name is biologically meaningful to the reader. + +Good: + +- Beta-catenin binds APC and Axin, placing it into the destruction-complex environment. +- CK1 and GSK3 phosphorylate beta-catenin in sequence, converting it into a form that is removed more rapidly. +- When beta-catenin is degraded, APC and Axin partners are released so the scaffold can participate in another cycle. + +Bad: + +- `bCat(ARM34) + AXIN(b) <-> bCat(ARM34!1).AXIN(b!1)`. + +#### `## What the model measures` + +Describe the plotted or tracked biological quantities. Use “readouts” or “measurements,” not “observables.” Explain what a biologist would see: active kinase, phosphorylated substrate, receptor complex, transcriptional output, degraded product, clustered polymer, pathway activity, and so on. + +#### `## Expected behavior in plots` + +Write model-specific plot guidance. Do not use reusable boilerplate about rising or falling curves. Say which particular readouts should rise, fall, peak, lag, oppose each other, or remain abstract for this model, and why. Avoid promising a specific trajectory unless the model comments or mechanism support it. + +#### `## Caveats` + +State limitations briefly. Examples: + +- The summary explains the encoded mechanism; it does not validate experimental correctness. +- Some molecule names are abstract, so identities are not invented. +- The model is a compact demonstration rather than a complete pathway model. + +Do not use this section to discuss local files or implementation logistics. + +## JSON Index Requirements + +When the user asks for a JSON index, write a clean machine-readable file such as `data/ai_summaries.json`. + +Each entry should include: + +```json +{ + "model_id": "...", + "title": "...", + "bngl_path": "...", + "yaml_path": "...", + "markdown_path": "...", + "summary": "...", + "key_events": ["...", "...", "..."] +} +``` + +JSON may include file paths because it is for site integration. Markdown summaries should not include those paths unless explicitly requested. + +The JSON `summary` should match the Markdown one-sentence summary. The JSON `key_events` should match the bullets in `## Key modeled events` or be a clean subset of them. + +## Workflow + +1. Read metadata first and record the clean title, id, category, source hints, and short description. +2. Read the BNGL comments before interpreting mechanisms; comments often contain the best biological description. +3. Identify the main biological players from molecule declarations, comments, metadata tags, and any anchors block. If anchors are present, translate them into plain localization statements such as “RCC1 is treated as nuclear-localized” or “EGFR is constrained to the membrane”; do not expose raw anchor syntax in the Markdown. +4. Identify the central mechanism: binding/assembly, activation, modification, feedback, degradation, transport, transcription, or other biological process. +5. Identify three to five key modeled events. These should be selective and biologically meaningful, not exhaustive. +6. Identify the model readouts and translate them into biological measurements. +7. Write the Markdown in the required structure. +8. Review the Markdown and remove raw syntax, file-path prose, implementation jargon, and generic filler. +9. If producing JSON, verify every referenced Markdown path exists and every entry has the required fields. + +## Same-directory Pairing Rule + +When tabulating or selecting models, pair a `.bngl` file with a YAML file only when the `.bngl` and `metadata.yaml` are in the same directory. Do not count inherited ancestor metadata pairs. If a directory has one `metadata.yaml` and multiple `.bngl` files in that same directory, each `.bngl` may be treated as a same-directory BNGL/YAML pair. Nested subdirectory `.bngl` files require their own same-directory `metadata.yaml` to count. + +## Anti-Boilerplate Requirements + +Every generated Markdown file must be specific from top to bottom. Never copy a generic paragraph across models. In particular: + +- `## Biological story` must name the specific model or pathway and describe its unique narrative. +- `## Expected behavior in plots` must name the model-specific readouts or behaviors to compare. +- `## Caveats` must identify the specific scope limitation of that model. +- Repeated stock phrases are allowed only for headings, not for section bodies. +- If two summaries have identical section-body text outside headings, rewrite them. + +## Quality Checklist + +Before finalizing, verify all of the following: + +- The summary is specific to this model, not reusable generic text. +- The reader can understand what the model shows without knowing BNGL. +- The mechanism section contains biological verbs and causal flow. +- The key modeled events include a few important modeled events without becoming a full rule dump. +- The readouts section explains what plotted quantities mean biologically. +- If the model uses anchors, the biological localization consequence is explained in prose without raw anchor syntax. +- The biological story, expected plot behavior, and caveats are unique to the model and not copied boilerplate. +- The Markdown contains no raw BNGL syntax, arrows, bond labels, file paths, or local-file logistics. +- The Markdown avoids the words “observables,” “seed species,” and “reaction rules.” +- The JSON is valid and points to existing Markdown files. diff --git a/skills/explain-model-detailed/SKILL.md b/skills/explain-model-detailed/SKILL.md new file mode 100644 index 00000000..1154d6f6 --- /dev/null +++ b/skills/explain-model-detailed/SKILL.md @@ -0,0 +1,290 @@ +--- +name: explain-rulehub-model-detailed +description: Generate standardized, technical RuleHub explanations from a same-directory BNGL/YAML pair. Use for detailed summaries that interpret model structure, grouped parameters and rules, molecule sites and states, observables, setup, simulation workflow, and model-specific caveats without copying BNGL blocks. +--- + +# Explain RuleHub Model in Detail + +## Purpose + +Write a detailed, technically accurate Markdown explanation of one RuleHub BNGL model and its same-directory metadata. The explanation is an interpretive guide for modelers and curators, not a transcription of the source. + +Optimize for usefulness: + +- Explain what constructs do in this particular model. +- Prefer concise grouping when many entries share a mechanism. +- Preserve site- and state-level accuracy without pasting BNGL patterns. +- Avoid boilerplate, repeated sentence frames, raw declaration lists, and code-block dumps. +- Use the word **Detailed**, not **Coder**, in the document title. + +## Reset Rule: Treat Every Model as New + +Discard assumptions and prose from previous summaries before starting another model. + +- Derive meanings only from the target directory's metadata, BNGL, comments, and nearby notes. +- Do not assume that an abbreviation has the same meaning across models. +- Do not infer an organism, cell type, residue identity, localization, or experimental claim that local files do not establish. +- Do not reuse stock descriptions of parameters, rules, observables, workflows, or caveats. +- Report unresolved meanings briefly in Section 9 instead of inventing them. + +## Required Inputs + +Read local files in this order: + +1. The target directory's metadata YAML. +2. The same-directory BNGL file. +3. Same-directory README files or notes, if present. +4. Comments in the BNGL, especially comments adjacent to parameters, functions, molecule types, rules, observables, and actions. + +A valid pair requires the BNGL and YAML to be in the same directory. Never inherit metadata from a parent directory. Do not treat `metadata_aigenerated.yaml` as the source metadata unless the user explicitly requests it. + +## Analyze Before Writing + +Build a private inventory before drafting: + +- active BNGL blocks and their counts; +- parameter families and the constructs that consume them; +- every active function and its dependencies; +- every declared molecule type, site, repeated site, and internal state; +- compartments, anchors, and biologically important initial pools; +- active reaction-rule families and the exact site/state/bond changes within them; +- every active observable and what it measures; +- active actions and their execution order. + +Ignore blank lines and comments when counting. Never include disabled/commented rules, observables, functions, or actions as active model behavior. + +## BNGL Interpretation Rules + +Apply these rules internally even when the final summary groups constructs: + +- Distinguish molecule types from their components. A component named `CK2` is not a `CK2` molecule unless that molecule actually occurs in the pattern. +- Treat bond labels as local identifiers. Explain the two sites connected or released; do not burden the reader with bond numbers unless a number is necessary to distinguish topology. +- Record exact internal-state changes in readable form, such as `IKK.st: n → a`. +- Distinguish reversible association from one-way catalysis, creation, degradation, transport, or state conversion. +- Identify source `0`, sink `0`, `Trash`, `Sink`, `DeleteMolecules`, population species, catalytic carry-through, and compartment changes when they affect interpretation. +- Treat anchors as localization constraints on molecules or complexes. +- Distinguish molecule-count observables from species-count observables and remember that pattern matches may count embeddings rather than unique complexes. +- Explain extended constructs such as compartments, anchors, population maps, local functions, energy patterns, or conditional rates only when they occur. + +## Required Markdown Structure + +Use exactly these headings unless the user requests another structure: + +```markdown +# Detailed Model Explanation: <specific model title> + +## 1. Model overview + +## 2. BNGL block inventory + +## 3. Parameters, functions, and rate laws + +## 4. Molecule types, sites, and states + +## 5. Compartments, anchors, initial species, and setup + +## 6. Reaction-rule inventory + +## 7. Observables and technical readouts + +## 8. Actions and simulation workflow + +## 9. Technical caveats and ambiguities +``` + +## Section Requirements + +### 1. Model overview + +Describe the model's big-picture purpose and mechanism in about two sentences. + +- Say what system or abstraction is modeled. +- Identify the principal input, mechanistic flow, and output or decision when supported locally. +- Do not list file paths, metadata fields, provenance, or a separate model id. +- Do not restate the title as a sentence. + +### 2. BNGL block inventory + +Give one concise paragraph or a compact table stating which blocks are present and their useful counts. Cover parameters, molecule types, species/seeds, functions, rules, observables, actions, compartments, and anchors when present. + +- Keep this section short. +- If anchors exist, state their count and general localization purpose only; reserve details for Section 5. +- Do not explain individual parameters, rules, or observables here. + +### 3. Parameters, functions, and rate laws + +Begin with one or two sentences explaining the parameter namespace and rate-law style. Then use concise tables rather than prose blocks or copied declarations. + +Use this parameter table: + +| Parameter group or names | Function in this model | +| --- | --- | + +Parameter guidance: + +- Group parameters that share a mechanistic role, such as initial pools, association/dissociation pairs, phosphorylation, transport, transcription, degradation, or simulation control. +- Name every important parameter or a clearly defined range/family. Do not hide unrelated parameters in a vague “other” group. +- Explain what each group controls in this model and where it acts. +- Include numerical values only when they are essential to understanding a scale, switch, asymmetry, initial condition, or unusual behavior. +- Do not paste source comments or reproduce the parameter block. +- Explain algebraic, conditional, multiplicative, saturation, local, or observable-dependent rate laws in words. + +If functions are present, add a separate table: + +| Function | Inputs/dependencies | Meaning and use in this model | +| --- | --- | --- | + +For every active function, explain what it computes, what controls it, and which rules or outputs use it. If no functions exist, say so in one sentence without adding an empty table. + +### 4. Molecule types, sites, and states + +Account for every declared molecule type, but group closely related types when this improves brevity and does not hide site or state differences. + +Use exactly this table: + +| Molecule type(s) | Site count | Sites/components | Internal states | Anchor/allowed compartments | Explanation | +| --- | ---: | --- | --- | --- | --- | + +- Count and name all declared components, including repeated components. +- List all declared internal-state alternatives. +- State anchor or allowed-compartment constraints when present; otherwise use “None.” +- Use the final column for one brief, model-specific explanation of the molecule's role. +- Do not include a separate Notes column. +- Do not paste declarations into the explanation column. +- If the model lacks a molecule-types block, identify effective players from active species/rules and explicitly mark that inference as a caveat. + +### 5. Compartments, anchors, initial species, and setup + +Explain the starting configuration in concise prose, using a short list only if it improves readability. + +- Describe compartment hierarchy, sizes, and movement only when relevant to model behavior. +- Explain each anchor localization or group closely related anchors by compartment. +- Identify the important initial pools and their starting states: stimulus, receptor, enzymes, substrates, scaffolds, feedback regulators, or zero-initialized outputs. +- Include initial amounts only when needed to understand stoichiometry, scale, an absent stimulus, or an important imbalance. +- Do not enumerate every seed merely because it exists. +- Never paste seed-species or anchor declarations. + +### 6. Reaction-rule inventory + +This section is the main mechanistic map. Explain rules verbally at site/state level; do not reproduce complete BNGL patterns. + +For small models, use one row per active rule. For medium or large models, group adjacent rules only when they implement the same mechanism and differ predictably by site, state, occupancy, ligand count, or family member. Every active rule must still be accounted for by an individual number or an explicit number range/list. + +Before the table, add a short, model-specific **Rule-family orientation** paragraph when the model has multiple families. Explain the sequence or relationship among those families; do not use a generic description of how to read a table. + +Use exactly this five-column table: + +| Rule number(s) | Direction | Involved molecules/sites | Exact modeled change and rate logic | Role within the model | +| ---: | --- | --- | --- | --- | + +Table requirements: + +- **Rule number(s):** use source order. A grouped row must enumerate the covered rules with a range or explicit list. +- **Direction:** state reversible, one-way, or mixed if a grouped family genuinely contains both; split the group if “mixed” would obscure behavior. +- **Involved molecules/sites:** list true molecule participants and the sites or states required for the rule to match. Do not list components as molecules. +- **Exact modeled change and rate logic:** verbally name the bond created/released, state transition, creation/removal event, localization change, or catalytic carry-through. Identify the applicable rate name or explain the full rate expression when its algebra changes behavior. Do not paste a BNGL rule. +- **Role within the model:** explain why the rule or family exists, how it advances or restrains the mechanism, and how it relates to nearby rules when useful. + +Grouping rules: + +- Group repetitive rules when a single precise row can state the shared mechanism and enumerate all varying sites, states, occupancies, or family members. +- Do not group rules that differ in direction, biological role, product semantics, localization, catalytic behavior, or materially different rate logic. +- For a grouped family, explicitly map rule numbers to their variants, for example: “12–15 target `l1`–`l4`, respectively.” +- Never replace interpretation with phrases such as “binding-pattern rewrite,” “see the pattern,” “same as above,” or “forms the explicitly site-matched bond.” +- Avoid repeated functional descriptions. Each row must add information specific to its rule or family. +- Omit local bond numbers unless topology cannot be explained without them. + +### 7. Observables and technical readouts + +Explain every active observable, grouping closely related readouts when that is clearer. + +Use this table: + +| Observable(s) | Type | What is measured | Technical interpretation | +| --- | --- | --- | --- | + +- Name every observable covered by each row. +- State molecule-count, species-count, population, or other type. +- Summarize the measured state, complex, localization, or family verbally; do not paste observable patterns. +- Explain how the readout should be interpreted and note double-counting or embedding behavior when relevant. + +### 8. Actions and simulation workflow + +Use two or three sentences describing how the model is run and what the workflow produces. + +- State the simulation method and essential duration/phase structure. +- Mention network generation, equilibration, stimulus changes, scans, continuation, exports, or bounded stoichiometry only when active. +- Explain the execution order when it affects interpretation. +- Do not list or paste action commands. +- Do not use reusable boilerplate; describe this model's actual workflow. + +### 9. Technical caveats and ambiguities + +Use a short model-specific list or paragraph. Include only caveats that materially affect interpretation or execution, such as: + +- ambiguous abbreviations or conflicting local metadata; +- abstract or lumped species that should not be overinterpreted; +- missing molecule-type declarations; +- pattern-match versus unique-complex counting; +- parser-sensitive syntax or unsupported extensions; +- bounded networks or commented-out rule families that alter scope; +- arbitrary/tutorial rate choices; +- uncertain biological mapping explicitly present in local files. + +Do not add generic caveats that could be attached to any BNGL model. + +## Anti-Clutter and Anti-Boilerplate Rules + +- Never paste a parameter, species, rule, observable, function, or action block. +- Do not include source paths in the generated summary. +- Do not repeat the same interpretation across multiple rule rows. +- Do not make every row follow the same empty sentence template. +- Do not create long prose paragraphs when a grouped table is clearer. +- Do not create a table merely to restate syntax. +- Prefer fewer, information-rich rows over exhaustive repetition, while explicitly accounting for all active rules and observables. +- Preserve technical precision through names of molecules, sites, states, directions, and meaningful rate logic—not through copied code. + +## JSON Index Requirements + +Create or update a JSON index only when requested. Use fields such as: + +```json +{ + "model_id": "...", + "title": "...", + "bngl_path": "...", + "yaml_path": "...", + "markdown_path": "...", + "audience": "technical", + "summary": "...", + "molecule_type_count": 0, + "reaction_rule_count": 0, + "reaction_rule_group_count": 0, + "observable_count": 0, + "uses_anchors": false, + "anchor_count": 0, + "key_constructs": ["..."], + "all_active_rules_accounted_for": true +} +``` + +Keep the JSON summary short. Do not duplicate Markdown tables in JSON. + +## Quality Checklist + +Before finalizing, verify: + +- The explanation is based only on the target model's local BNGL, same-directory YAML, and nearby local notes. +- The title begins `Detailed Model Explanation`, not `Coder Model Explanation`. +- Section 1 is about two interpretive sentences and contains no source listing. +- Section 2 is concise and its counts match active BNGL content. +- Section 3 groups parameters by model-specific function, explains rate-law style, and explains every active function without copied declarations. +- Section 4 accounts for every molecule type, component, repeated site, state, and anchor using the required six-column table. +- Section 5 explains spatial setup and important initial pools without dumping seeds. +- Section 6 uses the required five columns, contains no full BNGL rules, and accounts for every active rule individually or through an explicit, justified group. +- Every rule row names the true molecules/sites, exact verbal edit, direction, meaningful rate logic, and model-specific role. +- Grouped rules explicitly identify all rule numbers and all varying sites/states/occupancies. +- Section 7 accounts for every active observable and explains its type and interpretation without copied patterns. +- Section 8 is a two- or three-sentence account of the actual execution workflow. +- Section 9 contains only model-specific caveats. +- No section contains reusable boilerplate, copied source blocks, generic fallback language, or unnecessary provenance. diff --git a/skills/explain-model-detailed/agents/openai.yaml b/skills/explain-model-detailed/agents/openai.yaml new file mode 100644 index 00000000..31d5ea18 --- /dev/null +++ b/skills/explain-model-detailed/agents/openai.yaml @@ -0,0 +1,4 @@ +interface: + display_name: "Explain RuleHub Model (Coders)" + short_description: "Create technical BNGL/YAML model explanations for coders." + default_prompt: "Explain this RuleHub BNGL/YAML model for experienced coders with complete molecule sites and rule inventory." diff --git a/skills/metadata_auditing/SKILL.md b/skills/metadata_auditing/SKILL.md new file mode 100644 index 00000000..a194be4d --- /dev/null +++ b/skills/metadata_auditing/SKILL.md @@ -0,0 +1,246 @@ +--- +name: metadata-auditing +description: Audit RuleHub BNGL feature and citation metadata. Use when checking one or more model directories or same-directory BNGL/YAML pairs, creating source-derived *_metadata_aigenerated.yaml files, and writing a concise Markdown audit under data/. +--- + +# Audit RuleHub metadata + +Produce both deliverables for every audit: + +1. One concise Markdown report under `data/`. +2. One source-derived `*_metadata_aigenerated.yaml` for every auditable BNGL/YAML pair. + +Never overwrite a source YAML. Permit a report-only result only when a directory cannot be audited because its BNGL or source YAML is missing, and report that blockage explicitly. + +## Follow the schema + +Treat the repository-root `metadata-schema.yaml` as authoritative for section placement, field names, types, enum values, and formatting. Read it before editing metadata and consult it whenever uncertain. Do not relocate schema fields based on existing files that use an older layout. + +This workflow audits `features` and `citation`, not compatibility support. Preserve `compatibility` unchanged. Do not audit or infer `citation.doi`; preserve an existing DOI unchanged. + +## Process models independently + +Audit one model completely before starting the next: + +1. Record the exact folder, BNGL file, source YAML, and model identifier. +2. Collect evidence only for that model. +3. Resolve its features and citation, compare its original citation, write its generated YAML, and draft its report section. +4. Clear the prior model's candidate papers, identifiers, PMID, rationale, and notes before opening the next model. + +Never reuse a citation because two folders share an author or year. Disambiguate similar identifiers exactly—for example, treat `BaruaBCR2012` and `BaruaFceRI2012` as separate models and independently follow each model's own listing and paper link. Before accepting a paper, verify that its title, model name, pathway, or distinctive model content matches the current folder; a generic author/year match is insufficient. + +## Select inputs and name outputs + +Pair each `.bngl` file with metadata from the same directory; never inherit metadata from another directory. Choose the source YAML in this order: + +1. A file named by the user. +2. The model-specific `*_metadata.yaml` supplied by a collaborator (for example, `An_2009_metadata.yaml` for `An2009`). + +Do not use `metadata.yaml` or any `*_aigenerated.yaml` as a source. Do not count generated files as candidates. If several candidates remain at the same priority, do not choose silently; report the ambiguity and identify the files requiring confirmation. + +Append `_aigenerated` to the selected source stem: + +```text +An_2009_metadata.yaml -> An_2009_metadata_aigenerated.yaml +``` + +The output must remain in the source YAML's directory and must reveal which source it copies. + +## Audit feature fields + +Audit these fields under top-level `features:` exactly as defined by `metadata-schema.yaml`: + +```yaml +features: + uses_cbngl_compartments: boolean + uses_vcell_compartments: boolean + uses_energy: boolean + uses_functions: boolean + uses_moveconnected: boolean + uses_trash_molecules: boolean + uses_anchors: boolean + uses_multiple_identical_sites: boolean + uses_deletes_molecules: boolean + uses_exclude_include_reactants: boolean + uses_generate_network: boolean + default_sim_command: ode | ssa | nf | pla | hybrid | molclustpy | vcell +``` + +Never write these fields under `compatibility`. If `features:` is absent, create it. If audited feature keys incorrectly exist under `compatibility`, do not duplicate them there; write the audited values under `features` and report the legacy placement for review. + +### Preprocess active BNGL content + +- Inspect the complete BNGL file; do not infer features from metadata, filenames, or tags. +- Ignore blank lines and full-line comments. +- Strip trailing comments before analyzing a line. +- Ignore commented-out blocks, entries, rules, observables, actions, and modifiers. +- Treat a block entry as active only when it is uncommented and nonempty between matching `begin` and `end` lines. +- Do not count block delimiters as entries. + +### Detect compartment grammar + +Set compartment booleans from active species-pattern syntax, not merely from a `begin compartments` block: + +- `uses_vcell_compartments: true` for active prefix syntax: `@Compartment:Molecule(...)`. +- `uses_cbngl_compartments: true` for active suffix syntax: `Molecule(...)@Compartment`. +- Set both to `true` if both syntaxes occur; otherwise set each absent syntax to `false`. + +Do not confuse suffixes with molecule-site state or bond syntax. A compartment declaration alone proves neither pattern grammar. + +### Detect block and construct features + +Require at least one active entry; empty or comment-only blocks are false: + +- `uses_functions`: entry inside `begin functions`. +- `uses_anchors`: entry inside `begin anchors`. +- `uses_energy`: entry inside an energy-pattern block. +- `uses_moveconnected`: `moveConnected` call. +- `uses_trash_molecules`: `Trash(...)` molecule or sink pattern. +- `uses_multiple_identical_sites`: repeated component name in one molecule-type declaration, such as `L(r,r)`. +- `uses_deletes_molecules`: `DeleteMolecules` modifier or action. +- `uses_exclude_include_reactants`: `include_reactants` or `exclude_reactants` modifier. +- `uses_generate_network`: `generate_network(...)` action. + +Match complete identifiers case-sensitively where BNGL syntax is case-sensitive. Do not treat comments or similarly named identifiers as evidence. + +### Detect the default simulation command + +Use the first active simulation action, but store the schema enum value rather than the BNGL function name: + +- `simulate_ode(...)` -> `ode` +- `simulate_ssa(...)` -> `ssa` +- `simulate_nf(...)` -> `nf` +- other supported actions -> the corresponding `metadata-schema.yaml` enum + +Do not write `simulate`, `simulate_ode`, or another function name into `default_sim_command`. If a generic `simulate(...)` does not establish one supported method, preserve a valid source value or leave the field unset as the schema permits, and report the ambiguity. + +Mark a value ambiguous only after rechecking the relevant active syntax. Do not use ambiguity as a substitute for inspecting the model. + +## Audit citations + +Every generated YAML must contain or update: + +```yaml +citation: + year: "YYYY" + pmid: "PubMed ID" + # Use url instead of pmid only when no PMID can be established. + reference: "Author, Year" +``` + +Follow the reference formats in `metadata-schema.yaml`: `Author, Year` for one author, `Author & Author, Year` for two, and `Author et al., Year` for three or more. Require a four-digit `year`, a `reference`, and either `pmid` or `url`. Prefer `pmid` and store digits only. Use an article-specific journal, preprint, or website URL only if no PMID can be established. Ignore DOI for audit purposes and preserve it unchanged. + +### Establish citation evidence in strict order + +Use these sources in order and stop at the first source that identifies the model's paper reliably. Record only that highest-priority successful source in the rationale; do not write combined boilerplate such as “BNGLViz/BioNetGen listings.” + +1. **BNGLViz examples:** Open [BNGLViz examples](https://bnglviz.github.io/examples.html), match the exact model/folder identity, and follow its outbound paper link. +2. **BioNetGen applications:** Use [BioNetGen applications](https://bionetgen.org/applications) only if BNGLViz does not reliably identify the paper, then follow its outbound paper link. +3. **Same-directory evidence:** Inspect the BNGL header, `README.md`, and other descriptive files. Inspect a potentially relevant RTF, PDF, text, or similar artifact before moving on, and name the decisive artifact in the rationale. +4. **Independent literature search:** Search PubMed or the web only when the first three sources do not identify a paper, or when their reliable paper URL does not supply a PMID. Treat author/year-only search matches cautiously and verify the paper against model-specific content. + +Do not take shortcuts from a similar model, shared author, broad pathway, or search snippet. Open the actual listing link or paper record and check the title/authors before writing the reference. If both BNGLViz and BioNetGen list a model, use BNGLViz alone as provenance. If BNGLViz identifies the paper and links directly to PubMed, take the PMID from that link and say so plainly. + +### Resolve PMID and warnings + +- If the decisive listing links to PubMed, use that PMID. Rationale example: “PMID taken from the PubMed link on the BNGLViz entry for `BaruaBCR_2012`.” +- If the decisive source identifies an exact paper but links elsewhere, search PubMed by its exact title and authors. A matching PubMed result is corroboration of established source evidence and does **not** require a warning merely because PubMed was searched. +- If the BNGL header or another same-directory artifact identifies the exact paper, a matching PMID found from that title does **not** require a warning; state both the local evidence and PubMed provenance succinctly. +- If steps 1–3 fail and an independent search supplies the candidate paper, label the reference and PMID as low-confidence guesses requiring review and explain the model-specific match. +- If no PMID exists or can be established, write the best article-specific `url`, include the source link and a linked PubMed title/author search in the report, and warn that the PMID is unresolved. + +Never invent a PMID or claim a paper discusses a model feature without checking the paper record. A URL is a fallback, not a reason to skip PubMed. + +### Compare against the original citation + +First establish the audited citation independently using the sequence above. Then inspect the selected original model-specific YAML's `citation:` mapping, if present, and compare its `reference` and `pmid` with the audited values. + +- Report whether each present original value agrees. +- Report every mismatch explicitly, showing `original -> audited` and the evidence supporting the audited value. +- Treat a mismatch as requiring review; do not silently preserve or overwrite it. +- If the source YAML has no `citation:` mapping, skip this comparison. +- If only one of `reference` or `pmid` exists, compare that value and audit the missing field normally. + +The original YAML is comparison evidence, not authority and not a substitute for the ordered source search. + +### Write citation rationales + +Report the value and provenance for every audited citation. The year needs no separate rationale beyond its source. Give PMID, URL, and reference separate, short, model-specific rationales: + +- Name exactly one decisive source—the highest-priority successful source. +- For the reference, state how that source identifies this exact model/paper. +- For the PMID, state where the identifier came from; do not repeat the reference rationale. +- Add one brief corroborating detail only when needed to disambiguate the model. +- Never use generic claims such as “the record matches the model” without naming the identifying title, model ID, pathway, or distinctive content actually checked. + +## Add contributors + +Ensure every generated YAML contains this schema-compliant top-level list: + +```yaml +contributors: + - name: Vishnu Mukku + - name: Codex +``` + +If `contributors` already exists, preserve unrelated contributors and add any missing required names without duplication. `Vishnu Mukku` identifies the person running these audits; `Codex` identifies the auditing/generating agent. + +## Create generated YAML + +Copy the selected source to the derived same-directory output, then: + +- write every detected feature under exactly one top-level `features` mapping; +- write required citation values under exactly one top-level `citation` mapping; +- add the required contributors; +- insert missing false feature values without requesting review; +- flag inserted true values, changes to existing values, and genuine ambiguities for review; +- preserve all unaudited identity, compatibility, source, playground, DOI, contributors, ordering, quoting, and formatting as closely as practical. + +Treat a missing boolean as effectively false when deciding whether review is needed, but still write every audited boolean explicitly. Validate the completed YAML and confirm each audited key occurs once. + +## Write the audit report + +Start with a compact summary: + +```markdown +# <Audit title> + +Audited <N> models and created <N> `*_metadata_aigenerated.yaml` files. Inserted <N> missing values; <N> items require review. +``` + +Add one heading per model and keep all its information together: + +```markdown +## ModelName + +- Inserted false: `field_a`, `field_b`. +- Review insertion: `field_c: true` — <short active BNGL evidence>. +- Review change: `field_d: true` -> `false` — <short active BNGL evidence>. +- Review ambiguity: `field_e` — <what remains unclear>. +- Citation year: `YYYY`. +- Citation reference: `<reference>` — <one decisive source and exact model-paper match>. +- Citation PMID: `12345678` — <where PMID came from>; [PubMed](https://pubmed.ncbi.nlm.nih.gov/12345678/). +- Citation comparison: original `reference` and `pmid` agree with the audited values. +- Citation mismatch: `pmid`: `<original>` -> `<audited>` — <audited evidence>; **review required**. +- Citation URL: [source](<URL>) — <source and match>; **warning: PMID unresolved**; [PubMed search](<query URL>). +``` + +Omit bullet types that do not apply. Group routine false insertions. Give each inserted true, changed value, ambiguity, citation mismatch, or low-confidence citation one short review bullet. Always include concise citation provenance, but do not count routine high-confidence citation evidence as review. Do not include tables, pairing lists, unchanged feature values, evidence dumps, or generic boilerplate. Mention source selection only when ambiguous. + +## Verify + +Before finishing, confirm: + +- each model was processed independently and similar model names were not conflated; +- every audited model has a same-directory output derived from its selected `*_metadata.yaml`; +- no `metadata.yaml` or generated YAML was used as a source; +- every feature field is under `features`, occurs once, and agrees with active BNGL content; +- no audited feature was added under `compatibility`; +- `default_sim_command` uses a current schema enum value; +- every generated YAML has the required contributors; +- every generated YAML has a four-digit citation year, formatted reference, and either a digits-only PMID or working fallback URL; +- each citation uses the highest-priority successful source and has non-boilerplate rationales; +- source-YAML `reference` and `pmid` values were compared when its `citation` mapping existed, and every mismatch is reported; +- unresolved or independently guessed citations are warned and counted for review, while source-established PubMed lookups are not falsely warned; +- source YAML files remain unchanged; +- report totals match generated files, insertions, and review bullets.