Test changes to contact-inhibition-hippo-yap

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"
+

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

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"
+

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

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"

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

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"

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

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"

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

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"
+

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

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"

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

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"
+

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