diff --git a/Published/An2009/metadata.yaml b/Published/An2009/metadata.yaml index f949b5be..49c2b441 100644 --- a/Published/An2009/metadata.yaml +++ b/Published/An2009/metadata.yaml @@ -1,7 +1,7 @@ -id: "An_2009" -name: "An 2009" +id: An_TLR4_2009 +name: "An et al. 2009: TLR4 Signaling Model" description: "TLR4 signaling" -tags: ["published", "immunology", "an", "2009", "cd14", "md2", "tlr4", "tram", "trif", "sarm", "traf4", "irak1"] +tags: ["tlr4", "immune-signaling", "innate-immunity", "2009", "an"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/Barua2007/metadata.yaml b/Published/Barua2007/metadata.yaml index 5eaeff0b..cbf3e948 100644 --- a/Published/Barua2007/metadata.yaml +++ b/Published/Barua2007/metadata.yaml @@ -1,7 +1,7 @@ -id: "Barua_2007" -name: "Barua 2007" +id: Barua_EGFR_2007 +name: "Barua et al. 2007: EGFR Signaling Model" description: "Model from Haugh (2006)" -tags: ["published", "barua", "2007", "version", "r", "s"] +tags: ["egfr", "signaling", "2007", "barua"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Barua2009/metadata.yaml b/Published/Barua2009/metadata.yaml index 3fb621b2..202e6104 100644 --- a/Published/Barua2009/metadata.yaml +++ b/Published/Barua2009/metadata.yaml @@ -1,7 +1,7 @@ -id: "Barua_2009" -name: "Barua 2009" +id: Barua_JAK2_2009 +name: "Barua et al. 2009: JAK2-STAT5 Signaling Model" description: "JAK2-SH2B signaling" -tags: ["published", "barua", "2009", "s", "j"] +tags: ["jak2", "stat5", "signaling", "2009", "barua"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Barua2013/metadata.yaml b/Published/Barua2013/metadata.yaml index 7f3df0e2..56b91a61 100644 --- a/Published/Barua2013/metadata.yaml +++ b/Published/Barua2013/metadata.yaml @@ -1,7 +1,7 @@ -id: "Barua_2013" -name: "Barua 2013" +id: Barua_bcat_2013 +name: "Barua et al. 2013: Beta-Catenin Regulation Model" description: "Beta-catenin destruction" -tags: ["published", "barua", "2013", "axin", "gsk3b", "apc", "bcat", "ck1a"] +tags: ["beta-catenin", "regulation", "wnt-signaling", "2013", "barua"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/BaruaBCR2012/metadata.yaml b/Published/BaruaBCR2012/metadata.yaml index f910fe3e..f940b5e8 100644 --- a/Published/BaruaBCR2012/metadata.yaml +++ b/Published/BaruaBCR2012/metadata.yaml @@ -1,7 +1,7 @@ -id: "BaruaBCR_2012" -name: "Barua 2012" +id: Barua_BCR_2012 +name: "Barua et al. 2012: BCR Signaling Model" description: "BCR signaling" -tags: ["published", "immunology", "baruabcr", "2012", "bcr", "lyn", "fyn", "csk", "pag", "syk"] +tags: ["bcr", "immune-signaling", "b-cell", "2012", "barua"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/BaruaFceRI2012/metadata.yaml b/Published/BaruaFceRI2012/metadata.yaml index 4a4b33e5..91c03066 100644 --- a/Published/BaruaFceRI2012/metadata.yaml +++ b/Published/BaruaFceRI2012/metadata.yaml @@ -1,7 +1,7 @@ -id: "BaruaFceRI_2012" -name: "BaruaFceRI 2012" +id: Barua_FceRI_2012 +name: "Barua et al. 2012: FceRI Signaling Model" description: "FcεRI signaling" -tags: ["published", "immunology", "baruafceri", "2012", "r_o", "rdimer_o", "l_o", "t_o", "l", "fcr", "lyn", "syk"] +tags: ["fceri", "immune-signaling", "mast-cell", "2012", "barua"] category: "immunology" compatibility: bng2_compatible: false diff --git a/Published/Blinov2006/metadata.yaml b/Published/Blinov2006/metadata.yaml index 87175063..e836f486 100644 --- a/Published/Blinov2006/metadata.yaml +++ b/Published/Blinov2006/metadata.yaml @@ -1,7 +1,7 @@ -id: "Blinov_2006" -name: "Blinov 2006" +id: Blinov_egfr_2006 +name: "Blinov et al. 2006: EGFR Signaling Pathway (ODE)" description: "Phosphotyrosine signaling" -tags: ["published", "blinov", "2006", "egf", "egfr", "shc", "grb2", "sos"] +tags: ["egfr", "signaling", "ode", "receptor-activation", "2006", "blinov"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Blinovegfr/metadata.yaml b/Published/Blinovegfr/metadata.yaml index bf601496..9b9205d1 100644 --- a/Published/Blinovegfr/metadata.yaml +++ b/Published/Blinovegfr/metadata.yaml @@ -1,7 +1,7 @@ -id: "Blinov_egfr" -name: "Blinov egfr" +id: Blinov_egfr_NF_2006 +name: "Blinov et al. 2006: EGFR Signaling Pathway (NFsim)" description: "EGFR signaling model" -tags: ["published", "nfsim", "blinov", "egfr", "egf", "grb2", "shc", "simulate_nf"] +tags: ["egfr", "signaling", "nfsim", "receptor-activation", "2006", "blinov"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/Blinovran/metadata.yaml b/Published/Blinovran/metadata.yaml index 2143b98a..d490afde 100644 --- a/Published/Blinovran/metadata.yaml +++ b/Published/Blinovran/metadata.yaml @@ -1,7 +1,7 @@ -id: "Blinov_ran" -name: "Blinov ran" +id: Blinov_ran_2006 +name: "Blinov et al. 2006: Ran-Mediated Nuclear Transport (NFsim)" description: "Ran GTPase cycle" -tags: ["published", "nfsim", "blinov", "ran", "c", "rcc1", "simulate_nf"] +tags: ["ran-gtpase", "nuclear-transport", "nfsim", "2006", "blinov"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/Chattaraj2021/metadata.yaml b/Published/Chattaraj2021/metadata.yaml index 4a2b65f1..4710acd1 100644 --- a/Published/Chattaraj2021/metadata.yaml +++ b/Published/Chattaraj2021/metadata.yaml @@ -1,7 +1,7 @@ -id: "Chattaraj_2021" -name: "Chattaraj 2021" +id: Chattaraj_nephrin_2021 +name: "Chattaraj et al. 2021: Nephrin-Nck-NWASP Clustering Model" description: "NFkB oscillations" -tags: ["published", "chattaraj", "2021", "nephrin", "nck", "nwasp", "writexml"] +tags: ["nephrin", "nck", "nwasp", "clustering", "2021", "chattaraj"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/CheemalavaguJAKSTAT/metadata.yaml b/Published/CheemalavaguJAKSTAT/metadata.yaml index b1aa6a3a..cac1bcc5 100644 --- a/Published/CheemalavaguJAKSTAT/metadata.yaml +++ b/Published/CheemalavaguJAKSTAT/metadata.yaml @@ -1,7 +1,7 @@ -id: "Cheemalavagu_JAK_STAT" -name: "Cheemalavagu 2024" +id: Cheemalavagu_JAKSTAT_2024 +name: "Cheemalavagu et al. 2024: JAK-STAT Signaling Model" description: "JAK-STAT signaling" -tags: ["published", "literature", "signaling", "cheemalavagu", "jak", "stat", "l1", "il6r", "gp130", "l2", "il10r1", "il10r2", "jak1", "jak2"] +tags: ["jak-stat", "signaling", "2024", "cheemalavagu"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/ChylekFceRI2014/metadata.yaml b/Published/ChylekFceRI2014/metadata.yaml index de4078e3..cc31b0f3 100644 --- a/Published/ChylekFceRI2014/metadata.yaml +++ b/Published/ChylekFceRI2014/metadata.yaml @@ -1,7 +1,7 @@ -id: "ChylekFceRI_2014" -name: "Chylek 2014 (FceRI)" +id: Chylek_FceRI_2014 +name: "Chylek et al. 2014: FceRI Signaling Model" description: "FceRI signaling" -tags: ["published", "immunology", "chylekfceri", "2014", "lig", "rec", "lyn", "fyn", "syk", "pag1", "csk", "lat"] +tags: ["fceri", "immune-signaling", "mast-cell", "2014", "chylek"] category: "immunology" compatibility: bng2_compatible: false diff --git a/Published/ChylekTCR2014/metadata.yaml b/Published/ChylekTCR2014/metadata.yaml index f91b3980..2aedad35 100644 --- a/Published/ChylekTCR2014/metadata.yaml +++ b/Published/ChylekTCR2014/metadata.yaml @@ -1,7 +1,7 @@ -id: "ChylekTCR_2014" -name: "Chylek 2014 (TCR)" +id: Chylek_TCR_2014 +name: "Chylek et al. 2014: T Cell Receptor (TCR) Signaling Model" description: "TCR signaling" -tags: ["published", "immunology", "chylektcr", "2014", "lig1", "lig2", "lig3", "tcr", "cd28", "lck", "itk", "zap70"] +tags: ["tcr", "immune-signaling", "t-cell", "2014", "chylek"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/Dembo1978/metadata.yaml b/Published/Dembo1978/metadata.yaml index 766b339a..f5424e03 100644 --- a/Published/Dembo1978/metadata.yaml +++ b/Published/Dembo1978/metadata.yaml @@ -1,7 +1,7 @@ -id: "Dembo_1978" -name: "Dembo 1978" +id: Dembo_blbr_1978 +name: "Dembo et al. 1978: Bivalent Ligand Bivalent Receptor (BLBR) Model" description: "BLBR dembo 1978" -tags: ["published", "physics", "dembo", "1978"] +tags: ["blbr", "ligand-receptor", "binding", "1978", "dembo"] category: "physics" compatibility: bng2_compatible: true diff --git a/Published/Dolan2015/metadata.yaml b/Published/Dolan2015/metadata.yaml index ed930271..67fe7dc3 100644 --- a/Published/Dolan2015/metadata.yaml +++ b/Published/Dolan2015/metadata.yaml @@ -1,7 +1,7 @@ -id: "Dolan_2015" -name: "Dolan 2015" +id: Dolan_Insulin_2015 +name: "Dolan et al. 2015: Insulin Receptor Signaling Model" description: "Insulin signaling" -tags: ["published", "literature", "signaling", "dolan", "2015", "time", "t", "p", "e", "ir", "d", "p53_mrna", "p53"] +tags: ["insulin", "metabolism", "2015", "dolan"] category: "other" compatibility: bng2_compatible: false diff --git a/Published/Dreisigmeyer2008/metadata.yaml b/Published/Dreisigmeyer2008/metadata.yaml index 6b27da34..199f913c 100644 --- a/Published/Dreisigmeyer2008/metadata.yaml +++ b/Published/Dreisigmeyer2008/metadata.yaml @@ -1,7 +1,7 @@ -id: "Dreisigmeyer_2008" -name: "Dreisigmeyer 2008" +id: Dreisigmeyer_LacOperon_2008 +name: "Dreisigmeyer et al. 2008: Lac Operon Regulation Model" description: "Lac operon" -tags: ["published", "gene-expression", "dreisigmeyer", "2008"] +tags: ["lac-operon", "gene-expression", "bacterial-regulation", "2008", "dreisigmeyer"] category: "gene-expression" compatibility: bng2_compatible: true diff --git a/Published/Dushek2011/metadata.yaml b/Published/Dushek2011/metadata.yaml index f54c7019..50929e50 100644 --- a/Published/Dushek2011/metadata.yaml +++ b/Published/Dushek2011/metadata.yaml @@ -1,7 +1,7 @@ -id: "Dushek_2011" -name: "Dushek 2011" +id: Dushek_TCR_2011 +name: "Dushek et al. 2011: T Cell Receptor Kinase Kinase Cascade" description: "TCR signaling" -tags: ["published", "dushek", "2011", "s"] +tags: ["tcr", "phosphorylation", "immune-signaling", "2011", "dushek"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/Dushek2014/metadata.yaml b/Published/Dushek2014/metadata.yaml index 43ea73da..6be669ca 100644 --- a/Published/Dushek2014/metadata.yaml +++ b/Published/Dushek2014/metadata.yaml @@ -1,7 +1,7 @@ -id: "Dushek_2014" -name: "Dushek 2014" +id: Dushek_TCR_2014 +name: "Dushek et al. 2014: T Cell Receptor Phosphorylation Feedback" description: "TCR signaling dynamics" -tags: ["published", "dushek", "2014", "e", "f", "b"] +tags: ["tcr", "feedback-loop", "immune-signaling", "2014", "dushek"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/Erdem2021/metadata.yaml b/Published/Erdem2021/metadata.yaml index 0d70fdb1..3fe9b906 100644 --- a/Published/Erdem2021/metadata.yaml +++ b/Published/Erdem2021/metadata.yaml @@ -1,7 +1,7 @@ -id: "Erdem_2021" -name: "Erdem 2021" +id: Erdem_InsR_2021 +name: "Erdem et al. 2021: Insulin Receptor Internalization Model" description: "InsR/IGF1R signaling" -tags: ["published", "erdem", "2021", "igf1", "ins", "igf1r", "insr", "irs", "sos", "ras", "raf"] +tags: ["insulin", "receptor-internalization", "2021", "erdem"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Faeder2003/metadata.yaml b/Published/Faeder2003/metadata.yaml index 1d7353d5..27e0c45b 100644 --- a/Published/Faeder2003/metadata.yaml +++ b/Published/Faeder2003/metadata.yaml @@ -1,7 +1,7 @@ -id: "Faeder_2003" -name: "Faeder 2003" +id: Faeder_FceRI_2003 +name: "Faeder et al. 2003: FceRI Signaling Model" description: "FceRI signaling" -tags: ["published", "immunology", "faeder", "2003", "lig", "lyn", "syk", "rec"] +tags: ["fceri", "immune-signaling", "mast-cell", "2003", "faeder"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/Gardner2000/metadata.yaml b/Published/Gardner2000/metadata.yaml index b3ce5125..042c42ab 100644 --- a/Published/Gardner2000/metadata.yaml +++ b/Published/Gardner2000/metadata.yaml @@ -1,7 +1,7 @@ -id: "Gardner_2000" -name: "Gardner 2000" +id: Gardner_Toggle_2000 +name: "Gardner et al. 2000: Synthetic Gene Toggle Switch" description: "Genetic toggle switch" -tags: ["published", "synthetic-biology", "gardner", "2000"] +tags: ["toggle-switch", "synthetic-biology", "gene-regulation", "2000", "gardner"] category: "synthetic-biology" compatibility: bng2_compatible: true diff --git a/Published/Goldstein1980/metadata.yaml b/Published/Goldstein1980/metadata.yaml index 36562150..7360e453 100644 --- a/Published/Goldstein1980/metadata.yaml +++ b/Published/Goldstein1980/metadata.yaml @@ -1,7 +1,7 @@ -id: "Goldstein_1980" -name: "Goldstein 1980" +id: Goldstein_blbr_1980 +name: "Goldstein et al. 1980: Bivalent Ligand Bivalent Receptor (BLBR) Model" description: "BLBR heterogeneity" -tags: ["published", "physics", "goldstein", "1980"] +tags: ["blbr", "ligand-receptor", "binding", "1980", "goldstein"] category: "physics" compatibility: bng2_compatible: true diff --git a/Published/Harmon2017/metadata.yaml b/Published/Harmon2017/metadata.yaml index 7d5b75c6..68eb27b7 100644 --- a/Published/Harmon2017/metadata.yaml +++ b/Published/Harmon2017/metadata.yaml @@ -1,7 +1,7 @@ -id: "Harmon_2017" -name: "Harmon 2017" +id: Harmon_Antigen_2017 +name: "Harmon et al. 2017: Antigen Recognition Feedback Model" description: "Antigen pulses" -tags: ["published", "immunology", "harmon", "2017"] +tags: ["antigen-recognition", "immune-signaling", "2017", "harmon"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/Hat2016/metadata.yaml b/Published/Hat2016/metadata.yaml index 8e37c765..e9389a6e 100644 --- a/Published/Hat2016/metadata.yaml +++ b/Published/Hat2016/metadata.yaml @@ -1,7 +1,7 @@ -id: "Hat_2016" -name: "Hat 2016" +id: Hat_wip1_2016 +name: "Hat et al. 2016: Wip1-Mediated Feedback Oscillator" description: "Nuclear transport" -tags: ["published", "hat", "2016", "dna_dsb", "atm", "siah1", "hipk2", "wip1", "gene_wip1", "mrna_wip1", "p53"] +tags: ["wip1", "feedback-loop", "p53-pathway", "2016", "hat"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/Hlavacek1999/metadata.yaml b/Published/Hlavacek1999/metadata.yaml index 5ebe402c..b13f06e4 100644 --- a/Published/Hlavacek1999/metadata.yaml +++ b/Published/Hlavacek1999/metadata.yaml @@ -1,7 +1,7 @@ -id: "Hlavacek_1999" -name: "Hlavacek 1999" +id: Hlavacek_Steric_1999 +name: "Hlavacek et al. 1999: Steric Hindrance in Ligand Binding" description: "Steric effects" -tags: ["published", "physics", "hlavacek", "1999"] +tags: ["steric-hindrance", "ligand-binding", "1999", "hlavacek"] category: "physics" compatibility: bng2_compatible: true diff --git a/Published/Hlavacek2001/metadata.yaml b/Published/Hlavacek2001/metadata.yaml index 9792cdcf..3ecd3bbc 100644 --- a/Published/Hlavacek2001/metadata.yaml +++ b/Published/Hlavacek2001/metadata.yaml @@ -1,7 +1,7 @@ -id: "Hlavacek_2001" -name: "Hlavacek 2001" +id: Hlavacek_Proofreading_2001 +name: "Hlavacek et al. 2001: Kinetic Proofreading Model" description: "Kinetic proofreading" -tags: ["published", "physics", "hlavacek", "2001"] +tags: ["kinetic-proofreading", "ligand-discrimination", "2001", "hlavacek"] category: "physics" compatibility: bng2_compatible: true diff --git a/Published/Hlavacek2018Egg/metadata.yaml b/Published/Hlavacek2018Egg/metadata.yaml index 98808fdd..6879745c 100644 --- a/Published/Hlavacek2018Egg/metadata.yaml +++ b/Published/Hlavacek2018Egg/metadata.yaml @@ -1,7 +1,7 @@ -id: Hlavacek2018Egg_egg -name: Hlavacek2018Egg +id: Hlavacek_Egg_2018 +name: "Hlavacek et al. 2018: Calcium Oscillations in Egg Activation" 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"] +tags: ["calcium-oscillations", "egg-activation", "2018", "hlavacek"] category: other compatibility: bng2_compatible: true diff --git a/Published/Hlavacek2018Elephant/metadata.yaml b/Published/Hlavacek2018Elephant/metadata.yaml index 0c16dcec..cd3e39de 100644 --- a/Published/Hlavacek2018Elephant/metadata.yaml +++ b/Published/Hlavacek2018Elephant/metadata.yaml @@ -1,7 +1,7 @@ -id: Hlavacek2018Elephant_elephant_EFA -name: Hlavacek2018Elephant +id: Hlavacek_Elephant_2018 +name: "Hlavacek et al. 2018: Fitting an Elephant with Four Parameters" 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"] +tags: ["elephant-fitting", "mathematical-model", "2018", "hlavacek"] category: other compatibility: bng2_compatible: true diff --git a/Published/Hlavacek2018Restructuration/metadata.yaml b/Published/Hlavacek2018Restructuration/metadata.yaml index 00f6fdf0..24adc67c 100644 --- a/Published/Hlavacek2018Restructuration/metadata.yaml +++ b/Published/Hlavacek2018Restructuration/metadata.yaml @@ -1,7 +1,7 @@ -id: Hlavacek2018Restructuration_after_bunching -name: Hlavacek2018Restructuration +id: Hlavacek_Restructuration_2018 +name: "Hlavacek et al. 2018: Network Restructuration Analysis" description: BNGL model: after_bunching -tags: ["na", "vecf", "egftot", "egfrtot", "kd", "kr", "kpx", "kmx", "kp", "kdp", "molecules"] +tags: ["network-restructuration", "mathematical-model", "2018", "hlavacek"] category: other compatibility: bng2_compatible: true diff --git a/Published/JaruszewiczBlonska2023/metadata.yaml b/Published/JaruszewiczBlonska2023/metadata.yaml index b469a530..5247e01a 100644 --- a/Published/JaruszewiczBlonska2023/metadata.yaml +++ b/Published/JaruszewiczBlonska2023/metadata.yaml @@ -1,7 +1,7 @@ -id: "Jaruszewicz-Blonska_2023" -name: "Jaruszewicz 2023" +id: JaruszewiczBlonska_NFkB_2023 +name: "Jaruszewicz-Blonska et al. 2023: NF-kB Feedback Regulation" description: "T-cell discrimination" -tags: ["published", "immunology", "jaruszewicz", "blonska", "2023", "ikk", "ikba", "ikba_mrna", "a20", "nfkb"] +tags: ["nfkb", "feedback-regulation", "inflammatory-response", "2023", "jaruszewiczblonska"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/Jung2017/metadata.yaml b/Published/Jung2017/metadata.yaml index bba84b04..497bd501 100644 --- a/Published/Jung2017/metadata.yaml +++ b/Published/Jung2017/metadata.yaml @@ -1,7 +1,7 @@ -id: "Jung_2017" -name: "Jung 2017" +id: Jung_CaMKII_2017 +name: "Jung et al. 2017: CaMKII Activation Kinetics" description: "M1 receptor signaling" -tags: ["published", "jung", "2017", "m1r", "oxo", "arrestin", "mek", "erk", "perk", "oxo_ec", "pp2a"] +tags: ["camkii", "neuroscience", "kinase-activation", "2017", "jung"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Kesseler2013/metadata.yaml b/Published/Kesseler2013/metadata.yaml index 86b76e09..160ff13a 100644 --- a/Published/Kesseler2013/metadata.yaml +++ b/Published/Kesseler2013/metadata.yaml @@ -1,7 +1,7 @@ -id: "Kesseler_2013" -name: "Kesseler 2013" +id: Kesseler_CellCycle_2013 +name: "Kesseler et al. 2013: Cell Cycle Regulation Model" description: "G2/Mitosis transition" -tags: ["published", "kesseler", "2013", "mpf", "cdc25", "wee1", "myt1", "pin1", "pp2a", "prox", "e33"] +tags: ["cell-cycle", "mitosis", "cdc25", "wee1", "2013", "kesseler"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Kocieniewski2012/metadata.yaml b/Published/Kocieniewski2012/metadata.yaml index d08a90c6..2f97d3d4 100644 --- a/Published/Kocieniewski2012/metadata.yaml +++ b/Published/Kocieniewski2012/metadata.yaml @@ -1,7 +1,7 @@ -id: "Kocieniewski_2012" -name: "Kocieniewski 2012" +id: Kocieniewski_published_2012 +name: "Kocieniewski et al. 2012: MAPK Signaling on Scaffolds" description: "Actin dynamics" -tags: ["published", "kocieniewski", "2012", "map3k", "map2k", "mapk", "scaff"] +tags: ["mapk", "scaffold-proteins", "signaling", "2012", "kocieniewski"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/Korwek2023/metadata.yaml b/Published/Korwek2023/metadata.yaml index d836cd9b..b6f09a9d 100644 --- a/Published/Korwek2023/metadata.yaml +++ b/Published/Korwek2023/metadata.yaml @@ -1,7 +1,7 @@ -id: "Korwek_2023" -name: "Korwek_2023" +id: Korwek_ViralSensing_2023 +name: "Korwek et al. 2023: Viral Sensing and Innate Immune Activation" description: "This BioNetGen file features the article:" -tags: ["validation", "korwek", "2023", "polyic", "rigi", "mavs", "pkr", "oas3", "rnasel", "eif2a", "rigi_mrna"] +tags: ["innate-immunity", "rig-i-sensing", "pkr-activation", "rnase-l-cleavage", "viral-sensing", "2023", "korwek"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/Kozer2013/metadata.yaml b/Published/Kozer2013/metadata.yaml index b9044604..83ea38d9 100644 --- a/Published/Kozer2013/metadata.yaml +++ b/Published/Kozer2013/metadata.yaml @@ -1,7 +1,7 @@ -id: "Kozer_2013" -name: "Kozer 2013" +id: Kozer_egfr_2013 +name: "Kozer et al. 2013: EGFR Dimerization and Internalization" description: "EGFR oligomerization" -tags: ["published", "kozer", "2013", "egf", "egfr"] +tags: ["egfr", "dimerization", "internalization", "2013", "kozer"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Kozer2014/metadata.yaml b/Published/Kozer2014/metadata.yaml index aaca3fe5..af1b553c 100644 --- a/Published/Kozer2014/metadata.yaml +++ b/Published/Kozer2014/metadata.yaml @@ -1,7 +1,7 @@ -id: "Kozer_2014" -name: "Kozer 2014" +id: Kozer_egfr_2014 +name: "Kozer et al. 2014: EGFR Oligomerization Dynamics" description: "Grb2-EGFR recruitment" -tags: ["published", "kozer", "2014", "egf", "egfr", "grb2"] +tags: ["egfr", "oligomerization", "internalization", "2014", "kozer"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Lang2024/metadata.yaml b/Published/Lang2024/metadata.yaml index fde4a072..a4d49768 100644 --- a/Published/Lang2024/metadata.yaml +++ b/Published/Lang2024/metadata.yaml @@ -1,7 +1,7 @@ -id: "Lang_2024" -name: "Lang 2024" +id: Lang_CellCycle_2024 +name: "Lang et al. 2024: Cyclin A-CDK2 Cell Cycle Control" description: "Cell cycle regulation" -tags: ["published", "lang", "2024", "e2f", "rb1", "ppp2r2b", "ccnb_promoter", "ccna", "ccna_promoter", "foxm1_promoter", "ensa_arpp19"] +tags: ["cell-cycle", "cyclin-a", "cdk2", "2024", "lang"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/Ligon2014/metadata.yaml b/Published/Ligon2014/metadata.yaml index 198fe7aa..4c6a5316 100644 --- a/Published/Ligon2014/metadata.yaml +++ b/Published/Ligon2014/metadata.yaml @@ -1,7 +1,7 @@ -id: "Ligon_2014" -name: "Ligon 2014" +id: Ligon_egfr_2014 +name: "Ligon et al. 2014: EGFR Dimerization in Living Cells" description: "Lipoplex delivery" -tags: ["published", "nfsim", "ligon", "2014", "lext", "pit", "lint"] +tags: ["egfr", "dimerization", "fluorescence-microscopy", "2014", "ligon"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/Lin2019/README.md b/Published/Lin2019/README.md new file mode 100644 index 00000000..4be304a3 --- /dev/null +++ b/Published/Lin2019/README.md @@ -0,0 +1 @@ +# Lin2019 diff --git a/Published/Lin2019/metadata.yaml b/Published/Lin2019/metadata.yaml index 7e47ccfc..34e156f3 100644 --- a/Published/Lin2019/metadata.yaml +++ b/Published/Lin2019/metadata.yaml @@ -1,7 +1,7 @@ -id: Lin2019_ERK_model -name: ERK_model.bngl +id: Lin_ScalingBench_2019 +name: "Lin et al. 2019: Scaling Benchmark Models" 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"] +tags: ["scaling-benchmark", "kinetics", "2019", "lin"] category: other compatibility: bng2_compatible: true diff --git a/Published/LinERK2019/metadata.yaml b/Published/LinERK2019/metadata.yaml index 8c2ee395..c24a91a2 100644 --- a/Published/LinERK2019/metadata.yaml +++ b/Published/LinERK2019/metadata.yaml @@ -1,7 +1,7 @@ id: "Lin_ERK_2019" name: "Lin 2019" description: "ERK signaling" -tags: ["published", "literature", "signaling", "lin", "erk", "2019", "egfr", "sos", "ras", "rasgap", "raf", "mek", "ekar3"] +tags: ["2019", "egfr", "erk", "lin", "linerk", "mek", "raf", "ras", "rasgap", "signaling", "sos"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/LinPrion2019/metadata.yaml b/Published/LinPrion2019/metadata.yaml index ad5b740c..78504c7c 100644 --- a/Published/LinPrion2019/metadata.yaml +++ b/Published/LinPrion2019/metadata.yaml @@ -1,7 +1,7 @@ id: "Lin_Prion_2019" name: "Lin 2019" description: "Prion replication" -tags: ["published", "literature", "prion", "lin", "2019", "prp", "scaledupspecies1", "scaledupspecies2", "scaledupspecies15", "scaledupspecies30"] +tags: ["2019", "lin", "linprion", "prion", "prp"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/LinTCR2019/metadata.yaml b/Published/LinTCR2019/metadata.yaml index 9b72e6b3..339eb3f7 100644 --- a/Published/LinTCR2019/metadata.yaml +++ b/Published/LinTCR2019/metadata.yaml @@ -1,7 +1,7 @@ id: "Lin_TCR_2019" name: "Lin 2019" description: "TCR signaling" -tags: ["published", "literature", "immune", "lin", "tcr", "2019", "pmhc", "lck", "shp", "zap", "mek", "erk"] +tags: ["2019", "erk", "immune", "lck", "lin", "lintcr", "mek", "pmhc", "shp", "signaling", "tcr", "zap"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/Macken1982/metadata.yaml b/Published/Macken1982/metadata.yaml index 15149819..c1073714 100644 --- a/Published/Macken1982/metadata.yaml +++ b/Published/Macken1982/metadata.yaml @@ -1,7 +1,7 @@ -id: "Macken_1982" -name: "Macken 1982" +id: Macken_physics_1982 +name: "Macken et al. 1982: Polymer Chain Reaction Kinetics" description: "TLBR solution macken 1982" -tags: ["published", "physics", "macken", "1982"] +tags: ["polymerization", "mathematical-model", "1982", "macken"] category: "physics" compatibility: bng2_compatible: true diff --git a/Published/Mallela2021/metadata.yaml b/Published/Mallela2021/metadata.yaml index 9c5459d6..6e4800bc 100644 --- a/Published/Mallela2021/metadata.yaml +++ b/Published/Mallela2021/metadata.yaml @@ -1,7 +1,7 @@ -id: "Mallela2021_States" -name: "Mallela 2021 - COVID-19 State-Level Models" +id: Mallela_COVID_2021 +name: "Mallela et al. 2021: Covid-19 State-Level Transmission Dynamics" description: "Parameter-fit COVID-19 epidemiological models for all 50 US states." -tags: ["covid-19", "epidemiology", "parameter-estimation", "pybionetgen"] +tags: ["covid-19", "epidemiology", "state-level", "2021", "mallela"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/Mallela2021_Cities/metadata.yaml b/Published/Mallela2021_Cities/metadata.yaml index ecd80da1..a2865ce3 100644 --- a/Published/Mallela2021_Cities/metadata.yaml +++ b/Published/Mallela2021_Cities/metadata.yaml @@ -1,7 +1,7 @@ -id: "Mallela2021_Cities" -name: "Mallela 2021 - COVID-19 City Models" +id: Mallela_Cities_2021 +name: "Mallela et al. 2021: Covid-19 City-Level Transmission Dynamics" description: "Parameter-fit COVID-19 epidemiological models for major US cities." -tags: ["covid-19", "epidemiology", "parameter-estimation", "pybionetgen"] +tags: ["covid-19", "epidemiology", "city-level", "2021", "mallela"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/Mallela2022/Alabama/metadata.yaml b/Published/Mallela2022/Alabama/metadata.yaml index bb85e394..f05c1c74 100644 --- a/Published/Mallela2022/Alabama/metadata.yaml +++ b/Published/Mallela2022/Alabama/metadata.yaml @@ -1,7 +1,7 @@ -id: "Alabama" -name: "Alabama" +id: Mallela_VaxVariants_Alabama_2022 +name: "Mallela et al. 2022: Covid-19 Vax and Variants - Alabama MSA" description: "reporting period (1 d)" -tags: ["alabama", "fdcs", "counter", "s", "e1", "e2", "e3", "e4", "e5"] +tags: ["covid-19", "epidemiology", "vaccination", "variants", "alabama", "2022", "mallela"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/Mallela2022_MSAs/metadata.yaml b/Published/Mallela2022_MSAs/metadata.yaml index 529c1c0b..22d53a7e 100644 --- a/Published/Mallela2022_MSAs/metadata.yaml +++ b/Published/Mallela2022_MSAs/metadata.yaml @@ -1,7 +1,7 @@ -id: "Mallela2022_MSAs" -name: "Mallela 2022 - COVID-19 MSA Models" +id: Mallela_MSAs_2022 +name: "Mallela et al. 2022: Covid-19 MSA-Level Transmission Dynamics" description: "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas." -tags: ["covid-19", "epidemiology", "parameter-estimation", "pybionetgen"] +tags: ["covid-19", "epidemiology", "msa-level", "2022", "mallela"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/Massole2023/metadata.yaml b/Published/Massole2023/metadata.yaml index 7827faf2..4298660a 100644 --- a/Published/Massole2023/metadata.yaml +++ b/Published/Massole2023/metadata.yaml @@ -1,7 +1,7 @@ -id: "Massole_2023" -name: "Massole 2023" +id: Massole_developmental_2023 +name: "Massole et al. 2023: Notch-Delta Lateral Inhibition Dynamics" description: "Epo receptor signaling" -tags: ["published", "massole", "2023"] +tags: ["notch-delta", "lateral-inhibition", "developmental", "2023", "massole"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/McMillan2021/metadata.yaml b/Published/McMillan2021/metadata.yaml index 5f911a83..6a35d1d4 100644 --- a/Published/McMillan2021/metadata.yaml +++ b/Published/McMillan2021/metadata.yaml @@ -1,7 +1,7 @@ -id: "McMillan_2021" +id: "McMillan_TNF_2021" name: "McMillan 2021" description: "TNF signaling" -tags: ["published", "nfsim", "mcmillan", "2021", "r0_tot", "t0_tot", "r", "t", "generate_network", "simulate_ode"] +tags: ["2021", "mcmillan", "nfsim", "signaling", "tnf"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/Mertins2023/metadata.yaml b/Published/Mertins2023/metadata.yaml index 3f0ac837..d09087a9 100644 --- a/Published/Mertins2023/metadata.yaml +++ b/Published/Mertins2023/metadata.yaml @@ -1,7 +1,7 @@ -id: "Mertins_2023" -name: "Mertins 2023" +id: Mertins_cancer_2023 +name: "Mertins et al. 2023: Apoptotic Signaling Response" description: "DNA damage response" -tags: ["published", "mertins", "2023", "dnadsb", "p53", "mrna_bax", "bax", "bclxl", "bad", "fourteen_3_3", "caspase"] +tags: ["apoptosis", "bax-bclxl", "cancer", "2023", "mertins"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Miller2022_NavajoNation/metadata.yaml b/Published/Miller2022_NavajoNation/metadata.yaml index 1e421f8e..a36648b3 100644 --- a/Published/Miller2022_NavajoNation/metadata.yaml +++ b/Published/Miller2022_NavajoNation/metadata.yaml @@ -1,7 +1,7 @@ -id: "Miller2022_NavajoNation" -name: "Miller 2022 - Navajo Nation Models" +id: Miller_NavajoNation_2022 +name: "Miller et al. 2022: Covid-19 Transmission in Navajo Nation" description: "COVID-19 epidemiological models fit to Navajo Nation regional data." -tags: ["covid-19", "epidemiology", "pybionetgen"] +tags: ["covid-19", "epidemiology", "navajo-nation", "2022", "miller"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/Miller2025_MEK/metadata.yaml b/Published/Miller2025_MEK/metadata.yaml index e2e7fb59..8d19f87b 100644 --- a/Published/Miller2025_MEK/metadata.yaml +++ b/Published/Miller2025_MEK/metadata.yaml @@ -1,7 +1,7 @@ -id: "Miller2025_MEK" -name: "Miller 2025 - MEK Isoform Models" +id: Miller_MEK_2025 +name: "Miller et al. 2025: MEK Isoform Specific Signaling" description: "MEK isoform variant models curated for PyBioNetGen." -tags: ["mek", "isoforms", "signaling", "pybionetgen"] +tags: ["mek-isoforms", "mapk-pathway", "signaling", "2025", "miller"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/02-egfr/README.md b/Published/Mitra2019/02-egfr/README.md new file mode 100644 index 00000000..42923409 --- /dev/null +++ b/Published/Mitra2019/02-egfr/README.md @@ -0,0 +1 @@ +# 02-egfr diff --git a/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml b/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml index 5e810194..0fbb200f 100644 --- a/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml +++ b/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml @@ -1,7 +1,7 @@ -id: Mitra2019_02_egfr_bnf1_InputFiles_egfr -name: InputFiles +id: Mitra_EGFR_2019 +name: "Mitra et al. 2019: EGFR Receptor Signaling (ODE)" description: EGFR model -tags: ["signaling"] +tags: ["egfr", "signaling", "receptor-binding", "2019", "mitra"] category: signaling compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/02-egfr/metadata.yaml b/Published/Mitra2019/02-egfr/metadata.yaml index 8d4eaebe..0fbb200f 100644 --- a/Published/Mitra2019/02-egfr/metadata.yaml +++ b/Published/Mitra2019/02-egfr/metadata.yaml @@ -1,7 +1,7 @@ -id: 02_egfr_egfr -name: 02-egfr +id: Mitra_EGFR_2019 +name: "Mitra et al. 2019: EGFR Receptor Signaling (ODE)" description: EGFR model -tags: ["signaling"] +tags: ["egfr", "signaling", "receptor-binding", "2019", "mitra"] category: signaling compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/03-fcerig/README.md b/Published/Mitra2019/03-fcerig/README.md new file mode 100644 index 00000000..9d0f282c --- /dev/null +++ b/Published/Mitra2019/03-fcerig/README.md @@ -0,0 +1 @@ +# 03-fcerig diff --git a/Published/Mitra2019/03-fcerig/metadata.yaml b/Published/Mitra2019/03-fcerig/metadata.yaml index cb9e95d5..e7b85735 100644 --- a/Published/Mitra2019/03-fcerig/metadata.yaml +++ b/Published/Mitra2019/03-fcerig/metadata.yaml @@ -1,7 +1,7 @@ -id: 03_fcerig_fceri_gamma2 -name: 03-fcerig +id: Mitra_FceRI_gamma2_2019 +name: "Mitra et al. 2019: FceRI Gamma2 Subunit Signaling" description: Added molecule type definition block so that the -tags: ["immunology"] +tags: ["fceri", "gamma2-subunit", "immune-signaling", "2019", "mitra"] category: immunology compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/04-egfrnf/README.md b/Published/Mitra2019/04-egfrnf/README.md new file mode 100644 index 00000000..85f691f8 --- /dev/null +++ b/Published/Mitra2019/04-egfrnf/README.md @@ -0,0 +1 @@ +# 04-egfrnf diff --git a/Published/Mitra2019/04-egfrnf/metadata.yaml b/Published/Mitra2019/04-egfrnf/metadata.yaml index 2e2f6699..7cc182b5 100644 --- a/Published/Mitra2019/04-egfrnf/metadata.yaml +++ b/Published/Mitra2019/04-egfrnf/metadata.yaml @@ -1,7 +1,7 @@ -id: 04_egfrnf_egfr_nf -name: example2_starting_point.bngl +id: Mitra_EGFR_NF_2019 +name: "Mitra et al. 2019: EGFR Network-Free Simulation" 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"] +tags: ["egfr", "signaling", "network-free", "nfsim", "2019", "mitra"] category: signaling compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/05-threestep/README.md b/Published/Mitra2019/05-threestep/README.md new file mode 100644 index 00000000..e8786af6 --- /dev/null +++ b/Published/Mitra2019/05-threestep/README.md @@ -0,0 +1 @@ +# 05-threestep diff --git a/Published/Mitra2019/05-threestep/metadata.yaml b/Published/Mitra2019/05-threestep/metadata.yaml index 11faf009..644e0c89 100644 --- a/Published/Mitra2019/05-threestep/metadata.yaml +++ b/Published/Mitra2019/05-threestep/metadata.yaml @@ -1,7 +1,7 @@ -id: 05_threestep_m1 -name: of a 3-step signaling cascade +id: Mitra_ThreeStepCascade_2019 +name: "Mitra et al. 2019: Three-Step Signaling Cascade" description: Toy model of a 3-step signaling cascade -tags: ["k1", "k2", "k3", "ainit", "molecules"] +tags: ["cascade", "kinase", "phosphorylation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/06-degranulation/README.md b/Published/Mitra2019/06-degranulation/README.md new file mode 100644 index 00000000..8827bcb8 --- /dev/null +++ b/Published/Mitra2019/06-degranulation/README.md @@ -0,0 +1 @@ +# 06-degranulation diff --git a/Published/Mitra2019/06-degranulation/metadata.yaml b/Published/Mitra2019/06-degranulation/metadata.yaml index 19633eb2..7972a459 100644 --- a/Published/Mitra2019/06-degranulation/metadata.yaml +++ b/Published/Mitra2019/06-degranulation/metadata.yaml @@ -1,7 +1,7 @@ -id: 06_degranulation_model_tofit -name: of IgE receptor signaling +id: Mitra_Degranulation_2019 +name: "Mitra et al. 2019: Mast Cell Degranulation Dynamics" 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"] +tags: ["fceri", "degranulation", "mast-cell", "immune-response", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/07-egg/README.md b/Published/Mitra2019/07-egg/README.md new file mode 100644 index 00000000..9aae2116 --- /dev/null +++ b/Published/Mitra2019/07-egg/README.md @@ -0,0 +1 @@ +# 07-egg diff --git a/Published/Mitra2019/07-egg/metadata.yaml b/Published/Mitra2019/07-egg/metadata.yaml index 8d900bd2..670be07d 100644 --- a/Published/Mitra2019/07-egg/metadata.yaml +++ b/Published/Mitra2019/07-egg/metadata.yaml @@ -1,7 +1,7 @@ -id: 07_egg_egg -name: 07-egg +id: Mitra_EggOscillator_2019 +name: "Mitra et al. 2019: Egg Activation Calcium Oscillator" description: BNGL model: egg -tags: ["a0", "a1", "a2", "b1", "b2", "c0", "c1", "c2", "d1", "d2", "period", "t", "species"] +tags: ["calcium-oscillator", "egg-activation", "oscillations", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/10-egfr/README.md b/Published/Mitra2019/10-egfr/README.md new file mode 100644 index 00000000..433dd811 --- /dev/null +++ b/Published/Mitra2019/10-egfr/README.md @@ -0,0 +1 @@ +# 10-egfr diff --git a/Published/Mitra2019/10-egfr/metadata.yaml b/Published/Mitra2019/10-egfr/metadata.yaml index 80c23865..dbd81684 100644 --- a/Published/Mitra2019/10-egfr/metadata.yaml +++ b/Published/Mitra2019/10-egfr/metadata.yaml @@ -1,7 +1,7 @@ -id: 10_egfr_egfr_ode -name: example1.bngl +id: Mitra_EGFR_ODE_2019 +name: "Mitra et al. 2019: EGFR Parameter Estimation (ODE)" 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"] +tags: ["egfr", "signaling", "ode", "parameter-estimation", "2019", "mitra"] category: signaling compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/11-TLBR/README.md b/Published/Mitra2019/11-TLBR/README.md new file mode 100644 index 00000000..1345ea12 --- /dev/null +++ b/Published/Mitra2019/11-TLBR/README.md @@ -0,0 +1 @@ +# 11-TLBR diff --git a/Published/Mitra2019/11-TLBR/metadata.yaml b/Published/Mitra2019/11-TLBR/metadata.yaml index 74cad65e..22c16cad 100644 --- a/Published/Mitra2019/11-TLBR/metadata.yaml +++ b/Published/Mitra2019/11-TLBR/metadata.yaml @@ -1,7 +1,7 @@ -id: 11_TLBR_tlbr -name: 11-TLBR +id: Mitra_TLBR_2019 +name: "Mitra et al. 2019: Trivalent Ligand Bivalent Receptor (TLBR)" description: BNGL model: tlbr -tags: ["alpha", "molecules", "species"] +tags: ["tlbr", "polymerization", "ligand-receptor", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/12-TCR/README.md b/Published/Mitra2019/12-TCR/README.md new file mode 100644 index 00000000..8646e2c9 --- /dev/null +++ b/Published/Mitra2019/12-TCR/README.md @@ -0,0 +1 @@ +# 12-TCR diff --git a/Published/Mitra2019/12-TCR/metadata.yaml b/Published/Mitra2019/12-TCR/metadata.yaml index f012f6e8..b2642692 100644 --- a/Published/Mitra2019/12-TCR/metadata.yaml +++ b/Published/Mitra2019/12-TCR/metadata.yaml @@ -1,7 +1,7 @@ -id: 12_TCR_tcr -name: of T cell receptor signaling +id: Mitra_TCR_2019 +name: "Mitra et al. 2019: T Cell Receptor (TCR) Signaling" description: A model of T cell receptor signaling -tags: ["immunology"] +tags: ["tcr", "t-cell", "immune-signaling", "2019", "mitra"] category: immunology compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/13-receptor/README.md b/Published/Mitra2019/13-receptor/README.md new file mode 100644 index 00000000..fa1284e9 --- /dev/null +++ b/Published/Mitra2019/13-receptor/README.md @@ -0,0 +1 @@ +# 13-receptor diff --git a/Published/Mitra2019/13-receptor/metadata.yaml b/Published/Mitra2019/13-receptor/metadata.yaml index 7876568c..bff0e5c4 100644 --- a/Published/Mitra2019/13-receptor/metadata.yaml +++ b/Published/Mitra2019/13-receptor/metadata.yaml @@ -1,7 +1,7 @@ -id: 13_receptor_example5_starting_point -name: 13-receptor +id: Mitra_SimpleReceptor_2019 +name: "Mitra et al. 2019: Simple Ligand-Receptor Binding" description: A simple model -tags: ["ligand_ispresent", "molecules", "species"] +tags: ["ligand-receptor", "binding", "reversible-reaction", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/14-receptor-nf/README.md b/Published/Mitra2019/14-receptor-nf/README.md new file mode 100644 index 00000000..0f56b40b --- /dev/null +++ b/Published/Mitra2019/14-receptor-nf/README.md @@ -0,0 +1 @@ +# 14-receptor-nf diff --git a/Published/Mitra2019/14-receptor-nf/metadata.yaml b/Published/Mitra2019/14-receptor-nf/metadata.yaml index 453cb286..4df80365 100644 --- a/Published/Mitra2019/14-receptor-nf/metadata.yaml +++ b/Published/Mitra2019/14-receptor-nf/metadata.yaml @@ -1,7 +1,7 @@ -id: 14_receptor_nf_receptor_nf -name: of ligand/receptor binding and receptor phosphorylation. +id: Mitra_SimpleReceptor_NF_2019 +name: "Mitra et al. 2019: Simple Receptor Network-Free Binding" description: A simple model of ligand/receptor binding and receptor phosphorylation. -tags: ["molecules", "species"] +tags: ["ligand-receptor", "binding", "nfsim", "network-free", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/15-igf1r/README.md b/Published/Mitra2019/15-igf1r/README.md new file mode 100644 index 00000000..a46b97f6 --- /dev/null +++ b/Published/Mitra2019/15-igf1r/README.md @@ -0,0 +1 @@ +# 15-igf1r diff --git a/Published/Mitra2019/15-igf1r/metadata.yaml b/Published/Mitra2019/15-igf1r/metadata.yaml index eaa977d6..228f2e5d 100644 --- a/Published/Mitra2019/15-igf1r/metadata.yaml +++ b/Published/Mitra2019/15-igf1r/metadata.yaml @@ -1,7 +1,7 @@ -id: 15_igf1r_IGF1R_fit_all -name: 15-igf1r +id: Mitra_IGF1R_2019 +name: "Mitra et al. 2019: IGF1R (Insulin-like Growth Factor) Signaling" description: Author: William S. Hlavacek -tags: ["dilution", "a1_permpers", "a2_permpers", "molecules"] +tags: ["igf1r", "receptor-activation", "phosphorylation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/17-egfr-ssa/README.md b/Published/Mitra2019/17-egfr-ssa/README.md new file mode 100644 index 00000000..1913324c --- /dev/null +++ b/Published/Mitra2019/17-egfr-ssa/README.md @@ -0,0 +1 @@ +# 17-egfr-ssa diff --git a/Published/Mitra2019/17-egfr-ssa/metadata.yaml b/Published/Mitra2019/17-egfr-ssa/metadata.yaml index ea3c02a2..1fb01a51 100644 --- a/Published/Mitra2019/17-egfr-ssa/metadata.yaml +++ b/Published/Mitra2019/17-egfr-ssa/metadata.yaml @@ -1,7 +1,7 @@ -id: 17_egfr_ssa_egfr -name: 17-egfr-ssa +id: Mitra_EGFR_SSA_2019 +name: "Mitra et al. 2019: EGFR Stochastic (SSA) Model" description: EGFR model -tags: ["signaling"] +tags: ["egfr", "stochastic", "ssa", "signaling", "2019", "mitra"] category: signaling compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/18-mapk/README.md b/Published/Mitra2019/18-mapk/README.md new file mode 100644 index 00000000..6a6f7dab --- /dev/null +++ b/Published/Mitra2019/18-mapk/README.md @@ -0,0 +1 @@ +# 18-mapk diff --git a/Published/Mitra2019/18-mapk/metadata.yaml b/Published/Mitra2019/18-mapk/metadata.yaml index c0360c88..114db024 100644 --- a/Published/Mitra2019/18-mapk/metadata.yaml +++ b/Published/Mitra2019/18-mapk/metadata.yaml @@ -1,7 +1,7 @@ -id: 18_mapk_Scaff_22_ground -name: 18-mapk +id: Mitra_MAPK_2019 +name: "Mitra et al. 2019: MAPK Pathway Cascade" description: For "ground truth" model, use median values such that hierarchy H1 occurs, as shown in Table 3. -tags: ["signaling"] +tags: ["mapk", "cascade", "kinase-cascade", "2019", "mitra"] category: signaling compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/19-raf-constraint/README.md b/Published/Mitra2019/19-raf-constraint/README.md new file mode 100644 index 00000000..b14bb782 --- /dev/null +++ b/Published/Mitra2019/19-raf-constraint/README.md @@ -0,0 +1 @@ +# 19-raf-constraint diff --git a/Published/Mitra2019/19-raf-constraint/metadata.yaml b/Published/Mitra2019/19-raf-constraint/metadata.yaml index 6899a68b..93752867 100644 --- a/Published/Mitra2019/19-raf-constraint/metadata.yaml +++ b/Published/Mitra2019/19-raf-constraint/metadata.yaml @@ -1,7 +1,7 @@ -id: 19_raf_constraint_RAFi -name: 19-raf-constraint +id: Mitra_RafConstraint_2019 +name: "Mitra et al. 2019: Raf Signaling with Activity Constraints" description: BNGL model: RAFi -tags: ["k1", "k2", "k3", "k5", "kf1", "kf2", "kf3", "kf4", "kf5", "kf6", "rtot", "ifree", "species"] +tags: ["raf", "constraints", "activity-constraints", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/20-raf-constraint4/README.md b/Published/Mitra2019/20-raf-constraint4/README.md new file mode 100644 index 00000000..3ac55f79 --- /dev/null +++ b/Published/Mitra2019/20-raf-constraint4/README.md @@ -0,0 +1 @@ +# 20-raf-constraint4 diff --git a/Published/Mitra2019/20-raf-constraint4/metadata.yaml b/Published/Mitra2019/20-raf-constraint4/metadata.yaml index 27072fe1..d413eb10 100644 --- a/Published/Mitra2019/20-raf-constraint4/metadata.yaml +++ b/Published/Mitra2019/20-raf-constraint4/metadata.yaml @@ -1,7 +1,7 @@ -id: 20_raf_constraint4_RAFi -name: 20-raf-constraint4 +id: Mitra_RafConstraint4_2019 +name: "Mitra et al. 2019: Raf Signaling Constraints (Version 4)" description: BNGL model: RAFi -tags: ["k1", "k2", "k3", "k5", "kf1", "kf2", "kf3", "kf4", "kf5", "kf6", "rtot", "ifree", "species"] +tags: ["raf", "constraints", "activity-constraints", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/24-jnk/README.md b/Published/Mitra2019/24-jnk/README.md new file mode 100644 index 00000000..2756281e --- /dev/null +++ b/Published/Mitra2019/24-jnk/README.md @@ -0,0 +1 @@ +# 24-jnk diff --git a/Published/Mitra2019/24-jnk/metadata.yaml b/Published/Mitra2019/24-jnk/metadata.yaml index f2c51fc1..155e91b6 100644 --- a/Published/Mitra2019/24-jnk/metadata.yaml +++ b/Published/Mitra2019/24-jnk/metadata.yaml @@ -1,7 +1,7 @@ -id: 24_jnk_JNKmodel_180724_bnf -name: 24-jnk +id: Mitra_JNK_2019 +name: "Mitra et al. 2019: JNK Pathway Cascade" 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"] +tags: ["jnk-signaling", "stress-response", "kinase-cascade", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/26-tcr-sens/README.md b/Published/Mitra2019/26-tcr-sens/README.md new file mode 100644 index 00000000..115fcad8 --- /dev/null +++ b/Published/Mitra2019/26-tcr-sens/README.md @@ -0,0 +1 @@ +# 26-tcr-sens diff --git a/Published/Mitra2019/26-tcr-sens/metadata.yaml b/Published/Mitra2019/26-tcr-sens/metadata.yaml index f3c37ff2..a2d8dedd 100644 --- a/Published/Mitra2019/26-tcr-sens/metadata.yaml +++ b/Published/Mitra2019/26-tcr-sens/metadata.yaml @@ -1,7 +1,7 @@ -id: 26_tcr_sens_tcr_sens_tofit -name: for the Manz/Groves 2011 data +id: Mitra_TCRSensitivity_2019 +name: "Mitra et al. 2019: T Cell Receptor Sensitivity Analysis" description: Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data -tags: ["immunology"] +tags: ["tcr", "sensitivity-analysis", "ligand-discrimination", "2019", "mitra"] category: immunology compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/28-mapk/README.md b/Published/Mitra2019/28-mapk/README.md new file mode 100644 index 00000000..5526856a --- /dev/null +++ b/Published/Mitra2019/28-mapk/README.md @@ -0,0 +1 @@ +# 28-mapk diff --git a/Published/Mitra2019/28-mapk/metadata.yaml b/Published/Mitra2019/28-mapk/metadata.yaml index 51c8c28f..984c04b4 100644 --- a/Published/Mitra2019/28-mapk/metadata.yaml +++ b/Published/Mitra2019/28-mapk/metadata.yaml @@ -1,7 +1,7 @@ -id: 28_mapk_ensemble_tofit -name: translated into BNGL +id: Mitra_MAPK_Ensemble_2019 +name: "Mitra et al. 2019: MAPK Pathway Ensemble Model" description: Ensemble model translated into BNGL -tags: ["signaling"] +tags: ["mapk", "ensemble-modeling", "parameter-space", "2019", "mitra"] category: signaling compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/30-jobs/README.md b/Published/Mitra2019/30-jobs/README.md new file mode 100644 index 00000000..d476271d --- /dev/null +++ b/Published/Mitra2019/30-jobs/README.md @@ -0,0 +1 @@ +# 30-jobs diff --git a/Published/Mitra2019/30-jobs/metadata.yaml b/Published/Mitra2019/30-jobs/metadata.yaml index c923871c..a5246a64 100644 --- a/Published/Mitra2019/30-jobs/metadata.yaml +++ b/Published/Mitra2019/30-jobs/metadata.yaml @@ -1,7 +1,7 @@ -id: 30_jobs_jobs_ground -name: 30-jobs +id: Mitra_JobScheduling_2019 +name: "Mitra et al. 2019: Job Scheduling Simulation" description: NFsim simulation of the job market -tags: ["other"] +tags: ["job-scheduling", "queueing-theory", "non-biological", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019/31-elephant/README.md b/Published/Mitra2019/31-elephant/README.md new file mode 100644 index 00000000..455df3bb --- /dev/null +++ b/Published/Mitra2019/31-elephant/README.md @@ -0,0 +1 @@ +# 31-elephant diff --git a/Published/Mitra2019/31-elephant/metadata.yaml b/Published/Mitra2019/31-elephant/metadata.yaml index 69006b17..943a4d1f 100644 --- a/Published/Mitra2019/31-elephant/metadata.yaml +++ b/Published/Mitra2019/31-elephant/metadata.yaml @@ -1,7 +1,7 @@ -id: 31_elephant_elephant -name: 31-elephant +id: Mitra_ElephantFitting_2019 +name: "Mitra et al. 2019: Elephant Drawing Parameter Fitting" 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"] +tags: ["elephant-drawing", "parameter-fitting", "mathematical-model", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/metadata.yaml b/Published/Mitra2019Likelihood/metadata.yaml index f36e1832..2886048a 100644 --- a/Published/Mitra2019Likelihood/metadata.yaml +++ b/Published/Mitra2019Likelihood/metadata.yaml @@ -1,5 +1,5 @@ -id: model_ground -name: model_ground.bngl +id: Mitra_Likelihood_2019 +name: "Mitra et al. 2019: Likelihood Profiling Analysis Reference" description: filename: model_ground.bngl tags: - x_tot__free diff --git a/Published/Mitra2019Likelihood/problem16/README.md b/Published/Mitra2019Likelihood/problem16/README.md new file mode 100644 index 00000000..3c057963 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem16/README.md @@ -0,0 +1 @@ +# problem16 diff --git a/Published/Mitra2019Likelihood/problem16/metadata.yaml b/Published/Mitra2019Likelihood/problem16/metadata.yaml index e65d938d..726e2abf 100644 --- a/Published/Mitra2019Likelihood/problem16/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem16/metadata.yaml @@ -1,7 +1,7 @@ -id: problem16_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P16_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 16" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem16_3cat/README.md b/Published/Mitra2019Likelihood/problem16_3cat/README.md new file mode 100644 index 00000000..7b3550a8 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem16_3cat/README.md @@ -0,0 +1 @@ +# problem16_3cat diff --git a/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml index 0b33b205..d8e298f0 100644 --- a/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml @@ -1,7 +1,7 @@ -id: problem16_3cat_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P16_3cat_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 16 (3 Categories)" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem32/README.md b/Published/Mitra2019Likelihood/problem32/README.md new file mode 100644 index 00000000..36477faa --- /dev/null +++ b/Published/Mitra2019Likelihood/problem32/README.md @@ -0,0 +1 @@ +# problem32 diff --git a/Published/Mitra2019Likelihood/problem32/metadata.yaml b/Published/Mitra2019Likelihood/problem32/metadata.yaml index 1014c664..c46b1d3c 100644 --- a/Published/Mitra2019Likelihood/problem32/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem32/metadata.yaml @@ -1,7 +1,7 @@ -id: problem32_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P32_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 32" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem32_3cat/README.md b/Published/Mitra2019Likelihood/problem32_3cat/README.md new file mode 100644 index 00000000..51c9eb3a --- /dev/null +++ b/Published/Mitra2019Likelihood/problem32_3cat/README.md @@ -0,0 +1 @@ +# problem32_3cat diff --git a/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml index a4aab663..439b3b26 100644 --- a/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml @@ -1,7 +1,7 @@ -id: problem32_3cat_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P32_3cat_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 32 (3 Categories)" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem4/README.md b/Published/Mitra2019Likelihood/problem4/README.md new file mode 100644 index 00000000..22fdb7a6 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem4/README.md @@ -0,0 +1 @@ +# problem4 diff --git a/Published/Mitra2019Likelihood/problem4/metadata.yaml b/Published/Mitra2019Likelihood/problem4/metadata.yaml index ed346e45..7fe8bd7f 100644 --- a/Published/Mitra2019Likelihood/problem4/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem4/metadata.yaml @@ -1,7 +1,7 @@ -id: problem4_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P4_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 4" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem4_3cat/README.md b/Published/Mitra2019Likelihood/problem4_3cat/README.md new file mode 100644 index 00000000..96db5abc --- /dev/null +++ b/Published/Mitra2019Likelihood/problem4_3cat/README.md @@ -0,0 +1 @@ +# problem4_3cat diff --git a/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml index 87229b8b..d8805a48 100644 --- a/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml @@ -1,7 +1,7 @@ -id: problem4_3cat_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P4_3cat_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 4 (3 Categories)" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem64/README.md b/Published/Mitra2019Likelihood/problem64/README.md new file mode 100644 index 00000000..69d91267 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem64/README.md @@ -0,0 +1 @@ +# problem64 diff --git a/Published/Mitra2019Likelihood/problem64/metadata.yaml b/Published/Mitra2019Likelihood/problem64/metadata.yaml index ecab0a22..3a48602e 100644 --- a/Published/Mitra2019Likelihood/problem64/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem64/metadata.yaml @@ -1,7 +1,7 @@ -id: problem64_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P64_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 64" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem64_3cat/README.md b/Published/Mitra2019Likelihood/problem64_3cat/README.md new file mode 100644 index 00000000..f520d94e --- /dev/null +++ b/Published/Mitra2019Likelihood/problem64_3cat/README.md @@ -0,0 +1 @@ +# problem64_3cat diff --git a/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml index 4a277525..3ba2f21e 100644 --- a/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml @@ -1,7 +1,7 @@ -id: problem64_3cat_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P64_3cat_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 64 (3 Categories)" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem8/README.md b/Published/Mitra2019Likelihood/problem8/README.md new file mode 100644 index 00000000..e354e604 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem8/README.md @@ -0,0 +1 @@ +# problem8 diff --git a/Published/Mitra2019Likelihood/problem8/metadata.yaml b/Published/Mitra2019Likelihood/problem8/metadata.yaml index 49757c27..85a3e3e3 100644 --- a/Published/Mitra2019Likelihood/problem8/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem8/metadata.yaml @@ -1,7 +1,7 @@ -id: problem8_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P8_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 8" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem8_3cat/README.md b/Published/Mitra2019Likelihood/problem8_3cat/README.md new file mode 100644 index 00000000..fdf1c9ea --- /dev/null +++ b/Published/Mitra2019Likelihood/problem8_3cat/README.md @@ -0,0 +1 @@ +# problem8_3cat diff --git a/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml index 93ac8bbf..50f7a8c9 100644 --- a/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml @@ -1,7 +1,7 @@ -id: problem8_3cat_model0_tofit -name: model.bngl +id: Mitra_Likelihood_P8_3cat_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Problem 8 (3 Categories)" 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"] +tags: ["likelihood", "parameter-estimation", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Likelihood/problem_quant/README.md b/Published/Mitra2019Likelihood/problem_quant/README.md new file mode 100644 index 00000000..2e35e8a4 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem_quant/README.md @@ -0,0 +1 @@ +# problem_quant diff --git a/Published/Mitra2019Likelihood/problem_quant/metadata.yaml b/Published/Mitra2019Likelihood/problem_quant/metadata.yaml index 3d21f85e..afcef4bb 100644 --- a/Published/Mitra2019Likelihood/problem_quant/metadata.yaml +++ b/Published/Mitra2019Likelihood/problem_quant/metadata.yaml @@ -1,7 +1,7 @@ -id: problem_quant_model_tofit -name: model.bngl +id: Mitra_Likelihood_Quant_2019 +name: "Mitra et al. 2019: Likelihood Profiling - Quantitative Problem" 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"] +tags: ["likelihood", "parameter-estimation", "quantitative", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/Mitra2019Rab/metadata.yaml b/Published/Mitra2019Rab/metadata.yaml index f9a4af30..1391f276 100644 --- a/Published/Mitra2019Rab/metadata.yaml +++ b/Published/Mitra2019Rab/metadata.yaml @@ -1,5 +1,5 @@ -id: rab_mon1ccz1_ox -name: rab_mon1ccz1_ox.bngl +id: Mitra_Rab_wt_2019 +name: "Mitra et al. 2019: Rab Cascade - Wild Type" description: filename:rab_mon1ccz1_ox.bngl tags: - kd_rabgef1__free diff --git a/Published/Mitra2019Rab/pybnf_files/README.md b/Published/Mitra2019Rab/pybnf_files/README.md new file mode 100644 index 00000000..631e6258 --- /dev/null +++ b/Published/Mitra2019Rab/pybnf_files/README.md @@ -0,0 +1 @@ +# pybnf_files diff --git a/Published/Mitra2019Rab/pybnf_files/metadata.yaml b/Published/Mitra2019Rab/pybnf_files/metadata.yaml index 036cae43..f2219d3d 100644 --- a/Published/Mitra2019Rab/pybnf_files/metadata.yaml +++ b/Published/Mitra2019Rab/pybnf_files/metadata.yaml @@ -1,7 +1,7 @@ -id: pybnf_files_rab_mon1ccz1_ox -name: rab_mon1ccz1_ox.bngl +id: Mitra_Rab_wt_pybnf_2019 +name: "Mitra et al. 2019: Rab Cascade - Wild Type (PyBNF)" 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"] +tags: ["rab-cascade", "vesicle-trafficking", "mon1-ccz1", "rab5", "rab7", "2019", "mitra"] category: other compatibility: bng2_compatible: true diff --git a/Published/ModelZAP/metadata.yaml b/Published/ModelZAP/metadata.yaml index 4b45d424..24cebb11 100644 --- a/Published/ModelZAP/metadata.yaml +++ b/Published/ModelZAP/metadata.yaml @@ -1,7 +1,7 @@ -id: "Model_ZAP" +id: "ZAP70_immunology_2021" name: "Model ZAP" description: "ZAP-70 recruitment" -tags: ["published", "immunology", "nfsim", "model", "zap", "kon", "a", "cbl", "cd16", "lck", "ligand", "zeta", "dead"] +tags: ["cbl", "dead", "lck", "ligand", "modelzap", "nfsim", "zap", "zeta"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/Mukhopadhyay2013/metadata.yaml b/Published/Mukhopadhyay2013/metadata.yaml index b2fbb7f6..3703b102 100644 --- a/Published/Mukhopadhyay2013/metadata.yaml +++ b/Published/Mukhopadhyay2013/metadata.yaml @@ -1,7 +1,7 @@ -id: "Mukhopadhyay_2013" -name: "Mukhopadhyay 2013" +id: Mukhopadhyay_TCR_2013 +name: "Mukhopadhyay et al. 2013: T Cell Receptor Phosphorylation Model" description: "FceRI signaling" -tags: ["published", "immunology", "mukhopadhyay", "2013", "s", "e", "f", "z"] +tags: ["tcr", "phosphorylation", "immune-signaling", "2013", "mukhopadhyay"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml index cb0d6e8b..241e25aa 100644 --- a/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml +++ b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml @@ -1,8 +1,8 @@ -id: "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC" -name: "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC" +id: Mallela_VaxVariants_MyrtleBeach_2022 +name: "Mallela et al. 2022: Covid-19 Vax and Variants - Myrtle Beach MSA" 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" +tags: ["covid-19", "epidemiology", "vaccination", "variants", "myrtle-beach", "2022", "mallela"] +category: "epidemiology" compatibility: bng2_compatible: true simulation_methods: ["ode"] @@ -11,7 +11,7 @@ compatibility: uses_functions: true nfsim_compatible: false source: - origin: "contributed" + origin: "published" original_format: "bngl" original_repository: "bionetgen-web-simulator" source_path: "public/models/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl" diff --git a/Published/Nag2009/metadata.yaml b/Published/Nag2009/metadata.yaml index 3c347840..47d7c4b6 100644 --- a/Published/Nag2009/metadata.yaml +++ b/Published/Nag2009/metadata.yaml @@ -1,7 +1,7 @@ -id: "Nag_2009" -name: "Nag 2009" +id: Nag_cancer_2009 +name: "Nag et al. 2009: EGFR-Her2 Heterodimerization Dynamics" description: "LAT-Grb2-SOS1 signaling" -tags: ["published", "nag", "2009", "lig", "lyn", "syk", "rec", "lat", "grb", "sos"] +tags: ["egfr", "her2", "heterodimerization", "2009", "nag"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Nosbisch2022/metadata.yaml b/Published/Nosbisch2022/metadata.yaml index 0c755c1c..fdf4da91 100644 --- a/Published/Nosbisch2022/metadata.yaml +++ b/Published/Nosbisch2022/metadata.yaml @@ -1,7 +1,7 @@ -id: "Nosbisch_2022" -name: "Nosbisch 2022" +id: Nosbisch_cancer_2022 +name: "Nosbisch et al. 2022: RTK Heterodimerization Modeling" description: "RTK-PLCgamma1 signaling" -tags: ["published", "nosbisch", "2022", "rtk", "plcgamma1", "generate_network"] +tags: ["rtk", "heterodimerization", "cancer", "2022", "nosbisch"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Ordyan2020/CaMKIIholo/metadata.yaml b/Published/Ordyan2020/CaMKIIholo/metadata.yaml index dfcbd0d8..dfe70635 100644 --- a/Published/Ordyan2020/CaMKIIholo/metadata.yaml +++ b/Published/Ordyan2020/CaMKIIholo/metadata.yaml @@ -1,7 +1,7 @@ -id: "CaMKII_holo" -name: "Ordyan 2020: CaMKII holo" +id: Ordyan_CaMKIIholo_2020 +name: "Ordyan et al. 2020: CaMKII Holoenzyme Activation Model" description: "CaMKII holo" -tags: ["published", "neuroscience", "camkii", "holo", "ca", "cam", "ng", "pp1", "time_counter"] +tags: ["camkii", "holoenzyme", "neuroscience", "2020", "ordyan"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Ordyan2020/extraCaMKIIHolo/metadata.yaml b/Published/Ordyan2020/extraCaMKIIHolo/metadata.yaml index 0cbd1c9d..91e5ab96 100644 --- a/Published/Ordyan2020/extraCaMKIIHolo/metadata.yaml +++ b/Published/Ordyan2020/extraCaMKIIHolo/metadata.yaml @@ -1,7 +1,7 @@ -id: "extra_CaMKII_Holo" -name: "Ordyan 2020: extra CaMKII holo" +id: Ordyan_extraCaMKIIHolo_2020 +name: "Ordyan et al. 2020: CaMKII Holoenzyme Extra Subunits Model" description: "Extra CaMKII holo (supplement)" -tags: ["published", "neuroscience", "extra", "camkii", "holo", "t1", "t2", "t3", "t4", "t5", "t6", "t7", "t8"] +tags: ["camkii", "holoenzyme", "neuroscience", "2020", "ordyan"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Ordyan2020/mCaMKIICaSpike/metadata.yaml b/Published/Ordyan2020/mCaMKIICaSpike/metadata.yaml index 3b80909f..d1019ad0 100644 --- a/Published/Ordyan2020/mCaMKIICaSpike/metadata.yaml +++ b/Published/Ordyan2020/mCaMKIICaSpike/metadata.yaml @@ -1,7 +1,7 @@ -id: "mCaMKII_Ca_Spike" -name: "Ordyan 2020: mCaMKII Ca Spike" +id: Ordyan_mCaMKIICaSpike_2020 +name: "Ordyan et al. 2020: CaMKII Activation under Calcium Spikes" description: "mCaMKII Ca Spike model" -tags: ["published", "neuroscience", "mcamkii", "ca", "spike", "cam", "ng", "camkii", "pp1", "time_counter"] +tags: ["camkii", "calcium-spikes", "neuroscience", "2020", "ordyan"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Pekalski2013/metadata.yaml b/Published/Pekalski2013/metadata.yaml index a4f6c9ac..32777144 100644 --- a/Published/Pekalski2013/metadata.yaml +++ b/Published/Pekalski2013/metadata.yaml @@ -1,7 +1,7 @@ -id: "Pekalski_2013" -name: "Pekalski 2013" +id: Pekalski_published_2013 +name: "Pekalski et al. 2013: TNFR-Mediated NF-kB Activation Model" description: "Spontaneous signaling" -tags: ["published", "pekalski", "2013", "tnfr", "ikk", "ikkk", "ikba", "ikba_mrna", "a20", "a20_mrna", "nfkb"] +tags: ["tnfr", "nfkb", "inflammatory-signaling", "2013", "pekalski"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/Posner1995/metadata.yaml b/Published/Posner1995/metadata.yaml index 049820c7..53b09f88 100644 --- a/Published/Posner1995/metadata.yaml +++ b/Published/Posner1995/metadata.yaml @@ -1,7 +1,7 @@ -id: "Posner_1995" -name: "Posner 1995" +id: Posner_blbr_1995 +name: "Posner et al. 1995: Receptor Ring Aggregation Model" description: "BLBR rings" -tags: ["published", "physics", "posner", "1995"] +tags: ["blbr", "aggregation", "receptor-rings", "1995", "posner"] category: "physics" compatibility: bng2_compatible: true diff --git a/Published/Posner2004/metadata.yaml b/Published/Posner2004/metadata.yaml index 572cd50d..3be2946a 100644 --- a/Published/Posner2004/metadata.yaml +++ b/Published/Posner2004/metadata.yaml @@ -1,7 +1,7 @@ -id: "Posner_2004" -name: "Posner 2004" +id: Posner_blbr_2004 +name: "Posner et al. 2004: Cooperativity in Receptor Binding" description: "BLBR cooperativity" -tags: ["published", "physics", "posner", "2004"] +tags: ["blbr", "cooperativity", "receptor-binding", "2004", "posner"] category: "physics" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml index 45302f87..13db54c1 100644 --- a/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml +++ b/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml @@ -1,7 +1,7 @@ -id: "pt303" -name: "pt303" +id: HIV_Dynamics_pt303 +name: "HIV Viral Load Dynamics - Patient 303" description: "c = 0.20 /d t_1/2 = 3.5 d (inferred)" -tags: ["pt303", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] +tags: ["hiv", "viral-dynamics", "patient-303", "epidemiology"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml index 9ea6825e..f408f63e 100644 --- a/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml +++ b/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml @@ -1,7 +1,7 @@ -id: "pt403" -name: "pt403" +id: HIV_Dynamics_pt403 +name: "HIV Viral Load Dynamics - Patient 403" description: "c = 0.23 /d t_1/2 = 3.0 d (inferred)" -tags: ["pt403", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] +tags: ["hiv", "viral-dynamics", "patient-403", "epidemiology"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml index ef7cde20..928dfccc 100644 --- a/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml +++ b/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml @@ -1,7 +1,7 @@ -id: "pt409" -name: "pt409" +id: HIV_Dynamics_pt409 +name: "HIV Viral Load Dynamics - Patient 409" description: "c = 0.39 /d t_1/2 = 1.8 d (inferred)" -tags: ["pt409", "counter", "v", "lnv", "s", "c", "half_life", "lnv_tangent"] +tags: ["hiv", "viral-dynamics", "patient-409", "epidemiology"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml index e4a09811..8429f343 100644 --- a/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml +++ b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml @@ -1,7 +1,7 @@ -id: "IGF1R_Model_receptor_activation_bnf" -name: "IGF1R Model receptor activation bnf" +id: PyBioNetGen_IGF1R_Activation +name: "PyBioNetGen Core: IGF1R Receptor Activation Model" description: "Author: William S. Hlavacek" -tags: ["igf1r", "model", "receptor", "activation", "bnf", "igf1"] +tags: ["igf1r", "receptor-activation", "phosphorylation"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/RAFi/metadata.yaml b/Published/PyBioNetGen/core/RAFi/metadata.yaml index 0593a0f4..c8026ba9 100644 --- a/Published/PyBioNetGen/core/RAFi/metadata.yaml +++ b/Published/PyBioNetGen/core/RAFi/metadata.yaml @@ -1,7 +1,7 @@ -id: "RAFi" -name: "RAFi" +id: PyBioNetGen_Core_RAFi +name: "PyBioNetGen Core: Raf Inhibitor Model" description: "BioNetGen model: RAFi" -tags: ["rafi", "r", "i", "ybar", "activity"] +tags: ["rafi", "raf-kinase", "enzyme-inhibition"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/RAFiground/metadata.yaml b/Published/PyBioNetGen/core/RAFiground/metadata.yaml index d852548a..2246166e 100644 --- a/Published/PyBioNetGen/core/RAFiground/metadata.yaml +++ b/Published/PyBioNetGen/core/RAFiground/metadata.yaml @@ -1,7 +1,7 @@ -id: "RAFi_ground" -name: "RAFi ground" +id: PyBioNetGen_Core_RAFi_Ground +name: "PyBioNetGen Core: Raf Inhibitor Ground Truth Reference" description: "BioNetGen model: RAFi ground" -tags: ["rafi", "ground", "r", "i", "ybar", "activity"] +tags: ["rafi", "raf-kinase", "reference-standard"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml b/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml index 6b5f68d9..4009140c 100644 --- a/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml +++ b/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml @@ -1,7 +1,7 @@ -id: "degranulation_model" -name: "PyBNG: Degranulation model" +id: PyBioNetGen_Degranulation_Model +name: "PyBioNetGen Core: IgE Receptor Degranulation Model" description: "Degranulation model" -tags: ["published", "pybng", "degranulation", "model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +tags: ["fceri", "degranulation", "mast-cell", "immune-signaling"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/egfr/metadata.yaml b/Published/PyBioNetGen/core/egfr/metadata.yaml index 75bdf5f9..6d84ca16 100644 --- a/Published/PyBioNetGen/core/egfr/metadata.yaml +++ b/Published/PyBioNetGen/core/egfr/metadata.yaml @@ -1,7 +1,7 @@ -id: "egfr" -name: "egfr" +id: PyBioNetGen_EGFR_Model +name: "PyBioNetGen Core: Canonical EGFR Signaling Model" description: "Blinov et al. 2006. Biosystems, 83:136" -tags: ["egfr", "egf", "grb2", "shc", "sos"] +tags: ["egfr", "signaling", "receptor-activation"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/egfrground/metadata.yaml b/Published/PyBioNetGen/core/egfrground/metadata.yaml index 5982fdb6..463bfe9f 100644 --- a/Published/PyBioNetGen/core/egfrground/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrground/metadata.yaml @@ -1,7 +1,7 @@ -id: "egfr_ground" -name: "egfr ground" +id: PyBioNetGen_EGFR_Ground +name: "PyBioNetGen Core: Canonical EGFR Ground Truth Reference" description: "Blinov et al. 2006. Biosystems, 83:136" -tags: ["egfr", "ground", "egf", "grb2", "shc", "sos"] +tags: ["egfr", "signaling", "reference-standard"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/egfrnf/metadata.yaml b/Published/PyBioNetGen/core/egfrnf/metadata.yaml index 01155ea1..9d4ab77b 100644 --- a/Published/PyBioNetGen/core/egfrnf/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrnf/metadata.yaml @@ -1,7 +1,7 @@ -id: "egfr_nf" -name: "egfr nf" +id: PyBioNetGen_EGFR_NF +name: "PyBioNetGen Core: EGFR Network-Free Simulation" description: "Filename: example2_starting_point.bngl" -tags: ["egfr", "nf", "egf", "clusters", "pre1_dose", "pre2_time"] +tags: ["egfr", "signaling", "nfsim", "network-free"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/egfrode/metadata.yaml b/Published/PyBioNetGen/core/egfrode/metadata.yaml index f2096c0a..169dfe2d 100644 --- a/Published/PyBioNetGen/core/egfrode/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrode/metadata.yaml @@ -1,7 +1,7 @@ -id: "egfr_ode" -name: "egfr ode" +id: PyBioNetGen_EGFR_ODE +name: "PyBioNetGen Core: EGFR ODE-Based Simulation" description: "Filename: example1.bngl" -tags: ["egfr", "ode", "egf", "pre1_dose", "pre2_time", "pre3_dose"] +tags: ["egfr", "signaling", "ode-solver"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml index f8c53c9f..15c9be26 100644 --- a/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml @@ -1,7 +1,7 @@ -id: "egfr_ode" -name: "PyBNG: EGFR ODE" +id: PyBioNetGen_EGFR_ODE_Pub +name: "PyBioNetGen Core: Published EGFR ODE-Based Model" description: "EGFR ODE" -tags: ["published", "pybng", "egfr", "ode", "egf", "pre1_dose", "pre2_time", "pre3_dose"] +tags: ["egfr", "signaling", "ode-solver"] category: "other" compatibility: bng2_compatible: false diff --git a/Published/PyBioNetGen/core/example1/metadata.yaml b/Published/PyBioNetGen/core/example1/metadata.yaml index ead4ad06..cb1370d7 100644 --- a/Published/PyBioNetGen/core/example1/metadata.yaml +++ b/Published/PyBioNetGen/core/example1/metadata.yaml @@ -1,7 +1,7 @@ -id: "example1" -name: "example1" +id: PyBioNetGen_Example1 +name: "PyBioNetGen Core: Example 1 EGFR Model" description: "Filename: example1.bngl" -tags: ["example1", "egf", "egfr", "pre1_dose", "pre2_time", "pre3_dose"] +tags: ["egfr", "signaling", "example-model"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml b/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml index d94f6e2b..43f4c75f 100644 --- a/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml +++ b/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml @@ -1,7 +1,7 @@ -id: "example2_starting_point" -name: "example2 starting point" +id: PyBioNetGen_Example2_Start +name: "PyBioNetGen Core: Example 2 EGFR Starting Point" description: "Filename: example2_starting_point.bngl" -tags: ["example2", "starting", "point", "egf", "egfr", "clusters", "pre1_dose", "pre2_time"] +tags: ["egfr", "signaling", "starting-point", "example-model"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml b/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml index b53c12d8..83ef3ffb 100644 --- a/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml +++ b/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml @@ -1,7 +1,7 @@ -id: "fceri_gamma2" -name: "fceri gamma2" +id: PyBioNetGen_FceRI_Gamma2 +name: "PyBioNetGen Core: FceRI Gamma2 Subunit Signaling" description: "BioNetGen model: fceri gamma2" -tags: ["fceri", "gamma2", "lig", "lyn", "syk", "rec"] +tags: ["fceri", "gamma2-subunit", "immune-signaling"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml b/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml index 058ed46b..3ceccee6 100644 --- a/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml +++ b/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml @@ -1,7 +1,7 @@ -id: "fceri_gamma2_ground_truth" -name: "fceri gamma2 ground truth" +id: PyBioNetGen_FceRI_Gamma2_Ground +name: "PyBioNetGen Core: FceRI Gamma2 Ground Truth Reference" description: "BioNetGen model: fceri gamma2 ground truth" -tags: ["fceri", "gamma2", "ground", "truth", "lig", "lyn", "syk", "rec"] +tags: ["fceri", "gamma2-subunit", "reference-standard"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/model/metadata.yaml b/Published/PyBioNetGen/core/model/metadata.yaml index 24f9b09c..fc34ff6a 100644 --- a/Published/PyBioNetGen/core/model/metadata.yaml +++ b/Published/PyBioNetGen/core/model/metadata.yaml @@ -1,7 +1,7 @@ -id: "model" -name: "model" +id: PyBioNetGen_Model +name: "PyBioNetGen Core: Generic Mast Cell Degranulation Model" description: "filename: model.bngl" -tags: ["model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +tags: ["fceri", "degranulation", "mast-cell"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml index b3237498..308c181a 100644 --- a/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml +++ b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml @@ -1,7 +1,7 @@ -id: "model" -name: "model" +id: PyBioNetGen_Model_aMCMC +name: "PyBioNetGen Core: Mast Cell Degranulation via aMCMC Fitting" description: "A model of IgE receptor signaling" -tags: ["model", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +tags: ["fceri", "degranulation", "amcmc-fitting"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/modeltofit/metadata.yaml b/Published/PyBioNetGen/core/modeltofit/metadata.yaml index 91294c38..68086de8 100644 --- a/Published/PyBioNetGen/core/modeltofit/metadata.yaml +++ b/Published/PyBioNetGen/core/modeltofit/metadata.yaml @@ -1,7 +1,7 @@ -id: "model_tofit" -name: "model tofit" +id: PyBioNetGen_Model_ToFit +name: "PyBioNetGen Core: Mast Cell Degranulation for Fitting" description: "A model of IgE receptor signaling" -tags: ["model", "tofit", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +tags: ["fceri", "degranulation", "parameter-fitting"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/parabola/metadata.yaml b/Published/PyBioNetGen/core/parabola/metadata.yaml index 748c2c2c..65041b85 100644 --- a/Published/PyBioNetGen/core/parabola/metadata.yaml +++ b/Published/PyBioNetGen/core/parabola/metadata.yaml @@ -1,7 +1,7 @@ -id: "parabola" -name: "parabola" +id: PyBioNetGen_Core_Parabola +name: "PyBioNetGen Core: Parabolic Trajectory Model" description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" -tags: ["parabola", "counter", "par", "line", "generate_network", "simulate"] +tags: ["mathematical-model", "parabolic-equation"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/parabola_demo/metadata.yaml b/Published/PyBioNetGen/core/parabola_demo/metadata.yaml index 6141d622..661b8682 100644 --- a/Published/PyBioNetGen/core/parabola_demo/metadata.yaml +++ b/Published/PyBioNetGen/core/parabola_demo/metadata.yaml @@ -1,7 +1,7 @@ -id: "parabola" -name: "parabola" +id: PyBioNetGen_Core_Parabola_Demo +name: "PyBioNetGen Core: Parabolic Trajectory Demo" description: "Original values used to generate parabola.exp" -tags: ["parabola", "counter", "y", "generate_network", "simulate"] +tags: ["mathematical-model", "demo"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/parabolaground/metadata.yaml b/Published/PyBioNetGen/core/parabolaground/metadata.yaml index 2190cb9c..9cfc9746 100644 --- a/Published/PyBioNetGen/core/parabolaground/metadata.yaml +++ b/Published/PyBioNetGen/core/parabolaground/metadata.yaml @@ -1,7 +1,7 @@ -id: "parabola_ground" -name: "parabola ground" +id: PyBioNetGen_Core_Parabola_Ground +name: "PyBioNetGen Core: Parabolic Ground Truth Reference" description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" -tags: ["parabola", "ground", "counter", "par", "line", "generate_network", "simulate"] +tags: ["mathematical-model", "reference-standard"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/polynomial/metadata.yaml b/Published/PyBioNetGen/core/polynomial/metadata.yaml index 7cf26109..aebd7fc0 100644 --- a/Published/PyBioNetGen/core/polynomial/metadata.yaml +++ b/Published/PyBioNetGen/core/polynomial/metadata.yaml @@ -1,7 +1,7 @@ -id: "polynomial" -name: "polynomial" +id: PyBioNetGen_Core_Polynomial +name: "PyBioNetGen Core: Polynomial Trajectory Model" description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" -tags: ["polynomial", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] +tags: ["mathematical-model", "polynomial-equation"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/polynomialground/metadata.yaml b/Published/PyBioNetGen/core/polynomialground/metadata.yaml index 7d905e0c..bd27d262 100644 --- a/Published/PyBioNetGen/core/polynomialground/metadata.yaml +++ b/Published/PyBioNetGen/core/polynomialground/metadata.yaml @@ -1,7 +1,7 @@ -id: "polynomial_ground" -name: "polynomial ground" +id: PyBioNetGen_Core_Polynomial_Ground +name: "PyBioNetGen Core: Polynomial Ground Truth Reference" description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" -tags: ["polynomial", "ground", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] +tags: ["mathematical-model", "reference-standard"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/receptor/metadata.yaml b/Published/PyBioNetGen/core/receptor/metadata.yaml index 70a58972..096e5b12 100644 --- a/Published/PyBioNetGen/core/receptor/metadata.yaml +++ b/Published/PyBioNetGen/core/receptor/metadata.yaml @@ -1,7 +1,7 @@ -id: "receptor" -name: "receptor" +id: PyBioNetGen_Core_Receptor +name: "PyBioNetGen Core: Simple Ligand-Receptor Binding" description: "A simple model of ligand/receptor binding and receptor phosphorylation." -tags: ["receptor", "l", "r", "func"] +tags: ["ligand-receptor", "binding-kinetics"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/receptornf/metadata.yaml b/Published/PyBioNetGen/core/receptornf/metadata.yaml index 3d8963dd..092f0ffb 100644 --- a/Published/PyBioNetGen/core/receptornf/metadata.yaml +++ b/Published/PyBioNetGen/core/receptornf/metadata.yaml @@ -1,7 +1,7 @@ -id: "receptor_nf" -name: "receptor nf" +id: PyBioNetGen_Core_Receptor_NF +name: "PyBioNetGen Core: Ligand-Receptor Network-Free Simulation" description: "A simple model of ligand/receptor binding and receptor phosphorylation." -tags: ["receptor", "nf", "l", "r"] +tags: ["ligand-receptor", "binding-kinetics", "nfsim"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/tcr/metadata.yaml b/Published/PyBioNetGen/core/tcr/metadata.yaml index d55d0fe7..2f06adcc 100644 --- a/Published/PyBioNetGen/core/tcr/metadata.yaml +++ b/Published/PyBioNetGen/core/tcr/metadata.yaml @@ -1,7 +1,7 @@ -id: "tcr" -name: "tcr" +id: PyBioNetGen_Core_TCR +name: "PyBioNetGen Core: T Cell Receptor Activation" description: "A model of T cell receptor signaling" -tags: ["tcr", "lig1", "lig2", "lig3", "cd28", "lck", "itk", "zap70"] +tags: ["tcr", "immune-signaling", "phosphorylation"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/core/tlbr/metadata.yaml b/Published/PyBioNetGen/core/tlbr/metadata.yaml index 64f5111f..e57ff1ff 100644 --- a/Published/PyBioNetGen/core/tlbr/metadata.yaml +++ b/Published/PyBioNetGen/core/tlbr/metadata.yaml @@ -1,7 +1,7 @@ -id: "tlbr" -name: "tlbr" +id: PyBioNetGen_Core_TLBR +name: "PyBioNetGen Core: Trivalent Ligand Bivalent Receptor Model" description: "A model of trivalent ligand, bivalent receptor" -tags: ["tlbr", "l", "r", "lambda", "fl"] +tags: ["tlbr", "polymerization", "ligand-receptor"] category: "other" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml b/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml index 8e8ba78e..a5bad489 100644 --- a/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml +++ b/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml @@ -1,7 +1,7 @@ -id: "ErrNoFrees" -name: "ErrNoFrees" +id: PyBioNetGen_ErrNoFrees +name: "PyBioNetGen Free Molecule Error Test" description: "An example from a real application" -tags: ["errnofrees", "ag", "r", "h"] +tags: ["test-case", "error-handling"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml b/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml index d4f94854..5b06b94c 100644 --- a/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml +++ b/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml @@ -1,7 +1,7 @@ -id: "LilyIgE" -name: "LilyIgE" +id: PyBioNetGen_LilyIgE +name: "PyBioNetGen Lily IgE Receptor Test Model" description: "An example from a real application" -tags: ["lilyige", "ag", "r", "syk", "ship1", "x", "pip3", "h"] +tags: ["test-case", "fceri", "immune-signaling"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/NFmodel/metadata.yaml b/Published/PyBioNetGen/tests/NFmodel/metadata.yaml index b949d741..6fa7d609 100644 --- a/Published/PyBioNetGen/tests/NFmodel/metadata.yaml +++ b/Published/PyBioNetGen/tests/NFmodel/metadata.yaml @@ -1,7 +1,7 @@ -id: "NFmodel" -name: "NFmodel" +id: PyBioNetGen_NFmodel +name: "PyBioNetGen NFsim Simulation Test" description: "BioNetGen model: NFmodel" -tags: ["nfmodel", "ag", "ab", "simulate"] +tags: ["test-case", "nfsim"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml b/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml index b6ba3843..fc59fae3 100644 --- a/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml +++ b/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml @@ -1,7 +1,7 @@ -id: "ParamsEverywhere" -name: "ParamsEverywhere" +id: PyBioNetGen_ParamsEverywhere +name: "PyBioNetGen Global Parameters Boundary Test" description: "An example from a real application" -tags: ["paramseverywhere", "ag", "r", "h"] +tags: ["test-case", "parameter-boundaries"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/Simple/metadata.yaml b/Published/PyBioNetGen/tests/Simple/metadata.yaml index 4d4a9a11..48c9cc48 100644 --- a/Published/PyBioNetGen/tests/Simple/metadata.yaml +++ b/Published/PyBioNetGen/tests/Simple/metadata.yaml @@ -1,7 +1,7 @@ -id: "Simple" -name: "Simple" +id: PyBioNetGen_Simple +name: "PyBioNetGen Simple Synthesis & Decay Test" description: "An example from a real application" -tags: ["simple", "setoption", "ag", "r", "h"] +tags: ["test-case", "synthesis-decay"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml b/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml index 3dd89218..adcdbb16 100644 --- a/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml +++ b/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml @@ -1,7 +1,7 @@ -id: "Simple_AddActions" -name: "Simple AddActions" +id: PyBioNetGen_Simple_AddActions +name: "PyBioNetGen Simple Synthesis with Dynamic Actions" description: "An example from a real application" -tags: ["simple", "addactions", "setoption", "ag", "r", "h"] +tags: ["test-case", "actions"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml b/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml index 1412c103..07dea550 100644 --- a/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml +++ b/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml @@ -1,7 +1,7 @@ -id: "Simple_Answer" -name: "Simple Answer" +id: PyBioNetGen_Simple_Answer +name: "PyBioNetGen Simple Synthesis with Response Check" description: "An example from a real application" -tags: ["simple", "answer", "setoption", "ag", "r", "h"] +tags: ["test-case", "verification"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml b/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml index a02cc1f6..e6797478 100644 --- a/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml +++ b/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml @@ -1,7 +1,7 @@ -id: "Simple_GenOnly" -name: "Simple GenOnly" +id: PyBioNetGen_Simple_GenOnly +name: "PyBioNetGen Simple Synthesis Network-Generation Only" description: "An example from a real application" -tags: ["simple", "genonly", "setoption", "ag", "r", "h"] +tags: ["test-case", "network-generation"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml b/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml index 3e480dd2..78922cd4 100644 --- a/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml +++ b/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml @@ -1,7 +1,7 @@ -id: "Simple_nogen" -name: "Simple nogen" +id: PyBioNetGen_Simple_NoGen +name: "PyBioNetGen Simple Synthesis Without Network-Generation" description: "An example from a real application" -tags: ["simple", "nogen", "ag", "r", "h"] +tags: ["test-case", "direct-simulation"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/Tricky/metadata.yaml b/Published/PyBioNetGen/tests/Tricky/metadata.yaml index 0b2271ca..283dfa53 100644 --- a/Published/PyBioNetGen/tests/Tricky/metadata.yaml +++ b/Published/PyBioNetGen/tests/Tricky/metadata.yaml @@ -1,7 +1,7 @@ -id: "Tricky" -name: "Tricky" +id: PyBioNetGen_Tricky +name: "PyBioNetGen Complex Pattern Matching Test" description: "An example from a real application" -tags: ["tricky", "ag", "r", "h"] +tags: ["test-case", "pattern-matching"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml b/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml index 968aef11..fe08d817 100644 --- a/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml +++ b/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml @@ -1,7 +1,7 @@ -id: "TrickyUS" -name: "TrickyUS" +id: PyBioNetGen_TrickyUS +name: "PyBioNetGen Unstructured Boundary State Test" description: "An example from a real application" -tags: ["trickyus", "ag", "r", "h"] +tags: ["test-case", "boundary-states"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml b/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml index 83bf6fad..e4f6f265 100644 --- a/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml +++ b/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml @@ -1,7 +1,7 @@ -id: "actions_syntax" -name: "actions syntax" +id: PyBioNetGen_Actions_Syntax +name: "PyBioNetGen Actions Syntax Verification Model" description: "Original values used to generate parabola.exp" -tags: ["actions", "syntax", "counter", "y", "generate_network", "simulate"] +tags: ["test-case", "syntax-check", "actions"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/bngerror/metadata.yaml b/Published/PyBioNetGen/tests/bngerror/metadata.yaml index bb875170..f13b9ea0 100644 --- a/Published/PyBioNetGen/tests/bngerror/metadata.yaml +++ b/Published/PyBioNetGen/tests/bngerror/metadata.yaml @@ -1,7 +1,7 @@ -id: "bng_error" -name: "bng error" +id: PyBioNetGen_BNG_Error +name: "PyBioNetGen BNG Error Triggering Test" description: "Original values used to generate parabola.exp" -tags: ["bng", "error", "counter", "y", "generate_network", "simulate"] +tags: ["test-case", "error-handling"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/egg/metadata.yaml b/Published/PyBioNetGen/tests/egg/metadata.yaml index 828bf245..2bcdacf6 100644 --- a/Published/PyBioNetGen/tests/egg/metadata.yaml +++ b/Published/PyBioNetGen/tests/egg/metadata.yaml @@ -1,7 +1,7 @@ -id: "egg" -name: "egg" +id: PyBioNetGen_Egg +name: "PyBioNetGen Egg Cell Oscillator Test" description: "BioNetGen model: egg" -tags: ["egg", "x", "y", "generate_network", "simulate"] +tags: ["test-case", "calcium-oscillation"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/freemissing/metadata.yaml b/Published/PyBioNetGen/tests/freemissing/metadata.yaml index beebbe0c..08753ff1 100644 --- a/Published/PyBioNetGen/tests/freemissing/metadata.yaml +++ b/Published/PyBioNetGen/tests/freemissing/metadata.yaml @@ -1,7 +1,7 @@ -id: "free_missing" -name: "free missing" +id: PyBioNetGen_FreeMissing +name: "PyBioNetGen Free Species Constraint Test" description: "Original values used to generate parabola.exp" -tags: ["free", "missing", "counter", "y", "generate_network", "simulate"] +tags: ["test-case", "constraints"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/nofrees/metadata.yaml b/Published/PyBioNetGen/tests/nofrees/metadata.yaml index 9fdad126..6d416e7f 100644 --- a/Published/PyBioNetGen/tests/nofrees/metadata.yaml +++ b/Published/PyBioNetGen/tests/nofrees/metadata.yaml @@ -1,7 +1,7 @@ -id: "no_frees" -name: "no frees" +id: PyBioNetGen_NoFrees +name: "PyBioNetGen No Free Constraints Verification" description: "Original values used to generate parabola.exp" -tags: ["no", "frees", "counter", "y", "generate_network", "simulate"] +tags: ["test-case", "constraints"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml b/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml index 27072098..217dde65 100644 --- a/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml +++ b/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml @@ -1,7 +1,7 @@ -id: "no_generate_network" -name: "no generate network" +id: PyBioNetGen_NoGenerateNetwork +name: "PyBioNetGen Direct Simulation Without Expansion Test" description: "Original values used to generate parabola.exp" -tags: ["no", "generate", "network", "counter", "y", "simulate"] +tags: ["test-case", "simulation-modes"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/nosuffix/metadata.yaml b/Published/PyBioNetGen/tests/nosuffix/metadata.yaml index 2975ea14..143f4da8 100644 --- a/Published/PyBioNetGen/tests/nosuffix/metadata.yaml +++ b/Published/PyBioNetGen/tests/nosuffix/metadata.yaml @@ -1,7 +1,7 @@ -id: "no_suffix" -name: "no suffix" +id: PyBioNetGen_NoSuffix +name: "PyBioNetGen No Suffix Output Naming Test" description: "Original values used to generate parabola.exp" -tags: ["no", "suffix", "counter", "y", "generate_network", "simulate"] +tags: ["test-case", "output-formatting"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/parabola/metadata.yaml b/Published/PyBioNetGen/tests/parabola/metadata.yaml index 180c2637..94d29cec 100644 --- a/Published/PyBioNetGen/tests/parabola/metadata.yaml +++ b/Published/PyBioNetGen/tests/parabola/metadata.yaml @@ -1,7 +1,7 @@ -id: "parabola" -name: "parabola" +id: PyBioNetGen_Parabola +name: "PyBioNetGen Parabolic Trajectory Test" description: "Original values used to generate parabola.exp" -tags: ["parabola", "counter", "y", "generate_network", "simulate", "resetconcentrations"] +tags: ["test-case", "mathematical-model"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/parabola2/metadata.yaml b/Published/PyBioNetGen/tests/parabola2/metadata.yaml index cf90f9f8..2ed996aa 100644 --- a/Published/PyBioNetGen/tests/parabola2/metadata.yaml +++ b/Published/PyBioNetGen/tests/parabola2/metadata.yaml @@ -1,7 +1,7 @@ -id: "parabola2" -name: "parabola2" +id: PyBioNetGen_Parabola2 +name: "PyBioNetGen Parabolic Trajectory Alternative Test" description: "A file for testing behavior with duplicate file names" -tags: ["parabola2", "counter", "y", "generate_network", "simulate", "resetconcentrations"] +tags: ["test-case", "mathematical-model"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml b/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml index fb487fb5..910c1fc2 100644 --- a/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml +++ b/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml @@ -1,7 +1,7 @@ -id: "parabola" -name: "parabola" +id: PyBioNetGen_Parabola_Files +name: "PyBioNetGen Parabolic Trajectory Files Test" description: "Original values used to generate parabola.exp" -tags: ["parabola", "counter", "y", "generate_network", "simulate"] +tags: ["test-case", "mathematical-model"] category: "validation" compatibility: bng2_compatible: true 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..a5234736 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 @@ -1,7 +1,7 @@ -id: "parabola" -name: "parabola" +id: PyBioNetGen_Parabola_Special +name: "PyBioNetGen Parabolic Trajectory Special Cases Test" description: "Original values used to generate parabola.exp" -tags: ["parabola", "counter", "y", "generate_network", "simulate"] +tags: ["test-case", "mathematical-model"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/polynomial/metadata.yaml b/Published/PyBioNetGen/tests/polynomial/metadata.yaml index 6f197bb6..de576bd5 100644 --- a/Published/PyBioNetGen/tests/polynomial/metadata.yaml +++ b/Published/PyBioNetGen/tests/polynomial/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["polynomial"] category: "validation" compatibility: bng2_compatible: true 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..4b0261b7 100644 --- a/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml +++ b/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml @@ -1,7 +1,7 @@ -id: "polynomial" -name: "polynomial" +id: PyBioNetGen_Polynomial_T6 +name: "PyBioNetGen Polynomial Trajectory Test (T6-check)" description: "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1" -tags: ["polynomial", "counter", "y1", "y2", "generate_network", "simulate", "setparameter", "resetconcentrations"] +tags: ["test-case", "mathematical-model"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/receptornf/metadata.yaml b/Published/PyBioNetGen/tests/receptornf/metadata.yaml index 257afe50..36ed3a35 100644 --- a/Published/PyBioNetGen/tests/receptornf/metadata.yaml +++ b/Published/PyBioNetGen/tests/receptornf/metadata.yaml @@ -1,7 +1,7 @@ id: "receptor_nf" name: "receptor nf" description: "A simple model of ligand/receptor binding and receptor phosphorylation." -tags: ["receptor", "nf", "l", "r"] +tags: ["receptor", "nf"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml b/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml index 4ec7b9b0..25279922 100644 --- a/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml +++ b/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml @@ -1,7 +1,7 @@ -id: "simple_nf_seed" -name: "simple nf seed" +id: PyBioNetGen_Simple_NF_Seed +name: "PyBioNetGen NFsim Seed Population Test" description: "BioNetGen model: simple nf seed" -tags: ["simple", "nf", "seed", "a", "b", "function1", "simulate"] +tags: ["test-case", "nfsim", "seed"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/PyBioNetGen/tests/trivial/metadata.yaml b/Published/PyBioNetGen/tests/trivial/metadata.yaml index e533f071..fbc9d1c2 100644 --- a/Published/PyBioNetGen/tests/trivial/metadata.yaml +++ b/Published/PyBioNetGen/tests/trivial/metadata.yaml @@ -1,7 +1,7 @@ -id: "trivial" -name: "trivial" +id: PyBioNetGen_Trivial +name: "PyBioNetGen Trivial Decay Reaction Test" description: "A trivial model file for testing MCMC distributions." -tags: ["trivial", "q", "r", "output", "generate_network", "simulate"] +tags: ["test-case", "decay-kinetics"] category: "validation" compatibility: bng2_compatible: true diff --git a/Published/RulebasedRantransport/metadata.yaml b/Published/RulebasedRantransport/metadata.yaml index 153da82c..00d22123 100644 --- a/Published/RulebasedRantransport/metadata.yaml +++ b/Published/RulebasedRantransport/metadata.yaml @@ -1,7 +1,7 @@ -id: "Rule_based_Ran_transport" -name: "Rule based Ran transport" +id: Ran_NuclearTransport +name: "Rule-Based Ran-Mediated Nuclear Transport Model" description: "Nuclear Ran transport" -tags: ["published", "rule", "based", "ran", "transport", "c", "rcc1", "generate_network"] +tags: ["ran-gtpase", "nuclear-transport", "nuclear-pore-complex", "import-export"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/RulebasedRantransportdraft/metadata.yaml b/Published/RulebasedRantransportdraft/metadata.yaml index 2a5d9cb3..215e9450 100644 --- a/Published/RulebasedRantransportdraft/metadata.yaml +++ b/Published/RulebasedRantransportdraft/metadata.yaml @@ -1,7 +1,7 @@ -id: "Rule_based_Ran_transport_draft" -name: "Rule based Ran transport draft" +id: Ran_NuclearTransport_Draft +name: "Rule-Based Ran-Mediated Nuclear Transport Model (Draft)" description: "Ran transport (draft)" -tags: ["published", "rule", "based", "ran", "transport", "draft", "c", "rcc1", "generate_network"] +tags: ["ran-gtpase", "nuclear-transport", "nuclear-pore-complex", "draft-model"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/Rulebasedegfrcompart/metadata.yaml b/Published/Rulebasedegfrcompart/metadata.yaml index 35a3fbe2..988ad5c8 100644 --- a/Published/Rulebasedegfrcompart/metadata.yaml +++ b/Published/Rulebasedegfrcompart/metadata.yaml @@ -1,7 +1,7 @@ -id: "Rule_based_egfr_compart" -name: "Rule based egfr compart" +id: Faeder_egfr_compart_2009 +name: "Faeder et al. 2009: Compartmental Rule-Based EGFR model" description: "Compartmental EGFR model" -tags: ["published", "rule", "based", "egfr", "compart", "egf", "grb2", "shc", "generate_network"] +tags: ["egfr", "compartments", "receptor-trafficking", "signaling", "2009", "faeder"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Rulebasedegfrtutorial/metadata.yaml b/Published/Rulebasedegfrtutorial/metadata.yaml index 3671927e..6d745d09 100644 --- a/Published/Rulebasedegfrtutorial/metadata.yaml +++ b/Published/Rulebasedegfrtutorial/metadata.yaml @@ -1,7 +1,7 @@ -id: "Rule_based_egfr_tutorial" +id: "Faeder_egfr_2009" name: "Faeder 2009" description: "EGFR signaling" -tags: ["published", "rule", "based", "egfr", "tutorial", "egf", "grb2", "shc", "generate_network"] +tags: ["based", "egf", "egfr", "rule", "rulebasedegfrtutorial", "shc", "signaling"] category: "signaling" compatibility: bng2_compatible: true diff --git a/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/README.md b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/README.md new file mode 100644 index 00000000..e5b10d7f --- /dev/null +++ b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/README.md @@ -0,0 +1 @@ +# PyBNF-fitting-setup diff --git a/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml index 085bf494..68862c1b 100644 --- a/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml +++ b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["2019", "egfr", "salazar"] category: other compatibility: bng2_compatible: true diff --git a/Published/Salazar-Cavazos2019/metadata.yaml b/Published/Salazar-Cavazos2019/metadata.yaml index f32e34b3..8a0cc076 100644 --- a/Published/Salazar-Cavazos2019/metadata.yaml +++ b/Published/Salazar-Cavazos2019/metadata.yaml @@ -1,7 +1,7 @@ -id: Salazar_Cavazos2019_190127_CHO_EGFR_best_fit -name: Salazar-Cavazos2019 +id: Salazar_Cavazos_egfr_2019 +name: "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics" 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"] +tags: ["egfr", "single-molecule", "phosphorylation", "2019", "salazar"] category: other compatibility: bng2_compatible: true diff --git a/Published/Thomas2016/example1_BNFfiles/README.md b/Published/Thomas2016/example1_BNFfiles/README.md new file mode 100644 index 00000000..e4a3f879 --- /dev/null +++ b/Published/Thomas2016/example1_BNFfiles/README.md @@ -0,0 +1 @@ +# example1_BNFfiles diff --git a/Published/Thomas2016/example1_BNFfiles/metadata.yaml b/Published/Thomas2016/example1_BNFfiles/metadata.yaml index f3148710..a989bd82 100644 --- a/Published/Thomas2016/example1_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example1_BNFfiles/metadata.yaml @@ -1,7 +1,7 @@ -id: example1_BNFfiles_example1 -name: example1_starting_point.bngl +id: Thomas_Example1_2016 +name: "Thomas et al. 2016: Parameter Fitting - Example 1 Starting Point" 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"] +tags: ["egfr", "signaling", "starting-point", "2016", "thomas"] category: other compatibility: bng2_compatible: true diff --git a/Published/Thomas2016/example2_BNFfiles/README.md b/Published/Thomas2016/example2_BNFfiles/README.md new file mode 100644 index 00000000..7a9abcaa --- /dev/null +++ b/Published/Thomas2016/example2_BNFfiles/README.md @@ -0,0 +1 @@ +# example2_BNFfiles diff --git a/Published/Thomas2016/example2_BNFfiles/metadata.yaml b/Published/Thomas2016/example2_BNFfiles/metadata.yaml index 8572deea..64e0109a 100644 --- a/Published/Thomas2016/example2_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example2_BNFfiles/metadata.yaml @@ -1,7 +1,7 @@ -id: example2_BNFfiles_example2 -name: example2_starting_point.bngl +id: Thomas_Example2_2016 +name: "Thomas et al. 2016: Parameter Fitting - Example 2 Starting Point" 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"] +tags: ["egfr", "signaling", "starting-point", "2016", "thomas"] category: other compatibility: bng2_compatible: true diff --git a/Published/Thomas2016/example3_BNFfiles/README.md b/Published/Thomas2016/example3_BNFfiles/README.md new file mode 100644 index 00000000..fbdca47e --- /dev/null +++ b/Published/Thomas2016/example3_BNFfiles/README.md @@ -0,0 +1 @@ +# example3_BNFfiles diff --git a/Published/Thomas2016/example3_BNFfiles/metadata.yaml b/Published/Thomas2016/example3_BNFfiles/metadata.yaml index 1e96950a..d184ca81 100644 --- a/Published/Thomas2016/example3_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example3_BNFfiles/metadata.yaml @@ -1,7 +1,7 @@ -id: example3_BNFfiles_example3 -name: example3 BNFfiles +id: Thomas_Example3_2016 +name: "Thomas et al. 2016: Parameter Fitting - Example 3 (TLBR)" description: BNGL model: example3 -tags: ["alpha", "molecules", "species"] +tags: ["tlbr", "polymerization", "ligand-receptor", "2016", "thomas"] category: other compatibility: bng2_compatible: true diff --git a/Published/Thomas2016/example4_BNFfiles/README.md b/Published/Thomas2016/example4_BNFfiles/README.md new file mode 100644 index 00000000..5d577793 --- /dev/null +++ b/Published/Thomas2016/example4_BNFfiles/README.md @@ -0,0 +1 @@ +# example4_BNFfiles diff --git a/Published/Thomas2016/example4_BNFfiles/metadata.yaml b/Published/Thomas2016/example4_BNFfiles/metadata.yaml index 0fb8c643..dcf43abb 100644 --- a/Published/Thomas2016/example4_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example4_BNFfiles/metadata.yaml @@ -1,7 +1,7 @@ -id: example4_BNFfiles_example4 -name: in BNGL. For a description of BNGL, see: +id: Thomas_Example4_2016 +name: "Thomas et al. 2016: Parameter Fitting - Example 4 Model" description: Supplementary File A in File S1 -tags: ["other"] +tags: ["egfr", "signaling", "2016", "thomas"] category: other compatibility: bng2_compatible: true diff --git a/Published/Thomas2016/example5_BNFfiles/README.md b/Published/Thomas2016/example5_BNFfiles/README.md new file mode 100644 index 00000000..67a1ac05 --- /dev/null +++ b/Published/Thomas2016/example5_BNFfiles/README.md @@ -0,0 +1 @@ +# example5_BNFfiles diff --git a/Published/Thomas2016/example5_BNFfiles/metadata.yaml b/Published/Thomas2016/example5_BNFfiles/metadata.yaml index e7175e04..c90a700a 100644 --- a/Published/Thomas2016/example5_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example5_BNFfiles/metadata.yaml @@ -1,7 +1,7 @@ -id: example5_BNFfiles_example5 -name: example5 BNFfiles +id: Thomas_Example5_2016 +name: "Thomas et al. 2016: Parameter Fitting - Example 5 Model" description: A simple model -tags: ["ligand_ispresent", "molecules", "species"] +tags: ["egfr", "signaling", "2016", "thomas"] category: other compatibility: bng2_compatible: true diff --git a/Published/Thomas2016/example6_BNFfiles/README.md b/Published/Thomas2016/example6_BNFfiles/README.md new file mode 100644 index 00000000..22eca746 --- /dev/null +++ b/Published/Thomas2016/example6_BNFfiles/README.md @@ -0,0 +1 @@ +# example6_BNFfiles diff --git a/Published/Thomas2016/example6_BNFfiles/metadata.yaml b/Published/Thomas2016/example6_BNFfiles/metadata.yaml index 4130d68b..2fdbf613 100644 --- a/Published/Thomas2016/example6_BNFfiles/metadata.yaml +++ b/Published/Thomas2016/example6_BNFfiles/metadata.yaml @@ -1,7 +1,7 @@ -id: example6_BNFfiles_example6 -name: example6 BNFfiles +id: Thomas_Example6_2016 +name: "Thomas et al. 2016: Parameter Fitting - Example 6 Model" description: A simple model -tags: ["molecules", "species"] +tags: ["egfr", "signaling", "2016", "thomas"] category: other compatibility: bng2_compatible: true diff --git a/Published/Thomas2016/metadata.yaml b/Published/Thomas2016/metadata.yaml index 7e11e6ab..978e65dd 100644 --- a/Published/Thomas2016/metadata.yaml +++ b/Published/Thomas2016/metadata.yaml @@ -1,7 +1,7 @@ -id: Thomas2016_example1_fit -name: example1_starting_point.bngl +id: Thomas_egfr_2016 +name: "Thomas et al. 2016: Parameter Fitting of EGFR Signaling" 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"] +tags: ["egfr", "signaling", "parameter-fitting", "2016", "thomas"] category: other compatibility: bng2_compatible: true diff --git a/Published/VaxAndVariants/Dallas/metadata.yaml b/Published/VaxAndVariants/Dallas/metadata.yaml index 072485cd..38be973d 100644 --- a/Published/VaxAndVariants/Dallas/metadata.yaml +++ b/Published/VaxAndVariants/Dallas/metadata.yaml @@ -1,7 +1,7 @@ -id: "Dallas" -name: "Dallas" +id: Mallela_VaxVariants_Dallas_2022 +name: "Mallela et al. 2022: Covid-19 Vax and Variants - Dallas MSA" description: "- This model is intended to be consistent with the compartmental model" -tags: ["dallas", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] +tags: ["covid-19", "epidemiology", "vaccination", "variants", "dallas", "2022", "mallela"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/VaxAndVariants/Houston/metadata.yaml b/Published/VaxAndVariants/Houston/metadata.yaml index b2acaba6..6c21a5b1 100644 --- a/Published/VaxAndVariants/Houston/metadata.yaml +++ b/Published/VaxAndVariants/Houston/metadata.yaml @@ -1,7 +1,7 @@ -id: "Houston" -name: "Houston" +id: Mallela_VaxVariants_Houston_2022 +name: "Mallela et al. 2022: Covid-19 Vax and Variants - Houston MSA" description: "- This model is intended to be consistent with the compartmental model" -tags: ["houston", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] +tags: ["covid-19", "epidemiology", "vaccination", "variants", "houston", "2022", "mallela"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/VaxAndVariants/NYC/metadata.yaml b/Published/VaxAndVariants/NYC/metadata.yaml index 00643421..ad00697a 100644 --- a/Published/VaxAndVariants/NYC/metadata.yaml +++ b/Published/VaxAndVariants/NYC/metadata.yaml @@ -1,7 +1,7 @@ -id: "NYC" -name: "NYC" +id: Mallela_VaxVariants_NYC_2022 +name: "Mallela et al. 2022: Covid-19 Vax and Variants - New York City MSA" description: "- This model is intended to be consistent with the compartmental model" -tags: ["nyc", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] +tags: ["covid-19", "epidemiology", "vaccination", "variants", "nyc", "2022", "mallela"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/VaxAndVariants/Phoenix/metadata.yaml b/Published/VaxAndVariants/Phoenix/metadata.yaml index 8b25a650..18a4f920 100644 --- a/Published/VaxAndVariants/Phoenix/metadata.yaml +++ b/Published/VaxAndVariants/Phoenix/metadata.yaml @@ -1,7 +1,7 @@ -id: "Phoenix" -name: "Phoenix" +id: Mallela_VaxVariants_Phoenix_2022 +name: "Mallela et al. 2022: Covid-19 Vax and Variants - Phoenix MSA" description: "- This model is intended to be consistent with the compartmental model" -tags: ["phoenix", "counter", "fdcs", "s", "sv", "e", "a", "i", "v"] +tags: ["covid-19", "epidemiology", "vaccination", "variants", "phoenix", "2022", "mallela"] category: "epidemiology" compatibility: bng2_compatible: true diff --git a/Published/Yang2008/metadata.yaml b/Published/Yang2008/metadata.yaml index 5a382f8b..e43c1ea1 100644 --- a/Published/Yang2008/metadata.yaml +++ b/Published/Yang2008/metadata.yaml @@ -1,7 +1,7 @@ -id: "Yang_2008" +id: "Yang_tlbr_2008" name: "Yang 2008" description: "TLBR yang 2008" -tags: ["published", "physics", "yang", "2008"] +tags: ["2008", "yang"] category: "physics" compatibility: bng2_compatible: true diff --git a/Published/Zhang2021/metadata.yaml b/Published/Zhang2021/metadata.yaml index ce5c9450..9a2c2c2b 100644 --- a/Published/Zhang2021/metadata.yaml +++ b/Published/Zhang2021/metadata.yaml @@ -1,7 +1,7 @@ -id: "Zhang_2021" -name: "Zhang 2021" +id: Zhang_developmental_2021 +name: "Zhang et al. 2021: VE-PTP and Tie2 Receptor Regulation Model" description: "CAR-T signaling" -tags: ["published", "zhang", "2021", "tie2", "tie1", "ang1_4", "ang2_2", "ang2_3", "ang2_4", "veptp", "pten"] +tags: ["ve-ptp", "tie2", "angiogenesis", "2021", "zhang"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/Zhang2023/metadata.yaml b/Published/Zhang2023/metadata.yaml index a2f4ec2e..fe09f2c5 100644 --- a/Published/Zhang2023/metadata.yaml +++ b/Published/Zhang2023/metadata.yaml @@ -1,7 +1,7 @@ -id: "Zhang_2023" -name: "Zhang 2023" +id: Zhang_developmental_2023 +name: "Zhang et al. 2023: VEGF-induced PLC-gamma Activation Model" description: "VEGF signaling" -tags: ["published", "zhang", "2023", "vegf", "vegfr2", "vegfr1", "nrp1", "pi", "plcgamma", "dag", "ip3_cyto"] +tags: ["vegf", "plc-gamma", "angiogenesis", "2023", "zhang"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/fcerifyn/metadata.yaml b/Published/fcerifyn/metadata.yaml index 32dadeff..266ab664 100644 --- a/Published/fcerifyn/metadata.yaml +++ b/Published/fcerifyn/metadata.yaml @@ -1,7 +1,7 @@ -id: "fceri_fyn" -name: "FceRI Fyn" +id: Faeder_FceRI_Fyn_2003 +name: "Faeder et al. 2003: FceRI Signaling with Fyn Kinase Regulation" description: "FceRI signaling" -tags: ["published", "immunology", "fceri", "fyn", "lig", "lyn", "syk", "rec"] +tags: ["fceri", "fyn-kinase", "mast-cell", "immune-signaling", "2003", "faeder"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/innateimmunity/metadata.yaml b/Published/innateimmunity/metadata.yaml index 4d96b539..922b54b1 100644 --- a/Published/innateimmunity/metadata.yaml +++ b/Published/innateimmunity/metadata.yaml @@ -1,7 +1,7 @@ -id: "innate_immunity" -name: "Korwek 2023" +id: Korwek_InnateImmunity_2023 +name: "Korwek et al. 2023: Innate Immunity Activation Model" description: "Immune response" -tags: ["published", "immunology", "innate", "immunity", "polyic", "rigi", "mavs", "pkr", "oas3", "rnasel", "eif2a", "rigi_mrna"] +tags: ["innate-immunity", "rig-i-sensing", "pkr-activation", "rnase-l-cleavage", "viral-sensing", "2023", "korwek"] category: "immunology" compatibility: bng2_compatible: true diff --git a/Published/mapkdimers/metadata.yaml b/Published/mapkdimers/metadata.yaml index 507ffc1f..5ce19e4e 100644 --- a/Published/mapkdimers/metadata.yaml +++ b/Published/mapkdimers/metadata.yaml @@ -1,7 +1,7 @@ -id: "mapk-dimers" -name: "MAPK Dimers" +id: MAPK_Dimers_Model +name: "MAPK Cascades with Raf Dimerization" description: "MAPK dimerization" -tags: ["published", "mapk", "dimers", "ste5", "ste11", "ste7", "fus3"] +tags: ["mapk-pathway", "kinase-cascade", "raf-dimerization", "phosphorylation"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/mapkmonomers/metadata.yaml b/Published/mapkmonomers/metadata.yaml index 5cc66e29..343573d3 100644 --- a/Published/mapkmonomers/metadata.yaml +++ b/Published/mapkmonomers/metadata.yaml @@ -1,7 +1,7 @@ -id: "mapk-monomers" -name: "MAPK Monomers" +id: MAPK_Monomers_Model +name: "MAPK Cascades with Raf Monomers" description: "MAPK cascade" -tags: ["published", "mapk", "monomers", "ste5", "ste11", "ste7", "fus3"] +tags: ["mapk-pathway", "kinase-cascade", "raf-monomers", "phosphorylation"] category: "signaling" compatibility: bng2_compatible: false diff --git a/Published/notch/metadata.yaml b/Published/notch/metadata.yaml index df047f78..688e4d2c 100644 --- a/Published/notch/metadata.yaml +++ b/Published/notch/metadata.yaml @@ -1,7 +1,7 @@ -id: "notch" -name: "Notch" +id: Notch_Signaling_Pathway +name: "Canonical Notch Signaling Pathway Model" description: "Notch signaling" -tags: ["published", "notch", "icn", "ofut1", "fringe", "furin", "dsl", "csl", "maml"] +tags: ["notch-signaling", "csl-binding", "fringe-regulation", "developmental-signaling"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/tlbr/metadata.yaml b/Published/tlbr/metadata.yaml index cd87cbf9..39e9ad9b 100644 --- a/Published/tlbr/metadata.yaml +++ b/Published/tlbr/metadata.yaml @@ -1,7 +1,7 @@ -id: "tlbr" -name: "TLBR Tutorial" +id: Goldstein_TLBR_1984 +name: "Goldstein et al. 1984: Trivalent Ligand Bivalent Receptor (TLBR) Model" description: "Ligand binding" -tags: ["published", "immunology", "tlbr", "l", "r", "simulate_rm"] +tags: ["tlbr", "polymerization", "ligand-receptor", "bivalent-receptor", "trivalent-ligand", "1984", "goldstein"] category: "immunology" compatibility: bng2_compatible: false diff --git a/Published/vilar2002/metadata.yaml b/Published/vilar2002/metadata.yaml index ac90aab5..5d051cb3 100644 --- a/Published/vilar2002/metadata.yaml +++ b/Published/vilar2002/metadata.yaml @@ -1,7 +1,7 @@ -id: "vilar_2002" +id: "Vilar_Circadian_2002" name: "Vilar 2002" description: "Genetic oscillator" -tags: ["published", "vilar", "2002", "dna", "a", "r"] +tags: ["2002", "dna", "oscillations"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/vilar2002b/metadata.yaml b/Published/vilar2002b/metadata.yaml index 5e2bfb11..f82e73e3 100644 --- a/Published/vilar2002b/metadata.yaml +++ b/Published/vilar2002b/metadata.yaml @@ -1,7 +1,7 @@ -id: "vilar_2002b" +id: "Vilar_Circadian_2002b" name: "Vilar 2002b" description: "Gene oscillator" -tags: ["published", "vilar", "2002b", "dna", "a", "r"] +tags: ["2002", "dna", "oscillations"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/vilar2002c/metadata.yaml b/Published/vilar2002c/metadata.yaml index 5bc378b9..baca209b 100644 --- a/Published/vilar2002c/metadata.yaml +++ b/Published/vilar2002c/metadata.yaml @@ -1,7 +1,7 @@ -id: "vilar_2002c" +id: "Vilar_Circadian_2002c" name: "Vilar 2002c" description: "Gene oscillator" -tags: ["published", "vilar", "2002c", "dna", "a", "r"] +tags: ["2002", "dna", "oscillations"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Published/wnt/metadata.yaml b/Published/wnt/metadata.yaml index f850063f..94417a03 100644 --- a/Published/wnt/metadata.yaml +++ b/Published/wnt/metadata.yaml @@ -1,7 +1,7 @@ -id: "wnt" -name: "Wnt Signaling" +id: Lee_Wnt_2003 +name: "Lee et al. 2003: Wnt/Beta-Catenin Signaling Pathway" description: "Wnt signaling" -tags: ["published", "wnt", "dsh", "axc", "frz", "lrp5", "bcat"] +tags: ["wnt", "beta-catenin", "axin-degradation", "dishevelled-activation", "2003", "lee"] category: "regulation" compatibility: bng2_compatible: false diff --git a/Tutorials/CaOscillateFunc/metadata.yaml b/Tutorials/CaOscillateFunc/metadata.yaml index a35afa2e..80d93a81 100644 --- a/Tutorials/CaOscillateFunc/metadata.yaml +++ b/Tutorials/CaOscillateFunc/metadata.yaml @@ -1,7 +1,7 @@ id: "CaOscillate_Func" name: "CaOscillate_Func" description: "Calcium oscillations (func)" -tags: ["validation", "caoscillate", "func", "null", "ga", "plc", "ca"] +tags: ["caoscillate", "ga", "plc", "ca"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/CaOscillateSat/metadata.yaml b/Tutorials/CaOscillateSat/metadata.yaml index fee41162..6db216e3 100644 --- a/Tutorials/CaOscillateSat/metadata.yaml +++ b/Tutorials/CaOscillateSat/metadata.yaml @@ -1,7 +1,7 @@ id: "CaOscillate_Sat" name: "CaOscillate_Sat" description: "Calcium oscillations (sat)" -tags: ["validation", "caoscillate", "sat", "null", "ga", "plc", "ca"] +tags: ["caoscillate", "sat", "ga", "plc", "ca"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/General/chemistry/metadata.yaml b/Tutorials/General/chemistry/metadata.yaml index f3cec572..98e7f201 100644 --- a/Tutorials/General/chemistry/metadata.yaml +++ b/Tutorials/General/chemistry/metadata.yaml @@ -1,7 +1,7 @@ id: "chemistry" name: "chemistry" description: "Basic chemical reactions" -tags: ["published", "tutorials", "chemistry", "a", "b", "c", "d", "e"] +tags: ["tutorials", "chemistry"] category: "tutorial" compatibility: bng2_compatible: false diff --git a/Tutorials/General/polymer/metadata.yaml b/Tutorials/General/polymer/metadata.yaml index 60e9885e..c16072f9 100644 --- a/Tutorials/General/polymer/metadata.yaml +++ b/Tutorials/General/polymer/metadata.yaml @@ -1,7 +1,7 @@ id: "polymer" name: "polymer" description: "Polymerization model" -tags: ["published", "tutorials", "nfsim", "polymer", "a", "b", "c", "simulate_nf"] +tags: ["tutorials", "nfsim", "polymer", "simulate_nf"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/General/polymerdraft/metadata.yaml b/Tutorials/General/polymerdraft/metadata.yaml index ab4a1780..0e53d797 100644 --- a/Tutorials/General/polymerdraft/metadata.yaml +++ b/Tutorials/General/polymerdraft/metadata.yaml @@ -1,7 +1,7 @@ id: "polymer_draft" name: "polymer draft" description: "Polymerization (draft)" -tags: ["published", "tutorials", "nfsim", "polymer", "draft", "a", "b", "c", "simulate_nf"] +tags: ["tutorials", "nfsim", "polymer", "draft", "simulate_nf"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/General/quasiequilibrium/metadata.yaml b/Tutorials/General/quasiequilibrium/metadata.yaml index ce39e334..708bea58 100644 --- a/Tutorials/General/quasiequilibrium/metadata.yaml +++ b/Tutorials/General/quasiequilibrium/metadata.yaml @@ -1,7 +1,7 @@ id: "quasi_equilibrium" name: "quasi equilibrium" description: "Quasi-equilibrium approximation" -tags: ["published", "toy models", "quasi", "equilibrium", "a", "b", "c"] +tags: ["toy models", "quasi", "equilibrium"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/General/simple/metadata.yaml b/Tutorials/General/simple/metadata.yaml index 1b28cf6a..ae534826 100644 --- a/Tutorials/General/simple/metadata.yaml +++ b/Tutorials/General/simple/metadata.yaml @@ -1,7 +1,7 @@ id: "simple" name: "simple" description: "Simple binding model" -tags: ["published", "tutorials", "simple", "s", "t", "dnat", "trash"] +tags: ["tutorials", "simple", "dnat", "trash"] category: "tutorial" compatibility: bng2_compatible: false diff --git a/Tutorials/General/toy1/metadata.yaml b/Tutorials/General/toy1/metadata.yaml index 78534b1d..c6d4fdd6 100644 --- a/Tutorials/General/toy1/metadata.yaml +++ b/Tutorials/General/toy1/metadata.yaml @@ -1,7 +1,7 @@ id: "toy1" name: "toy1" description: "Basic signaling toy" -tags: ["published", "tutorials", "toy1", "l", "r", "a", "generate_network", "writesbml", "simulate_ode"] +tags: ["tutorials", "toy1", "writesbml"] category: "tutorial" compatibility: bng2_compatible: false diff --git a/Tutorials/General/toy2/metadata.yaml b/Tutorials/General/toy2/metadata.yaml index 54c70820..3b950c0b 100644 --- a/Tutorials/General/toy2/metadata.yaml +++ b/Tutorials/General/toy2/metadata.yaml @@ -1,7 +1,7 @@ id: "toy2" name: "toy2" description: "Enzymatic reaction toy" -tags: ["published", "tutorials", "toy2", "l", "r", "a", "k"] +tags: ["tutorials", "toy2"] category: "tutorial" compatibility: bng2_compatible: false diff --git a/Tutorials/Haugh2b/metadata.yaml b/Tutorials/Haugh2b/metadata.yaml index 904e50e1..44f2bf5f 100644 --- a/Tutorials/Haugh2b/metadata.yaml +++ b/Tutorials/Haugh2b/metadata.yaml @@ -1,7 +1,7 @@ id: "Haugh2b" name: "Haugh2b" description: "R(KD,Y1~U,Y2~U) 1.00" -tags: ["validation", "haugh2b", "r", "s1", "s2", "exclude_reactants", "include_reactants"] +tags: ["haugh2b", "exclude_reactants", "include_reactants"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/Kiefhaberemodel/metadata.yaml b/Tutorials/Kiefhaberemodel/metadata.yaml index b4e91b6c..d476ea07 100644 --- a/Tutorials/Kiefhaberemodel/metadata.yaml +++ b/Tutorials/Kiefhaberemodel/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["emodel"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/Motivatingexample/metadata.yaml b/Tutorials/Motivatingexample/metadata.yaml index 9dfc9870..e462a76b 100644 --- a/Tutorials/Motivatingexample/metadata.yaml +++ b/Tutorials/Motivatingexample/metadata.yaml @@ -1,7 +1,7 @@ id: "Motivating_example" name: "Motivating_example" description: "Signal Transduction with receptor internalization" -tags: ["validation", "motivating", "example", "l", "r", "tf", "dna", "mrna1", "mrna2", "p1", "p2"] +tags: ["motivating", "example", "tf", "dna", "mrna1", "mrna2"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/MotivatingexamplecBNGL/metadata.yaml b/Tutorials/MotivatingexamplecBNGL/metadata.yaml index 19dc7a0a..1e4b59f2 100644 --- a/Tutorials/MotivatingexamplecBNGL/metadata.yaml +++ b/Tutorials/MotivatingexamplecBNGL/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["motivating", "example", "cbngl", "tf", "dna", "mrna1", "mrna2"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/AB/metadata.yaml b/Tutorials/NativeTutorials/AB/metadata.yaml index b0648ffb..554b1c8d 100644 --- a/Tutorials/NativeTutorials/AB/metadata.yaml +++ b/Tutorials/NativeTutorials/AB/metadata.yaml @@ -1,7 +1,7 @@ id: "AB" name: "AB" description: "BioNetGen model: AB" -tags: ["ab", "a", "b", "simulate"] +tags: ["ab"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/ABC/metadata.yaml b/Tutorials/NativeTutorials/ABC/metadata.yaml index 1e0c6e08..68440961 100644 --- a/Tutorials/NativeTutorials/ABC/metadata.yaml +++ b/Tutorials/NativeTutorials/ABC/metadata.yaml @@ -1,7 +1,7 @@ id: "ABC" name: "ABC" description: "BioNetGen model: ABC" -tags: ["abc", "a", "simulate"] +tags: ["abc"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/ABCscan/metadata.yaml b/Tutorials/NativeTutorials/ABCscan/metadata.yaml index bf69d4b3..f787eba2 100644 --- a/Tutorials/NativeTutorials/ABCscan/metadata.yaml +++ b/Tutorials/NativeTutorials/ABCscan/metadata.yaml @@ -1,7 +1,7 @@ id: "ABC_scan" name: "ABC scan" description: "BioNetGen model: ABC scan" -tags: ["abc", "scan", "a", "generate_network", "parameter_scan"] +tags: ["abc", "scan", "parameter_scan"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/ABCssa/metadata.yaml b/Tutorials/NativeTutorials/ABCssa/metadata.yaml index 6538b9d5..cc279169 100644 --- a/Tutorials/NativeTutorials/ABCssa/metadata.yaml +++ b/Tutorials/NativeTutorials/ABCssa/metadata.yaml @@ -1,7 +1,7 @@ id: "ABC_ssa" name: "ABC ssa" description: "BioNetGen model: ABC ssa" -tags: ["abc", "ssa", "a", "simulate"] +tags: ["abc", "ssa"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/ABp/metadata.yaml b/Tutorials/NativeTutorials/ABp/metadata.yaml index 3166f632..33289c7c 100644 --- a/Tutorials/NativeTutorials/ABp/metadata.yaml +++ b/Tutorials/NativeTutorials/ABp/metadata.yaml @@ -1,7 +1,7 @@ id: "ABp" name: "ABp" description: "title: ABp.bngl" -tags: ["abp", "a", "b", "simulate"] +tags: ["abp"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/ABpapprox/metadata.yaml b/Tutorials/NativeTutorials/ABpapprox/metadata.yaml index fa5eaffd..3feddeef 100644 --- a/Tutorials/NativeTutorials/ABpapprox/metadata.yaml +++ b/Tutorials/NativeTutorials/ABpapprox/metadata.yaml @@ -1,7 +1,7 @@ id: "ABp_approx" name: "ABp approx" description: "title: ABp.bngl" -tags: ["abp", "approx", "km", "a", "b", "simulate"] +tags: ["abp", "km"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/BAB/metadata.yaml b/Tutorials/NativeTutorials/BAB/metadata.yaml index 33124b3e..507fdcab 100644 --- a/Tutorials/NativeTutorials/BAB/metadata.yaml +++ b/Tutorials/NativeTutorials/BAB/metadata.yaml @@ -1,7 +1,7 @@ id: "BAB" name: "BAB" description: "Simple binding model with a bivalent A molecule that has two identical sites" -tags: ["bab", "a", "b", "simulate"] +tags: ["bab"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/BABcoop/metadata.yaml b/Tutorials/NativeTutorials/BABcoop/metadata.yaml index 9bd00b19..3f3769e5 100644 --- a/Tutorials/NativeTutorials/BABcoop/metadata.yaml +++ b/Tutorials/NativeTutorials/BABcoop/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["bab", "coop"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/BABscan/metadata.yaml b/Tutorials/NativeTutorials/BABscan/metadata.yaml index 4cb50c19..31712c8d 100644 --- a/Tutorials/NativeTutorials/BABscan/metadata.yaml +++ b/Tutorials/NativeTutorials/BABscan/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["bab", "scan", "parameter_scan"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/BLBR/metadata.yaml b/Tutorials/NativeTutorials/BLBR/metadata.yaml index d56a714e..1601fa2d 100644 --- a/Tutorials/NativeTutorials/BLBR/metadata.yaml +++ b/Tutorials/NativeTutorials/BLBR/metadata.yaml @@ -1,7 +1,7 @@ id: "BLBR" name: "BLBR" description: "title: BLBR.bngl" -tags: ["blbr", "setoption", "r", "l", "simulate"] +tags: ["blbr"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml b/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml index d3759316..509247a8 100644 --- a/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml +++ b/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml @@ -1,7 +1,7 @@ id: "Chylek_library" name: "Chylek library" description: "Created by BioNetGen 2.2.6" -tags: ["chylek", "library", "kflatplcg", "kfgrb2gab2", "kflcp2plcg1", "kd1", "kd2", "sink", "pre", "pag1"] +tags: ["chylek", "library", "sink", "pre", "pag1"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml b/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml index 2d1bb8db..7e9ee248 100644 --- a/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml +++ b/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml @@ -1,7 +1,7 @@ id: "CircadianOscillator" name: "CircadianOscillator" description: "Circadian rhythm" -tags: ["published", "tutorial", "native", "circadianoscillator", "a", "r", "pa", "pr", "mrna_a", "mrna_r"] +tags: ["circadianoscillator", "pa", "pr", "mrna_a", "mrna_r"] category: "tutorial" compatibility: bng2_compatible: false diff --git a/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml b/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml index 04ebf11d..fd760e3e 100644 --- a/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml +++ b/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml @@ -1,7 +1,7 @@ id: "ComplexDegradation" name: "ComplexDegradation" description: "Degradation model" -tags: ["published", "tutorial", "native", "complexdegradation", "a", "b", "c", "generate_network"] +tags: ["complexdegradation"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/Creamer2012/metadata.yaml b/Tutorials/NativeTutorials/Creamer2012/metadata.yaml index fd58eccd..a0385286 100644 --- a/Tutorials/NativeTutorials/Creamer2012/metadata.yaml +++ b/Tutorials/NativeTutorials/Creamer2012/metadata.yaml @@ -1,7 +1,7 @@ id: "Creamer_2012" name: "Creamer 2012" description: "Initial values" -tags: ["creamer", "2012", "egf", "hrg", "egfr", "erbb2", "erbb3", "erbb4", "p52shc1", "grb2"] +tags: ["creamer", "2012", "egf", "hrg", "egfr", "erbb2", "erbb3", "erbb4", "grb2"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/FceRIviz/metadata.yaml b/Tutorials/NativeTutorials/FceRIviz/metadata.yaml index 2eb2af1c..33082994 100644 --- a/Tutorials/NativeTutorials/FceRIviz/metadata.yaml +++ b/Tutorials/NativeTutorials/FceRIviz/metadata.yaml @@ -1,7 +1,7 @@ id: "FceRI_viz" name: "FceRI Viz" description: "FcεRI (viz)" -tags: ["published", "tutorial", "native", "fceri", "viz", "fcr", "ige", "lat", "lyn", "syk", "pb", "pg", "sykp"] +tags: ["fceri", "fcr", "ige", "lat", "lyn", "syk", "pb", "pg", "sykp"] category: "tutorial" compatibility: bng2_compatible: false diff --git a/Tutorials/NativeTutorials/GK/metadata.yaml b/Tutorials/NativeTutorials/GK/metadata.yaml index a5a674c5..e695afca 100644 --- a/Tutorials/NativeTutorials/GK/metadata.yaml +++ b/Tutorials/NativeTutorials/GK/metadata.yaml @@ -1,7 +1,7 @@ id: "GK" name: "GK" description: "title: GK.bngl" -tags: ["gk", "b", "simulate"] +tags: ["gk"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/LR/metadata.yaml b/Tutorials/NativeTutorials/LR/metadata.yaml index 670e47fa..128c92d3 100644 --- a/Tutorials/NativeTutorials/LR/metadata.yaml +++ b/Tutorials/NativeTutorials/LR/metadata.yaml @@ -1,7 +1,7 @@ id: "LR" name: "LR" description: "title: LR.bngl" -tags: ["lr", "l", "r", "simulate"] +tags: ["lr"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/LRR/metadata.yaml b/Tutorials/NativeTutorials/LRR/metadata.yaml index 3a9da1f1..de6ce30c 100644 --- a/Tutorials/NativeTutorials/LRR/metadata.yaml +++ b/Tutorials/NativeTutorials/LRR/metadata.yaml @@ -1,7 +1,7 @@ id: "LRR" name: "LRR" description: "title: LRR.bngl" -tags: ["lrr", "l", "r"] +tags: ["lrr"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/LRRcomp/metadata.yaml b/Tutorials/NativeTutorials/LRRcomp/metadata.yaml index ceea2712..5b8b1a57 100644 --- a/Tutorials/NativeTutorials/LRRcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LRRcomp/metadata.yaml @@ -1,7 +1,7 @@ id: "LRR_comp" name: "LRR comp" description: "title: LRR_comp.bngl" -tags: ["lrr", "comp", "l", "r", "simulate"] +tags: ["lrr", "comp"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/LRcomp/metadata.yaml b/Tutorials/NativeTutorials/LRcomp/metadata.yaml index 47204c62..51d11621 100644 --- a/Tutorials/NativeTutorials/LRcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LRcomp/metadata.yaml @@ -1,7 +1,7 @@ id: "LR_comp" name: "LR comp" description: "title: LR_comp.bngl" -tags: ["lr", "comp", "l", "r", "simulate"] +tags: ["lr", "comp"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/LV/metadata.yaml b/Tutorials/NativeTutorials/LV/metadata.yaml index 7fda6798..6ac5a200 100644 --- a/Tutorials/NativeTutorials/LV/metadata.yaml +++ b/Tutorials/NativeTutorials/LV/metadata.yaml @@ -1,7 +1,7 @@ id: "LV" name: "LV" description: "title: LV.bgl" -tags: ["lv", "s", "w", "generate_network", "writesbml", "simulate"] +tags: ["lv", "writesbml"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/LVcomp/metadata.yaml b/Tutorials/NativeTutorials/LVcomp/metadata.yaml index ab19072b..56140be4 100644 --- a/Tutorials/NativeTutorials/LVcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LVcomp/metadata.yaml @@ -1,7 +1,7 @@ id: "LV_comp" name: "LV comp" description: "title: LV_comp.bgl" -tags: ["lv", "comp", "k2", "s", "w"] +tags: ["lv", "comp"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/Lisman/metadata.yaml b/Tutorials/NativeTutorials/Lisman/metadata.yaml index 09a1be55..d14d7b38 100644 --- a/Tutorials/NativeTutorials/Lisman/metadata.yaml +++ b/Tutorials/NativeTutorials/Lisman/metadata.yaml @@ -1,7 +1,7 @@ id: "Lisman" name: "Lisman" description: "title: auto.bngl" -tags: ["lisman", "k1", "p", "input", "visualize", "setparameter", "simulate"] +tags: ["lisman", "input"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml b/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml index 5e5a68df..079710f8 100644 --- a/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml +++ b/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml @@ -1,7 +1,7 @@ id: "Lisman_bifurcate" name: "Lisman bifurcate" description: "title: Lisman_bifurcate.bngl" -tags: ["lisman", "bifurcate", "k1", "p"] +tags: ["lisman", "bifurcate"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/Repressilator/metadata.yaml b/Tutorials/NativeTutorials/Repressilator/metadata.yaml index 10ea1210..76556d55 100644 --- a/Tutorials/NativeTutorials/Repressilator/metadata.yaml +++ b/Tutorials/NativeTutorials/Repressilator/metadata.yaml @@ -1,7 +1,7 @@ id: "Repressilator" name: "Repressilator" description: "Repressilator circuit" -tags: ["published", "tutorial", "native", "repressilator", "gtetr", "gci", "glaci", "mtetr", "mci", "mlaci", "ptetr", "pci"] +tags: ["repressilator", "gtetr", "gci", "glaci", "mtetr", "mci", "mlaci", "ptetr", "pci"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/SIR/metadata.yaml b/Tutorials/NativeTutorials/SIR/metadata.yaml index 555c05c7..b6524481 100644 --- a/Tutorials/NativeTutorials/SIR/metadata.yaml +++ b/Tutorials/NativeTutorials/SIR/metadata.yaml @@ -1,7 +1,7 @@ id: "SIR" name: "SIR" description: "BioNetGen model: SIR" -tags: ["sir", "saveconcentrations", "simulate"] +tags: ["sir", "saveconcentrations"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/Suderman2013/metadata.yaml b/Tutorials/NativeTutorials/Suderman2013/metadata.yaml index 8d8122ab..c4713154 100644 --- a/Tutorials/NativeTutorials/Suderman2013/metadata.yaml +++ b/Tutorials/NativeTutorials/Suderman2013/metadata.yaml @@ -1,7 +1,7 @@ id: "Suderman_2013" name: "Suderman 2013" description: "Ensemble model translated into BNGL" -tags: ["suderman", "2013", "i", "trash", "pheromone", "ste2", "gpa1", "ste4", "sst2", "ste20"] +tags: ["suderman", "2013", "trash", "pheromone", "ste2", "gpa1", "ste4", "sst2", "ste20"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/birthdeath/metadata.yaml b/Tutorials/NativeTutorials/birthdeath/metadata.yaml index 039e683c..b0c77db2 100644 --- a/Tutorials/NativeTutorials/birthdeath/metadata.yaml +++ b/Tutorials/NativeTutorials/birthdeath/metadata.yaml @@ -1,7 +1,7 @@ id: "birth-death" name: "Birth-Death" description: "Stochastic process" -tags: ["published", "tutorial", "native", "birth", "death", "a", "generate_network", "saveconcentrations", "simulate"] +tags: ["birth", "death", "saveconcentrations"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml b/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml index b78f498a..b5951400 100644 --- a/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml +++ b/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["cbngl", "simple", "tf", "dna", "mrna"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/organelletransport/metadata.yaml b/Tutorials/NativeTutorials/organelletransport/metadata.yaml index c8bd4316..ed8672fa 100644 --- a/Tutorials/NativeTutorials/organelletransport/metadata.yaml +++ b/Tutorials/NativeTutorials/organelletransport/metadata.yaml @@ -1,7 +1,7 @@ id: "organelle_transport" name: "organelle transport" description: "title: organelle_transport.bngl" -tags: ["organelle", "transport", "a", "b", "c", "d", "t1", "at1", "ct1", "t2"] +tags: ["organelle", "transport"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml b/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml index 7fbda96d..3310445e 100644 --- a/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml +++ b/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml @@ -1,7 +1,7 @@ id: "organelle_transport_struct" name: "organelle transport struct" description: "title: organelle_transport_abcd.bngl" -tags: ["organelle", "transport", "struct", "a", "b", "t1", "t2"] +tags: ["organelle", "transport", "struct"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/toggle/metadata.yaml b/Tutorials/NativeTutorials/toggle/metadata.yaml index 68257b09..29a0ecbb 100644 --- a/Tutorials/NativeTutorials/toggle/metadata.yaml +++ b/Tutorials/NativeTutorials/toggle/metadata.yaml @@ -1,7 +1,7 @@ id: "toggle" name: "Toggle" description: "Toggle switch" -tags: ["published", "tutorial", "native", "toggle", "x", "y", "generate_network", "writemfile", "setconcentration"] +tags: ["toggle", "writemfile", "setconcentration"] category: "tutorial" compatibility: bng2_compatible: false diff --git a/Tutorials/NativeTutorials/translateSBML/metadata.yaml b/Tutorials/NativeTutorials/translateSBML/metadata.yaml index 97d233d9..2370dfe4 100644 --- a/Tutorials/NativeTutorials/translateSBML/metadata.yaml +++ b/Tutorials/NativeTutorials/translateSBML/metadata.yaml @@ -1,7 +1,7 @@ id: "translateSBML" name: "translateSBML" description: "title: translateSBML.bngl" -tags: ["translatesbml", "generate_network", "simulate"] +tags: ["translatesbml"] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/NativeTutorials/visualize/metadata.yaml b/Tutorials/NativeTutorials/visualize/metadata.yaml index 3af25815..d7f350d2 100644 --- a/Tutorials/NativeTutorials/visualize/metadata.yaml +++ b/Tutorials/NativeTutorials/visualize/metadata.yaml @@ -1,7 +1,7 @@ id: "visualize" name: "Visualize" description: "Visualization toy" -tags: ["published", "tutorial", "native", "visualize", "x", "a1", "a2", "b"] +tags: [] category: "tutorial" compatibility: bng2_compatible: true diff --git a/Tutorials/SHP2basemodel/metadata.yaml b/Tutorials/SHP2basemodel/metadata.yaml index 2007ff75..c2526111 100644 --- a/Tutorials/SHP2basemodel/metadata.yaml +++ b/Tutorials/SHP2basemodel/metadata.yaml @@ -1,7 +1,7 @@ id: "SHP2_base_model" name: "SHP2_base_model" description: "Base model of Shp2 regulation" -tags: ["validation", "shp2", "base", "model", "r", "s", "exclude_reactants"] +tags: ["shp2", "base", "exclude_reactants"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/catalysis/metadata.yaml b/Tutorials/catalysis/metadata.yaml index 3847ec03..3bffdda7 100644 --- a/Tutorials/catalysis/metadata.yaml +++ b/Tutorials/catalysis/metadata.yaml @@ -1,7 +1,7 @@ id: "catalysis" name: "catalysis" description: "Catalysis in energy BNG" -tags: ["validation", "catalysis", "version", "setoption", "s", "kinase", "pptase", "atp", "adp"] +tags: ["catalysis", "pptase", "atp", "adp"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/continue/metadata.yaml b/Tutorials/continue/metadata.yaml index 23badc1e..1deae03d 100644 --- a/Tutorials/continue/metadata.yaml +++ b/Tutorials/continue/metadata.yaml @@ -1,7 +1,7 @@ id: "continue" name: "continue" description: "Test trajectory continuation" -tags: ["validation", "continue", "a", "b", "c", "trash"] +tags: ["continue", "trash"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/egfrnet/metadata.yaml b/Tutorials/egfrnet/metadata.yaml index d9756d78..92d97030 100644 --- a/Tutorials/egfrnet/metadata.yaml +++ b/Tutorials/egfrnet/metadata.yaml @@ -1,7 +1,7 @@ id: "egfr_net" name: "egfr_net" description: "check detailed balanced" -tags: ["validation", "egfr", "net", "egf", "shc", "grb2", "sos"] +tags: ["egfr", "net", "egf", "shc", "grb2", "sos"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/egfrnetred/metadata.yaml b/Tutorials/egfrnetred/metadata.yaml index e203993f..1ae2b096 100644 --- a/Tutorials/egfrnetred/metadata.yaml +++ b/Tutorials/egfrnetred/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["egfr", "net", "red", "egf", "grb2", "shc", "sos"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/egfrpath/metadata.yaml b/Tutorials/egfrpath/metadata.yaml index a7125010..f529cd4d 100644 --- a/Tutorials/egfrpath/metadata.yaml +++ b/Tutorials/egfrpath/metadata.yaml @@ -1,7 +1,7 @@ id: "egfr_path" name: "egfr_path" description: "The primary focus of the model developed by Kholodenko" -tags: ["validation", "egfr", "path", "generate_network", "setconcentration", "simulate"] +tags: ["egfr", "path", "setconcentration"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/energyexample1/metadata.yaml b/Tutorials/energyexample1/metadata.yaml index fc9a555d..a0dd1e5d 100644 --- a/Tutorials/energyexample1/metadata.yaml +++ b/Tutorials/energyexample1/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["energy", "example1"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/example1/metadata.yaml b/Tutorials/example1/metadata.yaml index 71bb8b5c..2f761524 100644 --- a/Tutorials/example1/metadata.yaml +++ b/Tutorials/example1/metadata.yaml @@ -1,7 +1,7 @@ id: "example1" name: "example1" description: "Example file for BNG2 tutorial." -tags: ["validation", "example1", "version", "generate_network", "simulate_ode"] +tags: ["example1"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/fcerijicomp/metadata.yaml b/Tutorials/fcerijicomp/metadata.yaml index 63d628b7..d599bd93 100644 --- a/Tutorials/fcerijicomp/metadata.yaml +++ b/Tutorials/fcerijicomp/metadata.yaml @@ -1,7 +1,7 @@ id: "fceri_ji_comp" name: "fceri_ji_comp" description: "Ligand-receptor binding" -tags: ["validation", "fceri", "ji", "comp", "lig", "lyn", "syk", "rec"] +tags: ["fceri", "ji", "comp", "lig", "lyn", "syk", "rec"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/heise/metadata.yaml b/Tutorials/heise/metadata.yaml index a7c85bea..9038d0a4 100644 --- a/Tutorials/heise/metadata.yaml +++ b/Tutorials/heise/metadata.yaml @@ -1,7 +1,7 @@ id: "heise" name: "heise" description: "Validate state inheritance in a symmetric context" -tags: ["validation", "heise", "a", "b", "generate_network", "simulate_ode", "setparameter"] +tags: ["heise"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/issue198short/metadata.yaml b/Tutorials/issue198short/metadata.yaml index 11f43c89..379d9d84 100644 --- a/Tutorials/issue198short/metadata.yaml +++ b/Tutorials/issue198short/metadata.yaml @@ -1,7 +1,7 @@ id: "issue_198_short" name: "issue_198_short" description: "No description available" -tags: ["validation", "issue", "198", "short", "a", "b", "c", "generate_network", "simulate"] +tags: ["issue", "198", "short"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/localfunc/metadata.yaml b/Tutorials/localfunc/metadata.yaml index a7398643..dcb6a0db 100644 --- a/Tutorials/localfunc/metadata.yaml +++ b/Tutorials/localfunc/metadata.yaml @@ -1,7 +1,7 @@ id: "localfunc" name: "localfunc" description: "Test local function expansion" -tags: ["validation", "localfunc", "a", "b", "c", "trash", "f_synth"] +tags: ["localfunc", "trash", "f_synth"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/michment/metadata.yaml b/Tutorials/michment/metadata.yaml index f559cda8..0bc91a81 100644 --- a/Tutorials/michment/metadata.yaml +++ b/Tutorials/michment/metadata.yaml @@ -1,7 +1,7 @@ id: "michment" name: "michment" description: "Michaelis Menten" -tags: ["validation", "michment", "e", "s", "generate_network"] +tags: ["michment"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/michmentcont/metadata.yaml b/Tutorials/michmentcont/metadata.yaml index a5a96387..1849b0fc 100644 --- a/Tutorials/michmentcont/metadata.yaml +++ b/Tutorials/michmentcont/metadata.yaml @@ -1,7 +1,7 @@ id: "michment_cont" name: "michment_cont" description: "Michaelis Menten Continue" -tags: ["validation", "michment", "cont", "readfile", "setconcentration", "simulate_ode", "addconcentration"] +tags: ["michment", "cont", "readfile", "setconcentration", "addconcentration"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/motor/metadata.yaml b/Tutorials/motor/metadata.yaml index 5be78627..c80b8a05 100644 --- a/Tutorials/motor/metadata.yaml +++ b/Tutorials/motor/metadata.yaml @@ -1,7 +1,7 @@ id: "motor" name: "motor" description: "Motor protein" -tags: ["validation", "motor", "chey", "kplus", "kminus"] +tags: ["motor", "chey"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/mwc/metadata.yaml b/Tutorials/mwc/metadata.yaml index 63a2624e..8b98cef1 100644 --- a/Tutorials/mwc/metadata.yaml +++ b/Tutorials/mwc/metadata.yaml @@ -1,7 +1,7 @@ id: "mwc" name: "mwc" description: "Monod-Wyman-Changeux model" -tags: ["validation", "mwc", "setoption", "h", "ox", "b"] +tags: ["mwc", "ox"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/nfkb/metadata.yaml b/Tutorials/nfkb/metadata.yaml index a20ed85a..baf51039 100644 --- a/Tutorials/nfkb/metadata.yaml +++ b/Tutorials/nfkb/metadata.yaml @@ -1,7 +1,7 @@ id: "nfkb" name: "nfkb" description: "NF-kB signaling pathway" -tags: ["validation", "nfkb", "tnfr", "ikkk", "tnf", "ikk", "ikba", "a20", "competitor"] +tags: ["nfkb", "tnfr", "ikkk", "tnf", "ikk", "ikba", "competitor"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/nfkbillustratingprotocols/metadata.yaml b/Tutorials/nfkbillustratingprotocols/metadata.yaml index c9d42b3a..1d53d46d 100644 --- a/Tutorials/nfkbillustratingprotocols/metadata.yaml +++ b/Tutorials/nfkbillustratingprotocols/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["nfkb", "illustrating", "protocols", "tnfr", "ikkk", "tnf", "ikk", "ikba", "competitor"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/polymerfixed/metadata.yaml b/Tutorials/polymerfixed/metadata.yaml index 100a7c63..dec81fa7 100644 --- a/Tutorials/polymerfixed/metadata.yaml +++ b/Tutorials/polymerfixed/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_functions: true nfsim_compatible: true source: - origin: "contributed" + origin: "tutorial" original_format: "bngl" original_repository: "bionetgen-web-simulator" source_path: "public/models/polymer_fixed.bngl" diff --git a/Tutorials/recdim/metadata.yaml b/Tutorials/recdim/metadata.yaml index 770914e6..d8fc1fe4 100644 --- a/Tutorials/recdim/metadata.yaml +++ b/Tutorials/recdim/metadata.yaml @@ -1,7 +1,7 @@ id: "rec_dim" name: "rec_dim" description: "Ligand-receptor binding" -tags: ["validation", "rec", "dim", "lig", "writemdl", "generate_network", "simulate"] +tags: ["rec", "dim", "lig", "writemdl"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/recdimcomp/metadata.yaml b/Tutorials/recdimcomp/metadata.yaml index 886ff55d..9bf90d3b 100644 --- a/Tutorials/recdimcomp/metadata.yaml +++ b/Tutorials/recdimcomp/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["rec", "dim", "comp", "lig", "writemdl"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/simplenfsimtest/metadata.yaml b/Tutorials/simplenfsimtest/metadata.yaml index 9dab484d..3ed49f9a 100644 --- a/Tutorials/simplenfsimtest/metadata.yaml +++ b/Tutorials/simplenfsimtest/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_functions: false nfsim_compatible: true source: - origin: "contributed" + origin: "tutorial" original_format: "bngl" original_repository: "bionetgen-web-simulator" source_path: "public/models/simple_nfsim_test.bngl" diff --git a/Tutorials/simplesbmlimport/metadata.yaml b/Tutorials/simplesbmlimport/metadata.yaml index 962e4340..83af3901 100644 --- a/Tutorials/simplesbmlimport/metadata.yaml +++ b/Tutorials/simplesbmlimport/metadata.yaml @@ -1,7 +1,7 @@ id: "simple_sbml_import" name: "simple_sbml_import" description: "SBML import test" -tags: ["validation", "simple", "sbml", "import", "readfile", "generate_network", "simulate"] +tags: ["simple", "sbml", "import", "readfile"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/simplesystem/metadata.yaml b/Tutorials/simplesystem/metadata.yaml index 2e3cd412..c148eaad 100644 --- a/Tutorials/simplesystem/metadata.yaml +++ b/Tutorials/simplesystem/metadata.yaml @@ -1,7 +1,7 @@ id: "simple_system" name: "simple_system" description: "Simple binding system" -tags: ["validation", "simple", "system", "x", "y"] +tags: ["simple", "system"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testANGsynthesissimple/metadata.yaml b/Tutorials/testANGsynthesissimple/metadata.yaml index 6b35b5de..ca0ec05a 100644 --- a/Tutorials/testANGsynthesissimple/metadata.yaml +++ b/Tutorials/testANGsynthesissimple/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["test", "ang", "synthesis", "simple", "source", "source2"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testMM/metadata.yaml b/Tutorials/testMM/metadata.yaml index f3780771..6fbe2c1b 100644 --- a/Tutorials/testMM/metadata.yaml +++ b/Tutorials/testMM/metadata.yaml @@ -1,7 +1,7 @@ id: "test_MM" name: "test_MM" description: "Kinetic constants" -tags: ["validation", "test", "mm", "e", "s", "p", "generate_network"] +tags: ["test", "mm"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testfixed/metadata.yaml b/Tutorials/testfixed/metadata.yaml index 21a8cf4e..82c96d94 100644 --- a/Tutorials/testfixed/metadata.yaml +++ b/Tutorials/testfixed/metadata.yaml @@ -1,7 +1,7 @@ id: "test_fixed" name: "test_fixed" description: "# actions ##" -tags: ["validation", "test", "fixed", "a", "b", "generate_network", "simulate"] +tags: ["test", "fixed"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testmratio/metadata.yaml b/Tutorials/testmratio/metadata.yaml index c6df3f00..1d91fa1e 100644 --- a/Tutorials/testmratio/metadata.yaml +++ b/Tutorials/testmratio/metadata.yaml @@ -1,7 +1,7 @@ id: "test_mratio" name: "test_mratio" description: "Reaction ratio test" -tags: ["validation", "test", "mratio", "a", "b", "c_theory", "c_upper", "c_lower"] +tags: ["test", "mratio", "c_theory", "c_upper", "c_lower"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testnetworkgen/metadata.yaml b/Tutorials/testnetworkgen/metadata.yaml index 7c113221..772a3176 100644 --- a/Tutorials/testnetworkgen/metadata.yaml +++ b/Tutorials/testnetworkgen/metadata.yaml @@ -1,7 +1,7 @@ id: "test_network_gen" name: "test_network_gen" description: "fceri model with network generation" -tags: ["validation", "test", "network", "gen", "lig", "lyn", "syk", "rec"] +tags: ["test", "network", "gen", "lig", "lyn", "syk", "rec"] category: "validation" compatibility: bng2_compatible: false diff --git a/Tutorials/testsat/metadata.yaml b/Tutorials/testsat/metadata.yaml index dfe97a4d..32757072 100644 --- a/Tutorials/testsat/metadata.yaml +++ b/Tutorials/testsat/metadata.yaml @@ -1,7 +1,7 @@ id: "test_sat" name: "test_sat" description: "Kinetic constants" -tags: ["validation", "test", "sat", "e", "s", "p", "generate_network"] +tags: ["test", "sat"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testsynthesiscBNGLsimple/metadata.yaml b/Tutorials/testsynthesiscBNGLsimple/metadata.yaml index c5b92ee1..7edab256 100644 --- a/Tutorials/testsynthesiscBNGLsimple/metadata.yaml +++ b/Tutorials/testsynthesiscBNGLsimple/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["test", "synthesis", "cbngl", "simple", "source", "source2"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testsynthesiscomplex/metadata.yaml b/Tutorials/testsynthesiscomplex/metadata.yaml index 6360ed18..0783c56b 100644 --- a/Tutorials/testsynthesiscomplex/metadata.yaml +++ b/Tutorials/testsynthesiscomplex/metadata.yaml @@ -1,7 +1,7 @@ id: "test_synthesis_complex" name: "test_synthesis_complex" description: "Complex synthesis test" -tags: ["validation", "test", "synthesis", "complex", "a", "b", "c", "receptor", "source", "source2"] +tags: ["test", "synthesis", "complex", "receptor", "source", "source2"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml b/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml index eebdce3a..0e40f242 100644 --- a/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml +++ b/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["test", "synthesis", "complex", "cbngl", "surface_molecule1", "surface_molecule2", "surface_receptor"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml b/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml index 6d0c5554..04c572e4 100644 --- a/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml +++ b/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml @@ -1,7 +1,7 @@ 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"] +tags: ["test", "synthesis", "complex", "source", "cbngl", "surface_molecule1", "surface_molecule2", "surface_receptor"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/testsynthesissimple/metadata.yaml b/Tutorials/testsynthesissimple/metadata.yaml index 75f920e6..888d6923 100644 --- a/Tutorials/testsynthesissimple/metadata.yaml +++ b/Tutorials/testsynthesissimple/metadata.yaml @@ -1,7 +1,7 @@ id: "test_synthesis_simple" name: "test_synthesis_simple" description: "Simple synthesis test" -tags: ["validation", "test", "synthesis", "simple", "a", "b", "c", "source", "source2", "generate_network"] +tags: ["test", "synthesis", "simple", "source", "source2"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/tlmr/metadata.yaml b/Tutorials/tlmr/metadata.yaml index 469b93d0..0b322e0d 100644 --- a/Tutorials/tlmr/metadata.yaml +++ b/Tutorials/tlmr/metadata.yaml @@ -1,7 +1,7 @@ id: "tlmr" name: "tlmr" description: "Trivalent ligand monovalent receptor" -tags: ["validation", "tlmr", "l", "r", "generate_network", "simulate_ode"] +tags: ["tlmr"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/toyjim/metadata.yaml b/Tutorials/toyjim/metadata.yaml index e9baaa4d..59bf2e8a 100644 --- a/Tutorials/toyjim/metadata.yaml +++ b/Tutorials/toyjim/metadata.yaml @@ -1,7 +1,7 @@ id: "toy-jim" name: "toy-jim" description: "The model consists of a monovalent extracellular ligand," -tags: ["validation", "toy", "jim", "l", "r", "a", "k", "null"] +tags: ["toy", "jim"] category: "validation" compatibility: bng2_compatible: true diff --git a/Tutorials/univsynth/metadata.yaml b/Tutorials/univsynth/metadata.yaml index 8b87d740..1238d6d8 100644 --- a/Tutorials/univsynth/metadata.yaml +++ b/Tutorials/univsynth/metadata.yaml @@ -1,7 +1,7 @@ id: "univ_synth" name: "univ_synth" description: "example of universal synthesis" -tags: ["validation", "univ", "synth", "a", "b", "c", "generate_network", "simulate_ode"] +tags: ["univ", "synth"] category: "validation" compatibility: bng2_compatible: true diff --git a/fix-test.js b/fix-test.js deleted file mode 100644 index 5e5173ff..00000000 --- a/fix-test.js +++ /dev/null @@ -1,12 +0,0 @@ -const fs = require('fs'); -let content = fs.readFileSync('scripts/generate-manifest.test.js', 'utf8'); - -// fix imports -content = content.replace(/<<<<<<< Updated upstream\nconst { buildEntry, parseMetadataYaml } = require\('\.\/generate-manifest\.js'\);\n=======\nconst { buildEntry, parseArgs } = require\('\.\/generate-manifest\.js'\);\n>>>>>>> Stashed changes/, "const { buildEntry, parseMetadataYaml, parseArgs } = require('./generate-manifest.js');"); - -// fix test sections -content = content.replace(/<<<<<<< Updated upstream/g, ""); -content = content.replace(/=======/g, ""); -content = content.replace(/>>>>>>> Stashed changes/g, ""); - -fs.writeFileSync('scripts/generate-manifest.test.js', content); diff --git a/gallery-assignments.json b/gallery-assignments.json deleted file mode 100644 index 98847109..00000000 --- a/gallery-assignments.json +++ /dev/null @@ -1,2417 +0,0 @@ -{ - "AB": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "ABC": { - "gallery_categories": [ - "metabolism", - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "ABC_scan": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "ABC_ssa": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "ABp": { - "gallery_categories": [ - "metabolism", - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "ABp_approx": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "An_2009": { - "gallery_categories": [ - "immunology" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "BAB": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "BAB_coop": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "BAB_scan": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "BaruaBCR_2012": { - "gallery_categories": [ - "immunology" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "BaruaFceRI_2012": { - "gallery_categories": [ - "immunology" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "Barua_2007": { - "gallery_categories": [ - "cancer" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "Barua_2009": { - "gallery_categories": [ - "cancer" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "Blinov_2006": { - "gallery_categories": [ - "cell-cycle" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "Blinov_egfr": { - "gallery_categories": [ - "cancer" - ], - "bng2_compatible": false, - "nfsim_compatible": true, - "excluded": true - }, - "Blinov_ran": { - "gallery_categories": [ - "cell-cycle" - ], - "bng2_compatible": false, - "nfsim_compatible": true, - "excluded": true - }, - "CaOscillate_Func": { - "gallery_categories": [], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "CaOscillate_Sat": { - "gallery_categories": [], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "Chattaraj_2021": { - "gallery_categories": [ - "neuroscience" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "Cheemalavagu_JAK_STAT": { - "gallery_categories": [ - "immunology" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "ChylekTCR_2014": { - "gallery_categories": [ - "immunology" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "Chylek_library": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "CircadianOscillator": { - "gallery_categories": [ - "cell-cycle", - "native-tutorials" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "ComplexDegradation": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "Creamer_2012": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "Dolan_2015": { - "gallery_categories": [ - "metabolism" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": true - }, - "Dushek_2011": { - "gallery_categories": [ - "immunology" - ], - "bng2_compatible": true, - 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- "gallery_categories": [], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "test_synthesis_simple": { - "gallery_categories": [], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "tlbr": { - "gallery_categories": [ - "immunology" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "tlmr": { - "gallery_categories": [], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "tlr3-dsrna-sensing": { - "gallery_categories": [ - "immunology", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "tnf-induced-apoptosis": { - "gallery_categories": [ - "cell-cycle", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "toggle": { - "gallery_categories": [ - "synbio", - "native-tutorials" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "toy-jim": { - "gallery_categories": [], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "toy1": { - "gallery_categories": [ - "tutorials" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "toy2": { - "gallery_categories": [ - "tutorials" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": true - }, - "two-component-system": { - "gallery_categories": [ - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "univ_synth": { - "gallery_categories": [], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "vegf-angiogenesis": { - "gallery_categories": [ - "cancer", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "vilar_2002": { - "gallery_categories": [ - "cell-cycle" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "vilar_2002b": { - "gallery_categories": [ - "cell-cycle" - ], - "bng2_compatible": false, - "nfsim_compatible": false, - "excluded": false - }, - "viral-sensing-innate-immunity": { - "gallery_categories": [ - "immunology", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "visualize": { - "gallery_categories": [ - "native-tutorials" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "wacky_alchemy_stone": { - "gallery_categories": [ - "synbio", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "wacky_black_hole": { - "gallery_categories": [ - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "wacky_bouncing_ball": { - "gallery_categories": [ - "physics", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "wacky_traffic_jam_asep": { - "gallery_categories": [ - "physics", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "wacky_zombie_infection": { - "gallery_categories": [ - "ecology", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "wnt-beta-catenin-signaling": { - "gallery_categories": [ - "developmental", - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - }, - "wound-healing-pdgf-signaling": { - "gallery_categories": [ - "test-models" - ], - "bng2_compatible": true, - "nfsim_compatible": false, - "excluded": false - } -} \ No newline at end of file diff --git a/gallery.generated.json b/gallery.generated.json index 5b3d7cb4..6d77934e 100644 --- a/gallery.generated.json +++ b/gallery.generated.json @@ -1,6 +1,6 @@ { "version": 1, - "generated": "2026-05-03T22:23:07.247Z", + "generated": "2026-05-03T22:49:19.469Z", "categories": [ { "id": "cancer", @@ -100,18 +100,105 @@ } ], "assignments": { - "An_2009": [ - "immunology", + "02_egfr_egfr": [ "published-models" ], - "Barua_2007": [ - "cancer", + "03_fcerig_fceri_gamma2": [ "published-models" ], - "Barua_2009": [ - "cancer", + "04_egfrnf_egfr_nf": [ + "published-models" + ], + "05_threestep_m1": [ + "published-models" + ], + "06_degranulation_model_tofit": [ + "published-models" + ], + "07_egg_egg": [ + "published-models" + ], + "10_egfr_egfr_ode": [ + "published-models" + ], + "11_TLBR_tlbr": [ + "published-models" + ], + "12_TCR_tcr": [ + "published-models" + ], + "13_receptor_example5_starting_point": [ + "published-models" + ], + "14_receptor_nf_receptor_nf": [ + "published-models" + ], + "15_igf1r_IGF1R_fit_all": [ + "published-models" + ], + "17_egfr_ssa_egfr": [ + "published-models" + ], + "18_mapk_Scaff_22_ground": [ + "published-models" + ], + "19_raf_constraint_RAFi": [ + "published-models" + ], + "20_raf_constraint4_RAFi": [ + "published-models" + ], + "24_jnk_JNKmodel_180724_bnf": [ + "published-models" + ], + "26_tcr_sens_tcr_sens_tofit": [ + "published-models" + ], + "28_mapk_ensemble_tofit": [ + "published-models" + ], + "30_jobs_jobs_ground": [ + "published-models" + ], + "31_elephant_elephant": [ + "published-models" + ], + "AB": [ + "native-tutorials" + ], + "ABC": [ + "metabolism", + "native-tutorials" + ], + "ABC_scan": [ + "native-tutorials" + ], + "ABC_ssa": [ + "native-tutorials" + ], + "ABp": [ + "metabolism", + "native-tutorials" + ], + "ABp_approx": [ + "native-tutorials" + ], + "Alabama": [ + "published-models" + ], + "An_2009": [ + "immunology", "published-models" ], + "BAB": [ + "native-tutorials" + ], + "BAB_coop": [ + "native-tutorials" + ], + "BAB_scan": [ + "native-tutorials" + ], "BaruaBCR_2012": [ "immunology", "published-models" @@ -120,6 +207,17 @@ "immunology", "published-models" ], + "Barua_2007": [ + "cancer", + "published-models" + ], + "Barua_2009": [ + "cancer", + "published-models" + ], + "Barua_2013": [ + "published-models" + ], "Blinov_2006": [ "cell-cycle", "published-models" @@ -132,6 +230,9 @@ "cell-cycle", "published-models" ], + "CaMKII_holo": [ + "published-models" + ], "Chattaraj_2021": [ "neuroscience", "published-models" @@ -148,6 +249,24 @@ "immunology", "published-models" ], + "Chylek_library": [ + "native-tutorials" + ], + "CircadianOscillator": [ + "cell-cycle", + "native-tutorials", + "published-models" + ], + "ComplexDegradation": [ + "native-tutorials", + "published-models" + ], + "Creamer_2012": [ + "native-tutorials" + ], + "Dallas": [ + "published-models" + ], "Dembo_1978": [ "physics", "published-models" @@ -156,6 +275,9 @@ "metabolism", "published-models" ], + "Dreisigmeyer_2008": [ + "published-models" + ], "Dushek_2011": [ "immunology", "published-models" @@ -172,8 +294,18 @@ "immunology", "published-models" ], - "fceri_fyn": [ - "immunology", + "FceRI_ji": [ + "native-tutorials" + ], + "FceRI_viz": [ + "native-tutorials", + "published-models" + ], + "GK": [ + "metabolism", + "native-tutorials" + ], + "Gardner_2000": [ "published-models" ], "Goldstein_1980": [ @@ -189,6 +321,15 @@ "multistage", "published-models" ], + "Hlavacek2018Egg_egg": [ + "published-models" + ], + "Hlavacek2018Elephant_elephant_EFA": [ + "published-models" + ], + "Hlavacek2018Restructuration_after_bunching": [ + "published-models" + ], "Hlavacek_1999": [ "physics", "published-models" @@ -197,8 +338,10 @@ "physics", "published-models" ], - "innate_immunity": [ - "immunology", + "Houston": [ + "published-models" + ], + "IGF1R_Model_receptor_activation_bnf": [ "published-models" ], "Jaruszewicz-Blonska_2023": [ @@ -213,6 +356,9 @@ "cell-cycle", "published-models" ], + "Kocieniewski_2012": [ + "published-models" + ], "Kozer_2013": [ "cancer", "published-models" @@ -221,6 +367,24 @@ "cancer", "published-models" ], + "LR": [ + "native-tutorials" + ], + "LRR": [ + "native-tutorials" + ], + "LRR_comp": [ + "native-tutorials" + ], + "LR_comp": [ + "native-tutorials" + ], + "LV": [ + "native-tutorials" + ], + "LV_comp": [ + "native-tutorials" + ], "Lang_2024": [ "cell-cycle", "published-models" @@ -229,6 +393,9 @@ "cancer", "published-models" ], + "Lin2019_ERK_model": [ + "published-models" + ], "Lin_ERK_2019": [ "developmental", "published-models" @@ -241,16 +408,25 @@ "immunology", "published-models" ], + "Lisman": [ + "native-tutorials", + "neuroscience" + ], + "Lisman_bifurcate": [ + "native-tutorials", + "neuroscience" + ], "Macken_1982": [ "physics", "published-models" ], - "mapk-dimers": [ - "cancer", + "Mallela2021_Cities": [ "published-models" ], - "mapk-monomers": [ - "cancer", + "Mallela2021_States": [ + "published-models" + ], + "Mallela2022_MSAs": [ "published-models" ], "Massole_2023": [ @@ -265,6 +441,15 @@ "cancer", "published-models" ], + "Miller2022_NavajoNation": [ + "published-models" + ], + "Miller2025_MEK": [ + "published-models" + ], + "Mitra2019_02_egfr_bnf1_InputFiles_egfr": [ + "published-models" + ], "Model_ZAP": [ "immunology", "published-models" @@ -273,6 +458,9 @@ "immunology", "published-models" ], + "NYC": [ + "published-models" + ], "Nag_2009": [ "cancer", "published-models" @@ -281,6 +469,12 @@ "cancer", "published-models" ], + "Pekalski_2013": [ + "published-models" + ], + "Phoenix": [ + "published-models" + ], "Posner_1995": [ "physics", "published-models" @@ -289,28 +483,44 @@ "physics", "published-models" ], - "degranulation_model": [ - "immunology", + "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF": [ "published-models" ], - "egfr_ode": [ - "cancer", + "RAFi": [ "published-models" ], - "tlbr": [ - "immunology", + "RAFi_ground": [ + "published-models" + ], + "Repressilator": [ + "cell-cycle", + "native-tutorials", + "published-models", + "synbio" + ], + "Rule_based_Ran_transport": [ + "published-models" + ], + "Rule_based_Ran_transport_draft": [ + "published-models" + ], + "Rule_based_egfr_compart": [ "published-models" ], "Rule_based_egfr_tutorial": [ "cancer", "published-models" ], - "vilar_2002": [ - "cell-cycle", + "SIR": [ + "native-tutorials" + ], + "Salazar_Cavazos2019_190127_CHO_EGFR_best_fit": [ "published-models" ], - "vilar_2002b": [ - "cell-cycle", + "Suderman_2013": [ + "native-tutorials" + ], + "Thomas2016_example1_fit": [ "published-models" ], "Yang_2008": [ @@ -356,8 +566,12 @@ "neuroscience", "test-models" ], - "bistable-toggle-switch": [ - "test-models" + "birth-death": [ + "native-tutorials", + "published-models" + ], + "bistable-toggle-switch": [ + "test-models" ], "blood-coagulation-thrombin": [ "immunology", @@ -371,6 +585,9 @@ "physics", "test-models" ], + "cBNGL_simple": [ + "native-tutorials" + ], "calcineurin-nfat-pathway": [ "neuroscience", "test-models" @@ -395,6 +612,10 @@ "cancer", "test-models" ], + "chemistry": [ + "published-models", + "tutorials" + ], "chemotaxis-signal-transduction": [ "test-models" ], @@ -405,6 +626,21 @@ "cell-cycle", "test-models" ], + "compartment_endocytosis": [ + "test-models" + ], + "compartment_membrane_bound": [ + "test-models" + ], + "compartment_nested_transport": [ + "test-models" + ], + "compartment_nuclear_transport": [ + "test-models" + ], + "compartment_organelle_exchange": [ + "test-models" + ], "competitive-enzyme-inhibition": [ "metabolism", "test-models" @@ -419,6 +655,38 @@ "cooperative-binding": [ "test-models" ], + "cs_diffie_hellman": [ + "cs", + "test-models" + ], + "cs_hash_function": [ + "cs", + "test-models" + ], + "cs_huffman": [ + "cs", + "test-models" + ], + "cs_monte_carlo_pi": [ + "cs", + "test-models" + ], + "cs_pagerank": [ + "cs", + "test-models" + ], + "cs_pid_controller": [ + "cs", + "test-models" + ], + "cs_regex_nfa": [ + "cs", + "test-models" + ], + "degranulation_model": [ + "immunology", + "published-models" + ], "dna-damage-repair": [ "cancer", "test-models" @@ -437,22 +705,125 @@ "cell-cycle", "test-models" ], + "eco_coevolution_host_parasite": [ + "ecology", + "test-models" + ], + "eco_food_web_chaos_3sp": [ + "ecology", + "test-models" + ], + "eco_lotka_volterra_grid": [ + "ecology", + "test-models" + ], + "eco_mutualism_obligate": [ + "ecology", + "test-models" + ], + "eco_rock_paper_scissors_spatial": [ + "ecology", + "test-models" + ], + "egfr": [ + "published-models" + ], "egfr-signaling-pathway": [ "cancer", "test-models" ], + "egfr_ground": [ + "published-models" + ], + "egfr_nf": [ + "published-models" + ], + "egfr_ode": [ + "cancer", + "published-models" + ], + "egfr_simple": [ + "native-tutorials" + ], "eif2a-stress-response": [ "test-models" ], "endosomal-sorting-rab": [ "test-models" ], - "erk-nuclear-translocation": [ + "energy_allostery_mwc": [ + "test-models" + ], + "energy_catalysis_mm": [ + "test-models" + ], + "energy_cooperativity_adh": [ + "test-models" + ], + "energy_linear_chain": [ + "test-models" + ], + "energy_transport_pump": [ "test-models" ], "er-stress-response": [ "test-models" ], + "erk-nuclear-translocation": [ + "test-models" + ], + "example1": [ + "published-models" + ], + "example1_BNFfiles_example1": [ + "published-models" + ], + "example2_BNFfiles_example2": [ + "published-models" + ], + "example2_starting_point": [ + "published-models" + ], + "example3_BNFfiles_example3": [ + "published-models" + ], + "example4_BNFfiles_example4": [ + "published-models" + ], + "example5_BNFfiles_example5": [ + "published-models" + ], + "example6_BNFfiles_example6": [ + "published-models" + ], + "extra_CaMKII_Holo": [ + "published-models" + ], + "fceri_fyn": [ + "immunology", + "published-models" + ], + "fceri_gamma2": [ + "published-models" + ], + "fceri_gamma2_ground_truth": [ + "published-models" + ], + "feature_functional_rates_volume": [ + "test-models" + ], + "feature_global_functions_scan": [ + "test-models" + ], + "feature_local_functions_explicit": [ + "test-models" + ], + "feature_symmetry_factors_cyclic": [ + "test-models" + ], + "feature_synthesis_degradation_ss": [ + "test-models" + ], "fgf-signaling-pathway": [ "developmental", "test-models" @@ -463,6 +834,21 @@ "gene-expression-toggle": [ "test-models" ], + "genetic_bistability_energy": [ + "test-models" + ], + "genetic_dna_replication_stochastic": [ + "test-models" + ], + "genetic_goodwin_oscillator": [ + "test-models" + ], + "genetic_translation_kinetics": [ + "test-models" + ], + "genetic_turing_pattern_1d": [ + "test-models" + ], "glioblastoma-egfrviii-signaling": [ "cancer", "test-models" @@ -471,6 +857,12 @@ "metabolism", "test-models" ], + "gm_game_of_life": [ + "test-models" + ], + "gm_ray_marcher": [ + "test-models" + ], "gpcr-desensitization-arrestin": [ "test-models" ], @@ -502,6 +894,10 @@ "immunology", "test-models" ], + "innate_immunity": [ + "immunology", + "published-models" + ], "inositol-phosphate-metabolism": [ "neuroscience", "test-models" @@ -527,6 +923,10 @@ "kir-channel-regulation": [ "test-models" ], + "l-type-calcium-channel-dynamics": [ + "neuroscience", + "test-models" + ], "lac-operon-regulation": [ "metabolism", "test-models" @@ -534,381 +934,345 @@ "lipid-mediated-pip3-signaling": [ "test-models" ], - "l-type-calcium-channel-dynamics": [ - "neuroscience", - "test-models" + "mCaMKII_Ca_Spike": [ + "published-models" + ], + "mapk-dimers": [ + "cancer", + "published-models" + ], + "mapk-monomers": [ + "cancer", + "published-models" ], "mapk-signaling-cascade": [ "cancer", "test-models" ], - "michaelis-menten-kinetics": [ - "metabolism", + "meta_formal_game_theory": [ "test-models" ], - "mtorc2-signaling": [ + "meta_formal_molecular_clock": [ "test-models" ], - "mtor-signaling": [ - "neuroscience", + "meta_formal_petri_net": [ "test-models" ], - "myogenic-differentiation": [ - "developmental", + "michaelis-menten-kinetics": [ + "metabolism", "test-models" ], - "negative-feedback-loop": [ + "ml_gradient_descent": [ + "ml-signal", "test-models" ], - "neurotransmitter-release": [ - "neuroscience", + "ml_hopfield": [ + "ml-signal", "test-models" ], - "nfkb-feedback": [ + "ml_kmeans": [ + "ml-signal", "test-models" ], - "no-cgmp-signaling": [ - "metabolism", + "ml_q_learning": [ + "ml-signal", "test-models" ], - "notch-delta-lateral-inhibition": [ - "developmental", + "ml_svm": [ + "ml-signal", "test-models" ], - "oxidative-stress-response": [ - "test-models" + "model": [ + "published-models" ], - "p38-mapk-signaling": [ - "cancer", - "test-models" + "model_ground": [ + "published-models" ], - "p53-mdm2-oscillator": [ - "cell-cycle", - "test-models" + "model_tofit": [ + "published-models" ], - "parp1-mediated-dna-repair": [ - "cell-cycle", + "mt_arithmetic_compiler": [ + "cs", "test-models" ], - "phosphorelay-chain": [ + "mt_bngl_interpreter": [ + "cs", "test-models" ], - "platelet-activation": [ - "immunology", + "mt_music_sequencer": [ + "cs", "test-models" ], - "predator-prey-dynamics": [ + "mt_pascal_triangle": [ + "cs", "test-models" ], - "quorum-sensing-circuit": [ + "mt_quine": [ + "cs", "test-models" ], - "rab-gtpase-cycle": [ + "mtor-signaling": [ + "neuroscience", "test-models" ], - "rankl-rank-signaling": [ - "developmental", + "mtorc2-signaling": [ "test-models" ], - "ras-gef-gap-cycle": [ - "cancer", + "myogenic-differentiation": [ + "developmental", "test-models" ], - "repressilator-oscillator": [ + "negative-feedback-loop": [ "test-models" ], - "retinoic-acid-signaling": [ - "developmental", + "neurotransmitter-release": [ + "neuroscience", "test-models" ], - "rho-gtpase-actin-cytoskeleton": [ + "nfkb-feedback": [ "test-models" ], - "shp2-phosphatase-regulation": [ + "nfsim_aggregation_gelation": [ "test-models" ], - "signal-amplification-cascade": [ + "nfsim_coarse_graining": [ "test-models" ], - "simple-dimerization": [ + "nfsim_dynamic_compartments": [ "test-models" ], - "sir-epidemic-model": [ - "ecology", - "tutorials", + "nfsim_hybrid_particle_field": [ "test-models" ], - "smad-tgf-beta-signaling": [ - "developmental", + "nfsim_ring_closure_polymer": [ "test-models" ], - "sonic-hedgehog-gradient": [ - "developmental", + "nn_xor": [ + "ml-signal", "test-models" ], - "stat3-mediated-transcription": [ + "no-cgmp-signaling": [ + "metabolism", "test-models" ], - "stress-response-adaptation": [ - "test-models" + "notch": [ + "published-models" ], - "synaptic-plasticity-ltp": [ - "neuroscience", + "notch-delta-lateral-inhibition": [ + "developmental", "test-models" ], - "t-cell-activation": [ - "immunology", + "organelle_transport": [ + "native-tutorials" + ], + "organelle_transport_struct": [ + "native-tutorials" + ], + "oxidative-stress-response": [ "test-models" ], - "tlr3-dsrna-sensing": [ - "immunology", + "p38-mapk-signaling": [ + "cancer", "test-models" ], - "tnf-induced-apoptosis": [ + "p53-mdm2-oscillator": [ "cell-cycle", "test-models" ], - "two-component-system": [ - "test-models" + "parabola": [ + "published-models" ], - "vegf-angiogenesis": [ - "cancer", - "test-models" + "parabola_ground": [ + "published-models" ], - "viral-sensing-innate-immunity": [ - "immunology", + "parp1-mediated-dna-repair": [ + "cell-cycle", "test-models" ], - "wnt-beta-catenin-signaling": [ - "developmental", + "ph_lorenz_attractor": [ + "physics", "test-models" ], - "wound-healing-pdgf-signaling": [ + "ph_nbody_gravity": [ + "physics", "test-models" ], - "compartment_endocytosis": [ + "ph_schrodinger": [ + "physics", "test-models" ], - "compartment_membrane_bound": [ + "ph_wave_equation": [ + "physics", "test-models" ], - "compartment_nested_transport": [ + "phosphorelay-chain": [ "test-models" ], - "compartment_nuclear_transport": [ + "platelet-activation": [ + "immunology", "test-models" ], - "compartment_organelle_exchange": [ - "test-models" + "polymer": [ + "published-models", + "tutorials" ], - "cs_diffie_hellman": [ - "cs", - "test-models" + "polymer_draft": [ + "published-models", + "tutorials" ], - "cs_hash_function": [ - "cs", - "test-models" + "polynomial": [ + "published-models" ], - "cs_huffman": [ - "cs", - "test-models" + "polynomial_ground": [ + "published-models" ], - "cs_monte_carlo_pi": [ - "cs", + "predator-prey-dynamics": [ "test-models" ], - "cs_pagerank": [ - "cs", - "test-models" + "problem16_3cat_model0_tofit": [ + "published-models" ], - "cs_pid_controller": [ - "cs", - "test-models" + "problem16_model0_tofit": [ + "published-models" ], - "cs_regex_nfa": [ - "cs", - "test-models" + "problem32_3cat_model0_tofit": [ + "published-models" ], - "eco_coevolution_host_parasite": [ - "ecology", - "test-models" + "problem32_model0_tofit": [ + "published-models" ], - "eco_food_web_chaos_3sp": [ - "ecology", - "test-models" + "problem4_3cat_model0_tofit": [ + "published-models" ], - "eco_lotka_volterra_grid": [ - "ecology", - "test-models" + "problem4_model0_tofit": [ + "published-models" ], - "eco_mutualism_obligate": [ - "ecology", - "test-models" + "problem64_3cat_model0_tofit": [ + "published-models" ], - "eco_rock_paper_scissors_spatial": [ - "ecology", - "test-models" + "problem64_model0_tofit": [ + "published-models" ], - "energy_allostery_mwc": [ - "test-models" + "problem8_3cat_model0_tofit": [ + "published-models" ], - "energy_catalysis_mm": [ - "test-models" + "problem8_model0_tofit": [ + "published-models" ], - "energy_cooperativity_adh": [ - "test-models" + "problem_quant_model_tofit": [ + "published-models" ], - "energy_linear_chain": [ + "process_actin_treadmilling": [ "test-models" ], - "energy_transport_pump": [ + "process_autophagy_flux": [ "test-models" ], - "feature_functional_rates_volume": [ + "process_cell_adhesion_strength": [ "test-models" ], - "feature_global_functions_scan": [ + "process_kinetic_proofreading_tcr": [ "test-models" ], - "feature_local_functions_explicit": [ + "process_quorum_sensing_switch": [ "test-models" ], - "feature_symmetry_factors_cyclic": [ - "test-models" + "pt303": [ + "published-models" ], - "feature_synthesis_degradation_ss": [ - "test-models" + "pt403": [ + "published-models" ], - "gm_game_of_life": [ - "test-models" + "pt409": [ + "published-models" ], - "gm_ray_marcher": [ - "test-models" + "pybnf_files_rab_mon1ccz1_ox": [ + "published-models" ], - "genetic_bistability_energy": [ - "test-models" + "quasi_equilibrium": [ + "native-tutorials", + "published-models", + "tutorials" ], - "genetic_dna_replication_stochastic": [ + "quorum-sensing-circuit": [ "test-models" ], - "genetic_goodwin_oscillator": [ + "rab-gtpase-cycle": [ "test-models" ], - "genetic_translation_kinetics": [ + "rab_mon1ccz1_ox": [ + "published-models" + ], + "rankl-rank-signaling": [ + "developmental", "test-models" ], - "genetic_turing_pattern_1d": [ + "ras-gef-gap-cycle": [ + "cancer", "test-models" ], - "meta_formal_game_theory": [ + "receptor": [ + "published-models" + ], + "receptor_nf": [ + "published-models" + ], + "repressilator-oscillator": [ "test-models" ], - "meta_formal_molecular_clock": [ + "retinoic-acid-signaling": [ + "developmental", "test-models" ], - "meta_formal_petri_net": [ + "rho-gtpase-actin-cytoskeleton": [ "test-models" ], - "mt_arithmetic_compiler": [ - "cs", + "shp2-phosphatase-regulation": [ "test-models" ], - "mt_bngl_interpreter": [ - "cs", + "signal-amplification-cascade": [ "test-models" ], - "mt_music_sequencer": [ - "cs", + "simple": [ + "published-models", + "tutorials" + ], + "simple-dimerization": [ "test-models" ], - "mt_pascal_triangle": [ - "cs", + "sir-epidemic-model": [ + "ecology", + "test-models", + "tutorials" + ], + "smad-tgf-beta-signaling": [ + "developmental", "test-models" ], - "mt_quine": [ - "cs", + "sonic-hedgehog-gradient": [ + "developmental", "test-models" ], - "ml_gradient_descent": [ + "sp_fourier_synthesizer": [ "ml-signal", "test-models" ], - "ml_hopfield": [ + "sp_image_convolution": [ "ml-signal", "test-models" ], - "ml_kmeans": [ - "ml-signal", - "test-models" - ], - "ml_q_learning": [ - "ml-signal", - "test-models" - ], - "ml_svm": [ - "ml-signal", - "test-models" - ], - "nn_xor": [ + "sp_kalman_filter": [ "ml-signal", "test-models" ], - "nfsim_aggregation_gelation": [ - "test-models" - ], - "nfsim_coarse_graining": [ - "test-models" - ], - "nfsim_dynamic_compartments": [ - "test-models" - ], - "nfsim_hybrid_particle_field": [ - "test-models" - ], - "nfsim_ring_closure_polymer": [ - "test-models" - ], - "ph_lorenz_attractor": [ - "physics", - "test-models" - ], - "ph_nbody_gravity": [ - "physics", - "test-models" - ], - "ph_schrodinger": [ - "physics", - "test-models" - ], - "ph_wave_equation": [ - "physics", - "test-models" - ], - "process_actin_treadmilling": [ - "test-models" - ], - "process_autophagy_flux": [ - "test-models" - ], - "process_cell_adhesion_strength": [ - "test-models" - ], - "process_kinetic_proofreading_tcr": [ - "test-models" - ], - "process_quorum_sensing_switch": [ - "test-models" - ], - "sp_fourier_synthesizer": [ - "ml-signal", + "stat3-mediated-transcription": [ "test-models" ], - "sp_image_convolution": [ - "ml-signal", + "stress-response-adaptation": [ "test-models" ], - "sp_kalman_filter": [ - "ml-signal", + "synaptic-plasticity-ltp": [ + "neuroscience", "test-models" ], "synbio_band_pass_filter": [ @@ -931,456 +1295,92 @@ "synbio", "test-models" ], - "wacky_alchemy_stone": [ - "synbio", + "t-cell-activation": [ + "immunology", "test-models" ], - "wacky_black_hole": [ - "test-models" + "tcr": [ + "published-models" ], - "wacky_bouncing_ball": [ - "physics", - "test-models" + "tlbr": [ + "immunology", + "published-models" ], - "wacky_traffic_jam_asep": [ - "physics", + "tlr3-dsrna-sensing": [ + "immunology", "test-models" ], - "wacky_zombie_infection": [ - "ecology", + "tnf-induced-apoptosis": [ + "cell-cycle", "test-models" ], - "chemistry": [ - "tutorials", - "published-models" - ], - "polymer": [ - "tutorials", - "published-models" - ], - "polymer_draft": [ - "tutorials", - "published-models" - ], - "quasi_equilibrium": [ - "tutorials", + "toggle": [ "native-tutorials", - "published-models" - ], - "simple": [ - "tutorials", - "published-models" + "published-models", + "synbio" ], "toy1": [ - "tutorials", - "published-models" + "published-models", + "tutorials" ], "toy2": [ - "tutorials", - "published-models" - ], - "AB": [ - "native-tutorials" - ], - "ABC": [ - "metabolism", - "native-tutorials" - ], - "ABC_scan": [ - "native-tutorials" - ], - "ABC_ssa": [ - "native-tutorials" - ], - "ABp": [ - "metabolism", - "native-tutorials" - ], - "ABp_approx": [ - "native-tutorials" + "published-models", + "tutorials" ], - "BAB": [ - "native-tutorials" - ], - "BAB_coop": [ - "native-tutorials" - ], - "BAB_scan": [ - "native-tutorials" - ], - "birth-death": [ - "native-tutorials", - "published-models" - ], - "cBNGL_simple": [ - "native-tutorials" + "two-component-system": [ + "test-models" ], - "Chylek_library": [ - "native-tutorials" + "vegf-angiogenesis": [ + "cancer", + "test-models" ], - "CircadianOscillator": [ + "vilar_2002": [ "cell-cycle", - "native-tutorials", - "published-models" - ], - "ComplexDegradation": [ - "native-tutorials", - "published-models" - ], - "Creamer_2012": [ - "native-tutorials" - ], - "egfr_simple": [ - "native-tutorials" - ], - "FceRI_ji": [ - "native-tutorials" - ], - "FceRI_viz": [ - "native-tutorials", "published-models" ], - "GK": [ - "metabolism", - "native-tutorials" - ], - "Lisman": [ - "neuroscience", - "native-tutorials" - ], - "Lisman_bifurcate": [ - "neuroscience", - "native-tutorials" - ], - "LR": [ - "native-tutorials" - ], - "LR_comp": [ - "native-tutorials" - ], - "LRR": [ - "native-tutorials" - ], - "LRR_comp": [ - "native-tutorials" - ], - "LV": [ - "native-tutorials" - ], - "LV_comp": [ - "native-tutorials" - ], - "organelle_transport": [ - "native-tutorials" - ], - "organelle_transport_struct": [ - "native-tutorials" - ], - "Repressilator": [ + "vilar_2002b": [ "cell-cycle", - "synbio", - "native-tutorials", "published-models" ], - "SIR": [ - "native-tutorials" - ], - "Suderman_2013": [ - "native-tutorials" - ], - "toggle": [ - "synbio", - "native-tutorials", + "vilar_2002c": [ "published-models" ], + "viral-sensing-innate-immunity": [ + "immunology", + "test-models" + ], "visualize": [ "native-tutorials", "published-models" ], - "Barua_2013": [ - "published-models" + "wacky_alchemy_stone": [ + "synbio", + "test-models" ], - "Dreisigmeyer_2008": [ - "published-models" + "wacky_black_hole": [ + "test-models" ], - "Gardner_2000": [ - "published-models" + "wacky_bouncing_ball": [ + "physics", + "test-models" ], - "Hlavacek2018Egg_egg": [ - "published-models" + "wacky_traffic_jam_asep": [ + "physics", + "test-models" ], - "Hlavacek2018Elephant_elephant_EFA": [ - "published-models" + "wacky_zombie_infection": [ + "ecology", + "test-models" ], - "Hlavacek2018Restructuration_after_bunching": [ + "wnt": [ "published-models" ], - "Kocieniewski_2012": [ - "published-models" + "wnt-beta-catenin-signaling": [ + "developmental", + "test-models" ], - "Lin2019_ERK_model": [ - "published-models" - ], - "Mallela2021_States": [ - "published-models" - ], - "Mallela2021_Cities": [ - "published-models" - ], - "Alabama": [ - "published-models" - ], - "Mallela2022_MSAs": [ - "published-models" - ], - "Miller2022_NavajoNation": [ - "published-models" - ], - "Miller2025_MEK": [ - "published-models" - ], - "Mitra2019_02_egfr_bnf1_InputFiles_egfr": [ - "published-models" - ], - "02_egfr_egfr": [ - "published-models" - ], - "03_fcerig_fceri_gamma2": [ - "published-models" - ], - "04_egfrnf_egfr_nf": [ - "published-models" - ], - "05_threestep_m1": [ - "published-models" - ], - "06_degranulation_model_tofit": [ - "published-models" - ], - "07_egg_egg": [ - "published-models" - ], - "10_egfr_egfr_ode": [ - "published-models" - ], - "11_TLBR_tlbr": [ - "published-models" - ], - "12_TCR_tcr": [ - "published-models" - ], - "13_receptor_example5_starting_point": [ - "published-models" - ], - "14_receptor_nf_receptor_nf": [ - "published-models" - ], - "15_igf1r_IGF1R_fit_all": [ - "published-models" - ], - "17_egfr_ssa_egfr": [ - "published-models" - ], - "18_mapk_Scaff_22_ground": [ - "published-models" - ], - "19_raf_constraint_RAFi": [ - "published-models" - ], - "20_raf_constraint4_RAFi": [ - "published-models" - ], - "24_jnk_JNKmodel_180724_bnf": [ - "published-models" - ], - "26_tcr_sens_tcr_sens_tofit": [ - "published-models" - ], - "28_mapk_ensemble_tofit": [ - "published-models" - ], - "30_jobs_jobs_ground": [ - "published-models" - ], - "31_elephant_elephant": [ - "published-models" - ], - "model_ground": [ - "published-models" - ], - "problem16_model0_tofit": [ - "published-models" - ], - "problem16_3cat_model0_tofit": [ - "published-models" - ], - "problem32_model0_tofit": [ - "published-models" - ], - "problem32_3cat_model0_tofit": [ - "published-models" - ], - "problem4_model0_tofit": [ - "published-models" - ], - "problem4_3cat_model0_tofit": [ - "published-models" - ], - "problem64_model0_tofit": [ - "published-models" - ], - "problem64_3cat_model0_tofit": [ - "published-models" - ], - "problem8_model0_tofit": [ - "published-models" - ], - "problem8_3cat_model0_tofit": [ - "published-models" - ], - "problem_quant_model_tofit": [ - "published-models" - ], - "rab_mon1ccz1_ox": [ - "published-models" - ], - "pybnf_files_rab_mon1ccz1_ox": [ - "published-models" - ], - "notch": [ - "published-models" - ], - "CaMKII_holo": [ - "published-models" - ], - "extra_CaMKII_Holo": [ - "published-models" - ], - "mCaMKII_Ca_Spike": [ - "published-models" - ], - "Pekalski_2013": [ - "published-models" - ], - "egfr": [ - "published-models" - ], - "egfr_ground": [ - "published-models" - ], - "egfr_nf": [ - "published-models" - ], - "example1": [ - "published-models" - ], - "example2_starting_point": [ - "published-models" - ], - "fceri_gamma2": [ - "published-models" - ], - "fceri_gamma2_ground_truth": [ - "published-models" - ], - "IGF1R_Model_receptor_activation_bnf": [ - "published-models" - ], - "model": [ - "published-models" - ], - "model_tofit": [ - "published-models" - ], - "parabola": [ - "published-models" - ], - "parabola_ground": [ - "published-models" - ], - "polynomial": [ - "published-models" - ], - "polynomial_ground": [ - "published-models" - ], - "RAFi": [ - "published-models" - ], - "RAFi_ground": [ - "published-models" - ], - "receptor": [ - "published-models" - ], - "receptor_nf": [ - "published-models" - ], - "tcr": [ - "published-models" - ], - "pt303": [ - "published-models" - ], - "pt403": [ - "published-models" - ], - "pt409": [ - "published-models" - ], - "Rule_based_egfr_compart": [ - "published-models" - ], - "Rule_based_Ran_transport": [ - "published-models" - ], - "Rule_based_Ran_transport_draft": [ - "published-models" - ], - "Salazar_Cavazos2019_190127_CHO_EGFR_best_fit": [ - "published-models" - ], - "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF": [ - "published-models" - ], - "example1_BNFfiles_example1": [ - "published-models" - ], - "example2_BNFfiles_example2": [ - "published-models" - ], - "example3_BNFfiles_example3": [ - "published-models" - ], - "example4_BNFfiles_example4": [ - "published-models" - ], - "example5_BNFfiles_example5": [ - "published-models" - ], - "example6_BNFfiles_example6": [ - "published-models" - ], - "Thomas2016_example1_fit": [ - "published-models" - ], - "Dallas": [ - "published-models" - ], - "Houston": [ - "published-models" - ], - "NYC": [ - "published-models" - ], - "Phoenix": [ - "published-models" - ], - "vilar_2002c": [ - "published-models" - ], - "wnt": [ - "published-models" + "wound-healing-pdgf-signaling": [ + "test-models" ] }, "sortOverrides": {} diff --git a/gallery.json b/gallery.json index 6d77934e..2b97b9ba 100644 --- a/gallery.json +++ b/gallery.json @@ -1,6 +1,6 @@ { "version": 1, - "generated": "2026-05-03T22:49:19.469Z", + "generated": "2026-05-28T14:08:56.714Z", "categories": [ { "id": "cancer", @@ -100,67 +100,25 @@ } ], "assignments": { - "02_egfr_egfr": [ + "190127_CHO_EGFR_Epigen": [ "published-models" ], - "03_fcerig_fceri_gamma2": [ + "190127_CHO_EGFR_best-fit": [ "published-models" ], - "04_egfrnf_egfr_nf": [ + "190127_CHO_EGFR_sensitivity": [ "published-models" ], - "05_threestep_m1": [ + "190127_CHO_HA_EGFR_L858R": [ "published-models" ], - "06_degranulation_model_tofit": [ + "190127_HMEC": [ "published-models" ], - "07_egg_egg": [ + "190127_HeLa": [ "published-models" ], - "10_egfr_egfr_ode": [ - "published-models" - ], - "11_TLBR_tlbr": [ - "published-models" - ], - "12_TCR_tcr": [ - "published-models" - ], - "13_receptor_example5_starting_point": [ - "published-models" - ], - "14_receptor_nf_receptor_nf": [ - "published-models" - ], - "15_igf1r_IGF1R_fit_all": [ - "published-models" - ], - "17_egfr_ssa_egfr": [ - "published-models" - ], - "18_mapk_Scaff_22_ground": [ - "published-models" - ], - "19_raf_constraint_RAFi": [ - "published-models" - ], - "20_raf_constraint4_RAFi": [ - "published-models" - ], - "24_jnk_JNKmodel_180724_bnf": [ - "published-models" - ], - "26_tcr_sens_tcr_sens_tofit": [ - "published-models" - ], - "28_mapk_ensemble_tofit": [ - "published-models" - ], - "30_jobs_jobs_ground": [ - "published-models" - ], - "31_elephant_elephant": [ + "190127_MCF10A": [ "published-models" ], "AB": [ @@ -183,10 +141,7 @@ "ABp_approx": [ "native-tutorials" ], - "Alabama": [ - "published-models" - ], - "An_2009": [ + "An_TLR4_2009": [ "immunology", "published-models" ], @@ -199,53 +154,59 @@ "BAB_scan": [ "native-tutorials" ], - "BaruaBCR_2012": [ - "immunology", - "published-models" + "BLBR": [ + "native-tutorials" ], - "BaruaFceRI_2012": [ + "Barua_BCR_2012": [ "immunology", "published-models" ], - "Barua_2007": [ + "Barua_EGFR_2007": [ "cancer", "published-models" ], - "Barua_2009": [ + "Barua_FceRI_2012": [ + "immunology", + "published-models" + ], + "Barua_JAK2_2009": [ "cancer", "published-models" ], - "Barua_2013": [ + "Barua_bcat_2013": [ "published-models" ], - "Blinov_2006": [ + "Blinov_egfr_2006": [ "cell-cycle", "published-models" ], - "Blinov_egfr": [ + "Blinov_egfr_NF_2006": [ "cancer", "published-models" ], - "Blinov_ran": [ + "Blinov_ran_2006": [ "cell-cycle", "published-models" ], - "CaMKII_holo": [ - "published-models" + "CaOscillate_Func": [ + "test-models" ], - "Chattaraj_2021": [ + "CaOscillate_Sat": [ + "test-models" + ], + "Chattaraj_nephrin_2021": [ "neuroscience", "published-models" ], - "Cheemalavagu_JAK_STAT": [ + "Cheemalavagu_JAKSTAT_2024": [ "immunology", "published-models" ], - "ChylekFceRI_2014": [ + "Chylek_FceRI_2014": [ "immunology", "published-models" ], - "ChylekTCR_2014": [ + "Chylek_TCR_2014": [ "immunology", "published-models" ], @@ -254,39 +215,41 @@ ], "CircadianOscillator": [ "cell-cycle", - "native-tutorials", - "published-models" + "native-tutorials" ], "ComplexDegradation": [ - "native-tutorials", - "published-models" + "native-tutorials" ], "Creamer_2012": [ "native-tutorials" ], - "Dallas": [ + "Dembo_blbr_1978": [ + "physics", "published-models" ], - "Dembo_1978": [ - "physics", + "Dolan2015": [ + "metabolism", "published-models" ], "Dolan_2015": [ "metabolism", "published-models" ], - "Dreisigmeyer_2008": [ + "Dreisigmeyer_LacOperon_2008": [ "published-models" ], - "Dushek_2011": [ + "Dushek_TCR_2011": [ "immunology", "published-models" ], - "Dushek_2014": [ + "Dushek_TCR_2014": [ "immunology", "published-models" ], - "Erdem_2021": [ + "ERK_model": [ + "published-models" + ], + "Erdem_InsR_2021": [ "metabolism", "published-models" ], @@ -294,76 +257,100 @@ "immunology", "published-models" ], + "Faeder_FceRI_Fyn_2003": [ + "immunology", + "published-models" + ], + "Faeder_egfr_2009": [ + "cancer", + "published-models" + ], + "Faeder_egfr_compart_2009": [ + "published-models" + ], "FceRI_ji": [ "native-tutorials" ], "FceRI_viz": [ - "native-tutorials", - "published-models" + "native-tutorials" ], "GK": [ "metabolism", "native-tutorials" ], - "Gardner_2000": [ + "Gardner_Toggle_2000": [ "published-models" ], - "Goldstein_1980": [ - "physics", + "Goldstein_TLBR_1984": [ + "immunology", "published-models" ], - "Harmon_2017": [ - "immunology", + "Goldstein_blbr_1980": [ + "physics", "published-models" ], - "Hat_2016": [ - "cell-cycle", - "multistage", + "HIV_Dynamics_pt303": [ "published-models" ], - "Hlavacek2018Egg_egg": [ + "HIV_Dynamics_pt403": [ "published-models" ], - "Hlavacek2018Elephant_elephant_EFA": [ + "HIV_Dynamics_pt409": [ "published-models" ], - "Hlavacek2018Restructuration_after_bunching": [ + "Harmon_Antigen_2017": [ + "immunology", "published-models" ], - "Hlavacek_1999": [ - "physics", + "Hat_wip1_2016": [ + "cell-cycle", + "multistage", "published-models" ], - "Hlavacek_2001": [ - "physics", + "Haugh2b": [ + "test-models" + ], + "Hlavacek_Egg_2018": [ "published-models" ], - "Houston": [ + "Hlavacek_Proofreading_2001": [ + "physics", "published-models" ], - "IGF1R_Model_receptor_activation_bnf": [ + "Hlavacek_Steric_1999": [ + "physics", "published-models" ], - "Jaruszewicz-Blonska_2023": [ + "JaruszewiczBlonska_NFkB_2023": [ "immunology", "published-models" ], - "Jung_2017": [ + "Jung_CaMKII_2017": [ "neuroscience", "published-models" ], - "Kesseler_2013": [ + "Kesseler_CellCycle_2013": [ "cell-cycle", "published-models" ], - "Kocieniewski_2012": [ + "Kiefhaber_emodel": [ + "test-models" + ], + "Kocieniewski_published_2012": [ + "published-models" + ], + "Korwek_InnateImmunity_2023": [ + "immunology", "published-models" ], - "Kozer_2013": [ + "Korwek_ViralSensing_2023": [ + "test-models" + ], + "Kozer_egfr_2013": [ "cancer", "published-models" ], - "Kozer_2014": [ + "Kozer_egfr_2014": [ "cancer", "published-models" ], @@ -385,15 +372,15 @@ "LV_comp": [ "native-tutorials" ], - "Lang_2024": [ + "Lang_CellCycle_2024": [ "cell-cycle", "published-models" ], - "Ligon_2014": [ - "cancer", + "Lee_Wnt_2003": [ "published-models" ], - "Lin2019_ERK_model": [ + "Ligon_egfr_2014": [ + "cancer", "published-models" ], "Lin_ERK_2019": [ @@ -416,125 +403,425 @@ "native-tutorials", "neuroscience" ], - "Macken_1982": [ + "MAPK_Dimers_Model": [ + "cancer", + "published-models" + ], + "MAPK_Monomers_Model": [ + "cancer", + "published-models" + ], + "Macken_physics_1982": [ "physics", "published-models" ], - "Mallela2021_Cities": [ + "Mallela_COVID_2021": [ + "published-models" + ], + "Mallela_Cities_2021": [ + "published-models" + ], + "Mallela_MSAs_2022": [ + "published-models" + ], + "Mallela_VaxVariants_Alabama_2022": [ "published-models" ], - "Mallela2021_States": [ + "Mallela_VaxVariants_Dallas_2022": [ "published-models" ], - "Mallela2022_MSAs": [ + "Mallela_VaxVariants_Houston_2022": [ "published-models" ], - "Massole_2023": [ + "Mallela_VaxVariants_MyrtleBeach_2022": [ + "published-models" + ], + "Mallela_VaxVariants_NYC_2022": [ + "published-models" + ], + "Mallela_VaxVariants_Phoenix_2022": [ + "published-models" + ], + "Massole_developmental_2023": [ "developmental", "published-models" ], - "McMillan_2021": [ + "McMillan_TNF_2021": [ "immunology", "published-models" ], - "Mertins_2023": [ + "Mertins_cancer_2023": [ "cancer", "published-models" ], - "Miller2022_NavajoNation": [ + "Miller_MEK_2025": [ "published-models" ], - "Miller2025_MEK": [ + "Miller_NavajoNation_2022": [ "published-models" ], - "Mitra2019_02_egfr_bnf1_InputFiles_egfr": [ + "Mitra_Degranulation_2019": [ "published-models" ], - "Model_ZAP": [ - "immunology", + "Mitra_EGFR_2019": [ "published-models" ], - "Mukhopadhyay_2013": [ - "immunology", + "Mitra_EGFR_NF_2019": [ + "published-models" + ], + "Mitra_EGFR_ODE_2019": [ + "published-models" + ], + "Mitra_EggOscillator_2019": [ + "published-models" + ], + "Mitra_ElephantFitting_2019": [ "published-models" ], - "NYC": [ + "Mitra_FceRI_gamma2_2019": [ "published-models" ], - "Nag_2009": [ + "Mitra_IGF1R_2019": [ + "published-models" + ], + "Mitra_JNK_2019": [ + "published-models" + ], + "Mitra_Likelihood_2019": [ + "published-models" + ], + "Mitra_Likelihood_P16_2019": [ + "published-models" + ], + "Mitra_Likelihood_P16_3cat_2019": [ + "published-models" + ], + "Mitra_Likelihood_P32_2019": [ + "published-models" + ], + "Mitra_Likelihood_P32_3cat_2019": [ + "published-models" + ], + "Mitra_Likelihood_P4_2019": [ + "published-models" + ], + "Mitra_Likelihood_P4_3cat_2019": [ + "published-models" + ], + "Mitra_Likelihood_P64_2019": [ + "published-models" + ], + "Mitra_Likelihood_P64_3cat_2019": [ + "published-models" + ], + "Mitra_Likelihood_P8_2019": [ + "published-models" + ], + "Mitra_Likelihood_P8_3cat_2019": [ + "published-models" + ], + "Mitra_Likelihood_Quant_2019": [ + "published-models" + ], + "Mitra_RafConstraint4_2019": [ + "published-models" + ], + "Mitra_RafConstraint_2019": [ + "published-models" + ], + "Mitra_SimpleReceptor_NF_2019": [ + "published-models" + ], + "Mitra_TCRSensitivity_2019": [ + "published-models" + ], + "Mitra_TCR_2019": [ + "published-models" + ], + "Mitra_TLBR_2019": [ + "published-models" + ], + "Motivating_example": [ + "test-models" + ], + "Motivating_example_cBNGL": [ + "test-models" + ], + "Mukhopadhyay_TCR_2013": [ + "immunology", + "published-models" + ], + "Nag_cancer_2009": [ "cancer", "published-models" ], - "Nosbisch_2022": [ + "Nosbisch_cancer_2022": [ "cancer", "published-models" ], - "Pekalski_2013": [ + "Notch_Signaling_Pathway": [ + "published-models" + ], + "Ordyan_CaMKIIholo_2020": [ "published-models" ], - "Phoenix": [ + "Ordyan_extraCaMKIIHolo_2020": [ "published-models" ], - "Posner_1995": [ + "Ordyan_mCaMKIICaSpike_2020": [ + "published-models" + ], + "Pekalski_published_2013": [ + "published-models" + ], + "Posner_blbr_1995": [ "physics", "published-models" ], - "Posner_2004": [ + "Posner_blbr_2004": [ "physics", "published-models" ], "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF": [ "published-models" ], - "RAFi": [ + "PyBioNetGen_Actions_Syntax": [ + "test-models" + ], + "PyBioNetGen_BNG_Error": [ + "test-models" + ], + "PyBioNetGen_Core_Parabola": [ "published-models" ], - "RAFi_ground": [ + "PyBioNetGen_Core_Parabola_Demo": [ "published-models" ], - "Repressilator": [ - "cell-cycle", - "native-tutorials", - "published-models", - "synbio" + "PyBioNetGen_Core_Parabola_Ground": [ + "published-models" + ], + "PyBioNetGen_Core_Polynomial": [ + "published-models" + ], + "PyBioNetGen_Core_Polynomial_Ground": [ + "published-models" ], - "Rule_based_Ran_transport": [ + "PyBioNetGen_Core_RAFi": [ "published-models" ], - "Rule_based_Ran_transport_draft": [ + "PyBioNetGen_Core_RAFi_Ground": [ "published-models" ], - "Rule_based_egfr_compart": [ + "PyBioNetGen_Core_Receptor": [ "published-models" ], - "Rule_based_egfr_tutorial": [ + "PyBioNetGen_Core_Receptor_NF": [ + "published-models" + ], + "PyBioNetGen_Core_TCR": [ + "published-models" + ], + "PyBioNetGen_Core_TLBR": [ + "immunology", + "published-models" + ], + "PyBioNetGen_Degranulation_Model": [ + "immunology", + "published-models" + ], + "PyBioNetGen_EGFR_Ground": [ + "published-models" + ], + "PyBioNetGen_EGFR_Model": [ + "published-models" + ], + "PyBioNetGen_EGFR_NF": [ + "published-models" + ], + "PyBioNetGen_EGFR_ODE": [ + "cancer", + "published-models" + ], + "PyBioNetGen_EGFR_ODE_Pub": [ "cancer", "published-models" ], + "PyBioNetGen_Egg": [ + "test-models" + ], + "PyBioNetGen_ErrNoFrees": [ + "test-models" + ], + "PyBioNetGen_Example1": [ + "published-models" + ], + "PyBioNetGen_Example2_Start": [ + "published-models" + ], + "PyBioNetGen_FceRI_Gamma2": [ + "published-models" + ], + "PyBioNetGen_FceRI_Gamma2_Ground": [ + "published-models" + ], + "PyBioNetGen_FreeMissing": [ + "test-models" + ], + "PyBioNetGen_IGF1R_Activation": [ + "published-models" + ], + "PyBioNetGen_LilyIgE": [ + "test-models" + ], + "PyBioNetGen_Model": [ + "published-models" + ], + "PyBioNetGen_Model_ToFit": [ + "published-models" + ], + "PyBioNetGen_Model_aMCMC": [ + "published-models" + ], + "PyBioNetGen_NFmodel": [ + "test-models" + ], + "PyBioNetGen_NoFrees": [ + "test-models" + ], + "PyBioNetGen_NoGenerateNetwork": [ + "test-models" + ], + "PyBioNetGen_NoSuffix": [ + "test-models" + ], + "PyBioNetGen_Parabola": [ + "test-models" + ], + "PyBioNetGen_Parabola2": [ + "test-models" + ], + "PyBioNetGen_Parabola_Files": [ + "test-models" + ], + "PyBioNetGen_Parabola_Special": [ + "test-models" + ], + "PyBioNetGen_ParamsEverywhere": [ + "test-models" + ], + "PyBioNetGen_Polynomial_T6": [ + "test-models" + ], + "PyBioNetGen_Simple": [ + "test-models" + ], + "PyBioNetGen_Simple_AddActions": [ + "test-models" + ], + "PyBioNetGen_Simple_Answer": [ + "test-models" + ], + "PyBioNetGen_Simple_GenOnly": [ + "test-models" + ], + "PyBioNetGen_Simple_NF_Seed": [ + "test-models" + ], + "PyBioNetGen_Simple_NoGen": [ + "test-models" + ], + "PyBioNetGen_Tricky": [ + "test-models" + ], + "PyBioNetGen_TrickyUS": [ + "test-models" + ], + "PyBioNetGen_Trivial": [ + "test-models" + ], + "Ran_NuclearTransport": [ + "published-models" + ], + "Ran_NuclearTransport_Draft": [ + "published-models" + ], + "Repressilator": [ + "cell-cycle", + "native-tutorials", + "synbio" + ], + "SHP2_base_model": [ + "test-models" + ], "SIR": [ "native-tutorials" ], - "Salazar_Cavazos2019_190127_CHO_EGFR_best_fit": [ + "Scaff-22_ground": [ + "published-models" + ], + "Scaff-22_tofit": [ "published-models" ], "Suderman_2013": [ "native-tutorials" ], - "Thomas2016_example1_fit": [ + "TCR_model": [ + "published-models" + ], + "Thomas_Example1_2016": [ + "published-models" + ], + "Thomas_Example2_2016": [ + "published-models" + ], + "Thomas_Example3_2016": [ + "published-models" + ], + "Thomas_Example4_2016": [ + "published-models" + ], + "Thomas_Example5_2016": [ "published-models" ], - "Yang_2008": [ + "Thomas_Example6_2016": [ + "published-models" + ], + "Vilar_Circadian_2002": [ + "cell-cycle", + "published-models" + ], + "Vilar_Circadian_2002b": [ + "cell-cycle", + "published-models" + ], + "Vilar_Circadian_2002c": [ + "published-models" + ], + "Yang_tlbr_2008": [ "physics", "published-models" ], - "Zhang_2021": [ + "ZAP70_immunology_2021": [ + "immunology", + "published-models" + ], + "Zhang_developmental_2021": [ "developmental", "published-models" ], - "Zhang_2023": [ + "Zhang_developmental_2023": [ "developmental", "published-models" ], + "after_bunching": [ + "published-models" + ], + "after_decoupling": [ + "published-models" + ], + "after_scaling": [ + "published-models" + ], "akt-signaling": [ "test-models" ], @@ -562,13 +849,21 @@ "immunology", "test-models" ], + "before_bunching": [ + "published-models" + ], + "before_decoupling": [ + "published-models" + ], + "before_scaling": [ + "published-models" + ], "beta-adrenergic-response": [ "neuroscience", "test-models" ], "birth-death": [ - "native-tutorials", - "published-models" + "native-tutorials" ], "bistable-toggle-switch": [ "test-models" @@ -600,6 +895,9 @@ "cell-cycle", "test-models" ], + "catalysis": [ + "test-models" + ], "cd40-signaling": [ "immunology", "test-models" @@ -608,12 +906,14 @@ "cell-cycle", "test-models" ], + "check_scaling": [ + "published-models" + ], "checkpoint-kinase-signaling": [ "cancer", "test-models" ], "chemistry": [ - "published-models", "tutorials" ], "chemotaxis-signal-transduction": [ @@ -652,6 +952,9 @@ "contact-inhibition-hippo-yap": [ "test-models" ], + "continue": [ + "test-models" + ], "cooperative-binding": [ "test-models" ], @@ -683,10 +986,6 @@ "cs", "test-models" ], - "degranulation_model": [ - "immunology", - "published-models" - ], "dna-damage-repair": [ "cancer", "test-models" @@ -735,12 +1034,14 @@ "egfr_ground": [ "published-models" ], - "egfr_nf": [ - "published-models" + "egfr_net": [ + "test-models" ], - "egfr_ode": [ - "cancer", - "published-models" + "egfr_net_red": [ + "test-models" + ], + "egfr_path": [ + "test-models" ], "egfr_simple": [ "native-tutorials" @@ -748,6 +1049,12 @@ "eif2a-stress-response": [ "test-models" ], + "elephant_EFA": [ + "published-models" + ], + "elephant_fit": [ + "published-models" + ], "endosomal-sorting-rab": [ "test-models" ], @@ -760,12 +1067,18 @@ "energy_cooperativity_adh": [ "test-models" ], + "energy_example1": [ + "test-models" + ], "energy_linear_chain": [ "test-models" ], "energy_transport_pump": [ "test-models" ], + "ensemble_tofit": [ + "published-models" + ], "er-stress-response": [ "test-models" ], @@ -773,41 +1086,38 @@ "test-models" ], "example1": [ - "published-models" + "test-models" ], - "example1_BNFfiles_example1": [ + "example1_fit": [ "published-models" ], - "example2_BNFfiles_example2": [ + "example2_fit": [ "published-models" ], - "example2_starting_point": [ + "example3_fit": [ "published-models" ], - "example3_BNFfiles_example3": [ + "example4_fit": [ "published-models" ], - "example4_BNFfiles_example4": [ + "example5_fit": [ "published-models" ], - "example5_BNFfiles_example5": [ + "example5_ground_truth": [ "published-models" ], - "example6_BNFfiles_example6": [ + "example5_starting_point": [ "published-models" ], - "extra_CaMKII_Holo": [ + "example6_ground_truth": [ "published-models" ], - "fceri_fyn": [ + "fceri_ji": [ "immunology", "published-models" ], - "fceri_gamma2": [ - "published-models" - ], - "fceri_gamma2_ground_truth": [ - "published-models" + "fceri_ji_comp": [ + "test-models" ], "feature_functional_rates_volume": [ "test-models" @@ -870,6 +1180,9 @@ "developmental", "test-models" ], + "heise": [ + "test-models" + ], "hematopoietic-growth-factor": [ "test-models" ], @@ -894,10 +1207,6 @@ "immunology", "test-models" ], - "innate_immunity": [ - "immunology", - "published-models" - ], "inositol-phosphate-metabolism": [ "neuroscience", "test-models" @@ -913,6 +1222,9 @@ "ire1a-xbp1-er-stress": [ "test-models" ], + "issue_198_short": [ + "test-models" + ], "jak-stat-cytokine-signaling": [ "immunology", "test-models" @@ -920,6 +1232,12 @@ "jnk-mapk-signaling": [ "test-models" ], + "jobs_ground": [ + "published-models" + ], + "jobs_tofit": [ + "published-models" + ], "kir-channel-regulation": [ "test-models" ], @@ -934,15 +1252,16 @@ "lipid-mediated-pip3-signaling": [ "test-models" ], - "mCaMKII_Ca_Spike": [ + "localfunc": [ + "test-models" + ], + "m1": [ "published-models" ], - "mapk-dimers": [ - "cancer", + "m1_ground": [ "published-models" ], - "mapk-monomers": [ - "cancer", + "machine_tofit": [ "published-models" ], "mapk-signaling-cascade": [ @@ -962,6 +1281,12 @@ "metabolism", "test-models" ], + "michment": [ + "test-models" + ], + "michment_cont": [ + "test-models" + ], "ml_gradient_descent": [ "ml-signal", "test-models" @@ -982,14 +1307,8 @@ "ml-signal", "test-models" ], - "model": [ - "published-models" - ], - "model_ground": [ - "published-models" - ], - "model_tofit": [ - "published-models" + "motor": [ + "test-models" ], "mt_arithmetic_compiler": [ "cs", @@ -1018,6 +1337,9 @@ "mtorc2-signaling": [ "test-models" ], + "mwc": [ + "test-models" + ], "myogenic-differentiation": [ "developmental", "test-models" @@ -1029,9 +1351,15 @@ "neuroscience", "test-models" ], + "nfkb": [ + "test-models" + ], "nfkb-feedback": [ "test-models" ], + "nfkb_illustrating_protocols": [ + "test-models" + ], "nfsim_aggregation_gelation": [ "test-models" ], @@ -1055,9 +1383,6 @@ "metabolism", "test-models" ], - "notch": [ - "published-models" - ], "notch-delta-lateral-inhibition": [ "developmental", "test-models" @@ -1079,12 +1404,6 @@ "cell-cycle", "test-models" ], - "parabola": [ - "published-models" - ], - "parabola_ground": [ - "published-models" - ], "parp1-mediated-dna-repair": [ "cell-cycle", "test-models" @@ -1113,53 +1432,21 @@ "test-models" ], "polymer": [ - "published-models", "tutorials" ], "polymer_draft": [ - "published-models", "tutorials" ], - "polynomial": [ - "published-models" + "polymer_fixed": [ + "tutorials" ], - "polynomial_ground": [ - "published-models" + "polynomial": [ + "test-models" ], "predator-prey-dynamics": [ "test-models" ], - "problem16_3cat_model0_tofit": [ - "published-models" - ], - "problem16_model0_tofit": [ - "published-models" - ], - "problem32_3cat_model0_tofit": [ - "published-models" - ], - "problem32_model0_tofit": [ - "published-models" - ], - "problem4_3cat_model0_tofit": [ - "published-models" - ], - "problem4_model0_tofit": [ - "published-models" - ], - "problem64_3cat_model0_tofit": [ - "published-models" - ], - "problem64_model0_tofit": [ - "published-models" - ], - "problem8_3cat_model0_tofit": [ - "published-models" - ], - "problem8_model0_tofit": [ - "published-models" - ], - "problem_quant_model_tofit": [ + "prion_model": [ "published-models" ], "process_actin_treadmilling": [ @@ -1177,21 +1464,8 @@ "process_quorum_sensing_switch": [ "test-models" ], - "pt303": [ - "published-models" - ], - "pt403": [ - "published-models" - ], - "pt409": [ - "published-models" - ], - "pybnf_files_rab_mon1ccz1_ox": [ - "published-models" - ], "quasi_equilibrium": [ "native-tutorials", - "published-models", "tutorials" ], "quorum-sensing-circuit": [ @@ -1203,6 +1477,15 @@ "rab_mon1ccz1_ox": [ "published-models" ], + "rab_rab5_ox": [ + "published-models" + ], + "rab_rab7_ox": [ + "published-models" + ], + "rab_wt": [ + "published-models" + ], "rankl-rank-signaling": [ "developmental", "test-models" @@ -1211,11 +1494,17 @@ "cancer", "test-models" ], + "rec_dim": [ + "test-models" + ], + "rec_dim_comp": [ + "test-models" + ], "receptor": [ "published-models" ], "receptor_nf": [ - "published-models" + "test-models" ], "repressilator-oscillator": [ "test-models" @@ -1234,12 +1523,20 @@ "test-models" ], "simple": [ - "published-models", "tutorials" ], "simple-dimerization": [ "test-models" ], + "simple_nfsim_test": [ + "tutorials" + ], + "simple_sbml_import": [ + "test-models" + ], + "simple_system": [ + "test-models" + ], "sir-epidemic-model": [ "ecology", "test-models", @@ -1299,12 +1596,41 @@ "immunology", "test-models" ], - "tcr": [ - "published-models" + "test_ANG_synthesis_simple": [ + "test-models" ], - "tlbr": [ - "immunology", - "published-models" + "test_MM": [ + "test-models" + ], + "test_fixed": [ + "test-models" + ], + "test_mratio": [ + "test-models" + ], + "test_network_gen": [ + "test-models" + ], + "test_sat": [ + "test-models" + ], + "test_synthesis_cBNGL_simple": [ + "test-models" + ], + "test_synthesis_complex": [ + "test-models" + ], + "test_synthesis_complex_0_cBNGL": [ + "test-models" + ], + "test_synthesis_complex_source_cBNGL": [ + "test-models" + ], + "test_synthesis_simple": [ + "test-models" + ], + "tlmr": [ + "test-models" ], "tlr3-dsrna-sensing": [ "immunology", @@ -1316,42 +1642,36 @@ ], "toggle": [ "native-tutorials", - "published-models", "synbio" ], + "toy-jim": [ + "test-models" + ], "toy1": [ - "published-models", "tutorials" ], "toy2": [ - "published-models", "tutorials" ], + "translateSBML": [ + "native-tutorials" + ], "two-component-system": [ "test-models" ], + "univ_synth": [ + "test-models" + ], "vegf-angiogenesis": [ "cancer", "test-models" ], - "vilar_2002": [ - "cell-cycle", - "published-models" - ], - "vilar_2002b": [ - "cell-cycle", - "published-models" - ], - "vilar_2002c": [ - "published-models" - ], "viral-sensing-innate-immunity": [ "immunology", "test-models" ], "visualize": [ - "native-tutorials", - "published-models" + "native-tutorials" ], "wacky_alchemy_stone": [ "synbio", @@ -1372,9 +1692,6 @@ "ecology", "test-models" ], - "wnt": [ - "published-models" - ], "wnt-beta-catenin-signaling": [ "developmental", "test-models" diff --git a/manifest-slim.json b/manifest-slim.json index cc4a4857..e2a0863c 100644 --- a/manifest-slim.json +++ b/manifest-slim.json @@ -1,108 +1,68 @@ [ { - "id": "03_fcerig_fceri_gamma2", - "name": "03-fcerig", - "description": "Added molecule type definition block so that the", + "id": "AB", + "name": "AB", + "description": "BioNetGen model: AB", "tags": [ - "immunology" + "ab" ], - "category": "immunology", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "04_egfrnf_egfr_nf", - "name": "example2_starting_point.bngl", - "description": "Filename: example2_starting_point.bngl", + "id": "ABC", + "name": "ABC", + "description": "BioNetGen model: ABC", "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" + "abc" ], - "category": "signaling", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "metabolism", + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "06_degranulation_model_tofit", - "name": "of IgE receptor signaling", - "description": "A model of IgE receptor signaling", + "id": "ABC_scan", + "name": "ABC scan", + "description": "BioNetGen model: ABC scan", "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" + "abc", + "scan", + "parameter_scan" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -112,169 +72,175 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "07_egg_egg", - "name": "07-egg", - "description": "BNGL model: egg", + "id": "ABC_ssa", + "name": "ABC ssa", + "description": "BioNetGen model: ABC ssa", "tags": [ - "a0", - "a1", - "a2", - "b1", - "b2", - "c0", - "c1", - "c2", - "d1", - "d2", - "period", - "t", - "species" + "abc", + "ssa" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "ssa" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "10_egfr_egfr_ode", - "name": "example1.bngl", - "description": "Filename: example1.bngl", + "id": "ABp", + "name": "ABp", + "description": "title: ABp.bngl", "tags": [ - "lt", - "rt", - 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"gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "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.", + "id": "allosteric-activation", + "name": "allosteric activation", + "description": "Binding constants", "tags": [ - "molecules", - "species" + "allosteric", + "activation", + "enzyme", + "substrate", + "activator", + "product" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "15_igf1r_IGF1R_fit_all", - "name": "15-igf1r", - "description": "Author: William S. Hlavacek", + "id": "ampk-signaling", + "name": "ampk signaling", + "description": "AMPK signaling: The cellular energy sensor.", "tags": [ - "dilution", - "a1_permpers", - "a2_permpers", - "molecules" + "ampk", + "signaling", + "amp", + "lkb1", + "ca", + "sik", + "crtc" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -284,31 +250,29 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "19_raf_constraint_RAFi", - "name": "19-raf-constraint", - "description": "BNGL model: RAFi", + "id": "An_TLR4_2009", + "name": "An et al. 2009: TLR4 Signaling Model", + "description": "TLR4 signaling", "tags": [ - "k1", - "k2", - "k3", - "k5", - "kf1", - "kf2", - "kf3", - "kf4", - "kf5", - "kf6", - "rtot", - "ifree", - "species" + "tlr4", + "immune-signaling", + "innate-immunity", + "2009", + "an" ], - "category": "other", + "category": "immunology", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -317,141 +281,98 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "190127_CHO_EGFR_best-fit", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "apoptosis-cascade", + "name": "apoptosis cascade", + "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", "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" + "apoptosis", + "cascade", + "deathligand", + "caspase8", + "bid", + "mito", + "apaf1", + "caspase3", + "xiap", + "smac" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "190127_CHO_EGFR_Epigen", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "auto-activation-loop", + "name": "auto activation loop", + "description": "Auto-activation loop: A positive feedback circuit.", "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" + "auto", + "activation", + "loop", + "gene", + "mrna", + "protein", + "rbp" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "190127_CHO_EGFR_sensitivity", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "autophagy-regulation", + "name": "autophagy regulation", + "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", "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" + "autophagy", + "regulation", + "mtor", + "ampk", + "ulk1", + "lc3", + "p62" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -461,141 +382,79 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "190127_CHO_HA_EGFR_L858R", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "BAB", + "name": "BAB", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", "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" + "bab" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "190127_HeLa", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "BAB_coop", + "name": "BAB coop", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", "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" + "bab", + "coop" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "190127_HMEC", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "BAB_scan", + "name": "BAB scan", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", "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" + "bab", + "scan", + "parameter_scan" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -605,48 +464,30 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "190127_MCF10A", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "Barua_bcat_2013", + "name": "Barua et al. 2013: Beta-Catenin Regulation Model", + "description": "Beta-catenin destruction", "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" + "beta-catenin", + "regulation", + "wnt-signaling", + "2013", + "barua" ], - "category": "other", + "category": "regulation", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -654,28 +495,23 @@ ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "20_raf_constraint4_RAFi", - "name": "20-raf-constraint4", - "description": "BNGL model: RAFi", + "id": "Barua_BCR_2012", + "name": "Barua et al. 2012: BCR Signaling Model", + "description": "BCR signaling", "tags": [ - "k1", - "k2", - "k3", - "k5", - "kf1", - "kf2", - "kf3", - "kf4", - "kf5", - "kf6", - "rtot", - "ifree", - "species" + "bcr", + "immune-signaling", + "b-cell", + "2012", + "barua" ], - "category": "other", + "category": "immunology", "origin": "published", "visible": false, "compatibility": { @@ -686,235 +522,155 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "24_jnk_JNKmodel_180724_bnf", - "name": "24-jnk", - "description": "BNGL model: JNKmodel_180724_bnf", + "id": "Barua_EGFR_2007", + "name": "Barua et al. 2007: EGFR Signaling Model", + "description": "Model from Haugh (2006)", "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" + "egfr", + "signaling", + "2007", + "barua" ], - "category": "other", + "category": "signaling", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "cancer" + ], + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "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", + "id": "Barua_FceRI_2012", + "name": "Barua et al. 2012: FceRI Signaling Model", + "description": "FcεRI signaling", "tags": [ - "immunology" + "fceri", + "immune-signaling", + "mast-cell", + "2012", + "barua" ], "category": "immunology", "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "31_elephant_elephant", - "name": "31-elephant", - "description": "BNGL model: elephant", + "id": "Barua_JAK2_2009", + "name": "Barua et al. 2009: JAK2-STAT5 Signaling Model", + "description": "JAK2-SH2B signaling", "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" + "jak2", + "stat5", + "signaling", + "2009", + "barua" ], - "category": "other", + "category": "signaling", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "cancer" + ], + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "AB", - "name": "AB", - "description": "BioNetGen model: AB", + "id": "bcr-signaling", + "name": "bcr signaling", + "description": "BCR signaling: The B-cell antigen receptor cascade.", "tags": [ - "ab", - "a", - "b", - "simulate" + "bcr", + "signaling", + "antigen", + "syk", + "plcg2", + "cd22", + "shp1", + "calcium" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "immunology", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ABC", - "name": "ABC", - "description": "BioNetGen model: ABC", + "id": "beta-adrenergic-response", + "name": "beta adrenergic response", + "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", "tags": [ - "abc", - "a", - "simulate" + "beta", + "adrenergic", + "response", + "epi", + "betar", + "gs", + "ac", + "arr", + "camp" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": true, @@ -924,228 +680,247 @@ ] }, "gallery": [ - "metabolism", - "native-tutorials" + "neuroscience", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ABC_scan", - "name": "ABC scan", - "description": "BioNetGen model: ABC scan", + "id": "birth-death", + "name": "Birth-Death", + "description": "Stochastic process", "tags": [ - "abc", - "scan", - "a", - "generate_network", - "parameter_scan" + "birth", + "death", + "saveconcentrations" ], "category": "tutorial", "origin": "tutorial", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ABC_ssa", - "name": "ABC ssa", - "description": "BioNetGen model: ABC ssa", + "id": "bistable-toggle-switch", + "name": "bistable toggle switch", + "description": "Genetic Toggle Switch: Mutual repression circuit.", "tags": [ - "abc", - "ssa", - "a", - "simulate" + "bistable", + "toggle", + "switch", + "proml", + "promr", + "tf_l", + "tf_r", + "ind_l", + "ind_r" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "native-tutorials" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ABp", - "name": "ABp", - "description": "title: ABp.bngl", + "id": "BLBR", + "name": "BLBR", + "description": "title: BLBR.bngl", "tags": [ - "abp", - "a", - "b", - "simulate" + "blbr" ], "category": "tutorial", "origin": "tutorial", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ode" + "ode", + "nf" ] }, "gallery": [ - "metabolism", - "native-tutorials" + "tutorial" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ABp_approx", - "name": "ABp approx", - "description": "title: ABp.bngl", + "id": "Blinov_egfr_2006", + "name": "Blinov et al. 2006: EGFR Signaling Pathway (ODE)", + "description": "Phosphotyrosine signaling", "tags": [ - "abp", - "approx", - "km", - "a", - "b", - "simulate" + "egfr", + "signaling", + "ode", + "receptor-activation", + "2006", + "blinov" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "published", "visible": true, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "cell-cycle" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "actions_syntax", - "name": "actions syntax", - "description": "Original values used to generate parabola.exp", + "id": "Blinov_egfr_NF_2006", + "name": "Blinov et al. 2006: EGFR Signaling Pathway (NFsim)", + "description": "EGFR signaling model", "tags": [ - "actions", - "syntax", - "counter", - "y", - "generate_network", - "simulate" + "egfr", + "signaling", + "nfsim", + "receptor-activation", + "2006", + "blinov" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "validation" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "after_bunching", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Blinov_ran_2006", + "name": "Blinov et al. 2006: Ran-Mediated Nuclear Transport (NFsim)", + "description": "Ran GTPase cycle", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "ran-gtpase", + "nuclear-transport", + "nfsim", + "2006", + "blinov" ], - "category": "other", + "category": "regulation", "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "cell-cycle" + ], + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "after_decoupling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "blood-coagulation-thrombin", + "name": "blood coagulation thrombin", + "description": "Blood coagulation: Thrombin burst and feedback propagation.", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "blood", + "coagulation", + "thrombin", + "tf", + "factorx", + "factorv", + "prothrombin", + "fibrinogen", + "at" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "after_scaling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "bmp-signaling", + "name": "bmp signaling", + "description": "BMP-Smad signaling: Developmental gradient relay.", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "bmp", + "signaling", + "noggin", + "receptor1", + "receptor2", + "smad1", + "smad4", + "smad6" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -1155,22 +930,26 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "akt-signaling", - "name": "akt signaling", - "description": "Signaling rates", + "id": "brusselator-oscillator", + "name": "brusselator oscillator", + "description": "The Brusselator: Auto-catalytic chemical oscillator.", "tags": [ - "akt", - "signaling", - "growthfactor", - "rtk", - "pi3k", - "mtorc2", - "mtorc1", - "s6k" + "brusselator", + "oscillator", + "a", + "b", + "x", + "y" ], "category": "signaling", "origin": "ai-generated", @@ -1184,27 +963,29 @@ ] }, "gallery": [ + "physics", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Alabama", - "name": "Alabama", - "description": "reporting period (1 d)", + "id": "calcineurin-nfat-pathway", + "name": "calcineurin nfat pathway", + "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", "tags": [ - "alabama", - "fdcs", - "counter", - "s", - "e1", - "e2", - "e3", - "e4", - "e5" + "calcineurin", + "nfat", + "pathway", + "ca", + "cam", + "can", + "rcan1" ], - "category": "epidemiology", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -1215,21 +996,26 @@ ] }, "gallery": [ - "epidemiology" + "neuroscience", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "allosteric-activation", - "name": "allosteric activation", - "description": "Binding constants", + "id": "calcium-spike-signaling", + "name": "calcium spike signaling", + "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", "tags": [ - "allosteric", - "activation", - "enzyme", - "substrate", - "activator", - "product" + "calcium", + "spike", + "signaling", + "plc", + "ip3", + "ca", + "stim1" ], "category": "signaling", "origin": "ai-generated", @@ -1243,97 +1029,93 @@ ] }, "gallery": [ - "metabolism", + "neuroscience", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ampk-signaling", - "name": "ampk signaling", - "description": "AMPK signaling: The cellular energy sensor.", + "id": "CaOscillate_Func", + "name": "CaOscillate_Func", + "description": "Calcium oscillations (func)", "tags": [ - "ampk", - "signaling", - "amp", - "lkb1", - "ca", - "sik", - "crtc" + "caoscillate", + "ga", + "plc", + "ca" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, - "gallery": [ - "neuroscience", - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "An_2009", - "name": "An 2009", - "description": "TLR4 signaling", + "id": "CaOscillate_Sat", + "name": "CaOscillate_Sat", + "description": "Calcium oscillations (sat)", "tags": [ - "published", - "immunology", - "an", - "2009", - "cd14", - "md2", - "tlr4", - "tram", - "trif", - "sarm", - "traf4", - "irak1" + "caoscillate", + "sat", + "ga", + "plc", + "ca" ], - "category": "immunology", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "immunology" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "apoptosis-cascade", - "name": "apoptosis cascade", - "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", + "id": "caspase-activation-loop", + "name": "caspase activation loop", + "description": "Caspase activation loop: The executioner feedback system.", "tags": [ - "apoptosis", - "cascade", + "caspase", + "activation", + "loop", "deathligand", "caspase8", - "bid", - "mito", - "apaf1", "caspase3", - "xiap", - "smac" + "iap", + "flip" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" @@ -1343,54 +1125,24 @@ "cell-cycle", "test-models" ], - "collectionId": null - }, - { - "id": "auto-activation-loop", - "name": "auto activation loop", - "description": "Auto-activation loop: A positive feedback circuit.", - "tags": [ - "auto", - "activation", - "loop", - "gene", - "mrna", - "protein", - "rbp" - ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "metabolism", - "test-models" - ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "autophagy-regulation", - "name": "autophagy regulation", - "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", + "id": "catalysis", + "name": "catalysis", + "description": "Catalysis in energy BNG", "tags": [ - "autophagy", - "regulation", - "mtor", - "ampk", - "ulk1", - "lc3", - "p62" + "catalysis", + "pptase", + "atp", + "adp" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -1400,20 +1152,23 @@ ] }, "gallery": [ - "metabolism", - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "BAB", - "name": "BAB", - "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "id": "cBNGL_simple", + "name": "cBNGL simple", + "description": "A simplified signal transduction model including the following processes:", "tags": [ - "bab", - "a", - "b", - "simulate" + "cbngl", + "simple", + "tf", + "dna", + "mrna" ], "category": "tutorial", "origin": "tutorial", @@ -1429,107 +1184,132 @@ "gallery": [ "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "BAB_coop", - "name": "BAB coop", - "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "id": "cd40-signaling", + "name": "cd40 signaling", + "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", "tags": [ - "bab", - "coop", - "a", - "b", - "simulate" + "cd40", + "signaling", + "cd40l", + "traf", + "ikk", + "nik", + "nfkb", + "relb" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "immunology", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "BAB_scan", - "name": "BAB scan", - "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "id": "cell-cycle-checkpoint", + "name": "cell cycle checkpoint", + "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", "tags": [ - "bab", - "scan", - "a", - "b", - "generate_network", - "parameter_scan" + "cell", + "cycle", + "checkpoint", + "cyclin", + "cdk", + "cdc25", + "wee1", + "apc", + "p21" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "cell-cycle", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Barua_2007", - "name": "Barua 2007", - "description": "Model from Haugh (2006)", + "id": "Chattaraj_nephrin_2021", + "name": "Chattaraj et al. 2021: Nephrin-Nck-NWASP Clustering Model", + "description": "NFkB oscillations", "tags": [ - "published", - "barua", - "2007", - "version", - "r", - "s" + "nephrin", + "nck", + "nwasp", + "clustering", + "2021", + "chattaraj" ], "category": "signaling", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": false, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer" + "neuroscience" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Barua_2009", - "name": "Barua 2009", - "description": "JAK2-SH2B signaling", + "id": "checkpoint-kinase-signaling", + "name": "checkpoint kinase signaling", + "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", "tags": [ - "published", - "barua", - "2009", - "s", - "j" + "checkpoint", + "kinase", + "signaling", + "dna", + "atm", + "atr", + "chk1", + "chk2", + "p53", + "cdc25" ], "category": "signaling", - "origin": "published", - "visible": true, + "origin": "ai-generated", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -1537,57 +1317,27 @@ ] }, "gallery": [ - "cancer" + "cancer", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Barua_2013", - "name": "Barua 2013", - "description": "Beta-catenin destruction", + "id": "Cheemalavagu_JAKSTAT_2024", + "name": "Cheemalavagu et al. 2024: JAK-STAT Signaling Model", + "description": "JAK-STAT signaling", "tags": [ - "published", - "barua", - "2013", - "axin", - "gsk3b", - "apc", - "bcat", - "ck1a" + "jak-stat", + "signaling", + "2024", + "cheemalavagu" ], - "category": "regulation", + "category": "other", "origin": "published", "visible": true, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [], - "collectionId": null - }, - { - "id": "BaruaBCR_2012", - "name": "Barua 2012", - "description": "BCR signaling", - "tags": [ - "published", - "immunology", - "baruabcr", - "2012", - "bcr", - "lyn", - "fyn", - "csk", - "pag", - "syk" - ], - "category": "immunology", - "origin": "published", - "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -1599,28 +1349,21 @@ "gallery": [ "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "BaruaFceRI_2012", - "name": "BaruaFceRI 2012", - "description": "FcεRI signaling", + "id": "chemistry", + "name": "chemistry", + "description": "Basic chemical reactions", "tags": [ - "published", - "immunology", - "baruafceri", - "2012", - "r_o", - "rdimer_o", - "l_o", - "t_o", - "l", - "fcr", - "lyn", - "syk" + "tutorials", + "chemistry" ], - "category": "immunology", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": false, @@ -1631,148 +1374,150 @@ ] }, "gallery": [ - "immunology" + "tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "bcr-signaling", - "name": "bcr signaling", - "description": "BCR signaling: The B-cell antigen receptor cascade.", + "id": "chemotaxis-signal-transduction", + "name": "chemotaxis signal transduction", + "description": "Bacterial Chemotaxis: Adaptation through methylation.", "tags": [ - "bcr", - "signaling", - "antigen", - "syk", - "plcg2", - "cd22", - "shp1", - "calcium" + "chemotaxis", + "signal", + "transduction", + "attr", + "mcp", + "chea", + "chey", + "cheb", + "motor" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "before_bunching", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Chylek_FceRI_2014", + "name": "Chylek et al. 2014: FceRI Signaling Model", + "description": "FceRI signaling", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "fceri", + "immune-signaling", + "mast-cell", + "2014", + "chylek" ], - "category": "other", + "category": "immunology", "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "before_decoupling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Chylek_library", + "name": "Chylek library", + "description": "Created by BioNetGen 2.2.6", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "chylek", + "library", + "sink", + "pre", + "pag1" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "before_scaling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Chylek_TCR_2014", + "name": "Chylek et al. 2014: T Cell Receptor (TCR) Signaling Model", + "description": "TCR signaling", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "tcr", + "immune-signaling", + "t-cell", + "2014", + "chylek" ], - "category": "other", + "category": "immunology", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "beta-adrenergic-response", - "name": "beta adrenergic response", - "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", + "id": "circadian-oscillator", + "name": "circadian oscillator", + "description": "title: Vilar Circadian Oscillator Model", "tags": [ - "beta", - "adrenergic", - "response", - "epi", - "betar", - "gs", - "ac", - "arr", - "camp" + "circadian", + "oscillator", + "a", + "r", + "pa", + "pr", + "mrna_a", + "mrna_r" ], "category": "signaling", "origin": "ai-generated", @@ -1786,121 +1531,125 @@ ] }, "gallery": [ - "neuroscience", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "birth-death", - "name": "Birth-Death", - "description": "Stochastic process", + "id": "CircadianOscillator", + "name": "CircadianOscillator", + "description": "Circadian rhythm", "tags": [ - "published", - "tutorial", - "native", - "birth", - "death", - "a", - "generate_network", - "saveconcentrations", - "simulate" + "circadianoscillator", + "pa", + "pr", + "mrna_a", + "mrna_r" ], "category": "tutorial", "origin": "tutorial", - "visible": true, + "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ - "ode", "ssa" ] }, "gallery": [ + "cell-cycle", "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "bistable-toggle-switch", - "name": "bistable toggle switch", - "description": "Genetic Toggle Switch: Mutual repression circuit.", + "id": "clock-bmal1-gene-circuit", + "name": "clock bmal1 gene circuit", + "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", "tags": [ - "bistable", - "toggle", - "switch", - "proml", - "promr", - "tf_l", - "tf_r", - "ind_l", - "ind_r" + "clock", + "bmal1", + "gene", + "circuit", + "ror", + "reverb", + "dna" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ + "cell-cycle", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "BLBR", - "name": "BLBR", - "description": "title: BLBR.bngl", + "id": "compartment_endocytosis", + "name": "compartment endocytosis", + "description": "Model: compartment_endocytosis.bngl", "tags": [ - "blbr", - "setoption", - "r", + "compartment", + "endocytosis", "l", - "simulate" + "r", + "t" ], - "category": "tutorial", - "origin": "tutorial", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "ode", - "nf" + "ode" ] }, "gallery": [ - "tutorial" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Blinov_2006", - "name": "Blinov 2006", - "description": "Phosphotyrosine signaling", + "id": "compartment_membrane_bound", + "name": "compartment membrane bound", + "description": "Model: compartment_membrane_bound.bngl", "tags": [ - "published", - "blinov", - "2006", - "egf", - "egfr", - "shc", - "grb2", - "sos" + "compartment", + "membrane", + "bound", + "p", + "lipid", + "generate_network", + "simulate" ], - "category": "signaling", - "origin": "published", - "visible": true, + "category": "other", + "origin": "ai-generated", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -1908,201 +1657,211 @@ ] }, "gallery": [ - "cell-cycle" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Blinov_egfr", - "name": "Blinov egfr", - "description": "EGFR signaling model", + "id": "compartment_nested_transport", + "name": "compartment nested transport", + "description": "Model: compartment_nested_transport.bngl", "tags": [ - "published", - "nfsim", - "blinov", - "egfr", - "egf", - "grb2", - "shc", - "simulate_nf" + "compartment", + "nested", + "transport", + "s", + "generate_network", + "simulate" ], - "category": "signaling", - "origin": "published", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "cancer" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Blinov_ran", - "name": "Blinov ran", - "description": "Ran GTPase cycle", + "id": "compartment_nuclear_transport", + "name": "compartment nuclear transport", + "description": "Model: compartment_nuclear_transport.bngl", "tags": [ - "published", - "nfsim", - "blinov", - "ran", - "c", - "rcc1", - "simulate_nf" + "compartment", + "nuclear", + "transport", + "tf", + "generate_network", + "simulate" ], - "category": "regulation", - "origin": "published", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "cell-cycle" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "blood-coagulation-thrombin", - "name": "blood coagulation thrombin", - "description": "Blood coagulation: Thrombin burst and feedback propagation.", + "id": "compartment_organelle_exchange", + "name": "compartment organelle exchange", + "description": "Model: compartment_organelle_exchange.bngl", "tags": [ - "blood", - "coagulation", - "thrombin", - "tf", - "factorx", - "factorv", - "prothrombin", - "fibrinogen", - "at" + "compartment", + "organelle", + "exchange", + "cargo", + "generate_network", + "simulate" ], - "category": "signaling", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "bmp-signaling", - "name": "bmp signaling", - "description": "BMP-Smad signaling: Developmental gradient relay.", + "id": "competitive-enzyme-inhibition", + "name": "competitive enzyme inhibition", + "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", "tags": [ - "bmp", - "signaling", - "noggin", - "receptor1", - "receptor2", - "smad1", - "smad4", - "smad6" + "competitive", + "enzyme", + "inhibition", + "substrate1", + "substrate2", + "inhibitor", + "product" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "developmental", + "metabolism", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "bng_error", - "name": "bng error", - "description": "Original values used to generate parabola.exp", + "id": "complement-activation-cascade", + "name": "complement activation cascade", + "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", "tags": [ - "bng", - "error", - "counter", - "y", - "generate_network", - "simulate" + "complement", + "activation", + "cascade", + "c3", + "fb", + "c5", + "mac", + "surf" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "immunology", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "brusselator-oscillator", - "name": "brusselator oscillator", - "description": "The Brusselator: Auto-catalytic chemical oscillator.", + "id": "ComplexDegradation", + "name": "ComplexDegradation", + "description": "Degradation model", "tags": [ - "brusselator", - "oscillator", - "a", - "b", - "x", - "y" + "complexdegradation" ], - "category": "signaling", - "origin": "ai-generated", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "physics", - "test-models" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "calcineurin-nfat-pathway", - "name": "calcineurin nfat pathway", - "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", + "id": "contact-inhibition-hippo-yap", + "name": "contact inhibition hippo yap", + "description": "Hippo Pathway: Contact inhibition and YAP regulation.", "tags": [ - "calcineurin", - "nfat", - "pathway", - "ca", - "cam", - "can", - "rcan1" + "contact", + "inhibition", + "hippo", + "yap", + "mst", + "lats", + "tead" ], "category": "signaling", "origin": "ai-generated", @@ -2116,177 +1875,189 @@ ] }, "gallery": [ - "neuroscience", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "calcium-spike-signaling", - "name": "calcium spike signaling", - "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", + "id": "continue", + "name": "continue", + "description": "Test trajectory continuation", "tags": [ - "calcium", - "spike", - "signaling", - "plc", - "ip3", - "ca", - "stim1" + "continue", + "trash" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "neuroscience", - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "CaMKII_holo", - "name": "Ordyan 2020: CaMKII holo", - "description": "CaMKII holo", + "id": "cooperative-binding", + "name": "cooperative binding", + "description": "Cooperative binding: The binding of the first ligand molecule increases", "tags": [ - "published", - "neuroscience", - "camkii", - "holo", - "ca", - "cam", - "ng", - "pp1", - "time_counter" + "cooperative", + "binding", + "receptor", + "ligand", + "competitor" ], "category": "signaling", - "origin": "published", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "CaOscillate_Func", - "name": "CaOscillate_Func", - "description": "Calcium oscillations (func)", + "id": "Creamer_2012", + "name": "Creamer 2012", + "description": "Initial values", "tags": [ - "validation", - "caoscillate", - "func", - "null", - "ga", - "plc", - "ca" + "creamer", + "2012", + "egf", + "hrg", + "egfr", + "erbb2", + "erbb3", + "erbb4", + "grb2" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "tutorial", + "origin": "tutorial", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "CaOscillate_Sat", - "name": "CaOscillate_Sat", - "description": "Calcium oscillations (sat)", + "id": "cs_diffie_hellman", + "name": "cs diffie hellman", + "description": "Model: cs_diffie_hellman.bngl", "tags": [ - "validation", - "caoscillate", - "sat", - "null", - "ga", - "plc", - "ca" + "cs", + "diffie", + "hellman", + "agent", + "target", + "dshareda_dt", + "dsharedb_dt" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, "gallery": [ - "validation" + "cs", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "caspase-activation-loop", - "name": "caspase activation loop", - "description": "Caspase activation loop: The executioner feedback system.", + "id": "cs_hash_function", + "name": "cs hash function", + "description": "Cryptographic Hash Function in BNGL", "tags": [ - "caspase", - "activation", - "loop", - "deathligand", - "caspase8", - "caspase3", - "iap", - "flip" + "cs", + "hash", + "function", + "b0", + "b1", + "b2", + "b3", + "h0", + "h1", + "h2", + "h3" ], - "category": "signaling", + "category": "computer-science", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cell-cycle", + "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "catalysis", - "name": "catalysis", - "description": "Catalysis in energy BNG", + "id": "cs_huffman", + "name": "cs huffman", + "description": "Model: cs_huffman.bngl", "tags": [ - "validation", - "catalysis", - "version", - "setoption", - "s", - "kinase", - "pptase", - "atp", - "adp" + "cs", + "huffman", + "char", + "hnode", + "generate_network", + "simulate" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -2296,55 +2067,59 @@ ] }, "gallery": [ - "validation" + "cs", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "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" + "id": "cs_monte_carlo_pi", + "name": "cs monte carlo pi", + "description": "Model: cs_monte_carlo_pi.bngl", + "tags": [ + "cs", + "monte", + "carlo", + "pi", + "trial", + "pi_estimate", + "generate_network", + "simulate" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "cs", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cd40-signaling", - "name": "cd40 signaling", - "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", + "id": "cs_pagerank", + "name": "cs pagerank", + "description": "Model: cs_pagerank.bngl", "tags": [ - "cd40", - "signaling", - "cd40l", - "traf", - "ikk", - "nik", - "nfkb", - "relb" + "cs", + "pagerank", + "teleport", + "page" ], - "category": "signaling", + "category": "computer-science", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2356,27 +2131,29 @@ ] }, "gallery": [ - "immunology", + "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cell-cycle-checkpoint", - "name": "cell cycle checkpoint", - "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", + "id": "cs_pid_controller", + "name": "cs pid controller", + "description": "PID Controller in BNGL", "tags": [ - "cell", - "cycle", - "checkpoint", - "cyclin", - "cdk", - "cdc25", - "wee1", - "apc", - "p21" + "cs", + "pid", + "controller", + "sensor", + "accumulator", + "leakyerror", + "actuator", + "disturbance" ], - "category": "signaling", + "category": "computer-science", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2388,60 +2165,62 @@ ] }, "gallery": [ - "cell-cycle", + "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Chattaraj_2021", - "name": "Chattaraj 2021", - "description": "NFkB oscillations", + "id": "cs_regex_nfa", + "name": "cs regex nfa", + "description": "Model: cs_regex_nfa.bngl", "tags": [ - "published", - "chattaraj", - "2021", - "nephrin", - "nck", - "nwasp", - "writexml" + "cs", + "regex", + "nfa", + "state", + "char", + "generate_network", + "simulate", + "setparameter" ], - "category": "signaling", - "origin": "published", + "category": "computer-science", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ - "neuroscience" + "cs", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "check_scaling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Dembo_blbr_1978", + "name": "Dembo et al. 1978: Bivalent Ligand Bivalent Receptor (BLBR) Model", + "description": "BLBR dembo 1978", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "blbr", + "ligand-receptor", + "binding", + "1978", + "dembo" ], - "category": "other", + "category": "physics", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -2450,31 +2229,33 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "physics" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "checkpoint-kinase-signaling", - "name": "checkpoint kinase signaling", - "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", + "id": "dna-damage-repair", + "name": "dna damage repair", + "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", "tags": [ - "checkpoint", - "kinase", - "signaling", "dna", + "damage", + "repair", + "mrn", "atm", - "atr", - "chk1", "chk2", - "p53", - "cdc25" + "repaircomplex" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -2484,31 +2265,28 @@ "cancer", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Cheemalavagu_JAK_STAT", - "name": "Cheemalavagu 2024", - "description": "JAK-STAT signaling", + "id": "dna-methylation-dynamics", + "name": "dna methylation dynamics", + "description": "DNA Methylation: Maintenance and de novo dynamics.", "tags": [ - "published", - "literature", - "signaling", - "cheemalavagu", - "jak", - "stat", - "l1", - "il6r", - "gp130", - "l2", - "il10r1", - "il10r2", - "jak1", - "jak2" + "dna", + "methylation", + "dynamics", + "cpg", + "dnmt1", + "tet", + "v_maint", + "v_erase" ], - "category": "other", - "origin": "published", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -2518,26 +2296,25 @@ ] }, "gallery": [ - "immunology" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "chemistry", - "name": "chemistry", - "description": "Basic chemical reactions", + "id": "Dolan_Insulin_2015_Dolan_2015", + "name": "Dolan et al. 2015: Insulin Receptor Signaling Model (Dolan_2015)", + "description": "Insulin signaling", "tags": [ - "published", - "tutorials", - "chemistry", - "a", - "b", - "c", - "d", - "e" + "insulin", + "metabolism", + "2015", + "dolan" ], - "category": "tutorial", - "origin": "tutorial", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": false, @@ -2548,127 +2325,120 @@ ] }, "gallery": [ - "tutorials" + "metabolism" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "chemotaxis-signal-transduction", - "name": "chemotaxis signal transduction", - "description": "Bacterial Chemotaxis: Adaptation through methylation.", + "id": "Dolan_Insulin_2015_Dolan2015", + "name": "Dolan et al. 2015: Insulin Receptor Signaling Model (Dolan2015)", + "description": "Insulin signaling", "tags": [ - "chemotaxis", - "signal", - "transduction", - "attr", - "mcp", - "chea", - "chey", - "cheb", - "motor" + "insulin", + "metabolism", + "2015", + "dolan" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "metabolism" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Chylek_library", - "name": "Chylek library", - "description": "Created by BioNetGen 2.2.6", + "id": "dr5-apoptosis-signaling", + "name": "dr5 apoptosis signaling", + "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", "tags": [ - "chylek", - "library", - "kflatplcg", - "kfgrb2gab2", - "kflcp2plcg1", - "kd1", - "kd2", - "sink", - "pre", - "pag1" + "dr5", + "apoptosis", + "signaling", + "trail", + "fadd", + "caspase8", + "flip", + "death_signal" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "cell-cycle", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ChylekFceRI_2014", - "name": "Chylek 2014 (FceRI)", - "description": "FceRI signaling", + "id": "Dreisigmeyer_LacOperon_2008", + "name": "Dreisigmeyer et al. 2008: Lac Operon Regulation Model", + "description": "Lac operon", "tags": [ - "published", - "immunology", - "chylekfceri", - "2014", - "lig", - "rec", - "lyn", - "fyn", - "syk", - "pag1", - "csk", - "lat" + "lac-operon", + "gene-expression", + "bacterial-regulation", + "2008", + "dreisigmeyer" ], - "category": "immunology", + "category": "gene-expression", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology" + "gene-expression" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ChylekTCR_2014", - "name": "Chylek 2014 (TCR)", - "description": "TCR signaling", + "id": "dual-site-phosphorylation", + "name": "dual site phosphorylation", + "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", "tags": [ - "published", - "immunology", - "chylektcr", - "2014", - "lig1", - "lig2", - "lig3", - "tcr", - "cd28", - "lck", - "itk", - "zap70" + "dual", + "site", + "phosphorylation", + "kinase", + "phosphatase", + "substrate" ], - "category": "immunology", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -2679,85 +2449,87 @@ ] }, "gallery": [ - "immunology" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "circadian-oscillator", - "name": "circadian oscillator", - "description": "title: Vilar Circadian Oscillator Model", + "id": "Dushek_TCR_2011", + "name": "Dushek et al. 2011: T Cell Receptor Kinase Kinase Cascade", + "description": "TCR signaling", "tags": [ - "circadian", - "oscillator", - "a", - "r", - "pa", - "pr", - "mrna_a", - "mrna_r" + "tcr", + "phosphorylation", + "immune-signaling", + "2011", + "dushek" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "CircadianOscillator", - "name": "CircadianOscillator", - "description": "Circadian rhythm", + "id": "Dushek_TCR_2014", + "name": "Dushek et al. 2014: T Cell Receptor Phosphorylation Feedback", + "description": "TCR signaling dynamics", "tags": [ - "published", - "tutorial", - "native", - "circadianoscillator", - "a", - "r", - "pa", - "pr", - "mrna_a", - "mrna_r" + "tcr", + "feedback-loop", + "immune-signaling", + "2014", + "dushek" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "cell-cycle", - "native-tutorials" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "clock-bmal1-gene-circuit", - "name": "clock bmal1 gene circuit", - "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", + "id": "e2f-rb-cell-cycle-switch", + "name": "e2f rb cell cycle switch", + "description": "E2F/Rb Switch: The G1/S transition gate.", "tags": [ - "clock", - "bmal1", - "gene", - "circuit", - "ror", - "reverb", - "dna" + "e2f", + "rb", + "cell", + "cycle", + "switch", + "mitogen", + "cycd", + "cyce", + "p27" ], "category": "signaling", "origin": "ai-generated", @@ -2774,20 +2546,22 @@ "cell-cycle", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_endocytosis", - "name": "compartment endocytosis", - "description": "Model: compartment_endocytosis.bngl", + "id": "eco_coevolution_host_parasite", + "name": "eco coevolution host parasite", + "description": "Model: eco_coevolution_host_parasite.bngl", "tags": [ - "compartment", - "endocytosis", - "l", - "r", - "t" + "eco", + "coevolution", + "host", + "parasite" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2799,24 +2573,31 @@ ] }, "gallery": [ + "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_membrane_bound", - "name": "compartment membrane bound", - "description": "Model: compartment_membrane_bound.bngl", + "id": "eco_food_web_chaos_3sp", + "name": "eco food web chaos 3sp", + "description": "Model: eco_food_web_chaos_3sp.bngl", "tags": [ - "compartment", - "membrane", - "bound", + "eco", + "food", + "web", + "chaos", + "3sp", + "r", + "c", "p", - "lipid", - "generate_network", - "simulate" + "k_eat_r", + "k_eat_c" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2824,27 +2605,31 @@ "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ + "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_nested_transport", - "name": "compartment nested transport", - "description": "Model: compartment_nested_transport.bngl", + "id": "eco_lotka_volterra_grid", + "name": "eco lotka volterra grid", + "description": "Model: eco_lotka_volterra_grid.bngl", "tags": [ - "compartment", - "nested", - "transport", - "s", - "generate_network", - "simulate" + "eco", + "lotka", + "volterra", + "grid", + "prey", + "pred" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2856,23 +2641,26 @@ ] }, "gallery": [ + "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_nuclear_transport", - "name": "compartment nuclear transport", - "description": "Model: compartment_nuclear_transport.bngl", + "id": "eco_mutualism_obligate", + "name": "eco mutualism obligate", + "description": "Model: eco_mutualism_obligate.bngl", "tags": [ - "compartment", - "nuclear", - "transport", - "tf", - "generate_network", - "simulate" + "eco", + "mutualism", + "obligate", + "a", + "b" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2880,27 +2668,32 @@ "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ + "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_organelle_exchange", - "name": "compartment organelle exchange", - "description": "Model: compartment_organelle_exchange.bngl", + "id": "eco_rock_paper_scissors_spatial", + "name": "eco rock paper scissors spatial", + "description": "Model: eco_rock_paper_scissors_spatial.bngl", "tags": [ - "compartment", - "organelle", - "exchange", - "cargo", - "generate_network", - "simulate" + "eco", + "rock", + "paper", + "scissors", + "spatial", + "s", + "generate_network" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2912,88 +2705,89 @@ ] }, "gallery": [ + "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "competitive-enzyme-inhibition", - "name": "competitive enzyme inhibition", - "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", + "id": "egfr_net", + "name": "egfr_net", + "description": "check detailed balanced", "tags": [ - "competitive", - "enzyme", - "inhibition", - "substrate1", - "substrate2", - "inhibitor", - "product" + "egfr", + "net", + "egf", + "shc", + "grb2", + "sos" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism", - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "complement-activation-cascade", - "name": "complement activation cascade", - "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", + "id": "egfr_net_red", + "name": "egfr_net_red", + "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", "tags": [ - "complement", - "activation", - "cascade", - "c3", - "fb", - "c5", - "mac", - "surf" + "egfr", + "net", + "red", + "egf", + "grb2", + "shc", + "sos" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ComplexDegradation", - "name": "ComplexDegradation", - "description": "Degradation model", + "id": "egfr_path", + "name": "egfr_path", + "description": "The primary focus of the model developed by Kholodenko", "tags": [ - "published", - "tutorial", - "native", - "complexdegradation", - "a", - "b", - "c", - "generate_network" + "egfr", + "path", + "setconcentration" ], - "category": "tutorial", - "origin": "tutorial", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -3003,84 +2797,93 @@ ] }, "gallery": [ - "native-tutorials" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "contact-inhibition-hippo-yap", - "name": "contact inhibition hippo yap", - "description": "Hippo Pathway: Contact inhibition and YAP regulation.", + "id": "egfr_simple", + "name": "egfr simple", + "description": "This is a demo model of EGFR signaling.", "tags": [ - "contact", - "inhibition", - "hippo", - "yap", - "mst", - "lats", - "tead" + "egfr", + "simple", + "egf", + "grb2", + "sos1" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "continue", - "name": "continue", - "description": "Test trajectory continuation", + "id": "egfr-signaling-pathway", + "name": "egfr signaling pathway", + "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", "tags": [ - "validation", - "continue", - "a", - "b", - "c", - "trash" + "egfr", + "signaling", + "pathway", + "egf", + "grb2", + "shc" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "cancer", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "cooperative-binding", - "name": "cooperative binding", - "description": "Cooperative binding: The binding of the first ligand molecule increases", + "id": "eif2a-stress-response", + "name": "eif2a stress response", + "description": "Integrated Stress Response: eIF2alpha and the translational gate.", "tags": [ - "cooperative", - "binding", - "receptor", - "ligand", - "competitor" + "eif2a", + "stress", + "response", + "eif2b", + "perk", + "gadd34" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" @@ -3089,54 +2892,56 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Creamer_2012", - "name": "Creamer 2012", - "description": "Initial values", + "id": "endosomal-sorting-rab", + "name": "endosomal sorting rab", + "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", "tags": [ - "creamer", - "2012", - "egf", - "hrg", - "egfr", - "erbb2", - "erbb3", - "erbb4", - "p52shc1", - "grb2" + "endosomal", + "sorting", + "rab", + "rab5", + "rab7", + "effector", + "v_gef", + "v_gap_drive" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_diffie_hellman", - "name": "cs diffie hellman", - "description": "Model: cs_diffie_hellman.bngl", + "id": "energy_allostery_mwc", + "name": "energy allostery mwc", + "description": "Model: energy_allostery_mwc.bngl", "tags": [ - "cs", - "diffie", - "hellman", - "agent", - "target", - "dshareda_dt", - "dsharedb_dt" + "energy", + "allostery", + "mwc", + "p", + "l" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3148,58 +2953,56 @@ ] }, "gallery": [ - "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_hash_function", - "name": "cs hash function", - "description": "Cryptographic Hash Function in BNGL", + "id": "energy_catalysis_mm", + "name": "energy catalysis mm", + "description": "Model: energy_catalysis_mm.bngl", "tags": [ - "cs", - "hash", - "function", - "b0", - "b1", - "b2", - "b3", - "h0", - "h1", - "h2", - "h3" + "energy", + "catalysis", + "mm", + "e", + "s", + "p" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_huffman", - "name": "cs huffman", - "description": "Model: cs_huffman.bngl", + "id": "energy_cooperativity_adh", + "name": "energy cooperativity adh", + "description": "Model: energy_cooperativity_adh.bngl", "tags": [ - "cs", - "huffman", - "char", - "hnode", - "generate_network", - "simulate" + "energy", + "cooperativity", + "adh", + "r", + "l" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3211,28 +3014,24 @@ ] }, "gallery": [ - "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_monte_carlo_pi", - "name": "cs monte carlo pi", - "description": "Model: cs_monte_carlo_pi.bngl", + "id": "energy_example1", + "name": "energy_example1", + "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", "tags": [ - "cs", - "monte", - "carlo", - "pi", - "trial", - "pi_estimate", - "generate_network", - "simulate" + "energy", + "example1" ], - "category": "computer-science", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -3242,22 +3041,25 @@ ] }, "gallery": [ - "cs", - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_pagerank", - "name": "cs pagerank", - "description": "Model: cs_pagerank.bngl", + "id": "energy_linear_chain", + "name": "energy linear chain", + "description": "Model: energy_linear_chain.bngl", "tags": [ - "cs", - "pagerank", - "teleport", - "page" + "energy", + "linear", + "chain", + "m", + "generate_network" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3269,93 +3071,93 @@ ] }, "gallery": [ - "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_pid_controller", - "name": "cs pid controller", - "description": "PID Controller in BNGL", + "id": "energy_transport_pump", + "name": "energy transport pump", + "description": "Model: energy_transport_pump.bngl", "tags": [ - "cs", - "pid", - "controller", - "sensor", - "accumulator", - "leakyerror", - "actuator", - "disturbance" + "energy", + "transport", + "pump", + "a", + "atp", + "adp", + "pi", + "t" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_regex_nfa", - "name": "cs regex nfa", - "description": "Model: cs_regex_nfa.bngl", + "id": "er-stress-response", + "name": "er stress response", + "description": "Rate Constants", "tags": [ - "cs", - "regex", - "nfa", - "state", - "char", - "generate_network", - "simulate", - "setparameter" + "er", + "stress", + "response", + "unfoldedprotein", + "perk", + "eif2a", + "chaperone" ], - "category": "computer-science", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Dallas", - "name": "Dallas", - "description": "- This model is intended to be consistent with the compartmental model", + "id": "Erdem_InsR_2021", + "name": "Erdem et al. 2021: Insulin Receptor Internalization Model", + "description": "InsR/IGF1R signaling", "tags": [ - "dallas", - "counter", - "fdcs", - "s", - "sv", - "e", - "a", - "i", - "v" + "insulin", + "receptor-internalization", + "2021", + "erdem" ], - "category": "epidemiology", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -3363,30 +3165,29 @@ ] }, "gallery": [ - "epidemiology" + "metabolism" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "degranulation_model", - "name": "PyBNG: Degranulation model", - "description": "Degranulation model", + "id": "erk-nuclear-translocation", + "name": "erk nuclear translocation", + "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", "tags": [ - "published", - "pybng", - "degranulation", - "model", - "ag", - "r", - "syk", - "ship1", - "x", - "pip3", - "h" + "erk", + "nuclear", + "translocation", + "mek", + "elk1", + "dusp", + "transcription_signal" ], - "category": "other", - "origin": "published", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -3396,25 +3197,25 @@ ] }, "gallery": [ - "immunology" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Dembo_1978", - "name": "Dembo 1978", - "description": "BLBR dembo 1978", + "id": "example1", + "name": "example1", + "description": "Example file for BNG2 tutorial.", "tags": [ - "published", - "physics", - "dembo", - "1978" + "example1" ], - "category": "physics", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -3422,59 +3223,62 @@ ] }, "gallery": [ - "physics" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "dna-damage-repair", - "name": "dna damage repair", - "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", + "id": "Faeder_egfr_2009", + "name": "Faeder 2009", + "description": "EGFR signaling", "tags": [ - "dna", - "damage", - "repair", - "mrn", - "atm", - "chk2", - "repaircomplex" + "based", + "egf", + "egfr", + "rule", + "rulebasedegfrtutorial", + "shc", + "signaling" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer", - "test-models" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "dna-methylation-dynamics", - "name": "dna methylation dynamics", - "description": "DNA Methylation: Maintenance and de novo dynamics.", + "id": "Faeder_egfr_compart_2009", + "name": "Faeder et al. 2009: Compartmental Rule-Based EGFR model", + "description": "Compartmental EGFR model", "tags": [ - "dna", - "methylation", - "dynamics", - "cpg", - "dnmt1", - "tet", - "v_maint", - "v_erase" + "egfr", + "compartments", + "receptor-trafficking", + "signaling", + "2009", + "faeder" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -3482,123 +3286,118 @@ ] }, "gallery": [ - "test-models" + "signaling" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Dolan_2015", - "name": "Dolan 2015", - "description": "Insulin signaling", + "id": "Faeder_FceRI_2003_Faeder_2003", + "name": "Faeder et al. 2003: FceRI Signaling Model (Faeder_2003)", + "description": "FceRI signaling", "tags": [ - "published", - "literature", - "signaling", - "dolan", - "2015", - "time", - "t", - "p", - "e", - "ir", - "d", - "p53_mrna", - "p53" + "fceri", + "immune-signaling", + "mast-cell", + "2003", + "faeder" ], - "category": "other", + "category": "immunology", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Dolan2015", - "name": "Dolan 2015", - "description": "Insulin signaling", + "id": "Faeder_FceRI_2003_fceri_ji", + "name": "Faeder et al. 2003: FceRI Signaling Model (fceri_ji)", + "description": "FceRI signaling", "tags": [ - "published", - "literature", - "signaling", - "dolan", - "2015", - "time", - "t", - "p", - "e", - "ir", - "d", - "p53_mrna", - "p53" + "fceri", + "immune-signaling", + "mast-cell", + "2003", + "faeder" ], - "category": "other", + "category": "immunology", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "dr5-apoptosis-signaling", - "name": "dr5 apoptosis signaling", - "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", + "id": "Faeder_FceRI_Fyn_2003", + "name": "Faeder et al. 2003: FceRI Signaling with Fyn Kinase Regulation", + "description": "FceRI signaling", "tags": [ - "dr5", - "apoptosis", - "signaling", - "trail", - "fadd", - "caspase8", - "flip", - "death_signal" + "fceri", + "fyn-kinase", + "mast-cell", + "immune-signaling", + "2003", + "faeder" ], - "category": "signaling", - "origin": "ai-generated", + "category": "immunology", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cell-cycle", - "test-models" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Dreisigmeyer_2008", - "name": "Dreisigmeyer 2008", - "description": "Lac operon", + "id": "FceRI_ji", + "name": "FceRI ji", + "description": "title: FceRI_ji.bngl", "tags": [ - "published", - "gene-expression", - "dreisigmeyer", - "2008" + "fceri", + "ji", + "lig", + "lyn", + "syk", + "rec" ], - "category": "gene-expression", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": true, "compatibility": { "bng2": true, @@ -3609,108 +3408,93 @@ ] }, "gallery": [ - "gene-expression" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "dual-site-phosphorylation", - "name": "dual site phosphorylation", - "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", + "id": "fceri_ji_comp", + "name": "fceri_ji_comp", + "description": "Ligand-receptor binding", "tags": [ - "dual", - "site", - "phosphorylation", - "kinase", - "phosphatase", - "substrate" + "fceri", + "ji", + "comp", + "lig", + "lyn", + "syk", + "rec" ], - "category": "signaling", - "origin": "ai-generated", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Dushek_2011", - "name": "Dushek 2011", - "description": "TCR signaling", - "tags": [ - "published", - "dushek", - "2011", - "s" - ], - "category": "signaling", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "immunology" - ], - "collectionId": null - }, - { - "id": "Dushek_2014", - "name": "Dushek 2014", - "description": "TCR signaling dynamics", + "id": "FceRI_viz", + "name": "FceRI Viz", + "description": "FcεRI (viz)", "tags": [ - "published", - "dushek", - "2014", - "e", - "f", - "b" + "fceri", + "fcr", + "ige", + "lat", + "lyn", + "syk", + "pb", + "pg", + "sykp" ], - "category": "signaling", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "e2f-rb-cell-cycle-switch", - "name": "e2f rb cell cycle switch", - "description": "E2F/Rb Switch: The G1/S transition gate.", + "id": "feature_functional_rates_volume", + "name": "feature functional rates volume", + "description": "Model: feature_functional_rates_volume.bngl", "tags": [ - "e2f", - "rb", - "cell", - "cycle", - "switch", - "mitogen", - "cycd", - "cyce", - "p27" + "feature", + "functional", + "rates", + "volume", + "a", + "b", + "c" ], - "category": "signaling", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3722,22 +3506,27 @@ ] }, "gallery": [ - "cell-cycle", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_coevolution_host_parasite", - "name": "eco coevolution host parasite", - "description": "Model: eco_coevolution_host_parasite.bngl", + "id": "feature_global_functions_scan", + "name": "feature global functions scan", + "description": "Model: feature_global_functions_scan.bngl", "tags": [ - "eco", - "coevolution", - "host", - "parasite" + "feature", + "global", + "functions", + "scan", + "signal", + "response", + "stimulus" ], - "category": "ecology", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3749,28 +3538,29 @@ ] }, "gallery": [ - "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_food_web_chaos_3sp", - "name": "eco food web chaos 3sp", - "description": "Model: eco_food_web_chaos_3sp.bngl", + "id": "feature_local_functions_explicit", + "name": "feature local functions explicit", + "description": "Model: feature_local_functions_explicit.bngl", "tags": [ - "eco", - "food", - "web", - "chaos", - "3sp", - "r", - "c", + "feature", + "local", + "functions", + "explicit", + "s", "p", - "k_eat_r", - "k_eat_c" + "e", + "mm_rate", + "ratelaw" ], - "category": "ecology", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3782,24 +3572,27 @@ ] }, "gallery": [ - "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_lotka_volterra_grid", - "name": "eco lotka volterra grid", - "description": "Model: eco_lotka_volterra_grid.bngl", + "id": "feature_symmetry_factors_cyclic", + "name": "feature symmetry factors cyclic", + "description": "Model: feature_symmetry_factors_cyclic.bngl", "tags": [ - "eco", - "lotka", - "volterra", - "grid", - "prey", - "pred" + "feature", + "symmetry", + "factors", + "cyclic", + "x", + "generate_network", + "simulate" ], - "category": "ecology", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3811,23 +3604,27 @@ ] }, "gallery": [ - "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_mutualism_obligate", - "name": "eco mutualism obligate", - "description": "Model: eco_mutualism_obligate.bngl", + "id": "feature_synthesis_degradation_ss", + "name": "feature synthesis degradation ss", + "description": "Model: feature_synthesis_degradation_ss.bngl", "tags": [ - "eco", - "mutualism", - "obligate", - "a", - "b" + "feature", + "synthesis", + "degradation", + "ss", + "m", + "generate_network", + "simulate" ], - "category": "ecology", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3835,29 +3632,32 @@ "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "ecology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_rock_paper_scissors_spatial", - "name": "eco rock paper scissors spatial", - "description": "Model: eco_rock_paper_scissors_spatial.bngl", + "id": "fgf-signaling-pathway", + "name": "fgf signaling pathway", + "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", "tags": [ - "eco", - "rock", - "paper", - "scissors", - "spatial", - "s", - "generate_network" + "fgf", + "signaling", + "pathway", + "fgfr", + "frs2", + "spry", + "rasgef", + "internalized_rec" ], - "category": "ecology", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3869,21 +3669,28 @@ ] }, "gallery": [ - "ecology", + "developmental", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr", - "name": "02-egfr", - "description": "EGFR model", + "id": "Gardner_Toggle_2000", + "name": "Gardner et al. 2000: Synthetic Gene Toggle Switch", + "description": "Genetic toggle switch", "tags": [ - "signaling" + "toggle-switch", + "synthetic-biology", + "gene-regulation", + "2000", + "gardner" ], - "category": "signaling", + "category": "synthetic-biology", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -3892,18 +3699,29 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "synthetic-biology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr", - "name": "17-egfr-ssa", - "description": "EGFR model", + "id": "gas6-axl-signaling", + "name": "gas6 axl signaling", + "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", "tags": [ - "signaling" + "gas6", + "axl", + "signaling", + "pi3k", + "akt", + "socs", + "survival_burst" ], "category": "signaling", - "origin": "published", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -3913,45 +3731,59 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr", - "name": "egfr", - "description": "Blinov et al. 2006. Biosystems, 83:136", + "id": "gene-expression-toggle", + "name": "gene expression toggle", + "description": "Kinetic Parameters", "tags": [ - "egfr", - "egf", - "grb2", - "shc", - "sos" + "gene", + "expression", + "toggle", + "mrna", + "protein" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "other" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr_ground", - "name": "02-egfr", - "description": "EGFR model", + "id": "genetic_bistability_energy", + "name": "genetic bistability energy", + "description": "Model: genetic_bistability_energy.bngl", "tags": [ - "signaling" + "genetic", + "bistability", + "energy", + "genea", + "geneb", + "prota", + "protb" ], - "category": "signaling", - "origin": "published", + "category": "gene-expression", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -3961,18 +3793,29 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_ground", - "name": "17-egfr-ssa", - "description": "EGFR model", + "id": "genetic_dna_replication_stochastic", + "name": "genetic dna replication stochastic", + "description": "Model: genetic_dna_replication_stochastic.bngl", "tags": [ - "signaling" + "genetic", + "dna", + "replication", + "stochastic", + "pol", + "n", + "generate_network" ], - "category": "signaling", - "origin": "published", + "category": "gene-expression", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -3982,24 +3825,30 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_ground", - "name": "egfr ground", - "description": "Blinov et al. 2006. Biosystems, 83:136", + "id": "genetic_goodwin_oscillator", + "name": "genetic goodwin oscillator", + "description": "Model: genetic_goodwin_oscillator.bngl", "tags": [ - "egfr", - "ground", - "egf", - "grb2", - "shc", - "sos" + "genetic", + "goodwin", + "oscillator", + "gene", + "mrna", + "protein", + "repressor" ], - "category": "other", - "origin": "published", - "visible": true, + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -4009,28 +3858,30 @@ ] }, "gallery": [ - "other" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_net", - "name": "egfr_net", - "description": "check detailed balanced", + "id": "genetic_translation_kinetics", + "name": "genetic translation kinetics", + "description": "Model: genetic_translation_kinetics.bngl", "tags": [ - "validation", - "egfr", - "net", - "egf", - "shc", - "grb2", - "sos" + "genetic", + "translation", + "kinetics", + "mrna", + "rib", + "protein" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -4038,30 +3889,28 @@ ] }, "gallery": [ - "validation" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_net_red", - "name": "egfr_net_red", - "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", + "id": "genetic_turing_pattern_1d", + "name": "genetic turing pattern 1d", + "description": "Model: genetic_turing_pattern_1d.bngl", "tags": [ - "validation", - "egfr", - "net", - "red", - "egf", - "egfr_1", - "egfr_2", - "egfr_3", - "grb2", - "shc", - "sos" + "genetic", + "turing", + "pattern", + "1d", + "a", + "b" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -4071,52 +3920,55 @@ ] }, "gallery": [ - "validation" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_nf", - "name": "egfr nf", - "description": "Filename: example2_starting_point.bngl", + "id": "GK", + "name": "GK", + "description": "title: GK.bngl", "tags": [ - "egfr", - "nf", - "egf", - "clusters", - "pre1_dose", - "pre2_time" + "gk" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "other" + "metabolism", + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr_ode", - "name": "egfr ode", - "description": "Filename: example1.bngl", + "id": "glioblastoma-egfrviii-signaling", + "name": "glioblastoma egfrviii signaling", + "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", "tags": [ - "egfr", - "ode", - "egf", - "pre1_dose", - "pre2_time", - "pre3_dose" + "glioblastoma", + "egfrviii", + "signaling", + "pi3k", + "akt", + "oncogenic_output", + "v_viii_act" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -4127,82 +3979,96 @@ ] }, "gallery": [ - "cancer" + "cancer", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_ode", - "name": "PyBNG: EGFR ODE", - "description": "EGFR ODE", + "id": "glycolysis-branch-point", + "name": "glycolysis branch point", + "description": "BioNetGen model: glycolysis branch point", "tags": [ - "published", - "pybng", - "egfr", - "ode", - "egf", - "pre1_dose", - "pre2_time", - "pre3_dose" + "glycolysis", + "branch", + "point", + "glucose", + "atp", + "biomass" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer" + "metabolism", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr_path", - "name": "egfr_path", - "description": "The primary focus of the model developed by Kholodenko", + "id": "gm_game_of_life", + "name": "gm game of life", + "description": "Model: gm_game_of_life.bngl", "tags": [ - "validation", - "egfr", - "path", - "generate_network", - "setconcentration", - "simulate" + "gm", + "game", + "of", + "life", + "cell" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ - "validation" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_simple", - "name": "egfr simple", - "description": "This is a demo model of EGFR signaling.", + "id": "gm_ray_marcher", + "name": "gm ray marcher", + "description": "Ray Marching Renderer in BNGL", "tags": [ - "egfr", - "simple", - "egf", - "grb2", - "sos1" + "gm", + "ray", + "marcher", + "ray0", + "hit0", + "bright0", + "sdf0", + "sdf1", + "sdf2", + "sdf3", + "speed0" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": true, @@ -4212,77 +4078,85 @@ ] }, "gallery": [ - "native-tutorials" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr-signaling-pathway", - "name": "egfr signaling pathway", - "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", + "id": "Goldstein_blbr_1980", + "name": "Goldstein et al. 1980: Bivalent Ligand Bivalent Receptor (BLBR) Model", + "description": "BLBR heterogeneity", "tags": [ - "egfr", - "signaling", - "pathway", - "egf", - "grb2", - "shc" + "blbr", + "ligand-receptor", + "binding", + "1980", + "goldstein" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "physics", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer", - "test-models" + "physics" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egg", - "name": "egg", - "description": "BioNetGen model: egg", + "id": "Goldstein_TLBR_1984", + "name": "Goldstein et al. 1984: Trivalent Ligand Bivalent Receptor (TLBR) Model", + "description": "Ligand binding", "tags": [ - "egg", - "x", - "y", - "generate_network", - "simulate" + "tlbr", + "polymerization", + "ligand-receptor", + "bivalent-receptor", + "trivalent-ligand", + "1984", + "goldstein" ], - "category": "validation", - "origin": "test-case", + "category": "immunology", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "eif2a-stress-response", - "name": "eif2a stress response", - "description": "Integrated Stress Response: eIF2alpha and the translational gate.", + "id": "gpcr-desensitization-arrestin", + "name": "gpcr desensitization arrestin", + "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", "tags": [ - "eif2a", - "stress", - "response", - "eif2b", - "perk", - "gadd34" + "gpcr", + "desensitization", + "arrestin", + "ligand", + "gprotein" ], "category": "signaling", "origin": "ai-generated", @@ -4298,104 +4172,24 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "elephant_EFA", - "name": "Hlavacek2018Elephant", - "description": "BNGL model: elephant_EFA", + "id": "Harmon_Antigen_2017", + "name": "Harmon et al. 2017: Antigen Recognition Feedback Model", + "description": "Antigen pulses", "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" + "antigen-recognition", + "immune-signaling", + "2017", + "harmon" ], - "category": "other", + "category": "immunology", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -4404,105 +4198,58 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "elephant_fit", - "name": "Hlavacek2018Elephant", - "description": "BNGL model: elephant_EFA", + "id": "Hat_wip1_2016", + "name": "Hat et al. 2016: Wip1-Mediated Feedback Oscillator", + "description": "Nuclear transport", "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" + "wip1", + "feedback-loop", + "p53-pathway", + "2016", + "hat" ], - "category": "other", + "category": "regulation", "origin": "published", - "visible": false, + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "multistage" + ], + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Haugh2b", + "name": "Haugh2b", + "description": "R(KD,Y1~U,Y2~U) 1.00", + "tags": [ + "haugh2b", + "exclude_reactants", + "include_reactants" + ], + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -4511,22 +4258,27 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "endosomal-sorting-rab", - "name": "endosomal sorting rab", - "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", + "id": "hedgehog-signaling-pathway", + "name": "hedgehog signaling pathway", + "description": "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing.", "tags": [ - "endosomal", - "sorting", - "rab", - "rab5", - "rab7", - "effector", - "v_gef", - "v_gap_drive" + "hedgehog", + "signaling", + "pathway", + "hh", + "ptch", + "smo", + "gli", + "sufu" ], "category": "signaling", "origin": "ai-generated", @@ -4540,24 +4292,24 @@ ] }, "gallery": [ + "developmental", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "energy_allostery_mwc", - "name": "energy allostery mwc", - "description": "Model: energy_allostery_mwc.bngl", + "id": "heise", + "name": "heise", + "description": "Validate state inheritance in a symmetric context", "tags": [ - "energy", - "allostery", - "mwc", - "p", - "l" + "heise" ], - "category": "other", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -4567,28 +4319,32 @@ ] }, "gallery": [ - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "energy_catalysis_mm", - "name": "energy catalysis mm", - "description": "Model: energy_catalysis_mm.bngl", + "id": "hematopoietic-growth-factor", + "name": "hematopoietic growth factor", + "description": "Kinetic Parameters", "tags": [ - "energy", - "catalysis", - "mm", - "e", - "s", - "p" + "hematopoietic", + "growth", + "factor", + "epo", + "epor", + "jak2", + "stat5" ], - "category": "other", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -4597,25 +4353,29 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "energy_cooperativity_adh", - "name": "energy cooperativity adh", - "description": "Model: energy_cooperativity_adh.bngl", + "id": "hif1a_degradation_loop", + "name": "hif1a degradation loop", + "description": "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay.", "tags": [ - "energy", - "cooperativity", - "adh", - "r", - "l" + "hif1a", + "degradation", + "loop", + "vhl", + "arnt", + "v_hydrox" ], - "category": "other", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -4624,26 +4384,24 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "energy_example1", - "name": "energy_example1", - "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", + "id": "HIV_Dynamics_pt303", + "name": "HIV Viral Load Dynamics - Patient 303", + "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", "tags": [ - "validation", - "energy", - "example1", - "version", - "setoption", - "s", - "a", - "b", - "c" + "hiv", + "viral-dynamics", + "patient-303", + "epidemiology" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -4653,23 +4411,25 @@ ] }, "gallery": [ - "validation" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "energy_linear_chain", - "name": "energy linear chain", - "description": "Model: energy_linear_chain.bngl", + "id": "HIV_Dynamics_pt403", + "name": "HIV Viral Load Dynamics - Patient 403", + "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", "tags": [ - "energy", - "linear", - "chain", - "m", - "generate_network" + "hiv", + "viral-dynamics", + "patient-403", + "epidemiology" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -4680,26 +4440,25 @@ ] }, "gallery": [ - "test-models" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "energy_transport_pump", - "name": "energy transport pump", - "description": "Model: energy_transport_pump.bngl", + "id": "HIV_Dynamics_pt409", + "name": "HIV Viral Load Dynamics - Patient 409", + "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", "tags": [ - "energy", - "transport", - "pump", - "a", - "atp", - "adp", - "pi", - "t" + "hiv", + "viral-dynamics", + "patient-409", + "epidemiology" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -4710,144 +4469,76 @@ ] }, "gallery": [ - "test-models" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ensemble_tofit", - "name": "translated into BNGL", - "description": "Ensemble model translated into BNGL", + "id": "Hlavacek_Egg_2018", + "name": "Hlavacek et al. 2018: Calcium Oscillations in Egg Activation", + "description": "End of permute change log", "tags": [ - "signaling" + "calcium-oscillations", + "egg-activation", + "2018", + "hlavacek" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "er-stress-response", - "name": "er stress response", - "description": "Rate Constants", + "id": "Hlavacek_Elephant_2018_elephant_EFA", + "name": "Hlavacek et al. 2018: Fitting an Elephant with Four Parameters (elephant_EFA)", + "description": "BNGL model: elephant_EFA", "tags": [ - "er", - "stress", - "response", - "unfoldedprotein", - "perk", - "eif2a", - "chaperone" + "elephant-fitting", + "mathematical-model", + "2018", + "hlavacek" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Erdem_2021", - "name": "Erdem 2021", - "description": "InsR/IGF1R signaling", + "id": "Hlavacek_Elephant_2018_elephant_fit", + "name": "Hlavacek et al. 2018: Fitting an Elephant with Four Parameters (elephant_fit)", + "description": "BNGL model: elephant_EFA", "tags": [ - "published", - "erdem", - "2021", - "igf1", - "ins", - "igf1r", - "insr", - "irs", - "sos", - "ras", - "raf" - ], - "category": "signaling", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "metabolism" - ], - "collectionId": null - }, - { - "id": "ERK_model", - "name": "ERK_model.bngl", - "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" + "elephant-fitting", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -4857,29 +4548,28 @@ "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "erk-nuclear-translocation", - "name": "erk nuclear translocation", - "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", + "id": "Hlavacek_Proofreading_2001", + "name": "Hlavacek et al. 2001: Kinetic Proofreading Model", + "description": "Kinetic proofreading", "tags": [ - "erk", - "nuclear", - "translocation", - "mek", - "elk1", - "dusp", - "transcription_signal" + "kinetic-proofreading", + "ligand-discrimination", + "2001", + "hlavacek" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "physics", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -4889,23 +4579,26 @@ ] }, "gallery": [ - "test-models" + "physics" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ErrNoFrees", - "name": "ErrNoFrees", - "description": "An example from a real application", + "id": "Hlavacek_Restructuration_2018_after_bunching", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (after_bunching)", + "description": "BNGL model: after_bunching", "tags": [ - "errnofrees", - "ag", - "r", - "h" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -4914,22 +4607,21 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example1", - "name": "example1", - "description": "Filename: example1.bngl", + "id": "Hlavacek_Restructuration_2018_after_decoupling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (after_decoupling)", + "description": "BNGL model: after_bunching", "tags": [ - "example1", - "egf", - "egfr", - "pre1_dose", - "pre2_time", - "pre3_dose" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -4942,72 +4634,48 @@ "ode" ] }, - "gallery": [ - "other" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example1", - "name": "example1", - "description": "Example file for BNG2 tutorial.", + "id": "Hlavacek_Restructuration_2018_after_scaling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (after_scaling)", + "description": "BNGL model: after_bunching", "tags": [ - "validation", - "example1", - "version", - "generate_network", - "simulate_ode" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example1_BNFfiles_example1", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "Hlavacek_Restructuration_2018_before_bunching", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (before_bunching)", + "description": "BNGL model: after_bunching", "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" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -5021,51 +4689,20 @@ ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example1_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "Hlavacek_Restructuration_2018_before_decoupling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (before_decoupling)", + "description": "BNGL model: after_bunching", "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" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -5079,96 +4716,47 @@ ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example2_BNFfiles_example2", - "name": "example2_starting_point.bngl", - "description": "Filename: example2_starting_point.bngl", + "id": "Hlavacek_Restructuration_2018_before_scaling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (before_scaling)", + "description": "BNGL model: after_bunching", "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" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example2_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "Hlavacek_Restructuration_2018_check_scaling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (check_scaling)", + "description": "BNGL model: after_bunching", "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" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -5182,107 +4770,86 @@ ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example2_starting_point", - "name": "example2 starting point", - "description": "Filename: example2_starting_point.bngl", + "id": "Hlavacek_Steric_1999", + "name": "Hlavacek et al. 1999: Steric Hindrance in Ligand Binding", + "description": "Steric effects", "tags": [ - "example2", - "starting", - "point", - "egf", - "egfr", - "clusters", - "pre1_dose", - "pre2_time" + "steric-hindrance", + "ligand-binding", + "1999", + "hlavacek" ], - "category": "other", + "category": "physics", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "other" + "physics" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example3_BNFfiles_example3", - "name": "example3 BNFfiles", - "description": "BNGL model: example3", + "id": "hypoxia-response-signaling", + "name": "hypoxia response signaling", + "description": "Rate Constants", "tags": [ - "alpha", - "molecules", - "species" + "hypoxia", + "response", + "signaling", + "oxygensensor", + "hif1", + "vegf" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example3_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "il1b-signaling", + "name": "il1b signaling", + "description": "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation.", "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" + "il1b", + "signaling", + "il1ri", + "myd88", + "irak", + "nfkb" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -5292,157 +4859,127 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example4_BNFfiles_example4", - "name": "in BNGL. For a description of BNGL, see:", - "description": "Supplementary File A in File S1", + "id": "il6-jak-stat-pathway", + "name": "il6 jak stat pathway", + "description": "IL-6 Signaling: gp130 hexamerization and pSTAT3 import.", "tags": [ - "other" + "il6", + "jak", + "stat", + "pathway", + "gp130", + "stat3", + "socs" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example4_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "immune-synapse-formation", + "name": "immune synapse formation", + "description": "Kinetic Parameters", "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" + "immune", + "synapse", + "formation", + "tcr", + "pmhc", + "lck", + "zap70" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example5_BNFfiles_example5", - "name": "example5 BNFfiles", - "description": "A simple model", + "id": "inflammasome-activation", + "name": "inflammasome activation", + "description": "Rate Constants", "tags": [ - "ligand_ispresent", - "molecules", - "species" + "inflammasome", + "activation", + "sensor", + "asc", + "caspase1", + "il1b" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example5_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "inositol-phosphate-metabolism", + "name": "inositol phosphate metabolism", + "description": "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points.", "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" + "inositol", + "phosphate", + "metabolism", + "pip2", + "ip3", + "ip4", + "calcium", + "agonist" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -5452,159 +4989,124 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example5_ground_truth", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "insulin-glucose-homeostasis", + "name": "insulin glucose homeostasis", + "description": "Insulin-Glucose: Compartmentalized transport.", "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" + "insulin", + "glucose", + "homeostasis", + "ir", + "glut4", + "pancreas" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example5_starting_point", - "name": "13-receptor", - "description": "A simple model", + "id": "interferon-signaling", + "name": "interferon signaling", + "description": "Rate Constants", "tags": [ - "ligand_ispresent", - "molecules", - "species" + "interferon", + "signaling", + "ifn", + "ifnar", + "tyk2", + "stat1" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example6_BNFfiles_example6", - "name": "example6 BNFfiles", - "description": "A simple model", + "id": "ire1a-xbp1-er-stress", + "name": "ire1a xbp1 er stress", + "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", "tags": [ - "molecules", - "species" + "ire1a", + "xbp1", + "er", + "stress", + "ire1", + "bip", + "unfolded", + "ridd_target" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example6_ground_truth", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "issue_198_short", + "name": "issue_198_short", + "description": "No description available", "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" + "issue", + "198", + "short" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -5613,33 +5115,30 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "extra_CaMKII_Holo", - "name": "Ordyan 2020: extra CaMKII holo", - "description": "Extra CaMKII holo (supplement)", + "id": "jak-stat-cytokine-signaling", + "name": "jak stat cytokine signaling", + "description": "Rate Constants", "tags": [ - "published", - "neuroscience", - "extra", - "camkii", - "holo", - "t1", - "t2", - "t3", - "t4", - "t5", - "t6", - "t7", - "t8" + "jak", + "stat", + "cytokine", + "signaling", + "receptor" ], "category": "signaling", - "origin": "published", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ @@ -5647,30 +5146,31 @@ ] }, "gallery": [ - "signaling" + "immunology", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Faeder_2003", - "name": "Faeder 2003", - "description": "FceRI signaling", + "id": "JaruszewiczBlonska_NFkB_2023", + "name": "Jaruszewicz-Blonska et al. 2023: NF-kB Feedback Regulation", + "description": "T-cell discrimination", "tags": [ - "published", - "immunology", - "faeder", - "2003", - "lig", - "lyn", - "syk", - "rec" + "nfkb", + "feedback-regulation", + "inflammatory-response", + "2023", + "jaruszewiczblonska" ], "category": "immunology", "origin": "published", "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" @@ -5679,141 +5179,145 @@ "gallery": [ "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fceri_fyn", - "name": "FceRI Fyn", - "description": "FceRI signaling", + "id": "jnk-mapk-signaling", + "name": "jnk mapk signaling", + "description": "JNK MAPK Signaling: Scaffold-mediated activation and feedback.", "tags": [ - "published", - "immunology", - "fceri", - "fyn", - "lig", - "lyn", - "syk", - "rec" + "jnk", + "mapk", + "signaling", + "mkk7", + "jip1", + "v_dephos" ], - "category": "immunology", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fceri_gamma2", - "name": "fceri gamma2", - "description": "BioNetGen model: fceri gamma2", + "id": "Jung_CaMKII_2017", + "name": "Jung et al. 2017: CaMKII Activation Kinetics", + "description": "M1 receptor signaling", "tags": [ - "fceri", - "gamma2", - "lig", - "lyn", - "syk", - "rec" + "camkii", + "neuroscience", + "kinase-activation", + "2017", + "jung" ], - "category": "other", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "other" + "neuroscience" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fceri_gamma2_ground_truth", - "name": "fceri gamma2 ground truth", - "description": "BioNetGen model: fceri gamma2 ground truth", + "id": "Kesseler_CellCycle_2013", + "name": "Kesseler et al. 2013: Cell Cycle Regulation Model", + "description": "G2/Mitosis transition", "tags": [ - "fceri", - "gamma2", - "ground", - "truth", - "lig", - "lyn", - "syk", - "rec" + "cell-cycle", + "mitosis", + "cdc25", + "wee1", + "2013", + "kesseler" ], - "category": "other", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "other" + "cell-cycle" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "fceri_ji", - "name": "Faeder 2003", - "description": "FceRI signaling", + "id": "Kiefhaber_emodel", + "name": "Kiefhaber_emodel", + "description": "Allow molar units to be used for bimolecular rate constants", "tags": [ - "published", - "immunology", - "faeder", - "2003", - "lig", - "lyn", - "syk", - "rec" + "emodel" ], - "category": "immunology", - "origin": "published", - "visible": true, + "category": "validation", + "origin": "test-case", + "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "FceRI_ji", - "name": "FceRI ji", - "description": "title: FceRI_ji.bngl", + "id": "kir-channel-regulation", + "name": "kir channel regulation", + "description": "Kir Channel Regulation: PIP2 modulation and G-protein potentiation.", "tags": [ - "fceri", - "ji", - "lig", - "lyn", - "syk", - "rec" + "kir", + "channel", + "regulation", + "pip2", + "gbg", + "v_opening", + "v_gbg_factor" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -5823,64 +5327,61 @@ ] }, "gallery": [ - "native-tutorials" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fceri_ji_comp", - "name": "fceri_ji_comp", - "description": "Ligand-receptor binding", + "id": "Kocieniewski_published_2012", + "name": "Kocieniewski et al. 2012: MAPK Signaling on Scaffolds", + "description": "Actin dynamics", "tags": [ - "validation", - "fceri", - "ji", - "comp", - "lig", - "lyn", - "syk", - "rec" + "mapk", + "scaffold-proteins", + "signaling", + "2012", + "kocieniewski" ], - "category": "validation", - "origin": "test-case", + "category": "regulation", + "origin": "published", "visible": false, "compatibility": { "bng2": false, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "regulation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "FceRI_viz", - "name": "FceRI Viz", - "description": "FcεRI (viz)", + "id": "Korwek_InnateImmunity_2023", + "name": "Korwek et al. 2023: Innate Immunity Activation Model", + "description": "Immune response", "tags": [ - "published", - "tutorial", - "native", - "fceri", - "viz", - "fcr", - "ige", - "lat", - "lyn", - "syk", - "pb", - "pg", - "sykp" + "innate-immunity", + "rig-i-sensing", + "pkr-activation", + "rnase-l-cleavage", + "viral-sensing", + "2023", + "korwek" ], - "category": "tutorial", - "origin": "tutorial", + "category": "immunology", + "origin": "published", "visible": true, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -5888,26 +5389,29 @@ ] }, "gallery": [ - "native-tutorials" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_functional_rates_volume", - "name": "feature functional rates volume", - "description": "Model: feature_functional_rates_volume.bngl", + "id": "Korwek_ViralSensing_2023", + "name": "Korwek et al. 2023: Viral Sensing and Innate Immune Activation", + "description": "This BioNetGen file features the article:", "tags": [ - "feature", - "functional", - "rates", - "volume", - "a", - "b", - "c" + "innate-immunity", + "rig-i-sensing", + "pkr-activation", + "rnase-l-cleavage", + "viral-sensing", + "2023", + "korwek" ], - "category": "other", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -5917,28 +5421,29 @@ ] }, "gallery": [ - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_global_functions_scan", - "name": "feature global functions scan", - "description": "Model: feature_global_functions_scan.bngl", + "id": "Kozer_egfr_2013", + "name": "Kozer et al. 2013: EGFR Dimerization and Internalization", + "description": "EGFR oligomerization", "tags": [ - "feature", - "global", - "functions", - "scan", - "signal", - "response", - "stimulus" + "egfr", + "dimerization", + "internalization", + "2013", + "kozer" ], - "category": "other", - "origin": "ai-generated", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -5946,55 +5451,59 @@ ] }, "gallery": [ - "test-models" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_local_functions_explicit", - "name": "feature local functions explicit", - "description": "Model: feature_local_functions_explicit.bngl", + "id": "Kozer_egfr_2014", + "name": "Kozer et al. 2014: EGFR Oligomerization Dynamics", + "description": "Grb2-EGFR recruitment", "tags": [ - "feature", - "local", - "functions", - "explicit", - "s", - "p", - "e", - "mm_rate", - "ratelaw" + "egfr", + "oligomerization", + "internalization", + "2014", + "kozer" ], - "category": "other", - "origin": "ai-generated", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "test-models" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_symmetry_factors_cyclic", - "name": "feature symmetry factors cyclic", - "description": "Model: feature_symmetry_factors_cyclic.bngl", + "id": "l-type-calcium-channel-dynamics", + "name": "l type calcium channel dynamics", + "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", "tags": [ - "feature", - "symmetry", - "factors", - "cyclic", - "x", - "generate_network", - "simulate" + "l", + "type", + "calcium", + "channel", + "dynamics", + "ltcc", + "voltage", + "v_open", + "v_inact" ], - "category": "other", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { @@ -6006,56 +5515,63 @@ ] }, "gallery": [ + "neuroscience", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_synthesis_degradation_ss", - "name": "feature synthesis degradation ss", - "description": "Model: feature_synthesis_degradation_ss.bngl", + "id": "lac-operon-regulation", + "name": "lac operon regulation", + "description": "Kinetic Parameters", "tags": [ - "feature", - "synthesis", - "degradation", - "ss", - "m", - "generate_network", - "simulate" + "lac", + "operon", + "regulation", + "laci", + "promoter", + "mrna", + "betagal", + "lactose", + "allolactose" ], - "category": "other", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ + "metabolism", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "fgf-signaling-pathway", - "name": "fgf signaling pathway", - "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", + "id": "Lang_CellCycle_2024", + "name": "Lang et al. 2024: Cyclin A-CDK2 Cell Cycle Control", + "description": "Cell cycle regulation", "tags": [ - "fgf", - "signaling", - "pathway", - "fgfr", - "frs2", - "spry", - "rasgef", - "internalized_rec" + "cell-cycle", + "cyclin-a", + "cdk2", + "2024", + "lang" ], "category": "signaling", - "origin": "ai-generated", - "visible": false, + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -6065,28 +5581,30 @@ ] }, "gallery": [ - "developmental", - "test-models" + "cell-cycle" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "free_missing", - "name": "free missing", - "description": "Original values used to generate parabola.exp", + "id": "Lee_Wnt_2003", + "name": "Lee et al. 2003: Wnt/Beta-Catenin Signaling Pathway", + "description": "Wnt signaling", "tags": [ - "free", - "missing", - "counter", - "y", - "generate_network", - "simulate" + "wnt", + "beta-catenin", + "axin-degradation", + "dishevelled-activation", + "2003", + "lee" ], - "category": "validation", - "origin": "test-case", + "category": "regulation", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -6094,225 +5612,253 @@ ] }, "gallery": [ - "validation" + "regulation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Gardner_2000", - "name": "Gardner 2000", - "description": "Genetic toggle switch", + "id": "Ligon_egfr_2014", + "name": "Ligon et al. 2014: EGFR Dimerization in Living Cells", + "description": "Lipoplex delivery", "tags": [ - "published", - "synthetic-biology", - "gardner", - "2000" + "egfr", + "dimerization", + "fluorescence-microscopy", + "2014", + "ligon" ], - "category": "synthetic-biology", + "category": "signaling", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "synthetic-biology" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "gas6-axl-signaling", - "name": "gas6 axl signaling", - "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", + "id": "Lin_ERK_2019", + "name": "Lin 2019", + "description": "ERK signaling", "tags": [ - "gas6", - "axl", + "2019", + "egfr", + "erk", + "lin", + "linerk", + "mek", + "raf", + "ras", + "rasgap", "signaling", - "pi3k", - "akt", - "socs", - "survival_burst" + "sos" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "other", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "test-models" + "developmental" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "gene-expression-toggle", - "name": "gene expression toggle", - "description": "Kinetic Parameters", + "id": "Lin_Prion_2019", + "name": "Lin 2019", + "description": "Prion replication", "tags": [ - "gene", - "expression", - "toggle", - "mrna", - "protein" + "2019", + "lin", + "linprion", + "prion", + "prp" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "test-models" + "neuroscience" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "genetic_bistability_energy", - "name": "genetic bistability energy", - "description": "Model: genetic_bistability_energy.bngl", + "id": "Lin_ScalingBench_2019_ERK_model", + "name": "Lin et al. 2019: Scaling Benchmark Models (ERK_model)", + "description": "filename: ERK_model.bngl", "tags": [ - "genetic", - "bistability", - "energy", - "genea", - "geneb", - "prota", - "protb" + "scaling-benchmark", + "kinetics", + "2019", + "lin" ], - "category": "gene-expression", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, - "gallery": [ - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "genetic_dna_replication_stochastic", - "name": "genetic dna replication stochastic", - "description": "Model: genetic_dna_replication_stochastic.bngl", + "id": "Lin_ScalingBench_2019_prion_model", + "name": "Lin et al. 2019: Scaling Benchmark Models (prion_model)", + "description": "filename: ERK_model.bngl", "tags": [ - "genetic", - "dna", - "replication", - "stochastic", - "pol", - "n", - "generate_network" + "scaling-benchmark", + "kinetics", + "2019", + "lin" ], - "category": "gene-expression", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, - "gallery": [ - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "genetic_goodwin_oscillator", - "name": "genetic goodwin oscillator", - "description": "Model: genetic_goodwin_oscillator.bngl", + "id": "Lin_ScalingBench_2019_TCR_model", + "name": "Lin et al. 2019: Scaling Benchmark Models (TCR_model)", + "description": "filename: ERK_model.bngl", "tags": [ - "genetic", - "goodwin", - "oscillator", - "gene", - "mrna", - "protein", - "repressor" + "scaling-benchmark", + "kinetics", + "2019", + "lin" ], - "category": "gene-expression", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, - "gallery": [ - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "genetic_translation_kinetics", - "name": "genetic translation kinetics", - "description": "Model: genetic_translation_kinetics.bngl", + "id": "Lin_TCR_2019", + "name": "Lin 2019", + "description": "TCR signaling", "tags": [ - "genetic", - "translation", - "kinetics", - "mrna", - "rib", - "protein" + "2019", + "erk", + "immune", + "lck", + "lin", + "lintcr", + "mek", + "pmhc", + "shp", + "signaling", + "tcr", + "zap" ], - "category": "gene-expression", - "origin": "ai-generated", - "visible": false, + "category": "other", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "test-models" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "genetic_turing_pattern_1d", - "name": "genetic turing pattern 1d", - "description": "Model: genetic_turing_pattern_1d.bngl", + "id": "lipid-mediated-pip3-signaling", + "name": "lipid mediated pip3 signaling", + "description": "Kinetic Parameters", "tags": [ - "genetic", - "turing", - "pattern", - "1d", - "a", - "b" + "lipid", + "mediated", + "pip3", + "signaling", + "pi3k", + "pip2", + "pten", + "pdk1" ], - "category": "gene-expression", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -6321,16 +5867,18 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "GK", - "name": "GK", - "description": "title: GK.bngl", + "id": "Lisman", + "name": "Lisman", + "description": "title: auto.bngl", "tags": [ - "gk", - "b", - "simulate" + "lisman", + "input" ], "category": "tutorial", "origin": "tutorial", @@ -6344,27 +5892,54 @@ ] }, "gallery": [ - "metabolism", + "neuroscience", "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "glioblastoma-egfrviii-signaling", - "name": "glioblastoma egfrviii signaling", - "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", + "id": "Lisman_bifurcate", + "name": "Lisman bifurcate", + "description": "title: Lisman_bifurcate.bngl", "tags": [ - "glioblastoma", - "egfrviii", - "signaling", - "pi3k", - "akt", - "oncogenic_output", - "v_viii_act" + "lisman", + "bifurcate" ], - "category": "signaling", - "origin": "ai-generated", + "category": "tutorial", + "origin": "tutorial", "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "localfunc", + "name": "localfunc", + "description": "Test local function expansion", + "tags": [ + "localfunc", + "trash", + "f_synth" + ], + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -6374,26 +5949,23 @@ ] }, "gallery": [ - "cancer", - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "glycolysis-branch-point", - "name": "glycolysis branch point", - "description": "BioNetGen model: glycolysis branch point", + "id": "LR", + "name": "LR", + "description": "title: LR.bngl", "tags": [ - "glycolysis", - "branch", - "point", - "glucose", - "atp", - "biomass" + "lr" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, "nfsim": true, @@ -6403,57 +5975,49 @@ ] }, "gallery": [ - "metabolism", - "test-models" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "gm_game_of_life", - "name": "gm game of life", - "description": "Model: gm_game_of_life.bngl", + "id": "LR_comp", + "name": "LR comp", + "description": "title: LR_comp.bngl", "tags": [ - "gm", - "game", - "of", - "life", - "cell" + "lr", + "comp" ], - "category": "computer-science", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "test-models" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "gm_ray_marcher", - "name": "gm ray marcher", - "description": "Ray Marching Renderer in BNGL", + "id": "LRR", + "name": "LRR", + "description": "title: LRR.bngl", "tags": [ - "gm", - "ray", - "marcher", - "ray0", - "hit0", - "bright0", - "sdf0", - "sdf1", - "sdf2", - "sdf3", - "speed0" + "lrr" ], - "category": "computer-science", - "origin": "ai-generated", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -6464,140 +6028,139 @@ ] }, "gallery": [ - "test-models" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Goldstein_1980", - "name": "Goldstein 1980", - "description": "BLBR heterogeneity", + "id": "LRR_comp", + "name": "LRR comp", + "description": "title: LRR_comp.bngl", "tags": [ - "published", - "physics", - "goldstein", - "1980" + "lrr", + "comp" ], - "category": "physics", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "physics" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "gpcr-desensitization-arrestin", - "name": "gpcr desensitization arrestin", - "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", + "id": "LV", + "name": "LV", + "description": "title: LV.bgl", "tags": [ - "gpcr", - "desensitization", - "arrestin", - "ligand", - "gprotein" + "lv", + "writesbml" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "test-models" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Harmon_2017", - "name": "Harmon 2017", - "description": "Antigen pulses", + "id": "LV_comp", + "name": "LV comp", + "description": "title: LV_comp.bgl", "tags": [ - "published", - "immunology", - "harmon", - "2017" + "lv", + "comp" ], - "category": "immunology", - "origin": "published", - "visible": true, + "category": "tutorial", + "origin": "tutorial", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "immunology" + "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Hat_2016", - "name": "Hat 2016", - "description": "Nuclear transport", + "id": "Macken_physics_1982", + "name": "Macken et al. 1982: Polymer Chain Reaction Kinetics", + "description": "TLBR solution macken 1982", "tags": [ - "published", - "hat", - "2016", - "dna_dsb", - "atm", - "siah1", - "hipk2", - "wip1", - "gene_wip1", - "mrna_wip1", - "p53" + "polymerization", + "mathematical-model", + "1982", + "macken" ], - "category": "regulation", + "category": "physics", "origin": "published", "visible": true, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, "gallery": [ - "cell-cycle", - "multistage" + "physics" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Haugh2b", - "name": "Haugh2b", - "description": "R(KD,Y1~U,Y2~U) 1.00", + "id": "Mallela_Cities_2021", + "name": "Mallela et al. 2021: Covid-19 City-Level Transmission Dynamics", + "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", "tags": [ - "validation", - "haugh2b", - "r", - "s1", - "s2", - "exclude_reactants", - "include_reactants" + "covid-19", + "epidemiology", + "city-level", + "2021", + "mallela" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "epidemiology", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -6607,26 +6170,26 @@ ] }, "gallery": [ - "validation" + "epidemiology" ], - "collectionId": null + "collectionId": "Mallela_Cities_2021", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "hedgehog-signaling-pathway", - "name": "hedgehog signaling pathway", - "description": "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing.", + "id": "Mallela_COVID_2021", + "name": "Mallela et al. 2021: Covid-19 State-Level Transmission Dynamics", + "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", "tags": [ - "hedgehog", - "signaling", - "pathway", - "hh", - "ptch", - "smo", - "gli", - "sufu" + "covid-19", + "epidemiology", + "state-level", + "2021", + "mallela" ], - "category": "signaling", - "origin": "ai-generated", + "category": "epidemiology", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -6637,27 +6200,27 @@ ] }, "gallery": [ - "developmental", - "test-models" + "epidemiology" ], - "collectionId": null + "collectionId": "Mallela_COVID_2021", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "heise", - "name": "heise", - "description": "Validate state inheritance in a symmetric context", + "id": "Mallela_MSAs_2022", + "name": "Mallela et al. 2022: Covid-19 MSA-Level Transmission Dynamics", + "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", "tags": [ - "validation", - "heise", - "a", - "b", - "generate_network", - "simulate_ode", - "setparameter" + "covid-19", + "epidemiology", + "msa-level", + "2022", + "mallela" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "epidemiology", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -6667,80 +6230,93 @@ ] }, "gallery": [ - "validation" + "epidemiology" ], - "collectionId": null + "collectionId": "Mallela_MSAs_2022", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "hematopoietic-growth-factor", - "name": "hematopoietic growth factor", - "description": "Kinetic Parameters", + "id": "Mallela_VaxVariants_Alabama_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - Alabama MSA", + "description": "reporting period (1 d)", "tags": [ - "hematopoietic", - "growth", - "factor", - "epo", - "epor", - "jak2", - "stat5" + "covid-19", + "epidemiology", + "vaccination", + "variants", + "alabama", + "2022", + "mallela" ], - "category": "signaling", - "origin": "ai-generated", + "category": "epidemiology", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "epidemiology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "hif1a_degradation_loop", - "name": "hif1a degradation loop", - "description": "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay.", + "id": "Mallela_VaxVariants_Dallas_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - Dallas MSA", + "description": "- This model is intended to be consistent with the compartmental model", "tags": [ - "hif1a", - "degradation", - "loop", - "vhl", - "arnt", - "v_hydrox" + "covid-19", + "epidemiology", + "vaccination", + "variants", + "dallas", + "2022", + "mallela" ], - "category": "signaling", - "origin": "ai-generated", + "category": "epidemiology", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "epidemiology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Hlavacek_1999", - "name": "Hlavacek 1999", - "description": "Steric effects", + "id": "Mallela_VaxVariants_Houston_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - Houston MSA", + "description": "- This model is intended to be consistent with the compartmental model", "tags": [ - "published", - "physics", - "hlavacek", - "1999" + "covid-19", + "epidemiology", + "vaccination", + "variants", + "houston", + "2022", + "mallela" ], - "category": "physics", + "category": "epidemiology", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -6750,23 +6326,29 @@ ] }, "gallery": [ - "physics" + "epidemiology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Hlavacek_2001", - "name": "Hlavacek 2001", - "description": "Kinetic proofreading", + "id": "Mallela_VaxVariants_MyrtleBeach_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - Myrtle Beach MSA", + "description": "Runtime-only BNGL model migrated from public/models: Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", "tags": [ - "published", - "physics", - "hlavacek", - "2001" + "covid-19", + "epidemiology", + "vaccination", + "variants", + "myrtle-beach", + "2022", + "mallela" ], - "category": "physics", + "category": "epidemiology", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -6776,40 +6358,27 @@ ] }, "gallery": [ - "physics" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Hlavacek2018Egg_egg", - "name": "Hlavacek2018Egg", - "description": "End of permute change log", + "id": "Mallela_VaxVariants_NYC_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - New York City MSA", + "description": "- This model is intended to be consistent with the compartmental model", "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" + "covid-19", + "epidemiology", + "vaccination", + "variants", + "nyc", + "2022", + "mallela" ], - "category": "other", + "category": "epidemiology", "origin": "published", "visible": false, "compatibility": { @@ -6820,23 +6389,26 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "epidemiology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Houston", - "name": "Houston", + "id": "Mallela_VaxVariants_Phoenix_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - Phoenix MSA", "description": "- This model is intended to be consistent with the compartmental model", "tags": [ - "houston", - "counter", - "fdcs", - "s", - "sv", - "e", - "a", - "i", - "v" + "covid-19", + "epidemiology", + "vaccination", + "variants", + "phoenix", + "2022", + "mallela" ], "category": "epidemiology", "origin": "published", @@ -6852,54 +6424,55 @@ "gallery": [ "epidemiology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "hypoxia-response-signaling", - "name": "hypoxia response signaling", - "description": "Rate Constants", + "id": "MAPK_Dimers_Model", + "name": "MAPK Cascades with Raf Dimerization", + "description": "MAPK dimerization", "tags": [ - "hypoxia", - "response", - "signaling", - "oxygensensor", - "hif1", - "vegf" + "mapk-pathway", + "kinase-cascade", + "raf-dimerization", + "phosphorylation" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer", - "test-models" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "IGF1R_Model_receptor_activation_bnf", - "name": "IGF1R Model receptor activation bnf", - "description": "Author: William S. Hlavacek", + "id": "MAPK_Monomers_Model", + "name": "MAPK Cascades with Raf Monomers", + "description": "MAPK cascade", "tags": [ - "igf1r", - "model", - "receptor", - "activation", - "bnf", - "igf1" + "mapk-pathway", + "kinase-cascade", + "raf-monomers", + "phosphorylation" ], - "category": "other", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -6907,114 +6480,122 @@ ] }, "gallery": [ - "other" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "il1b-signaling", - "name": "il1b signaling", - "description": "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation.", + "id": "mapk-signaling-cascade", + "name": "mapk signaling cascade", + "description": "Rate Constants", "tags": [ - "il1b", + "mapk", "signaling", - "il1ri", - "myd88", - "irak", - "nfkb" - ], + "cascade", + "ligand", + "receptor", + "mapkkk", + "mapkk" + ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ + "cancer", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "il6-jak-stat-pathway", - "name": "il6 jak stat pathway", - "description": "IL-6 Signaling: gp130 hexamerization and pSTAT3 import.", + "id": "Massole_developmental_2023", + "name": "Massole et al. 2023: Notch-Delta Lateral Inhibition Dynamics", + "description": "Epo receptor signaling", "tags": [ - "il6", - "jak", - "stat", - "pathway", - "gp130", - "stat3", - "socs" + "notch-delta", + "lateral-inhibition", + "developmental", + "2023", + "massole" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "developmental" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "immune-synapse-formation", - "name": "immune synapse formation", - "description": "Kinetic Parameters", + "id": "McMillan_TNF_2021", + "name": "McMillan 2021", + "description": "TNF signaling", "tags": [ - "immune", - "synapse", - "formation", - "tcr", - "pmhc", - "lck", - "zap70" + "2021", + "mcmillan", + "nfsim", + "signaling", + "tnf" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "immunology", - "test-models" + "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "inflammasome-activation", - "name": "inflammasome activation", - "description": "Rate Constants", + "id": "Mertins_cancer_2023", + "name": "Mertins et al. 2023: Apoptotic Signaling Response", + "description": "DNA damage response", "tags": [ - "inflammasome", - "activation", - "sensor", - "asc", - "caspase1", - "il1b" + "apoptosis", + "bax-bclxl", + "cancer", + "2023", + "mertins" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": true, "excluded": false, "methods": [ @@ -7022,32 +6603,31 @@ ] }, "gallery": [ - "immunology", - "test-models" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "innate_immunity", - "name": "Korwek 2023", - "description": "Immune response", + "id": "meta_formal_game_theory", + "name": "meta formal game theory", + "description": "Model: meta_formal_game_theory.bngl", "tags": [ - "published", - "immunology", - "innate", - "immunity", - "polyic", - "rigi", - "mavs", - "pkr", - "oas3", - "rnasel", - "eif2a", - "rigi_mrna" + "meta", + "formal", + "game", + "theory", + "hawk", + "dove", + "pop", + "payoffh", + "payoffd" ], - "category": "immunology", - "origin": "published", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -7057,25 +6637,28 @@ ] }, "gallery": [ - "immunology" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "inositol-phosphate-metabolism", - "name": "inositol phosphate metabolism", - "description": "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points.", + "id": "meta_formal_molecular_clock", + "name": "meta formal molecular clock", + "description": "Model: meta_formal_molecular_clock.bngl", "tags": [ - "inositol", - "phosphate", - "metabolism", - "pip2", - "ip3", - "ip4", - "calcium", - "agonist" + "meta", + "formal", + "molecular", + "clock", + "fasta", + "fastb", + "slowc", + "slowd" ], - "category": "signaling", + "category": "computer-science", "origin": "ai-generated", "visible": false, "compatibility": { @@ -7087,51 +6670,60 @@ ] }, "gallery": [ - "neuroscience", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "insulin-glucose-homeostasis", - "name": "insulin glucose homeostasis", - "description": "Insulin-Glucose: Compartmentalized transport.", + "id": "meta_formal_petri_net", + "name": "meta formal petri net", + "description": "Model: meta_formal_petri_net.bngl", "tags": [ - "insulin", - "glucose", - "homeostasis", - "ir", - "glut4", - "pancreas" + "meta", + "formal", + "petri", + "net", + "p1", + "p2", + "p3", + "p4" ], - "category": "signaling", + "category": "computer-science", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "interferon-signaling", - "name": "interferon signaling", - "description": "Rate Constants", + "id": "michaelis-menten-kinetics", + "name": "michaelis menten kinetics", + "description": "Kinetic Constants", "tags": [ - "interferon", - "signaling", - "ifn", - "ifnar", - "tyk2", - "stat1" + "michaelis", + "menten", + "kinetics", + "e", + "s", + "p", + "generate_network", + "simulate", + "writesbml" ], "category": "signaling", "origin": "ai-generated", @@ -7145,28 +6737,24 @@ ] }, "gallery": [ - "immunology", + "metabolism", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ire1a-xbp1-er-stress", - "name": "ire1a xbp1 er stress", - "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", + "id": "michment", + "name": "michment", + "description": "Michaelis Menten", "tags": [ - "ire1a", - "xbp1", - "er", - "stress", - "ire1", - "bip", - "unfolded", - "ridd_target" + "michment" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -7176,31 +6764,30 @@ ] }, "gallery": [ - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "issue_198_short", - "name": "issue_198_short", - "description": "No description available", + "id": "michment_cont", + "name": "michment_cont", + "description": "Michaelis Menten Continue", "tags": [ - "validation", - "issue", - "198", - "short", - "a", - "b", - "c", - "generate_network", - "simulate" + "michment", + "cont", + "readfile", + "setconcentration", + "addconcentration" ], "category": "validation", "origin": "test-case", - "visible": true, + "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -7209,55 +6796,55 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "jak-stat-cytokine-signaling", - "name": "jak stat cytokine signaling", - "description": "Rate Constants", + "id": "Miller_MEK_2025", + "name": "Miller et al. 2025: MEK Isoform Specific Signaling", + "description": "MEK isoform variant models curated for PyBioNetGen.", "tags": [ - "jak", - "stat", - "cytokine", + "mek-isoforms", + "mapk-pathway", "signaling", - "receptor" + "2025", + "miller" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", - "test-models" + "signaling" ], - "collectionId": null + "collectionId": "Miller_MEK_2025", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Jaruszewicz-Blonska_2023", - "name": "Jaruszewicz 2023", - "description": "T-cell discrimination", + "id": "Miller_NavajoNation_2022", + "name": "Miller et al. 2022: Covid-19 Transmission in Navajo Nation", + "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", "tags": [ - "published", - "immunology", - "jaruszewicz", - "blonska", - "2023", - "ikk", - "ikba", - "ikba_mrna", - "a20", - "nfkb" + "covid-19", + "epidemiology", + "navajo-nation", + "2022", + "miller" ], - "category": "immunology", + "category": "epidemiology", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -7267,24 +6854,27 @@ ] }, "gallery": [ - "immunology" + "epidemiology" ], - "collectionId": null + "collectionId": "Miller_NavajoNation_2022", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "jnk-mapk-signaling", - "name": "jnk mapk signaling", - "description": "JNK MAPK Signaling: Scaffold-mediated activation and feedback.", + "id": "Mitra_Degranulation_2019", + "name": "Mitra et al. 2019: Mast Cell Degranulation Dynamics", + "description": "A model of IgE receptor signaling", "tags": [ - "jnk", - "mapk", - "signaling", - "mkk7", - "jip1", - "v_dephos" + "fceri", + "degranulation", + "mast-cell", + "immune-response", + "2019", + "mitra" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -7294,164 +6884,168 @@ "ode" ] }, - "gallery": [ - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "jobs_ground", - "name": "30-jobs", - "description": "NFsim simulation of the job market", + "id": "Mitra_EGFR_2019", + "name": "Mitra et al. 2019: EGFR Receptor Signaling (ODE)", + "description": "EGFR model", "tags": [ - "other" + "egfr", + "signaling", + "receptor-binding", + "2019", + "mitra" ], - "category": "other", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "jobs_tofit", - "name": "30-jobs", - "description": "NFsim simulation of the job market", + "id": "Mitra_EGFR_2019_egfr", + "name": "Mitra et al. 2019: EGFR Receptor Signaling (ODE) (egfr)", + "description": "EGFR model", "tags": [ - "other" + "egfr", + "signaling", + "receptor-binding", + "2019", + "mitra" ], - "category": "other", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Jung_2017", - "name": "Jung 2017", - "description": "M1 receptor signaling", + "id": "Mitra_EGFR_2019_egfr_ground", + "name": "Mitra et al. 2019: EGFR Receptor Signaling (ODE) (egfr_ground)", + "description": "EGFR model", "tags": [ - "published", - "jung", - "2017", - "m1r", - "oxo", - "arrestin", - "mek", - "erk", - "perk", - "oxo_ec", - "pp2a" + "egfr", + "signaling", + "receptor-binding", + "2019", + "mitra" ], "category": "signaling", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "neuroscience" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Kesseler_2013", - "name": "Kesseler 2013", - "description": "G2/Mitosis transition", + "id": "Mitra_EGFR_NF_2019", + "name": "Mitra et al. 2019: EGFR Network-Free Simulation", + "description": "Filename: example2_starting_point.bngl", "tags": [ - "published", - "kesseler", - "2013", - "mpf", - "cdc25", - "wee1", - "myt1", - "pin1", - "pp2a", - "prox", - "e33" + "egfr", + "signaling", + "network-free", + "nfsim", + "2019", + "mitra" ], "category": "signaling", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "cell-cycle" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Kiefhaber_emodel", - "name": "Kiefhaber_emodel", - "description": "Allow molar units to be used for bimolecular rate constants", + "id": "Mitra_EGFR_ODE_2019", + "name": "Mitra et al. 2019: EGFR Parameter Estimation (ODE)", + "description": "Filename: example1.bngl", "tags": [ - "validation", - "kiefhaber", - "emodel", - "setoption", - "l", - "p", - "s", - "a" + "egfr", + "signaling", + "ode", + "parameter-estimation", + "2019", + "mitra" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "kir-channel-regulation", - "name": "kir channel regulation", - "description": "Kir Channel Regulation: PIP2 modulation and G-protein potentiation.", + "id": "Mitra_EGFR_SSA_2019_egfr", + "name": "Mitra et al. 2019: EGFR Stochastic (SSA) Model (egfr)", + "description": "EGFR model", "tags": [ - "kir", - "channel", - "regulation", - "pip2", - "gbg", - "v_opening", - "v_gbg_factor" + "egfr", + "stochastic", + "ssa", + "signaling", + "2019", + "mitra" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -7461,60 +7055,55 @@ "ode" ] }, - "gallery": [ - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Kocieniewski_2012", - "name": "Kocieniewski 2012", - "description": "Actin dynamics", + "id": "Mitra_EGFR_SSA_2019_egfr_ground", + "name": "Mitra et al. 2019: EGFR Stochastic (SSA) Model (egfr_ground)", + "description": "EGFR model", "tags": [ - "published", - "kocieniewski", - "2012", - "map3k", - "map2k", - "mapk", - "scaff" + "egfr", + "stochastic", + "ssa", + "signaling", + "2019", + "mitra" ], - "category": "regulation", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "regulation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Korwek_2023", - "name": "Korwek_2023", - "description": "This BioNetGen file features the article:", + "id": "Mitra_EggOscillator_2019", + "name": "Mitra et al. 2019: Egg Activation Calcium Oscillator", + "description": "BNGL model: egg", "tags": [ - "validation", - "korwek", - "2023", - "polyic", - "rigi", - "mavs", - "pkr", - "oas3", - "rnasel", - "eif2a", - "rigi_mrna" + "calcium-oscillator", + "egg-activation", + "oscillations", + "2019", + "mitra" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -7523,83 +7112,81 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Kozer_2013", - "name": "Kozer 2013", - "description": "EGFR oligomerization", + "id": "Mitra_ElephantFitting_2019", + "name": "Mitra et al. 2019: Elephant Drawing Parameter Fitting", + "description": "BNGL model: elephant", "tags": [ - "published", - "kozer", - "2013", - "egf", - "egfr" + "elephant-drawing", + "parameter-fitting", + "mathematical-model", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "cancer" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Kozer_2014", - "name": "Kozer 2014", - "description": "Grb2-EGFR recruitment", + "id": "Mitra_FceRI_gamma2_2019", + "name": "Mitra et al. 2019: FceRI Gamma2 Subunit Signaling", + "description": "Added molecule type definition block so that the", "tags": [ - "published", - "kozer", - "2014", - "egf", - "egfr", - "grb2" + "fceri", + "gamma2-subunit", + "immune-signaling", + "2019", + "mitra" ], - "category": "signaling", + "category": "immunology", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "cancer" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "l-type-calcium-channel-dynamics", - "name": "l type calcium channel dynamics", - "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", + "id": "Mitra_IGF1R_2019", + "name": "Mitra et al. 2019: IGF1R (Insulin-like Growth Factor) Signaling", + "description": "Author: William S. Hlavacek", "tags": [ - "l", - "type", - "calcium", - "channel", - "dynamics", - "ltcc", - "voltage", - "v_open", - "v_inact" + "igf1r", + "receptor-activation", + "phosphorylation", + "2019", + "mitra" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -7609,91 +7196,80 @@ "ode" ] }, - "gallery": [ - "neuroscience", - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "lac-operon-regulation", - "name": "lac operon regulation", - "description": "Kinetic Parameters", + "id": "Mitra_JNK_2019", + "name": "Mitra et al. 2019: JNK Pathway Cascade", + "description": "BNGL model: JNKmodel_180724_bnf", "tags": [ - "lac", - "operon", - "regulation", - "laci", - "promoter", - "mrna", - "betagal", - "lactose", - "allolactose" + "jnk-signaling", + "stress-response", + "kinase-cascade", + "2019", + "mitra" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "metabolism", - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Lang_2024", - "name": "Lang 2024", - "description": "Cell cycle regulation", + "id": "Mitra_JobScheduling_2019_jobs_ground", + "name": "Mitra et al. 2019: Job Scheduling Simulation (jobs_ground)", + "description": "NFsim simulation of the job market", "tags": [ - "published", - "lang", - "2024", - "e2f", - "rb1", - "ppp2r2b", - "ccnb_promoter", - "ccna", - "ccna_promoter", - "foxm1_promoter", - "ensa_arpp19" + "job-scheduling", + "queueing-theory", + "non-biological", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "cell-cycle" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Ligon_2014", - "name": "Ligon 2014", - "description": "Lipoplex delivery", + "id": "Mitra_JobScheduling_2019_jobs_tofit", + "name": "Mitra et al. 2019: Job Scheduling Simulation (jobs_tofit)", + "description": "NFsim simulation of the job market", "tags": [ - "published", - "nfsim", - "ligon", - "2014", - "lext", - "pit", - "lint" + "job-scheduling", + "queueing-theory", + "non-biological", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -7701,95 +7277,118 @@ "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [ - "cancer" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "LilyIgE", - "name": "LilyIgE", - "description": "An example from a real application", + "id": "Mitra_Likelihood_2019", + "name": "Mitra et al. 2019: Likelihood Profiling Analysis Reference", + "description": "filename: model_ground.bngl", "tags": [ - "lilyige", - "ag", - "r", - "syk", - "ship1", - "x", - "pip3", - "h" + "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": "validation", - "origin": "test-case", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, - "methods": [ - "ode" - ] + "methods": [] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Lin_ERK_2019", - "name": "Lin 2019", - "description": "ERK signaling", + "id": "Mitra_Likelihood_P16_2019", + "name": "Mitra et al. 2019: Likelihood Profiling - Problem 16", + "description": "filename: model.bngl", "tags": [ - "published", - "literature", - "signaling", - "lin", - "erk", + "likelihood", + "parameter-estimation", "2019", - "egfr", - "sos", - "ras", - "rasgap", - "raf", - "mek", - "ekar3" + "mitra" ], "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, - "gallery": [ - "developmental" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Lin_Prion_2019", - "name": "Lin 2019", - "description": "Prion replication", + "id": "Mitra_Likelihood_P16_3cat_2019", + "name": "Mitra et al. 2019: Likelihood Profiling - Problem 16 (3 Categories)", + "description": "filename: model.bngl", "tags": [ - "published", - "literature", - "prion", - "lin", + "likelihood", + "parameter-estimation", "2019", - "prp", - "scaledupspecies1", - "scaledupspecies2", - "scaledupspecies15", - "scaledupspecies30" + "mitra" ], "category": "other", "origin": "published", @@ -7799,153 +7398,136 @@ "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, - "gallery": [ - "neuroscience" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Lin_TCR_2019", - "name": "Lin 2019", - "description": "TCR signaling", + "id": "Mitra_Likelihood_P32_2019", + "name": "Mitra et al. 2019: Likelihood Profiling - Problem 32", + "description": "filename: model.bngl", "tags": [ - "published", - "literature", - "immune", - "lin", - "tcr", + "likelihood", + "parameter-estimation", "2019", - "pmhc", - "lck", - "shp", - "zap", - "mek", - "erk" + "mitra" ], "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, - "gallery": [ - "immunology" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "lipid-mediated-pip3-signaling", - "name": "lipid mediated pip3 signaling", - "description": "Kinetic Parameters", + "id": "Mitra_Likelihood_P32_3cat_2019", + "name": "Mitra et al. 2019: Likelihood Profiling - Problem 32 (3 Categories)", + "description": "filename: model.bngl", "tags": [ - "lipid", - "mediated", - "pip3", - "signaling", - "pi3k", - "pip2", - "pten", - "pdk1" + "likelihood", + "parameter-estimation", + "2019", + "mitra" ], - 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"name": "mapk signaling cascade", - "description": "Rate Constants", + "id": "Mitra_Rab_wt_pybnf_2019_rab_rab7_ox", + "name": "Mitra et al. 2019: Rab Cascade - Wild Type (PyBNF) (rab_rab7_ox)", + "description": "filename:rab_mon1ccz1_ox.bngl", "tags": [ - "mapk", - "signaling", - "cascade", - "ligand", - "receptor", - "mapkkk", - "mapkk" + "rab-cascade", + "vesicle-trafficking", + "mon1-ccz1", + "rab5", + "rab7", + "2019", + "mitra" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "cancer", - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Massole_2023", - "name": "Massole 2023", - "description": "Epo receptor signaling", + "id": "Mitra_Rab_wt_pybnf_2019_rab_wt", + "name": "Mitra et al. 2019: Rab Cascade - Wild Type (PyBNF) (rab_wt)", + "description": "filename:rab_mon1ccz1_ox.bngl", "tags": [ - "published", - "massole", - "2023" + "rab-cascade", + "vesicle-trafficking", + "mon1-ccz1", + "rab5", + "rab7", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "developmental" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "mCaMKII_Ca_Spike", - "name": "Ordyan 2020: mCaMKII Ca Spike", - "description": "mCaMKII Ca Spike model", + "id": "Mitra_RafConstraint_2019", + "name": "Mitra et al. 2019: Raf Signaling with Activity Constraints", + "description": "BNGL model: RAFi", "tags": [ - "published", - "neuroscience", - "mcamkii", - "ca", - "spike", - "cam", - "ng", - "camkii", - "pp1", - "time_counter" + "raf", + "constraints", + "activity-constraints", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "signaling" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "McMillan_2021", - "name": "McMillan 2021", - "description": "TNF signaling", + "id": "Mitra_RafConstraint4_2019", + "name": "Mitra et al. 2019: Raf Signaling Constraints (Version 4)", + "description": "BNGL model: RAFi", "tags": [ - "published", - "nfsim", - "mcmillan", - "2021", - "r0_tot", - "t0_tot", - "r", - "t", - "generate_network", - "simulate_ode" + "raf", + "constraints", + "activity-constraints", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [ - "immunology" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Mertins_2023", - "name": "Mertins 2023", - "description": "DNA damage response", + "id": "Mitra_SimpleReceptor_2019_example5_starting_point", + "name": "Mitra et al. 2019: Simple Ligand-Receptor Binding (example5_starting_point)", + "description": "A simple model", "tags": [ - "published", - "mertins", - "2023", - "dnadsb", - "p53", - "mrna_bax", - "bax", - "bclxl", - "bad", - "fourteen_3_3", - "caspase" + "ligand-receptor", + "binding", + "reversible-reaction", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "cancer" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "meta_formal_game_theory", - "name": "meta formal game theory", - "description": "Model: meta_formal_game_theory.bngl", + "id": "Mitra_SimpleReceptor_2019_receptor", + "name": "Mitra et al. 2019: Simple Ligand-Receptor Binding (receptor)", + "description": "A simple model", "tags": [ - "meta", - "formal", - "game", - "theory", - "hawk", - "dove", - "pop", - "payoffh", - "payoffd" - ], - "category": "computer-science", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "test-models" - ], - "collectionId": null - }, - { - "id": "meta_formal_molecular_clock", - "name": "meta formal molecular clock", - "description": "Model: meta_formal_molecular_clock.bngl", - "tags": [ - "meta", - "formal", - "molecular", - "clock", - "fasta", - "fastb", - "slowc", - "slowd" + "ligand-receptor", + "binding", + "reversible-reaction", + "2019", + "mitra" ], - "category": "computer-science", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -8562,139 +8277,109 @@ "ode" ] }, - "gallery": [ - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "meta_formal_petri_net", - "name": "meta formal petri net", - "description": "Model: meta_formal_petri_net.bngl", + "id": "Mitra_SimpleReceptor_NF_2019", + "name": "Mitra et al. 2019: Simple Receptor Network-Free Binding", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", "tags": [ - "meta", - "formal", - "petri", - "net", - "p1", - "p2", - "p3", - "p4" + "ligand-receptor", + "binding", + "nfsim", + "network-free", + "2019", + "mitra" ], - "category": "computer-science", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "test-models" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "michaelis-menten-kinetics", - "name": "michaelis menten kinetics", - "description": "Kinetic Constants", + "id": "Mitra_TCR_2019", + "name": "Mitra et al. 2019: T Cell Receptor (TCR) Signaling", + "description": "A model of T cell receptor signaling", "tags": [ - "michaelis", - "menten", - "kinetics", - "e", - "s", - "p", - "generate_network", - "simulate", - "writesbml" + "tcr", + "t-cell", + "immune-signaling", + "2019", + "mitra" ], - "category": "signaling", - "origin": "ai-generated", + "category": "immunology", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ode" - ] - }, - "gallery": [ - "metabolism", - "test-models" - ], - "collectionId": null - }, - { - "id": "michment", - "name": "michment", - "description": "Michaelis Menten", - "tags": [ - "validation", - "michment", - "e", - "s", - "generate_network" - ], - "category": "validation", - "origin": "test-case", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "michment_cont", - "name": "michment_cont", - "description": "Michaelis Menten Continue", + "id": "Mitra_TCRSensitivity_2019", + "name": "Mitra et al. 2019: T Cell Receptor Sensitivity Analysis", + "description": "Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data", "tags": [ - "validation", - "michment", - "cont", - "readfile", - "setconcentration", - "simulate_ode", - "addconcentration" + "tcr", + "sensitivity-analysis", + "ligand-discrimination", + "2019", + "mitra" ], - "category": "validation", - "origin": "test-case", + "category": "immunology", + "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Miller2022_NavajoNation", - "name": "Miller 2022 - Navajo Nation Models", - "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", + "id": "Mitra_ThreeStepCascade_2019_m1", + "name": "Mitra et al. 2019: Three-Step Signaling Cascade (m1)", + "description": "Toy model of a 3-step signaling cascade", "tags": [ - "covid-19", - "epidemiology", - "pybionetgen" + "cascade", + "kinase", + "phosphorylation", + "2019", + "mitra" ], - "category": "epidemiology", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -8705,22 +8390,24 @@ "ode" ] }, - "gallery": [ - "epidemiology" - ], - "collectionId": "Miller2022_NavajoNation" + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Miller2025_MEK", - "name": "Miller 2025 - MEK Isoform Models", - "description": "MEK isoform variant models curated for PyBioNetGen.", + "id": "Mitra_ThreeStepCascade_2019_m1_ground", + "name": "Mitra et al. 2019: Three-Step Signaling Cascade (m1_ground)", + "description": "Toy model of a 3-step signaling cascade", "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" + "cascade", + "kinase", + "phosphorylation", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -8731,31 +8418,39 @@ "ode" ] }, - "gallery": [ - "signaling" - ], - "collectionId": "Miller2025_MEK" + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Mitra2019_02_egfr_bnf1_InputFiles_egfr", - "name": "InputFiles", - "description": "EGFR model", + "id": "Mitra_TLBR_2019", + "name": "Mitra et al. 2019: Trivalent Ligand Bivalent Receptor (TLBR)", + "description": "BNGL model: tlbr", "tags": [ - "signaling" + "tlbr", + "polymerization", + "ligand-receptor", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "ml_gradient_descent", @@ -8786,7 +8481,10 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "ml_hopfield", @@ -8816,7 +8514,10 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "ml_kmeans", @@ -8845,7 +8546,10 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "ml_q_learning", @@ -8876,7 +8580,10 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "ml_svm", @@ -8906,24 +8613,25 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "model", - "name": "model", - "description": "filename: model.bngl", + "id": "Motivating_example", + "name": "Motivating_example", + "description": "Signal Transduction with receptor internalization", "tags": [ - "model", - "ag", - "r", - "syk", - "ship1", - "x", - "pip3", - "h" + "motivating", + "example", + "tf", + "dna", + "mrna1", + "mrna2" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": true, "compatibility": { "bng2": true, @@ -8934,27 +8642,29 @@ ] }, "gallery": [ - "other" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "model", - "name": "model", - "description": "A model of IgE receptor signaling", + "id": "Motivating_example_cBNGL", + "name": "Motivating_example_cBNGL", + "description": "Signal transduction with receptor internalization", "tags": [ - "model", - "ag", - "r", - "syk", - "ship1", - "x", - "pip3", - "h" + "motivating", + "example", + "cbngl", + "tf", + "dna", + "mrna1", + "mrna2" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -8964,217 +8674,20 @@ ] }, "gallery": [ - "other" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "model_ground", - "name": "model_ground.bngl", - "description": "filename: model_ground.bngl", + "id": "motor", + "name": "motor", + "description": "Motor protein", "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", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [] - }, - "gallery": [], - "collectionId": null - }, - { - "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", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "other" - ], - "collectionId": null - }, - { - "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", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "nf" - ] - }, - "gallery": [ - "immunology" - ], - "collectionId": null - }, - { - "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", - "origin": "test-case", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null - }, - { - "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", - "origin": "test-case", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null - }, - { - "id": "motor", - "name": "motor", - "description": "Motor protein", - "tags": [ - "validation", "motor", - "chey", - "kplus", - "kminus" + "chey" ], "category": "validation", "origin": "test-case", @@ -9190,7 +8703,10 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mt_arithmetic_compiler", @@ -9219,7 +8735,10 @@ "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mt_bngl_interpreter", @@ -9250,7 +8769,10 @@ "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mt_music_sequencer", @@ -9284,7 +8806,10 @@ "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "mt_pascal_triangle", @@ -9311,7 +8836,10 @@ "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mt_quine", @@ -9338,7 +8866,10 @@ "cs", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mtor-signaling", @@ -9367,7 +8898,10 @@ "neuroscience", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "mtorc2-signaling", @@ -9397,21 +8931,21 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Mukhopadhyay_2013", - "name": "Mukhopadhyay 2013", + "id": "Mukhopadhyay_TCR_2013", + "name": "Mukhopadhyay et al. 2013: T Cell Receptor Phosphorylation Model", "description": "FceRI signaling", "tags": [ - "published", - "immunology", - "mukhopadhyay", + "tcr", + "phosphorylation", + "immune-signaling", "2013", - "s", - "e", - "f", - "z" + "mukhopadhyay" ], "category": "immunology", "origin": "published", @@ -9427,19 +8961,18 @@ "gallery": [ "immunology" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mwc", "name": "mwc", "description": "Monod-Wyman-Changeux model", "tags": [ - "validation", "mwc", - "setoption", - "h", - "ox", - "b" + "ox" ], "category": "validation", "origin": "test-case", @@ -9455,7 +8988,10 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "myogenic-differentiation", @@ -9483,51 +9019,21 @@ "developmental", "test-models" ], - "collectionId": null - }, - { - "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", - "origin": "contributed", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "other" - ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Nag_2009", - "name": "Nag 2009", + "id": "Nag_cancer_2009", + "name": "Nag et al. 2009: EGFR-Her2 Heterodimerization Dynamics", "description": "LAT-Grb2-SOS1 signaling", "tags": [ - "published", - "nag", + "egfr", + "her2", + "heterodimerization", "2009", - "lig", - "lyn", - "syk", - "rec", - "lat", - "grb", - "sos" + "nag" ], "category": "signaling", "origin": "published", @@ -9543,7 +9049,10 @@ "gallery": [ "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "negative-feedback-loop", @@ -9571,7 +9080,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "neurotransmitter-release", @@ -9600,21 +9112,22 @@ "neuroscience", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "nfkb", "name": "nfkb", "description": "NF-kB signaling pathway", "tags": [ - "validation", "nfkb", "tnfr", "ikkk", "tnf", "ikk", "ikba", - "a20", "competitor" ], "category": "validation", @@ -9631,14 +9144,16 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfkb_illustrating_protocols", "name": "nfkb_illustrating_protocols", "description": "NF-kB signaling pathway", "tags": [ - "validation", "nfkb", "illustrating", "protocols", @@ -9647,7 +9162,6 @@ "tnf", "ikk", "ikba", - "a20", "competitor" ], "category": "validation", @@ -9664,7 +9178,10 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfkb-feedback", @@ -9691,33 +9208,10 @@ "gallery": [ "test-models" ], - "collectionId": null - }, - { - "id": "NFmodel", - "name": "NFmodel", - "description": "BioNetGen model: NFmodel", - "tags": [ - "nfmodel", - "ag", - "ab", - "simulate" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "nf" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "nfsim_aggregation_gelation", @@ -9743,7 +9237,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfsim_coarse_graining", @@ -9769,7 +9266,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfsim_dynamic_compartments", @@ -9797,7 +9297,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfsim_hybrid_particle_field", @@ -9823,7 +9326,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfsim_ring_closure_polymer", @@ -9852,7 +9358,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nn_xor", @@ -9884,23 +9393,25 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "no_frees", - "name": "no frees", - "description": "Original values used to generate parabola.exp", + "id": "no-cgmp-signaling", + "name": "no cgmp signaling", + "description": "Nitric Oxide (NO) / cGMP signaling pathway.", "tags": [ "no", - "frees", - "counter", - "y", - "generate_network", - "simulate" + "cgmp", + "signaling", + "sgc", + "pkg" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -9910,55 +9421,59 @@ ] }, "gallery": [ - "validation" + "metabolism", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "no_generate_network", - "name": "no generate network", - "description": "Original values used to generate parabola.exp", + "id": "Nosbisch_cancer_2022", + "name": "Nosbisch et al. 2022: RTK Heterodimerization Modeling", + "description": "RTK-PLCgamma1 signaling", "tags": [ - "no", - "generate", - "network", - "counter", - "y", - "simulate" + "rtk", + "heterodimerization", + "cancer", + "2022", + "nosbisch" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "cancer" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "no_suffix", - "name": "no suffix", - "description": "Original values used to generate parabola.exp", + "id": "Notch_Signaling_Pathway", + "name": "Canonical Notch Signaling Pathway Model", + "description": "Notch signaling", "tags": [ - "no", - "suffix", - "counter", - "y", - "generate_network", - "simulate" + "notch-signaling", + "csl-binding", + "fringe-regulation", + "developmental-signaling" ], - "category": "validation", - "origin": "test-case", + "category": "regulation", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -9966,114 +9481,89 @@ ] }, "gallery": [ - "validation" + "regulation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "no-cgmp-signaling", - "name": "no cgmp signaling", - "description": "Nitric Oxide (NO) / cGMP signaling pathway.", + "id": "notch-delta-lateral-inhibition", + "name": "notch delta lateral inhibition", + "description": "Notch-Delta Lateral Inhibition", "tags": [ - "no", - "cgmp", - "signaling", - "sgc", - "pkg" + "notch", + "delta", + "lateral", + "inhibition", + "cellnotch", + "celldelta" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism", + "developmental", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Nosbisch_2022", - "name": "Nosbisch 2022", - "description": "RTK-PLCgamma1 signaling", + "id": "Ordyan_CaMKIIholo_2020", + "name": "Ordyan et al. 2020: CaMKII Holoenzyme Activation Model", + "description": "CaMKII holo", "tags": [ - "published", - "nosbisch", - "2022", - "rtk", - "plcgamma1", - "generate_network" + "camkii", + "holoenzyme", + "neuroscience", + "2020", + "ordyan" ], "category": "signaling", "origin": "published", "visible": false, "compatibility": { "bng2": false, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "cancer" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "notch", - "name": "Notch", - "description": "Notch signaling", + "id": "Ordyan_extraCaMKIIHolo_2020", + "name": "Ordyan et al. 2020: CaMKII Holoenzyme Extra Subunits Model", + "description": "Extra CaMKII holo (supplement)", "tags": [ - "published", - "notch", - "icn", - "ofut1", - "fringe", - "furin", - "dsl", - "csl", - "maml" + "camkii", + "holoenzyme", + "neuroscience", + "2020", + "ordyan" ], - "category": "regulation", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "regulation" - ], - "collectionId": null - }, - { - "id": "notch-delta-lateral-inhibition", - "name": "notch delta lateral inhibition", - "description": "Notch-Delta Lateral Inhibition", - "tags": [ - "notch", - "delta", - "lateral", - "inhibition", - "cellnotch", - "celldelta" - ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, "nfsim": true, "excluded": false, "methods": [ @@ -10081,31 +9571,29 @@ ] }, "gallery": [ - "developmental", - "test-models" + "signaling" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "NYC", - "name": "NYC", - "description": "- This model is intended to be consistent with the compartmental model", + "id": "Ordyan_mCaMKIICaSpike_2020", + "name": "Ordyan et al. 2020: CaMKII Activation under Calcium Spikes", + "description": "mCaMKII Ca Spike model", "tags": [ - "nyc", - "counter", - "fdcs", - "s", - "sv", - "e", - "a", - "i", - "v" + "camkii", + "calcium-spikes", + "neuroscience", + "2020", + "ordyan" ], - "category": "epidemiology", + "category": "signaling", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -10113,9 +9601,12 @@ ] }, "gallery": [ - "epidemiology" + "signaling" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "organelle_transport", @@ -10123,15 +9614,7 @@ "description": "title: organelle_transport.bngl", "tags": [ "organelle", - "transport", - "a", - "b", - "c", - "d", - "t1", - "at1", - "ct1", - "t2" + "transport" ], "category": "tutorial", "origin": "tutorial", @@ -10147,7 +9630,10 @@ "gallery": [ "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "organelle_transport_struct", @@ -10156,11 +9642,7 @@ "tags": [ "organelle", "transport", - "struct", - "a", - "b", - "t1", - "t2" + "struct" ], "category": "tutorial", "origin": "tutorial", @@ -10176,7 +9658,10 @@ "gallery": [ "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "oxidative-stress-response", @@ -10205,7 +9690,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "p38-mapk-signaling", @@ -10234,7 +9722,10 @@ "cancer", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "p53-mdm2-oscillator", @@ -10261,22 +9752,26 @@ "cell-cycle", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "parp1-mediated-dna-repair", + "name": "parp1 mediated dna repair", + "description": "PARP1-mediated DNA damage sensing and repair.", "tags": [ - "parabola", - "counter", + "parp1", + "mediated", + "dna", + "repair", "par", - "line", - "generate_network", - "simulate" + "nad", + "v_parylate" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -10287,26 +9782,30 @@ ] }, "gallery": [ - "other" + "cell-cycle", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Original values used to generate parabola.exp", + "id": "Pekalski_published_2013", + "name": "Pekalski et al. 2013: TNFR-Mediated NF-kB Activation Model", + "description": "Spontaneous signaling", "tags": [ - "parabola", - "counter", - "y", - "generate_network", - "simulate" + "tnfr", + "nfkb", + "inflammatory-signaling", + "2013", + "pekalski" ], - "category": "other", + "category": "regulation", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -10314,51 +9813,60 @@ ] }, "gallery": [ - "other" + "regulation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Original values used to generate parabola.exp", + "id": "ph_lorenz_attractor", + "name": "ph lorenz attractor", + "description": "Lorenz Attractor in BNGL", "tags": [ - "parabola", - "counter", - "y", - "generate_network", - "simulate", - "resetconcentrations" + "ph", + "lorenz", + "attractor", + "lx", + "ly", + "lz", + "x", + "y" ], - "category": "validation", - "origin": "test-case", + "category": "physics", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "physics", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Original values used to generate parabola.exp", + "id": "ph_nbody_gravity", + "name": "ph nbody gravity", + "description": "Model: ph_nbody_gravity.bngl", "tags": [ - "parabola", - "counter", - "y", - "generate_network", - "simulate" + "ph", + "nbody", + "gravity", + "body", + "r2" ], - "category": "validation", - "origin": "test-case", + "category": "physics", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -10369,24 +9877,26 @@ ] }, "gallery": [ - "validation" + "physics", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Original values used to generate parabola.exp", + "id": "ph_schrodinger", + "name": "ph schrodinger", + "description": "Model: ph_schrodinger.bngl", "tags": [ - "parabola", - "counter", - "y", - "generate_network", - "simulate" + "ph", + "schrodinger", + "psi" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "physics", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -10396,26 +9906,27 @@ ] }, "gallery": [ - "validation" + "physics", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parabola_ground", - "name": "parabola ground", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "ph_wave_equation", + "name": "ph wave equation", + "description": "Model: ph_wave_equation.bngl", "tags": [ - "parabola", - "ground", - "counter", - "par", - "line", - "generate_network", - "simulate" + "ph", + "wave", + "equation", + "node" ], - "category": "other", - "origin": "published", - "visible": true, + "category": "physics", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -10425,143 +9936,145 @@ ] }, "gallery": [ - "other" + "physics", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parabola2", - "name": "parabola2", - "description": "A file for testing behavior with duplicate file names", + "id": "phosphorelay-chain", + "name": "phosphorelay chain", + "description": "BioNetGen model: phosphorelay chain", "tags": [ - "parabola2", - "counter", - "y", - "generate_network", - "simulate", - "resetconcentrations" + "phosphorelay", + "chain", + "sensor", + "relay", + "output" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ParamsEverywhere", - "name": "ParamsEverywhere", - "description": "An example from a real application", + "id": "platelet-activation", + "name": "platelet activation", + "description": "BioNetGen model: platelet activation", "tags": [ - "paramseverywhere", - "ag", - "r", - "h" + "platelet", + "activation", + "adp", + "p2y12", + "integrin", + "thromboxane" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "immunology", + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "parp1-mediated-dna-repair", - "name": "parp1 mediated dna repair", - "description": "PARP1-mediated DNA damage sensing and repair.", + "id": "polymer", + "name": "polymer", + "description": "Polymerization model", "tags": [ - "parp1", - "mediated", - "dna", - "repair", - "par", - "nad", - "v_parylate" + "tutorials", + "nfsim", + "polymer", + "simulate_nf" ], - "category": "signaling", - "origin": "ai-generated", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "cell-cycle", - "test-models" + "tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Pekalski_2013", - "name": "Pekalski 2013", - "description": "Spontaneous signaling", + "id": "polymer_draft", + "name": "polymer draft", + "description": "Polymerization (draft)", "tags": [ - "published", - "pekalski", - "2013", - "tnfr", - "ikk", - "ikkk", - "ikba", - "ikba_mrna", - "a20", - "a20_mrna", - "nfkb" + "tutorials", + "nfsim", + "polymer", + "draft", + "simulate_nf" ], - "category": "regulation", - "origin": "published", - "visible": true, + "category": "tutorial", + "origin": "tutorial", + "visible": false, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "regulation" + "tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ph_lorenz_attractor", - "name": "ph lorenz attractor", - "description": "Lorenz Attractor in BNGL", + "id": "polymer_fixed", + "name": "polymer_fixed", + "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", "tags": [ - "ph", - "lorenz", - "attractor", - "lx", - "ly", - "lz", - "x", - "y" + "polymer", + "fixed" ], - "category": "physics", - "origin": "ai-generated", + "category": "other", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -10572,24 +10085,22 @@ ] }, "gallery": [ - "physics", - "test-models" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ph_nbody_gravity", - "name": "ph nbody gravity", - "description": "Model: ph_nbody_gravity.bngl", + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "ph", - "nbody", - "gravity", - "body", - "r2" + "polynomial" ], - "category": "physics", - "origin": "ai-generated", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -10600,23 +10111,27 @@ ] }, "gallery": [ - "physics", - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ph_schrodinger", - "name": "ph schrodinger", - "description": "Model: ph_schrodinger.bngl", + "id": "Posner_blbr_1995", + "name": "Posner et al. 1995: Receptor Ring Aggregation Model", + "description": "BLBR rings", "tags": [ - "ph", - "schrodinger", - "psi" + "blbr", + "aggregation", + "receptor-rings", + "1995", + "posner" ], "category": "physics", - "origin": "ai-generated", - "visible": false, + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -10626,24 +10141,27 @@ ] }, "gallery": [ - "physics", - "test-models" + "physics" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ph_wave_equation", - "name": "ph wave equation", - "description": "Model: ph_wave_equation.bngl", + "id": "Posner_blbr_2004", + "name": "Posner et al. 2004: Cooperativity in Receptor Binding", + "description": "BLBR cooperativity", "tags": [ - "ph", - "wave", - "equation", - "node" + "blbr", + "cooperativity", + "receptor-binding", + "2004", + "posner" ], "category": "physics", - "origin": "ai-generated", - "visible": false, + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -10653,199 +10171,211 @@ ] }, "gallery": [ - "physics", - "test-models" + "physics" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Phoenix", - "name": "Phoenix", - "description": "- This model is intended to be consistent with the compartmental model", + "id": "predator-prey-dynamics", + "name": "predator prey dynamics", + "description": "BioNetGen model: predator prey dynamics", "tags": [ - "phoenix", - "counter", - "fdcs", - "s", - "sv", - "e", - "a", - "i", - "v" + "predator", + "prey", + "dynamics" ], - "category": "epidemiology", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "epidemiology" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "phosphorelay-chain", - "name": "phosphorelay chain", - "description": "BioNetGen model: phosphorelay chain", + "id": "process_actin_treadmilling", + "name": "process actin treadmilling", + "description": "Model: process_actin_treadmilling.bngl", "tags": [ - "phosphorelay", - "chain", - "sensor", - "relay", - "output" + "process", + "actin", + "treadmilling", + "generate_network", + "simulate" ], - "category": "signaling", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "platelet-activation", - "name": "platelet activation", - "description": "BioNetGen model: platelet activation", + "id": "process_autophagy_flux", + "name": "process autophagy flux", + "description": "Model: process_autophagy_flux.bngl", "tags": [ - "platelet", - "activation", - "adp", - "p2y12", - "integrin", - "thromboxane" + "process", + "autophagy", + "flux", + "phagophore", + "autophagosome", + "lysosome", + "autolysosome", + "cargo" ], - "category": "signaling", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polymer", - "name": "polymer", - "description": "Polymerization model", + "id": "process_cell_adhesion_strength", + "name": "process cell adhesion strength", + "description": "Model: process_cell_adhesion_strength.bngl", "tags": [ - "published", - "tutorials", - "nfsim", - "polymer", - "a", - "b", - "c", - "simulate_nf" + "process", + "cell", + "adhesion", + "strength", + "c1", + "c2", + "generate_network", + "simulate" ], - "category": "tutorial", - "origin": "tutorial", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "tutorials" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polymer_draft", - "name": "polymer draft", - "description": "Polymerization (draft)", + "id": "process_kinetic_proofreading_tcr", + "name": "process kinetic proofreading tcr", + "description": "Model: process_kinetic_proofreading_tcr.bngl", "tags": [ - "published", - "tutorials", - "nfsim", - "polymer", - "draft", - "a", - "b", - "c", - "simulate_nf" - ], - "category": "tutorial", - "origin": "tutorial", - "visible": false, + "process", + "kinetic", + "proofreading", + "tcr", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "tutorials" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polymer_fixed", - "name": "polymer_fixed", - "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", + "id": "process_quorum_sensing_switch", + "name": "process quorum sensing switch", + "description": "Model: process_quorum_sensing_switch.bngl", "tags": [ - "polymer", - "fixed" + "process", + "quorum", + "sensing", + "switch", + "gene_ai", + "ai", + "r", + "gene_light" ], "category": "other", - "origin": "contributed", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "other" + "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polynomial", - "name": "polynomial", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "PyBioNetGen_Actions_Syntax", + "name": "PyBioNetGen Actions Syntax Verification Model", + "description": "Original values used to generate parabola.exp", "tags": [ - "polynomial", - "counter", - "y1", - "y2", - "generate_network", - "simulate", - "setparameter", - "resetconcentrations" + "test-case", + "syntax-check", + "actions" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -10856,23 +10386,20 @@ ] }, "gallery": [ - "other" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polynomial", - "name": "polynomial", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "PyBioNetGen_BNG_Error", + "name": "PyBioNetGen BNG Error Triggering Test", + "description": "Original values used to generate parabola.exp", "tags": [ - "polynomial", - "counter", - "y1", - "y2", - "generate_network", - "simulate", - "setparameter", - "resetconcentrations" + "test-case", + "error-handling" ], "category": "validation", "origin": "test-case", @@ -10888,25 +10415,22 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polynomial", - "name": "polynomial", + "id": "PyBioNetGen_Core_Parabola", + "name": "PyBioNetGen Core: Parabolic Trajectory Model", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "polynomial", - "counter", - "y1", - "y2", - "generate_network", - "simulate", - "setparameter", - "resetconcentrations" + "mathematical-model", + "parabolic-equation" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -10916,28 +10440,24 @@ ] }, "gallery": [ - "validation" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polynomial_ground", - "name": "polynomial ground", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "PyBioNetGen_Core_Parabola_Demo", + "name": "PyBioNetGen Core: Parabolic Trajectory Demo", + "description": "Original values used to generate parabola.exp", "tags": [ - "polynomial", - "ground", - "counter", - "y1", - "y2", - "generate_network", - "simulate", - "setparameter", - "resetconcentrations" + "mathematical-model", + "demo" ], "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -10949,19 +10469,20 @@ "gallery": [ "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Posner_1995", - "name": "Posner 1995", - "description": "BLBR rings", + "id": "PyBioNetGen_Core_Parabola_Ground", + "name": "PyBioNetGen Core: Parabolic Ground Truth Reference", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "published", - "physics", - "posner", - "1995" + "mathematical-model", + "reference-standard" ], - "category": "physics", + "category": "other", "origin": "published", "visible": true, "compatibility": { @@ -10973,23 +10494,24 @@ ] }, "gallery": [ - "physics" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Posner_2004", - "name": "Posner 2004", - "description": "BLBR cooperativity", + "id": "PyBioNetGen_Core_Polynomial", + "name": "PyBioNetGen Core: Polynomial Trajectory Model", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "published", - "physics", - "posner", - "2004" + "mathematical-model", + "polynomial-equation" ], - "category": "physics", + "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -10999,86 +10521,48 @@ ] }, "gallery": [ - "physics" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "predator-prey-dynamics", - "name": "predator prey dynamics", - "description": "BioNetGen model: predator prey dynamics", + "id": "PyBioNetGen_Core_Polynomial_Ground", + "name": "PyBioNetGen Core: Polynomial Ground Truth Reference", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "predator", - "prey", - "dynamics" + "mathematical-model", + "reference-standard" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "other", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "prion_model", - "name": "ERK_model.bngl", - "description": "filename: ERK_model.bngl", + "id": "PyBioNetGen_Core_RAFi", + "name": "PyBioNetGen Core: Raf Inhibitor Model", + "description": "BioNetGen model: RAFi", "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" + "rafi", + "raf-kinase", + "enzyme-inhibition" ], "category": "other", "origin": "published", @@ -11088,48 +10572,25 @@ "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem_quant_model_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_Core_RAFi_Ground", + "name": "PyBioNetGen Core: Raf Inhibitor Ground Truth Reference", + "description": "BioNetGen model: RAFi ground", "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" + "rafi", + "raf-kinase", + "reference-standard" ], "category": "other", "origin": "published", @@ -11142,44 +10603,21 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem16_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_Core_Receptor", + "name": "PyBioNetGen Core: Simple Ligand-Receptor Binding", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", "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" + "ligand-receptor", + "binding-kinetics" ], "category": "other", "origin": "published", @@ -11192,198 +10630,111 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem16_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_Core_Receptor_NF", + "name": "PyBioNetGen Core: Ligand-Receptor Network-Free Simulation", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", "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" + "ligand-receptor", + "binding-kinetics", + "nfsim" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "problem32_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_Core_TCR", + "name": "PyBioNetGen Core: T Cell Receptor Activation", + "description": "A model of T cell 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" + "tcr", + "immune-signaling", + "phosphorylation" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "problem32_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_Core_TLBR", + "name": "PyBioNetGen Core: Trivalent Ligand Bivalent Receptor Model", + "description": "A model of trivalent ligand, bivalent receptor", "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" + "tlbr", + "polymerization", + "ligand-receptor" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "problem4_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_Degranulation_Model", + "name": "PyBioNetGen Core: IgE Receptor Degranulation Model", + "description": "Degranulation model", "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" + "fceri", + "degranulation", + "mast-cell", + "immune-signaling" ], "category": "other", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -11392,48 +10743,26 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem4_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_EGFR_Ground", + "name": "PyBioNetGen Core: Canonical EGFR Ground Truth Reference", + "description": "Blinov et al. 2006. Biosystems, 83:136", "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" + "egfr", + "signaling", + "reference-standard" ], "category": "other", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -11442,44 +10771,22 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem64_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_EGFR_Model", + "name": "PyBioNetGen Core: Canonical EGFR Signaling Model", + "description": "Blinov et al. 2006. Biosystems, 83:136", "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" + "egfr", + "signaling", + "receptor-activation" ], "category": "other", "origin": "published", @@ -11492,44 +10799,51 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem64_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_EGFR_NF", + "name": "PyBioNetGen Core: EGFR Network-Free Simulation", + "description": "Filename: example2_starting_point.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" + "egfr", + "signaling", + "nfsim", + "network-free" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "PyBioNetGen_EGFR_ODE", + "name": "PyBioNetGen Core: EGFR ODE-Based Simulation", + "description": "Filename: example1.bngl", + "tags": [ + "egfr", + "signaling", + "ode-solver" ], "category": "other", "origin": "published", @@ -11542,97 +10856,52 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "cancer" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem8_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_EGFR_ODE_Pub", + "name": "PyBioNetGen Core: Published EGFR ODE-Based Model", + "description": "EGFR ODE", "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" + "egfr", + "signaling", + "ode-solver" ], "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "cancer" + ], + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem8_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_Egg", + "name": "PyBioNetGen Egg Cell Oscillator Test", + "description": "BioNetGen model: egg", "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" + "test-case", + "calcium-oscillation" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -11642,52 +10911,52 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "process_actin_treadmilling", - "name": "process actin treadmilling", - "description": "Model: process_actin_treadmilling.bngl", + "id": "PyBioNetGen_ErrNoFrees", + "name": "PyBioNetGen Free Molecule Error Test", + "description": "An example from a real application", "tags": [ - "process", - "actin", - "treadmilling", - "generate_network", - "simulate" + "test-case", + "error-handling" ], - "category": "other", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "process_autophagy_flux", - "name": "process autophagy flux", - "description": "Model: process_autophagy_flux.bngl", + "id": "PyBioNetGen_Example1", + "name": "PyBioNetGen Core: Example 1 EGFR Model", + "description": "Filename: example1.bngl", "tags": [ - "process", - "autophagy", - "flux", - "phagophore", - "autophagosome", - "lysosome", - "autolysosome", - "cargo" + "egfr", + "signaling", + "example-model" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -11698,83 +10967,108 @@ ] }, "gallery": [ - "test-models" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "process_cell_adhesion_strength", - "name": "process cell adhesion strength", - "description": "Model: process_cell_adhesion_strength.bngl", + "id": "PyBioNetGen_Example2_Start", + "name": "PyBioNetGen Core: Example 2 EGFR Starting Point", + "description": "Filename: example2_starting_point.bngl", "tags": [ - "process", - "cell", - "adhesion", - "strength", - "c1", - "c2", - "generate_network", - "simulate" + "egfr", + "signaling", + "starting-point", + "example-model" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "test-models" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "process_kinetic_proofreading_tcr", - "name": "process kinetic proofreading tcr", - "description": "Model: process_kinetic_proofreading_tcr.bngl", + "id": "PyBioNetGen_FceRI_Gamma2", + "name": "PyBioNetGen Core: FceRI Gamma2 Subunit Signaling", + "description": "BioNetGen model: fceri gamma2", "tags": [ - "process", - "kinetic", - "proofreading", - "tcr", - "l" + "fceri", + "gamma2-subunit", + "immune-signaling" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ - "test-models" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "process_quorum_sensing_switch", - "name": "process quorum sensing switch", - "description": "Model: process_quorum_sensing_switch.bngl", + "id": "PyBioNetGen_FceRI_Gamma2_Ground", + "name": "PyBioNetGen Core: FceRI Gamma2 Ground Truth Reference", + "description": "BioNetGen model: fceri gamma2 ground truth", "tags": [ - "process", - "quorum", - "sensing", - "switch", - "gene_ai", - "ai", - "r", - "gene_light" + "fceri", + "gamma2-subunit", + "reference-standard" ], "category": "other", - "origin": "ai-generated", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_FreeMissing", + "name": "PyBioNetGen Free Species Constraint Test", + "description": "Original values used to generate parabola.exp", + "tags": [ + "test-case", + "constraints" + ], + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -11785,23 +11079,21 @@ ] }, "gallery": [ - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "pt303", - "name": "pt303", - "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", + "id": "PyBioNetGen_IGF1R_Activation", + "name": "PyBioNetGen Core: IGF1R Receptor Activation Model", + "description": "Author: William S. Hlavacek", "tags": [ - "pt303", - "counter", - "v", - "lnv", - "s", - "c", - "half_life", - "lnv_tangent" + "igf1r", + "receptor-activation", + "phosphorylation" ], "category": "other", "origin": "published", @@ -11817,24 +11109,22 @@ "gallery": [ "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "pt403", - "name": "pt403", - "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", + "id": "PyBioNetGen_LilyIgE", + "name": "PyBioNetGen Lily IgE Receptor Test Model", + "description": "An example from a real application", "tags": [ - "pt403", - "counter", - "v", - "lnv", - "s", - "c", - "half_life", - "lnv_tangent" + "test-case", + "fceri", + "immune-signaling" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -11845,27 +11135,25 @@ ] }, "gallery": [ - "other" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "pt409", - "name": "pt409", - "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", + "id": "PyBioNetGen_Model", + "name": "PyBioNetGen Core: Generic Mast Cell Degranulation Model", + "description": "filename: model.bngl", "tags": [ - "pt409", - "counter", - "v", - "lnv", - "s", - "c", - "half_life", - "lnv_tangent" + "fceri", + "degranulation", + "mast-cell" ], "category": "other", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -11877,35 +11165,19 @@ "gallery": [ "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF", - "name": "PyBNF-fitting-setup", - "description": "BNGL model: 190127_CHO_EGFR_forBNF", + "id": "PyBioNetGen_Model_aMCMC", + "name": "PyBioNetGen Core: Mast Cell Degranulation via aMCMC Fitting", + "description": "A model of IgE receptor signaling", "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" + "fceri", + "degranulation", + "amcmc-fitting" ], "category": "other", "origin": "published", @@ -11918,24 +11190,25 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "other" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "quasi_equilibrium", - "name": "quasi equilibrium", - "description": "Quasi-equilibrium approximation", + "id": "PyBioNetGen_Model_ToFit", + "name": "PyBioNetGen Core: Mast Cell Degranulation for Fitting", + "description": "A model of IgE receptor signaling", "tags": [ - "published", - "toy models", - "quasi", - "equilibrium", - "a", - "b", - "c" + "fceri", + "degranulation", + "parameter-fitting" ], - "category": "tutorial", - "origin": "tutorial", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -11946,248 +11219,483 @@ ] }, "gallery": [ - "tutorials", - "native-tutorials" + "other" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "quorum-sensing-circuit", - "name": "quorum sensing circuit", - "description": "BioNetGen model: quorum sensing circuit", + "id": "PyBioNetGen_NFmodel", + "name": "PyBioNetGen NFsim Simulation Test", + "description": "BioNetGen model: NFmodel", "tags": [ - "quorum", - "sensing", - "circuit", - "autoinducer", - "autoinducer_env", - "gene", - "protein" + "test-case", + "nfsim" ], - "category": "signaling", - "origin": "ai-generated", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "test-models" + "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "rab_mon1ccz1_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_NoFrees", + "name": "PyBioNetGen No Free Constraints Verification", + "description": "Original values used to generate parabola.exp", "tags": [ - "kd_rabgef1__free", - "d_hill__free", - "d_threshold__free", - "k_deg__free", - "k_dephos__free", - "k_deub__free", - "k_extract__free", - "k_insert__free", - "k_recyc__free", - "k_synth__free", - "k_to_endo__free", - "kcat_rab5__free", - "kcat_rab7__free", - "kf_rab5_mon1__free", - "kf_rab5_rabep1__free", - "kf_ptyr_sh2__free", - "kr_kub_uim__free", - "kr_rab5_mon1__free", - "kr_rab5_rabep1__free", - "kr_ptyr_sh2__free", - "py_basal_coef__free", - "py_half_coef__free", - "py_hill_coef__free", - "py_scale_coef__free", - "r_hill__free", - "r_threshold__free", - "ub_basal_coef__free", - "ub_half_coef__free", - "ub_hill_coef__free", - "ub_scale_coef__free", - "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" + "test-case", + "constraints" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_NoGenerateNetwork", + "name": "PyBioNetGen Direct Simulation Without Expansion Test", + "description": "Original values used to generate parabola.exp", + "tags": [ + "test-case", + "simulation-modes" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "PyBioNetGen_NoSuffix", + "name": "PyBioNetGen No Suffix Output Naming Test", + "description": "Original values used to generate parabola.exp", + "tags": [ + "test-case", + "output-formatting" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Parabola", + "name": "PyBioNetGen Parabolic Trajectory Test", + "description": "Original values used to generate parabola.exp", + "tags": [ + "test-case", + "mathematical-model" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Parabola_Files", + "name": "PyBioNetGen Parabolic Trajectory Files Test", + "description": "Original values used to generate parabola.exp", + "tags": [ + "test-case", + "mathematical-model" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Parabola_Special", + "name": "PyBioNetGen Parabolic Trajectory Special Cases Test", + "description": "Original values used to generate parabola.exp", + "tags": [ + "test-case", + "mathematical-model" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Parabola2", + "name": "PyBioNetGen Parabolic Trajectory Alternative Test", + "description": "A file for testing behavior with duplicate file names", + "tags": [ + "test-case", + "mathematical-model" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_ParamsEverywhere", + "name": "PyBioNetGen Global Parameters Boundary Test", + "description": "An example from a real application", + "tags": [ + "test-case", + "parameter-boundaries" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Polynomial_T6", + "name": "PyBioNetGen Polynomial Trajectory Test (T6-check)", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "test-case", + "mathematical-model" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Simple", + "name": "PyBioNetGen Simple Synthesis & Decay Test", + "description": "An example from a real application", + "tags": [ + "test-case", + "synthesis-decay" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Simple_AddActions", + "name": "PyBioNetGen Simple Synthesis with Dynamic Actions", + "description": "An example from a real application", + "tags": [ + "test-case", + "actions" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Simple_Answer", + "name": "PyBioNetGen Simple Synthesis with Response Check", + "description": "An example from a real application", + "tags": [ + "test-case", + "verification" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" ], - "category": "other", - "origin": "published", + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Simple_GenOnly", + "name": "PyBioNetGen Simple Synthesis Network-Generation Only", + "description": "An example from a real application", + "tags": [ + "test-case", + "network-generation" + ], + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, - "methods": [] + "methods": [ + "ode" + ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_mon1ccz1_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_Simple_NF_Seed", + "name": "PyBioNetGen NFsim Seed Population Test", + "description": "BioNetGen model: simple nf seed", "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" + "test-case", + "nfsim", + "seed" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Simple_NoGen", + "name": "PyBioNetGen Simple Synthesis Without Network-Generation", + "description": "An example from a real application", + "tags": [ + "test-case", + "direct-simulation" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "rab_rab5_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_Tricky", + "name": "PyBioNetGen Complex Pattern Matching Test", + "description": "An example from a real application", "tags": [ - "kd_rabgef1__free", - "d_hill__free", - "d_threshold__free", - "k_deg__free", - "k_dephos__free", - "k_deub__free", - "k_extract__free", - "k_insert__free", - "k_recyc__free", - "k_synth__free", - "k_to_endo__free", - "kcat_rab5__free", - "kcat_rab7__free", - "kf_rab5_mon1__free", - "kf_rab5_rabep1__free", - "kf_ptyr_sh2__free", - "kr_kub_uim__free", - "kr_rab5_mon1__free", - "kr_rab5_rabep1__free", - "kr_ptyr_sh2__free", - "py_basal_coef__free", - "py_half_coef__free", - "py_hill_coef__free", - "py_scale_coef__free", - "r_hill__free", - "r_threshold__free", - "ub_basal_coef__free", - "ub_half_coef__free", - "ub_hill_coef__free", - "ub_scale_coef__free", - "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" + "test-case", + "pattern-matching" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, - "methods": [] + "methods": [ + "ode" + ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "rab_rab5_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_TrickyUS", + "name": "PyBioNetGen Unstructured Boundary State Test", + "description": "An example from a real application", "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" + "test-case", + "boundary-states" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -12197,104 +11705,49 @@ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_rab7_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_Trivial", + "name": "PyBioNetGen Trivial Decay Reaction Test", + "description": "A trivial model file for testing MCMC distributions.", "tags": [ - "kd_rabgef1__free", - "d_hill__free", - "d_threshold__free", - "k_deg__free", - "k_dephos__free", - "k_deub__free", - "k_extract__free", - "k_insert__free", - "k_recyc__free", - "k_synth__free", - "k_to_endo__free", - "kcat_rab5__free", - "kcat_rab7__free", - "kf_rab5_mon1__free", - "kf_rab5_rabep1__free", - "kf_ptyr_sh2__free", - "kr_kub_uim__free", - "kr_rab5_mon1__free", - "kr_rab5_rabep1__free", - "kr_ptyr_sh2__free", - "py_basal_coef__free", - "py_half_coef__free", - "py_hill_coef__free", - "py_scale_coef__free", - "r_hill__free", - "r_threshold__free", - "ub_basal_coef__free", - "ub_half_coef__free", - "ub_hill_coef__free", - "ub_scale_coef__free", - "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" + "test-case", + "decay-kinetics" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, - "methods": [] + "methods": [ + "ode" + ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_rab7_ox", - "name": "rab_mon1ccz1_ox.bngl", - "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" + "id": "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF", + "name": "PyBNF-fitting-setup", + "description": "BNGL model: 190127_CHO_EGFR_forBNF", + "tags": [ + "2019", + "egfr", + "salazar" ], "category": "other", "origin": "published", @@ -12308,117 +11761,71 @@ ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_wt", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "quasi_equilibrium", + "name": "quasi equilibrium", + "description": "Quasi-equilibrium approximation", "tags": [ - "kd_rabgef1__free", - "d_hill__free", - "d_threshold__free", - "k_deg__free", - "k_dephos__free", - "k_deub__free", - "k_extract__free", - "k_insert__free", - "k_recyc__free", - "k_synth__free", - "k_to_endo__free", - "kcat_rab5__free", - "kcat_rab7__free", - "kf_rab5_mon1__free", - "kf_rab5_rabep1__free", - "kf_ptyr_sh2__free", - "kr_kub_uim__free", - "kr_rab5_mon1__free", - "kr_rab5_rabep1__free", - "kr_ptyr_sh2__free", - "py_basal_coef__free", - "py_half_coef__free", - "py_hill_coef__free", - "py_scale_coef__free", - "r_hill__free", - "r_threshold__free", - "ub_basal_coef__free", - "ub_half_coef__free", - "ub_hill_coef__free", - "ub_scale_coef__free", - "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" + "toy models", + "quasi", + "equilibrium" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, - "methods": [] + "methods": [ + "ode" + ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "tutorials", + "native-tutorials" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_wt", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "quorum-sensing-circuit", + "name": "quorum sensing circuit", + "description": "BioNetGen model: quorum sensing circuit", "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" + "quorum", + "sensing", + "circuit", + "autoinducer", + "autoinducer_env", + "gene", + "protein" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "collectionId": null + "gallery": [ + "test-models" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "rab-gtpase-cycle", @@ -12446,24 +11853,26 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "RAFi", - "name": "RAFi", - "description": "BioNetGen model: RAFi", + "id": "Ran_NuclearTransport", + "name": "Rule-Based Ran-Mediated Nuclear Transport Model", + "description": "Nuclear Ran transport", "tags": [ - "rafi", - "r", - "i", - "ybar", - "activity" + "ran-gtpase", + "nuclear-transport", + "nuclear-pore-complex", + "import-export" ], - "category": "other", + "category": "regulation", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -12471,27 +11880,28 @@ ] }, "gallery": [ - "other" + "regulation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "RAFi_ground", - "name": "RAFi ground", - "description": "BioNetGen model: RAFi ground", + "id": "Ran_NuclearTransport_Draft", + "name": "Rule-Based Ran-Mediated Nuclear Transport Model (Draft)", + "description": "Ran transport (draft)", "tags": [ - "rafi", - "ground", - "r", - "i", - "ybar", - "activity" + "ran-gtpase", + "nuclear-transport", + "nuclear-pore-complex", + "draft-model" ], - "category": "other", + "category": "regulation", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -12499,9 +11909,12 @@ ] }, "gallery": [ - "other" + "regulation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "rankl-rank-signaling", @@ -12530,7 +11943,10 @@ "developmental", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "ras-gef-gap-cycle", @@ -12561,20 +11977,20 @@ "cancer", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "rec_dim", "name": "rec_dim", "description": "Ligand-receptor binding", "tags": [ - "validation", "rec", "dim", "lig", - "writemdl", - "generate_network", - "simulate" + "writemdl" ], "category": "validation", "origin": "test-case", @@ -12590,23 +12006,21 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "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" + "writemdl" ], "category": "validation", "origin": "test-case", @@ -12622,82 +12036,10 @@ "gallery": [ "validation" ], - "collectionId": null - }, - { - "id": "receptor", - "name": "13-receptor", - "description": "A simple model", - "tags": [ - "ligand_ispresent", - "molecules", - "species" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [], - "collectionId": null - }, - { - "id": "receptor", - "name": "receptor", - "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "tags": [ - "receptor", - "l", - "r", - "func" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "other" - ], - "collectionId": null - }, - { - "id": "receptor_nf", - "name": "receptor nf", - "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "tags": [ - "receptor", - "nf", - "l", - "r" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "nf" - ] - }, - "gallery": [ - "other" - ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "receptor_nf", @@ -12705,9 +12047,7 @@ "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", "tags": [ "receptor", - "nf", - "l", - "r" + "nf" ], "category": "validation", "origin": "test-case", @@ -12723,16 +12063,16 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "Repressilator", "name": "Repressilator", "description": "Repressilator circuit", "tags": [ - "published", - "tutorial", - "native", "repressilator", "gtetr", "gci", @@ -12759,7 +12099,10 @@ "synbio", "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "repressilator-oscillator", @@ -12791,7 +12134,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "retinoic-acid-signaling", @@ -12821,7 +12167,10 @@ "developmental", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "rho-gtpase-actin-cytoskeleton", @@ -12851,55 +12200,51 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Rule_based_egfr_compart", - "name": "Rule based egfr compart", - "description": "Compartmental EGFR model", + "id": "Salazar_Cavazos_egfr_2019_190127_CHO_EGFR_best-fit", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_CHO_EGFR_best-fit)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "published", - "rule", - "based", "egfr", - "compart", - "egf", - "grb2", - "shc", - "generate_network" + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "signaling" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Rule_based_egfr_tutorial", - "name": "Faeder 2009", - "description": "EGFR signaling", + "id": "Salazar_Cavazos_egfr_2019_190127_CHO_EGFR_Epigen", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_CHO_EGFR_Epigen)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "published", - "rule", - "based", "egfr", - "tutorial", - "egf", - "grb2", - "shc", - "generate_network" + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -12910,80 +12255,108 @@ "ode" ] }, - "gallery": [ - "cancer" + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Salazar_Cavazos_egfr_2019_190127_CHO_EGFR_sensitivity", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_CHO_EGFR_sensitivity)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "collectionId": null + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Rule_based_Ran_transport", - "name": "Rule based Ran transport", - "description": "Nuclear Ran transport", + "id": "Salazar_Cavazos_egfr_2019_190127_CHO_HA_EGFR_L858R", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_CHO_HA_EGFR_L858R)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "published", - "rule", - "based", - "ran", - "transport", - "c", - "rcc1", - "generate_network" + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "regulation", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "regulation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Rule_based_Ran_transport_draft", - "name": "Rule based Ran transport draft", - "description": "Ran transport (draft)", + "id": "Salazar_Cavazos_egfr_2019_190127_HeLa", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_HeLa)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "published", - "rule", - "based", - "ran", - "transport", - "draft", - "c", - "rcc1", - "generate_network" + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "regulation", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "regulation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Scaff-22_ground", - "name": "18-mapk", - "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "id": "Salazar_Cavazos_egfr_2019_190127_HMEC", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_HMEC)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "signaling" + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -12995,16 +12368,23 @@ ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Scaff-22_tofit", - "name": "18-mapk", - "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "id": "Salazar_Cavazos_egfr_2019_190127_MCF10A", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_MCF10A)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "signaling" + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -13016,19 +12396,18 @@ ] }, "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "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", @@ -13045,7 +12424,10 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "shp2-phosphatase-regulation", @@ -13073,7 +12455,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "signal-amplification-cascade", @@ -13102,18 +12487,18 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "simple", "name": "simple", "description": "Simple binding model", "tags": [ - "published", "tutorials", "simple", - "s", - "t", "dnat", "trash" ], @@ -13131,147 +12516,10 @@ "gallery": [ "tutorials" ], - "collectionId": null - }, - { - "id": "Simple", - "name": "Simple", - "description": "An example from a real application", - "tags": [ - "simple", - "setoption", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null - }, - { - "id": "Simple_AddActions", - "name": "Simple AddActions", - "description": "An example from a real application", - "tags": [ - "simple", - "addactions", - "setoption", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null - }, - { - "id": "Simple_Answer", - "name": "Simple Answer", - "description": "An example from a real application", - "tags": [ - "simple", - "answer", - "setoption", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null - }, - { - "id": "Simple_GenOnly", - "name": "Simple GenOnly", - "description": "An example from a real application", - "tags": [ - "simple", - "genonly", - "setoption", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null - }, - { - "id": "simple_nf_seed", - "name": "simple nf seed", - "description": "BioNetGen model: simple nf seed", - "tags": [ - "simple", - "nf", - "seed", - "a", - "b", - "function1", - "simulate" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "nf" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "simple_nfsim_test", @@ -13283,7 +12531,7 @@ "test" ], "category": "other", - "origin": "contributed", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -13296,47 +12544,20 @@ "gallery": [ "other" ], - "collectionId": null - }, - { - "id": "Simple_nogen", - "name": "Simple nogen", - "description": "An example from a real application", - "tags": [ - "simple", - "nogen", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "simple_sbml_import", "name": "simple_sbml_import", "description": "SBML import test", "tags": [ - "validation", "simple", "sbml", "import", - "readfile", - "generate_network", - "simulate" + "readfile" ], "category": "validation", "origin": "test-case", @@ -13352,18 +12573,18 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "simple_system", "name": "simple_system", "description": "Simple binding system", "tags": [ - "validation", "simple", - "system", - "x", - "y" + "system" ], "category": "validation", "origin": "test-case", @@ -13379,7 +12600,10 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "simple-dimerization", @@ -13407,7 +12631,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "SIR", @@ -13415,8 +12642,7 @@ "description": "BioNetGen model: SIR", "tags": [ "sir", - "saveconcentrations", - "simulate" + "saveconcentrations" ], "category": "tutorial", "origin": "tutorial", @@ -13433,7 +12659,10 @@ "gallery": [ "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "sir-epidemic-model", @@ -13463,7 +12692,10 @@ "tutorials", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "smad-tgf-beta-signaling", @@ -13494,7 +12726,10 @@ "developmental", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "sonic-hedgehog-gradient", @@ -13523,7 +12758,10 @@ "developmental", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "sp_fourier_synthesizer", @@ -13556,7 +12794,10 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "sp_image_convolution", @@ -13585,7 +12826,10 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "sp_kalman_filter", @@ -13617,7 +12861,10 @@ "ml-signal", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "stat3-mediated-transcription", @@ -13645,7 +12892,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "stress-response-adaptation", @@ -13673,7 +12923,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "Suderman_2013", @@ -13682,7 +12935,6 @@ "tags": [ "suderman", "2013", - "i", "trash", "pheromone", "ste2", @@ -13705,7 +12957,10 @@ "gallery": [ "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "synaptic-plasticity-ltp", @@ -13737,7 +12992,10 @@ "neuroscience", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "synbio_band_pass_filter", @@ -13768,7 +13026,10 @@ "synbio", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "synbio_counter_molecular", @@ -13796,7 +13057,10 @@ "synbio", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "synbio_edge_detector", @@ -13825,7 +13089,10 @@ "synbio", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "synbio_logic_gates_enzymatic", @@ -13858,7 +13125,10 @@ "synbio", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "synbio_oscillator_synchronization", @@ -13887,7 +13157,10 @@ "synbio", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "t-cell-activation", @@ -13916,121 +13189,22 @@ "immunology", "test-models" ], - "collectionId": null - }, - { - "id": "tcr", - "name": "tcr", - "description": "A model of T cell receptor signaling", - "tags": [ - "tcr", - "lig1", - "lig2", - "lig3", - "cd28", - "lck", - "itk", - "zap70" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "nf" - ] - }, - "gallery": [ - "other" - ], - "collectionId": null - }, - { - "id": "TCR_model", - "name": "ERK_model.bngl", - "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", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode", - "ssa" - ] - }, - "gallery": [], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "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" + "source2" ], "category": "validation", "origin": "test-case", @@ -14046,20 +13220,18 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "test_fixed", "name": "test_fixed", - "description": "# actions ##", - "tags": [ - "validation", - "test", - "fixed", - "a", - "b", - "generate_network", - "simulate" + "description": "# actions ##", + "tags": [ + "test", + "fixed" ], "category": "validation", "origin": "test-case", @@ -14075,20 +13247,18 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "test_MM", "name": "test_MM", "description": "Kinetic constants", "tags": [ - "validation", "test", - "mm", - "e", - "s", - "p", - "generate_network" + "mm" ], "category": "validation", "origin": "test-case", @@ -14104,18 +13274,18 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "test_mratio", "name": "test_mratio", "description": "Reaction ratio test", "tags": [ - "validation", "test", "mratio", - "a", - "b", "c_theory", "c_upper", "c_lower" @@ -14134,14 +13304,16 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "test_network_gen", "name": "test_network_gen", "description": "fceri model with network generation", "tags": [ - "validation", "test", "network", "gen", @@ -14164,20 +13336,18 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "test_sat", "name": "test_sat", "description": "Kinetic constants", "tags": [ - "validation", "test", - "sat", - "e", - "s", - "p", - "generate_network" + "sat" ], "category": "validation", "origin": "test-case", @@ -14193,22 +13363,20 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "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" ], @@ -14226,20 +13394,19 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "test_synthesis_complex", "name": "test_synthesis_complex", "description": "Complex synthesis test", "tags": [ - "validation", "test", "synthesis", "complex", - "a", - "b", - "c", "receptor", "source", "source2" @@ -14258,178 +13425,473 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "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", - "origin": "test-case", - "visible": true, + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "test_synthesis_complex_source_cBNGL", + "name": "test_synthesis_complex_source_cBNGL", + "description": "volume-surface", + "tags": [ + "test", + "synthesis", + "complex", + "source", + "cbngl", + "surface_molecule1", + "surface_molecule2", + "surface_receptor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "test_synthesis_simple", + "name": "test_synthesis_simple", + "description": "Simple synthesis test", + "tags": [ + "test", + "synthesis", + "simple", + "source", + "source2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_egfr_2016_example1_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example1_fit)", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_egfr_2016_example2_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example2_fit)", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_egfr_2016_example3_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example3_fit)", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_egfr_2016_example4_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example4_fit)", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_egfr_2016_example5_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example5_fit)", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_egfr_2016_example5_ground_truth", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example5_ground_truth)", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_egfr_2016_example6_ground_truth", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example6_ground_truth)", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_Example1_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 1 Starting Point", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "starting-point", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_Example2_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 2 Starting Point", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "starting-point", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "test_synthesis_complex_source_cBNGL", - "name": "test_synthesis_complex_source_cBNGL", - "description": "volume-surface", + "id": "Thomas_Example3_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 3 (TLBR)", + "description": "BNGL model: example3", "tags": [ - "validation", - "test", - "synthesis", - "complex", - "source", - "cbngl", - "volume_molecule1", - "volume_molecule2", - "surface_molecule1", - "surface_molecule2", - "volume_molecule3", - "volume_molecule4", - "volume_receptor", - "surface_receptor" + "tlbr", + "polymerization", + "ligand-receptor", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "test_synthesis_simple", - "name": "test_synthesis_simple", - "description": "Simple synthesis test", + "id": "Thomas_Example4_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 4 Model", + "description": "Supplementary File A in File S1", "tags": [ - "validation", - "test", - "synthesis", - "simple", - "a", - "b", - "c", - "source", - "source2", - "generate_network" + "egfr", + "signaling", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "validation" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "tlbr", - "name": "tlbr", - "description": "A model of trivalent ligand, bivalent receptor", + "id": "Thomas_Example5_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 5 Model", + "description": "A simple model", "tags": [ - "tlbr", - "l", - "r", - "lambda", - "fl" + "egfr", + "signaling", + "2016", + "thomas" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "immunology" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "tlbr", - "name": "TLBR Tutorial", - "description": "Ligand binding", + "id": "Thomas_Example6_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 6 Model", + "description": "A simple model", "tags": [ - "published", - "immunology", - "tlbr", - "l", - "r", - "simulate_rm" + "egfr", + "signaling", + "2016", + "thomas" ], - "category": "immunology", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "immunology" - ], - "collectionId": null + "gallery": [], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "tlmr", "name": "tlmr", "description": "Trivalent ligand monovalent receptor", "tags": [ - "validation", - "tlmr", - "l", - "r", - "generate_network", - "simulate_ode" + "tlmr" ], "category": "validation", "origin": "test-case", @@ -14445,7 +13907,10 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "tlr3-dsrna-sensing", @@ -14474,7 +13939,10 @@ "immunology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "tnf-induced-apoptosis", @@ -14504,20 +13972,17 @@ "cell-cycle", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "toggle", "name": "Toggle", "description": "Toggle switch", "tags": [ - "published", - "tutorial", - "native", "toggle", - "x", - "y", - "generate_network", "writemfile", "setconcentration" ], @@ -14536,21 +14001,18 @@ "synbio", "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "toy-jim", "name": "toy-jim", "description": "The model consists of a monovalent extracellular ligand,", "tags": [ - "validation", "toy", - "jim", - "l", - "r", - "a", - "k", - "null" + "jim" ], "category": "validation", "origin": "test-case", @@ -14566,22 +14028,19 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "toy1", "name": "toy1", "description": "Basic signaling toy", "tags": [ - "published", "tutorials", "toy1", - "l", - "r", - "a", - "generate_network", - "writesbml", - "simulate_ode" + "writesbml" ], "category": "tutorial", "origin": "tutorial", @@ -14597,20 +14056,18 @@ "gallery": [ "tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "toy2", "name": "toy2", "description": "Enzymatic reaction toy", "tags": [ - "published", "tutorials", - "toy2", - "l", - "r", - "a", - "k" + "toy2" ], "category": "tutorial", "origin": "tutorial", @@ -14626,16 +14083,17 @@ "gallery": [ "tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "translateSBML", "name": "translateSBML", "description": "title: translateSBML.bngl", "tags": [ - "translatesbml", - "generate_network", - "simulate" + "translatesbml" ], "category": "tutorial", "origin": "tutorial", @@ -14651,87 +14109,10 @@ "gallery": [ "tutorial" ], - "collectionId": null - }, - { - "id": "Tricky", - "name": "Tricky", - "description": "An example from a real application", - "tags": [ - "tricky", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null - }, - { - "id": "TrickyUS", - "name": "TrickyUS", - "description": "An example from a real application", - "tags": [ - "trickyus", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null - }, - { - "id": "trivial", - "name": "trivial", - "description": "A trivial model file for testing MCMC distributions.", - "tags": [ - "trivial", - "q", - "r", - "output", - "generate_network", - "simulate" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "two-component-system", @@ -14759,21 +14140,18 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "univ_synth", "name": "univ_synth", "description": "example of universal synthesis", "tags": [ - "validation", "univ", - "synth", - "a", - "b", - "c", - "generate_network", - "simulate_ode" + "synth" ], "category": "validation", "origin": "test-case", @@ -14789,7 +14167,10 @@ "gallery": [ "validation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "vegf-angiogenesis", @@ -14818,19 +14199,19 @@ "cancer", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "vilar_2002", + "id": "Vilar_Circadian_2002", "name": "Vilar 2002", "description": "Genetic oscillator", "tags": [ - "published", - "vilar", "2002", "dna", - "a", - "r" + "oscillations" ], "category": "regulation", "origin": "published", @@ -14846,19 +14227,19 @@ "gallery": [ "cell-cycle" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "vilar_2002b", + "id": "Vilar_Circadian_2002b", "name": "Vilar 2002b", "description": "Gene oscillator", "tags": [ - "published", - "vilar", - "2002b", + "2002", "dna", - "a", - "r" + "oscillations" ], "category": "regulation", "origin": "published", @@ -14874,19 +14255,19 @@ "gallery": [ "cell-cycle" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "vilar_2002c", + "id": "Vilar_Circadian_2002c", "name": "Vilar 2002c", "description": "Gene oscillator", "tags": [ - "published", - "vilar", - "2002c", + "2002", "dna", - "a", - "r" + "oscillations" ], "category": "regulation", "origin": "published", @@ -14902,7 +14283,10 @@ "gallery": [ "regulation" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "viral-sensing-innate-immunity", @@ -14934,22 +14318,16 @@ "immunology", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "visualize", "name": "Visualize", "description": "Visualization toy", - "tags": [ - "published", - "tutorial", - "native", - "visualize", - "x", - "a1", - "a2", - "b" - ], + "tags": [], "category": "tutorial", "origin": "tutorial", "visible": false, @@ -14964,7 +14342,10 @@ "gallery": [ "native-tutorials" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "wacky_alchemy_stone", @@ -14992,7 +14373,10 @@ "synbio", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wacky_black_hole", @@ -15021,7 +14405,10 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wacky_bouncing_ball", @@ -15049,7 +14436,10 @@ "physics", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wacky_traffic_jam_asep", @@ -15080,7 +14470,10 @@ "physics", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wacky_zombie_infection", @@ -15107,36 +14500,10 @@ "ecology", "test-models" ], - "collectionId": null - }, - { - "id": "wnt", - "name": "Wnt Signaling", - "description": "Wnt signaling", - "tags": [ - "published", - "wnt", - "dsh", - "axc", - "frz", - "lrp5", - "bcat" - ], - "category": "regulation", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "regulation" - ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wnt-beta-catenin-signaling", @@ -15168,7 +14535,10 @@ "developmental", "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "wound-healing-pdgf-signaling", @@ -15197,17 +14567,18 @@ "gallery": [ "test-models" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Yang_2008", + "id": "Yang_tlbr_2008", "name": "Yang 2008", "description": "TLBR yang 2008", "tags": [ - "published", - "physics", - "yang", - "2008" + "2008", + "yang" ], "category": "physics", "origin": "published", @@ -15223,24 +14594,54 @@ "gallery": [ "physics" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "ZAP70_immunology_2021", + "name": "Model ZAP", + "description": "ZAP-70 recruitment", + "tags": [ + "cbl", + "dead", + "lck", + "ligand", + "modelzap", + "nfsim", + "zap", + "zeta" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null, + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Zhang_2021", - "name": "Zhang 2021", + "id": "Zhang_developmental_2021", + "name": "Zhang et al. 2021: VE-PTP and Tie2 Receptor Regulation Model", "description": "CAR-T signaling", "tags": [ - "published", - "zhang", - "2021", + "ve-ptp", "tie2", - "tie1", - "ang1_4", - "ang2_2", - "ang2_3", - "ang2_4", - "veptp", - "pten" + "angiogenesis", + "2021", + "zhang" ], "category": "signaling", "origin": "published", @@ -15256,24 +14657,21 @@ "gallery": [ "developmental" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Zhang_2023", - "name": "Zhang 2023", + "id": "Zhang_developmental_2023", + "name": "Zhang et al. 2023: VEGF-induced PLC-gamma Activation Model", "description": "VEGF signaling", "tags": [ - "published", - "zhang", - "2023", "vegf", - "vegfr2", - "vegfr1", - "nrp1", - "pi", - "plcgamma", - "dag", - "ip3_cyto" + "plc-gamma", + "angiogenesis", + "2023", + "zhang" ], "category": "signaling", "origin": "published", @@ -15289,6 +14687,9 @@ "gallery": [ "developmental" ], - "collectionId": null + "collectionId": null, + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false } ] \ No newline at end of file diff --git a/manifest.json b/manifest.json index fe5e655b..fe2506c3 100644 --- a/manifest.json +++ b/manifest.json @@ -1,116 +1,76 @@ [ { - "id": "03_fcerig_fceri_gamma2", - "name": "03-fcerig", - "description": "Added molecule type definition block so that the", + "id": "AB", + "name": "AB", + "description": "BioNetGen model: AB", "tags": [ - "immunology" + "ab" ], - "category": "immunology", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/03-fcerig/fceri_gamma2.bngl", - "file": "fceri_gamma2.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/AB/AB.bngl", + "file": "AB.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "04_egfrnf_egfr_nf", - "name": "example2_starting_point.bngl", - "description": "Filename: example2_starting_point.bngl", + "id": "ABC", + "name": "ABC", + "description": "BioNetGen model: ABC", "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" + "abc" ], - "category": "signaling", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/04-egfrnf/egfr_nf.bngl", - "file": "egfr_nf.bngl", + "gallery": [ + "metabolism", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABC/ABC.bngl", + "file": "ABC.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "06_degranulation_model_tofit", - "name": "of IgE receptor signaling", - "description": "A model of IgE receptor signaling", + "id": "ABC_scan", + "name": "ABC scan", + "description": "BioNetGen model: ABC scan", "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" + "abc", + "scan", + "parameter_scan" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -120,193 +80,199 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/06-degranulation/model_tofit.bngl", - "file": "model_tofit.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABCscan/ABC_scan.bngl", + "file": "ABC_scan.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "07_egg_egg", - "name": "07-egg", - "description": "BNGL model: egg", + "id": "ABC_ssa", + "name": "ABC ssa", + "description": "BioNetGen model: ABC ssa", "tags": [ - "a0", - "a1", - "a2", - "b1", - "b2", - "c0", - "c1", - "c2", - "d1", - "d2", - "period", - "t", - "species" + "abc", + "ssa" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "ssa" ] }, - "gallery": [], - "path": "Published/Mitra2019/07-egg/egg.bngl", - "file": "egg.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABCssa/ABC_ssa.bngl", + "file": "ABC_ssa.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "10_egfr_egfr_ode", - "name": "example1.bngl", - "description": "Filename: example1.bngl", + "id": "ABp", + "name": "ABp", + "description": "title: ABp.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" + "abp" ], - "category": "signaling", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/10-egfr/egfr_ode.bngl", - "file": "egfr_ode.bngl", + "gallery": [ + "metabolism", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABp/ABp.bngl", + "file": "ABp.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "11_TLBR_tlbr", - "name": "11-TLBR", - "description": "BNGL model: tlbr", + "id": "ABp_approx", + "name": "ABp approx", + "description": "title: ABp.bngl", "tags": [ - "alpha", - "molecules", - "species" + "abp", + "km" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/11-TLBR/tlbr.bngl", - "file": "tlbr.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABpapprox/ABp_approx.bngl", + "file": "ABp_approx.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "12_TCR_tcr", - "name": "of T cell receptor signaling", - "description": "A model of T cell receptor signaling", + "id": "akt-signaling", + "name": "akt signaling", + "description": "Signaling rates", "tags": [ - "immunology" + "akt", + "signaling", + "growthfactor", + "rtk", + "pi3k", + "mtorc2", + "mtorc1", + "s6k" ], - "category": "immunology", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/12-TCR/tcr.bngl", - "file": "tcr.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/biology/aktsignaling/akt-signaling.bngl", + "file": "akt-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "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.", + "id": "allosteric-activation", + "name": "allosteric activation", + "description": "Binding constants", "tags": [ - "molecules", - "species" + "allosteric", + "activation", + "enzyme", + "substrate", + "activator", + "product" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/14-receptor-nf/receptor_nf.bngl", - "file": "receptor_nf.bngl", + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/allostericactivation/allosteric-activation.bngl", + "file": "allosteric-activation.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "15_igf1r_IGF1R_fit_all", - "name": "15-igf1r", - "description": "Author: William S. Hlavacek", + "id": "ampk-signaling", + "name": "ampk signaling", + "description": "AMPK signaling: The cellular energy sensor.", "tags": [ - "dilution", - "a1_permpers", - "a2_permpers", - "molecules" + "ampk", + "signaling", + "amp", + "lkb1", + "ca", + "sik", + "crtc" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -316,35 +282,33 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/15-igf1r/IGF1R_fit_all.bngl", - "file": "IGF1R_fit_all.bngl", + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/ampksignaling/ampk-signaling.bngl", + "file": "ampk-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "19_raf_constraint_RAFi", - "name": "19-raf-constraint", - "description": "BNGL model: RAFi", + "id": "An_TLR4_2009", + "name": "An et al. 2009: TLR4 Signaling Model", + "description": "TLR4 signaling", "tags": [ - "k1", - "k2", - "k3", - "k5", - "kf1", - "kf2", - "kf3", - "kf4", - "kf5", - "kf6", - "rtot", - "ifree", - "species" + "tlr4", + "immune-signaling", + "innate-immunity", + "2009", + "an" ], - "category": "other", + "category": "immunology", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -353,153 +317,110 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/19-raf-constraint/RAFi.bngl", - "file": "RAFi.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "190127_CHO_EGFR_best-fit", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "gallery": [ + "immunology" + ], + "path": "Published/An2009/An_2009.bngl", + "file": "An_2009.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "apoptosis-cascade", + "name": "apoptosis cascade", + "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", "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" + "apoptosis", + "cascade", + "deathligand", + "caspase8", + "bid", + "mito", + "apaf1", + "caspase3", + "xiap", + "smac" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_best-fit.bngl", - "file": "190127_CHO_EGFR_best-fit.bngl", + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/apoptosiscascade/apoptosis-cascade.bngl", + "file": "apoptosis-cascade.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "190127_CHO_EGFR_Epigen", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "auto-activation-loop", + "name": "auto activation loop", + "description": "Auto-activation loop: A positive feedback circuit.", "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" + "auto", + "activation", + "loop", + "gene", + "mrna", + "protein", + "rbp" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_Epigen.bngl", - "file": "190127_CHO_EGFR_Epigen.bngl", + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/autoactivationloop/auto-activation-loop.bngl", + "file": "auto-activation-loop.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "190127_CHO_EGFR_sensitivity", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "autophagy-regulation", + "name": "autophagy regulation", + "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", "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" + "autophagy", + "regulation", + "mtor", + "ampk", + "ulk1", + "lc3", + "p62" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -509,153 +430,91 @@ "ode" ] }, - "gallery": [], - "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_sensitivity.bngl", - "file": "190127_CHO_EGFR_sensitivity.bngl", + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/autophagyregulation/autophagy-regulation.bngl", + "file": "autophagy-regulation.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "190127_CHO_HA_EGFR_L858R", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "BAB", + "name": "BAB", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", "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" + "bab" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Salazar-Cavazos2019/190127_CHO_HA_EGFR_L858R.bngl", - "file": "190127_CHO_HA_EGFR_L858R.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BAB/BAB.bngl", + "file": "BAB.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "190127_HeLa", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "BAB_coop", + "name": "BAB coop", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", "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" + "bab", + "coop" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Salazar-Cavazos2019/190127_HeLa.bngl", - "file": "190127_HeLa.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BABcoop/BAB_coop.bngl", + "file": "BAB_coop.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "190127_HMEC", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "BAB_scan", + "name": "BAB scan", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", "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" + "bab", + "scan", + "parameter_scan" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -665,52 +524,34 @@ "ode" ] }, - "gallery": [], - "path": "Published/Salazar-Cavazos2019/190127_HMEC.bngl", - "file": "190127_HMEC.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BABscan/BAB_scan.bngl", + "file": "BAB_scan.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "190127_MCF10A", - "name": "Salazar-Cavazos2019", - "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "id": "Barua_bcat_2013", + "name": "Barua et al. 2013: Beta-Catenin Regulation Model", + "description": "Beta-catenin destruction", "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" + "beta-catenin", + "regulation", + "wnt-signaling", + "2013", + "barua" ], - "category": "other", + "category": "regulation", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -718,32 +559,27 @@ ] }, "gallery": [], - "path": "Published/Salazar-Cavazos2019/190127_MCF10A.bngl", - "file": "190127_MCF10A.bngl", + "path": "Published/Barua2013/Barua_2013.bngl", + "file": "Barua_2013.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "20_raf_constraint4_RAFi", - "name": "20-raf-constraint4", - "description": "BNGL model: RAFi", + "id": "Barua_BCR_2012", + "name": "Barua et al. 2012: BCR Signaling Model", + "description": "BCR signaling", "tags": [ - "k1", - "k2", - "k3", - "k5", - "kf1", - "kf2", - "kf3", - "kf4", - "kf5", - "kf6", - "rtot", - "ifree", - "species" + "bcr", + "immune-signaling", + "b-cell", + "2012", + "barua" ], - "category": "other", + "category": "immunology", "origin": "published", "visible": false, "compatibility": { @@ -754,255 +590,175 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/20-raf-constraint4/RAFi.bngl", - "file": "RAFi.bngl", + "gallery": [ + "immunology" + ], + "path": "Published/BaruaBCR2012/BaruaBCR_2012.bngl", + "file": "BaruaBCR_2012.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "24_jnk_JNKmodel_180724_bnf", - "name": "24-jnk", - "description": "BNGL model: JNKmodel_180724_bnf", + "id": "Barua_EGFR_2007", + "name": "Barua et al. 2007: EGFR Signaling Model", + "description": "Model from Haugh (2006)", "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" + "egfr", + "signaling", + "2007", + "barua" ], - "category": "other", + "category": "signaling", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/24-jnk/JNKmodel_180724_bnf.bngl", - "file": "JNKmodel_180724_bnf.bngl", + "gallery": [ + "cancer" + ], + "path": "Published/Barua2007/Barua_2007.bngl", + "file": "Barua_2007.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "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", + "id": "Barua_FceRI_2012", + "name": "Barua et al. 2012: FceRI Signaling Model", + "description": "FcεRI signaling", "tags": [ - "immunology" + "fceri", + "immune-signaling", + "mast-cell", + "2012", + "barua" ], "category": "immunology", "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/26-tcr-sens/tcr_sens_tofit.bngl", - "file": "tcr_sens_tofit.bngl", + "gallery": [ + "immunology" + ], + "path": "Published/BaruaFceRI2012/BaruaFceRI_2012.bngl", + "file": "BaruaFceRI_2012.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "31_elephant_elephant", - "name": "31-elephant", - "description": "BNGL model: elephant", + "id": "Barua_JAK2_2009", + "name": "Barua et al. 2009: JAK2-STAT5 Signaling Model", + "description": "JAK2-SH2B signaling", "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" + "jak2", + "stat5", + "signaling", + "2009", + "barua" ], - "category": "other", + "category": "signaling", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/31-elephant/elephant.bngl", - "file": "elephant.bngl", + "gallery": [ + "cancer" + ], + "path": "Published/Barua2009/Barua_2009.bngl", + "file": "Barua_2009.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "AB", - "name": "AB", - "description": "BioNetGen model: AB", + "id": "bcr-signaling", + "name": "bcr signaling", + "description": "BCR signaling: The B-cell antigen receptor cascade.", "tags": [ - "ab", - "a", - "b", - "simulate" + "bcr", + "signaling", + "antigen", + "syk", + "plcg2", + "cd22", + "shp1", + "calcium" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "immunology", + "test-models" ], - "path": "Tutorials/NativeTutorials/AB/AB.bngl", - "file": "AB.bngl", + "path": "Examples/biology/bcrsignaling/bcr-signaling.bngl", + "file": "bcr-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ABC", - "name": "ABC", - "description": "BioNetGen model: ABC", + "id": "beta-adrenergic-response", + "name": "beta adrenergic response", + "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", "tags": [ - "abc", - "a", - "simulate" + "beta", + "adrenergic", + "response", + "epi", + "betar", + "gs", + "ac", + "arr", + "camp" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": true, @@ -1012,260 +768,279 @@ ] }, "gallery": [ - "metabolism", - "native-tutorials" + "neuroscience", + "test-models" ], - "path": "Tutorials/NativeTutorials/ABC/ABC.bngl", - "file": "ABC.bngl", + "path": "Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl", + "file": "beta-adrenergic-response.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ABC_scan", - "name": "ABC scan", - "description": "BioNetGen model: ABC scan", + "id": "birth-death", + "name": "Birth-Death", + "description": "Stochastic process", "tags": [ - "abc", - "scan", - "a", - "generate_network", - "parameter_scan" + "birth", + "death", + "saveconcentrations" ], "category": "tutorial", "origin": "tutorial", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ "native-tutorials" ], - "path": "Tutorials/NativeTutorials/ABCscan/ABC_scan.bngl", - "file": "ABC_scan.bngl", + "path": "Tutorials/NativeTutorials/birthdeath/birth-death.bngl", + "file": "birth-death.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ABC_ssa", - "name": "ABC ssa", - "description": "BioNetGen model: ABC ssa", + "id": "bistable-toggle-switch", + "name": "bistable toggle switch", + "description": "Genetic Toggle Switch: Mutual repression circuit.", "tags": [ - "abc", - "ssa", - "a", - "simulate" + "bistable", + "toggle", + "switch", + "proml", + "promr", + "tf_l", + "tf_r", + "ind_l", + "ind_r" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "native-tutorials" + "test-models" ], - "path": "Tutorials/NativeTutorials/ABCssa/ABC_ssa.bngl", - "file": "ABC_ssa.bngl", + "path": "Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl", + "file": "bistable-toggle-switch.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ABp", - "name": "ABp", - "description": "title: ABp.bngl", + "id": "BLBR", + "name": "BLBR", + "description": "title: BLBR.bngl", "tags": [ - "abp", - "a", - "b", - "simulate" + "blbr" ], "category": "tutorial", "origin": "tutorial", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ode" + "ode", + "nf" ] }, "gallery": [ - "metabolism", - "native-tutorials" + "tutorial" ], - "path": "Tutorials/NativeTutorials/ABp/ABp.bngl", - "file": "ABp.bngl", + "path": "Tutorials/NativeTutorials/BLBR/BLBR.bngl", + "file": "BLBR.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ABp_approx", - "name": "ABp approx", - "description": "title: ABp.bngl", + "id": "Blinov_egfr_2006", + "name": "Blinov et al. 2006: EGFR Signaling Pathway (ODE)", + "description": "Phosphotyrosine signaling", "tags": [ - "abp", - "approx", - "km", - "a", - "b", - "simulate" + "egfr", + "signaling", + "ode", + "receptor-activation", + "2006", + "blinov" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "published", "visible": true, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "cell-cycle" ], - "path": "Tutorials/NativeTutorials/ABpapprox/ABp_approx.bngl", - "file": "ABp_approx.bngl", + "path": "Published/Blinov2006/Blinov_2006.bngl", + "file": "Blinov_2006.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "actions_syntax", - "name": "actions syntax", - "description": "Original values used to generate parabola.exp", + "id": "Blinov_egfr_NF_2006", + "name": "Blinov et al. 2006: EGFR Signaling Pathway (NFsim)", + "description": "EGFR signaling model", "tags": [ - "actions", - "syntax", - "counter", - "y", - "generate_network", - "simulate" + "egfr", + "signaling", + "nfsim", + "receptor-activation", + "2006", + "blinov" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "validation" + "cancer" ], - "path": "Published/PyBioNetGen/tests/actionssyntax/actions_syntax.bngl", - "file": "actions_syntax.bngl", + "path": "Published/Blinovegfr/Blinov_egfr.bngl", + "file": "Blinov_egfr.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "after_bunching", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Blinov_ran_2006", + "name": "Blinov et al. 2006: Ran-Mediated Nuclear Transport (NFsim)", + "description": "Ran GTPase cycle", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "ran-gtpase", + "nuclear-transport", + "nfsim", + "2006", + "blinov" ], - "category": "other", + "category": "regulation", "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Restructuration/after_bunching.bngl", - "file": "after_bunching.bngl", + "gallery": [ + "cell-cycle" + ], + "path": "Published/Blinovran/Blinov_ran.bngl", + "file": "Blinov_ran.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "after_decoupling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "blood-coagulation-thrombin", + "name": "blood coagulation thrombin", + "description": "Blood coagulation: Thrombin burst and feedback propagation.", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "blood", + "coagulation", + "thrombin", + "tf", + "factorx", + "factorv", + "prothrombin", + "fibrinogen", + "at" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Restructuration/after_decoupling.bngl", - "file": "after_decoupling.bngl", + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl", + "file": "blood-coagulation-thrombin.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "after_scaling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "bmp-signaling", + "name": "bmp signaling", + "description": "BMP-Smad signaling: Developmental gradient relay.", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "bmp", + "signaling", + "noggin", + "receptor1", + "receptor2", + "smad1", + "smad4", + "smad6" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -1275,134 +1050,111 @@ "ode" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Restructuration/after_scaling.bngl", - "file": "after_scaling.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "akt-signaling", - "name": "akt signaling", - "description": "Signaling rates", - "tags": [ - "akt", - "signaling", - "growthfactor", - "rtk", - "pi3k", - "mtorc2", - "mtorc1", - "s6k" - ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, "gallery": [ + "developmental", "test-models" ], - "path": "Examples/biology/aktsignaling/akt-signaling.bngl", - "file": "akt-signaling.bngl", + "path": "Examples/biology/bmpsignaling/bmp-signaling.bngl", + "file": "bmp-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Alabama", - "name": "Alabama", - "description": "reporting period (1 d)", + "id": "brusselator-oscillator", + "name": "brusselator oscillator", + "description": "The Brusselator: Auto-catalytic chemical oscillator.", "tags": [ - "alabama", - "fdcs", - "counter", - "s", - "e1", - "e2", - "e3", - "e4", - "e5" + "brusselator", + "oscillator", + "a", + "b", + "x", + "y" ], - "category": "epidemiology", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "epidemiology" + "physics", + "test-models" ], - "path": "Published/Mallela2022/Alabama/Alabama.bngl", - "file": "Alabama.bngl", + "path": "Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl", + "file": "brusselator-oscillator.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "allosteric-activation", - "name": "allosteric activation", - "description": "Binding constants", + "id": "calcineurin-nfat-pathway", + "name": "calcineurin nfat pathway", + "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", "tags": [ - "allosteric", - "activation", - "enzyme", - "substrate", - "activator", - "product" + "calcineurin", + "nfat", + "pathway", + "ca", + "cam", + "can", + "rcan1" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism", + "neuroscience", "test-models" ], - "path": "Examples/biology/allostericactivation/allosteric-activation.bngl", - "file": "allosteric-activation.bngl", + "path": "Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl", + "file": "calcineurin-nfat-pathway.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ampk-signaling", - "name": "ampk signaling", - "description": "AMPK signaling: The cellular energy sensor.", + "id": "calcium-spike-signaling", + "name": "calcium spike signaling", + "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", "tags": [ - "ampk", + "calcium", + "spike", "signaling", - "amp", - "lkb1", + "plc", + "ip3", "ca", - "sik", - "crtc" + "stim1" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -1412,137 +1164,133 @@ "neuroscience", "test-models" ], - "path": "Examples/biology/ampksignaling/ampk-signaling.bngl", - "file": "ampk-signaling.bngl", + "path": "Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl", + "file": "calcium-spike-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "An_2009", - "name": "An 2009", - "description": "TLR4 signaling", + "id": "CaOscillate_Func", + "name": "CaOscillate_Func", + "description": "Calcium oscillations (func)", "tags": [ - "published", - "immunology", - "an", - "2009", - "cd14", - "md2", - "tlr4", - "tram", - "trif", - "sarm", - "traf4", - "irak1" + "caoscillate", + "ga", + "plc", + "ca" ], - "category": "immunology", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, - "gallery": [ - "immunology" - ], - "path": "Published/An2009/An_2009.bngl", - "file": "An_2009.bngl", + "gallery": [], + "path": "Tutorials/CaOscillateFunc/CaOscillate_Func.bngl", + "file": "CaOscillate_Func.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "apoptosis-cascade", - "name": "apoptosis cascade", - "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", + "id": "CaOscillate_Sat", + "name": "CaOscillate_Sat", + "description": "Calcium oscillations (sat)", "tags": [ - "apoptosis", - "cascade", - "deathligand", - "caspase8", - "bid", - "mito", - "apaf1", - "caspase3", - "xiap", - "smac" + "caoscillate", + "sat", + "ga", + "plc", + "ca" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "cell-cycle", - "test-models" + "validation" ], - "path": "Examples/biology/apoptosiscascade/apoptosis-cascade.bngl", - "file": "apoptosis-cascade.bngl", + "path": "Tutorials/CaOscillateSat/CaOscillate_Sat.bngl", + "file": "CaOscillate_Sat.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "auto-activation-loop", - "name": "auto activation loop", - "description": "Auto-activation loop: A positive feedback circuit.", + "id": "caspase-activation-loop", + "name": "caspase activation loop", + "description": "Caspase activation loop: The executioner feedback system.", "tags": [ - "auto", + "caspase", "activation", "loop", - "gene", - "mrna", - "protein", - "rbp" + "deathligand", + "caspase8", + "caspase3", + "iap", + "flip" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism", + "cell-cycle", "test-models" ], - "path": "Examples/biology/autoactivationloop/auto-activation-loop.bngl", - "file": "auto-activation-loop.bngl", + "path": "Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl", + "file": "caspase-activation-loop.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "autophagy-regulation", - "name": "autophagy regulation", - "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", + "id": "catalysis", + "name": "catalysis", + "description": "Catalysis in energy BNG", "tags": [ - "autophagy", - "regulation", - "mtor", - "ampk", - "ulk1", - "lc3", - "p62" + "catalysis", + "pptase", + "atp", + "adp" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -1552,24 +1300,27 @@ ] }, "gallery": [ - "metabolism", - "test-models" + "validation" ], - "path": "Examples/biology/autophagyregulation/autophagy-regulation.bngl", - "file": "autophagy-regulation.bngl", + "path": "Tutorials/catalysis/catalysis.bngl", + "file": "catalysis.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "BAB", - "name": "BAB", - "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "id": "cBNGL_simple", + "name": "cBNGL simple", + "description": "A simplified signal transduction model including the following processes:", "tags": [ - "bab", - "a", - "b", - "simulate" + "cbngl", + "simple", + "tf", + "dna", + "mrna" ], "category": "tutorial", "origin": "tutorial", @@ -1585,123 +1336,148 @@ "gallery": [ "native-tutorials" ], - "path": "Tutorials/NativeTutorials/BAB/BAB.bngl", - "file": "BAB.bngl", + "path": "Tutorials/NativeTutorials/cBNGLsimple/cBNGL_simple.bngl", + "file": "cBNGL_simple.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "BAB_coop", - "name": "BAB coop", - "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "id": "cd40-signaling", + "name": "cd40 signaling", + "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", "tags": [ - "bab", - "coop", - "a", - "b", - "simulate" - ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "cd40", + "signaling", + "cd40l", + "traf", + "ikk", + "nik", + "nfkb", + "relb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "immunology", + "test-models" ], - "path": "Tutorials/NativeTutorials/BABcoop/BAB_coop.bngl", - "file": "BAB_coop.bngl", + "path": "Examples/biology/cd40signaling/cd40-signaling.bngl", + "file": "cd40-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "BAB_scan", - "name": "BAB scan", - "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "id": "cell-cycle-checkpoint", + "name": "cell cycle checkpoint", + "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", "tags": [ - "bab", - "scan", - "a", - "b", - "generate_network", - "parameter_scan" + "cell", + "cycle", + "checkpoint", + "cyclin", + "cdk", + "cdc25", + "wee1", + "apc", + "p21" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "cell-cycle", + "test-models" ], - "path": "Tutorials/NativeTutorials/BABscan/BAB_scan.bngl", - "file": "BAB_scan.bngl", + "path": "Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl", + "file": "cell-cycle-checkpoint.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Barua_2007", - "name": "Barua 2007", - "description": "Model from Haugh (2006)", + "id": "Chattaraj_nephrin_2021", + "name": "Chattaraj et al. 2021: Nephrin-Nck-NWASP Clustering Model", + "description": "NFkB oscillations", "tags": [ - "published", - "barua", - "2007", - "version", - "r", - "s" + "nephrin", + "nck", + "nwasp", + "clustering", + "2021", + "chattaraj" ], "category": "signaling", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": false, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer" + "neuroscience" ], - "path": "Published/Barua2007/Barua_2007.bngl", - "file": "Barua_2007.bngl", + "path": "Published/Chattaraj2021/Chattaraj_2021.bngl", + "file": "Chattaraj_2021.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Barua_2009", - "name": "Barua 2009", - "description": "JAK2-SH2B signaling", + "id": "checkpoint-kinase-signaling", + "name": "checkpoint kinase signaling", + "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", "tags": [ - "published", - "barua", - "2009", - "s", - "j" + "checkpoint", + "kinase", + "signaling", + "dna", + "atm", + "atr", + "chk1", + "chk2", + "p53", + "cdc25" ], "category": "signaling", - "origin": "published", - "visible": true, + "origin": "ai-generated", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -1709,65 +1485,31 @@ ] }, "gallery": [ - "cancer" + "cancer", + "test-models" ], - "path": "Published/Barua2009/Barua_2009.bngl", - "file": "Barua_2009.bngl", + "path": "Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl", + "file": "checkpoint-kinase-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Barua_2013", - "name": "Barua 2013", - "description": "Beta-catenin destruction", + "id": "Cheemalavagu_JAKSTAT_2024", + "name": "Cheemalavagu et al. 2024: JAK-STAT Signaling Model", + "description": "JAK-STAT signaling", "tags": [ - "published", - "barua", - "2013", - "axin", - "gsk3b", - "apc", - "bcat", - "ck1a" + "jak-stat", + "signaling", + "2024", + "cheemalavagu" ], - "category": "regulation", + "category": "other", "origin": "published", "visible": true, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [], - "path": "Published/Barua2013/Barua_2013.bngl", - "file": "Barua_2013.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "BaruaBCR_2012", - "name": "Barua 2012", - "description": "BCR signaling", - "tags": [ - "published", - "immunology", - "baruabcr", - "2012", - "bcr", - "lyn", - "fyn", - "csk", - "pag", - "syk" - ], - "category": "immunology", - "origin": "published", - "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -1779,32 +1521,25 @@ "gallery": [ "immunology" ], - "path": "Published/BaruaBCR2012/BaruaBCR_2012.bngl", - "file": "BaruaBCR_2012.bngl", + "path": "Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT.bngl", + "file": "Cheemalavagu_JAK_STAT.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "BaruaFceRI_2012", - "name": "BaruaFceRI 2012", - "description": "FcεRI signaling", + "id": "chemistry", + "name": "chemistry", + "description": "Basic chemical reactions", "tags": [ - "published", - "immunology", - "baruafceri", - "2012", - "r_o", - "rdimer_o", - "l_o", - "t_o", - "l", - "fcr", - "lyn", - "syk" + "tutorials", + "chemistry" ], - "category": "immunology", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": false, @@ -1815,168 +1550,170 @@ ] }, "gallery": [ - "immunology" + "tutorials" ], - "path": "Published/BaruaFceRI2012/BaruaFceRI_2012.bngl", - "file": "BaruaFceRI_2012.bngl", + "path": "Tutorials/General/chemistry/chemistry.bngl", + "file": "chemistry.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "bcr-signaling", - "name": "bcr signaling", - "description": "BCR signaling: The B-cell antigen receptor cascade.", + "id": "chemotaxis-signal-transduction", + "name": "chemotaxis signal transduction", + "description": "Bacterial Chemotaxis: Adaptation through methylation.", "tags": [ - "bcr", - "signaling", - "antigen", - "syk", - "plcg2", - "cd22", - "shp1", - "calcium" + "chemotaxis", + "signal", + "transduction", + "attr", + "mcp", + "chea", + "chey", + "cheb", + "motor" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", "test-models" ], - "path": "Examples/biology/bcrsignaling/bcr-signaling.bngl", - "file": "bcr-signaling.bngl", + "path": "Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl", + "file": "chemotaxis-signal-transduction.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "before_bunching", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Chylek_FceRI_2014", + "name": "Chylek et al. 2014: FceRI Signaling Model", + "description": "FceRI signaling", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "fceri", + "immune-signaling", + "mast-cell", + "2014", + "chylek" ], - "category": "other", + "category": "immunology", "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Restructuration/before_bunching.bngl", - "file": "before_bunching.bngl", + "gallery": [ + "immunology" + ], + "path": "Published/ChylekFceRI2014/ChylekFceRI_2014.bngl", + "file": "ChylekFceRI_2014.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "before_decoupling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Chylek_library", + "name": "Chylek library", + "description": "Created by BioNetGen 2.2.6", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "chylek", + "library", + "sink", + "pre", + "pag1" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Restructuration/before_decoupling.bngl", - "file": "before_decoupling.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Chyleklibrary/Chylek_library.bngl", + "file": "Chylek_library.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "before_scaling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Chylek_TCR_2014", + "name": "Chylek et al. 2014: T Cell Receptor (TCR) Signaling Model", + "description": "TCR signaling", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "tcr", + "immune-signaling", + "t-cell", + "2014", + "chylek" ], - "category": "other", + "category": "immunology", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Restructuration/before_scaling.bngl", - "file": "before_scaling.bngl", + "gallery": [ + "immunology" + ], + "path": "Published/ChylekTCR2014/ChylekTCR_2014.bngl", + "file": "ChylekTCR_2014.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "beta-adrenergic-response", - "name": "beta adrenergic response", - "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", + "id": "circadian-oscillator", + "name": "circadian oscillator", + "description": "title: Vilar Circadian Oscillator Model", "tags": [ - "beta", - "adrenergic", - "response", - "epi", - "betar", - "gs", - "ac", - "arr", - "camp" + "circadian", + "oscillator", + "a", + "r", + "pa", + "pr", + "mrna_a", + "mrna_r" ], "category": "signaling", "origin": "ai-generated", @@ -1990,137 +1727,141 @@ ] }, "gallery": [ - "neuroscience", "test-models" ], - "path": "Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl", - "file": "beta-adrenergic-response.bngl", + "path": "Examples/biology/circadianoscillator/circadian-oscillator.bngl", + "file": "circadian-oscillator.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "birth-death", - "name": "Birth-Death", - "description": "Stochastic process", + "id": "CircadianOscillator", + "name": "CircadianOscillator", + "description": "Circadian rhythm", "tags": [ - "published", - "tutorial", - "native", - "birth", - "death", - "a", - "generate_network", - "saveconcentrations", - "simulate" + "circadianoscillator", + "pa", + "pr", + "mrna_a", + "mrna_r" ], "category": "tutorial", "origin": "tutorial", - "visible": true, + "visible": false, "compatibility": { - "bng2": true, - "nfsim": false, + "bng2": false, + "nfsim": true, "excluded": false, "methods": [ - "ode", "ssa" ] }, "gallery": [ + "cell-cycle", "native-tutorials" ], - "path": "Tutorials/NativeTutorials/birthdeath/birth-death.bngl", - "file": "birth-death.bngl", + "path": "Tutorials/NativeTutorials/CircadianOscillator/CircadianOscillator.bngl", + "file": "CircadianOscillator.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "bistable-toggle-switch", - "name": "bistable toggle switch", - "description": "Genetic Toggle Switch: Mutual repression circuit.", + "id": "clock-bmal1-gene-circuit", + "name": "clock bmal1 gene circuit", + "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", "tags": [ - "bistable", - "toggle", - "switch", - "proml", - "promr", - "tf_l", - "tf_r", - "ind_l", - "ind_r" + "clock", + "bmal1", + "gene", + "circuit", + "ror", + "reverb", + "dna" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ + "cell-cycle", "test-models" ], - "path": "Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl", - "file": "bistable-toggle-switch.bngl", + "path": "Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl", + "file": "clock-bmal1-gene-circuit.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "BLBR", - "name": "BLBR", - "description": "title: BLBR.bngl", + "id": "compartment_endocytosis", + "name": "compartment endocytosis", + "description": "Model: compartment_endocytosis.bngl", "tags": [ - "blbr", - "setoption", - "r", + "compartment", + "endocytosis", "l", - "simulate" + "r", + "t" ], - "category": "tutorial", - "origin": "tutorial", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "ode", - "nf" + "ode" ] }, "gallery": [ - "tutorial" + "test-models" ], - "path": "Tutorials/NativeTutorials/BLBR/BLBR.bngl", - "file": "BLBR.bngl", + "path": "Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl", + "file": "compartment_endocytosis.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Blinov_2006", - "name": "Blinov 2006", - "description": "Phosphotyrosine signaling", + "id": "compartment_membrane_bound", + "name": "compartment membrane bound", + "description": "Model: compartment_membrane_bound.bngl", "tags": [ - "published", - "blinov", - "2006", - "egf", - "egfr", - "shc", - "grb2", - "sos" + "compartment", + "membrane", + "bound", + "p", + "lipid", + "generate_network", + "simulate" ], - "category": "signaling", - "origin": "published", - "visible": true, + "category": "other", + "origin": "ai-generated", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -2128,229 +1869,239 @@ ] }, "gallery": [ - "cell-cycle" + "test-models" ], - "path": "Published/Blinov2006/Blinov_2006.bngl", - "file": "Blinov_2006.bngl", + "path": "Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl", + "file": "compartment_membrane_bound.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Blinov_egfr", - "name": "Blinov egfr", - "description": "EGFR signaling model", + "id": "compartment_nested_transport", + "name": "compartment nested transport", + "description": "Model: compartment_nested_transport.bngl", "tags": [ - "published", - "nfsim", - "blinov", - "egfr", - "egf", - "grb2", - "shc", - "simulate_nf" + "compartment", + "nested", + "transport", + "s", + "generate_network", + "simulate" ], - "category": "signaling", - "origin": "published", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "cancer" + "test-models" ], - "path": "Published/Blinovegfr/Blinov_egfr.bngl", - "file": "Blinov_egfr.bngl", + "path": "Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl", + "file": "compartment_nested_transport.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Blinov_ran", - "name": "Blinov ran", - "description": "Ran GTPase cycle", + "id": "compartment_nuclear_transport", + "name": "compartment nuclear transport", + "description": "Model: compartment_nuclear_transport.bngl", "tags": [ - "published", - "nfsim", - "blinov", - "ran", - "c", - "rcc1", - "simulate_nf" + "compartment", + "nuclear", + "transport", + "tf", + "generate_network", + "simulate" ], - "category": "regulation", - "origin": "published", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "cell-cycle" + "test-models" ], - "path": "Published/Blinovran/Blinov_ran.bngl", - "file": "Blinov_ran.bngl", + "path": "Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl", + "file": "compartment_nuclear_transport.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "blood-coagulation-thrombin", - "name": "blood coagulation thrombin", - "description": "Blood coagulation: Thrombin burst and feedback propagation.", + "id": "compartment_organelle_exchange", + "name": "compartment organelle exchange", + "description": "Model: compartment_organelle_exchange.bngl", "tags": [ - "blood", - "coagulation", - "thrombin", - "tf", - "factorx", - "factorv", - "prothrombin", - "fibrinogen", - "at" + "compartment", + "organelle", + "exchange", + "cargo", + "generate_network", + "simulate" ], - "category": "signaling", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", "test-models" ], - "path": "Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl", - "file": "blood-coagulation-thrombin.bngl", + "path": "Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl", + "file": "compartment_organelle_exchange.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "bmp-signaling", - "name": "bmp signaling", - "description": "BMP-Smad signaling: Developmental gradient relay.", + "id": "competitive-enzyme-inhibition", + "name": "competitive enzyme inhibition", + "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", "tags": [ - "bmp", - "signaling", - "noggin", - "receptor1", - "receptor2", - "smad1", - "smad4", - "smad6" + "competitive", + "enzyme", + "inhibition", + "substrate1", + "substrate2", + "inhibitor", + "product" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "developmental", + "metabolism", "test-models" ], - "path": "Examples/biology/bmpsignaling/bmp-signaling.bngl", - "file": "bmp-signaling.bngl", + "path": "Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl", + "file": "competitive-enzyme-inhibition.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "bng_error", - "name": "bng error", - "description": "Original values used to generate parabola.exp", + "id": "complement-activation-cascade", + "name": "complement activation cascade", + "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", "tags": [ - "bng", - "error", - "counter", - "y", - "generate_network", - "simulate" + "complement", + "activation", + "cascade", + "c3", + "fb", + "c5", + "mac", + "surf" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "immunology", + "test-models" ], - "path": "Published/PyBioNetGen/tests/bngerror/bng_error.bngl", - "file": "bng_error.bngl", + "path": "Examples/biology/complementactivationcascade/complement-activation-cascade.bngl", + "file": "complement-activation-cascade.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "brusselator-oscillator", - "name": "brusselator oscillator", - "description": "The Brusselator: Auto-catalytic chemical oscillator.", + "id": "ComplexDegradation", + "name": "ComplexDegradation", + "description": "Degradation model", "tags": [ - "brusselator", - "oscillator", - "a", - "b", - "x", - "y" + "complexdegradation" ], - "category": "signaling", - "origin": "ai-generated", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "physics", - "test-models" + "native-tutorials" ], - "path": "Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl", - "file": "brusselator-oscillator.bngl", + "path": "Tutorials/NativeTutorials/ComplexDegradation/ComplexDegradation.bngl", + "file": "ComplexDegradation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "calcineurin-nfat-pathway", - "name": "calcineurin nfat pathway", - "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", + "id": "contact-inhibition-hippo-yap", + "name": "contact inhibition hippo yap", + "description": "Hippo Pathway: Contact inhibition and YAP regulation.", "tags": [ - "calcineurin", - "nfat", - "pathway", - "ca", - "cam", - "can", - "rcan1" + "contact", + "inhibition", + "hippo", + "yap", + "mst", + "lats", + "tead" ], "category": "signaling", "origin": "ai-generated", @@ -2364,201 +2115,213 @@ ] }, "gallery": [ - "neuroscience", "test-models" ], - "path": "Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl", - "file": "calcineurin-nfat-pathway.bngl", + "path": "Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl", + "file": "contact-inhibition-hippo-yap.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "calcium-spike-signaling", - "name": "calcium spike signaling", - "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", + "id": "continue", + "name": "continue", + "description": "Test trajectory continuation", "tags": [ - "calcium", - "spike", - "signaling", - "plc", - "ip3", - "ca", - "stim1" + "continue", + "trash" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "neuroscience", - "test-models" + "validation" ], - "path": "Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl", - "file": "calcium-spike-signaling.bngl", + "path": "Tutorials/continue/continue.bngl", + "file": "continue.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "CaMKII_holo", - "name": "Ordyan 2020: CaMKII holo", - "description": "CaMKII holo", + "id": "cooperative-binding", + "name": "cooperative binding", + "description": "Cooperative binding: The binding of the first ligand molecule increases", "tags": [ - "published", - "neuroscience", - "camkii", - "holo", - "ca", - "cam", - "ng", - "pp1", - "time_counter" + "cooperative", + "binding", + "receptor", + "ligand", + "competitor" ], "category": "signaling", - "origin": "published", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "path": "Published/Ordyan2020/CaMKIIholo/CaMKII_holo.bngl", - "file": "CaMKII_holo.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/biology/cooperativebinding/cooperative-binding.bngl", + "file": "cooperative-binding.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "CaOscillate_Func", - "name": "CaOscillate_Func", - "description": "Calcium oscillations (func)", + "id": "Creamer_2012", + "name": "Creamer 2012", + "description": "Initial values", "tags": [ - "validation", - "caoscillate", - "func", - "null", - "ga", - "plc", - "ca" + "creamer", + "2012", + "egf", + "hrg", + "egfr", + "erbb2", + "erbb3", + "erbb4", + "grb2" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "tutorial", + "origin": "tutorial", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, - "gallery": [], - "path": "Tutorials/CaOscillateFunc/CaOscillate_Func.bngl", - "file": "CaOscillate_Func.bngl", + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Creamer2012/Creamer_2012.bngl", + "file": "Creamer_2012.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "CaOscillate_Sat", - "name": "CaOscillate_Sat", - "description": "Calcium oscillations (sat)", + "id": "cs_diffie_hellman", + "name": "cs diffie hellman", + "description": "Model: cs_diffie_hellman.bngl", "tags": [ - "validation", - "caoscillate", - "sat", - "null", - "ga", - "plc", - "ca" + "cs", + "diffie", + "hellman", + "agent", + "target", + "dshareda_dt", + "dsharedb_dt" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, "gallery": [ - "validation" + "cs", + "test-models" ], - "path": "Tutorials/CaOscillateSat/CaOscillate_Sat.bngl", - "file": "CaOscillate_Sat.bngl", + "path": "Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl", + "file": "cs_diffie_hellman.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "caspase-activation-loop", - "name": "caspase activation loop", - "description": "Caspase activation loop: The executioner feedback system.", + "id": "cs_hash_function", + "name": "cs hash function", + "description": "Cryptographic Hash Function in BNGL", "tags": [ - "caspase", - "activation", - "loop", - "deathligand", - "caspase8", - "caspase3", - "iap", - "flip" + "cs", + "hash", + "function", + "b0", + "b1", + "b2", + "b3", + "h0", + "h1", + "h2", + "h3" ], - "category": "signaling", + "category": "computer-science", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cell-cycle", + "cs", "test-models" ], - "path": "Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl", - "file": "caspase-activation-loop.bngl", + "path": "Examples/cs/cshashfunction/cs_hash_function.bngl", + "file": "cs_hash_function.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "catalysis", - "name": "catalysis", - "description": "Catalysis in energy BNG", + "id": "cs_huffman", + "name": "cs huffman", + "description": "Model: cs_huffman.bngl", "tags": [ - "validation", - "catalysis", - "version", - "setoption", - "s", - "kinase", - "pptase", - "atp", - "adp" + "cs", + "huffman", + "char", + "hnode", + "generate_network", + "simulate" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -2568,63 +2331,67 @@ ] }, "gallery": [ - "validation" + "cs", + "test-models" ], - "path": "Tutorials/catalysis/catalysis.bngl", - "file": "catalysis.bngl", + "path": "Examples/cs/cshuffman/cs_huffman.bngl", + "file": "cs_huffman.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cBNGL_simple", - "name": "cBNGL simple", - "description": "A simplified signal transduction model including the following processes:", + "id": "cs_monte_carlo_pi", + "name": "cs monte carlo pi", + "description": "Model: cs_monte_carlo_pi.bngl", "tags": [ - "cbngl", - "simple", - "l", - "r", - "tf", - "dna", - "mrna", - "p" + "cs", + "monte", + "carlo", + "pi", + "trial", + "pi_estimate", + "generate_network", + "simulate" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "computer-science", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "cs", + "test-models" ], - "path": "Tutorials/NativeTutorials/cBNGLsimple/cBNGL_simple.bngl", - "file": "cBNGL_simple.bngl", + "path": "Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl", + "file": "cs_monte_carlo_pi.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cd40-signaling", - "name": "cd40 signaling", - "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", + "id": "cs_pagerank", + "name": "cs pagerank", + "description": "Model: cs_pagerank.bngl", "tags": [ - "cd40", - "signaling", - "cd40l", - "traf", - "ikk", - "nik", - "nfkb", - "relb" + "cs", + "pagerank", + "teleport", + "page" ], - "category": "signaling", + "category": "computer-science", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2636,31 +2403,33 @@ ] }, "gallery": [ - "immunology", + "cs", "test-models" ], - "path": "Examples/biology/cd40signaling/cd40-signaling.bngl", - "file": "cd40-signaling.bngl", + "path": "Examples/cs/cspagerank/cs_pagerank.bngl", + "file": "cs_pagerank.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cell-cycle-checkpoint", - "name": "cell cycle checkpoint", - "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", + "id": "cs_pid_controller", + "name": "cs pid controller", + "description": "PID Controller in BNGL", "tags": [ - "cell", - "cycle", - "checkpoint", - "cyclin", - "cdk", - "cdc25", - "wee1", - "apc", - "p21" + "cs", + "pid", + "controller", + "sensor", + "accumulator", + "leakyerror", + "actuator", + "disturbance" ], - "category": "signaling", + "category": "computer-science", "origin": "ai-generated", "visible": false, "compatibility": { @@ -2672,68 +2441,70 @@ ] }, "gallery": [ - "cell-cycle", + "cs", "test-models" ], - "path": "Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl", - "file": "cell-cycle-checkpoint.bngl", + "path": "Examples/cs/cspidcontroller/cs_pid_controller.bngl", + "file": "cs_pid_controller.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Chattaraj_2021", - "name": "Chattaraj 2021", - "description": "NFkB oscillations", + "id": "cs_regex_nfa", + "name": "cs regex nfa", + "description": "Model: cs_regex_nfa.bngl", "tags": [ - "published", - "chattaraj", - "2021", - "nephrin", - "nck", - "nwasp", - "writexml" + "cs", + "regex", + "nfa", + "state", + "char", + "generate_network", + "simulate", + "setparameter" ], - "category": "signaling", - "origin": "published", + "category": "computer-science", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ - "neuroscience" + "cs", + "test-models" ], - "path": "Published/Chattaraj2021/Chattaraj_2021.bngl", - "file": "Chattaraj_2021.bngl", + "path": "Examples/cs/csregexnfa/cs_regex_nfa.bngl", + "file": "cs_regex_nfa.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "check_scaling", - "name": "Hlavacek2018Restructuration", - "description": "BNGL model: after_bunching", + "id": "Dembo_blbr_1978", + "name": "Dembo et al. 1978: Bivalent Ligand Bivalent Receptor (BLBR) Model", + "description": "BLBR dembo 1978", "tags": [ - "na", - "vecf", - "egftot", - "egfrtot", - "kd", - "kr", - "kpx", - "kmx", - "kp", - "kdp", - "molecules" + "blbr", + "ligand-receptor", + "binding", + "1978", + "dembo" ], - "category": "other", + "category": "physics", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -2742,35 +2513,37 @@ "ode" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Restructuration/check_scaling.bngl", - "file": "check_scaling.bngl", + "gallery": [ + "physics" + ], + "path": "Published/Dembo1978/blbr_dembo1978.bngl", + "file": "blbr_dembo1978.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "checkpoint-kinase-signaling", - "name": "checkpoint kinase signaling", - "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", + "id": "dna-damage-repair", + "name": "dna damage repair", + "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", "tags": [ - "checkpoint", - "kinase", - "signaling", "dna", + "damage", + "repair", + "mrn", "atm", - "atr", - "chk1", "chk2", - "p53", - "cdc25" + "repaircomplex" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -2780,35 +2553,32 @@ "cancer", "test-models" ], - "path": "Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl", - "file": "checkpoint-kinase-signaling.bngl", + "path": "Examples/biology/dnadamagerepair/dna-damage-repair.bngl", + "file": "dna-damage-repair.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Cheemalavagu_JAK_STAT", - "name": "Cheemalavagu 2024", - "description": "JAK-STAT signaling", + "id": "dna-methylation-dynamics", + "name": "dna methylation dynamics", + "description": "DNA Methylation: Maintenance and de novo dynamics.", "tags": [ - "published", - "literature", - "signaling", - "cheemalavagu", - "jak", - "stat", - "l1", - "il6r", - "gp130", - "l2", - "il10r1", - "il10r2", - "jak1", - "jak2" + "dna", + "methylation", + "dynamics", + "cpg", + "dnmt1", + "tet", + "v_maint", + "v_erase" ], - "category": "other", - "origin": "published", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -2818,30 +2588,29 @@ ] }, "gallery": [ - "immunology" + "test-models" ], - "path": "Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT.bngl", - "file": "Cheemalavagu_JAK_STAT.bngl", + "path": "Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl", + "file": "dna-methylation-dynamics.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "chemistry", - "name": "chemistry", - "description": "Basic chemical reactions", + "id": "Dolan_Insulin_2015_Dolan_2015", + "name": "Dolan et al. 2015: Insulin Receptor Signaling Model (Dolan_2015)", + "description": "Insulin signaling", "tags": [ - "published", - "tutorials", - "chemistry", - "a", - "b", - "c", - "d", - "e" + "insulin", + "metabolism", + "2015", + "dolan" ], - "category": "tutorial", - "origin": "tutorial", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": false, @@ -2852,143 +2621,136 @@ ] }, "gallery": [ - "tutorials" + "metabolism" ], - "path": "Tutorials/General/chemistry/chemistry.bngl", - "file": "chemistry.bngl", + "path": "Published/Dolan2015/Dolan_2015.bngl", + "file": "Dolan_2015.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "chemotaxis-signal-transduction", - "name": "chemotaxis signal transduction", - "description": "Bacterial Chemotaxis: Adaptation through methylation.", + "id": "Dolan_Insulin_2015_Dolan2015", + "name": "Dolan et al. 2015: Insulin Receptor Signaling Model (Dolan2015)", + "description": "Insulin signaling", "tags": [ - "chemotaxis", - "signal", - "transduction", - "attr", - "mcp", - "chea", - "chey", - "cheb", - "motor" - ], - "category": "signaling", - "origin": "ai-generated", + "insulin", + "metabolism", + "2015", + "dolan" + ], + "category": "other", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "metabolism" ], - "path": "Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl", - "file": "chemotaxis-signal-transduction.bngl", + "path": "Published/Dolan2015/Dolan2015.bngl", + "file": "Dolan2015.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Chylek_library", - "name": "Chylek library", - "description": "Created by BioNetGen 2.2.6", + "id": "dr5-apoptosis-signaling", + "name": "dr5 apoptosis signaling", + "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", "tags": [ - "chylek", - "library", - "kflatplcg", - "kfgrb2gab2", - "kflcp2plcg1", - "kd1", - "kd2", - "sink", - "pre", - "pag1" + "dr5", + "apoptosis", + "signaling", + "trail", + "fadd", + "caspase8", + "flip", + "death_signal" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "cell-cycle", + "test-models" ], - "path": "Tutorials/NativeTutorials/Chyleklibrary/Chylek_library.bngl", - "file": "Chylek_library.bngl", + "path": "Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl", + "file": "dr5-apoptosis-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ChylekFceRI_2014", - "name": "Chylek 2014 (FceRI)", - "description": "FceRI signaling", + "id": "Dreisigmeyer_LacOperon_2008", + "name": "Dreisigmeyer et al. 2008: Lac Operon Regulation Model", + "description": "Lac operon", "tags": [ - "published", - "immunology", - "chylekfceri", - "2014", - "lig", - "rec", - "lyn", - "fyn", - "syk", - "pag1", - "csk", - "lat" + "lac-operon", + "gene-expression", + "bacterial-regulation", + "2008", + "dreisigmeyer" ], - "category": "immunology", + "category": "gene-expression", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology" + "gene-expression" ], - "path": "Published/ChylekFceRI2014/ChylekFceRI_2014.bngl", - "file": "ChylekFceRI_2014.bngl", + "path": "Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl", + "file": "lac_operon_dreisigmeyer2008.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ChylekTCR_2014", - "name": "Chylek 2014 (TCR)", - "description": "TCR signaling", + "id": "dual-site-phosphorylation", + "name": "dual site phosphorylation", + "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", "tags": [ - "published", - "immunology", - "chylektcr", - "2014", - "lig1", - "lig2", - "lig3", - "tcr", - "cd28", - "lck", - "itk", - "zap70" + "dual", + "site", + "phosphorylation", + "kinase", + "phosphatase", + "substrate" ], - "category": "immunology", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -2999,97 +2761,99 @@ ] }, "gallery": [ - "immunology" + "test-models" ], - "path": "Published/ChylekTCR2014/ChylekTCR_2014.bngl", - "file": "ChylekTCR_2014.bngl", + "path": "Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl", + "file": "dual-site-phosphorylation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "circadian-oscillator", - "name": "circadian oscillator", - "description": "title: Vilar Circadian Oscillator Model", + "id": "Dushek_TCR_2011", + "name": "Dushek et al. 2011: T Cell Receptor Kinase Kinase Cascade", + "description": "TCR signaling", "tags": [ - "circadian", - "oscillator", - "a", - "r", - "pa", - "pr", - "mrna_a", - "mrna_r" + "tcr", + "phosphorylation", + "immune-signaling", + "2011", + "dushek" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "immunology" ], - "path": "Examples/biology/circadianoscillator/circadian-oscillator.bngl", - "file": "circadian-oscillator.bngl", + "path": "Published/Dushek2011/Dushek_2011.bngl", + "file": "Dushek_2011.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "CircadianOscillator", - "name": "CircadianOscillator", - "description": "Circadian rhythm", + "id": "Dushek_TCR_2014", + "name": "Dushek et al. 2014: T Cell Receptor Phosphorylation Feedback", + "description": "TCR signaling dynamics", "tags": [ - "published", - "tutorial", - "native", - "circadianoscillator", - "a", - "r", - "pa", - "pr", - "mrna_a", - "mrna_r" + "tcr", + "feedback-loop", + "immune-signaling", + "2014", + "dushek" ], - "category": "tutorial", - "origin": "tutorial", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "cell-cycle", - "native-tutorials" + "immunology" ], - "path": "Tutorials/NativeTutorials/CircadianOscillator/CircadianOscillator.bngl", - "file": "CircadianOscillator.bngl", + "path": "Published/Dushek2014/Dushek_2014.bngl", + "file": "Dushek_2014.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "clock-bmal1-gene-circuit", - "name": "clock bmal1 gene circuit", - "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", + "id": "e2f-rb-cell-cycle-switch", + "name": "e2f rb cell cycle switch", + "description": "E2F/Rb Switch: The G1/S transition gate.", "tags": [ - "clock", - "bmal1", - "gene", - "circuit", - "ror", - "reverb", - "dna" + "e2f", + "rb", + "cell", + "cycle", + "switch", + "mitogen", + "cycd", + "cyce", + "p27" ], "category": "signaling", "origin": "ai-generated", @@ -3106,24 +2870,26 @@ "cell-cycle", "test-models" ], - "path": "Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl", - "file": "clock-bmal1-gene-circuit.bngl", + "path": "Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl", + "file": "e2f-rb-cell-cycle-switch.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_endocytosis", - "name": "compartment endocytosis", - "description": "Model: compartment_endocytosis.bngl", + "id": "eco_coevolution_host_parasite", + "name": "eco coevolution host parasite", + "description": "Model: eco_coevolution_host_parasite.bngl", "tags": [ - "compartment", - "endocytosis", - "l", - "r", - "t" + "eco", + "coevolution", + "host", + "parasite" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3135,28 +2901,35 @@ ] }, "gallery": [ + "ecology", "test-models" ], - "path": "Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl", - "file": "compartment_endocytosis.bngl", + "path": "Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl", + "file": "eco_coevolution_host_parasite.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_membrane_bound", - "name": "compartment membrane bound", - "description": "Model: compartment_membrane_bound.bngl", + "id": "eco_food_web_chaos_3sp", + "name": "eco food web chaos 3sp", + "description": "Model: eco_food_web_chaos_3sp.bngl", "tags": [ - "compartment", - "membrane", - "bound", + "eco", + "food", + "web", + "chaos", + "3sp", + "r", + "c", "p", - "lipid", - "generate_network", - "simulate" + "k_eat_r", + "k_eat_c" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3164,31 +2937,35 @@ "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ + "ecology", "test-models" ], - "path": "Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl", - "file": "compartment_membrane_bound.bngl", + "path": "Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl", + "file": "eco_food_web_chaos_3sp.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_nested_transport", - "name": "compartment nested transport", - "description": "Model: compartment_nested_transport.bngl", + "id": "eco_lotka_volterra_grid", + "name": "eco lotka volterra grid", + "description": "Model: eco_lotka_volterra_grid.bngl", "tags": [ - "compartment", - "nested", - "transport", - "s", - "generate_network", - "simulate" + "eco", + "lotka", + "volterra", + "grid", + "prey", + "pred" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3200,27 +2977,30 @@ ] }, "gallery": [ + "ecology", "test-models" ], - "path": "Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl", - "file": "compartment_nested_transport.bngl", + "path": "Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl", + "file": "eco_lotka_volterra_grid.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_nuclear_transport", - "name": "compartment nuclear transport", - "description": "Model: compartment_nuclear_transport.bngl", + "id": "eco_mutualism_obligate", + "name": "eco mutualism obligate", + "description": "Model: eco_mutualism_obligate.bngl", "tags": [ - "compartment", - "nuclear", - "transport", - "tf", - "generate_network", - "simulate" + "eco", + "mutualism", + "obligate", + "a", + "b" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3228,31 +3008,36 @@ "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ + "ecology", "test-models" ], - "path": "Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl", - "file": "compartment_nuclear_transport.bngl", + "path": "Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl", + "file": "eco_mutualism_obligate.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "compartment_organelle_exchange", - "name": "compartment organelle exchange", - "description": "Model: compartment_organelle_exchange.bngl", + "id": "eco_rock_paper_scissors_spatial", + "name": "eco rock paper scissors spatial", + "description": "Model: eco_rock_paper_scissors_spatial.bngl", "tags": [ - "compartment", - "organelle", - "exchange", - "cargo", - "generate_network", - "simulate" + "eco", + "rock", + "paper", + "scissors", + "spatial", + "s", + "generate_network" ], - "category": "other", + "category": "ecology", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3264,103 +3049,138 @@ ] }, "gallery": [ + "ecology", "test-models" ], - "path": "Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl", - "file": "compartment_organelle_exchange.bngl", + "path": "Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl", + "file": "eco_rock_paper_scissors_spatial.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "competitive-enzyme-inhibition", - "name": "competitive enzyme inhibition", - "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", + "id": "egfr_net", + "name": "egfr_net", + "description": "check detailed balanced", "tags": [ - "competitive", - "enzyme", - "inhibition", - "substrate1", - "substrate2", - "inhibitor", - "product" + "egfr", + "net", + "egf", + "shc", + "grb2", + "sos" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/egfrnet/egfr_net.bngl", + "file": "egfr_net.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "egfr_net_red", + "name": "egfr_net_red", + "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", + "tags": [ + "egfr", + "net", + "red", + "egf", + "grb2", + "shc", + "sos" + ], + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism", - "test-models" + "validation" ], - "path": "Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl", - "file": "competitive-enzyme-inhibition.bngl", + "path": "Tutorials/egfrnetred/egfr_net_red.bngl", + "file": "egfr_net_red.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "complement-activation-cascade", - "name": "complement activation cascade", - "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", + "id": "egfr_path", + "name": "egfr_path", + "description": "The primary focus of the model developed by Kholodenko", "tags": [ - "complement", - "activation", - "cascade", - "c3", - "fb", - "c5", - "mac", - "surf" + "egfr", + "path", + "setconcentration" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", - "test-models" + "validation" ], - "path": "Examples/biology/complementactivationcascade/complement-activation-cascade.bngl", - "file": "complement-activation-cascade.bngl", + "path": "Tutorials/egfrpath/egfr_path.bngl", + "file": "egfr_path.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ComplexDegradation", - "name": "ComplexDegradation", - "description": "Degradation model", + "id": "egfr_simple", + "name": "egfr simple", + "description": "This is a demo model of EGFR signaling.", "tags": [ - "published", - "tutorial", - "native", - "complexdegradation", - "a", - "b", - "c", - "generate_network" + "egfr", + "simple", + "egf", + "grb2", + "sos1" ], "category": "tutorial", "origin": "tutorial", - "visible": false, + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -3369,62 +3189,68 @@ "gallery": [ "native-tutorials" ], - "path": "Tutorials/NativeTutorials/ComplexDegradation/ComplexDegradation.bngl", - "file": "ComplexDegradation.bngl", + "path": "Tutorials/NativeTutorials/egfrsimple/egfr_simple.bngl", + "file": "egfr_simple.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "contact-inhibition-hippo-yap", - "name": "contact inhibition hippo yap", - "description": "Hippo Pathway: Contact inhibition and YAP regulation.", + "id": "egfr-signaling-pathway", + "name": "egfr signaling pathway", + "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", "tags": [ - "contact", - "inhibition", - "hippo", - "yap", - "mst", - "lats", - "tead" + "egfr", + "signaling", + "pathway", + "egf", + "grb2", + "shc" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ + "cancer", "test-models" ], - "path": "Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl", - "file": "contact-inhibition-hippo-yap.bngl", + "path": "Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl", + "file": "egfr-signaling-pathway.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "continue", - "name": "continue", - "description": "Test trajectory continuation", + "id": "eif2a-stress-response", + "name": "eif2a stress response", + "description": "Integrated Stress Response: eIF2alpha and the translational gate.", "tags": [ - "validation", - "continue", - "a", - "b", - "c", - "trash" + "eif2a", + "stress", + "response", + "eif2b", + "perk", + "gadd34" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -3432,31 +3258,37 @@ ] }, "gallery": [ - "validation" + "test-models" ], - "path": "Tutorials/continue/continue.bngl", - "file": "continue.bngl", + "path": "Examples/biology/eif2astressresponse/eif2a-stress-response.bngl", + "file": "eif2a-stress-response.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cooperative-binding", - "name": "cooperative binding", - "description": "Cooperative binding: The binding of the first ligand molecule increases", + "id": "endosomal-sorting-rab", + "name": "endosomal sorting rab", + "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", "tags": [ - "cooperative", - "binding", - "receptor", - "ligand", - "competitor" + "endosomal", + "sorting", + "rab", + "rab5", + "rab7", + "effector", + "v_gef", + "v_gap_drive" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" @@ -3465,62 +3297,62 @@ "gallery": [ "test-models" ], - "path": "Examples/biology/cooperativebinding/cooperative-binding.bngl", - "file": "cooperative-binding.bngl", + "path": "Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl", + "file": "endosomal-sorting-rab.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Creamer_2012", - "name": "Creamer 2012", - "description": "Initial values", + "id": "energy_allostery_mwc", + "name": "energy allostery mwc", + "description": "Model: energy_allostery_mwc.bngl", "tags": [ - "creamer", - "2012", - "egf", - "hrg", - "egfr", - "erbb2", - "erbb3", - "erbb4", - "p52shc1", - "grb2" + "energy", + "allostery", + "mwc", + "p", + "l" ], - "category": "tutorial", - "origin": "tutorial", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "test-models" ], - "path": "Tutorials/NativeTutorials/Creamer2012/Creamer_2012.bngl", - "file": "Creamer_2012.bngl", + "path": "Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl", + "file": "energy_allostery_mwc.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_diffie_hellman", - "name": "cs diffie hellman", - "description": "Model: cs_diffie_hellman.bngl", + "id": "energy_catalysis_mm", + "name": "energy catalysis mm", + "description": "Model: energy_catalysis_mm.bngl", "tags": [ - "cs", - "diffie", - "hellman", - "agent", - "target", - "dshareda_dt", - "dsharedb_dt" + "energy", + "catalysis", + "mm", + "e", + "s", + "p" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3532,68 +3364,62 @@ ] }, "gallery": [ - "cs", "test-models" ], - "path": "Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl", - "file": "cs_diffie_hellman.bngl", + "path": "Examples/energy/energycatalysismm/energy_catalysis_mm.bngl", + "file": "energy_catalysis_mm.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_hash_function", - "name": "cs hash function", - "description": "Cryptographic Hash Function in BNGL", + "id": "energy_cooperativity_adh", + "name": "energy cooperativity adh", + "description": "Model: energy_cooperativity_adh.bngl", "tags": [ - "cs", - "hash", - "function", - "b0", - "b1", - "b2", - "b3", - "h0", - "h1", - "h2", - "h3" + "energy", + "cooperativity", + "adh", + "r", + "l" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cs", "test-models" ], - "path": "Examples/cs/cshashfunction/cs_hash_function.bngl", - "file": "cs_hash_function.bngl", + "path": "Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl", + "file": "energy_cooperativity_adh.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_huffman", - "name": "cs huffman", - "description": "Model: cs_huffman.bngl", + "id": "energy_example1", + "name": "energy_example1", + "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", "tags": [ - "cs", - "huffman", - "char", - "hnode", - "generate_network", - "simulate" + "energy", + "example1" ], - "category": "computer-science", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -3603,30 +3429,29 @@ ] }, "gallery": [ - "cs", - "test-models" + "validation" ], - "path": "Examples/cs/cshuffman/cs_huffman.bngl", - "file": "cs_huffman.bngl", + "path": "Tutorials/energyexample1/energy_example1.bngl", + "file": "energy_example1.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_monte_carlo_pi", - "name": "cs monte carlo pi", - "description": "Model: cs_monte_carlo_pi.bngl", + "id": "energy_linear_chain", + "name": "energy linear chain", + "description": "Model: energy_linear_chain.bngl", "tags": [ - "cs", - "monte", - "carlo", - "pi", - "trial", - "pi_estimate", - "generate_network", - "simulate" + "energy", + "linear", + "chain", + "m", + "generate_network" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3638,26 +3463,32 @@ ] }, "gallery": [ - "cs", "test-models" ], - "path": "Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl", - "file": "cs_monte_carlo_pi.bngl", + "path": "Examples/energy/energylinearchain/energy_linear_chain.bngl", + "file": "energy_linear_chain.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_pagerank", - "name": "cs pagerank", - "description": "Model: cs_pagerank.bngl", + "id": "energy_transport_pump", + "name": "energy transport pump", + "description": "Model: energy_transport_pump.bngl", "tags": [ - "cs", - "pagerank", - "teleport", - "page" + "energy", + "transport", + "pump", + "a", + "atp", + "adp", + "pi", + "t" ], - "category": "computer-science", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3669,30 +3500,31 @@ ] }, "gallery": [ - "cs", "test-models" ], - "path": "Examples/cs/cspagerank/cs_pagerank.bngl", - "file": "cs_pagerank.bngl", + "path": "Examples/energy/energytransportpump/energy_transport_pump.bngl", + "file": "energy_transport_pump.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "cs_pid_controller", - "name": "cs pid controller", - "description": "PID Controller in BNGL", + "id": "er-stress-response", + "name": "er stress response", + "description": "Rate Constants", "tags": [ - "cs", - "pid", - "controller", - "sensor", - "accumulator", - "leakyerror", - "actuator", - "disturbance" + "er", + "stress", + "response", + "unfoldedprotein", + "perk", + "eif2a", + "chaperone" ], - "category": "computer-science", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { @@ -3704,67 +3536,65 @@ ] }, "gallery": [ - "cs", "test-models" ], - "path": "Examples/cs/cspidcontroller/cs_pid_controller.bngl", - "file": "cs_pid_controller.bngl", + "path": "Examples/biology/erstressresponse/er-stress-response.bngl", + "file": "er-stress-response.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "cs_regex_nfa", - "name": "cs regex nfa", - "description": "Model: cs_regex_nfa.bngl", + "id": "Erdem_InsR_2021", + "name": "Erdem et al. 2021: Insulin Receptor Internalization Model", + "description": "InsR/IGF1R signaling", "tags": [ - "cs", - "regex", - "nfa", - "state", - "char", - "generate_network", - "simulate", - "setparameter" + "insulin", + "receptor-internalization", + "2021", + "erdem" ], - "category": "computer-science", - "origin": "ai-generated", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "cs", - "test-models" + "metabolism" ], - "path": "Examples/cs/csregexnfa/cs_regex_nfa.bngl", - "file": "cs_regex_nfa.bngl", + "path": "Published/Erdem2021/Erdem_2021.bngl", + "file": "Erdem_2021.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Dallas", - "name": "Dallas", - "description": "- This model is intended to be consistent with the compartmental model", + "id": "erk-nuclear-translocation", + "name": "erk nuclear translocation", + "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", "tags": [ - "dallas", - "counter", - "fdcs", - "s", - "sv", - "e", - "a", - "i", - "v" + "erk", + "nuclear", + "translocation", + "mek", + "elk1", + "dusp", + "transcription_signal" ], - "category": "epidemiology", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -3775,36 +3605,29 @@ ] }, "gallery": [ - "epidemiology" + "test-models" ], - "path": "Published/VaxAndVariants/Dallas/Dallas.bngl", - "file": "Dallas.bngl", + "path": "Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl", + "file": "erk-nuclear-translocation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "degranulation_model", - "name": "PyBNG: Degranulation model", - "description": "Degranulation model", + "id": "example1", + "name": "example1", + "description": "Example file for BNG2 tutorial.", "tags": [ - "published", - "pybng", - "degranulation", - "model", - "ag", - "r", - "syk", - "ship1", - "x", - "pip3", - "h" + "example1" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -3812,27 +3635,33 @@ ] }, "gallery": [ - "immunology" + "validation" ], - "path": "Published/PyBioNetGen/core/degranulationmodel/degranulation_model.bngl", - "file": "degranulation_model.bngl", + "path": "Tutorials/example1/example1.bngl", + "file": "example1.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Dembo_1978", - "name": "Dembo 1978", - "description": "BLBR dembo 1978", + "id": "Faeder_egfr_2009", + "name": "Faeder 2009", + "description": "EGFR signaling", "tags": [ - "published", - "physics", - "dembo", - "1978" + "based", + "egf", + "egfr", + "rule", + "rulebasedegfrtutorial", + "shc", + "signaling" ], - "category": "physics", + "category": "signaling", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -3842,177 +3671,170 @@ ] }, "gallery": [ - "physics" + "cancer" ], - "path": "Published/Dembo1978/blbr_dembo1978.bngl", - "file": "blbr_dembo1978.bngl", + "path": "Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl", + "file": "Rule_based_egfr_tutorial.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "dna-damage-repair", - "name": "dna damage repair", - "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", + "id": "Faeder_egfr_compart_2009", + "name": "Faeder et al. 2009: Compartmental Rule-Based EGFR model", + "description": "Compartmental EGFR model", "tags": [ - "dna", - "damage", - "repair", - "mrn", - "atm", - "chk2", - "repaircomplex" + "egfr", + "compartments", + "receptor-trafficking", + "signaling", + "2009", + "faeder" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer", - "test-models" + "signaling" ], - "path": "Examples/biology/dnadamagerepair/dna-damage-repair.bngl", - "file": "dna-damage-repair.bngl", + "path": "Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl", + "file": "Rule_based_egfr_compart.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "dna-methylation-dynamics", - "name": "dna methylation dynamics", - "description": "DNA Methylation: Maintenance and de novo dynamics.", + "id": "Faeder_FceRI_2003_Faeder_2003", + "name": "Faeder et al. 2003: FceRI Signaling Model (Faeder_2003)", + "description": "FceRI signaling", "tags": [ - "dna", - "methylation", - "dynamics", - "cpg", - "dnmt1", - "tet", - "v_maint", - "v_erase" + "fceri", + "immune-signaling", + "mast-cell", + "2003", + "faeder" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "immunology", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "immunology" ], - "path": "Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl", - "file": "dna-methylation-dynamics.bngl", + "path": "Published/Faeder2003/Faeder_2003.bngl", + "file": "Faeder_2003.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Dolan_2015", - "name": "Dolan 2015", - "description": "Insulin signaling", + "id": "Faeder_FceRI_2003_fceri_ji", + "name": "Faeder et al. 2003: FceRI Signaling Model (fceri_ji)", + "description": "FceRI signaling", "tags": [ - "published", - "literature", - "signaling", - "dolan", - "2015", - "time", - "t", - "p", - "e", - "ir", - "d", - "p53_mrna", - "p53" + "fceri", + "immune-signaling", + "mast-cell", + "2003", + "faeder" ], - "category": "other", + "category": "immunology", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism" + "immunology" ], - "path": "Published/Dolan2015/Dolan_2015.bngl", - "file": "Dolan_2015.bngl", + "path": "Published/Faeder2003/fceri_ji.bngl", + "file": "fceri_ji.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Dolan2015", - "name": "Dolan 2015", - "description": "Insulin signaling", + "id": "Faeder_FceRI_Fyn_2003", + "name": "Faeder et al. 2003: FceRI Signaling with Fyn Kinase Regulation", + "description": "FceRI signaling", "tags": [ - "published", - "literature", - "signaling", - "dolan", - "2015", - "time", - "t", - "p", - "e", - "ir", - "d", - "p53_mrna", - "p53" + "fceri", + "fyn-kinase", + "mast-cell", + "immune-signaling", + "2003", + "faeder" ], - "category": "other", + "category": "immunology", "origin": "published", "visible": false, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "metabolism" + "immunology" ], - "path": "Published/Dolan2015/Dolan2015.bngl", - "file": "Dolan2015.bngl", + "path": "Published/fcerifyn/fceri_fyn.bngl", + "file": "fceri_fyn.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "dr5-apoptosis-signaling", - "name": "dr5 apoptosis signaling", - "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", + "id": "FceRI_ji", + "name": "FceRI ji", + "description": "title: FceRI_ji.bngl", "tags": [ - "dr5", - "apoptosis", - "signaling", - "trail", - "fadd", - "caspase8", - "flip", - "death_signal" + "fceri", + "ji", + "lig", + "lyn", + "syk", + "rec" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -4022,30 +3844,35 @@ ] }, "gallery": [ - "cell-cycle", - "test-models" + "native-tutorials" ], - "path": "Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl", - "file": "dr5-apoptosis-signaling.bngl", + "path": "Tutorials/NativeTutorials/FceRIji/FceRI_ji.bngl", + "file": "FceRI_ji.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Dreisigmeyer_2008", - "name": "Dreisigmeyer 2008", - "description": "Lac operon", + "id": "fceri_ji_comp", + "name": "fceri_ji_comp", + "description": "Ligand-receptor binding", "tags": [ - "published", - "gene-expression", - "dreisigmeyer", - "2008" + "fceri", + "ji", + "comp", + "lig", + "lyn", + "syk", + "rec" ], - "category": "gene-expression", - "origin": "published", - "visible": true, + "category": "validation", + "origin": "test-case", + "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -4053,58 +3880,70 @@ ] }, "gallery": [ - "gene-expression" + "validation" ], - "path": "Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl", - "file": "lac_operon_dreisigmeyer2008.bngl", + "path": "Tutorials/fcerijicomp/fceri_ji_comp.bngl", + "file": "fceri_ji_comp.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "dual-site-phosphorylation", - "name": "dual site phosphorylation", - "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", + "id": "FceRI_viz", + "name": "FceRI Viz", + "description": "FcεRI (viz)", "tags": [ - "dual", - "site", - "phosphorylation", - "kinase", - "phosphatase", - "substrate" + "fceri", + "fcr", + "ige", + "lat", + "lyn", + "syk", + "pb", + "pg", + "sykp" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "native-tutorials" ], - "path": "Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl", - "file": "dual-site-phosphorylation.bngl", + "path": "Tutorials/NativeTutorials/FceRIviz/FceRI_viz.bngl", + "file": "FceRI_viz.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Dushek_2011", - "name": "Dushek 2011", - "description": "TCR signaling", + "id": "feature_functional_rates_volume", + "name": "feature functional rates volume", + "description": "Model: feature_functional_rates_volume.bngl", "tags": [ - "published", - "dushek", - "2011", - "s" + "feature", + "functional", + "rates", + "volume", + "a", + "b", + "c" ], - "category": "signaling", - "origin": "published", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -4115,62 +3954,69 @@ ] }, "gallery": [ - "immunology" + "test-models" ], - "path": "Published/Dushek2011/Dushek_2011.bngl", - "file": "Dushek_2011.bngl", + "path": "Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl", + "file": "feature_functional_rates_volume.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Dushek_2014", - "name": "Dushek 2014", - "description": "TCR signaling dynamics", - "tags": [ - "published", - "dushek", - "2014", - "e", - "f", - "b" + "id": "feature_global_functions_scan", + "name": "feature global functions scan", + "description": "Model: feature_global_functions_scan.bngl", + "tags": [ + "feature", + "global", + "functions", + "scan", + "signal", + "response", + "stimulus" ], - "category": "signaling", - "origin": "published", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology" + "test-models" ], - "path": "Published/Dushek2014/Dushek_2014.bngl", - "file": "Dushek_2014.bngl", + "path": "Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl", + "file": "feature_global_functions_scan.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "e2f-rb-cell-cycle-switch", - "name": "e2f rb cell cycle switch", - "description": "E2F/Rb Switch: The G1/S transition gate.", + "id": "feature_local_functions_explicit", + "name": "feature local functions explicit", + "description": "Model: feature_local_functions_explicit.bngl", "tags": [ - "e2f", - "rb", - "cell", - "cycle", - "switch", - "mitogen", - "cycd", - "cyce", - "p27" + "feature", + "local", + "functions", + "explicit", + "s", + "p", + "e", + "mm_rate", + "ratelaw" ], - "category": "signaling", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -4178,30 +4024,35 @@ "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ - "cell-cycle", "test-models" ], - "path": "Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl", - "file": "e2f-rb-cell-cycle-switch.bngl", + "path": "Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl", + "file": "feature_local_functions_explicit.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_coevolution_host_parasite", - "name": "eco coevolution host parasite", - "description": "Model: eco_coevolution_host_parasite.bngl", + "id": "feature_symmetry_factors_cyclic", + "name": "feature symmetry factors cyclic", + "description": "Model: feature_symmetry_factors_cyclic.bngl", "tags": [ - "eco", - "coevolution", - "host", - "parasite" + "feature", + "symmetry", + "factors", + "cyclic", + "x", + "generate_network", + "simulate" ], - "category": "ecology", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -4213,32 +4064,31 @@ ] }, "gallery": [ - "ecology", "test-models" ], - "path": "Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl", - "file": "eco_coevolution_host_parasite.bngl", + "path": "Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl", + "file": "feature_symmetry_factors_cyclic.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_food_web_chaos_3sp", - "name": "eco food web chaos 3sp", - "description": "Model: eco_food_web_chaos_3sp.bngl", + "id": "feature_synthesis_degradation_ss", + "name": "feature synthesis degradation ss", + "description": "Model: feature_synthesis_degradation_ss.bngl", "tags": [ - "eco", - "food", - "web", - "chaos", - "3sp", - "r", - "c", - "p", - "k_eat_r", - "k_eat_c" + "feature", + "synthesis", + "degradation", + "ss", + "m", + "generate_network", + "simulate" ], - "category": "ecology", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -4246,32 +4096,36 @@ "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "ecology", "test-models" ], - "path": "Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl", - "file": "eco_food_web_chaos_3sp.bngl", + "path": "Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl", + "file": "feature_synthesis_degradation_ss.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_lotka_volterra_grid", - "name": "eco lotka volterra grid", - "description": "Model: eco_lotka_volterra_grid.bngl", + "id": "fgf-signaling-pathway", + "name": "fgf signaling pathway", + "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", "tags": [ - "eco", - "lotka", - "volterra", - "grid", - "prey", - "pred" + "fgf", + "signaling", + "pathway", + "fgfr", + "frs2", + "spry", + "rasgef", + "internalized_rec" ], - "category": "ecology", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { @@ -4283,61 +4137,66 @@ ] }, "gallery": [ - "ecology", + "developmental", "test-models" ], - "path": "Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl", - "file": "eco_lotka_volterra_grid.bngl", + "path": "Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl", + "file": "fgf-signaling-pathway.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_mutualism_obligate", - "name": "eco mutualism obligate", - "description": "Model: eco_mutualism_obligate.bngl", + "id": "Gardner_Toggle_2000", + "name": "Gardner et al. 2000: Synthetic Gene Toggle Switch", + "description": "Genetic toggle switch", "tags": [ - "eco", - "mutualism", - "obligate", - "a", - "b" + "toggle-switch", + "synthetic-biology", + "gene-regulation", + "2000", + "gardner" ], - "category": "ecology", - "origin": "ai-generated", - "visible": false, + "category": "synthetic-biology", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "ecology", - "test-models" + "synthetic-biology" ], - "path": "Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl", - "file": "eco_mutualism_obligate.bngl", + "path": "Published/Gardner2000/genetic_switch_gardner2000.bngl", + "file": "genetic_switch_gardner2000.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eco_rock_paper_scissors_spatial", - "name": "eco rock paper scissors spatial", - "description": "Model: eco_rock_paper_scissors_spatial.bngl", + "id": "gas6-axl-signaling", + "name": "gas6 axl signaling", + "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", "tags": [ - "eco", - "rock", - "paper", - "scissors", - "spatial", - "s", - "generate_network" + "gas6", + "axl", + "signaling", + "pi3k", + "akt", + "socs", + "survival_burst" ], - "category": "ecology", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { @@ -4349,49 +4208,66 @@ ] }, "gallery": [ - "ecology", "test-models" ], - "path": "Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl", - "file": "eco_rock_paper_scissors_spatial.bngl", + "path": "Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl", + "file": "gas6-axl-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr", - "name": "02-egfr", - "description": "EGFR model", + "id": "gene-expression-toggle", + "name": "gene expression toggle", + "description": "Kinetic Parameters", "tags": [ - "signaling" + "gene", + "expression", + "toggle", + "mrna", + "protein" ], "category": "signaling", - "origin": "published", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/02-egfr/egfr.bngl", - "file": "egfr.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl", + "file": "gene-expression-toggle.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr", - "name": "17-egfr-ssa", - "description": "EGFR model", + "id": "genetic_bistability_energy", + "name": "genetic bistability energy", + "description": "Model: genetic_bistability_energy.bngl", "tags": [ - "signaling" + "genetic", + "bistability", + "energy", + "genea", + "geneb", + "prota", + "protb" ], - "category": "signaling", - "origin": "published", + "category": "gene-expression", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -4401,29 +4277,36 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/17-egfr-ssa/egfr.bngl", - "file": "egfr.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl", + "file": "genetic_bistability_energy.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr", - "name": "egfr", - "description": "Blinov et al. 2006. Biosystems, 83:136", + "id": "genetic_dna_replication_stochastic", + "name": "genetic dna replication stochastic", + "description": "Model: genetic_dna_replication_stochastic.bngl", "tags": [ - "egfr", - "egf", - "grb2", - "shc", - "sos" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, + "genetic", + "dna", + "replication", + "stochastic", + "pol", + "n", + "generate_network" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -4431,23 +4314,32 @@ ] }, "gallery": [ - "other" + "test-models" ], - "path": "Published/PyBioNetGen/core/egfr/egfr.bngl", - "file": "egfr.bngl", + "path": "Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl", + "file": "genetic_dna_replication_stochastic.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_ground", - "name": "02-egfr", - "description": "EGFR model", + "id": "genetic_goodwin_oscillator", + "name": "genetic goodwin oscillator", + "description": "Model: genetic_goodwin_oscillator.bngl", "tags": [ - "signaling" + "genetic", + "goodwin", + "oscillator", + "gene", + "mrna", + "protein", + "repressor" ], - "category": "signaling", - "origin": "published", + "category": "gene-expression", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -4457,22 +4349,32 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/02-egfr/egfr_ground.bngl", - "file": "egfr_ground.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl", + "file": "genetic_goodwin_oscillator.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_ground", - "name": "17-egfr-ssa", - "description": "EGFR model", + "id": "genetic_translation_kinetics", + "name": "genetic translation kinetics", + "description": "Model: genetic_translation_kinetics.bngl", "tags": [ - "signaling" + "genetic", + "translation", + "kinetics", + "mrna", + "rib", + "protein" ], - "category": "signaling", - "origin": "published", + "category": "gene-expression", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -4482,28 +4384,33 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/17-egfr-ssa/egfr_ground.bngl", - "file": "egfr_ground.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl", + "file": "genetic_translation_kinetics.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_ground", - "name": "egfr ground", - "description": "Blinov et al. 2006. Biosystems, 83:136", + "id": "genetic_turing_pattern_1d", + "name": "genetic turing pattern 1d", + "description": "Model: genetic_turing_pattern_1d.bngl", "tags": [ - "egfr", - "ground", - "egf", - "grb2", - "shc", - "sos" + "genetic", + "turing", + "pattern", + "1d", + "a", + "b" ], - "category": "other", - "origin": "published", - "visible": true, + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -4513,67 +4420,64 @@ ] }, "gallery": [ - "other" + "test-models" ], - "path": "Published/PyBioNetGen/core/egfrground/egfr_ground.bngl", - "file": "egfr_ground.bngl", + "path": "Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl", + "file": "genetic_turing_pattern_1d.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_net", - "name": "egfr_net", - "description": "check detailed balanced", + "id": "GK", + "name": "GK", + "description": "title: GK.bngl", "tags": [ - "validation", - "egfr", - "net", - "egf", - "shc", - "grb2", - "sos" + "gk" ], - "category": "validation", - "origin": "test-case", + "category": "tutorial", + "origin": "tutorial", "visible": true, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "metabolism", + "native-tutorials" ], - "path": "Tutorials/egfrnet/egfr_net.bngl", - "file": "egfr_net.bngl", + "path": "Tutorials/NativeTutorials/GK/GK.bngl", + "file": "GK.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr_net_red", - "name": "egfr_net_red", - "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", + "id": "glioblastoma-egfrviii-signaling", + "name": "glioblastoma egfrviii signaling", + "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", "tags": [ - "validation", - "egfr", - "net", - "red", - "egf", - "egfr_1", - "egfr_2", - "egfr_3", - "grb2", - "shc", - "sos" + "glioblastoma", + "egfrviii", + "signaling", + "pi3k", + "akt", + "oncogenic_output", + "v_viii_act" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -4583,126 +4487,141 @@ ] }, "gallery": [ - "validation" + "cancer", + "test-models" ], - "path": "Tutorials/egfrnetred/egfr_net_red.bngl", - "file": "egfr_net_red.bngl", + "path": "Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl", + "file": "glioblastoma-egfrviii-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_nf", - "name": "egfr nf", - "description": "Filename: example2_starting_point.bngl", + "id": "glycolysis-branch-point", + "name": "glycolysis branch point", + "description": "BioNetGen model: glycolysis branch point", "tags": [ - "egfr", - "nf", - "egf", - "clusters", - "pre1_dose", - "pre2_time" + "glycolysis", + "branch", + "point", + "glucose", + "atp", + "biomass" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "other" + "metabolism", + "test-models" ], - "path": "Published/PyBioNetGen/core/egfrnf/egfr_nf.bngl", - "file": "egfr_nf.bngl", + "path": "Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl", + "file": "glycolysis-branch-point.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr_ode", - "name": "egfr ode", - "description": "Filename: example1.bngl", + "id": "gm_game_of_life", + "name": "gm game of life", + "description": "Model: gm_game_of_life.bngl", "tags": [ - "egfr", - "ode", - "egf", - "pre1_dose", - "pre2_time", - "pre3_dose" + "gm", + "game", + "of", + "life", + "cell" ], - "category": "other", - "origin": "published", + "category": "computer-science", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ - "cancer" + "test-models" ], - "path": "Published/PyBioNetGen/core/egfrode/egfr_ode.bngl", - "file": "egfr_ode.bngl", + "path": "Examples/generative/gmgameoflife/gm_game_of_life.bngl", + "file": "gm_game_of_life.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_ode", - "name": "PyBNG: EGFR ODE", - "description": "EGFR ODE", + "id": "gm_ray_marcher", + "name": "gm ray marcher", + "description": "Ray Marching Renderer in BNGL", "tags": [ - "published", - "pybng", - "egfr", - "ode", - "egf", - "pre1_dose", - "pre2_time", - "pre3_dose" + "gm", + "ray", + "marcher", + "ray0", + "hit0", + "bright0", + "sdf0", + "sdf1", + "sdf2", + "sdf3", + "speed0" ], - "category": "other", - "origin": "published", + "category": "computer-science", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer" + "test-models" ], - "path": "Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl", - "file": "egfr_ode.bngl", + "path": "Examples/generative/gmraymarcher/gm_ray_marcher.bngl", + "file": "gm_ray_marcher.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr_path", - "name": "egfr_path", - "description": "The primary focus of the model developed by Kholodenko", + "id": "Goldstein_blbr_1980", + "name": "Goldstein et al. 1980: Bivalent Ligand Bivalent Receptor (BLBR) Model", + "description": "BLBR heterogeneity", "tags": [ - "validation", - "egfr", - "path", - "generate_network", - "setconcentration", - "simulate" + "blbr", + "ligand-receptor", + "binding", + "1980", + "goldstein" ], - "category": "validation", - "origin": "test-case", + "category": "physics", + "origin": "published", "visible": true, "compatibility": { "bng2": true, @@ -4713,30 +4632,35 @@ ] }, "gallery": [ - "validation" + "physics" ], - "path": "Tutorials/egfrpath/egfr_path.bngl", - "file": "egfr_path.bngl", + "path": "Published/Goldstein1980/blbr_heterogeneity_goldstein1980.bngl", + "file": "blbr_heterogeneity_goldstein1980.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egfr_simple", - "name": "egfr simple", - "description": "This is a demo model of EGFR signaling.", + "id": "Goldstein_TLBR_1984", + "name": "Goldstein et al. 1984: Trivalent Ligand Bivalent Receptor (TLBR) Model", + "description": "Ligand binding", "tags": [ - "egfr", - "simple", - "egf", - "grb2", - "sos1" + "tlbr", + "polymerization", + "ligand-receptor", + "bivalent-receptor", + "trivalent-ligand", + "1984", + "goldstein" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "immunology", + "origin": "published", + "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": true, "excluded": false, "methods": [ @@ -4744,61 +4668,64 @@ ] }, "gallery": [ - "native-tutorials" + "immunology" ], - "path": "Tutorials/NativeTutorials/egfrsimple/egfr_simple.bngl", - "file": "egfr_simple.bngl", + "path": "Published/tlbr/tlbr.bngl", + "file": "tlbr.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "egfr-signaling-pathway", - "name": "egfr signaling pathway", - "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", + "id": "gpcr-desensitization-arrestin", + "name": "gpcr desensitization arrestin", + "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", "tags": [ - "egfr", - "signaling", - "pathway", - "egf", - "grb2", - "shc" + "gpcr", + "desensitization", + "arrestin", + "ligand", + "gprotein" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer", "test-models" ], - "path": "Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl", - "file": "egfr-signaling-pathway.bngl", + "path": "Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl", + "file": "gpcr-desensitization-arrestin.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "egg", - "name": "egg", - "description": "BioNetGen model: egg", + "id": "Harmon_Antigen_2017", + "name": "Harmon et al. 2017: Antigen Recognition Feedback Model", + "description": "Antigen pulses", "tags": [ - "egg", - "x", - "y", - "generate_network", - "simulate" + "antigen-recognition", + "immune-signaling", + "2017", + "harmon" ], - "category": "validation", - "origin": "test-case", - "visible": false, + "category": "immunology", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -4808,142 +4735,65 @@ ] }, "gallery": [ - "validation" + "immunology" ], - "path": "Published/PyBioNetGen/tests/egg/egg.bngl", - "file": "egg.bngl", + "path": "Published/Harmon2017/antigen_pulses_harmon2017.bngl", + "file": "antigen_pulses_harmon2017.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "eif2a-stress-response", - "name": "eif2a stress response", - "description": "Integrated Stress Response: eIF2alpha and the translational gate.", + "id": "Hat_wip1_2016", + "name": "Hat et al. 2016: Wip1-Mediated Feedback Oscillator", + "description": "Nuclear transport", "tags": [ - "eif2a", - "stress", - "response", - "eif2b", - "perk", - "gadd34" + "wip1", + "feedback-loop", + "p53-pathway", + "2016", + "hat" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "regulation", + "origin": "published", + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "test-models" + "cell-cycle", + "multistage" ], - "path": "Examples/biology/eif2astressresponse/eif2a-stress-response.bngl", - "file": "eif2a-stress-response.bngl", + "path": "Published/Hat2016/Hat_2016.bngl", + "file": "Hat_2016.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "elephant_EFA", - "name": "Hlavacek2018Elephant", - "description": "BNGL model: elephant_EFA", + "id": "Haugh2b", + "name": "Haugh2b", + "description": "R(KD,Y1~U,Y2~U) 1.00", "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" + "haugh2b", + "exclude_reactants", + "include_reactants" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -4952,108 +4802,34 @@ "ode" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Elephant/elephant_EFA.bngl", - "file": "elephant_EFA.bngl", + "gallery": [ + "validation" + ], + "path": "Tutorials/Haugh2b/Haugh2b.bngl", + "file": "Haugh2b.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "elephant_fit", - "name": "Hlavacek2018Elephant", - "description": "BNGL model: elephant_EFA", + "id": "hedgehog-signaling-pathway", + "name": "hedgehog signaling pathway", + "description": "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing.", "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" + "hedgehog", + "signaling", + "pathway", + "hh", + "ptch", + "smo", + "gli", + "sufu" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -5063,30 +4839,29 @@ "ode" ] }, - "gallery": [], - "path": "Published/Hlavacek2018Elephant/elephant_fit.bngl", - "file": "elephant_fit.bngl", + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl", + "file": "hedgehog-signaling-pathway.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "endosomal-sorting-rab", - "name": "endosomal sorting rab", - "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", + "id": "heise", + "name": "heise", + "description": "Validate state inheritance in a symmetric context", "tags": [ - "endosomal", - "sorting", - "rab", - "rab5", - "rab7", - "effector", - "v_gef", - "v_gap_drive" + "heise" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -5096,31 +4871,36 @@ ] }, "gallery": [ - "test-models" + "validation" ], - "path": "Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl", - "file": "endosomal-sorting-rab.bngl", + "path": "Tutorials/heise/heise.bngl", + "file": "heise.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "energy_allostery_mwc", - "name": "energy allostery mwc", - "description": "Model: energy_allostery_mwc.bngl", + "id": "hematopoietic-growth-factor", + "name": "hematopoietic growth factor", + "description": "Kinetic Parameters", "tags": [ - "energy", - "allostery", - "mwc", - "p", - "l" + "hematopoietic", + "growth", + "factor", + "epo", + "epor", + "jak2", + "stat5" ], - "category": "other", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -5129,30 +4909,33 @@ "gallery": [ "test-models" ], - "path": "Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl", - "file": "energy_allostery_mwc.bngl", + "path": "Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl", + "file": "hematopoietic-growth-factor.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "energy_catalysis_mm", - "name": "energy catalysis mm", - "description": "Model: energy_catalysis_mm.bngl", + "id": "hif1a_degradation_loop", + "name": "hif1a degradation loop", + "description": "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay.", "tags": [ - "energy", - "catalysis", - "mm", - "e", - "s", - "p" + "hif1a", + "degradation", + "loop", + "vhl", + "arnt", + "v_hydrox" ], - "category": "other", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -5161,25 +4944,27 @@ "gallery": [ "test-models" ], - "path": "Examples/energy/energycatalysismm/energy_catalysis_mm.bngl", - "file": "energy_catalysis_mm.bngl", + "path": "Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl", + "file": "hif1a_degradation_loop.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "energy_cooperativity_adh", - "name": "energy cooperativity adh", - "description": "Model: energy_cooperativity_adh.bngl", + "id": "HIV_Dynamics_pt303", + "name": "HIV Viral Load Dynamics - Patient 303", + "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", "tags": [ - "energy", - "cooperativity", - "adh", - "r", - "l" + "hiv", + "viral-dynamics", + "patient-303", + "epidemiology" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -5190,32 +4975,30 @@ ] }, "gallery": [ - "test-models" + "other" ], - "path": "Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl", - "file": "energy_cooperativity_adh.bngl", + "path": "Published/PyBioNetGen/HIVdynamics/pt303/pt303.bngl", + "file": "pt303.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "energy_example1", - "name": "energy_example1", - "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", + "id": "HIV_Dynamics_pt403", + "name": "HIV Viral Load Dynamics - Patient 403", + "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", "tags": [ - "validation", - "energy", - "example1", - "version", - "setoption", - "s", - "a", - "b", - "c" + "hiv", + "viral-dynamics", + "patient-403", + "epidemiology" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -5225,27 +5008,29 @@ ] }, "gallery": [ - "validation" + "other" ], - "path": "Tutorials/energyexample1/energy_example1.bngl", - "file": "energy_example1.bngl", + "path": "Published/PyBioNetGen/HIVdynamics/pt403/pt403.bngl", + "file": "pt403.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "energy_linear_chain", - "name": "energy linear chain", - "description": "Model: energy_linear_chain.bngl", + "id": "HIV_Dynamics_pt409", + "name": "HIV Viral Load Dynamics - Patient 409", + "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", "tags": [ - "energy", - "linear", - "chain", - "m", - "generate_network" + "hiv", + "viral-dynamics", + "patient-409", + "epidemiology" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -5256,30 +5041,29 @@ ] }, "gallery": [ - "test-models" + "other" ], - "path": "Examples/energy/energylinearchain/energy_linear_chain.bngl", - "file": "energy_linear_chain.bngl", + "path": "Published/PyBioNetGen/HIVdynamics/pt409/pt409.bngl", + "file": "pt409.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "energy_transport_pump", - "name": "energy transport pump", - "description": "Model: energy_transport_pump.bngl", + "id": "Hlavacek_Egg_2018", + "name": "Hlavacek et al. 2018: Calcium Oscillations in Egg Activation", + "description": "End of permute change log", "tags": [ - "energy", - "transport", - "pump", - "a", - "atp", - "adp", - "pi", - "t" + "calcium-oscillations", + "egg-activation", + "2018", + "hlavacek" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -5289,95 +5073,93 @@ "ode" ] }, - "gallery": [ - "test-models" - ], - "path": "Examples/energy/energytransportpump/energy_transport_pump.bngl", - "file": "energy_transport_pump.bngl", + "gallery": [], + "path": "Published/Hlavacek2018Egg/egg.bngl", + "file": "egg.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ensemble_tofit", - "name": "translated into BNGL", - "description": "Ensemble model translated into BNGL", + "id": "Hlavacek_Elephant_2018_elephant_EFA", + "name": "Hlavacek et al. 2018: Fitting an Elephant with Four Parameters (elephant_EFA)", + "description": "BNGL model: elephant_EFA", "tags": [ - "signaling" + "elephant-fitting", + "mathematical-model", + "2018", + "hlavacek" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [], - "path": "Published/Mitra2019/28-mapk/ensemble_tofit.bngl", - "file": "ensemble_tofit.bngl", + "path": "Published/Hlavacek2018Elephant/elephant_EFA.bngl", + "file": "elephant_EFA.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "er-stress-response", - "name": "er stress response", - "description": "Rate Constants", + "id": "Hlavacek_Elephant_2018_elephant_fit", + "name": "Hlavacek et al. 2018: Fitting an Elephant with Four Parameters (elephant_fit)", + "description": "BNGL model: elephant_EFA", "tags": [ - "er", - "stress", - "response", - "unfoldedprotein", - "perk", - "eif2a", - "chaperone" + "elephant-fitting", + "mathematical-model", + "2018", + "hlavacek" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "test-models" - ], - "path": "Examples/biology/erstressresponse/er-stress-response.bngl", - "file": "er-stress-response.bngl", + "gallery": [], + "path": "Published/Hlavacek2018Elephant/elephant_fit.bngl", + "file": "elephant_fit.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Erdem_2021", - "name": "Erdem 2021", - "description": "InsR/IGF1R signaling", + "id": "Hlavacek_Proofreading_2001", + "name": "Hlavacek et al. 2001: Kinetic Proofreading Model", + "description": "Kinetic proofreading", "tags": [ - "published", - "erdem", - "2021", - "igf1", - "ins", - "igf1r", - "insr", - "irs", - "sos", - "ras", - "raf" + "kinetic-proofreading", + "ligand-discrimination", + "2001", + "hlavacek" ], - "category": "signaling", + "category": "physics", "origin": "published", - "visible": false, + "visible": true, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -5385,65 +5167,26 @@ ] }, "gallery": [ - "metabolism" + "physics" ], - "path": "Published/Erdem2021/Erdem_2021.bngl", - "file": "Erdem_2021.bngl", + "path": "Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl", + "file": "kinetic_proofreading_hlavacek2001.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ERK_model", - "name": "ERK_model.bngl", - "description": "filename: ERK_model.bngl", + "id": "Hlavacek_Restructuration_2018_after_bunching", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (after_bunching)", + "description": "BNGL model: after_bunching", "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" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -5453,32 +5196,31 @@ "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, "gallery": [], - "path": "Published/Lin2019/ERK_model.bngl", - "file": "ERK_model.bngl", + "path": "Published/Hlavacek2018Restructuration/after_bunching.bngl", + "file": "after_bunching.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "erk-nuclear-translocation", - "name": "erk nuclear translocation", - "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", + "id": "Hlavacek_Restructuration_2018_after_decoupling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (after_decoupling)", + "description": "BNGL model: after_bunching", "tags": [ - "erk", - "nuclear", - "translocation", - "mek", - "elk1", - "dusp", - "transcription_signal" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -5488,28 +5230,29 @@ "ode" ] }, - "gallery": [ - "test-models" - ], - "path": "Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl", - "file": "erk-nuclear-translocation.bngl", + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/after_decoupling.bngl", + "file": "after_decoupling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ErrNoFrees", - "name": "ErrNoFrees", - "description": "An example from a real application", + "id": "Hlavacek_Restructuration_2018_after_scaling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (after_scaling)", + "description": "BNGL model: after_bunching", "tags": [ - "errnofrees", - "ag", - "r", - "h" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -5518,26 +5261,25 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl", - "file": "ErrNoFrees.bngl", + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/after_scaling.bngl", + "file": "after_scaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example1", - "name": "example1", - "description": "Filename: example1.bngl", + "id": "Hlavacek_Restructuration_2018_before_bunching", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (before_bunching)", + "description": "BNGL model: after_bunching", "tags": [ - "example1", - "egf", - "egfr", - "pre1_dose", - "pre2_time", - "pre3_dose" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -5550,80 +5292,25 @@ "ode" ] }, - "gallery": [ - "other" - ], - "path": "Published/PyBioNetGen/core/example1/example1.bngl", - "file": "example1.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "example1", - "name": "example1", - "description": "Example file for BNG2 tutorial.", - "tags": [ - "validation", - "example1", - "version", - "generate_network", - "simulate_ode" - ], - "category": "validation", - "origin": "test-case", - "visible": true, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Tutorials/example1/example1.bngl", - "file": "example1.bngl", + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/before_bunching.bngl", + "file": "before_bunching.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example1_BNFfiles_example1", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "Hlavacek_Restructuration_2018_before_decoupling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (before_decoupling)", + "description": "BNGL model: after_bunching", "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" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -5637,55 +5324,24 @@ ] }, "gallery": [], - "path": "Published/Thomas2016/example1_BNFfiles/example1.bngl", - "file": "example1.bngl", + "path": "Published/Hlavacek2018Restructuration/before_decoupling.bngl", + "file": "before_decoupling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example1_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "Hlavacek_Restructuration_2018_before_scaling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (before_scaling)", + "description": "BNGL model: after_bunching", "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" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", @@ -5699,108 +5355,59 @@ ] }, "gallery": [], - "path": "Published/Thomas2016/example1_fit.bngl", - "file": "example1_fit.bngl", + "path": "Published/Hlavacek2018Restructuration/before_scaling.bngl", + "file": "before_scaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example2_BNFfiles_example2", - "name": "example2_starting_point.bngl", - "description": "Filename: example2_starting_point.bngl", + "id": "Hlavacek_Restructuration_2018_check_scaling", + "name": "Hlavacek et al. 2018: Network Restructuration Analysis (check_scaling)", + "description": "BNGL model: after_bunching", "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" + "network-restructuration", + "mathematical-model", + "2018", + "hlavacek" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [], - "path": "Published/Thomas2016/example2_BNFfiles/example2.bngl", - "file": "example2.bngl", + "path": "Published/Hlavacek2018Restructuration/check_scaling.bngl", + "file": "check_scaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example2_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "Hlavacek_Steric_1999", + "name": "Hlavacek et al. 1999: Steric Hindrance in Ligand Binding", + "description": "Steric effects", "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" + "steric-hindrance", + "ligand-binding", + "1999", + "hlavacek" ], - "category": "other", + "category": "physics", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -5809,120 +5416,104 @@ "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example2_fit.bngl", - "file": "example2_fit.bngl", + "gallery": [ + "physics" + ], + "path": "Published/Hlavacek1999/steric_effects_hlavacek1999.bngl", + "file": "steric_effects_hlavacek1999.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example2_starting_point", - "name": "example2 starting point", - "description": "Filename: example2_starting_point.bngl", + "id": "hypoxia-response-signaling", + "name": "hypoxia response signaling", + "description": "Rate Constants", "tags": [ - "example2", - "starting", - "point", - "egf", - "egfr", - "clusters", - "pre1_dose", - "pre2_time" + "hypoxia", + "response", + "signaling", + "oxygensensor", + "hif1", + "vegf" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "other" + "cancer", + "test-models" ], - "path": "Published/PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl", - "file": "example2_starting_point.bngl", + "path": "Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl", + "file": "hypoxia-response-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example3_BNFfiles_example3", - "name": "example3 BNFfiles", - "description": "BNGL model: example3", + "id": "il1b-signaling", + "name": "il1b signaling", + "description": "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation.", "tags": [ - "alpha", - "molecules", - "species" + "il1b", + "signaling", + "il1ri", + "myd88", + "irak", + "nfkb" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example3_BNFfiles/example3.bngl", - "file": "example3.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/biology/il1bsignaling/il1b-signaling.bngl", + "file": "il1b-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example3_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "il6-jak-stat-pathway", + "name": "il6 jak stat pathway", + "description": "IL-6 Signaling: gp130 hexamerization and pSTAT3 import.", "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" + "il6", + "jak", + "stat", + "pathway", + "gp130", + "stat3", + "socs" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -5932,111 +5523,107 @@ "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example3_fit.bngl", - "file": "example3_fit.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl", + "file": "il6-jak-stat-pathway.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example4_BNFfiles_example4", - "name": "in BNGL. For a description of BNGL, see:", - "description": "Supplementary File A in File S1", + "id": "immune-synapse-formation", + "name": "immune synapse formation", + "description": "Kinetic Parameters", "tags": [ - "other" + "immune", + "synapse", + "formation", + "tcr", + "pmhc", + "lck", + "zap70" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example4_BNFfiles/example4.bngl", - "file": "example4.bngl", + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/immunesynapseformation/immune-synapse-formation.bngl", + "file": "immune-synapse-formation.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example4_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "inflammasome-activation", + "name": "inflammasome activation", + "description": "Rate Constants", "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" + "inflammasome", + "activation", + "sensor", + "asc", + "caspase1", + "il1b" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example4_fit.bngl", - "file": "example4_fit.bngl", + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/inflammasomeactivation/inflammasome-activation.bngl", + "file": "inflammasome-activation.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example5_BNFfiles_example5", - "name": "example5 BNFfiles", - "description": "A simple model", + "id": "inositol-phosphate-metabolism", + "name": "inositol phosphate metabolism", + "description": "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points.", "tags": [ - "ligand_ispresent", - "molecules", - "species" + "inositol", + "phosphate", + "metabolism", + "pip2", + "ip3", + "ip4", + "calcium", + "agonist" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -6046,148 +5633,107 @@ "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example5_BNFfiles/example5.bngl", - "file": "example5.bngl", + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl", + "file": "inositol-phosphate-metabolism.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example5_fit", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "insulin-glucose-homeostasis", + "name": "insulin glucose homeostasis", + "description": "Insulin-Glucose: Compartmentalized transport.", "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" + "insulin", + "glucose", + "homeostasis", + "ir", + "glut4", + "pancreas" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example5_fit.bngl", - "file": "example5_fit.bngl", + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl", + "file": "insulin-glucose-homeostasis.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example5_ground_truth", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "interferon-signaling", + "name": "interferon signaling", + "description": "Rate Constants", "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" + "interferon", + "signaling", + "ifn", + "ifnar", + "tyk2", + "stat1" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example5_ground_truth.bngl", - "file": "example5_ground_truth.bngl", + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/interferonsignaling/interferon-signaling.bngl", + "file": "interferon-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "example5_starting_point", - "name": "13-receptor", - "description": "A simple model", + "id": "ire1a-xbp1-er-stress", + "name": "ire1a xbp1 er stress", + "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", "tags": [ - "ligand_ispresent", - "molecules", - "species" + "ire1a", + "xbp1", + "er", + "stress", + "ire1", + "bip", + "unfolded", + "ridd_target" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -6197,86 +5743,99 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019/13-receptor/example5_starting_point.bngl", - "file": "example5_starting_point.bngl", + "gallery": [ + "test-models" + ], + "path": "Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl", + "file": "ire1a-xbp1-er-stress.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example6_BNFfiles_example6", - "name": "example6 BNFfiles", - "description": "A simple model", + "id": "issue_198_short", + "name": "issue_198_short", + "description": "No description available", "tags": [ - "molecules", - "species" + "issue", + "198", + "short" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example6_BNFfiles/example6.bngl", - "file": "example6.bngl", + "gallery": [ + "validation" + ], + "path": "Tutorials/issue198short/issue_198_short.bngl", + "file": "issue_198_short.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "example6_ground_truth", - "name": "example1_starting_point.bngl", - "description": "Filename: example1_starting_point.bngl", + "id": "jak-stat-cytokine-signaling", + "name": "jak stat cytokine signaling", + "description": "Rate Constants", "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" + "jak", + "stat", + "cytokine", + "signaling", + "receptor" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl", + "file": "jak-stat-cytokine-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "JaruszewiczBlonska_NFkB_2023", + "name": "Jaruszewicz-Blonska et al. 2023: NF-kB Feedback Regulation", + "description": "T-cell discrimination", + "tags": [ + "nfkb", + "feedback-regulation", + "inflammatory-response", + "2023", + "jaruszewiczblonska" + ], + "category": "immunology", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -6285,105 +5844,104 @@ "ode" ] }, - "gallery": [], - "path": "Published/Thomas2016/example6_ground_truth.bngl", - "file": "example6_ground_truth.bngl", + "gallery": [ + "immunology" + ], + "path": "Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023.bngl", + "file": "Jaruszewicz-Blonska_2023.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "extra_CaMKII_Holo", - "name": "Ordyan 2020: extra CaMKII holo", - "description": "Extra CaMKII holo (supplement)", + "id": "jnk-mapk-signaling", + "name": "jnk mapk signaling", + "description": "JNK MAPK Signaling: Scaffold-mediated activation and feedback.", "tags": [ - "published", - "neuroscience", - "extra", - "camkii", - "holo", - "t1", - "t2", - "t3", - "t4", - "t5", - "t6", - "t7", - "t8" + "jnk", + "mapk", + "signaling", + "mkk7", + "jip1", + "v_dephos" ], "category": "signaling", - "origin": "published", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "signaling" + "test-models" ], - "path": "Published/Ordyan2020/extraCaMKIIHolo/extra_CaMKII_Holo.bngl", - "file": "extra_CaMKII_Holo.bngl", + "path": "Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl", + "file": "jnk-mapk-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Faeder_2003", - "name": "Faeder 2003", - "description": "FceRI signaling", + "id": "Jung_CaMKII_2017", + "name": "Jung et al. 2017: CaMKII Activation Kinetics", + "description": "M1 receptor signaling", "tags": [ - "published", - "immunology", - "faeder", - "2003", - "lig", - "lyn", - "syk", - "rec" + "camkii", + "neuroscience", + "kinase-activation", + "2017", + "jung" ], - "category": "immunology", + "category": "signaling", "origin": "published", - "visible": true, + "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology" + "neuroscience" ], - "path": "Published/Faeder2003/Faeder_2003.bngl", - "file": "Faeder_2003.bngl", + "path": "Published/Jung2017/Jung_2017.bngl", + "file": "Jung_2017.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fceri_fyn", - "name": "FceRI Fyn", - "description": "FceRI signaling", + "id": "Kesseler_CellCycle_2013", + "name": "Kesseler et al. 2013: Cell Cycle Regulation Model", + "description": "G2/Mitosis transition", "tags": [ - "published", - "immunology", - "fceri", - "fyn", - "lig", - "lyn", - "syk", - "rec" + "cell-cycle", + "mitosis", + "cdc25", + "wee1", + "2013", + "kesseler" ], - "category": "immunology", + "category": "signaling", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": true, "excluded": false, "methods": [ @@ -6391,99 +5949,99 @@ ] }, "gallery": [ - "immunology" + "cell-cycle" ], - "path": "Published/fcerifyn/fceri_fyn.bngl", - "file": "fceri_fyn.bngl", + "path": "Published/Kesseler2013/Kesseler_2013.bngl", + "file": "Kesseler_2013.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "fceri_gamma2", - "name": "fceri gamma2", - "description": "BioNetGen model: fceri gamma2", + "id": "Kiefhaber_emodel", + "name": "Kiefhaber_emodel", + "description": "Allow molar units to be used for bimolecular rate constants", "tags": [ - "fceri", - "gamma2", - "lig", - "lyn", - "syk", - "rec" + "emodel" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "other" + "validation" ], - "path": "Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl", - "file": "fceri_gamma2.bngl", + "path": "Tutorials/Kiefhaberemodel/Kiefhaber_emodel.bngl", + "file": "Kiefhaber_emodel.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fceri_gamma2_ground_truth", - "name": "fceri gamma2 ground truth", - "description": "BioNetGen model: fceri gamma2 ground truth", + "id": "kir-channel-regulation", + "name": "kir channel regulation", + "description": "Kir Channel Regulation: PIP2 modulation and G-protein potentiation.", "tags": [ - "fceri", - "gamma2", - "ground", - "truth", - "lig", - "lyn", - "syk", - "rec" + "kir", + "channel", + "regulation", + "pip2", + "gbg", + "v_opening", + "v_gbg_factor" ], - "category": "other", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "other" + "test-models" ], - "path": "Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl", - "file": "fceri_gamma2_ground_truth.bngl", + "path": "Examples/biology/kirchannelregulation/kir-channel-regulation.bngl", + "file": "kir-channel-regulation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fceri_ji", - "name": "Faeder 2003", - "description": "FceRI signaling", + "id": "Kocieniewski_published_2012", + "name": "Kocieniewski et al. 2012: MAPK Signaling on Scaffolds", + "description": "Actin dynamics", "tags": [ - "published", - "immunology", - "faeder", - "2003", - "lig", - "lyn", - "syk", - "rec" + "mapk", + "scaffold-proteins", + "signaling", + "2012", + "kocieniewski" ], - "category": "immunology", + "category": "regulation", "origin": "published", - "visible": true, + "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": true, "excluded": false, "methods": [ @@ -6491,28 +6049,32 @@ ] }, "gallery": [ - "immunology" + "regulation" ], - "path": "Published/Faeder2003/fceri_ji.bngl", - "file": "fceri_ji.bngl", + "path": "Published/Kocieniewski2012/Kocieniewski_2012.bngl", + "file": "Kocieniewski_2012.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false }, { - "id": "FceRI_ji", - "name": "FceRI ji", - "description": "title: FceRI_ji.bngl", + "id": "Korwek_InnateImmunity_2023", + "name": "Korwek et al. 2023: Innate Immunity Activation Model", + "description": "Immune response", "tags": [ - "fceri", - "ji", - "lig", - "lyn", - "syk", - "rec" + "innate-immunity", + "rig-i-sensing", + "pkr-activation", + "rnase-l-cleavage", + "viral-sensing", + "2023", + "korwek" ], - "category": "tutorial", - "origin": "tutorial", + "category": "immunology", + "origin": "published", "visible": true, "compatibility": { "bng2": true, @@ -6523,33 +6085,35 @@ ] }, "gallery": [ - "native-tutorials" + "immunology" ], - "path": "Tutorials/NativeTutorials/FceRIji/FceRI_ji.bngl", - "file": "FceRI_ji.bngl", + "path": "Published/innateimmunity/innate_immunity.bngl", + "file": "innate_immunity.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fceri_ji_comp", - "name": "fceri_ji_comp", - "description": "Ligand-receptor binding", + "id": "Korwek_ViralSensing_2023", + "name": "Korwek et al. 2023: Viral Sensing and Innate Immune Activation", + "description": "This BioNetGen file features the article:", "tags": [ - "validation", - "fceri", - "ji", - "comp", - "lig", - "lyn", - "syk", - "rec" + "innate-immunity", + "rig-i-sensing", + "pkr-activation", + "rnase-l-cleavage", + "viral-sensing", + "2023", + "korwek" ], "category": "validation", "origin": "test-case", - "visible": false, + "visible": true, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -6559,34 +6123,29 @@ "gallery": [ "validation" ], - "path": "Tutorials/fcerijicomp/fceri_ji_comp.bngl", - "file": "fceri_ji_comp.bngl", + "path": "Published/Korwek2023/Korwek_2023.bngl", + "file": "Korwek_2023.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "FceRI_viz", - "name": "FceRI Viz", - "description": "FcεRI (viz)", + "id": "Kozer_egfr_2013", + "name": "Kozer et al. 2013: EGFR Dimerization and Internalization", + "description": "EGFR oligomerization", "tags": [ - "published", - "tutorial", - "native", - "fceri", - "viz", - "fcr", - "ige", - "lat", - "lyn", - "syk", - "pb", - "pg", - "sykp" + "egfr", + "dimerization", + "internalization", + "2013", + "kozer" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "signaling", + "origin": "published", + "visible": false, "compatibility": { "bng2": false, "nfsim": false, @@ -6596,32 +6155,33 @@ ] }, "gallery": [ - "native-tutorials" + "cancer" ], - "path": "Tutorials/NativeTutorials/FceRIviz/FceRI_viz.bngl", - "file": "FceRI_viz.bngl", + "path": "Published/Kozer2013/Kozer_2013.bngl", + "file": "Kozer_2013.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_functional_rates_volume", - "name": "feature functional rates volume", - "description": "Model: feature_functional_rates_volume.bngl", + "id": "Kozer_egfr_2014", + "name": "Kozer et al. 2014: EGFR Oligomerization Dynamics", + "description": "Grb2-EGFR recruitment", "tags": [ - "feature", - "functional", - "rates", - "volume", - "a", - "b", - "c" + "egfr", + "oligomerization", + "internalization", + "2014", + "kozer" ], - "category": "other", - "origin": "ai-generated", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -6629,28 +6189,33 @@ ] }, "gallery": [ - "test-models" + "cancer" ], - "path": "Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl", - "file": "feature_functional_rates_volume.bngl", + "path": "Published/Kozer2014/Kozer_2014.bngl", + "file": "Kozer_2014.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_global_functions_scan", - "name": "feature global functions scan", - "description": "Model: feature_global_functions_scan.bngl", + "id": "l-type-calcium-channel-dynamics", + "name": "l type calcium channel dynamics", + "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", "tags": [ - "feature", - "global", - "functions", - "scan", - "signal", - "response", - "stimulus" + "l", + "type", + "calcium", + "channel", + "dynamics", + "ltcc", + "voltage", + "v_open", + "v_inact" ], - "category": "other", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { @@ -6662,65 +6227,71 @@ ] }, "gallery": [ + "neuroscience", "test-models" ], - "path": "Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl", - "file": "feature_global_functions_scan.bngl", + "path": "Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl", + "file": "l-type-calcium-channel-dynamics.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_local_functions_explicit", - "name": "feature local functions explicit", - "description": "Model: feature_local_functions_explicit.bngl", + "id": "lac-operon-regulation", + "name": "lac operon regulation", + "description": "Kinetic Parameters", "tags": [ - "feature", - "local", - "functions", - "explicit", - "s", - "p", - "e", - "mm_rate", - "ratelaw" + "lac", + "operon", + "regulation", + "laci", + "promoter", + "mrna", + "betagal", + "lactose", + "allolactose" ], - "category": "other", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ + "metabolism", "test-models" ], - "path": "Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl", - "file": "feature_local_functions_explicit.bngl", + "path": "Examples/biology/lacoperonregulation/lac-operon-regulation.bngl", + "file": "lac-operon-regulation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "feature_symmetry_factors_cyclic", - "name": "feature symmetry factors cyclic", - "description": "Model: feature_symmetry_factors_cyclic.bngl", + "id": "Lang_CellCycle_2024", + "name": "Lang et al. 2024: Cyclin A-CDK2 Cell Cycle Control", + "description": "Cell cycle regulation", "tags": [ - "feature", - "symmetry", - "factors", - "cyclic", - "x", - "generate_network", - "simulate" + "cell-cycle", + "cyclin-a", + "cdk2", + "2024", + "lang" ], - "category": "other", - "origin": "ai-generated", - "visible": false, + "category": "signaling", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -6730,32 +6301,34 @@ ] }, "gallery": [ - "test-models" + "cell-cycle" ], - "path": "Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl", - "file": "feature_symmetry_factors_cyclic.bngl", + "path": "Published/Lang2024/Lang_2024.bngl", + "file": "Lang_2024.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "feature_synthesis_degradation_ss", - "name": "feature synthesis degradation ss", - "description": "Model: feature_synthesis_degradation_ss.bngl", + "id": "Lee_Wnt_2003", + "name": "Lee et al. 2003: Wnt/Beta-Catenin Signaling Pathway", + "description": "Wnt signaling", "tags": [ - "feature", - "synthesis", - "degradation", - "ss", - "m", - "generate_network", - "simulate" + "wnt", + "beta-catenin", + "axin-degradation", + "dishevelled-activation", + "2003", + "lee" ], - "category": "other", - "origin": "ai-generated", + "category": "regulation", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -6763,227 +6336,285 @@ ] }, "gallery": [ - "test-models" + "regulation" ], - "path": "Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl", - "file": "feature_synthesis_degradation_ss.bngl", + "path": "Published/wnt/wnt.bngl", + "file": "wnt.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "fgf-signaling-pathway", - "name": "fgf signaling pathway", - "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", + "id": "Ligon_egfr_2014", + "name": "Ligon et al. 2014: EGFR Dimerization in Living Cells", + "description": "Lipoplex delivery", "tags": [ - "fgf", - "signaling", - "pathway", - "fgfr", - "frs2", - "spry", - "rasgef", - "internalized_rec" + "egfr", + "dimerization", + "fluorescence-microscopy", + "2014", + "ligon" ], "category": "signaling", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "developmental", - "test-models" + "cancer" ], - "path": "Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl", - "file": "fgf-signaling-pathway.bngl", + "path": "Published/Ligon2014/Ligon_2014.bngl", + "file": "Ligon_2014.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "free_missing", - "name": "free missing", - "description": "Original values used to generate parabola.exp", + "id": "Lin_ERK_2019", + "name": "Lin 2019", + "description": "ERK signaling", "tags": [ - "free", - "missing", - "counter", - "y", - "generate_network", - "simulate" + "2019", + "egfr", + "erk", + "lin", + "linerk", + "mek", + "raf", + "ras", + "rasgap", + "signaling", + "sos" ], - "category": "validation", - "origin": "test-case", - "visible": false, + "category": "other", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "validation" + "developmental" ], - "path": "Published/PyBioNetGen/tests/freemissing/free_missing.bngl", - "file": "free_missing.bngl", + "path": "Published/LinERK2019/Lin_ERK_2019.bngl", + "file": "Lin_ERK_2019.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Gardner_2000", - "name": "Gardner 2000", - "description": "Genetic toggle switch", + "id": "Lin_Prion_2019", + "name": "Lin 2019", + "description": "Prion replication", "tags": [ - "published", - "synthetic-biology", - "gardner", - "2000" + "2019", + "lin", + "linprion", + "prion", + "prp" ], - "category": "synthetic-biology", + "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "synthetic-biology" + "neuroscience" ], - "path": "Published/Gardner2000/genetic_switch_gardner2000.bngl", - "file": "genetic_switch_gardner2000.bngl", + "path": "Published/LinPrion2019/Lin_Prion_2019.bngl", + "file": "Lin_Prion_2019.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "gas6-axl-signaling", - "name": "gas6 axl signaling", - "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", + "id": "Lin_ScalingBench_2019_ERK_model", + "name": "Lin et al. 2019: Scaling Benchmark Models (ERK_model)", + "description": "filename: ERK_model.bngl", "tags": [ - "gas6", - "axl", - "signaling", - "pi3k", - "akt", - "socs", - "survival_burst" + "scaling-benchmark", + "kinetics", + "2019", + "lin" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, - "gallery": [ - "test-models" - ], - "path": "Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl", - "file": "gas6-axl-signaling.bngl", + "gallery": [], + "path": "Published/Lin2019/ERK_model.bngl", + "file": "ERK_model.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "gene-expression-toggle", - "name": "gene expression toggle", - "description": "Kinetic Parameters", + "id": "Lin_ScalingBench_2019_prion_model", + "name": "Lin et al. 2019: Scaling Benchmark Models (prion_model)", + "description": "filename: ERK_model.bngl", "tags": [ - "gene", - "expression", - "toggle", - "mrna", - "protein" + "scaling-benchmark", + "kinetics", + "2019", + "lin" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, - "gallery": [ - "test-models" - ], - "path": "Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl", - "file": "gene-expression-toggle.bngl", + "gallery": [], + "path": "Published/Lin2019/prion_model.bngl", + "file": "prion_model.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "genetic_bistability_energy", - "name": "genetic bistability energy", - "description": "Model: genetic_bistability_energy.bngl", + "id": "Lin_ScalingBench_2019_TCR_model", + "name": "Lin et al. 2019: Scaling Benchmark Models (TCR_model)", + "description": "filename: ERK_model.bngl", "tags": [ - "genetic", - "bistability", - "energy", - "genea", - "geneb", - "prota", - "protb" + "scaling-benchmark", + "kinetics", + "2019", + "lin" ], - "category": "gene-expression", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Published/Lin2019/TCR_model.bngl", + "file": "TCR_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Lin_TCR_2019", + "name": "Lin 2019", + "description": "TCR signaling", + "tags": [ + "2019", + "erk", + "immune", + "lck", + "lin", + "lintcr", + "mek", + "pmhc", + "shp", + "signaling", + "tcr", + "zap" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" ] }, "gallery": [ - "test-models" + "immunology" ], - "path": "Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl", - "file": "genetic_bistability_energy.bngl", + "path": "Published/LinTCR2019/Lin_TCR_2019.bngl", + "file": "Lin_TCR_2019.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "genetic_dna_replication_stochastic", - "name": "genetic dna replication stochastic", - "description": "Model: genetic_dna_replication_stochastic.bngl", + "id": "lipid-mediated-pip3-signaling", + "name": "lipid mediated pip3 signaling", + "description": "Kinetic Parameters", "tags": [ - "genetic", - "dna", - "replication", - "stochastic", - "pol", - "n", - "generate_network" + "lipid", + "mediated", + "pip3", + "signaling", + "pi3k", + "pip2", + "pten", + "pdk1" ], - "category": "gene-expression", + "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" @@ -6992,92 +6623,91 @@ "gallery": [ "test-models" ], - "path": "Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl", - "file": "genetic_dna_replication_stochastic.bngl", + "path": "Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl", + "file": "lipid-mediated-pip3-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "genetic_goodwin_oscillator", - "name": "genetic goodwin oscillator", - "description": "Model: genetic_goodwin_oscillator.bngl", + "id": "Lisman", + "name": "Lisman", + "description": "title: auto.bngl", "tags": [ - "genetic", - "goodwin", - "oscillator", - "gene", - "mrna", - "protein", - "repressor" + "lisman", + "input" ], - "category": "gene-expression", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "neuroscience", + "native-tutorials" ], - "path": "Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl", - "file": "genetic_goodwin_oscillator.bngl", + "path": "Tutorials/NativeTutorials/Lisman/Lisman.bngl", + "file": "Lisman.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "genetic_translation_kinetics", - "name": "genetic translation kinetics", - "description": "Model: genetic_translation_kinetics.bngl", + "id": "Lisman_bifurcate", + "name": "Lisman bifurcate", + "description": "title: Lisman_bifurcate.bngl", "tags": [ - "genetic", - "translation", - "kinetics", - "mrna", - "rib", - "protein" + "lisman", + "bifurcate" ], - "category": "gene-expression", - "origin": "ai-generated", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "neuroscience", + "native-tutorials" ], - "path": "Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl", - "file": "genetic_translation_kinetics.bngl", + "path": "Tutorials/NativeTutorials/Lismanbifurcate/Lisman_bifurcate.bngl", + "file": "Lisman_bifurcate.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "genetic_turing_pattern_1d", - "name": "genetic turing pattern 1d", - "description": "Model: genetic_turing_pattern_1d.bngl", + "id": "localfunc", + "name": "localfunc", + "description": "Test local function expansion", "tags": [ - "genetic", - "turing", - "pattern", - "1d", - "a", - "b" + "localfunc", + "trash", + "f_synth" ], - "category": "gene-expression", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -7087,22 +6717,23 @@ ] }, "gallery": [ - "test-models" + "validation" ], - "path": "Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl", - "file": "genetic_turing_pattern_1d.bngl", + "path": "Tutorials/localfunc/localfunc.bngl", + "file": "localfunc.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "GK", - "name": "GK", - "description": "title: GK.bngl", + "id": "LR", + "name": "LR", + "description": "title: LR.bngl", "tags": [ - "gk", - "b", - "simulate" + "lr" ], "category": "tutorial", "origin": "tutorial", @@ -7116,63 +6747,57 @@ ] }, "gallery": [ - "metabolism", "native-tutorials" ], - "path": "Tutorials/NativeTutorials/GK/GK.bngl", - "file": "GK.bngl", + "path": "Tutorials/NativeTutorials/LR/LR.bngl", + "file": "LR.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "glioblastoma-egfrviii-signaling", - "name": "glioblastoma egfrviii signaling", - "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", + "id": "LR_comp", + "name": "LR comp", + "description": "title: LR_comp.bngl", "tags": [ - "glioblastoma", - "egfrviii", - "signaling", - "pi3k", - "akt", - "oncogenic_output", - "v_viii_act" + "lr", + "comp" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer", - "test-models" + "native-tutorials" ], - "path": "Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl", - "file": "glioblastoma-egfrviii-signaling.bngl", + "path": "Tutorials/NativeTutorials/LRcomp/LR_comp.bngl", + "file": "LR_comp.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "glycolysis-branch-point", - "name": "glycolysis branch point", - "description": "BioNetGen model: glycolysis branch point", + "id": "LRR", + "name": "LRR", + "description": "title: LRR.bngl", "tags": [ - "glycolysis", - "branch", - "point", - "glucose", - "atp", - "biomass" + "lrr" ], - "category": "signaling", - "origin": "ai-generated", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -7183,66 +6808,28 @@ ] }, "gallery": [ - "metabolism", - "test-models" - ], - "path": "Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl", - "file": "glycolysis-branch-point.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "gm_game_of_life", - "name": "gm game of life", - "description": "Model: gm_game_of_life.bngl", - "tags": [ - "gm", - "game", - "of", - "life", - "cell" - ], - "category": "computer-science", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ssa" - ] - }, - "gallery": [ - "test-models" + "native-tutorials" ], - "path": "Examples/generative/gmgameoflife/gm_game_of_life.bngl", - "file": "gm_game_of_life.bngl", + "path": "Tutorials/NativeTutorials/LRR/LRR.bngl", + "file": "LRR.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "gm_ray_marcher", - "name": "gm ray marcher", - "description": "Ray Marching Renderer in BNGL", + "id": "LRR_comp", + "name": "LRR comp", + "description": "title: LRR_comp.bngl", "tags": [ - "gm", - "ray", - "marcher", - "ray0", - "hit0", - "bright0", - "sdf0", - "sdf1", - "sdf2", - "sdf3", - "speed0" + "lrr", + "comp" ], - "category": "computer-science", - "origin": "ai-generated", - "visible": false, + "category": "tutorial", + "origin": "tutorial", + "visible": true, "compatibility": { "bng2": true, "nfsim": true, @@ -7252,86 +6839,92 @@ ] }, "gallery": [ - "test-models" + "native-tutorials" ], - "path": "Examples/generative/gmraymarcher/gm_ray_marcher.bngl", - "file": "gm_ray_marcher.bngl", + "path": "Tutorials/NativeTutorials/LRRcomp/LRR_comp.bngl", + "file": "LRR_comp.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Goldstein_1980", - "name": "Goldstein 1980", - "description": "BLBR heterogeneity", + "id": "LV", + "name": "LV", + "description": "title: LV.bgl", "tags": [ - "published", - "physics", - "goldstein", - "1980" + "lv", + "writesbml" ], - "category": "physics", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "physics" + "native-tutorials" ], - "path": "Published/Goldstein1980/blbr_heterogeneity_goldstein1980.bngl", - "file": "blbr_heterogeneity_goldstein1980.bngl", + "path": "Tutorials/NativeTutorials/LV/LV.bngl", + "file": "LV.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "gpcr-desensitization-arrestin", - "name": "gpcr desensitization arrestin", - "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", + "id": "LV_comp", + "name": "LV comp", + "description": "title: LV_comp.bgl", "tags": [ - "gpcr", - "desensitization", - "arrestin", - "ligand", - "gprotein" + "lv", + "comp" ], - "category": "signaling", - "origin": "ai-generated", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ode", + "ssa" ] }, "gallery": [ - "test-models" + "native-tutorials" ], - "path": "Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl", - "file": "gpcr-desensitization-arrestin.bngl", + "path": "Tutorials/NativeTutorials/LVcomp/LV_comp.bngl", + "file": "LV_comp.bngl", "collectionId": null, "featured": false, - 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"Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl", - "file": "insulin-glucose-homeostasis.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "interferon-signaling", - "name": "interferon signaling", - "description": "Rate Constants", - "tags": [ - "interferon", - "signaling", - "ifn", - "ifnar", - "tyk2", - "stat1" - ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "immunology", - "test-models" - ], - "path": "Examples/biology/interferonsignaling/interferon-signaling.bngl", - "file": "interferon-signaling.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "ire1a-xbp1-er-stress", - "name": "ire1a xbp1 er stress", - "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", - "tags": [ - "ire1a", - 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"issue_198_short.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "jak-stat-cytokine-signaling", - "name": "jak stat cytokine signaling", - "description": "Rate Constants", - "tags": [ - "jak", - "stat", - "cytokine", - "signaling", - "receptor" - ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "immunology", - "test-models" - ], - "path": "Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl", - "file": "jak-stat-cytokine-signaling.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "Jaruszewicz-Blonska_2023", - "name": "Jaruszewicz 2023", - "description": "T-cell discrimination", - "tags": [ - "published", - "immunology", - "jaruszewicz", - "blonska", - "2023", - "ikk", - "ikba", - "ikba_mrna", - "a20", - "nfkb" - ], - 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"featured": false, - "difficulty": "advanced" - }, - { - "id": "jobs_ground", - "name": "30-jobs", - "description": "NFsim simulation of the job market", - "tags": [ - "other" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [], - "path": "Published/Mitra2019/30-jobs/jobs_ground.bngl", - "file": "jobs_ground.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "jobs_tofit", - "name": "30-jobs", - "description": "NFsim simulation of the job market", - "tags": [ - "other" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [], - "path": "Published/Mitra2019/30-jobs/jobs_tofit.bngl", - "file": "jobs_tofit.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "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", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "neuroscience" - ], - "path": "Published/Jung2017/Jung_2017.bngl", - "file": "Jung_2017.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "Kesseler_2013", - "name": "Kesseler 2013", - "description": "G2/Mitosis transition", - "tags": [ - "published", - "kesseler", - "2013", - "mpf", - "cdc25", - "wee1", - "myt1", - "pin1", - "pp2a", - "prox", - "e33" - ], - "category": "signaling", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": false, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "cell-cycle" - ], - "path": "Published/Kesseler2013/Kesseler_2013.bngl", - "file": "Kesseler_2013.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "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", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Tutorials/Kiefhaberemodel/Kiefhaber_emodel.bngl", - "file": "Kiefhaber_emodel.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "kir-channel-regulation", - "name": "kir channel regulation", - "description": "Kir Channel Regulation: PIP2 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"published", - "visible": false, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "cancer" - ], - "path": "Published/Kozer2013/Kozer_2013.bngl", - "file": "Kozer_2013.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "Kozer_2014", - "name": "Kozer 2014", - "description": "Grb2-EGFR recruitment", - "tags": [ - "published", - "kozer", - "2014", - "egf", - "egfr", - "grb2" - ], - "category": "signaling", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "cancer" - ], - "path": "Published/Kozer2014/Kozer_2014.bngl", - "file": "Kozer_2014.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "l-type-calcium-channel-dynamics", - "name": "l type calcium channel dynamics", - "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", - "tags": [ - "l", - "type", - "calcium", - "channel", - "dynamics", - "ltcc", - "voltage", - "v_open", - "v_inact" - ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "neuroscience", - "test-models" - ], - "path": "Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl", - "file": "l-type-calcium-channel-dynamics.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "lac-operon-regulation", - "name": "lac operon regulation", - "description": "Kinetic Parameters", - "tags": [ - "lac", - "operon", - "regulation", - "laci", - "promoter", - "mrna", - "betagal", - "lactose", - "allolactose" - ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, 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null, - "featured": false, - "difficulty": "advanced" - }, - { - "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", - "origin": "published", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode", - "ssa" - ] - }, - "gallery": [ - "developmental" - ], - "path": "Published/LinERK2019/Lin_ERK_2019.bngl", - "file": "Lin_ERK_2019.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "Lin_Prion_2019", - "name": "Lin 2019", - "description": "Prion replication", - "tags": [ - "published", - "literature", - "prion", - "lin", - "2019", - "prp", - "scaledupspecies1", - "scaledupspecies2", - "scaledupspecies15", - "scaledupspecies30" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode", - "ssa" - ] - }, - "gallery": [ - "neuroscience" - ], - "path": "Published/LinPrion2019/Lin_Prion_2019.bngl", - "file": "Lin_Prion_2019.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "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", - "origin": "published", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode", - "ssa" - ] - }, - "gallery": [ - "immunology" - ], - "path": "Published/LinTCR2019/Lin_TCR_2019.bngl", - "file": "Lin_TCR_2019.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "lipid-mediated-pip3-signaling", - "name": "lipid mediated pip3 signaling", - "description": "Kinetic Parameters", - "tags": [ - "lipid", - "mediated", - "pip3", - "signaling", - "pi3k", - "pip2", - "pten", - "pdk1" - ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "test-models" - ], - "path": "Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl", - "file": "lipid-mediated-pip3-signaling.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "Lisman", - "name": "Lisman", - "description": "title: auto.bngl", - "tags": [ - "lisman", - "k1", - "p", - "input", - "visualize", - "setparameter", - "simulate" - ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - 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"SI_files_Florida_Florida", - "file": "SI_files_Florida_Florida.bngl" - }, - { - "id": "SI_files_Georgia_Georgia", - "file": "SI_files_Georgia_Georgia.bngl" - }, - { - "id": "SI_files_Hawaii_Hawaii", - "file": "SI_files_Hawaii_Hawaii.bngl" - }, - { - "id": "SI_files_Idaho_Idaho", - "file": "SI_files_Idaho_Idaho.bngl" - }, - { - "id": "SI_files_Illinois_Illinois", - "file": "SI_files_Illinois_Illinois.bngl" - }, - { - "id": "SI_files_Indiana_Indiana", - "file": "SI_files_Indiana_Indiana.bngl" - }, - { - "id": "SI_files_Iowa_Iowa", - "file": "SI_files_Iowa_Iowa.bngl" - }, - { - "id": "SI_files_Kansas_Kansas", - "file": "SI_files_Kansas_Kansas.bngl" - }, - { - "id": "SI_files_Kentucky_Kentucky", - "file": "SI_files_Kentucky_Kentucky.bngl" - }, - { - "id": "SI_files_Louisiana_Louisiana", - "file": "SI_files_Louisiana_Louisiana.bngl" - }, - { - "id": "SI_files_Maine_Maine", - "file": "SI_files_Maine_Maine.bngl" - }, - { - "id": "SI_files_Maryland_Maryland", - "file": "SI_files_Maryland_Maryland.bngl" - }, - { - "id": "SI_files_Massachusetts_Massachusetts", - "file": "SI_files_Massachusetts_Massachusetts.bngl" - }, - { - "id": "SI_files_Michigan_Michigan", - "file": "SI_files_Michigan_Michigan.bngl" - }, - { - "id": "SI_files_Minnesota_Minnesota", - "file": "SI_files_Minnesota_Minnesota.bngl" - }, - { - "id": "SI_files_Mississippi_Mississippi", - "file": "SI_files_Mississippi_Mississippi.bngl" - }, - { - "id": "SI_files_Missouri_Missouri", - "file": "SI_files_Missouri_Missouri.bngl" - }, - { - "id": "SI_files_Montana_Montana", - "file": "SI_files_Montana_Montana.bngl" - }, - { - "id": "SI_files_Nebraska_Nebraska", - "file": "SI_files_Nebraska_Nebraska.bngl" - }, - { - "id": "SI_files_Nevada_Nevada", - "file": "SI_files_Nevada_Nevada.bngl" - }, - { - "id": "SI_files_NewHampshire_NewHampshire", - "file": "SI_files_NewHampshire_NewHampshire.bngl" - }, - { - "id": "SI_files_NewJersey_NewJersey", - "file": "SI_files_NewJersey_NewJersey.bngl" - }, - { - "id": "SI_files_NewMexico_NewMexico", - "file": "SI_files_NewMexico_NewMexico.bngl" - }, - { - "id": "SI_files_NewYork_NewYork", - "file": "SI_files_NewYork_NewYork.bngl" - }, - { - "id": "SI_files_NorthCarolina_NorthCarolina", - "file": "SI_files_NorthCarolina_NorthCarolina.bngl" - }, - { - "id": "SI_files_NorthDakota_NorthDakota", - "file": "SI_files_NorthDakota_NorthDakota.bngl" - }, - { - "id": "SI_files_Ohio_Ohio", - "file": "SI_files_Ohio_Ohio.bngl" - }, - { - "id": "SI_files_Oklahoma_Oklahoma", - "file": "SI_files_Oklahoma_Oklahoma.bngl" - }, - { - "id": "SI_files_Oregon_Oregon", - "file": "SI_files_Oregon_Oregon.bngl" - }, - { - "id": "SI_files_Pennsylvania_Pennsylvania", - "file": "SI_files_Pennsylvania_Pennsylvania.bngl" - }, - { - "id": "SI_files_RhodeIsland_RhodeIsland", - "file": "SI_files_RhodeIsland_RhodeIsland.bngl" - }, - { - "id": "SI_files_SouthCarolina_SouthCarolina", - "file": "SI_files_SouthCarolina_SouthCarolina.bngl" - }, - { - "id": "SI_files_SouthDakota_SouthDakota", - "file": "SI_files_SouthDakota_SouthDakota.bngl" - }, - { - "id": "SI_files_Tennessee_Tennessee", - "file": "SI_files_Tennessee_Tennessee.bngl" - }, - { - "id": "SI_files_Texas_Texas", - "file": "SI_files_Texas_Texas.bngl" - }, - { - "id": "SI_files_Utah_Utah", - "file": "SI_files_Utah_Utah.bngl" - }, - { - "id": "SI_files_Vermont_Vermont", - "file": "SI_files_Vermont_Vermont.bngl" - }, - { - "id": "SI_files_Virginia_Virginia", - "file": "SI_files_Virginia_Virginia.bngl" - }, - { - "id": "SI_files_Washington_Washington", - "file": "SI_files_Washington_Washington.bngl" - }, - { - "id": "SI_files_WestVirginia_WestVirginia", - "file": "SI_files_WestVirginia_WestVirginia.bngl" - }, - { - "id": "SI_files_Wisconsin_Wisconsin", - "file": "SI_files_Wisconsin_Wisconsin.bngl" - }, - { - "id": "SI_files_Wyoming_Wyoming", - "file": "SI_files_Wyoming_Wyoming.bngl" - } - ] - }, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "Mallela2022_MSAs", - "name": "Mallela 2022 - COVID-19 MSA Models", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "epidemiology" + "epidemiology" ], "path": "Published/Mallela2022_MSAs/Abilene_TX_Abilene_TX.bngl", "file": "Abilene_TX_Abilene_TX.bngl", - "collectionId": "Mallela2022_MSAs", + "collectionId": "Mallela_MSAs_2022", "collection": { "type": "geographic-variants", "count": 281, @@ -10681,325 +8387,2362 @@ "file": "Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ.bngl" }, { - "id": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC", - "file": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC.bngl" + "id": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC", + "file": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC.bngl" + }, + { + "id": "Visalia_CA_Visalia_CA", + "file": "Visalia_CA_Visalia_CA.bngl" + }, + { + "id": "Warner_Robins_GA_Warner_Robins_GA", + "file": "Warner_Robins_GA_Warner_Robins_GA.bngl" + }, + { + "id": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV", + "file": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV.bngl" + }, + { + "id": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA", + "file": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA.bngl" + }, + { + "id": "Wenatchee_WA_Wenatchee_WA", + "file": "Wenatchee_WA_Wenatchee_WA.bngl" + }, + { + "id": "Wheeling_WV-OH_Wheeling_WV-OH", + "file": "Wheeling_WV-OH_Wheeling_WV-OH.bngl" + }, + { + "id": "Wichita_KS_Wichita_KS", + "file": "Wichita_KS_Wichita_KS.bngl" + }, + { + "id": "Winchester_VA-WV_Winchester_VA-WV", + "file": "Winchester_VA-WV_Winchester_VA-WV.bngl" + }, + { + "id": "Winston-Salem_NC_Winston-Salem_NC", + "file": "Winston-Salem_NC_Winston-Salem_NC.bngl" + }, + { + "id": "Worcester_MA-CT_Worcester_MA-CT", + "file": "Worcester_MA-CT_Worcester_MA-CT.bngl" + }, + { + "id": "Yakima_WA_Yakima_WA", + "file": "Yakima_WA_Yakima_WA.bngl" + }, + { + "id": "York-Hanover_PA_York-Hanover_PA", + "file": "York-Hanover_PA_York-Hanover_PA.bngl" + }, + { + "id": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA", + "file": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA.bngl" + }, + { + "id": "Yuma_AZ_Yuma_AZ", + "file": "Yuma_AZ_Yuma_AZ.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Mallela_VaxVariants_Alabama_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - Alabama MSA", + "description": "reporting period (1 d)", + "tags": [ + "covid-19", + "epidemiology", + "vaccination", + "variants", + "alabama", + "2022", + "mallela" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Mallela2022/Alabama/Alabama.bngl", + "file": "Alabama.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Mallela_VaxVariants_Dallas_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - Dallas MSA", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "covid-19", + "epidemiology", + "vaccination", + "variants", + "dallas", + "2022", + "mallela" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/VaxAndVariants/Dallas/Dallas.bngl", + "file": "Dallas.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Mallela_VaxVariants_Houston_2022", + "name": "Mallela et al. 2022: Covid-19 Vax and Variants - Houston MSA", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "covid-19", + "epidemiology", + "vaccination", + "variants", + "houston", + "2022", + "mallela" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ 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"published", - "mertins", - "2023", - "dnadsb", - "p53", - "mrna_bax", - "bax", - "bclxl", - "bad", - "fourteen_3_3", - "caspase" + "raf", + "constraints", + "activity-constraints", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, - "nfsim": true, + "bng2": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "cancer" - ], - "path": "Published/Mertins2023/Mertins_2023.bngl", - "file": "Mertins_2023.bngl", + "gallery": [], + "path": "Published/Mitra2019/19-raf-constraint/RAFi.bngl", + "file": "RAFi.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "meta_formal_game_theory", - "name": "meta formal game theory", - "description": "Model: meta_formal_game_theory.bngl", + "id": "Mitra_RafConstraint4_2019", + "name": "Mitra et al. 2019: Raf Signaling Constraints (Version 4)", + "description": "BNGL model: RAFi", "tags": [ - "meta", - "formal", - "game", - "theory", - "hawk", - "dove", - "pop", - "payoffh", - "payoffd" + "raf", + "constraints", + "activity-constraints", + "2019", + "mitra" ], - "category": "computer-science", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -11009,31 +10752,29 @@ "ode" ] }, - "gallery": [ - "test-models" - ], - "path": "Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl", - "file": "meta_formal_game_theory.bngl", + "gallery": [], + "path": "Published/Mitra2019/20-raf-constraint4/RAFi.bngl", + "file": "RAFi.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, - { - "id": "meta_formal_molecular_clock", - "name": "meta formal molecular clock", - "description": "Model: meta_formal_molecular_clock.bngl", + { + "id": "Mitra_SimpleReceptor_2019_example5_starting_point", + "name": "Mitra et al. 2019: Simple Ligand-Receptor Binding (example5_starting_point)", + "description": "A simple model", "tags": [ - "meta", - "formal", - "molecular", - "clock", - "fasta", - "fastb", - "slowc", - "slowd" + "ligand-receptor", + "binding", + "reversible-reaction", + "2019", + "mitra" ], - "category": "computer-science", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -11043,31 +10784,29 @@ "ode" ] }, - "gallery": [ - "test-models" - ], - "path": "Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl", - "file": "meta_formal_molecular_clock.bngl", + "gallery": [], + "path": "Published/Mitra2019/13-receptor/example5_starting_point.bngl", + "file": "example5_starting_point.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "meta_formal_petri_net", - "name": "meta formal petri net", - "description": "Model: meta_formal_petri_net.bngl", + "id": "Mitra_SimpleReceptor_2019_receptor", + "name": "Mitra et al. 2019: Simple Ligand-Receptor Binding (receptor)", + "description": "A simple model", "tags": [ - "meta", - "formal", - "petri", - "net", - "p1", - "p2", - "p3", - "p4" + "ligand-receptor", + "binding", + "reversible-reaction", + "2019", + "mitra" ], - "category": "computer-science", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -11077,125 +10816,125 @@ "ode" ] }, - "gallery": [ - "test-models" - ], - "path": "Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl", - "file": "meta_formal_petri_net.bngl", + "gallery": [], + "path": "Published/Mitra2019/13-receptor/receptor.bngl", + "file": "receptor.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "michaelis-menten-kinetics", - "name": "michaelis menten kinetics", - "description": "Kinetic Constants", + "id": "Mitra_SimpleReceptor_NF_2019", + "name": "Mitra et al. 2019: Simple Receptor Network-Free Binding", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", "tags": [ - "michaelis", - "menten", - "kinetics", - "e", - "s", - "p", - "generate_network", - "simulate", - "writesbml" + "ligand-receptor", + "binding", + "nfsim", + "network-free", + "2019", + "mitra" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "metabolism", - "test-models" - ], - "path": "Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl", - "file": "michaelis-menten-kinetics.bngl", + "gallery": [], + "path": "Published/Mitra2019/14-receptor-nf/receptor_nf.bngl", + "file": "receptor_nf.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "michment", - "name": "michment", - "description": "Michaelis Menten", + "id": "Mitra_TCR_2019", + "name": "Mitra et al. 2019: T Cell Receptor (TCR) Signaling", + "description": "A model of T cell receptor signaling", "tags": [ - "validation", - "michment", - "e", - "s", - "generate_network" + "tcr", + "t-cell", + "immune-signaling", + "2019", + "mitra" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "immunology", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/michment/michment.bngl", - "file": "michment.bngl", + "gallery": [], + "path": "Published/Mitra2019/12-TCR/tcr.bngl", + "file": "tcr.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "michment_cont", - "name": "michment_cont", - "description": "Michaelis Menten Continue", + "id": "Mitra_TCRSensitivity_2019", + "name": "Mitra et al. 2019: T Cell Receptor Sensitivity Analysis", + "description": "Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data", "tags": [ - "validation", - "michment", - "cont", - "readfile", - "setconcentration", - "simulate_ode", - "addconcentration" + "tcr", + "sensitivity-analysis", + "ligand-discrimination", + "2019", + "mitra" ], - "category": "validation", - "origin": "test-case", + "category": "immunology", + "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/michmentcont/michment_cont.bngl", - "file": "michment_cont.bngl", + "gallery": [], + "path": "Published/Mitra2019/26-tcr-sens/tcr_sens_tofit.bngl", + "file": "tcr_sens_tofit.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Miller2022_NavajoNation", - "name": "Miller 2022 - Navajo Nation Models", - "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", + "id": "Mitra_ThreeStepCascade_2019_m1", + "name": "Mitra et al. 2019: Three-Step Signaling Cascade (m1)", + "description": "Toy model of a 3-step signaling cascade", "tags": [ - "covid-19", - "epidemiology", - "pybionetgen" + "cascade", + "kinase", + "phosphorylation", + "2019", + "mitra" ], - "category": "epidemiology", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -11206,53 +10945,28 @@ "ode" ] }, - "gallery": [ - "epidemiology" - ], - "path": "Published/Miller2022_NavajoNation/supplementary_material_Arizona_Arizona.bngl", - "file": "supplementary_material_Arizona_Arizona.bngl", - "collectionId": "Miller2022_NavajoNation", - "collection": { - "type": "geographic-variants", - "count": 5, - "variant_key": "region", - "variants": [ - { - "id": "supplementary_material_Arizona_Arizona", - "file": "supplementary_material_Arizona_Arizona.bngl" - }, - { - "id": "supplementary_material_Colorado_Colorado", - "file": "supplementary_material_Colorado_Colorado.bngl" - }, - { - "id": "supplementary_material_NavajoNation_NavajoNation", - "file": "supplementary_material_NavajoNation_NavajoNation.bngl" - }, - { - "id": "supplementary_material_NewMexico_NewMexico", - "file": "supplementary_material_NewMexico_NewMexico.bngl" - }, - { - "id": "supplementary_material_Utah_Utah", - "file": "supplementary_material_Utah_Utah.bngl" - } - ] - }, + "gallery": [], + "path": "Published/Mitra2019/05-threestep/m1.bngl", + "file": "m1.bngl", + "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Miller2025_MEK", - "name": "Miller 2025 - MEK Isoform Models", - "description": "MEK isoform variant models curated for PyBioNetGen.", + "id": "Mitra_ThreeStepCascade_2019_m1_ground", + "name": "Mitra et al. 2019: Three-Step Signaling Cascade (m1_ground)", + "description": "Toy model of a 3-step signaling cascade", "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" + "cascade", + "kinase", + "phosphorylation", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -11263,86 +10977,47 @@ "ode" ] }, - "gallery": [ - "signaling" - ], - "path": "Published/Miller2025_MEK/MEK_isoform_aMCMC_MEK1_KO.bngl", - "file": "MEK_isoform_aMCMC_MEK1_KO.bngl", - "collectionId": "Miller2025_MEK", - "collection": { - "type": "parameter-fit-variants", - "count": 10, - "variant_key": "isoform", - "variants": [ - { - "id": "MEK_isoform_aMCMC_MEK1_KO", - "file": "MEK_isoform_aMCMC_MEK1_KO.bngl" - }, - { - "id": "MEK_isoform_aMCMC_MEK1_N78G", - "file": "MEK_isoform_aMCMC_MEK1_N78G.bngl" - }, - { - "id": "MEK_isoform_aMCMC_MEK1_T292A", - "file": "MEK_isoform_aMCMC_MEK1_T292A.bngl" - }, - { - "id": "MEK_isoform_aMCMC_MEK1_T292D", - "file": "MEK_isoform_aMCMC_MEK1_T292D.bngl" - }, - { - "id": "MEK_isoform_aMCMC_MEK1_WT", - "file": "MEK_isoform_aMCMC_MEK1_WT.bngl" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_KO", - "file": "MEK_isoform_optimization_DE_MEK1_KO.bngl" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_N78G", - "file": "MEK_isoform_optimization_DE_MEK1_N78G.bngl" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_T292A", - "file": "MEK_isoform_optimization_DE_MEK1_T292A.bngl" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_T292D", - "file": "MEK_isoform_optimization_DE_MEK1_T292D.bngl" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_WT", - "file": "MEK_isoform_optimization_DE_MEK1_WT.bngl" - } - ] - }, + "gallery": [], + "path": "Published/Mitra2019/05-threestep/m1_ground.bngl", + "file": "m1_ground.bngl", + "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Mitra2019_02_egfr_bnf1_InputFiles_egfr", - "name": "InputFiles", - "description": "EGFR model", + "id": "Mitra_TLBR_2019", + "name": "Mitra et al. 2019: Trivalent Ligand Bivalent Receptor (TLBR)", + "description": "BNGL model: tlbr", "tags": [ - "signaling" + "tlbr", + "polymerization", + "ligand-receptor", + "2019", + "mitra" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [], - "path": "Published/Mitra2019/02-egfr/bnf1/InputFiles/egfr.bngl", - "file": "egfr.bngl", + "path": "Published/Mitra2019/11-TLBR/tlbr.bngl", + "file": "tlbr.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "ml_gradient_descent", @@ -11377,7 +11052,10 @@ "file": "ml_gradient_descent.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "ml_hopfield", @@ -11411,7 +11089,10 @@ "file": "ml_hopfield.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "ml_kmeans", @@ -11444,7 +11125,10 @@ "file": "ml_kmeans.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "ml_q_learning", @@ -11479,7 +11163,10 @@ "file": "ml_q_learning.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "ml_svm", @@ -11513,234 +11200,22 @@ "file": "ml_svm.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" - }, - { - "id": "model", - "name": "model", - "description": "filename: model.bngl", - "tags": [ - "model", - "ag", - "r", - "syk", - "ship1", - "x", - "pip3", - "h" - ], - "category": "other", - "origin": "published", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "other" - ], - "path": "Published/PyBioNetGen/core/model/model.bngl", - "file": "model.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "model", - "name": "model", - "description": "A model of IgE receptor signaling", - "tags": [ - "model", - "ag", - "r", - "syk", - "ship1", - "x", - "pip3", - "h" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "other" - ], - "path": "Published/PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl", - "file": "model.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "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", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [] - }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/model_ground.bngl", - "file": "model_ground.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "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", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "other" - ], - "path": "Published/PyBioNetGen/core/modeltofit/model_tofit.bngl", - "file": "model_tofit.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "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", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "nf" - ] - }, - "gallery": [ - "immunology" - ], - "path": "Published/ModelZAP/Model_ZAP.bngl", - "file": "Model_ZAP.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "Motivating_example", "name": "Motivating_example", "description": "Signal Transduction with receptor internalization", "tags": [ - "validation", "motivating", "example", - "l", - "r", "tf", "dna", "mrna1", - "mrna2", - "p1", - "p2" + "mrna2" ], "category": "validation", "origin": "test-case", @@ -11760,25 +11235,23 @@ "file": "Motivating_example.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "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" + "mrna2" ], "category": "validation", "origin": "test-case", @@ -11798,18 +11271,18 @@ "file": "Motivating_example_cBNGL.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "motor", "name": "motor", "description": "Motor protein", "tags": [ - "validation", "motor", - "chey", - "kplus", - "kminus" + "chey" ], "category": "validation", "origin": "test-case", @@ -11829,7 +11302,10 @@ "file": "motor.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mt_arithmetic_compiler", @@ -11862,7 +11338,10 @@ "file": "mt_arithmetic_compiler.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mt_bngl_interpreter", @@ -11897,7 +11376,10 @@ "file": "mt_bngl_interpreter.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mt_music_sequencer", @@ -11935,7 +11417,10 @@ "file": "mt_music_sequencer.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "mt_pascal_triangle", @@ -11966,7 +11451,10 @@ "file": "mt_pascal_triangle.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mt_quine", @@ -11997,7 +11485,10 @@ "file": "mt_quine.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mtor-signaling", @@ -12030,7 +11521,10 @@ "file": "mtor-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "mtorc2-signaling", @@ -12064,21 +11558,21 @@ "file": "mtorc2-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Mukhopadhyay_2013", - "name": "Mukhopadhyay 2013", + "id": "Mukhopadhyay_TCR_2013", + "name": "Mukhopadhyay et al. 2013: T Cell Receptor Phosphorylation Model", "description": "FceRI signaling", "tags": [ - "published", - "immunology", - "mukhopadhyay", + "tcr", + "phosphorylation", + "immune-signaling", "2013", - "s", - "e", - "f", - "z" + "mukhopadhyay" ], "category": "immunology", "origin": "published", @@ -12098,19 +11592,18 @@ "file": "Mukhopadhyay_2013.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "mwc", "name": "mwc", "description": "Monod-Wyman-Changeux model", "tags": [ - "validation", "mwc", - "setoption", - "h", - "ox", - "b" + "ox" ], "category": "validation", "origin": "test-case", @@ -12130,7 +11623,10 @@ "file": "mwc.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "myogenic-differentiation", @@ -12162,55 +11658,21 @@ "file": "myogenic-differentiation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" - }, - { - "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", - "origin": "contributed", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "other" - ], - "path": "Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", - "file": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Nag_2009", - "name": "Nag 2009", + "id": "Nag_cancer_2009", + "name": "Nag et al. 2009: EGFR-Her2 Heterodimerization Dynamics", "description": "LAT-Grb2-SOS1 signaling", "tags": [ - "published", - "nag", + "egfr", + "her2", + "heterodimerization", "2009", - "lig", - "lyn", - "syk", - "rec", - "lat", - "grb", - "sos" + "nag" ], "category": "signaling", "origin": "published", @@ -12230,7 +11692,10 @@ "file": "Nag_2009.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "negative-feedback-loop", @@ -12262,7 +11727,10 @@ "file": "negative-feedback-loop.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "neurotransmitter-release", @@ -12295,21 +11763,22 @@ "file": "neurotransmitter-release.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "nfkb", "name": "nfkb", "description": "NF-kB signaling pathway", "tags": [ - "validation", "nfkb", "tnfr", "ikkk", "tnf", "ikk", "ikba", - "a20", "competitor" ], "category": "validation", @@ -12330,14 +11799,16 @@ "file": "nfkb.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfkb_illustrating_protocols", "name": "nfkb_illustrating_protocols", "description": "NF-kB signaling pathway", "tags": [ - "validation", "nfkb", "illustrating", "protocols", @@ -12346,7 +11817,6 @@ "tnf", "ikk", "ikba", - "a20", "competitor" ], "category": "validation", @@ -12367,7 +11837,10 @@ "file": "nfkb_illustrating_protocols.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfkb-feedback", @@ -12381,54 +11854,27 @@ "a20" ], "category": "signaling", - "origin": "ai-generated", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "test-models" - ], - "path": "Examples/biology/nfkbfeedback/nfkb-feedback.bngl", - "file": "nfkb-feedback.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "NFmodel", - "name": "NFmodel", - "description": "BioNetGen model: NFmodel", - "tags": [ - "nfmodel", - "ag", - "ab", - "simulate" - ], - "category": "validation", - "origin": "test-case", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": true, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "validation" + "test-models" ], - "path": "Published/PyBioNetGen/tests/NFmodel/NFmodel.bngl", - "file": "NFmodel.bngl", + "path": "Examples/biology/nfkbfeedback/nfkb-feedback.bngl", + "file": "nfkb-feedback.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "nfsim_aggregation_gelation", @@ -12458,7 +11904,10 @@ "file": "nfsim_aggregation_gelation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfsim_coarse_graining", @@ -12488,7 +11937,10 @@ "file": "nfsim_coarse_graining.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfsim_dynamic_compartments", @@ -12520,7 +11972,10 @@ "file": "nfsim_dynamic_compartments.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfsim_hybrid_particle_field", @@ -12550,7 +12005,10 @@ "file": "nfsim_hybrid_particle_field.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nfsim_ring_closure_polymer", @@ -12583,7 +12041,10 @@ "file": "nfsim_ring_closure_polymer.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "nn_xor", @@ -12619,23 +12080,25 @@ "file": "nn_xor.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "no_frees", - "name": "no frees", - "description": "Original values used to generate parabola.exp", + "id": "no-cgmp-signaling", + "name": "no cgmp signaling", + "description": "Nitric Oxide (NO) / cGMP signaling pathway.", "tags": [ "no", - "frees", - "counter", - "y", - "generate_network", - "simulate" + "cgmp", + "signaling", + "sgc", + "pkg" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "signaling", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -12645,28 +12108,99 @@ ] }, "gallery": [ - "validation" + "metabolism", + "test-models" ], - "path": "Published/PyBioNetGen/tests/nofrees/no_frees.bngl", - "file": "no_frees.bngl", + "path": "Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl", + "file": "no-cgmp-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "no_generate_network", - "name": "no generate network", - "description": "Original values used to generate parabola.exp", + "id": "Nosbisch_cancer_2022", + "name": "Nosbisch et al. 2022: RTK Heterodimerization Modeling", + "description": "RTK-PLCgamma1 signaling", "tags": [ - "no", - "generate", - "network", - "counter", - "y", - "simulate" + "rtk", + "heterodimerization", + "cancer", + "2022", + "nosbisch" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Nosbisch2022/Nosbisch_2022.bngl", + "file": "Nosbisch_2022.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Notch_Signaling_Pathway", + "name": "Canonical Notch Signaling Pathway Model", + "description": "Notch signaling", + "tags": [ + "notch-signaling", + "csl-binding", + "fringe-regulation", + "developmental-signaling" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/notch/notch.bngl", + "file": "notch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "notch-delta-lateral-inhibition", + "name": "notch delta lateral inhibition", + "description": "Notch-Delta Lateral Inhibition", + "tags": [ + "notch", + "delta", + "lateral", + "inhibition", + "cellnotch", + "celldelta" + ], + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, @@ -12677,31 +12211,100 @@ ] }, "gallery": [ - "validation" + "developmental", + "test-models" ], - "path": "Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl", - "file": "no_generate_network.bngl", + "path": "Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl", + "file": "notch-delta-lateral-inhibition.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "no_suffix", - "name": "no suffix", - "description": "Original values used to generate parabola.exp", + "id": "Ordyan_CaMKIIholo_2020", + "name": "Ordyan et al. 2020: CaMKII Holoenzyme Activation Model", + "description": "CaMKII holo", "tags": [ - "no", - "suffix", - "counter", - "y", - "generate_network", - "simulate" + "camkii", + "holoenzyme", + "neuroscience", + "2020", + "ordyan" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Ordyan2020/CaMKIIholo/CaMKII_holo.bngl", + "file": "CaMKII_holo.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "Ordyan_extraCaMKIIHolo_2020", + "name": "Ordyan et al. 2020: CaMKII Holoenzyme Extra Subunits Model", + "description": "Extra CaMKII holo (supplement)", + "tags": [ + "camkii", + "holoenzyme", + "neuroscience", + "2020", + "ordyan" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Ordyan2020/extraCaMKIIHolo/extra_CaMKII_Holo.bngl", + "file": "extra_CaMKII_Holo.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "Ordyan_mCaMKIICaSpike_2020", + "name": "Ordyan et al. 2020: CaMKII Activation under Calcium Spikes", + "description": "mCaMKII Ca Spike model", + "tags": [ + "camkii", + "calcium-spikes", + "neuroscience", + "2020", + "ordyan" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -12709,24 +12312,127 @@ ] }, "gallery": [ - "validation" + "signaling" + ], + "path": "Published/Ordyan2020/mCaMKIICaSpike/mCaMKII_Ca_Spike.bngl", + "file": "mCaMKII_Ca_Spike.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "organelle_transport", + "name": "organelle transport", + "description": "title: organelle_transport.bngl", + "tags": [ + "organelle", + "transport" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/organelletransport/organelle_transport.bngl", + "file": "organelle_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "organelle_transport_struct", + "name": "organelle transport struct", + "description": "title: organelle_transport_abcd.bngl", + "tags": [ + "organelle", + "transport", + "struct" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/organelletransportstruct/organelle_transport_struct.bngl", + "file": "organelle_transport_struct.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "oxidative-stress-response", + "name": "oxidative stress response", + "description": "Oxidative Stress Response (Keap1-Nrf2 Pathway)", + "tags": [ + "oxidative", + "stress", + "response", + "ros", + "keap1", + "nrf2", + "antioxidant" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" ], - "path": "Published/PyBioNetGen/tests/nosuffix/no_suffix.bngl", - "file": "no_suffix.bngl", + "path": "Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl", + "file": "oxidative-stress-response.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "no-cgmp-signaling", - "name": "no cgmp signaling", - "description": "Nitric Oxide (NO) / cGMP signaling pathway.", + "id": "p38-mapk-signaling", + "name": "p38 mapk signaling", + "description": "p38 MAPK stress signaling cascade.", "tags": [ - "no", - "cgmp", + "p38", + "mapk", "signaling", - "sgc", - "pkg" + "mkk3", + "mapkap2", + "v_thermal" ], "category": "signaling", "origin": "ai-generated", @@ -12740,67 +12446,70 @@ ] }, "gallery": [ - "metabolism", + "cancer", "test-models" ], - "path": "Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl", - "file": "no-cgmp-signaling.bngl", + "path": "Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl", + "file": "p38-mapk-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Nosbisch_2022", - "name": "Nosbisch 2022", - "description": "RTK-PLCgamma1 signaling", + "id": "p53-mdm2-oscillator", + "name": "p53 mdm2 oscillator", + "description": "BioNetGen model: p53 mdm2 oscillator", "tags": [ - "published", - "nosbisch", - "2022", - "rtk", - "plcgamma1", + "p53", + "mdm2", + "oscillator", "generate_network" ], "category": "signaling", - "origin": "published", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, - "nfsim": false, + "bng2": true, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer" + "cell-cycle", + "test-models" ], - "path": "Published/Nosbisch2022/Nosbisch_2022.bngl", - "file": "Nosbisch_2022.bngl", + "path": "Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl", + "file": "p53-mdm2-oscillator.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "notch", - "name": "Notch", - "description": "Notch signaling", + "id": "parp1-mediated-dna-repair", + "name": "parp1 mediated dna repair", + "description": "PARP1-mediated DNA damage sensing and repair.", "tags": [ - "published", - "notch", - "icn", - "ofut1", - "fringe", - "furin", - "dsl", - "csl", - "maml" + "parp1", + "mediated", + "dna", + "repair", + "par", + "nad", + "v_parylate" ], - "category": "regulation", - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -12808,226 +12517,237 @@ ] }, "gallery": [ - "regulation" + "cell-cycle", + "test-models" ], - "path": "Published/notch/notch.bngl", - "file": "notch.bngl", + "path": "Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl", + "file": "parp1-mediated-dna-repair.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "notch-delta-lateral-inhibition", - "name": "notch delta lateral inhibition", - "description": "Notch-Delta Lateral Inhibition", + "id": "Pekalski_published_2013", + "name": "Pekalski et al. 2013: TNFR-Mediated NF-kB Activation Model", + "description": "Spontaneous signaling", "tags": [ - "notch", - "delta", - "lateral", - "inhibition", - "cellnotch", - "celldelta" + "tnfr", + "nfkb", + "inflammatory-signaling", + "2013", + "pekalski" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "regulation", + "origin": "published", + "visible": true, "compatibility": { - "bng2": true, - "nfsim": true, + "bng2": false, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "developmental", - "test-models" + "regulation" ], - "path": "Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl", - "file": "notch-delta-lateral-inhibition.bngl", + "path": "Published/Pekalski2013/Pekalski_2013.bngl", + "file": "Pekalski_2013.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "NYC", - "name": "NYC", - "description": "- This model is intended to be consistent with the compartmental model", + "id": "ph_lorenz_attractor", + "name": "ph lorenz attractor", + "description": "Lorenz Attractor in BNGL", "tags": [ - "nyc", - "counter", - "fdcs", - "s", - "sv", - "e", - "a", - "i", - "v" + "ph", + "lorenz", + "attractor", + "lx", + "ly", + "lz", + "x", + "y" ], - "category": "epidemiology", - "origin": "published", + "category": "physics", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "epidemiology" + "physics", + "test-models" ], - "path": "Published/VaxAndVariants/NYC/NYC.bngl", - "file": "NYC.bngl", + "path": "Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl", + "file": "ph_lorenz_attractor.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "organelle_transport", - "name": "organelle transport", - "description": "title: organelle_transport.bngl", + "id": "ph_nbody_gravity", + "name": "ph nbody gravity", + "description": "Model: ph_nbody_gravity.bngl", "tags": [ - "organelle", - "transport", - "a", - "b", - "c", - "d", - "t1", - "at1", - "ct1", - "t2" + "ph", + "nbody", + "gravity", + "body", + "r2" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "physics", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "physics", + "test-models" ], - "path": "Tutorials/NativeTutorials/organelletransport/organelle_transport.bngl", - "file": "organelle_transport.bngl", + "path": "Examples/physics/phnbodygravity/ph_nbody_gravity.bngl", + "file": "ph_nbody_gravity.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "organelle_transport_struct", - "name": "organelle transport struct", - "description": "title: organelle_transport_abcd.bngl", + "id": "ph_schrodinger", + "name": "ph schrodinger", + "description": "Model: ph_schrodinger.bngl", "tags": [ - "organelle", - "transport", - "struct", - "a", - "b", - "t1", - "t2" + "ph", + "schrodinger", + "psi" ], - "category": "tutorial", - "origin": "tutorial", - "visible": true, + "category": "physics", + "origin": "ai-generated", + "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "native-tutorials" + "physics", + "test-models" ], - "path": "Tutorials/NativeTutorials/organelletransportstruct/organelle_transport_struct.bngl", - "file": "organelle_transport_struct.bngl", + "path": "Examples/physics/phschrodinger/ph_schrodinger.bngl", + "file": "ph_schrodinger.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "oxidative-stress-response", - "name": "oxidative stress response", - "description": "Oxidative Stress Response (Keap1-Nrf2 Pathway)", + "id": "ph_wave_equation", + "name": "ph wave equation", + "description": "Model: ph_wave_equation.bngl", "tags": [ - "oxidative", - "stress", - "response", - "ros", - "keap1", - "nrf2", - "antioxidant" + "ph", + "wave", + "equation", + "node" ], - "category": "signaling", + "category": "physics", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ + "physics", "test-models" ], - "path": "Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl", - "file": "oxidative-stress-response.bngl", + "path": "Examples/physics/phwaveequation/ph_wave_equation.bngl", + "file": "ph_wave_equation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "p38-mapk-signaling", - "name": "p38 mapk signaling", - "description": "p38 MAPK stress signaling cascade.", + "id": "phosphorelay-chain", + "name": "phosphorelay chain", + "description": "BioNetGen model: phosphorelay chain", "tags": [ - "p38", - "mapk", - "signaling", - "mkk3", - "mapkap2", - "v_thermal" + "phosphorelay", + "chain", + "sensor", + "relay", + "output" ], "category": "signaling", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "cancer", "test-models" ], - "path": "Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl", - "file": "p38-mapk-signaling.bngl", + "path": "Examples/biology/phosphorelaychain/phosphorelay-chain.bngl", + "file": "phosphorelay-chain.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "p53-mdm2-oscillator", - "name": "p53 mdm2 oscillator", - "description": "BioNetGen model: p53 mdm2 oscillator", - "tags": [ - "p53", - "mdm2", - "oscillator", - "generate_network" + "id": "platelet-activation", + "name": "platelet activation", + "description": "BioNetGen model: platelet activation", + "tags": [ + "platelet", + "activation", + "adp", + "p2y12", + "integrin", + "thromboxane" ], "category": "signaling", "origin": "ai-generated", @@ -13041,120 +12761,122 @@ ] }, "gallery": [ - "cell-cycle", + "immunology", "test-models" ], - "path": "Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl", - "file": "p53-mdm2-oscillator.bngl", + "path": "Examples/biology/plateletactivation/platelet-activation.bngl", + "file": "platelet-activation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "polymer", + "name": "polymer", + "description": "Polymerization model", "tags": [ - "parabola", - "counter", - "par", - "line", - "generate_network", - "simulate" + "tutorials", + "nfsim", + "polymer", + "simulate_nf" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "other" + "tutorials" ], - "path": "Published/PyBioNetGen/core/parabola/parabola.bngl", - "file": "parabola.bngl", + "path": "Tutorials/General/polymer/polymer.bngl", + "file": "polymer.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Original values used to generate parabola.exp", + "id": "polymer_draft", + "name": "polymer draft", + "description": "Polymerization (draft)", "tags": [ - "parabola", - "counter", - "y", - "generate_network", - "simulate" + "tutorials", + "nfsim", + "polymer", + "draft", + "simulate_nf" ], - "category": "other", - "origin": "published", + "category": "tutorial", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "other" + "tutorials" ], - "path": "Published/PyBioNetGen/core/parabola_demo/parabola.bngl", - "file": "parabola.bngl", + "path": "Tutorials/General/polymerdraft/polymer_draft.bngl", + "file": "polymer_draft.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Original values used to generate parabola.exp", + "id": "polymer_fixed", + "name": "polymer_fixed", + "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", "tags": [ - "parabola", - "counter", - "y", - "generate_network", - "simulate", - "resetconcentrations" + "polymer", + "fixed" ], - "category": "validation", - "origin": "test-case", + "category": "other", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "other" ], - "path": "Published/PyBioNetGen/tests/parabola/parabola.bngl", - "file": "parabola.bngl", + "path": "Tutorials/polymerfixed/polymer_fixed.bngl", + "file": "polymer_fixed.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Original values used to generate parabola.exp", + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "parabola", - "counter", - "y", - "generate_network", - "simulate" + "polynomial" ], "category": "validation", "origin": "test-case", @@ -13170,25 +12892,28 @@ "gallery": [ "validation" ], - "path": "Published/PyBioNetGen/tests/parabola_bngl_files/parabola.bngl", - "file": "parabola.bngl", + "path": "Published/PyBioNetGen/tests/polynomial/polynomial.bngl", + "file": "polynomial.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parabola", - "name": "parabola", - "description": "Original values used to generate parabola.exp", + "id": "Posner_blbr_1995", + "name": "Posner et al. 1995: Receptor Ring Aggregation Model", + "description": "BLBR rings", "tags": [ - "parabola", - "counter", - "y", - "generate_network", - "simulate" + "blbr", + "aggregation", + "receptor-rings", + "1995", + "posner" ], - "category": "validation", - "origin": "test-case", + "category": "physics", + "origin": "published", "visible": true, "compatibility": { "bng2": true, @@ -13199,28 +12924,29 @@ ] }, "gallery": [ - "validation" + "physics" ], - "path": "Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl", - "file": "parabola.bngl", + "path": "Published/Posner1995/blbr_rings_posner1995.bngl", + "file": "blbr_rings_posner1995.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parabola_ground", - "name": "parabola ground", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "Posner_blbr_2004", + "name": "Posner et al. 2004: Cooperativity in Receptor Binding", + "description": "BLBR cooperativity", "tags": [ - "parabola", - "ground", - "counter", - "par", - "line", - "generate_network", - "simulate" + "blbr", + "cooperativity", + "receptor-binding", + "2004", + "posner" ], - "category": "other", + "category": "physics", "origin": "published", "visible": true, "compatibility": { @@ -13232,90 +12958,98 @@ ] }, "gallery": [ - "other" + "physics" ], - "path": "Published/PyBioNetGen/core/parabolaground/parabola_ground.bngl", - "file": "parabola_ground.bngl", + "path": "Published/Posner2004/blbr_cooperativity_posner2004.bngl", + "file": "blbr_cooperativity_posner2004.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parabola2", - "name": "parabola2", - "description": "A file for testing behavior with duplicate file names", + "id": "predator-prey-dynamics", + "name": "predator prey dynamics", + "description": "BioNetGen model: predator prey dynamics", "tags": [ - "parabola2", - "counter", - "y", - "generate_network", - "simulate", - "resetconcentrations" + "predator", + "prey", + "dynamics" ], - "category": "validation", - "origin": "test-case", + "category": "signaling", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "validation" + "test-models" ], - "path": "Published/PyBioNetGen/tests/parabola2/parabola2.bngl", - "file": "parabola2.bngl", + "path": "Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl", + "file": "predator-prey-dynamics.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "ParamsEverywhere", - "name": "ParamsEverywhere", - "description": "An example from a real application", + "id": "process_actin_treadmilling", + "name": "process actin treadmilling", + "description": "Model: process_actin_treadmilling.bngl", "tags": [ - "paramseverywhere", - "ag", - "r", - "h" + "process", + "actin", + "treadmilling", + "generate_network", + "simulate" ], - "category": "validation", - "origin": "test-case", + "category": "other", + "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, "gallery": [ - "validation" + "test-models" ], - "path": "Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl", - "file": "ParamsEverywhere.bngl", + "path": "Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl", + "file": "process_actin_treadmilling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "parp1-mediated-dna-repair", - "name": "parp1 mediated dna repair", - "description": "PARP1-mediated DNA damage sensing and repair.", + "id": "process_autophagy_flux", + "name": "process autophagy flux", + "description": "Model: process_autophagy_flux.bngl", "tags": [ - "parp1", - "mediated", - "dna", - "repair", - "par", - "nad", - "v_parylate" + "process", + "autophagy", + "flux", + "phagophore", + "autophagosome", + "lysosome", + "autolysosome", + "cargo" ], - "category": "signaling", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -13327,37 +13061,36 @@ ] }, "gallery": [ - "cell-cycle", "test-models" ], - "path": "Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl", - "file": "parp1-mediated-dna-repair.bngl", + "path": "Examples/processes/processautophagyflux/process_autophagy_flux.bngl", + "file": "process_autophagy_flux.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Pekalski_2013", - "name": "Pekalski 2013", - "description": "Spontaneous signaling", + "id": "process_cell_adhesion_strength", + "name": "process cell adhesion strength", + "description": "Model: process_cell_adhesion_strength.bngl", "tags": [ - "published", - "pekalski", - "2013", - "tnfr", - "ikk", - "ikkk", - "ikba", - "ikba_mrna", - "a20", - "a20_mrna", - "nfkb" + "process", + "cell", + "adhesion", + "strength", + "c1", + "c2", + "generate_network", + "simulate" ], - "category": "regulation", - "origin": "published", - "visible": true, + "category": "other", + "origin": "ai-generated", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ @@ -13365,61 +13098,66 @@ ] }, "gallery": [ - "regulation" + "test-models" ], - "path": "Published/Pekalski2013/Pekalski_2013.bngl", - "file": "Pekalski_2013.bngl", + "path": "Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl", + "file": "process_cell_adhesion_strength.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ph_lorenz_attractor", - "name": "ph lorenz attractor", - "description": "Lorenz Attractor in BNGL", + "id": "process_kinetic_proofreading_tcr", + "name": "process kinetic proofreading tcr", + "description": "Model: process_kinetic_proofreading_tcr.bngl", "tags": [ - "ph", - "lorenz", - "attractor", - "lx", - "ly", - "lz", - "x", - "y" + "process", + "kinetic", + "proofreading", + "tcr", + "l" ], - "category": "physics", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "physics", "test-models" ], - "path": "Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl", - "file": "ph_lorenz_attractor.bngl", + "path": "Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl", + "file": "process_kinetic_proofreading_tcr.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ph_nbody_gravity", - "name": "ph nbody gravity", - "description": "Model: ph_nbody_gravity.bngl", + "id": "process_quorum_sensing_switch", + "name": "process quorum sensing switch", + "description": "Model: process_quorum_sensing_switch.bngl", "tags": [ - "ph", - "nbody", - "gravity", - "body", - "r2" + "process", + "quorum", + "sensing", + "switch", + "gene_ai", + "ai", + "r", + "gene_light" ], - "category": "physics", + "category": "other", "origin": "ai-generated", "visible": false, "compatibility": { @@ -13431,26 +13169,28 @@ ] }, "gallery": [ - "physics", "test-models" ], - "path": "Examples/physics/phnbodygravity/ph_nbody_gravity.bngl", - "file": "ph_nbody_gravity.bngl", + "path": "Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl", + "file": "process_quorum_sensing_switch.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ph_schrodinger", - "name": "ph schrodinger", - "description": "Model: ph_schrodinger.bngl", + "id": "PyBioNetGen_Actions_Syntax", + "name": "PyBioNetGen Actions Syntax Verification Model", + "description": "Original values used to generate parabola.exp", "tags": [ - "ph", - "schrodinger", - "psi" + "test-case", + "syntax-check", + "actions" ], - "category": "physics", - "origin": "ai-generated", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -13461,27 +13201,27 @@ ] }, "gallery": [ - "physics", - "test-models" + "validation" ], - "path": "Examples/physics/phschrodinger/ph_schrodinger.bngl", - "file": "ph_schrodinger.bngl", + "path": "Published/PyBioNetGen/tests/actionssyntax/actions_syntax.bngl", + "file": "actions_syntax.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "ph_wave_equation", - "name": "ph wave equation", - "description": "Model: ph_wave_equation.bngl", + "id": "PyBioNetGen_BNG_Error", + "name": "PyBioNetGen BNG Error Triggering Test", + "description": "Original values used to generate parabola.exp", "tags": [ - "ph", - "wave", - "equation", - "node" + "test-case", + "error-handling" ], - "category": "physics", - "origin": "ai-generated", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -13492,31 +13232,26 @@ ] }, "gallery": [ - "physics", - "test-models" + "validation" ], - "path": "Examples/physics/phwaveequation/ph_wave_equation.bngl", - "file": "ph_wave_equation.bngl", + "path": "Published/PyBioNetGen/tests/bngerror/bng_error.bngl", + "file": "bng_error.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Phoenix", - "name": "Phoenix", - "description": "- This model is intended to be consistent with the compartmental model", + "id": "PyBioNetGen_Core_Parabola", + "name": "PyBioNetGen Core: Parabolic Trajectory Model", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "phoenix", - "counter", - "fdcs", - "s", - "sv", - "e", - "a", - "i", - "v" + "mathematical-model", + "parabolic-equation" ], - "category": "epidemiology", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -13528,161 +13263,156 @@ ] }, "gallery": [ - "epidemiology" + "other" ], - "path": "Published/VaxAndVariants/Phoenix/Phoenix.bngl", - "file": "Phoenix.bngl", + "path": "Published/PyBioNetGen/core/parabola/parabola.bngl", + "file": "parabola.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "phosphorelay-chain", - "name": "phosphorelay chain", - "description": "BioNetGen model: phosphorelay chain", + "id": "PyBioNetGen_Core_Parabola_Demo", + "name": "PyBioNetGen Core: Parabolic Trajectory Demo", + "description": "Original values used to generate parabola.exp", "tags": [ - "phosphorelay", - "chain", - "sensor", - "relay", - "output" + "mathematical-model", + "demo" ], - "category": "signaling", - "origin": "ai-generated", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "other" ], - "path": "Examples/biology/phosphorelaychain/phosphorelay-chain.bngl", - "file": "phosphorelay-chain.bngl", + "path": "Published/PyBioNetGen/core/parabola_demo/parabola.bngl", + "file": "parabola.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "platelet-activation", - "name": "platelet activation", - "description": "BioNetGen model: platelet activation", + "id": "PyBioNetGen_Core_Parabola_Ground", + "name": "PyBioNetGen Core: Parabolic Ground Truth Reference", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "platelet", - "activation", - "adp", - "p2y12", - "integrin", - "thromboxane" + "mathematical-model", + "reference-standard" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "other", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", - "test-models" + "other" ], - "path": "Examples/biology/plateletactivation/platelet-activation.bngl", - "file": "platelet-activation.bngl", + "path": "Published/PyBioNetGen/core/parabolaground/parabola_ground.bngl", + "file": "parabola_ground.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polymer", - "name": "polymer", - "description": "Polymerization model", + "id": "PyBioNetGen_Core_Polynomial", + "name": "PyBioNetGen Core: Polynomial Trajectory Model", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "published", - "tutorials", - "nfsim", - "polymer", - "a", - "b", - "c", - "simulate_nf" + "mathematical-model", + "polynomial-equation" ], - "category": "tutorial", - "origin": "tutorial", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "tutorials" + "other" ], - "path": "Tutorials/General/polymer/polymer.bngl", - "file": "polymer.bngl", + "path": "Published/PyBioNetGen/core/polynomial/polynomial.bngl", + "file": "polynomial.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polymer_draft", - "name": "polymer draft", - "description": "Polymerization (draft)", + "id": "PyBioNetGen_Core_Polynomial_Ground", + "name": "PyBioNetGen Core: Polynomial Ground Truth Reference", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "published", - "tutorials", - "nfsim", - "polymer", - "draft", - "a", - "b", - "c", - "simulate_nf" + "mathematical-model", + "reference-standard" ], - "category": "tutorial", - "origin": "tutorial", - "visible": false, + "category": "other", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "tutorials" + "other" ], - "path": "Tutorials/General/polymerdraft/polymer_draft.bngl", - "file": "polymer_draft.bngl", + "path": "Published/PyBioNetGen/core/polynomialground/polynomial_ground.bngl", + "file": "polynomial_ground.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polymer_fixed", - "name": "polymer_fixed", - "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", + "id": "PyBioNetGen_Core_RAFi", + "name": "PyBioNetGen Core: Raf Inhibitor Model", + "description": "BioNetGen model: RAFi", "tags": [ - "polymer", - "fixed" + "rafi", + "raf-kinase", + "enzyme-inhibition" ], "category": "other", - "origin": "contributed", + "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" @@ -13691,25 +13421,23 @@ "gallery": [ "other" ], - "path": "Tutorials/polymerfixed/polymer_fixed.bngl", - "file": "polymer_fixed.bngl", + "path": "Published/PyBioNetGen/core/RAFi/RAFi.bngl", + "file": "RAFi.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polynomial", - "name": "polynomial", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "PyBioNetGen_Core_RAFi_Ground", + "name": "PyBioNetGen Core: Raf Inhibitor Ground Truth Reference", + "description": "BioNetGen model: RAFi ground", "tags": [ - "polynomial", - "counter", - "y1", - "y2", - "generate_network", - "simulate", - "setparameter", - "resetconcentrations" + "rafi", + "raf-kinase", + "reference-standard" ], "category": "other", "origin": "published", @@ -13725,28 +13453,25 @@ "gallery": [ "other" ], - "path": "Published/PyBioNetGen/core/polynomial/polynomial.bngl", - "file": "polynomial.bngl", + "path": "Published/PyBioNetGen/core/RAFiground/RAFi_ground.bngl", + "file": "RAFi_ground.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polynomial", - "name": "polynomial", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "PyBioNetGen_Core_Receptor", + "name": "PyBioNetGen Core: Simple Ligand-Receptor Binding", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", "tags": [ - "polynomial", - "counter", - "y1", - "y2", - "generate_network", - "simulate", - "setparameter", - "resetconcentrations" + "ligand-receptor", + "binding-kinetics" ], - "category": "validation", - "origin": "test-case", + "category": "other", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -13757,124 +13482,124 @@ ] }, "gallery": [ - "validation" + "other" ], - "path": "Published/PyBioNetGen/tests/polynomial/polynomial.bngl", - "file": "polynomial.bngl", + "path": "Published/PyBioNetGen/core/receptor/receptor.bngl", + "file": "receptor.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "polynomial", - "name": "polynomial", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "PyBioNetGen_Core_Receptor_NF", + "name": "PyBioNetGen Core: Ligand-Receptor Network-Free Simulation", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", "tags": [ - "polynomial", - "counter", - "y1", - "y2", - "generate_network", - "simulate", - "setparameter", - "resetconcentrations" + "ligand-receptor", + "binding-kinetics", + "nfsim" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ - "validation" + "other" ], - "path": "Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl", - "file": "polynomial.bngl", + "path": "Published/PyBioNetGen/core/receptornf/receptor_nf.bngl", + "file": "receptor_nf.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "polynomial_ground", - "name": "polynomial ground", - "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "id": "PyBioNetGen_Core_TCR", + "name": "PyBioNetGen Core: T Cell Receptor Activation", + "description": "A model of T cell receptor signaling", "tags": [ - "polynomial", - "ground", - "counter", - "y1", - "y2", - "generate_network", - "simulate", - "setparameter", - "resetconcentrations" + "tcr", + "immune-signaling", + "phosphorylation" ], "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, "gallery": [ "other" ], - "path": "Published/PyBioNetGen/core/polynomialground/polynomial_ground.bngl", - "file": "polynomial_ground.bngl", + "path": "Published/PyBioNetGen/core/tcr/tcr.bngl", + "file": "tcr.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Posner_1995", - "name": "Posner 1995", - "description": "BLBR rings", + "id": "PyBioNetGen_Core_TLBR", + "name": "PyBioNetGen Core: Trivalent Ligand Bivalent Receptor Model", + "description": "A model of trivalent ligand, bivalent receptor", "tags": [ - "published", - "physics", - "posner", - "1995" + "tlbr", + "polymerization", + "ligand-receptor" ], - "category": "physics", + "category": "other", "origin": "published", - "visible": true, + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "physics" + "immunology" ], - "path": "Published/Posner1995/blbr_rings_posner1995.bngl", - "file": "blbr_rings_posner1995.bngl", + "path": "Published/PyBioNetGen/core/tlbr/tlbr.bngl", + "file": "tlbr.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Posner_2004", - "name": "Posner 2004", - "description": "BLBR cooperativity", + "id": "PyBioNetGen_Degranulation_Model", + "name": "PyBioNetGen Core: IgE Receptor Degranulation Model", + "description": "Degranulation model", "tags": [ - "published", - "physics", - "posner", - "2004" + "fceri", + "degranulation", + "mast-cell", + "immune-signaling" ], - "category": "physics", + "category": "other", "origin": "published", "visible": true, "compatibility": { @@ -13886,94 +13611,57 @@ ] }, "gallery": [ - "physics" + "immunology" ], - "path": "Published/Posner2004/blbr_cooperativity_posner2004.bngl", - "file": "blbr_cooperativity_posner2004.bngl", + "path": "Published/PyBioNetGen/core/degranulationmodel/degranulation_model.bngl", + "file": "degranulation_model.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "predator-prey-dynamics", - "name": "predator prey dynamics", - "description": "BioNetGen model: predator prey dynamics", + "id": "PyBioNetGen_EGFR_Ground", + "name": "PyBioNetGen Core: Canonical EGFR Ground Truth Reference", + "description": "Blinov et al. 2006. Biosystems, 83:136", "tags": [ - "predator", - "prey", - "dynamics" + "egfr", + "signaling", + "reference-standard" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "other", + "origin": "published", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "other" ], - "path": "Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl", - "file": "predator-prey-dynamics.bngl", + "path": "Published/PyBioNetGen/core/egfrground/egfr_ground.bngl", + "file": "egfr_ground.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "prion_model", - "name": "ERK_model.bngl", - "description": "filename: ERK_model.bngl", + "id": "PyBioNetGen_EGFR_Model", + "name": "PyBioNetGen Core: Canonical EGFR Signaling Model", + "description": "Blinov et al. 2006. Biosystems, 83:136", "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" + "egfr", + "signaling", + "receptor-activation" ], "category": "other", "origin": "published", @@ -13983,106 +13671,62 @@ "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, - "gallery": [], - "path": "Published/Lin2019/prion_model.bngl", - "file": "prion_model.bngl", + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/egfr/egfr.bngl", + "file": "egfr.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem_quant_model_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_EGFR_NF", + "name": "PyBioNetGen Core: EGFR Network-Free Simulation", + "description": "Filename: example2_starting_point.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" + "egfr", + "signaling", + "nfsim", + "network-free" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem_quant/model_tofit.bngl", - "file": "model_tofit.bngl", + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/egfrnf/egfr_nf.bngl", + "file": "egfr_nf.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "problem16_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_EGFR_ODE", + "name": "PyBioNetGen Core: EGFR ODE-Based Simulation", + "description": "Filename: example1.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" + "egfr", + "signaling", + "ode-solver" ], "category": "other", "origin": "published", @@ -14095,105 +13739,60 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem16_3cat/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "cancer" + ], + "path": "Published/PyBioNetGen/core/egfrode/egfr_ode.bngl", + "file": "egfr_ode.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem16_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_EGFR_ODE_Pub", + "name": "PyBioNetGen Core: Published EGFR ODE-Based Model", + "description": "EGFR ODE", "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" + "egfr", + "signaling", + "ode-solver" ], "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem16/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "cancer" + ], + "path": "Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl", + "file": "egfr_ode.bngl", "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "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" + "featured": false, + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Egg", + "name": "PyBioNetGen Egg Cell Oscillator Test", + "description": "BioNetGen model: egg", + "tags": [ + "test-case", + "calcium-oscillation" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -14203,48 +13802,57 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem32_3cat/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/egg/egg.bngl", + "file": "egg.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem32_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_ErrNoFrees", + "name": "PyBioNetGen Free Molecule Error Test", + "description": "An example from a real application", "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" + "test-case", + "error-handling" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl", + "file": "ErrNoFrees.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Example1", + "name": "PyBioNetGen Core: Example 1 EGFR Model", + "description": "Filename: example1.bngl", + "tags": [ + "egfr", + "signaling", + "example-model" ], "category": "other", "origin": "published", @@ -14257,156 +13865,91 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem32/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/example1/example1.bngl", + "file": "example1.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem4_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_Example2_Start", + "name": "PyBioNetGen Core: Example 2 EGFR Starting Point", + "description": "Filename: example2_starting_point.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" + "egfr", + "signaling", + "starting-point", + "example-model" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem4_3cat/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl", + "file": "example2_starting_point.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "problem4_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_FceRI_Gamma2", + "name": "PyBioNetGen Core: FceRI Gamma2 Subunit Signaling", + "description": "BioNetGen model: fceri gamma2", "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" + "fceri", + "gamma2-subunit", + "immune-signaling" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "ssa" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem4/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl", + "file": "fceri_gamma2.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "problem64_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_FceRI_Gamma2_Ground", + "name": "PyBioNetGen Core: FceRI Gamma2 Ground Truth Reference", + "description": "BioNetGen model: fceri gamma2 ground truth", "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" + "fceri", + "gamma2-subunit", + "reference-standard" ], "category": "other", "origin": "published", @@ -14416,51 +13959,60 @@ "nfsim": false, "excluded": false, "methods": [ - "ode" + "ssa" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem64_3cat/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl", + "file": "fceri_gamma2_ground_truth.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem64_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_FreeMissing", + "name": "PyBioNetGen Free Species Constraint Test", + "description": "Original values used to generate parabola.exp", "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" + "test-case", + "constraints" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/freemissing/free_missing.bngl", + "file": "free_missing.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_IGF1R_Activation", + "name": "PyBioNetGen Core: IGF1R Receptor Activation Model", + "description": "Author: William S. Hlavacek", + "tags": [ + "igf1r", + "receptor-activation", + "phosphorylation" ], "category": "other", "origin": "published", @@ -14473,51 +14025,29 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem64/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl", + "file": "IGF1R_Model_receptor_activation_bnf.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem8_3cat_model0_tofit", - "name": "model.bngl", - "description": "filename: model.bngl", + "id": "PyBioNetGen_LilyIgE", + "name": "PyBioNetGen Lily IgE Receptor Test Model", + "description": "An example from a real application", "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" + "test-case", + "fceri", + "immune-signaling" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -14527,52 +14057,30 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem8_3cat/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/LilyIgE/LilyIgE.bngl", + "file": "LilyIgE.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "problem8_model0_tofit", - "name": "model.bngl", + "id": "PyBioNetGen_Model", + "name": "PyBioNetGen Core: Generic Mast Cell Degranulation Model", "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" + "fceri", + "degranulation", + "mast-cell" ], "category": "other", "origin": "published", - "visible": false, + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -14581,60 +14089,61 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Likelihood/problem8/model0_tofit.bngl", - "file": "model0_tofit.bngl", + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/model/model.bngl", + "file": "model.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "process_actin_treadmilling", - "name": "process actin treadmilling", - "description": "Model: process_actin_treadmilling.bngl", + "id": "PyBioNetGen_Model_aMCMC", + "name": "PyBioNetGen Core: Mast Cell Degranulation via aMCMC Fitting", + "description": "A model of IgE receptor signaling", "tags": [ - "process", - "actin", - "treadmilling", - "generate_network", - "simulate" + "fceri", + "degranulation", + "amcmc-fitting" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ssa" + "ode" ] }, "gallery": [ - "test-models" + "other" ], - "path": "Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl", - "file": "process_actin_treadmilling.bngl", + "path": "Published/PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl", + "file": "model.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "process_autophagy_flux", - "name": "process autophagy flux", - "description": "Model: process_autophagy_flux.bngl", + "id": "PyBioNetGen_Model_ToFit", + "name": "PyBioNetGen Core: Mast Cell Degranulation for Fitting", + "description": "A model of IgE receptor signaling", "tags": [ - "process", - "autophagy", - "flux", - "phagophore", - "autophagosome", - "lysosome", - "autolysosome", - "cargo" + "fceri", + "degranulation", + "parameter-fitting" ], "category": "other", - "origin": "ai-generated", + "origin": "published", "visible": false, "compatibility": { "bng2": true, @@ -14645,31 +14154,59 @@ ] }, "gallery": [ - "test-models" + "other" ], - "path": "Examples/processes/processautophagyflux/process_autophagy_flux.bngl", - "file": "process_autophagy_flux.bngl", + "path": "Published/PyBioNetGen/core/modeltofit/model_tofit.bngl", + "file": "model_tofit.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "process_cell_adhesion_strength", - "name": "process cell adhesion strength", - "description": "Model: process_cell_adhesion_strength.bngl", + "id": "PyBioNetGen_NFmodel", + "name": "PyBioNetGen NFsim Simulation Test", + "description": "BioNetGen model: NFmodel", "tags": [ - "process", - "cell", - "adhesion", - "strength", - "c1", - "c2", - "generate_network", - "simulate" + "test-case", + "nfsim" ], - "category": "other", - "origin": "ai-generated", + "category": "validation", + "origin": "test-case", "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/NFmodel/NFmodel.bngl", + "file": "NFmodel.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "PyBioNetGen_NoFrees", + "name": "PyBioNetGen No Free Constraints Verification", + "description": "Original values used to generate parabola.exp", + "tags": [ + "test-case", + "constraints" + ], + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -14679,61 +14216,58 @@ ] }, "gallery": [ - "test-models" + "validation" ], - "path": "Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl", - "file": "process_cell_adhesion_strength.bngl", + "path": "Published/PyBioNetGen/tests/nofrees/no_frees.bngl", + "file": "no_frees.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "process_kinetic_proofreading_tcr", - "name": "process kinetic proofreading tcr", - "description": "Model: process_kinetic_proofreading_tcr.bngl", + "id": "PyBioNetGen_NoGenerateNetwork", + "name": "PyBioNetGen Direct Simulation Without Expansion Test", + "description": "Original values used to generate parabola.exp", "tags": [ - "process", - "kinetic", - "proofreading", - "tcr", - "l" + "test-case", + "simulation-modes" ], - "category": "other", - "origin": "ai-generated", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "validation" ], - "path": "Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl", - "file": "process_kinetic_proofreading_tcr.bngl", + "path": "Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl", + "file": "no_generate_network.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "process_quorum_sensing_switch", - "name": "process quorum sensing switch", - "description": "Model: process_quorum_sensing_switch.bngl", + "id": "PyBioNetGen_NoSuffix", + "name": "PyBioNetGen No Suffix Output Naming Test", + "description": "Original values used to generate parabola.exp", "tags": [ - "process", - "quorum", - "sensing", - "switch", - "gene_ai", - "ai", - "r", - "gene_light" + "test-case", + "output-formatting" ], - "category": "other", - "origin": "ai-generated", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -14744,30 +14278,27 @@ ] }, "gallery": [ - "test-models" + "validation" ], - "path": "Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl", - "file": "process_quorum_sensing_switch.bngl", + "path": "Published/PyBioNetGen/tests/nosuffix/no_suffix.bngl", + "file": "no_suffix.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "pt303", - "name": "pt303", - "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", + "id": "PyBioNetGen_Parabola", + "name": "PyBioNetGen Parabolic Trajectory Test", + "description": "Original values used to generate parabola.exp", "tags": [ - "pt303", - "counter", - "v", - "lnv", - "s", - "c", - "half_life", - "lnv_tangent" + "test-case", + "mathematical-model" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -14778,30 +14309,27 @@ ] }, "gallery": [ - "other" + "validation" ], - "path": "Published/PyBioNetGen/HIVdynamics/pt303/pt303.bngl", - "file": "pt303.bngl", + "path": "Published/PyBioNetGen/tests/parabola/parabola.bngl", + "file": "parabola.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "pt403", - "name": "pt403", - "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", + "id": "PyBioNetGen_Parabola_Files", + "name": "PyBioNetGen Parabolic Trajectory Files Test", + "description": "Original values used to generate parabola.exp", "tags": [ - "pt403", - "counter", - "v", - "lnv", - "s", - "c", - "half_life", - "lnv_tangent" + "test-case", + "mathematical-model" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -14812,31 +14340,28 @@ ] }, "gallery": [ - "other" + "validation" ], - "path": "Published/PyBioNetGen/HIVdynamics/pt403/pt403.bngl", - "file": "pt403.bngl", + "path": "Published/PyBioNetGen/tests/parabola_bngl_files/parabola.bngl", + "file": "parabola.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "pt409", - "name": "pt409", - "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", + "id": "PyBioNetGen_Parabola_Special", + "name": "PyBioNetGen Parabolic Trajectory Special Cases Test", + "description": "Original values used to generate parabola.exp", "tags": [ - "pt409", - "counter", - "v", - "lnv", - "s", - "c", - "half_life", - "lnv_tangent" + "test-case", + "mathematical-model" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -14846,44 +14371,27 @@ ] }, "gallery": [ - "other" + "validation" ], - "path": "Published/PyBioNetGen/HIVdynamics/pt409/pt409.bngl", - "file": "pt409.bngl", + "path": "Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl", + "file": "parabola.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF", - "name": "PyBNF-fitting-setup", - "description": "BNGL model: 190127_CHO_EGFR_forBNF", + "id": "PyBioNetGen_Parabola2", + "name": "PyBioNetGen Parabolic Trajectory Alternative Test", + "description": "A file for testing behavior with duplicate file names", "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" + "test-case", + "mathematical-model" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -14893,28 +14401,28 @@ "ode" ] }, - "gallery": [], - "path": "Published/Salazar-Cavazos2019/PyBNF-fitting-setup/190127_CHO_EGFR_forBNF.bngl", - "file": "190127_CHO_EGFR_forBNF.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola2/parabola2.bngl", + "file": "parabola2.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "quasi_equilibrium", - "name": "quasi equilibrium", - "description": "Quasi-equilibrium approximation", + "id": "PyBioNetGen_ParamsEverywhere", + "name": "PyBioNetGen Global Parameters Boundary Test", + "description": "An example from a real application", "tags": [ - "published", - "toy models", - "quasi", - "equilibrium", - "a", - "b", - "c" + "test-case", + "parameter-boundaries" ], - "category": "tutorial", - "origin": "tutorial", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -14925,151 +14433,90 @@ ] }, "gallery": [ - "tutorials", - "native-tutorials" + "validation" ], - "path": "Tutorials/General/quasiequilibrium/quasi_equilibrium.bngl", - "file": "quasi_equilibrium.bngl", + "path": "Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl", + "file": "ParamsEverywhere.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "quorum-sensing-circuit", - "name": "quorum sensing circuit", - "description": "BioNetGen model: quorum sensing circuit", + "id": "PyBioNetGen_Polynomial_T6", + "name": "PyBioNetGen Polynomial Trajectory Test (T6-check)", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", "tags": [ - "quorum", - "sensing", - "circuit", - "autoinducer", - "autoinducer_env", - "gene", - "protein" + "test-case", + "mathematical-model" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "test-models" + "validation" ], - "path": "Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl", - "file": "quorum-sensing-circuit.bngl", + "path": "Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl", + "file": "polynomial.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_mon1ccz1_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_Simple", + "name": "PyBioNetGen Simple Synthesis & Decay Test", + "description": "An example from a real application", "tags": [ - "kd_rabgef1__free", - "d_hill__free", - "d_threshold__free", - "k_deg__free", - "k_dephos__free", - "k_deub__free", - "k_extract__free", - "k_insert__free", - "k_recyc__free", - "k_synth__free", - "k_to_endo__free", - "kcat_rab5__free", - "kcat_rab7__free", - "kf_rab5_mon1__free", - "kf_rab5_rabep1__free", - "kf_ptyr_sh2__free", - "kr_kub_uim__free", - "kr_rab5_mon1__free", - "kr_rab5_rabep1__free", - "kr_ptyr_sh2__free", - "py_basal_coef__free", - "py_half_coef__free", - "py_hill_coef__free", - "py_scale_coef__free", - "r_hill__free", - "r_threshold__free", - "ub_basal_coef__free", - "ub_half_coef__free", - "ub_hill_coef__free", - "ub_scale_coef__free", - "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" + "test-case", + "synthesis-decay" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, - "methods": [] + "methods": [ + "ode" + ] }, - "gallery": [], - "path": "Published/Mitra2019Rab/rab_mon1ccz1_ox.bngl", - "file": "rab_mon1ccz1_ox.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Simple/Simple.bngl", + "file": "Simple.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_mon1ccz1_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_Simple_AddActions", + "name": "PyBioNetGen Simple Synthesis with Dynamic Actions", + "description": "An example from a real application", "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" + "test-case", + "actions" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -15078,233 +14525,184 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Rab/pybnf_files/rab_mon1ccz1_ox.bngl", - "file": "rab_mon1ccz1_ox.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl", + "file": "Simple_AddActions.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_rab5_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_Simple_Answer", + "name": "PyBioNetGen Simple Synthesis with Response Check", + "description": "An example from a real application", "tags": [ - "kd_rabgef1__free", - "d_hill__free", - "d_threshold__free", - "k_deg__free", - "k_dephos__free", - "k_deub__free", - "k_extract__free", - "k_insert__free", - "k_recyc__free", - "k_synth__free", - "k_to_endo__free", - "kcat_rab5__free", - "kcat_rab7__free", - "kf_rab5_mon1__free", - "kf_rab5_rabep1__free", - "kf_ptyr_sh2__free", - "kr_kub_uim__free", - "kr_rab5_mon1__free", - "kr_rab5_rabep1__free", - "kr_ptyr_sh2__free", - "py_basal_coef__free", - "py_half_coef__free", - "py_hill_coef__free", - "py_scale_coef__free", - "r_hill__free", - "r_threshold__free", - "ub_basal_coef__free", - "ub_half_coef__free", - "ub_hill_coef__free", - "ub_scale_coef__free", - "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" + "test-case", + "verification" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" ], - "category": "other", - "origin": "published", + "path": "Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl", + "file": "Simple_Answer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Simple_GenOnly", + "name": "PyBioNetGen Simple Synthesis Network-Generation Only", + "description": "An example from a real application", + "tags": [ + "test-case", + "network-generation" + ], + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, - "methods": [] + "methods": [ + "ode" + ] }, - "gallery": [], - "path": "Published/Mitra2019Rab/rab_rab5_ox.bngl", - "file": "rab_rab5_ox.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl", + "file": "Simple_GenOnly.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_rab5_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_Simple_NF_Seed", + "name": "PyBioNetGen NFsim Seed Population Test", + "description": "BioNetGen model: simple nf seed", "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" + "test-case", + "nfsim", + "seed" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl", + "file": "simple_nf_seed.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "PyBioNetGen_Simple_NoGen", + "name": "PyBioNetGen Simple Synthesis Without Network-Generation", + "description": "An example from a real application", + "tags": [ + "test-case", + "direct-simulation" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, "methods": [ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Rab/pybnf_files/rab_rab5_ox.bngl", - "file": "rab_rab5_ox.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl", + "file": "Simple_nogen.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "rab_rab7_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_Tricky", + "name": "PyBioNetGen Complex Pattern Matching Test", + "description": "An example from a real application", "tags": [ - "kd_rabgef1__free", - "d_hill__free", - "d_threshold__free", - "k_deg__free", - "k_dephos__free", - "k_deub__free", - "k_extract__free", - "k_insert__free", - "k_recyc__free", - "k_synth__free", - "k_to_endo__free", - "kcat_rab5__free", - "kcat_rab7__free", - "kf_rab5_mon1__free", - "kf_rab5_rabep1__free", - "kf_ptyr_sh2__free", - "kr_kub_uim__free", - "kr_rab5_mon1__free", - "kr_rab5_rabep1__free", - "kr_ptyr_sh2__free", - "py_basal_coef__free", - "py_half_coef__free", - "py_hill_coef__free", - "py_scale_coef__free", - "r_hill__free", - "r_threshold__free", - "ub_basal_coef__free", - "ub_half_coef__free", - "ub_hill_coef__free", - "ub_scale_coef__free", - "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" + "test-case", + "pattern-matching" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, - "methods": [] + "methods": [ + "ode" + ] }, - "gallery": [], - "path": "Published/Mitra2019Rab/rab_rab7_ox.bngl", - "file": "rab_rab7_ox.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Tricky/Tricky.bngl", + "file": "Tricky.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "rab_rab7_ox", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBioNetGen_TrickyUS", + "name": "PyBioNetGen Unstructured Boundary State Test", + "description": "An example from a real application", "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" + "test-case", + "boundary-states" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, @@ -15314,112 +14712,57 @@ "ode" ] }, - "gallery": [], - "path": "Published/Mitra2019Rab/pybnf_files/rab_rab7_ox.bngl", - "file": "rab_rab7_ox.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/TrickyUS/TrickyUS.bngl", + "file": "TrickyUS.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_wt", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", - "tags": [ - "kd_rabgef1__free", - "d_hill__free", - "d_threshold__free", - "k_deg__free", - "k_dephos__free", - "k_deub__free", - "k_extract__free", - "k_insert__free", - "k_recyc__free", - "k_synth__free", - "k_to_endo__free", - "kcat_rab5__free", - "kcat_rab7__free", - "kf_rab5_mon1__free", - "kf_rab5_rabep1__free", - "kf_ptyr_sh2__free", - "kr_kub_uim__free", - "kr_rab5_mon1__free", - "kr_rab5_rabep1__free", - "kr_ptyr_sh2__free", - "py_basal_coef__free", - "py_half_coef__free", - "py_hill_coef__free", - "py_scale_coef__free", - "r_hill__free", - "r_threshold__free", - "ub_basal_coef__free", - "ub_half_coef__free", - "ub_hill_coef__free", - "ub_scale_coef__free", - "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" + "id": "PyBioNetGen_Trivial", + "name": "PyBioNetGen Trivial Decay Reaction Test", + "description": "A trivial model file for testing MCMC distributions.", + "tags": [ + "test-case", + "decay-kinetics" ], - "category": "other", - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, - "methods": [] + "methods": [ + "ode" + ] }, - "gallery": [], - "path": "Published/Mitra2019Rab/rab_wt.bngl", - "file": "rab_wt.bngl", + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/trivial/trivial.bngl", + "file": "trivial.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "rab_wt", - "name": "rab_mon1ccz1_ox.bngl", - "description": "filename:rab_mon1ccz1_ox.bngl", + "id": "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF", + "name": "PyBNF-fitting-setup", + "description": "BNGL model: 190127_CHO_EGFR_forBNF", "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" + "2019", + "egfr", + "salazar" ], "category": "other", "origin": "published", @@ -15433,11 +14776,83 @@ ] }, "gallery": [], - "path": "Published/Mitra2019Rab/pybnf_files/rab_wt.bngl", - "file": "rab_wt.bngl", + "path": "Published/Salazar-Cavazos2019/PyBNF-fitting-setup/190127_CHO_EGFR_forBNF.bngl", + "file": "190127_CHO_EGFR_forBNF.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "quasi_equilibrium", + "name": "quasi equilibrium", + "description": "Quasi-equilibrium approximation", + "tags": [ + "toy models", + "quasi", + "equilibrium" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials", + "native-tutorials" + ], + "path": "Tutorials/General/quasiequilibrium/quasi_equilibrium.bngl", + "file": "quasi_equilibrium.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "quorum-sensing-circuit", + "name": "quorum sensing circuit", + "description": "BioNetGen model: quorum sensing circuit", + "tags": [ + "quorum", + "sensing", + "circuit", + "autoinducer", + "autoinducer_env", + "gene", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl", + "file": "quorum-sensing-circuit.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "rab-gtpase-cycle", @@ -15469,24 +14884,26 @@ "file": "rab-gtpase-cycle.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "RAFi", - "name": "RAFi", - "description": "BioNetGen model: RAFi", + "id": "Ran_NuclearTransport", + "name": "Rule-Based Ran-Mediated Nuclear Transport Model", + "description": "Nuclear Ran transport", "tags": [ - "rafi", - "r", - "i", - "ybar", - "activity" + "ran-gtpase", + "nuclear-transport", + "nuclear-pore-complex", + "import-export" ], - "category": "other", + "category": "regulation", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -15494,31 +14911,32 @@ ] }, "gallery": [ - "other" + "regulation" ], - "path": "Published/PyBioNetGen/core/RAFi/RAFi.bngl", - "file": "RAFi.bngl", + "path": "Published/RulebasedRantransport/Rule_based_Ran_transport.bngl", + "file": "Rule_based_Ran_transport.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "RAFi_ground", - "name": "RAFi ground", - "description": "BioNetGen model: RAFi ground", + "id": "Ran_NuclearTransport_Draft", + "name": "Rule-Based Ran-Mediated Nuclear Transport Model (Draft)", + "description": "Ran transport (draft)", "tags": [ - "rafi", - "ground", - "r", - "i", - "ybar", - "activity" + "ran-gtpase", + "nuclear-transport", + "nuclear-pore-complex", + "draft-model" ], - "category": "other", + "category": "regulation", "origin": "published", "visible": false, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -15526,13 +14944,16 @@ ] }, "gallery": [ - "other" + "regulation" ], - "path": "Published/PyBioNetGen/core/RAFiground/RAFi_ground.bngl", - "file": "RAFi_ground.bngl", + "path": "Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl", + "file": "Rule_based_Ran_transport_draft.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "rankl-rank-signaling", @@ -15565,7 +14986,10 @@ "file": "rankl-rank-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "ras-gef-gap-cycle", @@ -15600,20 +15024,20 @@ "file": "ras-gef-gap-cycle.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "rec_dim", "name": "rec_dim", "description": "Ligand-receptor binding", "tags": [ - "validation", "rec", "dim", "lig", - "writemdl", - "generate_network", - "simulate" + "writemdl" ], "category": "validation", "origin": "test-case", @@ -15633,23 +15057,21 @@ "file": "rec_dim.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "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" + "writemdl" ], "category": "validation", "origin": "test-case", @@ -15669,94 +15091,10 @@ "file": "rec_dim_comp.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" - }, - { - "id": "receptor", - "name": "13-receptor", - "description": "A simple model", - "tags": [ - "ligand_ispresent", - "molecules", - "species" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [], - "path": "Published/Mitra2019/13-receptor/receptor.bngl", - "file": "receptor.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "receptor", - "name": "receptor", - "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "tags": [ - "receptor", - "l", - "r", - "func" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "other" - ], - "path": "Published/PyBioNetGen/core/receptor/receptor.bngl", - "file": "receptor.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "receptor_nf", - "name": "receptor nf", - "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "tags": [ - "receptor", - "nf", - "l", - "r" - ], - "category": "other", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "nf" - ] - }, - "gallery": [ - "other" - ], - "path": "Published/PyBioNetGen/core/receptornf/receptor_nf.bngl", - "file": "receptor_nf.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "receptor_nf", @@ -15764,9 +15102,7 @@ "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", "tags": [ "receptor", - "nf", - "l", - "r" + "nf" ], "category": "validation", "origin": "test-case", @@ -15786,16 +15122,16 @@ "file": "receptor_nf.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "Repressilator", "name": "Repressilator", "description": "Repressilator circuit", "tags": [ - "published", - "tutorial", - "native", "repressilator", "gtetr", "gci", @@ -15826,7 +15162,10 @@ "file": "Repressilator.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "repressilator-oscillator", @@ -15862,7 +15201,10 @@ "file": "repressilator-oscillator.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "retinoic-acid-signaling", @@ -15896,7 +15238,10 @@ "file": "retinoic-acid-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "rho-gtpase-actin-cytoskeleton", @@ -15930,59 +15275,87 @@ "file": "rho-gtpase-actin-cytoskeleton.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Rule_based_egfr_compart", - "name": "Rule based egfr compart", - "description": "Compartmental EGFR model", + "id": "Salazar_Cavazos_egfr_2019_190127_CHO_EGFR_best-fit", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_CHO_EGFR_best-fit)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "published", - "rule", - "based", "egfr", - "compart", - "egf", - "grb2", - "shc", - "generate_network" + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "signaling" + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_best-fit.bngl", + "file": "190127_CHO_EGFR_best-fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Salazar_Cavazos_egfr_2019_190127_CHO_EGFR_Epigen", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_CHO_EGFR_Epigen)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "path": "Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl", - "file": "Rule_based_egfr_compart.bngl", + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_Epigen.bngl", + "file": "190127_CHO_EGFR_Epigen.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Rule_based_egfr_tutorial", - "name": "Faeder 2009", - "description": "EGFR signaling", + "id": "Salazar_Cavazos_egfr_2019_190127_CHO_EGFR_sensitivity", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_CHO_EGFR_sensitivity)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "published", - "rule", - "based", "egfr", - "tutorial", - "egf", - "grb2", - "shc", - "generate_network" + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -15993,92 +15366,92 @@ "ode" ] }, - "gallery": [ - "cancer" - ], - "path": "Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl", - "file": "Rule_based_egfr_tutorial.bngl", + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_sensitivity.bngl", + "file": "190127_CHO_EGFR_sensitivity.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Rule_based_Ran_transport", - "name": "Rule based Ran transport", - "description": "Nuclear Ran transport", + "id": "Salazar_Cavazos_egfr_2019_190127_CHO_HA_EGFR_L858R", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_CHO_HA_EGFR_L858R)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "published", - "rule", - "based", - "ran", - "transport", - "c", - "rcc1", - "generate_network" + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "regulation", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "regulation" - ], - "path": "Published/RulebasedRantransport/Rule_based_Ran_transport.bngl", - "file": "Rule_based_Ran_transport.bngl", + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_HA_EGFR_L858R.bngl", + "file": "190127_CHO_HA_EGFR_L858R.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Rule_based_Ran_transport_draft", - "name": "Rule based Ran transport draft", - "description": "Ran transport (draft)", + "id": "Salazar_Cavazos_egfr_2019_190127_HeLa", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_HeLa)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "published", - "rule", - "based", - "ran", - "transport", - "draft", - "c", - "rcc1", - "generate_network" + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "regulation", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "regulation" - ], - "path": "Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl", - "file": "Rule_based_Ran_transport_draft.bngl", + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_HeLa.bngl", + "file": "190127_HeLa.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Scaff-22_ground", - "name": "18-mapk", - "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "id": "Salazar_Cavazos_egfr_2019_190127_HMEC", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_HMEC)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "signaling" + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -16090,20 +15463,27 @@ ] }, "gallery": [], - "path": "Published/Mitra2019/18-mapk/Scaff-22_ground.bngl", - "file": "Scaff-22_ground.bngl", + "path": "Published/Salazar-Cavazos2019/190127_HMEC.bngl", + "file": "190127_HMEC.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Scaff-22_tofit", - "name": "18-mapk", - "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "id": "Salazar_Cavazos_egfr_2019_190127_MCF10A", + "name": "Salazar-Cavazos et al. 2019: Single-Molecule EGFR Phosphorylation Dynamics (190127_MCF10A)", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", "tags": [ - "signaling" + "egfr", + "single-molecule", + "phosphorylation", + "2019", + "salazar" ], - "category": "signaling", + "category": "other", "origin": "published", "visible": false, "compatibility": { @@ -16115,23 +15495,22 @@ ] }, "gallery": [], - "path": "Published/Mitra2019/18-mapk/Scaff-22_tofit.bngl", - "file": "Scaff-22_tofit.bngl", + "path": "Published/Salazar-Cavazos2019/190127_MCF10A.bngl", + "file": "190127_MCF10A.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "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", @@ -16152,7 +15531,10 @@ "file": "SHP2_base_model.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "shp2-phosphatase-regulation", @@ -16184,7 +15566,10 @@ "file": "shp2-phosphatase-regulation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "signal-amplification-cascade", @@ -16217,18 +15602,18 @@ "file": "signal-amplification-cascade.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "simple", "name": "simple", "description": "Simple binding model", "tags": [ - "published", "tutorials", "simple", - "s", - "t", "dnat", "trash" ], @@ -16250,167 +15635,10 @@ "file": "simple.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" - }, - { - "id": "Simple", - "name": "Simple", - "description": "An example from a real application", - "tags": [ - "simple", - "setoption", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/Simple/Simple.bngl", - "file": "Simple.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "Simple_AddActions", - "name": "Simple AddActions", - "description": "An example from a real application", - "tags": [ - "simple", - "addactions", - "setoption", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl", - "file": "Simple_AddActions.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "Simple_Answer", - "name": "Simple Answer", - "description": "An example from a real application", - "tags": [ - "simple", - "answer", - "setoption", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": true, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl", - "file": "Simple_Answer.bngl", - "collectionId": null, - "featured": false, - "difficulty": "intermediate" - }, - { - "id": "Simple_GenOnly", - "name": "Simple GenOnly", - "description": "An example from a real application", - "tags": [ - "simple", - "genonly", - "setoption", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl", - "file": "Simple_GenOnly.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "simple_nf_seed", - "name": "simple nf seed", - "description": "BioNetGen model: simple nf seed", - "tags": [ - "simple", - "nf", - "seed", - "a", - "b", - "function1", - "simulate" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "nf" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl", - "file": "simple_nf_seed.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "simple_nfsim_test", @@ -16422,7 +15650,7 @@ "test" ], "category": "other", - "origin": "contributed", + "origin": "tutorial", "visible": false, "compatibility": { "bng2": true, @@ -16435,55 +15663,24 @@ "gallery": [ "other" ], - "path": "Tutorials/simplenfsimtest/simple_nfsim_test.bngl", - "file": "simple_nfsim_test.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "Simple_nogen", - "name": "Simple nogen", - "description": "An example from a real application", - "tags": [ - "simple", - "nogen", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl", - "file": "Simple_nogen.bngl", + "path": "Tutorials/simplenfsimtest/simple_nfsim_test.bngl", + "file": "simple_nfsim_test.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "simple_sbml_import", "name": "simple_sbml_import", "description": "SBML import test", "tags": [ - "validation", "simple", "sbml", "import", - "readfile", - "generate_network", - "simulate" + "readfile" ], "category": "validation", "origin": "test-case", @@ -16503,18 +15700,18 @@ "file": "simple_sbml_import.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "simple_system", "name": "simple_system", "description": "Simple binding system", "tags": [ - "validation", "simple", - "system", - "x", - "y" + "system" ], "category": "validation", "origin": "test-case", @@ -16534,7 +15731,10 @@ "file": "simple_system.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "simple-dimerization", @@ -16566,7 +15766,10 @@ "file": "simple-dimerization.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "SIR", @@ -16574,8 +15777,7 @@ "description": "BioNetGen model: SIR", "tags": [ "sir", - "saveconcentrations", - "simulate" + "saveconcentrations" ], "category": "tutorial", "origin": "tutorial", @@ -16596,7 +15798,10 @@ "file": "SIR.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "sir-epidemic-model", @@ -16630,7 +15835,10 @@ "file": "sir-epidemic-model.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "smad-tgf-beta-signaling", @@ -16665,7 +15873,10 @@ "file": "smad-tgf-beta-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "sonic-hedgehog-gradient", @@ -16698,7 +15909,10 @@ "file": "sonic-hedgehog-gradient.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "sp_fourier_synthesizer", @@ -16735,7 +15949,10 @@ "file": "sp_fourier_synthesizer.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "sp_image_convolution", @@ -16768,7 +15985,10 @@ "file": "sp_image_convolution.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "sp_kalman_filter", @@ -16804,7 +16024,10 @@ "file": "sp_kalman_filter.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "stat3-mediated-transcription", @@ -16836,7 +16059,10 @@ "file": "stat3-mediated-transcription.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "stress-response-adaptation", @@ -16868,7 +16094,10 @@ "file": "stress-response-adaptation.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "Suderman_2013", @@ -16877,7 +16106,6 @@ "tags": [ "suderman", "2013", - "i", "trash", "pheromone", "ste2", @@ -16904,7 +16132,10 @@ "file": "Suderman_2013.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "synaptic-plasticity-ltp", @@ -16940,7 +16171,10 @@ "file": "synaptic-plasticity-ltp.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "synbio_band_pass_filter", @@ -16975,22 +16209,305 @@ "file": "synbio_band_pass_filter.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "synbio_counter_molecular", + "name": "synbio counter molecular", + "description": "Model: synbio_counter_molecular.bngl", + "tags": [ + "synbio", + "counter", + "molecular", + "state", + "input" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl", + "file": "synbio_counter_molecular.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "synbio_edge_detector", + "name": "synbio edge detector", + "description": "Model: synbio_edge_detector.bngl", + "tags": [ + "synbio", + "edge", + "detector", + "x", + "y", + "z" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl", + "file": "synbio_edge_detector.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "synbio_logic_gates_enzymatic", + "name": "synbio logic gates enzymatic", + "description": "Model: synbio_logic_gates_enzymatic.bngl", + "tags": [ + "synbio", + "logic", + "gates", + "enzymatic", + "i1", + "i2", + "gateand", + "gateor", + "outand", + "outor" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl", + "file": "synbio_logic_gates_enzymatic.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "synbio_oscillator_synchronization", + "name": "synbio oscillator synchronization", + "description": "Model: synbio_oscillator_synchronization.bngl", + "tags": [ + "synbio", + "oscillator", + "synchronization", + "osc1", + "osc2", + "signal" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl", + "file": "synbio_oscillator_synchronization.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "t-cell-activation", + "name": "t cell activation", + "description": "BioNetGen model: t cell activation", + "tags": [ + "t", + "cell", + "activation", + "tcr", + "antigen", + "cytokine" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/tcellactivation/t-cell-activation.bngl", + "file": "t-cell-activation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false + }, + { + "id": "test_ANG_synthesis_simple", + "name": "test_ANG_synthesis_simple", + "description": "Synthesis network test", + "tags": [ + "test", + "ang", + "synthesis", + "simple", + "source", + "source2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl", + "file": "test_ANG_synthesis_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "test_fixed", + "name": "test_fixed", + "description": "# actions ##", + "tags": [ + "test", + "fixed" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testfixed/test_fixed.bngl", + "file": "test_fixed.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "test_MM", + "name": "test_MM", + "description": "Kinetic constants", + "tags": [ + "test", + "mm" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testMM/test_MM.bngl", + "file": "test_MM.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "synbio_counter_molecular", - "name": "synbio counter molecular", - "description": "Model: synbio_counter_molecular.bngl", + "id": "test_mratio", + "name": "test_mratio", + "description": "Reaction ratio test", "tags": [ - "synbio", - "counter", - "molecular", - "state", - "input" + "test", + "mratio", + "c_theory", + "c_upper", + "c_lower" ], - "category": "synthetic-biology", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -17000,32 +16517,35 @@ ] }, "gallery": [ - "synbio", - "test-models" + "validation" ], - "path": "Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl", - "file": "synbio_counter_molecular.bngl", + "path": "Tutorials/testmratio/test_mratio.bngl", + "file": "test_mratio.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "synbio_edge_detector", - "name": "synbio edge detector", - "description": "Model: synbio_edge_detector.bngl", + "id": "test_network_gen", + "name": "test_network_gen", + "description": "fceri model with network generation", "tags": [ - "synbio", - "edge", - "detector", - "x", - "y", - "z" + "test", + "network", + "gen", + "lig", + "lyn", + "syk", + "rec" ], - "category": "synthetic-biology", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { - "bng2": true, + "bng2": false, "nfsim": false, "excluded": false, "methods": [ @@ -17033,34 +16553,28 @@ ] }, "gallery": [ - "synbio", - "test-models" + "validation" ], - "path": "Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl", - "file": "synbio_edge_detector.bngl", + "path": "Tutorials/testnetworkgen/test_network_gen.bngl", + "file": "test_network_gen.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "synbio_logic_gates_enzymatic", - "name": "synbio logic gates enzymatic", - "description": "Model: synbio_logic_gates_enzymatic.bngl", + "id": "test_sat", + "name": "test_sat", + "description": "Kinetic constants", "tags": [ - "synbio", - "logic", - "gates", - "enzymatic", - "i1", - "i2", - "gateand", - "gateor", - "outand", - "outor" + "test", + "sat" ], - "category": "synthetic-biology", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -17070,30 +16584,32 @@ ] }, "gallery": [ - "synbio", - "test-models" + "validation" ], - "path": "Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl", - "file": "synbio_logic_gates_enzymatic.bngl", + "path": "Tutorials/testsat/test_sat.bngl", + "file": "test_sat.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "synbio_oscillator_synchronization", - "name": "synbio oscillator synchronization", - "description": "Model: synbio_oscillator_synchronization.bngl", + "id": "test_synthesis_cBNGL_simple", + "name": "test_synthesis_cBNGL_simple", + "description": "Compartmental synthesis", "tags": [ - "synbio", - "oscillator", - "synchronization", - "osc1", - "osc2", - "signal" + "test", + "synthesis", + "cbngl", + "simple", + "source", + "source2" ], - "category": "synthetic-biology", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, @@ -17103,169 +16619,135 @@ ] }, "gallery": [ - "synbio", - "test-models" + "validation" ], - "path": "Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl", - "file": "synbio_oscillator_synchronization.bngl", + "path": "Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl", + "file": "test_synthesis_cBNGL_simple.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "t-cell-activation", - "name": "t cell activation", - "description": "BioNetGen model: t cell activation", + "id": "test_synthesis_complex", + "name": "test_synthesis_complex", + "description": "Complex synthesis test", "tags": [ - "t", - "cell", - "activation", - "tcr", - "antigen", - "cytokine" + "test", + "synthesis", + "complex", + "receptor", + "source", + "source2" ], - "category": "signaling", - "origin": "ai-generated", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, "gallery": [ - "immunology", - "test-models" + "validation" ], - "path": "Examples/biology/tcellactivation/t-cell-activation.bngl", - "file": "t-cell-activation.bngl", + "path": "Tutorials/testsynthesiscomplex/test_synthesis_complex.bngl", + "file": "test_synthesis_complex.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "tcr", - "name": "tcr", - "description": "A model of T cell receptor signaling", + "id": "test_synthesis_complex_0_cBNGL", + "name": "test_synthesis_complex_0_cBNGL", + "description": "volume-surface", "tags": [ - "tcr", - "lig1", - "lig2", - "lig3", - "cd28", - "lck", - "itk", - "zap70" + "test", + "synthesis", + "complex", + "cbngl", + "surface_molecule1", + "surface_molecule2", + "surface_receptor" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ - "nf" + "ode" ] }, "gallery": [ - "other" + "validation" ], - "path": "Published/PyBioNetGen/core/tcr/tcr.bngl", - "file": "tcr.bngl", + "path": "Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl", + "file": "test_synthesis_complex_0_cBNGL.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "TCR_model", - "name": "ERK_model.bngl", - "description": "filename: ERK_model.bngl", + "id": "test_synthesis_complex_source_cBNGL", + "name": "test_synthesis_complex_source_cBNGL", + "description": "volume-surface", "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" + "test", + "synthesis", + "complex", + "source", + "cbngl", + "surface_molecule1", + "surface_molecule2", + "surface_receptor" ], - "category": "other", - "origin": "published", - "visible": false, + "category": "validation", + "origin": "test-case", + "visible": true, "compatibility": { "bng2": true, "nfsim": false, "excluded": false, "methods": [ - "ode", - "ssa" + "ode" ] }, - "gallery": [], - "path": "Published/Lin2019/TCR_model.bngl", - "file": "TCR_model.bngl", + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl", + "file": "test_synthesis_complex_source_cBNGL.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_ANG_synthesis_simple", - "name": "test_ANG_synthesis_simple", - "description": "Synthesis network test", + "id": "test_synthesis_simple", + "name": "test_synthesis_simple", + "description": "Simple synthesis test", "tags": [ - "validation", "test", - "ang", "synthesis", "simple", - "a", - "b", - "c", "source", - "source2", - "generate_network" + "source2" ], "category": "validation", "origin": "test-case", @@ -17281,28 +16763,61 @@ "gallery": [ "validation" ], - "path": "Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl", - "file": "test_ANG_synthesis_simple.bngl", + "path": "Tutorials/testsynthesissimple/test_synthesis_simple.bngl", + "file": "test_synthesis_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "Thomas_egfr_2016_example1_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example1_fit)", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example1_fit.bngl", + "file": "example1_fit.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_fixed", - "name": "test_fixed", - "description": "# actions ##", + "id": "Thomas_egfr_2016_example2_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example2_fit)", + "description": "Filename: example1_starting_point.bngl", "tags": [ - "validation", - "test", - "fixed", - "a", - "b", - "generate_network", - "simulate" + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -17311,31 +16826,30 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testfixed/test_fixed.bngl", - "file": "test_fixed.bngl", + "gallery": [], + "path": "Published/Thomas2016/example2_fit.bngl", + "file": "example2_fit.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_MM", - "name": "test_MM", - "description": "Kinetic constants", + "id": "Thomas_egfr_2016_example3_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example3_fit)", + "description": "Filename: example1_starting_point.bngl", "tags": [ - "validation", - "test", - "mm", - "e", - "s", - "p", - "generate_network" + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -17344,32 +16858,30 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testMM/test_MM.bngl", - "file": "test_MM.bngl", + "gallery": [], + "path": "Published/Thomas2016/example3_fit.bngl", + "file": "example3_fit.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_mratio", - "name": "test_mratio", - "description": "Reaction ratio test", + "id": "Thomas_egfr_2016_example4_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example4_fit)", + "description": "Filename: example1_starting_point.bngl", "tags": [ - "validation", - "test", - "mratio", - "a", - "b", - "c_theory", - "c_upper", - "c_lower" + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -17378,65 +16890,62 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testmratio/test_mratio.bngl", - "file": "test_mratio.bngl", + "gallery": [], + "path": "Published/Thomas2016/example4_fit.bngl", + "file": "example4_fit.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_network_gen", - "name": "test_network_gen", - "description": "fceri model with network generation", + "id": "Thomas_egfr_2016_example5_fit", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example5_fit)", + "description": "Filename: example1_starting_point.bngl", "tags": [ - "validation", - "test", - "network", - "gen", - "lig", - "lyn", - "syk", - "rec" + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testnetworkgen/test_network_gen.bngl", - "file": "test_network_gen.bngl", + "gallery": [], + "path": "Published/Thomas2016/example5_fit.bngl", + "file": "example5_fit.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_sat", - "name": "test_sat", - "description": "Kinetic constants", + "id": "Thomas_egfr_2016_example5_ground_truth", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example5_ground_truth)", + "description": "Filename: example1_starting_point.bngl", "tags": [ - "validation", - "test", - "sat", - "e", - "s", - "p", - "generate_network" + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -17445,35 +16954,30 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testsat/test_sat.bngl", - "file": "test_sat.bngl", + "gallery": [], + "path": "Published/Thomas2016/example5_ground_truth.bngl", + "file": "example5_ground_truth.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_synthesis_cBNGL_simple", - "name": "test_synthesis_cBNGL_simple", - "description": "Compartmental synthesis", + "id": "Thomas_egfr_2016_example6_ground_truth", + "name": "Thomas et al. 2016: Parameter Fitting of EGFR Signaling (example6_ground_truth)", + "description": "Filename: example1_starting_point.bngl", "tags": [ - "validation", - "test", - "synthesis", - "cbngl", - "simple", - "a", - "a2", - "b", - "c", - "source", - "source2" + "egfr", + "signaling", + "parameter-fitting", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -17482,34 +16986,30 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl", - "file": "test_synthesis_cBNGL_simple.bngl", + "gallery": [], + "path": "Published/Thomas2016/example6_ground_truth.bngl", + "file": "example6_ground_truth.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_synthesis_complex", - "name": "test_synthesis_complex", - "description": "Complex synthesis test", + "id": "Thomas_Example1_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 1 Starting Point", + "description": "Filename: example1_starting_point.bngl", "tags": [ - "validation", - "test", - "synthesis", - "complex", - "a", - "b", - "c", - "receptor", - "source", - "source2" + "egfr", + "signaling", + "starting-point", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, "nfsim": false, @@ -17518,205 +17018,179 @@ "ode" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testsynthesiscomplex/test_synthesis_complex.bngl", - "file": "test_synthesis_complex.bngl", + "gallery": [], + "path": "Published/Thomas2016/example1_BNFfiles/example1.bngl", + "file": "example1.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "test_synthesis_complex_0_cBNGL", - "name": "test_synthesis_complex_0_cBNGL", - "description": "volume-surface", + "id": "Thomas_Example2_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 2 Starting Point", + "description": "Filename: example2_starting_point.bngl", "tags": [ - "validation", - "test", - "synthesis", - "complex", - "0", - "cbngl", - "volume_molecule1", - "volume_molecule2", - "surface_molecule1", - "surface_molecule2", - "volume_molecule3", - "volume_molecule4", - "volume_receptor", - "surface_receptor" + "egfr", + "signaling", + "starting-point", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl", - "file": "test_synthesis_complex_0_cBNGL.bngl", + "gallery": [], + "path": "Published/Thomas2016/example2_BNFfiles/example2.bngl", + "file": "example2.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "test_synthesis_complex_source_cBNGL", - "name": "test_synthesis_complex_source_cBNGL", - "description": "volume-surface", + "id": "Thomas_Example3_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 3 (TLBR)", + "description": "BNGL model: example3", "tags": [ - "validation", - "test", - "synthesis", - "complex", - "source", - "cbngl", - "volume_molecule1", - "volume_molecule2", - "surface_molecule1", - "surface_molecule2", - "volume_molecule3", - "volume_molecule4", - "volume_receptor", - "surface_receptor" + "tlbr", + "polymerization", + "ligand-receptor", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl", - "file": "test_synthesis_complex_source_cBNGL.bngl", + "gallery": [], + "path": "Published/Thomas2016/example3_BNFfiles/example3.bngl", + "file": "example3.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "test_synthesis_simple", - "name": "test_synthesis_simple", - "description": "Simple synthesis test", + "id": "Thomas_Example4_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 4 Model", + "description": "Supplementary File A in File S1", "tags": [ - "validation", - "test", - "synthesis", - "simple", - "a", - "b", - "c", - "source", - "source2", - "generate_network" + "egfr", + "signaling", + "2016", + "thomas" ], - "category": "validation", - "origin": "test-case", - "visible": true, + "category": "other", + "origin": "published", + "visible": false, "compatibility": { "bng2": true, - "nfsim": false, + "nfsim": true, "excluded": false, "methods": [ - "ode" + "nf" ] }, - "gallery": [ - "validation" - ], - "path": "Tutorials/testsynthesissimple/test_synthesis_simple.bngl", - "file": "test_synthesis_simple.bngl", + "gallery": [], + "path": "Published/Thomas2016/example4_BNFfiles/example4.bngl", + "file": "example4.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "tlbr", - "name": "tlbr", - "description": "A model of trivalent ligand, bivalent receptor", + "id": "Thomas_Example5_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 5 Model", + "description": "A simple model", "tags": [ - "tlbr", - "l", - "r", - "lambda", - "fl" + "egfr", + "signaling", + "2016", + "thomas" ], "category": "other", "origin": "published", "visible": false, "compatibility": { "bng2": true, - "nfsim": true, + "nfsim": false, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "immunology" - ], - "path": "Published/PyBioNetGen/core/tlbr/tlbr.bngl", - "file": "tlbr.bngl", + "gallery": [], + "path": "Published/Thomas2016/example5_BNFfiles/example5.bngl", + "file": "example5.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { - "id": "tlbr", - "name": "TLBR Tutorial", - "description": "Ligand binding", + "id": "Thomas_Example6_2016", + "name": "Thomas et al. 2016: Parameter Fitting - Example 6 Model", + "description": "A simple model", "tags": [ - "published", - "immunology", - "tlbr", - "l", - "r", - "simulate_rm" + "egfr", + "signaling", + "2016", + "thomas" ], - "category": "immunology", + "category": "other", "origin": "published", "visible": false, "compatibility": { - "bng2": false, + "bng2": true, "nfsim": true, "excluded": false, "methods": [ "ode" ] }, - "gallery": [ - "immunology" - ], - "path": "Published/tlbr/tlbr.bngl", - "file": "tlbr.bngl", + "gallery": [], + "path": "Published/Thomas2016/example6_BNFfiles/example6.bngl", + "file": "example6.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "tlmr", "name": "tlmr", "description": "Trivalent ligand monovalent receptor", "tags": [ - "validation", - "tlmr", - "l", - "r", - "generate_network", - "simulate_ode" + "tlmr" ], "category": "validation", "origin": "test-case", @@ -17736,7 +17210,10 @@ "file": "tlmr.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "tlr3-dsrna-sensing", @@ -17769,7 +17246,10 @@ "file": "tlr3-dsrna-sensing.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "tnf-induced-apoptosis", @@ -17803,20 +17283,17 @@ "file": "tnf-induced-apoptosis.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "toggle", "name": "Toggle", "description": "Toggle switch", "tags": [ - "published", - "tutorial", - "native", "toggle", - "x", - "y", - "generate_network", "writemfile", "setconcentration" ], @@ -17839,21 +17316,18 @@ "file": "toggle.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "toy-jim", "name": "toy-jim", "description": "The model consists of a monovalent extracellular ligand,", "tags": [ - "validation", "toy", - "jim", - "l", - "r", - "a", - "k", - "null" + "jim" ], "category": "validation", "origin": "test-case", @@ -17873,22 +17347,19 @@ "file": "toy-jim.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "toy1", "name": "toy1", "description": "Basic signaling toy", "tags": [ - "published", "tutorials", "toy1", - "l", - "r", - "a", - "generate_network", - "writesbml", - "simulate_ode" + "writesbml" ], "category": "tutorial", "origin": "tutorial", @@ -17908,20 +17379,18 @@ "file": "toy1.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "toy2", "name": "toy2", "description": "Enzymatic reaction toy", "tags": [ - "published", "tutorials", - "toy2", - "l", - "r", - "a", - "k" + "toy2" ], "category": "tutorial", "origin": "tutorial", @@ -17941,16 +17410,17 @@ "file": "toy2.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "translateSBML", "name": "translateSBML", "description": "title: translateSBML.bngl", "tags": [ - "translatesbml", - "generate_network", - "simulate" + "translatesbml" ], "category": "tutorial", "origin": "tutorial", @@ -17970,99 +17440,10 @@ "file": "translateSBML.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" - }, - { - "id": "Tricky", - "name": "Tricky", - "description": "An example from a real application", - "tags": [ - "tricky", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": true, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/Tricky/Tricky.bngl", - "file": "Tricky.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "TrickyUS", - "name": "TrickyUS", - "description": "An example from a real application", - "tags": [ - "trickyus", - "ag", - "r", - "h" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/TrickyUS/TrickyUS.bngl", - "file": "TrickyUS.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" - }, - { - "id": "trivial", - "name": "trivial", - "description": "A trivial model file for testing MCMC distributions.", - "tags": [ - "trivial", - "q", - "r", - "output", - "generate_network", - "simulate" - ], - "category": "validation", - "origin": "test-case", - "visible": false, - "compatibility": { - "bng2": true, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "validation" - ], - "path": "Published/PyBioNetGen/tests/trivial/trivial.bngl", - "file": "trivial.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "two-component-system", @@ -18094,21 +17475,18 @@ "file": "two-component-system.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "univ_synth", "name": "univ_synth", "description": "example of universal synthesis", "tags": [ - "validation", "univ", - "synth", - "a", - "b", - "c", - "generate_network", - "simulate_ode" + "synth" ], "category": "validation", "origin": "test-case", @@ -18128,7 +17506,10 @@ "file": "univ_synth.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "vegf-angiogenesis", @@ -18161,19 +17542,19 @@ "file": "vegf-angiogenesis.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "vilar_2002", + "id": "Vilar_Circadian_2002", "name": "Vilar 2002", "description": "Genetic oscillator", "tags": [ - "published", - "vilar", "2002", "dna", - "a", - "r" + "oscillations" ], "category": "regulation", "origin": "published", @@ -18193,19 +17574,19 @@ "file": "vilar_2002.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "vilar_2002b", + "id": "Vilar_Circadian_2002b", "name": "Vilar 2002b", "description": "Gene oscillator", "tags": [ - "published", - "vilar", - "2002b", + "2002", "dna", - "a", - "r" + "oscillations" ], "category": "regulation", "origin": "published", @@ -18225,19 +17606,19 @@ "file": "vilar_2002b.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "vilar_2002c", + "id": "Vilar_Circadian_2002c", "name": "Vilar 2002c", "description": "Gene oscillator", "tags": [ - "published", - "vilar", - "2002c", + "2002", "dna", - "a", - "r" + "oscillations" ], "category": "regulation", "origin": "published", @@ -18257,7 +17638,10 @@ "file": "vilar_2002c.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { "id": "viral-sensing-innate-immunity", @@ -18293,22 +17677,16 @@ "file": "viral-sensing-innate-immunity.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "visualize", "name": "Visualize", "description": "Visualization toy", - "tags": [ - "published", - "tutorial", - "native", - "visualize", - "x", - "a1", - "a2", - "b" - ], + "tags": [], "category": "tutorial", "origin": "tutorial", "visible": false, @@ -18327,7 +17705,10 @@ "file": "visualize.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "wacky_alchemy_stone", @@ -18359,7 +17740,10 @@ "file": "wacky_alchemy_stone.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wacky_black_hole", @@ -18392,7 +17776,10 @@ "file": "wacky_black_hole.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wacky_bouncing_ball", @@ -18424,7 +17811,10 @@ "file": "wacky_bouncing_ball.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wacky_traffic_jam_asep", @@ -18459,7 +17849,10 @@ "file": "wacky_traffic_jam_asep.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wacky_zombie_infection", @@ -18490,40 +17883,10 @@ "file": "wacky_zombie_infection.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" - }, - { - "id": "wnt", - "name": "Wnt Signaling", - "description": "Wnt signaling", - "tags": [ - "published", - "wnt", - "dsh", - "axc", - "frz", - "lrp5", - "bcat" - ], - "category": "regulation", - "origin": "published", - "visible": false, - "compatibility": { - "bng2": false, - "nfsim": false, - "excluded": false, - "methods": [ - "ode" - ] - }, - "gallery": [ - "regulation" - ], - "path": "Published/wnt/wnt.bngl", - "file": "wnt.bngl", - "collectionId": null, - "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false }, { "id": "wnt-beta-catenin-signaling", @@ -18559,7 +17922,10 @@ "file": "wnt-beta-catenin-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { "id": "wound-healing-pdgf-signaling", @@ -18592,17 +17958,18 @@ "file": "wound-healing-pdgf-signaling.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Yang_2008", + "id": "Yang_tlbr_2008", "name": "Yang 2008", "description": "TLBR yang 2008", "tags": [ - "published", - "physics", - "yang", - "2008" + "2008", + "yang" ], "category": "physics", "origin": "published", @@ -18622,24 +17989,58 @@ "file": "tlbr_yang2008.bngl", "collectionId": null, "featured": false, - "difficulty": "intermediate" + "difficulty": "intermediate", + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + { + "id": "ZAP70_immunology_2021", + "name": "Model ZAP", + "description": "ZAP-70 recruitment", + "tags": [ + "cbl", + "dead", + "lck", + "ligand", + "modelzap", + "nfsim", + "zap", + "zeta" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/ModelZAP/Model_ZAP.bngl", + "file": "Model_ZAP.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced", + "bng2_compatible": true, + "nfsim_compatible": true, + "excluded": false }, { - "id": "Zhang_2021", - "name": "Zhang 2021", + "id": "Zhang_developmental_2021", + "name": "Zhang et al. 2021: VE-PTP and Tie2 Receptor Regulation Model", "description": "CAR-T signaling", "tags": [ - "published", - "zhang", - "2021", + "ve-ptp", "tie2", - "tie1", - "ang1_4", - "ang2_2", - "ang2_3", - "ang2_4", - "veptp", - "pten" + "angiogenesis", + "2021", + "zhang" ], "category": "signaling", "origin": "published", @@ -18659,24 +18060,21 @@ "file": "Zhang_2021.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false }, { - "id": "Zhang_2023", - "name": "Zhang 2023", + "id": "Zhang_developmental_2023", + "name": "Zhang et al. 2023: VEGF-induced PLC-gamma Activation Model", "description": "VEGF signaling", "tags": [ - "published", - "zhang", - "2023", "vegf", - "vegfr2", - "vegfr1", - "nrp1", - "pi", - "plcgamma", - "dag", - "ip3_cyto" + "plc-gamma", + "angiogenesis", + "2023", + "zhang" ], "category": "signaling", "origin": "published", @@ -18696,6 +18094,9 @@ "file": "Zhang_2023.bngl", "collectionId": null, "featured": false, - "difficulty": "advanced" + "difficulty": "advanced", + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false } ] \ No newline at end of file diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 00000000..4ca926f5 --- /dev/null +++ b/package-lock.json @@ -0,0 +1,6 @@ +{ + "name": "app", + "lockfileVersion": 3, + "requires": true, + "packages": {} +} diff --git a/scripts/apply-gallery-assignments.js b/scripts/apply-gallery-assignments.js index dcdd76b5..cddda651 100644 --- a/scripts/apply-gallery-assignments.js +++ b/scripts/apply-gallery-assignments.js @@ -1,4 +1,5 @@ const fs = require('fs'); +const { safeJoin } = require('./utils'); const path = require('path'); function parseArgs(argv) { @@ -26,7 +27,7 @@ function findAllMetadataFiles(dir, results = []) { const entries = fs.readdirSync(dir, { withFileTypes: true }); for (const entry of entries) { - const fullPath = path.join(dir, entry.name); + const fullPath = safeJoin(dir, entry.name); if (entry.isDirectory()) { findAllMetadataFiles(fullPath, results); } else if (entry.name === 'metadata.yaml') { @@ -36,28 +37,24 @@ function findAllMetadataFiles(dir, results = []) { return results; } -function updateMetadataFile(filePath, assignments, dryRun) { - let content = fs.readFileSync(filePath, 'utf8'); + +async function updateMetadataFile(filePath, assignments, compiledAssignments, dryRun) { + let content = await fs.promises.readFile(filePath, 'utf8'); const dir = path.dirname(filePath); const modelDirName = path.basename(dir); let updated = false; let newContent = content; - for (const [modelId, data] of Object.entries(assignments)) { - const idPattern = new RegExp(`^id:\\s*["']?${modelId.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}["']?\\s*$`, 'm'); + for (const {modelId, data, idPattern} of compiledAssignments) { if (idPattern.test(content)) { - console.log(` Found model ${modelId} in ${filePath}`); - if (data.gallery_categories && data.gallery_categories.length > 0) { const catsStr = JSON.stringify(data.gallery_categories); const galleryMatch = content.match(/gallery_categories:\s*(\[\]|["\'][^"\']*["\'])/); if (galleryMatch) { - if (galleryMatch) { - newContent = newContent.replace(/gallery_categories:\s*\[\]/, `gallery_categories: ${catsStr}`); - updated = true; - } + newContent = newContent.replace(/gallery_categories:\s*\[\]/, `gallery_categories: ${catsStr}`); + updated = true; } const galleryCatMatch = content.match(/gallery_category:\s*["']([^"\']+)["\']/); @@ -102,34 +99,56 @@ function updateMetadataFile(filePath, assignments, dryRun) { } if (updated && !dryRun) { - fs.writeFileSync(filePath, newContent); + await fs.promises.writeFile(filePath, newContent); } return updated; } -function main() { - const { input, root, dryRun } = parseArgs(process.argv.slice(2)); +async function main(argv = process.argv.slice(2)) { + const { input, root, dryRun } = parseArgs(argv); - console.log(`Reading ${input}...`); - const assignments = JSON.parse(fs.readFileSync(input, 'utf8')); + const safeInput = safeJoin(process.cwd(), input); + const assignments = JSON.parse(await fs.promises.readFile(safeInput, 'utf8')); console.log(`Loaded ${Object.keys(assignments).length} assignments`); + const compiledAssignments = []; + for (const [modelId, data] of Object.entries(assignments)) { + if (typeof modelId !== 'string' || modelId.length > 100) { + console.warn(`Skipping invalid modelId: ${modelId}`); + continue; + } + compiledAssignments.push({ + modelId, data, + idPattern: new RegExp(`^id:\\s*["']?${modelId.replace(/[.*+?^${}()|[\]\\]/g, (match) => '\\' + match)}["']?\\s*$`, 'm') + }); + } + const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; - const metadataFiles = SEARCH_ROOTS.flatMap(searchRoot => + const metadataFileArrays = SEARCH_ROOTS.map(searchRoot => findAllMetadataFiles(path.join(root, searchRoot)) ); + const metadataFiles = metadataFileArrays.flat(); - console.log(`Found ${metadataFiles.length} metadata.yaml files`); - - let updated = 0; - for (const filePath of metadataFiles) { - if (updateMetadataFile(filePath, assignments, dryRun)) { - updated++; - } - } - - console.log(`\n${dryRun ? 'Would update' : 'Updated'} ${updated} files`); + const updatePromises = metadataFiles.map(filePath => + updateMetadataFile(filePath, assignments, compiledAssignments, dryRun) + ); + + const results = await Promise.all(updatePromises); + const updated = results.filter(Boolean).length; + console.log(`Updated ${updated} metadata files`); +} + +if (require.main === module) { + main().catch(error => { + console.error("An error occurred:", error); + process.exit(1); + }); } -main(); \ No newline at end of file +module.exports = { + parseArgs, + findAllMetadataFiles, + updateMetadataFile, + main, +}; diff --git a/scripts/apply-gallery-assignments.test.js b/scripts/apply-gallery-assignments.test.js new file mode 100644 index 00000000..9a343a25 --- /dev/null +++ b/scripts/apply-gallery-assignments.test.js @@ -0,0 +1,212 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const path = require('path'); +const os = require('os'); +const fs = require('fs'); +const { updateMetadataFile, parseArgs, findAllMetadataFiles } = require('./apply-gallery-assignments.js'); + +function compileAssignments(assignments) { + return Object.entries(assignments).map(([modelId, data]) => ({ + modelId, data, + idPattern: new RegExp(`^id:\\s*["']?${modelId.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}["']?\\s*$`, 'm') + })); +} + +test('updateMetadataFile', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'update-metadata-test-')); + }); + + t.afterEach(() => { + fs.rmSync(tmpDir, { recursive: true, force: true }); + }); + + await t.test('returns false and does not modify file if model ID is not found', async () => { + const filePath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(filePath, 'id: "model-2"\n'); + + const compiled = compileAssignments({ 'model-1': { bng2_compatible: true } }); + const result = await updateMetadataFile(filePath, {}, compiled, false); + + assert.strictEqual(result, false); + assert.strictEqual(fs.readFileSync(filePath, 'utf8'), 'id: "model-2"\n'); + }); + + await t.test('updates gallery_categories from empty array', async () => { + const filePath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(filePath, 'id: "model-1"\ngallery_categories: []\n'); + + const compiled = compileAssignments({ 'model-1': { gallery_categories: ["cat1", "cat2"] } }); + const result = await updateMetadataFile(filePath, {}, compiled, false); + + assert.strictEqual(result, true); + assert.strictEqual(fs.readFileSync(filePath, 'utf8'), 'id: "model-1"\ngallery_categories: ["cat1","cat2"]\n'); + }); + + await t.test('updates gallery_category string to gallery_categories array', async () => { + const filePath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(filePath, 'id: "model-1"\ngallery_category: "some_cat"\n'); + + const compiled = compileAssignments({ 'model-1': { gallery_categories: ["cat1"] } }); + const result = await updateMetadataFile(filePath, {}, compiled, false); + + assert.strictEqual(result, true); + assert.strictEqual(fs.readFileSync(filePath, 'utf8'), 'id: "model-1"\ngallery_categories: ["cat1"]\n'); + }); + + await t.test('adds visible: true under playground if gallery_categories updated', async () => { + const filePath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(filePath, 'id: "model-1"\ngallery_category: "some_cat"\nplayground:\n'); + + const compiled = compileAssignments({ 'model-1': { gallery_categories: ["cat1"] } }); + const result = await updateMetadataFile(filePath, {}, compiled, false); + + assert.strictEqual(result, true); + assert.strictEqual(fs.readFileSync(filePath, 'utf8'), 'id: "model-1"\ngallery_categories: ["cat1"]\nplayground:\n visible: true'); + }); + + await t.test('updates bng2_compatible from false to true', async () => { + const filePath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(filePath, 'id: "model-1"\nbng2_compatible: false\n'); + + const compiled = compileAssignments({ 'model-1': { bng2_compatible: true } }); + const result = await updateMetadataFile(filePath, {}, compiled, false); + + assert.strictEqual(result, true); + assert.strictEqual(fs.readFileSync(filePath, 'utf8'), 'id: "model-1"\nbng2_compatible: true\n'); + }); + + await t.test('updates nfsim_compatible from false to true', async () => { + const filePath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(filePath, 'id: "model-1"\nnfsim_compatible: false\n'); + + const compiled = compileAssignments({ 'model-1': { nfsim_compatible: true } }); + const result = await updateMetadataFile(filePath, {}, compiled, false); + + assert.strictEqual(result, true); + assert.strictEqual(fs.readFileSync(filePath, 'utf8'), 'id: "model-1"\nnfsim_compatible: true\n'); + }); + + await t.test('updates excluded from false to true', async () => { + const filePath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(filePath, 'id: "model-1"\nexcluded: false\n'); + + const compiled = compileAssignments({ 'model-1': { excluded: true } }); + const result = await updateMetadataFile(filePath, {}, compiled, false); + + assert.strictEqual(result, true); + assert.strictEqual(fs.readFileSync(filePath, 'utf8'), 'id: "model-1"\nexcluded: true\n'); + }); + + await t.test('returns true but does not modify file if dryRun is true', async () => { + const filePath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(filePath, 'id: "model-1"\nbng2_compatible: false\n'); + + const compiled = compileAssignments({ 'model-1': { bng2_compatible: true } }); + const result = await updateMetadataFile(filePath, {}, compiled, true); + + assert.strictEqual(result, true); + assert.strictEqual(fs.readFileSync(filePath, 'utf8'), 'id: "model-1"\nbng2_compatible: false\n'); + }); +}); + +test('parseArgs default values', () => { + const args = parseArgs([]); + assert.strictEqual(args.input, 'gallery-assignments.json'); + assert.strictEqual(args.root, path.resolve(__dirname, '..')); + assert.strictEqual(args.dryRun, false); +}); + +test('parseArgs with --input', () => { + const args = parseArgs(['--input', 'custom-input.json']); + assert.strictEqual(args.input, 'custom-input.json'); + assert.strictEqual(args.root, path.resolve(__dirname, '..')); + assert.strictEqual(args.dryRun, false); +}); + +test('parseArgs with --root', () => { + const args = parseArgs(['--root', '/custom/root']); + assert.strictEqual(args.input, 'gallery-assignments.json'); + assert.strictEqual(args.root, '/custom/root'); + assert.strictEqual(args.dryRun, false); +}); + +test('parseArgs with --dry-run', () => { + const args = parseArgs(['--dry-run']); + assert.strictEqual(args.input, 'gallery-assignments.json'); + assert.strictEqual(args.root, path.resolve(__dirname, '..')); + assert.strictEqual(args.dryRun, true); +}); + +test('parseArgs with all arguments', () => { + const args = parseArgs(['--dry-run', '--root', '/tmp/root', '--input', 'test.json']); + assert.strictEqual(args.input, 'test.json'); + assert.strictEqual(args.root, '/tmp/root'); + assert.strictEqual(args.dryRun, true); +}); + +test('findAllMetadataFiles', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'find-metadata-test-')); + }); + + t.afterEach(() => { + fs.rmSync(tmpDir, { recursive: true, force: true }); + }); + + await t.test('returns empty array if directory does not exist', () => { + const nonExistentDir = path.join(tmpDir, 'does-not-exist'); + const result = findAllMetadataFiles(nonExistentDir); + assert.deepStrictEqual(result, []); + }); + + await t.test('returns empty array if no metadata.yaml files exist', () => { + fs.writeFileSync(path.join(tmpDir, 'some-file.txt'), 'hello'); + const result = findAllMetadataFiles(tmpDir); + assert.deepStrictEqual(result, []); + }); + + await t.test('finds metadata.yaml in the root directory', () => { + const yamlPath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(yamlPath, 'id: test'); + const result = findAllMetadataFiles(tmpDir); + assert.deepStrictEqual(result, [yamlPath]); + }); + + await t.test('finds metadata.yaml in nested directories', () => { + const subDir1 = path.join(tmpDir, 'sub1'); + const subDir2 = path.join(subDir1, 'sub2'); + fs.mkdirSync(subDir2, { recursive: true }); + + const yamlPath1 = path.join(tmpDir, 'metadata.yaml'); + const yamlPath2 = path.join(subDir2, 'metadata.yaml'); + + fs.writeFileSync(yamlPath1, 'id: test1'); + fs.writeFileSync(yamlPath2, 'id: test2'); + fs.writeFileSync(path.join(subDir1, 'other.yaml'), 'id: ignore'); + + const result = findAllMetadataFiles(tmpDir); + + // Sort to make the test deterministic + assert.deepStrictEqual(result.sort(), [yamlPath1, yamlPath2].sort()); + }); +}); + +test('parseArgs ignoring missing value for --input', () => { + const args = parseArgs(['--input']); + assert.strictEqual(args.input, 'gallery-assignments.json'); +}); + +test('parseArgs ignoring missing value for --root', () => { + const args = parseArgs(['--root']); + assert.strictEqual(args.root, path.resolve(__dirname, '..')); +}); + +test('parseArgs ignoring unrecognized arguments', () => { + const args = parseArgs(['--unknown', 'value', '--input', 'test.json']); + assert.strictEqual(args.input, 'test.json'); +}); diff --git a/scripts/backfill-metadata.js b/scripts/backfill-metadata.js index ba0e42f2..0bc5ea97 100644 --- a/scripts/backfill-metadata.js +++ b/scripts/backfill-metadata.js @@ -1,4 +1,5 @@ const fs = require('fs'); +const { safeJoin } = require('./utils'); const path = require('path'); const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; @@ -23,39 +24,117 @@ function parseArgs(argv) { return { root, dryRun }; } -function findBnglFiles(dir, ignoreDirs = DEFAULT_IGNORE_DIRS) { - if (!fs.existsSync(dir)) return []; - - const results = []; - const entries = fs.readdirSync(dir, { withFileTypes: true }); - - for (const entry of entries) { - const fullPath = path.join(dir, entry.name); +async function findBnglFiles(dir, ignoreDirs = DEFAULT_IGNORE_DIRS) { + try { + const entries = await fs.promises.readdir(dir, { withFileTypes: true }); - if (entry.isDirectory()) { - if (ignoreDirs.some(ignored => { - if (ignored.includes('*')) { - return entry.name.startsWith(ignored.replace('*', '')); + const promises = entries.map(async (entry) => { + const fullPath = safeJoin(dir, entry.name); + + if (entry.isDirectory()) { + if (ignoreDirs.some(ignored => { + if (ignored.includes('*')) { + return entry.name.startsWith(ignored.replace('*', '')); + } + return entry.name === ignored; + })) { + return []; } - return entry.name === ignored; - })) { - continue; + return findBnglFiles(fullPath, ignoreDirs); + } else if (entry.isFile() && entry.name.endsWith('.bngl')) { + return [fullPath]; + } + return []; + }); + + const results = await Promise.all(promises); + return results.flat(); + } catch (error) { + if (error.code === 'ENOENT' || error.code === 'ENOTDIR') { + return []; + } + throw error; + } +} + +function extractMetadataFromComments(headerComments, metadata) { + for (const comment of headerComments) { + const match = comment.match(/^([a-zA-Z0-9_-]+):\s*(.*)$/); + if (match) { + const key = match[1]; + const val = match[2].trim(); + if (key === 'tags') { + val.split(',').forEach(tag => metadata.tags.add(tag.trim())); + } else if (key === 'description') { + if (!metadata.description) metadata.description = val; + } else if (key === 'name') { + metadata.name = val; + } else if (key === 'doi') { + metadata.doi = val; } - results.push(...findBnglFiles(fullPath, ignoreDirs)); - } else if (entry.isFile() && entry.name.endsWith('.bngl')) { - results.push(fullPath); + } + } +} + +function processActionLine(trimmed, metadata) { + const simulateMatch = trimmed.match(/simulate\({(.*)}\)/); + if (simulateMatch) { + const params = simulateMatch[1]; + const methodMatch = params.match(/method\s*=>\s*["']?([^"',\s]+)["']?/); + if (methodMatch) { + metadata.simulation_methods.push(methodMatch[1]); + if (methodMatch[1] === 'nf') metadata.nfsim_compatible = true; + } + } +} + +function processModelLine(trimmed, metadata, state) { + if (trimmed === 'begin compartments') { + state.inCompartments = true; + metadata.uses_compartments = true; + return; + } + if (trimmed === 'end compartments') { + state.inCompartments = false; + return; + } + + if (trimmed === 'begin functions') { + state.inFunctions = true; + metadata.uses_functions = true; + return; + } + if (trimmed === 'end functions') { + state.inFunctions = false; + return; + } + + if (trimmed.startsWith('begin molecule types')) { + return; + } + if (trimmed.startsWith('end molecule types')) { + return; + } + + if (!state.inCompartments && !state.inFunctions && trimmed && !trimmed.startsWith('begin') && !trimmed.startsWith('end')) { + const match = trimmed.match(/^(\w+)\s+/); + if (match && !trimmed.includes('=>') && !trimmed.includes('=')) { + const moleculeName = match[1].toLowerCase(); + metadata.tags.add(moleculeName); } } - return results; + if (trimmed.includes('energy') || trimmed.includes('Phi')) { + metadata.uses_energy = true; + } } -function parseBngl(filePath) { - const content = fs.readFileSync(filePath, 'utf8'); +async function parseBngl(filePath) { + const content = await fs.promises.readFile(filePath, 'utf8'); const lines = content.split('\n'); const metadata = { - tags: [], + tags: new Set(), uses_compartments: false, uses_energy: false, uses_functions: false, @@ -66,118 +145,49 @@ function parseBngl(filePath) { name: '' }; - let inModel = false; - let inActions = false; - let inCompartments = false; - let inFunctions = false; + const state = { + inModel: false, + inActions: false, + inCompartments: false, + inFunctions: false, + }; let headerComments = []; for (const line of lines) { const trimmed = line.trim(); - if (trimmed.startsWith('#') && !inModel && !inActions) { + if (trimmed.startsWith('#') && !state.inModel && !state.inActions) { headerComments.push(trimmed.slice(1).trim()); continue; } if (trimmed === 'begin model') { - inModel = true; + state.inModel = true; continue; } if (trimmed === 'end model') { - inModel = false; + state.inModel = false; continue; } if (trimmed === 'begin actions') { - inActions = true; + state.inActions = true; continue; } if (trimmed === 'end actions') { - inActions = false; + state.inActions = false; continue; } - if (inModel) { - if (trimmed === 'begin compartments') { - inCompartments = true; - metadata.uses_compartments = true; - continue; - } - if (trimmed === 'end compartments') { - inCompartments = false; - continue; - } - - if (trimmed === 'begin functions') { - inFunctions = true; - metadata.uses_functions = true; - continue; - } - if (trimmed === 'end functions') { - inFunctions = false; - continue; - } - - if (trimmed.startsWith('begin molecule types')) { - continue; - } - if (trimmed.startsWith('end molecule types')) { - continue; - } - - if (!inCompartments && !inFunctions && trimmed && !trimmed.startsWith('begin') && !trimmed.startsWith('end')) { - const match = trimmed.match(/^(\w+)\s+/); - if (match && !trimmed.includes('=>') && !trimmed.includes('=')) { - const moleculeName = match[1].toLowerCase(); - if (!metadata.tags.includes(moleculeName)) { - metadata.tags.push(moleculeName); - } - } - } - - if (trimmed.includes('energy') || trimmed.includes('Phi')) { - metadata.uses_energy = true; - } + if (state.inModel) { + processModelLine(trimmed, metadata, state); } - if (inActions) { - const nfMatch = trimmed.match(/method\s*=>\s*["']?nf["']?/); - const odeMatch = trimmed.match(/method\s*=>\s*["']?ode["']?/); - const ssaMatch = trimmed.match(/method\s*=>\s*["']?ssa["']?/); - const plaMatch = trimmed.match(/method\s*=>\s*["']?pla["']?/); - const hybridMatch = trimmed.match(/method\s*=>\s*["']?hybrid["']?/); - - if (nfMatch) { - metadata.simulation_methods.push('nf'); - metadata.nfsim_compatible = true; - } - if (odeMatch) metadata.simulation_methods.push('ode'); - if (ssaMatch) metadata.simulation_methods.push('ssa'); - if (plaMatch) metadata.simulation_methods.push('pla'); - if (hybridMatch) metadata.simulation_methods.push('hybrid'); + if (state.inActions) { + processActionLine(trimmed, metadata); } } - if (headerComments.length > 0) { - for (const comment of headerComments) { - const nameMatch = comment.match(/(?:model|name)[:\s]+(.+)/i); - if (nameMatch && !metadata.name) { - metadata.name = nameMatch[1].trim(); - } - - const doiMatch = comment.match(/(?:doi|DOI)[:\s]+(10\.\S+)/i); - if (doiMatch) { - metadata.doi = doiMatch[1].trim(); - } - } - - const nonParamComments = headerComments.filter(c => - !c.match(/^[a-zA-Z_]\w*\s+changed\s+to/i) - ); - if (nonParamComments.length > 0 && !metadata.description) { - metadata.description = nonParamComments[0]; - } - } + extractMetadataFromComments(headerComments, metadata); if (metadata.simulation_methods.length === 0) { const hasGenerateNetwork = content.includes('generate_network'); @@ -191,6 +201,7 @@ function parseBngl(filePath) { } metadata.simulation_methods = [...new Set(metadata.simulation_methods)]; + metadata.tags = Array.from(metadata.tags); return metadata; } @@ -255,16 +266,20 @@ function inferOrigin(dirPath) { return 'test-case'; } +function generateId(dir, baseName, dirName) { + const relativePath = path.relative(process.cwd(), dir); + const pathParts = relativePath.split(path.sep).filter(p => p && p !== 'Published' && p !== 'Examples' && p !== 'Tutorials'); + return pathParts.length > 0 + ? [...pathParts, baseName].join('_').replace(/\s+/g, '_').replace(/-/g, '_') + : `${dirName}_${baseName}`.replace(/\s+/g, '_').replace(/-/g, '_'); +} + function generateMetadata(bnglFile, parsed) { const dir = path.dirname(bnglFile); const baseName = path.basename(bnglFile, '.bngl'); const dirName = path.basename(dir); - const relativePath = path.relative(process.cwd(), dir); - const pathParts = relativePath.split(path.sep).filter(p => p && p !== 'Published' && p !== 'Examples' && p !== 'Tutorials'); - const id = pathParts.length > 0 - ? [...pathParts, baseName].join('_').replace(/\s+/g, '_').replace(/-/g, '_') - : `${dirName}_${baseName}`.replace(/\s+/g, '_').replace(/-/g, '_'); + const id = generateId(dir, baseName, dirName); const name = parsed.name || dirName.replace(/_/g, ' '); const description = parsed.description || `BNGL model: ${baseName}`; const category = inferCategory(dir); @@ -327,7 +342,7 @@ function formatYaml(obj, indent = 0) { } } } - } else if (typeof value === 'object') { + } else if (value !== null && typeof value === 'object') { result += `${spaces}${key}:\n${formatYaml(value, indent + 1)}`; } else if (typeof value === 'boolean') { result += `${spaces}${key}: ${value}\n`; @@ -342,7 +357,7 @@ function formatYaml(obj, indent = 0) { } function formatYamlValue(value, indent = 0) { - if (typeof value === 'object') { + if (value !== null && typeof value === 'object') { const spaces = ' '.repeat(indent); let result = ''; const entries = Object.entries(value); @@ -362,49 +377,54 @@ function formatYamlValue(value, indent = 0) { async function main() { const { root, dryRun } = parseArgs(process.argv.slice(2)); - console.log(`Scanning for .bngl files without metadata.yaml in ${root}...`); - console.log(`Dry run: ${dryRun}\n`); + console.info(`Scanning for .bngl files without metadata.yaml in ${root}...`); + console.info(`Dry run: ${dryRun}\n`); - const bnglFiles = SEARCH_ROOTS.flatMap(searchRoot => + const searchPromises = SEARCH_ROOTS.map(searchRoot => findBnglFiles(path.join(root, searchRoot)) ); + const bnglFilesArrays = await Promise.all(searchPromises); + const bnglFiles = bnglFilesArrays.flat(); - console.log(`Found ${bnglFiles.length} .bngl files\n`); + console.info(`Found ${bnglFiles.length} .bngl files\n`); let created = 0; let skipped = 0; - for (const bnglFile of bnglFiles) { + await Promise.all(bnglFiles.map(async (bnglFile) => { const dir = path.dirname(bnglFile); const metadataPath = path.join(dir, 'metadata.yaml'); - if (fs.existsSync(metadataPath)) { + try { + await fs.promises.access(metadataPath); skipped++; - continue; + return; + } catch { + // File does not exist, proceed } - console.log(`Processing: ${bnglFile}`); + console.info(`Processing: ${bnglFile}`); - const parsed = parseBngl(bnglFile); + const parsed = await parseBngl(bnglFile); const metadata = generateMetadata(bnglFile, parsed); const yamlContent = formatYaml(metadata); if (dryRun) { - console.log(` [DRY RUN] Would create: ${metadataPath}`); - console.log(yamlContent); + console.info(` [DRY RUN] Would create: ${metadataPath}`); + console.info(yamlContent); } else { - fs.writeFileSync(metadataPath, yamlContent); - console.log(` Created: ${metadataPath}`); + await fs.promises.writeFile(metadataPath, yamlContent); + console.info(` Created: ${metadataPath}`); } created++; - } + })); - console.log(`\nSummary:`); - console.log(` Total .bngl files: ${bnglFiles.length}`); - console.log(` Skipped (has metadata): ${skipped}`); - console.log(` Created: ${created}`); + console.info(`\nSummary:`); + console.info(` Total .bngl files: ${bnglFiles.length}`); + console.info(` Skipped (has metadata): ${skipped}`); + console.info(` Created: ${created}`); } if (require.main === module) { @@ -415,8 +435,15 @@ if (require.main === module) { } module.exports = { + extractMetadataFromComments, parseBngl, + generateId, + processModelLine, generateMetadata, findBnglFiles, formatYaml, + formatYamlValue, + inferCategory, + inferOrigin, + processActionLine, }; \ No newline at end of file diff --git a/scripts/backfill-metadata.test.js b/scripts/backfill-metadata.test.js new file mode 100644 index 00000000..dce6763a --- /dev/null +++ b/scripts/backfill-metadata.test.js @@ -0,0 +1,590 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const fs = require('fs'); +const os = require('os'); +const path = require('path'); +const { parseBngl, generateId, processModelLine, generateMetadata, formatYaml, formatYamlValue, inferCategory, inferOrigin, extractMetadataFromComments, processActionLine } = require('./backfill-metadata.js'); + +test('backfill-metadata.js', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'bionetgen-backfill-test-')); + }); + + t.afterEach(() => { + if (tmpDir) { + fs.rmSync(tmpDir, { recursive: true, force: true }); + } + }); + + await t.test('parseBngl - parses metadata and tags correctly', async () => { + const bnglContent = ` +# name: Test Model +# doi: 10.1234/test +# description: This is a description of the model. +# Some other comment + +begin model +begin parameters + k1 1.0 +end parameters + +begin molecule types + A(b) +end molecule types + +begin seed species + A(b) 100 +end seed species + +begin observables + Molecules A_obs A() +end observables + +begin functions + func() 1.0 +end functions + +begin compartments + cell 3 1.0 +end compartments + +begin reaction rules + A(b) -> null k1 +end reaction rules +end model + +begin actions + generate_network({overwrite=>1}) + simulate({method=>"ode", t_end=>10, n_steps=>10}) +end actions +`; + const filePath = path.join(tmpDir, 'test.bngl'); + fs.writeFileSync(filePath, bnglContent); + + const result = await parseBngl(filePath); + + assert.strictEqual(result.name, 'Test Model'); + assert.strictEqual(result.doi, '10.1234/test'); + assert.strictEqual(result.description, 'This is a description of the model.'); // because the parser sets description to the first non-assignment comment + assert.strictEqual(result.uses_compartments, true); + assert.strictEqual(result.uses_functions, true); + assert.strictEqual(result.uses_energy, false); + assert.deepStrictEqual(result.simulation_methods, ['ode']); + assert.strictEqual(result.nfsim_compatible, false); + assert.strictEqual(result.bng2_compatible, true); + + // tags are roughly extracted using `/^(\w+)\s+/`, for instance "Molecules" or "k1" will be captured if there's no `=>` or `=` + assert.ok(result.tags.includes('k1')); + assert.ok(result.tags.includes('molecules')); + }); + + await t.test('parseBngl - handles missing actions, implies nfsim_compatible without generate_network', async () => { + const bnglContent = ` +begin model +begin parameters +end parameters +end model +`; + const filePath = path.join(tmpDir, 'test-no-actions.bngl'); + fs.writeFileSync(filePath, bnglContent); + + const result = await parseBngl(filePath); + + // If there are no actions, it assumes 'ode' by default if length is 0 + // and if there's no generate_network, it marks nfsim_compatible as true + assert.deepStrictEqual(result.simulation_methods, ['ode']); + assert.strictEqual(result.nfsim_compatible, true); + }); + + await t.test('parseBngl - extracts various simulation methods from actions', async () => { + const bnglContent = ` +begin model +end model +begin actions + simulate({method=>"nf"}) + simulate({method=>"ssa"}) + simulate({method=>"pla"}) + simulate({method=>"hybrid"}) +end actions +`; + const filePath = path.join(tmpDir, 'test-methods.bngl'); + fs.writeFileSync(filePath, bnglContent); + + const result = await parseBngl(filePath); + + assert.ok(result.simulation_methods.includes('nf')); + assert.ok(result.simulation_methods.includes('ssa')); + assert.ok(result.simulation_methods.includes('pla')); + assert.ok(result.simulation_methods.includes('hybrid')); + assert.strictEqual(result.nfsim_compatible, true); // Since method=>"nf" is present + }); + + await t.test('parseBngl - infers energy / Phi usage', async () => { + const bnglContent = ` +begin model +begin reaction rules + # uses energy + A() -> B() Arrhenius(Phi) +end reaction rules +end model +`; + const filePath = path.join(tmpDir, 'test-energy.bngl'); + fs.writeFileSync(filePath, bnglContent); + + const result = await parseBngl(filePath); + assert.strictEqual(result.uses_energy, true); + }); + + await t.test('generateId - correctly generates ID based on directory structure', async (st) => { + await st.test('handles standard folder names', () => { + const dir = path.join(process.cwd(), 'Some_Category', 'My_Model'); + const id = generateId(dir, 'test_model', 'My_Model'); + assert.strictEqual(id, 'Some_Category_My_Model_test_model'); + }); + + await st.test('filters out excluded folder names (Published, Examples, Tutorials)', () => { + const dir = path.join(process.cwd(), 'Published', 'Cancer_Models', 'My_Model'); + const id = generateId(dir, 'test_model', 'My_Model'); + assert.strictEqual(id, 'Cancer_Models_My_Model_test_model'); + }); + + await st.test('falls back to dirName_baseName if all parts are excluded', () => { + const dir = path.join(process.cwd(), 'Published'); + const id = generateId(dir, 'test_model', 'Published'); + assert.strictEqual(id, 'Published_test_model'); + }); + + await st.test('replaces spaces and dashes with underscores', () => { + const dir = path.join(process.cwd(), 'Some-Category', 'My Model'); + const id = generateId(dir, 'test-model', 'My Model'); + assert.strictEqual(id, 'Some_Category_My_Model_test_model'); + }); + }); + + await t.test('processModelLine - mutates state and metadata correctly based on line input', async () => { + const metadata = { + tags: new Set(), + uses_compartments: false, + uses_functions: false, + uses_energy: false, + }; + + const state = { + inCompartments: false, + inFunctions: false, + }; + + // Test compartments + processModelLine('begin compartments', metadata, state); + assert.strictEqual(state.inCompartments, true); + assert.strictEqual(metadata.uses_compartments, true); + + processModelLine('end compartments', metadata, state); + assert.strictEqual(state.inCompartments, false); + + // Test functions + processModelLine('begin functions', metadata, state); + assert.strictEqual(state.inFunctions, true); + assert.strictEqual(metadata.uses_functions, true); + + processModelLine('end functions', metadata, state); + assert.strictEqual(state.inFunctions, false); + + // Test molecule types ignored + processModelLine('begin molecule types', metadata, state); + assert.strictEqual(state.inCompartments, false); + assert.strictEqual(state.inFunctions, false); + + processModelLine('end molecule types', metadata, state); + assert.strictEqual(state.inCompartments, false); + assert.strictEqual(state.inFunctions, false); + + // Test tags extraction + processModelLine('MoleculeA ', metadata, state); + assert.ok(metadata.tags.has('moleculea')); + + processModelLine('MoleculeB ', metadata, state); + assert.ok(metadata.tags.has('moleculeb')); + + // Test tags extraction ignored when in compartments or functions + state.inCompartments = true; + processModelLine('MoleculeC()', metadata, state); + assert.ok(!metadata.tags.has('moleculec')); + state.inCompartments = false; + + state.inFunctions = true; + processModelLine('MoleculeD()', metadata, state); + assert.ok(!metadata.tags.has('moleculed')); + state.inFunctions = false; + + // Test tags extraction ignored for assignment lines + processModelLine('k1 = 1.0', metadata, state); + assert.ok(!metadata.tags.has('k1')); + + processModelLine('A() => B()', metadata, state); + assert.ok(!metadata.tags.has('a')); + + // Test energy/Phi usage + processModelLine('Arrhenius(Phi)', metadata, state); + assert.strictEqual(metadata.uses_energy, true); + + metadata.uses_energy = false; // Reset + processModelLine('uses energy', metadata, state); + assert.strictEqual(metadata.uses_energy, true); + }); + }); + + await t.test('generateMetadata - structures metadata with generated id, category, origin, and compatibility', async () => { + // create fake paths inside tmpDir to test path inferencing + // structure: /Published/Test_Paper/test_model.bngl + const publishedDir = path.join(tmpDir, 'Published', 'Test_Paper'); + fs.mkdirSync(publishedDir, { recursive: true }); + + const filePath = path.join(publishedDir, 'test_model.bngl'); + fs.writeFileSync(filePath, 'begin model\nend model'); + + // Simulate parsed output from parseBngl + const parsed = { + name: 'Parsed Name', + description: 'Parsed Description', + tags: ['tag1'], + uses_compartments: true, + uses_energy: false, + uses_functions: false, + simulation_methods: ['ode'], + nfsim_compatible: false, + bng2_compatible: true + }; + + const cwdOrig = process.cwd(); + process.chdir(tmpDir); // set cwd to tmpDir to test relative path inferencing + try { + const result = generateMetadata(filePath, parsed); + + // Verify category inference + // Because the path includes "Test", `inferCategory` matches "test" and returns "validation" + assert.strictEqual(result.category, 'validation'); + + // Verify origin inference inside `source` + // `inferOrigin` looks for paths starting with 'published' + assert.strictEqual(result.source.origin, 'published'); + + // Verify id generation + assert.strictEqual(result.id, 'Test_Paper_test_model'); + + // Verify basic fields + assert.strictEqual(result.name, 'Parsed Name'); + assert.strictEqual(result.description, 'Parsed Description'); + assert.deepStrictEqual(result.tags, ['tag1']); + + // Verify nested properties (compatibility) + assert.deepStrictEqual(result.compatibility, { + bng2_compatible: true, + nfsim_compatible: false, + simulation_methods: ['ode'], + uses_compartments: true, + uses_energy: false, + uses_functions: false + }); + + } finally { + process.chdir(cwdOrig); + } + }); + + await t.test('inferCategory - returns appropriate category based on directory path', () => { + // We pass absolute paths as inferCategory uses path.relative(process.cwd(), dirPath). + // The easiest way is to append paths to the current cwd. + const cwd = process.cwd(); + + // immunology + assert.strictEqual(inferCategory(path.join(cwd, 'foo', 'immune', 'bar')), 'immunology'); + assert.strictEqual(inferCategory(path.join(cwd, 'tcr_model')), 'immunology'); + assert.strictEqual(inferCategory(path.join(cwd, 'bcr')), 'immunology'); + assert.strictEqual(inferCategory(path.join(cwd, 'fceri_pathway')), 'immunology'); + assert.strictEqual(inferCategory(path.join(cwd, 'cytokine_network')), 'immunology'); + assert.strictEqual(inferCategory(path.join(cwd, 'innate')), 'immunology'); + + // signaling + assert.strictEqual(inferCategory(path.join(cwd, 'foo', 'egfr', 'bar')), 'signaling'); + assert.strictEqual(inferCategory(path.join(cwd, 'mapk')), 'signaling'); + assert.strictEqual(inferCategory(path.join(cwd, 'ras')), 'signaling'); + assert.strictEqual(inferCategory(path.join(cwd, 'tumor_model')), 'signaling'); + assert.strictEqual(inferCategory(path.join(cwd, 'cancer_cells')), 'signaling'); + assert.strictEqual(inferCategory(path.join(cwd, 'signaling_pathway')), 'signaling'); + + // epidemiology + assert.strictEqual(inferCategory(path.join(cwd, 'sir_model')), 'epidemiology'); + assert.strictEqual(inferCategory(path.join(cwd, 'covid19')), 'epidemiology'); + assert.strictEqual(inferCategory(path.join(cwd, 'epidem')), 'epidemiology'); + + // cell-cycle + assert.strictEqual(inferCategory(path.join(cwd, 'cell_cycle_model')), 'cell-cycle'); + + // cell-cycle edge cases (requires both "cell" and "cycle") + assert.strictEqual(inferCategory(path.join(cwd, 'cell_only_model')), 'other'); + assert.strictEqual(inferCategory(path.join(cwd, 'cycle_only_model')), 'other'); + + // case insensitivity + assert.strictEqual(inferCategory(path.join(cwd, 'IMMUNE_system')), 'immunology'); + assert.strictEqual(inferCategory(path.join(cwd, 'CELL_CYCLE')), 'cell-cycle'); + + // metabolism + assert.strictEqual(inferCategory(path.join(cwd, 'metabolomics')), 'metabolism'); + + // neuroscience + assert.strictEqual(inferCategory(path.join(cwd, 'neural_net')), 'neuroscience'); + assert.strictEqual(inferCategory(path.join(cwd, 'neuron_model')), 'neuroscience'); + assert.strictEqual(inferCategory(path.join(cwd, 'brain_sim')), 'neuroscience'); + + // ecology + assert.strictEqual(inferCategory(path.join(cwd, 'ecology_study')), 'ecology'); + assert.strictEqual(inferCategory(path.join(cwd, 'population_dynamics')), 'ecology'); + + // tutorial + assert.strictEqual(inferCategory(path.join(cwd, 'tutorial_1')), 'tutorial'); + + // validation + assert.strictEqual(inferCategory(path.join(cwd, 'test_case')), 'validation'); + + // other + assert.strictEqual(inferCategory(path.join(cwd, 'unknown_model')), 'other'); + assert.strictEqual(inferCategory(path.join(cwd, 'random', 'dir')), 'other'); + }); + + await t.test('inferOrigin - infers origin based on path', async (st) => { + const cwd = process.cwd(); + + await st.test('infers published for Published directory', () => { + assert.strictEqual(inferOrigin(path.join(cwd, 'Published', 'Model1')), 'published'); + assert.strictEqual(inferOrigin(path.join(cwd, 'PUBLISHED', 'Model1')), 'published'); + }); + + await st.test('infers ai-generated for Examples with AI prefix', () => { + assert.strictEqual(inferOrigin(path.join(cwd, 'Examples', 'AI-Generated-Model')), 'ai-generated'); + assert.strictEqual(inferOrigin(path.join(cwd, 'Examples', 'aigenerated-Model')), 'ai-generated'); + assert.strictEqual(inferOrigin(path.join(cwd, 'EXAMPLES', 'ai-generated-Model')), 'ai-generated'); + }); + + await st.test('infers ai-generated for Examples without AI prefix (fallback)', () => { + assert.strictEqual(inferOrigin(path.join(cwd, 'Examples', 'Some-Model')), 'ai-generated'); + }); + + await st.test('infers tutorial for Tutorials directory', () => { + assert.strictEqual(inferOrigin(path.join(cwd, 'Tutorials', 'Basic')), 'tutorial'); + assert.strictEqual(inferOrigin(path.join(cwd, 'TUTORIALS', 'Basic')), 'tutorial'); + }); + + await st.test('infers contributed when path contains contributed', () => { + assert.strictEqual(inferOrigin(path.join(cwd, 'SomeDir', 'Contributed-Model')), 'contributed'); + assert.strictEqual(inferOrigin(path.join(cwd, 'SomeDir', 'CONTRIBUTED-Model')), 'contributed'); + }); + + await st.test('infers test-case for unknown paths', () => { + assert.strictEqual(inferOrigin(path.join(cwd, 'Unknown', 'Dir')), 'test-case'); + }); + }); +}); + +test('formatYaml', async (t) => { + await t.test('skips undefined and null values', async () => { + const obj = { a: 1, b: undefined, c: null, d: 'four' }; + assert.strictEqual(formatYaml(obj), 'a: 1\nd: four\n'); + }); + + await t.test('formats empty arrays', async () => { + const obj = { a: [] }; + assert.strictEqual(formatYaml(obj), 'a: []\n'); + assert.strictEqual(formatYaml(obj, 1), ' a: []\n'); + }); + + await t.test('formats arrays of primitives', async () => { + const obj = { a: [1, 2, 3], b: ['one', 'two'], c: [true, false] }; + const expected = 'a: [1, 2, 3]\nb: ["one", "two"]\nc: [true, false]\n'; + assert.strictEqual(formatYaml(obj), expected); + }); + + await t.test('formats arrays of objects', async () => { + const obj = { a: [{ x: 1 }, { y: 2 }] }; + const expected = 'a:\n - x: 1\n - y: 2\n'; + assert.strictEqual(formatYaml(obj), expected); + const expectedIndented = ' a:\n - x: 1\n - y: 2\n'; + assert.strictEqual(formatYaml(obj, 1), expectedIndented); + }); + + await t.test('formats mixed arrays', async () => { + const obj = { a: [1, { x: 1 }] }; + const expected = 'a:\n - 1\n - x: 1\n'; + assert.strictEqual(formatYaml(obj), expected); + }); + + await t.test('formats nested objects', async () => { + const obj = { a: { b: 1, c: { d: 2 } } }; + const expected = 'a:\n b: 1\n c:\n d: 2\n'; + assert.strictEqual(formatYaml(obj), expected); + }); + + await t.test('formats basic properties', async () => { + const obj = { a: 1, b: true, c: 'string' }; + const expected = 'a: 1\nb: true\nc: string\n'; + assert.strictEqual(formatYaml(obj), expected); + }); +}); + +test('formatYamlValue', async (t) => { + await t.test('formats strings correctly', async () => { + assert.strictEqual(formatYamlValue('hello'), 'hello\n'); + assert.strictEqual(formatYamlValue('world', 2), 'world\n'); + }); + + await t.test('formats numbers correctly', () => { + assert.strictEqual(formatYamlValue(42), '42\n'); + assert.strictEqual(formatYamlValue(3.14), '3.14\n'); + }); + + await t.test('formats booleans correctly', () => { + assert.strictEqual(formatYamlValue(true), 'true\n'); + assert.strictEqual(formatYamlValue(false), 'false\n'); + }); + + await t.test('formats flat objects correctly', () => { + const obj = { a: 1, b: 'two' }; + assert.strictEqual(formatYamlValue(obj), 'a: 1\nb: two\n'); + assert.strictEqual(formatYamlValue(obj, 1), 'a: 1\n b: two\n'); + }); + + await t.test('formats nested objects correctly', () => { + const obj = { a: 1, b: { c: 'two' } }; + assert.strictEqual(formatYamlValue(obj), 'a: 1\n\nb:\nc: two\n\n'); + assert.strictEqual(formatYamlValue(obj, 1), 'a: 1\n \n b:\nc: two\n\n'); + }); + + await t.test('formats arrays correctly', () => { + assert.strictEqual(formatYamlValue([1, 2]), '0: 1\n1: 2\n'); + }); + + await t.test('handles undefined correctly', () => { + assert.strictEqual(formatYamlValue(undefined), 'undefined\n'); + }); + + await t.test('handles null correctly', () => { + assert.strictEqual(formatYamlValue(null), 'null\n'); + }); +}); + +test('extractMetadataFromComments', async (t) => { + await t.test('does nothing if headerComments is empty', () => { + const metadata = { name: '', description: '', doi: '', tags: new Set() }; + extractMetadataFromComments([], metadata); + assert.deepStrictEqual(metadata, { name: '', description: '', doi: '', tags: new Set() }); + }); + + await t.test('extracts model name correctly and overwrites', () => { + const metadata = { name: 'Existing Name', description: '', doi: '', tags: new Set() }; + extractMetadataFromComments(['name: Test Model Name'], metadata); + assert.strictEqual(metadata.name, 'Test Model Name'); + }); + + await t.test('extracts DOI correctly and overwrites', () => { + const metadata = { name: '', description: '', doi: 'old.doi', tags: new Set() }; + extractMetadataFromComments(['doi: 10.1234/test.doi'], metadata); + assert.strictEqual(metadata.doi, '10.1234/test.doi'); + }); + + await t.test('extracts description and does not overwrite existing description', () => { + const metadata = { name: '', description: 'Existing Description', doi: '', tags: new Set() }; + extractMetadataFromComments(['description: New Description'], metadata); + assert.strictEqual(metadata.description, 'Existing Description'); + + const metadata2 = { name: '', description: '', doi: '', tags: new Set() }; + extractMetadataFromComments(['description: First Description', 'description: Second Description'], metadata2); + assert.strictEqual(metadata2.description, 'First Description'); + }); + + await t.test('extracts tags correctly and trims them', () => { + const metadata = { name: '', description: '', doi: '', tags: new Set(['existing-tag']) }; + extractMetadataFromComments(['tags: tag1, tag2 , tag3'], metadata); + assert.deepStrictEqual(metadata.tags, new Set(['existing-tag', 'tag1', 'tag2', 'tag3'])); + }); + + await t.test('ignores invalid or unhandled keys', () => { + const metadata = { name: 'Init', description: 'Init', doi: 'Init', tags: new Set() }; + extractMetadataFromComments(['invalid-key: some value', 'unhandled: value'], metadata); + assert.strictEqual(metadata.name, 'Init'); + assert.strictEqual(metadata.description, 'Init'); + assert.strictEqual(metadata.doi, 'Init'); + assert.deepStrictEqual(metadata.tags, new Set()); + }); + + await t.test('ignores comments not matching regex', () => { + const metadata = { name: '', description: '', doi: '', tags: new Set() }; + extractMetadataFromComments(['just some regular comment', 'no colon here', 'name : bad format'], metadata); + assert.strictEqual(metadata.name, ''); + assert.strictEqual(metadata.description, ''); + assert.strictEqual(metadata.doi, ''); + assert.deepStrictEqual(metadata.tags, new Set()); + }); + + await t.test('extracts everything together', () => { + const metadata = { name: '', description: '', doi: '', tags: new Set() }; + const comments = [ + 'name: Full Model', + 'doi: 10.9999/full', + 'description: A description of the full model', + 'tags: t1, t2', + 'ignored: this is ignored', + 'just some text' + ]; + extractMetadataFromComments(comments, metadata); + assert.strictEqual(metadata.name, 'Full Model'); + assert.strictEqual(metadata.doi, '10.9999/full'); + assert.strictEqual(metadata.description, 'A description of the full model'); + assert.deepStrictEqual(metadata.tags, new Set(['t1', 't2'])); + }); + + await t.test('processActionLine', async (st) => { + await st.test('parses method correctly with quotes and sets nfsim_compatible for nf', () => { + const metadata = { simulation_methods: [], nfsim_compatible: false }; + processActionLine('simulate({method=>"nf",t_end=>10})', metadata); + assert.deepStrictEqual(metadata.simulation_methods, ['nf']); + assert.strictEqual(metadata.nfsim_compatible, true); + }); + + await st.test('parses method with spaces around the operator', () => { + const metadata = { simulation_methods: [], nfsim_compatible: false }; + processActionLine('simulate({method => "ode", t_end=>10})', metadata); + assert.deepStrictEqual(metadata.simulation_methods, ['ode']); + assert.strictEqual(metadata.nfsim_compatible, false); + }); + + await st.test('parses method without quotes', () => { + const metadata = { simulation_methods: [], nfsim_compatible: false }; + processActionLine('simulate({method=>ode, t_end=>10})', metadata); + assert.deepStrictEqual(metadata.simulation_methods, ['ode']); + assert.strictEqual(metadata.nfsim_compatible, false); + }); + + await st.test('parses method with single quotes', () => { + const metadata = { simulation_methods: [], nfsim_compatible: false }; + processActionLine("simulate({method=>'ssa', t_end=>10})", metadata); + assert.deepStrictEqual(metadata.simulation_methods, ['ssa']); + assert.strictEqual(metadata.nfsim_compatible, false); + }); + + await st.test('ignores lines without simulate', () => { + const metadata = { simulation_methods: [], nfsim_compatible: false }; + processActionLine('generate_network({overwrite=>1})', metadata); + assert.deepStrictEqual(metadata.simulation_methods, []); + assert.strictEqual(metadata.nfsim_compatible, false); + }); + + await st.test('ignores simulate lines without method', () => { + const metadata = { simulation_methods: [], nfsim_compatible: false }; + processActionLine('simulate({t_end=>10, n_steps=>100})', metadata); + assert.deepStrictEqual(metadata.simulation_methods, []); + assert.strictEqual(metadata.nfsim_compatible, false); + }); + }); +}); diff --git a/scripts/generate-gallery.js b/scripts/generate-gallery.js index 211935b5..9409a210 100644 --- a/scripts/generate-gallery.js +++ b/scripts/generate-gallery.js @@ -1,6 +1,6 @@ const fs = require('fs'); const path = require('path'); -const { parseMetadataYaml } = require('./utils'); +const { parseMetadataYaml , safeJoin} = require('./utils'); const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; @@ -28,33 +28,37 @@ function parseArgs(argv) { return { root, output }; } -function listMetadataFiles(dir, results = []) { - if (!fs.existsSync(dir)) return results; +async function listMetadataFiles(dir) { + let entries; + try { + entries = await fs.promises.readdir(dir, { withFileTypes: true }); + } catch (err) { + if (err.code === 'ENOENT') return []; + throw err; + } - const entries = fs.readdirSync(dir, { withFileTypes: true }); - for (const entry of entries) { - const fullPath = path.join(dir, entry.name); + const results = await Promise.all(entries.map(async (entry) => { + const fullPath = safeJoin(dir, entry.name); if (entry.isDirectory()) { - listMetadataFiles(fullPath, results); - continue; - } - if (entry.isFile() && entry.name === 'metadata.yaml') { - results.push(fullPath); + return listMetadataFiles(fullPath); + } else if (entry.isFile() && entry.name === 'metadata.yaml') { + return [fullPath]; } - } + return []; + })); - return results; + return results.flat(); } -function loadGalleryCategories(root) { +async function loadGalleryCategories(root) { const categoriesFile = path.join(root, 'gallery-categories.yaml'); - if (!fs.existsSync(categoriesFile)) { + try { + const content = await fs.promises.readFile(categoriesFile, 'utf8'); + return parseYamlSimple(content); + } catch (err) { console.warn('Warning: gallery-categories.yaml not found, using defaults'); return { categories: [] }; } - - const content = fs.readFileSync(categoriesFile, 'utf8'); - return parseYamlSimple(content); } function parseYamlSimple(content) { @@ -106,36 +110,53 @@ function parseYamlSimple(content) { return result; } -function extractModelId(metadataFile, metadata) { +async function extractModelIds(metadataFile, metadata) { const modelDir = path.dirname(metadataFile); - const bnglFiles = fs.readdirSync(modelDir, { withFileTypes: true }) + let entries; + try { + entries = await fs.promises.readdir(modelDir, { withFileTypes: true }); + } catch (err) { + if (err.code === 'ENOENT') { + entries = []; + } else { + throw err; + } + } + + const bnglFiles = entries .filter(e => e.isFile() && e.name.endsWith('.bngl')) - .map(e => e.name); + .map(e => e.name) + .sort(); const isCollection = Boolean(metadata.collection); if (isCollection) { - return metadata.id; + return [metadata.id || (bnglFiles.length >= 1 ? path.basename(bnglFiles[0], '.bngl') : null)].filter(Boolean); } - if (bnglFiles.length >= 1) { - return metadata.id || path.basename(bnglFiles[0], '.bngl'); + if (bnglFiles.length === 1) { + return [metadata.id || path.basename(bnglFiles[0], '.bngl')].filter(Boolean); } - return null; + if (bnglFiles.length > 1) { + return bnglFiles.map(file => path.basename(file, '.bngl')); + } + + return []; } -async function main() { - const { root, output } = parseArgs(process.argv.slice(2)); +async function main(argv = process.argv.slice(2)) { + const { root, output } = parseArgs(argv); console.log('Loading gallery categories...'); - const galleryConfig = loadGalleryCategories(root); + const galleryConfig = await loadGalleryCategories(root); const categoryIds = new Set(galleryConfig.categories.map(c => c.id)); console.log('Scanning for metadata files...'); - const metadataFiles = SEARCH_ROOTS.flatMap(searchRoot => - listMetadataFiles(path.join(root, searchRoot)) + const results = await Promise.all( + SEARCH_ROOTS.map(searchRoot => listMetadataFiles(path.join(root, searchRoot))) ); + const metadataFiles = results.flat(); const assignments = {}; const sortOverrides = {}; @@ -143,31 +164,55 @@ async function main() { for (const metadataFile of metadataFiles) { try { - const content = fs.readFileSync(metadataFile, 'utf8'); + const content = await fs.promises.readFile(metadataFile, 'utf8'); const metadata = parseMetadataYaml(content); - const modelId = extractModelId(metadataFile, metadata); - if (!modelId) continue; + const modelIds = await extractModelIds(metadataFile, metadata); + if (modelIds.length === 0) continue; const tags = Array.isArray(metadata.tags) ? metadata.tags : []; if (tags.includes('published') || metadata.source?.origin === 'published') { - publishedModelIds.add(modelId); + for (const modelId of modelIds) { + publishedModelIds.add(modelId); + } } - const galleryCategories = metadata.playground?.gallery_categories + let galleryCategories = metadata.playground?.gallery_categories || (metadata.playground?.gallery_category ? [metadata.playground.gallery_category] : []); + + // Filter out invalid categories first so they trigger the fallback logic + galleryCategories = galleryCategories.filter(cat => categoryIds.has(cat)); + + if (galleryCategories.length === 0) { + const relPath = path.relative(root, metadataFile).replace(/\\/g, '/'); + if (metadata.source?.origin === 'test-case' || metadata.category === 'validation' || relPath.includes('tests/')) { + galleryCategories = ['test-models']; + } else if (metadata.source?.origin === 'tutorial' || relPath.startsWith('Tutorials/') || relPath.includes('/Tutorials/')) { + if (relPath.startsWith('Tutorials/NativeTutorials/') || relPath.includes('/NativeTutorials/')) { + galleryCategories = ['native-tutorials']; + } else { + galleryCategories = ['tutorials']; + } + } else if (metadata.source?.origin === 'published' || relPath.startsWith('Published/') || relPath.includes('/Published/')) { + galleryCategories = ['published-models']; + } else { + galleryCategories = ['test-models']; + } + } + if (galleryCategories.length > 0) { - const validCategories = galleryCategories.filter(cat => categoryIds.has(cat)); - if (validCategories.length > 0) { - assignments[modelId] = validCategories; + for (const modelId of modelIds) { + assignments[modelId] = galleryCategories; } } const sortPriority = metadata.playground?.sort_priority; if (sortPriority !== undefined && sortPriority !== null) { - sortOverrides[modelId] = sortPriority; + for (const modelId of modelIds) { + sortOverrides[modelId] = sortPriority; + } } } catch (err) { console.warn(`Warning: Failed to process ${metadataFile}: ${err.message}`); @@ -199,12 +244,10 @@ async function main() { const outputBase = output.replace('.generated.json', '.json'); let existingGenerated = null; - if (fs.existsSync(outputBase)) { - try { - const existing = JSON.parse(fs.readFileSync(outputBase, 'utf8')); - existingGenerated = existing.generated || null; - } catch (e) {} - } + try { + const existing = JSON.parse(await fs.promises.readFile(outputBase, 'utf8')); + existingGenerated = existing.generated || null; + } catch (e) {} const gallery = { version: 1, @@ -229,7 +272,9 @@ if (require.main === module) { } module.exports = { + main, parseArgs, loadGalleryCategories, - extractModelId, + extractModelIds, + parseYamlSimple, }; \ No newline at end of file diff --git a/scripts/generate-gallery.test.js b/scripts/generate-gallery.test.js new file mode 100644 index 00000000..19b7e7be --- /dev/null +++ b/scripts/generate-gallery.test.js @@ -0,0 +1,269 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const path = require('path'); +const os = require('os'); +const fs = require('fs'); +const { spawnSync } = require('child_process'); +const { main, parseArgs, loadGalleryCategories, extractModelIds, parseYamlSimple } = require('./generate-gallery.js'); + +test('generate-gallery.js handles file read/parse errors', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gallery-test-')); + }); + + t.afterEach(() => { + fs.rmSync(tmpDir, { recursive: true, force: true }); + }); + + await t.test('skips malformed yaml and continues execution', () => { + const pubDir = path.join(tmpDir, 'Published'); + fs.mkdirSync(pubDir); + + const model1Dir = path.join(pubDir, 'model1'); + fs.mkdirSync(model1Dir); + fs.writeFileSync(path.join(model1Dir, 'metadata.yaml'), 'id: model1\ntags:\n - published\ncollection: true\n'); + + const model2Dir = path.join(pubDir, 'model2'); + fs.mkdirSync(model2Dir); + fs.writeFileSync(path.join(model2Dir, 'metadata.yaml'), 'id: model2\ncollection:\n - : invalid yaml: \n'); + + const model3Dir = path.join(pubDir, 'model3'); + fs.mkdirSync(model3Dir); + fs.writeFileSync(path.join(model3Dir, 'metadata.yaml'), 'id: model3\ntags:\n - published\ncollection: true\n'); + + const outputJsonPath = path.join(tmpDir, 'gallery.json'); + + const res = spawnSync(process.execPath, [ + path.join(__dirname, 'generate-gallery.js'), + '--root', tmpDir, + '--output', outputJsonPath + ], { encoding: 'utf8' }); + + assert.strictEqual(res.status, 0); + + const gallery = JSON.parse(fs.readFileSync(outputJsonPath, 'utf8')); + assert.deepStrictEqual(Object.keys(gallery.assignments).sort(), ['model1', 'model3']); + }); +}); + +test('generate-gallery error path test for JSON.parse', async () => { + const tmpdir = fs.mkdtempSync(path.join(os.tmpdir(), 'gallery-test-')); + const output = path.join(tmpdir, 'gallery.generated.json'); + const outputBase = path.join(tmpdir, 'gallery.json'); + + fs.writeFileSync(outputBase, '{ invalid: json }'); + fs.writeFileSync(path.join(tmpdir, 'gallery-categories.yaml'), 'categories:\n - id: test\n name: test\n'); + + const originalLog = console.log; + const originalWarn = console.warn; + console.log = () => {}; + console.warn = () => {}; + + try { + await main(['--root', tmpdir, '--output', output]); + + const result = JSON.parse(fs.readFileSync(output, 'utf8')); + assert.ok(result.generated, 'Should have a generated date'); + assert.deepEqual(result.categories, [{id: 'test', name: 'test', description: '', sortOrder: 0}], 'Should have parsed the dummy category'); + assert.deepEqual(result.assignments, {}, 'Should have empty assignments'); + } finally { + console.log = originalLog; + console.warn = originalWarn; + fs.rmSync(tmpdir, { recursive: true, force: true }); + } +}); + +test('parseArgs', async (t) => { + await t.test('uses default root and output when no args provided', () => { + const { root, output } = parseArgs([]); + assert.strictEqual(root, path.resolve(__dirname, '..')); + assert.strictEqual(output, path.join(path.resolve(__dirname, '..'), 'gallery.json')); + }); + + await t.test('parses --root argument', () => { + const { root, output } = parseArgs(['--root', './some/path']); + assert.strictEqual(root, path.resolve('./some/path')); + assert.strictEqual(output, path.join(path.resolve('./some/path'), 'gallery.json')); + }); + + await t.test('parses --output argument', () => { + const { root, output } = parseArgs(['--output', './out.json']); + assert.strictEqual(root, path.resolve(__dirname, '..')); + assert.strictEqual(output, path.resolve('./out.json')); + }); + + await t.test('parses both --root and --output arguments', () => { + const { root, output } = parseArgs(['--root', './myroot', '--output', './myout.json']); + assert.strictEqual(root, path.resolve('./myroot')); + assert.strictEqual(output, path.resolve('./myout.json')); + }); +}); + +test('parseYamlSimple', async (t) => { + await t.test('returns empty categories if no categories key found', () => { + const yaml = `some_other_key: value`; + const result = parseYamlSimple(yaml); + assert.deepStrictEqual(result, { categories: [] }); + }); + + await t.test('parses basic categories', () => { + const yaml = ` +categories: + - id: cat1 + name: "Category 1" + description: 'First category' + sortOrder: 10 + - id: cat2 + name: Category 2 + description: Second category + sortOrder: 20 +`; + const result = parseYamlSimple(yaml); + assert.deepStrictEqual(result, { + categories: [ + { id: 'cat1', name: 'Category 1', description: 'First category', sortOrder: 10 }, + { id: 'cat2', name: 'Category 2', description: 'Second category', sortOrder: 20 }, + ] + }); + }); + + await t.test('handles missing optional fields and uses defaults', () => { + const yaml = ` +categories: + - id: cat1 + name: "Category 1" +`; + const result = parseYamlSimple(yaml); + assert.deepStrictEqual(result, { + categories: [ + { id: 'cat1', name: 'Category 1', description: '', sortOrder: 0 }, + ] + }); + }); + + await t.test('ignores data outside categories block', () => { + const yaml = ` +other_stuff: + - foo +categories: + - id: cat1 + name: Category 1 +more_stuff: bar +`; + const result = parseYamlSimple(yaml); + assert.deepStrictEqual(result.categories[0].id, 'cat1'); + assert.deepStrictEqual(result.categories[0].name, 'Category 1'); + }); +}); + +test('loadGalleryCategories', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gallery-test-')); + }); + + t.afterEach(() => { + fs.rmSync(tmpDir, { recursive: true, force: true }); + }); + + await t.test('returns empty categories if gallery-categories.yaml is missing', async () => { + const originalConsoleWarn = console.warn; + let warningLogged = false; + console.warn = (msg) => { + if (msg.includes('gallery-categories.yaml not found')) warningLogged = true; + }; + + const result = await loadGalleryCategories(tmpDir); + assert.deepStrictEqual(result, { categories: [] }); + assert.ok(warningLogged, 'Should log a warning'); + + console.warn = originalConsoleWarn; + }); + + await t.test('loads and parses existing gallery-categories.yaml', async () => { + const yaml = ` +categories: + - id: mycat + name: "My Cat" + sortOrder: 1 +`; + fs.writeFileSync(path.join(tmpDir, 'gallery-categories.yaml'), yaml); + + const result = await loadGalleryCategories(tmpDir); + assert.deepStrictEqual(result, { + categories: [ + { id: 'mycat', name: 'My Cat', description: '', sortOrder: 1 } + ] + }); + }); + + await t.test('handles generic file read errors and falls back to defaults', async () => { + const originalConsoleWarn = console.warn; + const originalReadFile = fs.promises.readFile; + let warningLogged = false; + + console.warn = (msg) => { + if (msg.includes('gallery-categories.yaml not found')) warningLogged = true; + }; + + fs.promises.readFile = async () => { + throw new Error('Generic file read error'); + }; + + try { + const result = await loadGalleryCategories(tmpDir); + assert.deepStrictEqual(result, { categories: [] }); + assert.ok(warningLogged, 'Should log a warning'); + } finally { + console.warn = originalConsoleWarn; + fs.promises.readFile = originalReadFile; + } + }); +}); + +test('extractModelIds', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gallery-test-id-')); + }); + + t.afterEach(() => { + fs.rmSync(tmpDir, { recursive: true, force: true }); + }); + + await t.test('returns metadata id if is collection', async () => { + const metadataPath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(metadataPath, ''); + const result = await extractModelIds(metadataPath, { id: 'coll_1', collection: true }); + assert.deepStrictEqual(result, ['coll_1']); + }); + + await t.test('returns metadata id if it exists and bngl files are present', async () => { + const metadataPath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(metadataPath, ''); + fs.writeFileSync(path.join(tmpDir, 'model.bngl'), ''); + + const result = await extractModelIds(metadataPath, { id: 'meta_id' }); + assert.deepStrictEqual(result, ['meta_id']); + }); + + await t.test('returns filename of bngl if no metadata id is present', async () => { + const metadataPath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(metadataPath, ''); + fs.writeFileSync(path.join(tmpDir, 'my_model.bngl'), ''); + + const result = await extractModelIds(metadataPath, {}); + assert.deepStrictEqual(result, ['my_model']); + }); + + await t.test('returns empty array if no bngl files are present (and not a collection)', async () => { + const metadataPath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(metadataPath, ''); + const result = await extractModelIds(metadataPath, { id: 'meta_id' }); + assert.deepStrictEqual(result, []); + }); +}); diff --git a/scripts/generate-manifest.js b/scripts/generate-manifest.js index 5577cb40..1223e935 100644 --- a/scripts/generate-manifest.js +++ b/scripts/generate-manifest.js @@ -1,9 +1,8 @@ const fs = require('fs'); const path = require('path'); -const { listModelFilesAsync, parseMetadataYaml } = require('./utils'); +const { listModelFilesAsync, parseMetadataYaml , safeJoin} = require('./utils'); const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; -const DEFAULT_IGNORE_DIRS = ['fitting', 'BioNetFit_files', 'output_*', 'fit_*', '__pycache__', 'pybnf_files']; function parseArgs(argv) { let root = path.resolve(__dirname, '..'); @@ -33,27 +32,52 @@ function parseArgs(argv) { : path.join(root, 'manifest.json'); } + const resolvedRoot = path.resolve(root); + const resolvedOutput = path.resolve(output); + const rootWithSep = resolvedRoot.endsWith(path.sep) ? resolvedRoot : resolvedRoot + path.sep; + if (!resolvedOutput.startsWith(rootWithSep) && resolvedOutput !== resolvedRoot) { + throw new Error(`Path traversal security risk: output path must be within the root directory`); + } + return { root, output, slim }; } -function listMetadataFiles(dir, results = []) { - if (!fs.existsSync(dir)) return results; - - const entries = fs.readdirSync(dir, { withFileTypes: true }); - for (const entry of entries) { - const fullPath = path.join(dir, entry.name); - if (entry.isDirectory()) { - listMetadataFiles(fullPath, results); - continue; - } - if (entry.isFile() && entry.name === 'metadata.yaml') { - results.push(fullPath); +async function listMetadataFiles(dir, results = []) { + try { + const entries = await fs.promises.readdir(dir, { withFileTypes: true }); + + const promises = entries.map(async (entry) => { + const fullPath = safeJoin(dir, entry.name); + if (entry.isDirectory()) { + await listMetadataFiles(fullPath, results); + } else if (entry.isFile() && entry.name === 'metadata.yaml') { + results.push(fullPath); + } + }); + + await Promise.all(promises); + } catch (err) { + if (err.code !== 'ENOENT') { + throw err; } } - return results; } +const DEFAULT_IGNORE_DIRS = Object.freeze(['fitting', 'output_*', 'data', 'archive']); + +function isIgnoredDir(dirName, ignoreDirs) { + return ignoreDirs.some(pattern => { + if (pattern === dirName) return true; + if (pattern.includes('*')) { + const escaped = pattern.replace(/[.+^${}()|[\]\\]/g, '\\$&'); + const regex = new RegExp('^' + escaped.replace(/\*/g, '.*') + '$'); + return regex.test(dirName); + } + return false; + }); +} + function getIgnoreDirs(metadata) { const auxDirs = metadata?.source?.aux_dirs; if (auxDirs && Array.isArray(auxDirs)) { @@ -62,15 +86,6 @@ function getIgnoreDirs(metadata) { return DEFAULT_IGNORE_DIRS; } -function isIgnoredDir(dirName, ignoreDirs) { - return ignoreDirs.some(ignored => { - if (ignored.includes('*')) { - return dirName.startsWith(ignored.replace('*', '')); - } - return dirName === ignored; - }); -} - async function listModelFilesFiltered(dir, metadata) { const entries = await fs.promises.readdir(dir, { withFileTypes: true }); @@ -80,14 +95,17 @@ async function listModelFilesFiltered(dir, metadata) { .sort(); } -function buildEntry(root, metadata, metadataFile, modelFile, isCollection, slim, modelFiles) { +async function buildEntry(root, metadata, metadataFile, modelFile, isCollection, slim, modelFiles) { + modelFiles = modelFiles || [modelFile]; const modelDir = path.dirname(metadataFile); const relativeModelPath = path.relative(root, path.join(modelDir, modelFile)).replace(/\\/g, '/'); - const id = isCollection - ? metadata.id || path.basename(modelFile, '.bngl') - : (metadata.id && modelFiles.length === 1) - ? metadata.id - : path.basename(modelFile, '.bngl'); + const fileBaseName = path.basename(modelFile, '.bngl'); + let id = metadata.id || fileBaseName; + if (!isCollection && modelFiles.length > 1 && metadata.id) { + if (!metadata.id.endsWith(fileBaseName) && metadata.id !== fileBaseName) { + id = `${metadata.id}_${fileBaseName}`; + } + } const compatibility = { bng2: metadata.compatibility?.bng2_compatible ?? false, @@ -103,7 +121,13 @@ function buildEntry(root, metadata, metadataFile, modelFile, isCollection, slim, const baseEntry = { id, - name: isCollection ? metadata.name : (metadata.name || id), + name: isCollection + ? (metadata.name || fileBaseName) + : (metadata.name && modelFiles.length === 1) + ? metadata.name + : (metadata.name + ? `${metadata.name} (${path.basename(modelFile, '.bngl')})` + : path.basename(modelFile, '.bngl')), description: metadata.description || '', tags: Array.isArray(metadata.tags) ? metadata.tags : [], category: metadata.category || 'other', @@ -122,12 +146,12 @@ function buildEntry(root, metadata, metadataFile, modelFile, isCollection, slim, baseEntry.collectionId = metadata.id || null; if (!slim && metadata.collection) { - const modelFiles = fs.readdirSync(modelDir, { withFileTypes: true }) - .filter(e => e.isFile() && e.name.endsWith('.bngl')) - .map(e => e.name) - .sort(); + let filesToUse = modelFiles; + if (fs.existsSync(modelDir)) { + filesToUse = await listModelFilesAsync(modelDir); + } - const variants = modelFiles.map(file => ({ + const variants = filesToUse.map(file => ({ id: path.basename(file, '.bngl'), file: file, })); @@ -155,6 +179,11 @@ function buildEntry(root, metadata, metadataFile, modelFile, isCollection, slim, } } + // Backwards-compatible top-level compatibility flags + baseEntry.bng2_compatible = compatibility.bng2 || false; + baseEntry.nfsim_compatible = compatibility.nfsim || false; + baseEntry.excluded = compatibility.excluded || false; + return baseEntry; } @@ -164,7 +193,8 @@ function isCollectionEntry(metadata, modelFiles) { async function main() { const { root, output, slim } = parseArgs(process.argv.slice(2)); - const metadataFiles = SEARCH_ROOTS.flatMap(searchRoot => listMetadataFiles(path.join(root, searchRoot))); + const metadataFilesArrays = await Promise.all(SEARCH_ROOTS.map(searchRoot => listMetadataFiles(path.join(root, searchRoot)))); + const metadataFiles = metadataFilesArrays.flat(); const entryPromises = metadataFiles.map(async (metadataFile) => { const content = await fs.promises.readFile(metadataFile, 'utf8'); @@ -176,19 +206,18 @@ async function main() { const isCollection = isCollectionEntry(metadata, modelFiles); if (isCollection) { - return [buildEntry(root, metadata, metadataFile, modelFiles[0], true, slim, modelFiles)]; + return [await buildEntry(root, metadata, metadataFile, modelFiles[0], true, slim, modelFiles)]; } - return modelFiles.map(modelFile => + return Promise.all(modelFiles.map(modelFile => buildEntry(root, metadata, metadataFile, modelFile, false, slim, modelFiles) - ); + )); }); const manifestEntries = (await Promise.all(entryPromises)).flat(); manifestEntries.sort((left, right) => left.id.localeCompare(right.id)); await fs.promises.writeFile(output, JSON.stringify(manifestEntries, null, 2)); - console.log(`Generated ${manifestEntries.length} manifest entries at ${output}${slim ? ' (slim)' : ''}`); } if (require.main === module) { @@ -199,8 +228,13 @@ if (require.main === module) { } module.exports = { + getIgnoreDirs, + DEFAULT_IGNORE_DIRS, parseArgs, buildEntry, listMetadataFiles, isCollectionEntry, + parseMetadataYaml, + isIgnoredDir, + listModelFilesFiltered, }; \ No newline at end of file diff --git a/scripts/generate-manifest.test.js b/scripts/generate-manifest.test.js index b7227c24..99848059 100644 --- a/scripts/generate-manifest.test.js +++ b/scripts/generate-manifest.test.js @@ -3,7 +3,8 @@ const assert = require('node:assert'); const path = require('path'); const os = require('os'); const fs = require('fs'); -const { buildEntry, parseMetadataYaml, listMetadataFiles } = require('./generate-manifest.js'); +const { buildEntry, listMetadataFiles, parseArgs, isIgnoredDir, isCollectionEntry, getIgnoreDirs, DEFAULT_IGNORE_DIRS, listModelFilesFiltered } = require('./generate-manifest.js'); +const { parseMetadataYaml } = require('./utils.js'); test('listMetadataFiles', async (t) => { let tmpDir; @@ -16,25 +17,25 @@ test('listMetadataFiles', async (t) => { fs.rmSync(tmpDir, { recursive: true, force: true }); }); - await t.test('returns empty array for non-existent directory', () => { - const results = listMetadataFiles(path.join(tmpDir, 'non-existent')); + await t.test('returns empty array for non-existent directory', async () => { + const results = await listMetadataFiles(path.join(tmpDir, 'non-existent')); assert.deepStrictEqual(results, []); }); - await t.test('returns empty array when no metadata files exist', () => { + await t.test('returns empty array when no metadata files exist', async () => { fs.writeFileSync(path.join(tmpDir, 'somefile.txt'), ''); - const results = listMetadataFiles(tmpDir); + const results = await listMetadataFiles(tmpDir); assert.deepStrictEqual(results, []); }); - await t.test('finds metadata.yaml in root directory', () => { + await t.test('finds metadata.yaml in root directory', async () => { const yamlPath = path.join(tmpDir, 'metadata.yaml'); fs.writeFileSync(yamlPath, ''); - const results = listMetadataFiles(tmpDir); + const results = await listMetadataFiles(tmpDir); assert.deepStrictEqual(results, [yamlPath]); }); - await t.test('finds metadata.yaml in nested directories', () => { + await t.test('finds metadata.yaml in nested directories', async () => { const dir1 = path.join(tmpDir, 'dir1'); const dir2 = path.join(tmpDir, 'dir2'); fs.mkdirSync(dir1); @@ -46,13 +47,13 @@ test('listMetadataFiles', async (t) => { fs.writeFileSync(yaml1, ''); fs.writeFileSync(yaml2, ''); - const results = listMetadataFiles(tmpDir); + const results = await listMetadataFiles(tmpDir); assert.strictEqual(results.length, 2); assert.ok(results.includes(yaml1)); assert.ok(results.includes(yaml2)); }); - await t.test('ignores other files named metadata.yaml if they are directories', () => { + await t.test('ignores other files named metadata.yaml if they are directories', async () => { const fakeYamlDir = path.join(tmpDir, 'metadata.yaml'); fs.mkdirSync(fakeYamlDir); @@ -60,13 +61,13 @@ test('listMetadataFiles', async (t) => { fs.mkdirSync(path.join(tmpDir, 'dir1')); fs.writeFileSync(realYaml, ''); - const results = listMetadataFiles(tmpDir); + const results = await listMetadataFiles(tmpDir); assert.deepStrictEqual(results, [realYaml]); }); }); test('buildEntry', async (t) => { - await t.test('handles a single model with full metadata', () => { + await t.test('handles a single model with full metadata', async () => { const root = '/path/to/root'; const metadataFile = '/path/to/root/Published/ModelA/metadata.yaml'; const modelFile = 'model_a.bngl'; @@ -83,7 +84,7 @@ test('buildEntry', async (t) => { playground: { visible: true }, }; - const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + const entry = await buildEntry(root, metadata, metadataFile, modelFile, isCollection, false, [modelFile]); assert.strictEqual(entry.id, 'model_a'); assert.strictEqual(entry.name, 'Model A'); @@ -93,16 +94,20 @@ test('buildEntry', async (t) => { assert.strictEqual(entry.file, 'model_a.bngl'); assert.deepStrictEqual(entry.tags, ['test', 'model']); assert.strictEqual(entry.category, 'validation'); - assert.strictEqual(entry.bng2_compatible, true); + assert.strictEqual(entry.compatibility.bng2, true); assert.strictEqual(entry.origin, 'published'); assert.strictEqual(entry.visible, true); assert.strictEqual(entry.collectionId, null); }); - await t.test('handles a collection entry', () => { - const root = '/path/to/root'; - const metadataFile = '/path/to/root/Contributed/CollectionB/metadata.yaml'; + await t.test('handles a collection entry', async () => { + // Create a temporary directory since listModelFilesAsync will read it + const tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'buildEntry-test-')); + const metadataFile = path.join(tmpDir, 'metadata.yaml'); const modelFile = 'variant_1.bngl'; + fs.writeFileSync(path.join(tmpDir, 'variant_1.bngl'), ''); + fs.writeFileSync(path.join(tmpDir, 'variant_2.bngl'), ''); + const isCollection = true; const metadata = { @@ -111,14 +116,17 @@ test('buildEntry', async (t) => { collection: { type: 'parameter-fit-variants' } }; - const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + const entry = await buildEntry(tmpDir, metadata, metadataFile, modelFile, isCollection, false, [modelFile, 'variant_2.bngl']); - assert.strictEqual(entry.id, 'variant_1'); - assert.strictEqual(entry.name, 'Collection B - variant_1'); + assert.strictEqual(entry.id, 'collection_b'); + assert.strictEqual(entry.name, 'Collection B'); assert.strictEqual(entry.collectionId, 'collection_b'); + assert.strictEqual(entry.collection.variants.length, 2); + + fs.rmSync(tmpDir, { recursive: true, force: true }); }); - await t.test('handles missing metadata with appropriate fallbacks', () => { + await t.test('handles missing metadata with appropriate fallbacks', async () => { const root = '/path/to/root'; const metadataFile = '/path/to/root/Tutorials/ModelC/metadata.yaml'; const modelFile = 'model_c.bngl'; @@ -126,20 +134,20 @@ test('buildEntry', async (t) => { const metadata = {}; - const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + const entry = await buildEntry(root, metadata, metadataFile, modelFile, isCollection, false, [modelFile]); assert.strictEqual(entry.id, 'model_c'); assert.strictEqual(entry.name, 'model_c'); assert.strictEqual(entry.description, ''); assert.deepStrictEqual(entry.tags, []); assert.strictEqual(entry.category, 'other'); - assert.strictEqual(entry.bng2_compatible, false); + assert.strictEqual(entry.compatibility.bng2, false); assert.strictEqual(entry.origin, 'other'); assert.strictEqual(entry.visible, false); assert.strictEqual(entry.collectionId, null); }); - await t.test('handles partial compatibility and playground metadata', () => { + await t.test('handles partial compatibility and playground metadata', async () => { const root = '/path/to/root'; const metadataFile = '/path/to/root/Tutorials/ModelD/metadata.yaml'; const modelFile = 'model_d.bngl'; @@ -150,9 +158,9 @@ test('buildEntry', async (t) => { playground: {} }; - const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + const entry = await buildEntry(root, metadata, metadataFile, modelFile, isCollection, false, [modelFile]); - assert.strictEqual(entry.bng2_compatible, false); + assert.strictEqual(entry.compatibility.bng2, false); assert.strictEqual(entry.visible, false); }); }); @@ -173,21 +181,27 @@ test('parseArgs', async (t) => { }); await t.test('parses --output argument', () => { - const args = parseArgs(['--output', 'custom/output.json']); const expectedRoot = path.resolve(__dirname, '..'); - const expectedOutput = path.resolve('custom/output.json'); + const outputArg = path.join(expectedRoot, 'custom/output.json'); + const args = parseArgs(['--output', outputArg]); assert.strictEqual(args.root, expectedRoot); - assert.strictEqual(args.output, expectedOutput); + assert.strictEqual(args.output, outputArg); }); await t.test('parses both --root and --output arguments', () => { - const args = parseArgs(['--root', 'custom/root', '--output', 'custom/output.json']); const expectedRoot = path.resolve('custom/root'); - const expectedOutput = path.resolve('custom/output.json'); + const expectedOutput = path.resolve('custom/root/custom/output.json'); + const args = parseArgs(['--root', 'custom/root', '--output', expectedOutput]); assert.strictEqual(args.root, expectedRoot); assert.strictEqual(args.output, expectedOutput); }); + await t.test('throws an error if output is outside root directory', () => { + assert.throws(() => { + parseArgs(['--root', '/custom/root', '--output', '/etc/passwd']); + }, /Path traversal security risk/); + }); + await t.test('ignores flags at the end of the array', () => { const args = parseArgs(['--root']); const expectedRoot = path.resolve(__dirname, '..'); @@ -323,20 +337,26 @@ test('parseArgs', async (t) => { }); await t.test('parses --output argument', () => { - const customOutput = path.resolve('/custom/output.json'); - const result = parseArgs(['--output', '/custom/output.json']); + const customOutput = path.join(defaultRoot, 'custom/output.json'); + const result = parseArgs(['--output', customOutput]); assert.strictEqual(result.root, defaultRoot); assert.strictEqual(result.output, customOutput); }); await t.test('parses both --root and --output arguments', () => { const customRoot = path.resolve('/custom/root'); - const customOutput = path.resolve('/custom/output.json'); - const result = parseArgs(['--root', '/custom/root', '--output', '/custom/output.json']); + const customOutput = path.resolve('/custom/root/output.json'); + const result = parseArgs(['--root', '/custom/root', '--output', customOutput]); assert.strictEqual(result.root, customRoot); assert.strictEqual(result.output, customOutput); }); + await t.test('throws an error if output is outside root directory', () => { + assert.throws(() => { + parseArgs(['--root', '/custom/root', '--output', '/etc/passwd']); + }, /Path traversal security risk/); + }); + await t.test('ignores flags missing a subsequent value', () => { const result1 = parseArgs(['--root']); assert.strictEqual(result1.root, defaultRoot); @@ -348,3 +368,130 @@ test('parseArgs', async (t) => { }); }); + +test('isIgnoredDir', async (t) => { + await t.test('returns true for exact match', () => { + assert.strictEqual(isIgnoredDir('fitting', ['fitting', 'output_*']), true); + }); + + await t.test('returns false for non-match', () => { + assert.strictEqual(isIgnoredDir('data', ['fitting', 'output_*']), false); + }); + + await t.test('returns true for wildcard match', () => { + assert.strictEqual(isIgnoredDir('output_123', ['fitting', 'output_*']), true); + }); + + await t.test('returns false for partial match without wildcard', () => { + assert.strictEqual(isIgnoredDir('fitting_dir', ['fitting', 'output_*']), false); + }); + + await t.test('returns false for empty ignoreDirs array', () => { + assert.strictEqual(isIgnoredDir('fitting', []), false); + }); +}); + +test('isCollectionEntry', async (t) => { + await t.test('returns true when metadata has a collection property', () => { + const metadata = { collection: { type: 'parameter-fit-variants' } }; + assert.strictEqual(isCollectionEntry(metadata), true); + }); + + await t.test('returns false when metadata has no collection property', () => { + const metadata = { id: 'model_a' }; + assert.strictEqual(isCollectionEntry(metadata), false); + }); + + await t.test('returns false when collection property is null or undefined', () => { + const metadataWithNull = { collection: null }; + const metadataWithUndefined = { collection: undefined }; + assert.strictEqual(isCollectionEntry(metadataWithNull), false); + assert.strictEqual(isCollectionEntry(metadataWithUndefined), false); + }); +}); + +test('getIgnoreDirs', async (t) => { + await t.test('returns DEFAULT_IGNORE_DIRS when metadata is undefined', () => { + const result = getIgnoreDirs(undefined); + assert.deepStrictEqual(result, DEFAULT_IGNORE_DIRS); + }); + + await t.test('returns DEFAULT_IGNORE_DIRS when metadata.source is undefined', () => { + const metadata = { id: 'model_1' }; + const result = getIgnoreDirs(metadata); + assert.deepStrictEqual(result, DEFAULT_IGNORE_DIRS); + }); + + await t.test('returns DEFAULT_IGNORE_DIRS when metadata.source.aux_dirs is not an array', () => { + const metadata = { + source: { + aux_dirs: 'not_an_array' + } + }; + const result = getIgnoreDirs(metadata); + assert.deepStrictEqual(result, DEFAULT_IGNORE_DIRS); + }); + + await t.test('returns combined array when metadata.source.aux_dirs is an array', () => { + const metadata = { + source: { + aux_dirs: ['custom_dir_1', 'custom_dir_2'] + } + }; + const result = getIgnoreDirs(metadata); + const expected = [...DEFAULT_IGNORE_DIRS, 'custom_dir_1', 'custom_dir_2']; + assert.deepStrictEqual(result, expected); + }); +}); + +test('listModelFilesFiltered', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'listModelFilesFiltered-test-')); + }); + + t.afterEach(() => { + fs.rmSync(tmpDir, { recursive: true, force: true }); + }); + + await t.test('returns an empty array for an empty directory', async () => { + const results = await listModelFilesFiltered(tmpDir, {}); + assert.deepStrictEqual(results, []); + }); + + await t.test('matches only .bngl files and ignores other extensions', async () => { + fs.writeFileSync(path.join(tmpDir, 'model1.bngl'), ''); + fs.writeFileSync(path.join(tmpDir, 'model2.bngl'), ''); + fs.writeFileSync(path.join(tmpDir, 'data.txt'), ''); + fs.writeFileSync(path.join(tmpDir, 'script.py'), ''); + + const results = await listModelFilesFiltered(tmpDir, {}); + assert.deepStrictEqual(results, ['model1.bngl', 'model2.bngl']); + }); + + await t.test('ignores directories, even if they end in .bngl', async () => { + fs.writeFileSync(path.join(tmpDir, 'model1.bngl'), ''); + fs.mkdirSync(path.join(tmpDir, 'fake.bngl')); + + const results = await listModelFilesFiltered(tmpDir, {}); + assert.deepStrictEqual(results, ['model1.bngl']); + }); + + await t.test('returns results sorted alphabetically', async () => { + fs.writeFileSync(path.join(tmpDir, 'z_model.bngl'), ''); + fs.writeFileSync(path.join(tmpDir, 'a_model.bngl'), ''); + fs.writeFileSync(path.join(tmpDir, 'm_model.bngl'), ''); + + const results = await listModelFilesFiltered(tmpDir, {}); + assert.deepStrictEqual(results, ['a_model.bngl', 'm_model.bngl', 'z_model.bngl']); + }); + + await t.test('throws ENOENT for non-existent directories', async () => { + const fakeDir = path.join(tmpDir, 'does-not-exist'); + await assert.rejects( + async () => await listModelFilesFiltered(fakeDir, {}), + { code: 'ENOENT' } + ); + }); +}); diff --git a/scripts/migration/curate-published-tags.js b/scripts/migration/curate-published-tags.js new file mode 100644 index 00000000..996b7f1d --- /dev/null +++ b/scripts/migration/curate-published-tags.js @@ -0,0 +1,205 @@ +const { safeJoin } = require('../utils'); +const fs = require('fs'); +const path = require('path'); + +const BLACKLIST = new Set([ + 'generate_network', 'simulate', 'simulate_ode', 'simulate_ssa', 'simulate_nf', 'writexml', + 'setoption', 'exclude_reactants', 'include_reactants', 'species', 'molecules', 'time', + 'counter', 'trash', 'null', 'setparameter', 'resetconcentrations', 'tmax', 't', + 'version', 'source', 'origin', 'published', 'literature', 'tofit', 'ground', 'exact', + 'fit', 'best_fit', 'bnf', 'bnf1', 'pybnf', 'pybng', 'validation', 'showcase', 'tutorial', + 'test-case', 'other', 'signaling', 'immunology', 'cancer', 'metabolism', 'cell-cycle', + 'developmental', 'physics', 'cs', 'ecology', 'synbio' +]); + +function parseArgs(argv) { + const args = { + root: path.resolve(__dirname, '../../') + }; + + for (let i = 0; i < argv.length; i++) { + if (argv[i] === '--root' && i + 1 < argv.length) { + args.root = argv[i + 1]; + i++; + } + } + return args; +} + +async function listMetadataFiles(dir) { + try { + const entries = await fs.promises.readdir(dir, { withFileTypes: true }); + const promises = entries.map(async (entry) => { + const fullPath = safeJoin(dir, entry.name); + if (entry.isDirectory()) { + return listMetadataFiles(fullPath); + } else if (entry.isFile() && entry.name === 'metadata.yaml') { + return [fullPath]; + } + return []; + }); + const results = await Promise.all(promises); + return results.flat(); + } catch (err) { + if (err.code === 'ENOENT') return []; + throw err; + } +} + +function parseMetadataYaml(content) { + const lines = content.split('\n'); + const metadata = {}; + for (const line of lines) { + const trimmed = line.trim(); + if (!trimmed || trimmed.startsWith('#')) continue; + const match = line.match(/^([a-zA-Z0-9_-]+):\s*(.*)$/); + if (match) { + const key = match[1]; + let val = match[2].trim(); + if (val.startsWith('"') && val.endsWith('"')) val = val.slice(1, -1); + if (val.startsWith("'") && val.endsWith("'")) val = val.slice(1, -1); + metadata[key] = val; + } + } + return metadata; +} + +async function main(argv = process.argv.slice(2)) { + const args = parseArgs(argv); + const rulehubRoot = args.root; + const publishedDir = path.join(rulehubRoot, 'Published'); + + const metadataFiles = await listMetadataFiles(publishedDir); + let count = 0; + + for (const metaFile of metadataFiles) { + const relPath = path.relative(publishedDir, path.dirname(metaFile)).replace(/\\/g, '/'); + + // Skip PyBioNetGen internal files + if (relPath.startsWith('PyBioNetGen')) { + continue; + } + + let content = await fs.promises.readFile(metaFile, 'utf8'); + let meta = parseMetadataYaml(content); + + // 1. Rename McMillan_immunology_2021 to McMillan_TNF_2021 + if (meta.id === 'McMillan_immunology_2021') { + content = content.replace(/^id:\s*(["']?)McMillan_immunology_2021\1\s*$/m, 'id: "McMillan_TNF_2021"'); + meta.id = 'McMillan_TNF_2021'; + } + + // 2. Rename ZAP_immunology_2021 to ZAP70_immunology_2021 + if (meta.id === 'ZAP_immunology_2021') { + content = content.replace(/^id:\s*(["']?)ZAP_immunology_2021\1\s*$/m, 'id: "ZAP70_immunology_2021"'); + meta.id = 'ZAP70_immunology_2021'; + } + + // 3. Parse and clean up tags + const tagsMatch = content.match(/^tags:\s*\[(.*?)\]\s*$/m); + if (tagsMatch) { + const rawTags = tagsMatch[1].split(',') + .map(t => t.trim().replace(/^["']|["']$/g, '')) + .filter(Boolean); + + let cleanTags = []; + for (const tag of rawTags) { + const lowerTag = tag.toLowerCase(); + + // Filter blacklisted words + if (BLACKLIST.has(lowerTag)) continue; + + // Filter length <= 2 (except common ones if necessary, but generally raw variables are short) + if (lowerTag.length <= 2) continue; + + // Filter raw variables and parameter names: e.g. starts with letter, has digit, not a 4-digit year + if (/^[a-zA-Z]+.*\d+.*$/.test(tag) && !/^\d{4}$/.test(tag)) { + continue; + } + + // Filter other raw variable patterns like grb2_total__free + if (lowerTag.includes('_') || lowerTag.includes('__')) { + // Only keep if it is a well-known biological concept containing underscore (like cell_cycle) + const okTags = ['cell_cycle', 'signal_transduction', 'gene_expression', 'feed_forward', 'feedback_loop']; + if (!okTags.includes(lowerTag)) { + continue; + } + } + + cleanTags.push(lowerTag); + } + + // 4. Add clean biological tags based on author, category, description, and year + // Extract year + const yearMatch = relPath.match(/\d{4}/); + if (yearMatch) { + cleanTags.push(yearMatch[0]); + } + + // Extract author + const authorMatch = relPath.match(/^([A-Za-z]+)/); + if (authorMatch && authorMatch[1].toLowerCase() !== 'rulebased' && authorMatch[1].toLowerCase() !== 'vaxandvariants') { + cleanTags.push(authorMatch[1].toLowerCase()); + } + + // Add category/subject terms from description + const desc = (meta.description || '').toLowerCase(); + if (desc.includes('tnf')) cleanTags.push('tnf'); + if (desc.includes('egfr') || desc.includes('egf')) cleanTags.push('egfr'); + if (desc.includes('tcr') || desc.includes('t cell')) cleanTags.push('tcr'); + if (desc.includes('bcr') || desc.includes('b cell')) cleanTags.push('bcr'); + if (desc.includes('fceri') || desc.includes('ige')) cleanTags.push('fceri'); + if (desc.includes('camkii')) cleanTags.push('camkii'); + if (desc.includes('circadian') || desc.includes('clock')) cleanTags.push('circadian'); + if (desc.includes('signaling') || desc.includes('cascade')) cleanTags.push('signaling'); + if (desc.includes('transport') || desc.includes('import')) cleanTags.push('transport'); + if (desc.includes('oscillation') || desc.includes('oscillator')) cleanTags.push('oscillations'); + + // Deduplicate and sort + const finalTags = Array.from(new Set(cleanTags)).sort(); + + // Replace the tags line in-place + const tagsString = finalTags.map(t => `"${t}"`).join(', '); + const updatedContent = content.replace(/^tags:\s*\[(.*?)\]\s*$/m, `tags: [${tagsString}]`); + + if (content !== updatedContent) { + await fs.promises.writeFile(metaFile, updatedContent, 'utf8'); + console.log(`Curated tags in ${metaFile} -> [${tagsString}]`); + count++; + } + } + } + + // 5. Update our ID_MAP in normalize-published-ids.js to map McMillan2021 to McMillan_TNF_2021 + const normalizerPath = path.join(rulehubRoot, 'scripts', 'migration', 'normalize-published-ids.js'); + try { + let normalizerContent = await fs.promises.readFile(normalizerPath, 'utf8'); + normalizerContent = normalizerContent.replace( + /"McMillan2021": "McMillan_immunology_2021"/, + '"McMillan2021": "McMillan_TNF_2021"' + ).replace( + /"ModelZAP": "ZAP_immunology_2021"/, + '"ModelZAP": "ZAP70_immunology_2021"' + ); + await fs.promises.writeFile(normalizerPath, normalizerContent, 'utf8'); + console.log('Updated normalize-published-ids.js map values.'); + } catch (err) { + if (err.code !== 'ENOENT') throw err; + } + + console.log(`\nSuccessfully curated tags in ${count} Published metadata files!`); +} + +if (require.main === module) { + main().catch(error => { + console.error('An error occurred:', error); + process.exit(1); + }); +} + +module.exports = { + parseArgs, + listMetadataFiles, + parseMetadataYaml, + main +}; diff --git a/scripts/migration/curate-published-tags.test.js b/scripts/migration/curate-published-tags.test.js new file mode 100644 index 00000000..555c11cb --- /dev/null +++ b/scripts/migration/curate-published-tags.test.js @@ -0,0 +1,249 @@ +const assert = require('assert'); +const test = require('node:test'); +const fs = require('fs'); +const path = require('path'); +const os = require('os'); +const { parseArgs, listMetadataFiles, parseMetadataYaml, main } = require('./curate-published-tags.js'); + +test('parseArgs', async (t) => { + await t.test('uses default root when no args provided', () => { + const args = parseArgs([]); + assert.strictEqual(args.root, path.resolve(__dirname, '../../')); + }); + + await t.test('parses --root argument', () => { + const args = parseArgs(['--root', '/custom/root']); + assert.strictEqual(args.root, '/custom/root'); + }); + + await t.test('ignores other arguments', () => { + const args = parseArgs(['--other', 'value', '--root', '/custom/root']); + assert.strictEqual(args.root, '/custom/root'); + }); +}); + +test('parseMetadataYaml', async (t) => { + await t.test('parses simple key-value pairs', () => { + const yaml = ` +id: "test_model" +title: "Test Model" +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { id: 'test_model', title: 'Test Model' }); + }); + + await t.test('handles single quotes', () => { + const yaml = ` +id: 'test_model' +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { id: 'test_model' }); + }); + + await t.test('handles unquoted values', () => { + const yaml = ` +year: 2021 +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { year: '2021' }); + }); + + await t.test('ignores comments and empty lines', () => { + const yaml = ` +# This is a comment + +id: "test" +# Another comment +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { id: 'test' }); + }); + + await t.test('handles malformed lines without colons', () => { + const yaml = ` +id: "test" +malformed line here +title: "Test Model" +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { id: 'test', title: 'Test Model' }); + }); + + await t.test('ignores lines with invalid keys', () => { + const yaml = ` +invalid key: "value" +id: "test" +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { id: 'test' }); + }); + + await t.test('handles multiple colons in the value part', () => { + const yaml = ` +url: "https://example.com/test:123" +description: 'A description: with colon' +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { url: 'https://example.com/test:123', description: 'A description: with colon' }); + }); + + await t.test('handles arrays parsed as strings', () => { + const yaml = ` +tags: ["one", "two"] +categories: ['a', 'b'] +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { tags: '["one", "two"]', categories: "['a', 'b']" }); + }); + + await t.test('preserves internal quotes', () => { + const yaml = ` +title: "Model's Title" +desc: 'He said "Hello"' +mixed: "\\'value\\'" +`; + const result = parseMetadataYaml(yaml); + assert.deepEqual(result, { title: "Model's Title", desc: 'He said "Hello"', mixed: "\\'value\\'" }); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', async () => { + const results = await listMetadataFiles('/non/existent/dir'); + assert.deepEqual(results, []); + }); + + await t.test('finds metadata.yaml files in directory tree', async () => { + const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'test-')); + try { + const dir1 = path.join(tempDir, 'dir1'); + const dir2 = path.join(tempDir, 'dir2'); + fs.mkdirSync(dir1); + fs.mkdirSync(dir2); + + fs.writeFileSync(path.join(dir1, 'metadata.yaml'), 'id: test1'); + fs.writeFileSync(path.join(dir2, 'metadata.yaml'), 'id: test2'); + fs.writeFileSync(path.join(dir1, 'other.txt'), 'not a metadata file'); + + const results = await listMetadataFiles(tempDir); + assert.strictEqual(results.length, 2); + assert.ok(results.includes(path.join(dir1, 'metadata.yaml'))); + assert.ok(results.includes(path.join(dir2, 'metadata.yaml'))); + } finally { + fs.rmSync(tempDir, { recursive: true, force: true }); + } + }); +}); + +test('main functionality', async (t) => { + await t.test('curates tags correctly', async () => { + const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'test-curate-')); + try { + // Setup directory structure + const publishedDir = path.join(tempDir, 'Published'); + const modelDir = path.join(publishedDir, 'ModelAuthor2021'); + fs.mkdirSync(publishedDir); + fs.mkdirSync(modelDir, { recursive: true }); + + // Create a metadata file + const metadataContent = ` +id: "test_model" +description: "Model with tnf and egfr signaling." +tags: ["generate_network", "my_var_123", "goodtag", "tnf", "cell_cycle"] +`; + const metaFile = path.join(modelDir, 'metadata.yaml'); + fs.writeFileSync(metaFile, metadataContent); + + // Run main + const originalConsoleLog = console.log; + console.log = () => {}; // Silence output + try { + await main(['--root', tempDir]); + } finally { + console.log = originalConsoleLog; + } + + // Verify updated content + const updatedContent = fs.readFileSync(metaFile, 'utf8'); + const meta = parseMetadataYaml(updatedContent); + + // Expected tags logic: + // 1. "generate_network" is blacklisted -> removed + // 2. "my_var_123" is variable-like -> removed + // 3. "goodtag" is kept (cleanTags) + // 4. "tnf" is kept and duplicated (from desc) -> deduplicated + // 5. "cell_cycle" is kept + // 6. Year "2021" is extracted from path "ModelAuthor2021" + // 7. Author "modelauthor" is extracted from path + // 8. "egfr" added from description + // 9. "signaling" added from description + + const expectedTagsMatch = updatedContent.match(/^tags:\s*\[(.*?)\]\s*$/m); + assert.ok(expectedTagsMatch, 'Tags line should exist'); + + const expectedTags = [ + '2021', + 'cell_cycle', + 'egfr', + 'goodtag', + 'modelauthor', + 'signaling', + 'tnf' + ].map(t => '"' + t + '"').join(', '); + + assert.strictEqual(expectedTagsMatch[1], expectedTags); + + } finally { + fs.rmSync(tempDir, { recursive: true, force: true }); + } + }); + + await t.test('updates specific model IDs', async () => { + const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'test-rename-')); + try { + // Setup directory structure + const publishedDir = path.join(tempDir, 'Published'); + const modelDir1 = path.join(publishedDir, 'McMillan2021'); + const modelDir2 = path.join(publishedDir, 'ZAP2021'); + fs.mkdirSync(publishedDir); + fs.mkdirSync(modelDir1, { recursive: true }); + fs.mkdirSync(modelDir2, { recursive: true }); + + // Create a metadata file + const meta1 = path.join(modelDir1, 'metadata.yaml'); + fs.writeFileSync(meta1, 'id: "McMillan_immunology_2021"\ntags: ["test"]'); + + const meta2 = path.join(modelDir2, 'metadata.yaml'); + fs.writeFileSync(meta2, 'id: "ZAP_immunology_2021"\ntags: ["test"]'); + + // Also mock normalizer script to test that logic + const scriptsDir = path.join(tempDir, 'scripts', 'migration'); + fs.mkdirSync(scriptsDir, { recursive: true }); + const normalizerPath = path.join(scriptsDir, 'normalize-published-ids.js'); + fs.writeFileSync(normalizerPath, 'const map = { "McMillan2021": "McMillan_immunology_2021", "ModelZAP": "ZAP_immunology_2021" };'); + + // Run main + const originalConsoleLog = console.log; + console.log = () => {}; // Silence output + try { + await main(['--root', tempDir]); + } finally { + console.log = originalConsoleLog; + } + + // Verify updated content + const updated1 = fs.readFileSync(meta1, 'utf8'); + assert.match(updated1, /id: "McMillan_TNF_2021"/); + + const updated2 = fs.readFileSync(meta2, 'utf8'); + assert.match(updated2, /id: "ZAP70_immunology_2021"/); + + const updatedNormalizer = fs.readFileSync(normalizerPath, 'utf8'); + assert.match(updatedNormalizer, /"McMillan2021": "McMillan_TNF_2021"/); + assert.match(updatedNormalizer, /"ModelZAP": "ZAP70_immunology_2021"/); + + } finally { + fs.rmSync(tempDir, { recursive: true, force: true }); + } + }); +}); diff --git a/scripts/migration/extract-gallery-from-constants.js b/scripts/migration/extract-gallery-from-constants.js index 819cfc1b..fbf6ad27 100644 --- a/scripts/migration/extract-gallery-from-constants.js +++ b/scripts/migration/extract-gallery-from-constants.js @@ -28,7 +28,7 @@ function parseSetFromString(content, setName) { if (startIdx === -1) return new Set(); const arrayStart = startIdx + searchStr.length; - let depth = 0; + let depth = 1; let arrayEnd = arrayStart; for (let i = arrayStart; i < content.length; i++) { @@ -71,7 +71,7 @@ function extractAllModelIds(content) { if (startIdx === -1) continue; const arrayStart = startIdx + searchStr.length; - let depth = 0; + let depth = 1; let arrayEnd = arrayStart; for (let i = arrayStart; i < content.length; i++) { @@ -97,88 +97,29 @@ function extractAllModelIds(content) { } function extractCategoryMappings(content) { - const mappings = {}; - - const categoryPatterns = [ - { pattern: /CANCER_MODELS.*?egfr-signaling-pathway.*?glioblastoma.*?hif1a.*?hypoxia.*?vegf.*?dna-damage.*?checkpoint.*?ras-gef.*?p38.*?mapk-signaling-cascade/s, category: 'cancer' }, - { pattern: /IMMUNOLOGY_MODELS.*?bcr-signaling.*?cd40.*?complement.*?immune-synapse/s, category: 'immunology' }, - { pattern: /NEUROSCIENCE_MODELS.*?ampk-signaling.*?calcineurin.*?calcium.*?mtor.*?neurotransmitter.*?synaptic/s, category: 'neuroscience' }, - { pattern: /CELL_CYCLE_MODELS.*?apoptosis.*?caspase.*?cell-cycle.*?dr5.*?e2f.*?tnf.*?p53.*?clock-bmal1/s, category: 'cell-cycle' }, - { pattern: /METABOLISM_MODELS.*?allosteric.*?auto-activation.*?autophagy.*?glycolysis.*?insulin.*?lac-operon/s, category: 'metabolism' }, - { pattern: /DEVELOPMENTAL_MODELS.*?hedgehog.*?myogenic.*?notch.*?rankl.*?sonic-hedgehog.*?wnt.*?fgf.*?smad.*?retinoic.*?bmp/s, category: 'developmental' }, - { pattern: /ECOLOGY_MODELS.*?eco_/s, category: 'ecology' }, - { pattern: /PHYSICS_MODELS.*?ph_/s, category: 'physics' }, - { pattern: /COMPUTER_SCIENCE_MODELS.*?cs_/s, category: 'cs' }, - { pattern: /ML_SIGNAL_MODELS.*?ml_|sp_/s, category: 'ml-signal' }, - { pattern: /SYNBIO_MODELS.*?synbio/s, category: 'synbio' }, - ]; - const modelIdToCategory = {}; - const cancertest = content.match(/CANCER_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (cancertest) { - const ids = cancertest[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'cancer'); - } - - const immunetest = content.match(/IMMUNOLOGY_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (immunetest) { - const ids = immunetest[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'immunology'); - } - - const neuroscience = content.match(/NEUROSCIENCE_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (neuroscience) { - const ids = neuroscience[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'neuroscience'); - } - - const cellcycle = content.match(/CELL_CYCLE_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (cellcycle) { - const ids = cellcycle[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'cell-cycle'); - } - - const metabolism = content.match(/METABOLISM_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (metabolism) { - const ids = metabolism[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'metabolism'); - } - - const developmental = content.match(/DEVELOPMENTAL_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (developmental) { - const ids = developmental[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'developmental'); - } - - const ecology = content.match(/ECOLOGY_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (ecology) { - const ids = ecology[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'ecology'); - } - - const physics = content.match(/PHYSICS_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (physics) { - const ids = physics[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'physics'); - } - - const cs = content.match(/COMPUTER_SCIENCE_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (cs) { - const ids = cs[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'cs'); - } - - const ml = content.match(/ML_SIGNAL_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (ml) { - const ids = ml[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'ml-signal'); - } + const simpleCategories = [ + { prefix: 'CANCER_MODELS', category: 'cancer' }, + { prefix: 'IMMUNOLOGY_MODELS', category: 'immunology' }, + { prefix: 'NEUROSCIENCE_MODELS', category: 'neuroscience' }, + { prefix: 'CELL_CYCLE_MODELS', category: 'cell-cycle' }, + { prefix: 'METABOLISM_MODELS', category: 'metabolism' }, + { prefix: 'DEVELOPMENTAL_MODELS', category: 'developmental' }, + { prefix: 'ECOLOGY_MODELS', category: 'ecology' }, + { prefix: 'PHYSICS_MODELS', category: 'physics' }, + { prefix: 'COMPUTER_SCIENCE_MODELS', category: 'cs' }, + { prefix: 'ML_SIGNAL_MODELS', category: 'ml-signal' }, + { prefix: 'SYNBIO_MODELS', category: 'synbio' }, + ]; - const synbio = content.match(/SYNBIO_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); - if (synbio) { - const ids = synbio[1].match(/["']([^"']+)["']/g) || []; - ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'synbio'); + for (const { prefix, category } of simpleCategories) { + const regex = new RegExp(`${prefix}\\.filter\\(m => \\[\([^\\]]+\)\\]\\.includes\\(m\\.id\\)\\)`); + const match = content.match(regex); + if (match) { + const ids = match[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = category); + } } const tutorials = content.match(/const TUTORIALS: Example\[\] = \[([\s\S]*?)\];/); @@ -194,7 +135,7 @@ function extractCategoryMappings(content) { }); } - const native = content.match(/NATIVE_TUTORIALS\.filter\(m => \["([^"]+)"\]/); + const native = content.match(/NATIVE_TUTORIALS\.filter\(m => \["([^\]]+)"\]/); if (native) { const ids = native[1].split(',').map(s => s.trim().replace(/["']/g, '')); ids.forEach(id => { @@ -209,8 +150,8 @@ function extractCategoryMappings(content) { return modelIdToCategory; } -function main() { - const { constantsPath, output } = parseArgs(process.argv.slice(2)); +function main(argv = process.argv.slice(2)) { + const { constantsPath, output } = parseArgs(argv); console.log(`Reading ${constantsPath}...`); const content = fs.readFileSync(constantsPath, 'utf8'); @@ -270,4 +211,14 @@ function main() { console.log(` NFsim compatible: ${nfsimCount}`); } -main(); \ No newline at end of file +if (require.main === module) { + main(); +} + +module.exports = { + parseArgs, + parseSetFromString, + extractAllModelIds, + extractCategoryMappings, + main +}; \ No newline at end of file diff --git a/scripts/migration/normalize-published-ids.js b/scripts/migration/normalize-published-ids.js new file mode 100644 index 00000000..dfb61556 --- /dev/null +++ b/scripts/migration/normalize-published-ids.js @@ -0,0 +1,173 @@ +const { safeJoin } = require('../utils'); +const fs = require('fs'); +const path = require('path'); + +function parseArgs(argv) { + const args = { + root: path.resolve(__dirname, '../../') + }; + + for (let i = 0; i < argv.length; i++) { + if (argv[i] === '--root' && i + 1 < argv.length) { + args.root = argv[++i]; + } + } + return args; +} + +const ID_MAP = { + "An2009": "An_TLR4_2009", + "Barua2007": "Barua_EGFR_2007", + "Barua2009": "Barua_JAK2_2009", + "Barua2013": "Barua_bcat_2013", + "BaruaBCR2012": "Barua_BCR_2012", + "BaruaFceRI2012": "Barua_FceRI_2012", + "Blinov2006": "Blinov_egfr_2006", + "Blinovegfr": "Blinov_egfr_2006", + "Blinovran": "Blinov_ran_2006", + "Chattaraj2021": "Chattaraj_nephrin_2021", + "CheemalavaguJAKSTAT": "Cheemalavagu_JAKSTAT_2024", + "ChylekFceRI2014": "Chylek_FceRI_2014", + "ChylekTCR2014": "Chylek_TCR_2014", + "Dembo1978": "Dembo_blbr_1978", + "Dolan2015": "Dolan_Insulin_2015", + "Dreisigmeyer2008": "Dreisigmeyer_LacOperon_2008", + "Dushek2011": "Dushek_TCR_2011", + "Dushek2014": "Dushek_TCR_2014", + "Erdem2021": "Erdem_InsR_2021", + "Faeder2003": "Faeder_FceRI_2003", + "Gardner2000": "Gardner_Toggle_2000", + "Goldstein1980": "Goldstein_blbr_1980", + "Harmon2017": "Harmon_Antigen_2017", + "Hat2016": "Hat_wip1_2016", + "Hlavacek1999": "Hlavacek_Steric_1999", + "Hlavacek2001": "Hlavacek_Proofreading_2001", + "Hlavacek2018Egg": "Hlavacek_Egg_2018", + "Hlavacek2018Elephant": "Hlavacek_Elephant_2018", + "Hlavacek2018Restructuration": "Hlavacek_Restructuration_2018", + "JaruszewiczBlonska2023": "JaruszewiczBlonska_NFkB_2023", + "Jung2017": "Jung_CaMKII_2017", + "Kesseler2013": "Kesseler_CellCycle_2013", + "Kocieniewski2012": "Kocieniewski_published_2012", + "Korwek2023": "Korwek_published_2023", + "Kozer2013": "Kozer_egfr_2013", + "Kozer2014": "Kozer_egfr_2014", + "Lang2024": "Lang_CellCycle_2024", + "Ligon2014": "Ligon_egfr_2014", + "LinERK2019": "Lin_ERK_2019", + "LinPrion2019": "Lin_Prion_2019", + "LinTCR2019": "Lin_TCR_2019", + "Macken1982": "Macken_physics_1982", + "Mallela2021": "Mallela_COVID_2021", + "Mallela2021_Cities": "Mallela_Cities_2021", + "Mallela2022": "Mallela_COVID_2022", + "Mallela2022_MSAs": "Mallela_MSAs_2022", + "Massole2023": "Massole_developmental_2023", + "McMillan2021": "McMillan_TNF_2021", + "Mertins2023": "Mertins_cancer_2023", + "Miller2022_NavajoNation": "Miller_NavajoNation_2022", + "Miller2025_MEK": "Miller_MEK_2025", + "Mitra2019/02-egfr": "Mitra_egfr_2019", + "Mitra2019/05-threestep": "Mitra_threestep_2019", + "Mitra2019/13-receptor": "Mitra_receptor_2019", + "Mitra2019/17-egfr-ssa": "Mitra_egfr_ssa_2019", + "Mitra2019/18-mapk": "Mitra_mapk_2019", + "Mitra2019/28-mapk": "Mitra_mapk_ensemble_2019", + "Mitra2019/30-jobs": "Mitra_jobs_2019", + "Mitra2019Likelihood": "Mitra_likelihood_2019", + "Mitra2019Rab": "Mitra_Rab_2019", + "Mitra2019Rab/pybnf_files": "Mitra_Rab_pybnf_2019", + "ModelZAP": "ZAP70_immunology_2021", + "Mukhopadhyay2013": "Mukhopadhyay_TCR_2013", + "Nag2009": "Nag_cancer_2009", + "Nosbisch2022": "Nosbisch_cancer_2022", + "Ordyan2020": "Ordyan_CaMKII_2020", + "Pekalski2013": "Pekalski_published_2013", + "Posner1995": "Posner_blbr_1995", + "Posner2004": "Posner_blbr_2004", + "RulebasedRantransport": "Rule_based_Ran_transport", + "RulebasedRantransportdraft": "Rule_based_Ran_transport_draft", + "Rulebasedegfrcompart": "Rule_based_egfr_compart", + "Rulebasedegfrtutorial": "Faeder_egfr_2009", + "Salazar-Cavazos2019": "Salazar_Cavazos_egfr_2019", + "Thomas2016": "Thomas_egfr_2016", + "vilar2002": "Vilar_Circadian_2002", + "vilar2002b": "Vilar_Circadian_2002b", + "vilar2002c": "Vilar_Circadian_2002c", + "Yang2008": "Yang_tlbr_2008", + "Zhang2021": "Zhang_developmental_2021", + "Zhang2023": "Zhang_developmental_2023", + "VaxAndVariants/NYC": "VaxAndVariants_NYC", + "VaxAndVariants/Phoenix": "VaxAndVariants_Phoenix" +}; + +async function listMetadataFiles(dir, results = []) { + try { + const entries = await fs.promises.readdir(dir, { withFileTypes: true }); + const promises = entries.map(async entry => { + const fullPath = safeJoin(dir, entry.name); + if (entry.isDirectory()) { + await listMetadataFiles(fullPath, results); + } else if (entry.isFile() && entry.name === 'metadata.yaml') { + results.push(fullPath); + } + }); + await Promise.all(promises); + } catch (error) { + if (error.code !== 'ENOENT') throw error; + } + return results; +} + +async function updateMetadataId(filePath, newId) { + let content = await fs.promises.readFile(filePath, 'utf8'); + + // Replace the id property in yaml + // Match id: "..." or id: '...' or id: ... + const updatedContent = content.replace(/^id:\s*(["']?)(.*?)\1\s*$/m, `id: "${newId}"`); + + if (content !== updatedContent) { + await fs.promises.writeFile(filePath, updatedContent, 'utf8'); + console.log(`Updated ID in ${filePath} to "${newId}"`); + return true; + } + return false; +} + +async function main(argv = process.argv.slice(2)) { + const args = parseArgs(argv); + const publishedDir = path.join(args.root, 'Published'); + + const metadataFiles = await listMetadataFiles(publishedDir); + let count = 0; + + for (const metaFile of metadataFiles) { + const relPath = path.relative(publishedDir, path.dirname(metaFile)).replace(/\\/g, '/'); + + // Skip PyBioNetGen internal files + if (relPath.startsWith('PyBioNetGen')) { + continue; + } + + // Find key in mapping + const newId = ID_MAP[relPath]; + if (newId) { + if (await updateMetadataId(metaFile, newId)) { + count++; + } + } else { + console.log(`No explicit mapping for ${relPath}, skipped.`); + } + } + + console.log(`\nSuccessfully updated ${count} metadata files in Published/!`); +} + +if (require.main === module) { + main().catch(error => { + console.error('An error occurred:', error); + process.exit(1); + }); +} + +module.exports = { parseArgs, listMetadataFiles, updateMetadataId, main }; diff --git a/scripts/migration/normalize-published-ids.test.js b/scripts/migration/normalize-published-ids.test.js new file mode 100644 index 00000000..4b49db5e --- /dev/null +++ b/scripts/migration/normalize-published-ids.test.js @@ -0,0 +1,92 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const fs = require('fs'); +const os = require('os'); +const path = require('path'); +const { parseArgs, updateMetadataId } = require('./normalize-published-ids'); + +test('normalize-published-ids.js tests', async (t) => { + await t.test('parseArgs', async (t) => { + await t.test('defaults --root to resolved directory if missing', () => { + const args = parseArgs([]); + assert.ok(args.root.endsWith('RuleHub')); + }); + + await t.test('parses --root /path/to/root', () => { + const args = parseArgs(['--root', '/path/to/root']); + assert.strictEqual(args.root, '/path/to/root'); + }); + + await t.test('ignores --root if no argument is provided after it', () => { + const args = parseArgs(['--root']); + assert.ok(args.root.endsWith('RuleHub')); + }) + }); + + await t.test('updateMetadataId', async (t) => { + let tempDir; + + t.before(() => { + tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'normalize-ids-test-')); + }); + + t.after(() => { + if (tempDir) { + fs.rmSync(tempDir, { recursive: true, force: true }); + } + }); + + await t.test('replaces an unquoted id', async () => { + const filePath = path.join(tempDir, 'metadata_unquoted.yaml'); + fs.writeFileSync(filePath, 'name: "test"\nid: oldId\nother: "value"', 'utf8'); + + const result = await updateMetadataId(filePath, 'newId'); + + assert.strictEqual(result, true); + const content = fs.readFileSync(filePath, 'utf8'); + assert.strictEqual(content, 'name: "test"\nid: "newId"\nother: "value"'); + }); + + await t.test('replaces a single-quoted id', async () => { + const filePath = path.join(tempDir, 'metadata_single_quoted.yaml'); + fs.writeFileSync(filePath, "name: 'test'\nid: 'oldId'\nother: 'value'", 'utf8'); + + const result = await updateMetadataId(filePath, 'newId'); + + assert.strictEqual(result, true); + const content = fs.readFileSync(filePath, 'utf8'); + assert.strictEqual(content, "name: 'test'\nid: \"newId\"\nother: 'value'"); + }); + + await t.test('replaces a double-quoted id', async () => { + const filePath = path.join(tempDir, 'metadata_double_quoted.yaml'); + fs.writeFileSync(filePath, 'name: "test"\nid: "oldId"\nother: "value"', 'utf8'); + + const result = await updateMetadataId(filePath, 'newId'); + + assert.strictEqual(result, true); + const content = fs.readFileSync(filePath, 'utf8'); + assert.strictEqual(content, 'name: "test"\nid: "newId"\nother: "value"'); + }); + + await t.test('returns false if id is already correct', async () => { + const filePath = path.join(tempDir, 'metadata_correct.yaml'); + fs.writeFileSync(filePath, 'name: "test"\nid: "newId"\nother: "value"', 'utf8'); + + const result = await updateMetadataId(filePath, 'newId'); + + assert.strictEqual(result, false); + const content = fs.readFileSync(filePath, 'utf8'); + assert.strictEqual(content, 'name: "test"\nid: "newId"\nother: "value"'); // Unchanged + }); + + await t.test('handles spacing correctly', async () => { + const filePath = path.join(tempDir, 'metadata_spaces.yaml'); + fs.writeFileSync(filePath, 'name: "test"\n id: oldId \nother: "value"', 'utf8'); + + const result = await updateMetadataId(filePath, 'newId'); + + assert.strictEqual(result, false, "Original regex shouldn't match indented id"); + }) + }); +}); \ No newline at end of file diff --git a/scripts/tests/apply-gallery-assignments.test.js b/scripts/tests/apply-gallery-assignments.test.js new file mode 100644 index 00000000..415002d0 --- /dev/null +++ b/scripts/tests/apply-gallery-assignments.test.js @@ -0,0 +1,165 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const path = require('path'); +const fs = require('fs'); +const os = require('os'); + +const { parseArgs, updateMetadataFile } = require('../apply-gallery-assignments.js'); + +function compileAssignments(assignments) { + return Object.entries(assignments).map(([modelId, data]) => ({ + modelId, data, + idPattern: new RegExp(`^id:\\s*["']?${modelId.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}["']?\\s*$`, 'm') + })); +} + +test('parseArgs', async (t) => { + await t.test('uses default values', () => { + const args = parseArgs([]); + assert.strictEqual(args.input, 'gallery-assignments.json'); + assert.strictEqual(args.root, path.resolve(__dirname, '..', '..')); + assert.strictEqual(args.dryRun, false); + }); + + await t.test('parses --input', () => { + const args = parseArgs(['--input', 'custom.json']); + assert.strictEqual(args.input, 'custom.json'); + }); + + await t.test('parses --root', () => { + const args = parseArgs(['--root', '/custom/root']); + assert.strictEqual(args.root, '/custom/root'); + }); + + await t.test('parses --dry-run', () => { + const args = parseArgs(['--dry-run']); + assert.strictEqual(args.dryRun, true); + }); + + await t.test('parses multiple arguments', () => { + const args = parseArgs(['--input', 'custom.json', '--dry-run', '--root', '/custom/root']); + assert.strictEqual(args.input, 'custom.json'); + assert.strictEqual(args.root, '/custom/root'); + assert.strictEqual(args.dryRun, true); + }); +}); + +test('updateMetadataFile', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'bionetgen-test-')); + }); + + t.afterEach(() => { + if (tmpDir) { + fs.rmSync(tmpDir, { recursive: true, force: true }); + } + }); + + await t.test('updates gallery_categories, playground visible flag', async () => { + const modelDir = path.join(tmpDir, 'model1'); + fs.mkdirSync(modelDir); + const metadataPath = path.join(modelDir, 'metadata.yaml'); + + const initialContent = `id: "model1" +gallery_categories: [] +playground: + some_other_key: true`; + + fs.writeFileSync(metadataPath, initialContent); + + const compiled = compileAssignments({ model1: { gallery_categories: ["cat1", "cat2"] } }); + + const updated = await updateMetadataFile(metadataPath, {}, compiled, false); + + assert.strictEqual(updated, true); + const newContent = fs.readFileSync(metadataPath, 'utf8'); + + assert.ok(newContent.includes('gallery_categories: ["cat1","cat2"]')); + assert.ok(newContent.includes('visible: true')); + }); + + await t.test('updates single gallery_category to gallery_categories', async () => { + const modelDir = path.join(tmpDir, 'model2'); + fs.mkdirSync(modelDir); + const metadataPath = path.join(modelDir, 'metadata.yaml'); + + const initialContent = `id: "model2" +gallery_category: "old_cat"`; + + fs.writeFileSync(metadataPath, initialContent); + + const compiled = compileAssignments({ model2: { gallery_categories: ["cat1", "cat2"] } }); + + const updated = await updateMetadataFile(metadataPath, {}, compiled, false); + + assert.strictEqual(updated, true); + const newContent = fs.readFileSync(metadataPath, 'utf8'); + + assert.ok(newContent.includes('gallery_categories: ["cat1","cat2"]')); + assert.ok(!newContent.includes('gallery_category: "old_cat"')); + }); + + await t.test('updates compatibility flags', async () => { + const modelDir = path.join(tmpDir, 'model3'); + fs.mkdirSync(modelDir); + const metadataPath = path.join(modelDir, 'metadata.yaml'); + + const initialContent = `id: "model3" +bng2_compatible: false +nfsim_compatible: false +excluded: false`; + + fs.writeFileSync(metadataPath, initialContent); + + const compiled = compileAssignments({ model3: { bng2_compatible: true, nfsim_compatible: true, excluded: true } }); + + const updated = await updateMetadataFile(metadataPath, {}, compiled, false); + + assert.strictEqual(updated, true); + const newContent = fs.readFileSync(metadataPath, 'utf8'); + + assert.ok(newContent.includes('bng2_compatible: true')); + assert.ok(newContent.includes('nfsim_compatible: true')); + assert.ok(newContent.includes('excluded: true')); + }); + + await t.test('does not modify if dryRun is true', async () => { + const modelDir = path.join(tmpDir, 'model4'); + fs.mkdirSync(modelDir); + const metadataPath = path.join(modelDir, 'metadata.yaml'); + + const initialContent = `id: "model4" +bng2_compatible: false`; + + fs.writeFileSync(metadataPath, initialContent); + + const compiled = compileAssignments({ model4: { bng2_compatible: true } }); + + const updated = await updateMetadataFile(metadataPath, {}, compiled, true); // dryRun = true + + assert.strictEqual(updated, true); // It should still report that it *would* update + + const newContent = fs.readFileSync(metadataPath, 'utf8'); + assert.strictEqual(newContent, initialContent); // File shouldn't be changed + }); + + await t.test('does not update if model id not found', async () => { + const modelDir = path.join(tmpDir, 'model5'); + fs.mkdirSync(modelDir); + const metadataPath = path.join(modelDir, 'metadata.yaml'); + + const initialContent = `id: "other_model" +bng2_compatible: false`; + + fs.writeFileSync(metadataPath, initialContent); + + const compiled = compileAssignments({ model5: { bng2_compatible: true } }); + + const updated = await updateMetadataFile(metadataPath, {}, compiled, false); + + assert.strictEqual(updated, false); + }); + +}); diff --git a/scripts/tests/generate-gallery.test.js b/scripts/tests/generate-gallery.test.js new file mode 100644 index 00000000..03ac7b47 --- /dev/null +++ b/scripts/tests/generate-gallery.test.js @@ -0,0 +1,87 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const fs = require('fs'); +const path = require('path'); +const os = require('os'); +const { main } = require('../generate-gallery.js'); + +test('generate-gallery main function', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gallery-test-')); + }); + + t.afterEach(() => { + fs.rmSync(tmpDir, { recursive: true, force: true }); + }); + + await t.test('continues processing if a metadata.yaml is unreadable and warns', async () => { + const publishedDir = path.join(tmpDir, 'Published'); + fs.mkdirSync(path.join(publishedDir, 'ModelA'), { recursive: true }); + fs.mkdirSync(path.join(publishedDir, 'ModelB'), { recursive: true }); + + // Provide default categories + fs.writeFileSync(path.join(tmpDir, 'gallery-categories.yaml'), ` +categories: + - id: goodcat + name: "Good Category" +`); + + // ModelA: Valid + fs.writeFileSync(path.join(publishedDir, 'ModelA', 'metadata.yaml'), ` +id: modelA +playground: + gallery_category: goodcat +`); + fs.writeFileSync(path.join(publishedDir, 'ModelA', 'modelA.bngl'), `begin model\\nend model`); + + // ModelB: Unreadable + const badPath = path.join(publishedDir, 'ModelB', 'metadata.yaml'); + fs.writeFileSync(badPath, `id: modelB\\nplayground:\\n gallery_category: goodcat`); + fs.writeFileSync(path.join(publishedDir, 'ModelB', 'modelB.bngl'), `begin model\\nend model`); + + // Make unreadable + fs.chmodSync(badPath, 0o000); + + const outPath = path.join(tmpDir, 'gallery.json'); + + // Capture console.warn + const originalWarn = console.warn; + const warnings = []; + console.warn = (msg) => warnings.push(msg); + + // Capture console.log to avoid spam + const originalLog = console.log; + console.log = () => {}; + + try { + await main(['--root', tmpDir, '--output', outPath]); + } finally { + console.warn = originalWarn; + console.log = originalLog; + // Restore permissions so rmSync can delete it + try { + fs.chmodSync(badPath, 0o666); + } catch (e) { + // ignore + } + } + + if (process.platform !== 'win32') { + assert.ok(warnings.some(msg => msg.includes('Failed to process') && msg.includes(badPath)), 'Should log a warning for unreadable metadata'); + + const result = JSON.parse(fs.readFileSync(outPath, 'utf8')); + + assert.strictEqual(typeof result.assignments, 'object'); + assert.ok('modelA' in result.assignments, 'Valid modelA should be processed'); + assert.strictEqual(result.assignments['modelB'], undefined, 'Unreadable modelB should not be processed'); + } else { + // On Windows chmod 0 may not make a file unreadable; at minimum + // ensure valid modelA is processed and output exists. + const result = JSON.parse(fs.readFileSync(outPath, 'utf8')); + assert.strictEqual(typeof result.assignments, 'object'); + assert.ok('modelA' in result.assignments, 'Valid modelA should be processed'); + } + }); +}); diff --git a/scripts/tests/validate-metadata.test.js b/scripts/tests/validate-metadata.test.js index c977fe45..d7fea8bf 100644 --- a/scripts/tests/validate-metadata.test.js +++ b/scripts/tests/validate-metadata.test.js @@ -1,6 +1,6 @@ const { test } = require('node:test'); const assert = require('node:assert'); -const { parseScalar, normalizeModelKey } = require('../validate-metadata.js'); +const { parseScalar, normalizeModelKey, expectArray, expectEnum } = require('../validate-metadata.js'); test('parseScalar', async (t) => { await t.test('parses boolean strings', () => { @@ -41,16 +41,16 @@ test('parseScalar', async (t) => { }); test('normalizeModelKey', async (t) => { - await t.test('removes .bngl extension case-insensitively', () => { - assert.strictEqual(normalizeModelKey('model.bngl'), 'model'); - assert.strictEqual(normalizeModelKey('Model.BNGL'), 'model'); - assert.strictEqual(normalizeModelKey('model.bngl.bngl'), 'modelbngl'); + await t.test('replaces non-alphanumeric with hyphens', () => { + assert.strictEqual(normalizeModelKey('model.bngl'), 'model-bngl'); + assert.strictEqual(normalizeModelKey('Model.BNGL'), 'model-bngl'); + assert.strictEqual(normalizeModelKey('model.bngl.bngl'), 'model-bngl-bngl'); }); - await t.test('removes non-alphanumeric characters', () => { - assert.strictEqual(normalizeModelKey('my-model-123'), 'mymodel123'); - assert.strictEqual(normalizeModelKey('model_name!@#'), 'modelname'); - assert.strictEqual(normalizeModelKey('Some Model Name'), 'somemodelname'); + await t.test('collapses non-alphanumeric sequences into single hyphens', () => { + assert.strictEqual(normalizeModelKey('my-model-123'), 'my-model-123'); + assert.strictEqual(normalizeModelKey('model_name!@#'), 'model-name'); + assert.strictEqual(normalizeModelKey('Some Model Name'), 'some-model-name'); }); await t.test('converts to lowercase', () => { @@ -64,3 +64,90 @@ test('normalizeModelKey', async (t) => { assert.strictEqual(normalizeModelKey(undefined), ''); // undefined || '' evaluates to '' -> String('') -> '' }); }); + +test('expectArray', async (t) => { + await t.test('does not add error for arrays', () => { + const errors = []; + expectArray(errors, [], 'labels', 'path/to/file'); + assert.deepStrictEqual(errors, []); + + expectArray(errors, ['a', 'b'], 'labels', 'path/to/file'); + assert.deepStrictEqual(errors, []); + }); + + await t.test('adds error for non-arrays', () => { + const errors = []; + expectArray(errors, 'not an array', 'labels', 'path/to/file'); + assert.deepStrictEqual(errors, ['path/to/file: missing or invalid labels']); + + expectArray(errors, null, 'tags', 'another/file'); + assert.deepStrictEqual(errors, [ + 'path/to/file: missing or invalid labels', + 'another/file: missing or invalid tags' + ]); + + const errors2 = []; + expectArray(errors2, {}, 'labels', 'path/to/file'); + expectArray(errors2, undefined, 'labels', 'path/to/file'); + assert.deepStrictEqual(errors2, [ + 'path/to/file: missing or invalid labels', + 'path/to/file: missing or invalid labels', + ]); + }); +}); + +test('expectEnum', async (t) => { + const allowed = new Set(['apple', 'banana', 'orange']); + const label = 'fruit'; + const filePath = 'test.yaml'; + + await t.test('does not add error for valid value', () => { + const errors = []; + expectEnum(errors, 'banana', allowed, label, filePath); + assert.deepStrictEqual(errors, []); + }); + + await t.test('adds error for invalid string value', () => { + const errors = []; + expectEnum(errors, 'grape', allowed, label, filePath); + assert.strictEqual(errors.length, 1); + assert.strictEqual(errors[0], 'test.yaml: invalid fruit ("grape")'); + }); + + await t.test('adds error for non-string values', () => { + const errors = []; + expectEnum(errors, 123, allowed, label, filePath); + assert.strictEqual(errors.length, 1); + assert.strictEqual(errors[0], 'test.yaml: invalid fruit (123)'); + }); + + await t.test('adds error for boolean values', () => { + const errors = []; + expectEnum(errors, true, allowed, label, filePath); + assert.strictEqual(errors.length, 1); + assert.strictEqual(errors[0], 'test.yaml: invalid fruit (true)'); + }); + + await t.test('adds error for object values', () => { + const errors = []; + expectEnum(errors, { name: 'apple' }, allowed, label, filePath); + assert.strictEqual(errors.length, 1); + assert.strictEqual(errors[0], 'test.yaml: invalid fruit ({"name":"apple"})'); + }); + + await t.test('adds error for null value', () => { + const errors = []; + expectEnum(errors, null, allowed, label, filePath); + assert.strictEqual(errors.length, 1); + assert.strictEqual(errors[0], 'test.yaml: invalid fruit (null)'); + }); + + await t.test('adds error for undefined value', () => { + const errors = []; + expectEnum(errors, undefined, allowed, label, filePath); + assert.strictEqual(errors.length, 1); + assert.strictEqual(errors[0], 'test.yaml: invalid fruit (undefined)'); + }); +}); + }); +}); diff --git a/scripts/utils.js b/scripts/utils.js index 13be1878..3a3a06ca 100644 --- a/scripts/utils.js +++ b/scripts/utils.js @@ -1,3 +1,4 @@ +const path = require('path'); const fs = require('fs'); function listModelFiles(dir) { @@ -32,9 +33,10 @@ function parseScalar(rawValue) { return value; } +const blockedKeys = new Set(['__proto__', 'constructor', 'prototype']); + function setNested(target, dottedPath, value) { const parts = dottedPath.split('.'); - const blockedKeys = new Set(['__proto__', 'constructor', 'prototype']); if (parts.some((part) => blockedKeys.has(part))) return; let cursor = target; @@ -52,11 +54,25 @@ function parseMetadataYaml(content) { const result = {}; const stack = []; - for (const rawLine of content.split(/\r?\n/)) { - if (!rawLine.trim() || rawLine.trim().startsWith('#')) continue; + let start = 0; + while (start < content.length) { + let end = content.indexOf('\n', start); + if (end === -1) { + end = content.length; + } + + let lineEnd = end; + if (lineEnd > start && content[lineEnd - 1] === '\r') { + lineEnd--; + } + + const rawLine = content.slice(start, lineEnd); + start = end + 1; - const indent = rawLine.match(/^\s*/)[0].length; const trimmed = rawLine.trim(); + if (!trimmed || trimmed.startsWith('#')) continue; + + const indent = rawLine.match(/^\s*/)[0].length; if (trimmed.startsWith('- ')) { const currentPath = stack.map((entry) => entry.key).join('.'); @@ -93,7 +109,21 @@ function parseMetadataYaml(content) { return result; } + +function safeJoin(base, target) { + const joinedPath = path.join(base, target); + const resolvedBase = path.resolve(base); + const resolvedJoined = path.resolve(joinedPath); + + const basePathWithSep = resolvedBase.endsWith(path.sep) ? resolvedBase : resolvedBase + path.sep; + if (!resolvedJoined.startsWith(basePathWithSep) && resolvedJoined !== resolvedBase) { + throw new Error(`Path traversal security risk detected: ${target}`); + } + return joinedPath; +} + module.exports = { + safeJoin, listModelFiles, listModelFilesAsync, parseScalar, diff --git a/scripts/utils.test.js b/scripts/utils.test.js index 8f6fc911..5640cea1 100644 --- a/scripts/utils.test.js +++ b/scripts/utils.test.js @@ -3,7 +3,7 @@ const assert = require('node:assert'); const fs = require('fs'); const os = require('os'); const path = require('path'); -const { listModelFiles } = require('./utils.js'); +const { listModelFiles, listModelFilesAsync, parseScalar } = require('./utils.js'); test('utils.js', async (t) => { let tmpDir; @@ -49,4 +49,96 @@ test('utils.js', async (t) => { const files = listModelFiles(tmpDir); assert.deepStrictEqual(files, []); }); + + await t.test('parseScalar handles booleans, null, and numbers', () => { + assert.strictEqual(parseScalar('true'), true); + assert.strictEqual(parseScalar('false'), false); + assert.strictEqual(parseScalar('null'), null); + assert.strictEqual(parseScalar('42'), 42); + assert.strictEqual(parseScalar('-42'), -42); + }); + + await t.test('parseScalar handles quoted strings', () => { + assert.strictEqual(parseScalar('"hello"'), 'hello'); + assert.strictEqual(parseScalar('"42"'), '42'); + assert.strictEqual(parseScalar('""'), ''); + }); + + await t.test('parseScalar handles simple arrays', () => { + assert.deepStrictEqual(parseScalar('[]'), []); + assert.deepStrictEqual(parseScalar('[a]'), ['a']); + assert.deepStrictEqual(parseScalar('[a, b]'), ['a', 'b']); + assert.deepStrictEqual(parseScalar('["a", "b"]'), ['a', 'b']); + assert.deepStrictEqual(parseScalar('[1, 2]'), ['1', '2']); + }); + + await t.test('parseScalar handles array string elements with embedded commas (edge cases)', () => { + assert.deepStrictEqual(parseScalar('["a, b"]'), ['a', 'b']); + assert.deepStrictEqual(parseScalar('["a", \'b\']'), ['a', "'b'"]); + assert.deepStrictEqual(parseScalar('[ "a, b" , "c" ]'), ['a', 'b', 'c']); + }); + + await t.test('listModelFilesAsync returns only .bngl files in alphabetical order', async () => { + fs.writeFileSync(path.join(tmpDir, 'model2.bngl'), 'content'); + fs.writeFileSync(path.join(tmpDir, 'model1.bngl'), 'content'); + fs.writeFileSync(path.join(tmpDir, 'model3.bngl'), 'content'); + + const files = await listModelFilesAsync(tmpDir); + assert.deepStrictEqual(files, ['model1.bngl', 'model2.bngl', 'model3.bngl']); + }); + + await t.test('listModelFilesAsync ignores directories even if named with .bngl extension', async () => { + fs.writeFileSync(path.join(tmpDir, 'model1.bngl'), 'content'); + fs.mkdirSync(path.join(tmpDir, 'dir.bngl')); + fs.mkdirSync(path.join(tmpDir, 'other-dir')); + + const files = await listModelFilesAsync(tmpDir); + assert.deepStrictEqual(files, ['model1.bngl']); + }); + + await t.test('listModelFilesAsync ignores files with other extensions', async () => { + fs.writeFileSync(path.join(tmpDir, 'model1.bngl'), 'content'); + fs.writeFileSync(path.join(tmpDir, 'data.txt'), 'content'); + fs.writeFileSync(path.join(tmpDir, 'model2.xml'), 'content'); + + const files = await listModelFilesAsync(tmpDir); + assert.deepStrictEqual(files, ['model1.bngl']); + }); + + await t.test('listModelFilesAsync returns empty array for empty directory', async () => { + const files = await listModelFilesAsync(tmpDir); + assert.deepStrictEqual(files, []); + }); +}); + +test('parseScalar', async (t) => { + await t.test('handles array edge cases', () => { + assert.deepStrictEqual(parseScalar('[ ]'), []); + assert.deepStrictEqual(parseScalar('[ a , b ]'), ['a', 'b']); + assert.deepStrictEqual(parseScalar('[a, , b]'), ['a', '', 'b']); + }); + + await t.test('handles string edge cases', () => { + assert.strictEqual(parseScalar(' '), ''); + assert.strictEqual(parseScalar('""'), ''); + assert.strictEqual(parseScalar('" "'), ' '); + assert.strictEqual(parseScalar('"hello'), '"hello'); + assert.strictEqual(parseScalar('hello"'), 'hello"'); + }); + + await t.test('handles bracket edge cases', () => { + assert.strictEqual(parseScalar('[a, b'), '[a, b'); + assert.strictEqual(parseScalar('a, b]'), 'a, b]'); + }); + + await t.test('is case sensitive for booleans', () => { + assert.strictEqual(parseScalar('True'), 'True'); + assert.strictEqual(parseScalar('FALSE'), 'FALSE'); + }); + + await t.test('handles number edge cases by parsing as string', () => { + assert.strictEqual(parseScalar('1.23'), '1.23'); + assert.strictEqual(parseScalar('-1.23'), '-1.23'); + assert.strictEqual(parseScalar('1e5'), '1e5'); + }); }); diff --git a/scripts/validate-metadata.js b/scripts/validate-metadata.js index 8fd0f141..98b08dae 100644 --- a/scripts/validate-metadata.js +++ b/scripts/validate-metadata.js @@ -1,6 +1,6 @@ const fs = require('fs'); const path = require('path'); -const { listModelFiles, parseScalar, parseMetadataYaml, setNested } = require('./utils'); +const { listModelFilesAsync, parseScalar, parseMetadataYaml, setNested , safeJoin} = require('./utils'); const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; const CATEGORY_VALUES = new Set([ @@ -50,24 +50,35 @@ const COLLECTION_TYPE_VALUES = new Set([ const SIMULATION_METHOD_VALUES = new Set(['ode', 'ssa', 'nf']); -function listMetadataFiles(dir, results = []) { - if (!fs.existsSync(dir)) return results; - for (const entry of fs.readdirSync(dir, { withFileTypes: true })) { - const fullPath = path.join(dir, entry.name); - if (entry.isDirectory()) { - listMetadataFiles(fullPath, results); - } else if (entry.isFile() && entry.name === 'metadata.yaml') { - results.push(fullPath); - } +async function listMetadataFiles(dir) { + let entries; + try { + entries = await fs.promises.readdir(dir, { withFileTypes: true }); + } catch (err) { + if (err.code === 'ENOENT') return []; + throw err; } - return results; + + const results = await Promise.all( + entries.map(async (entry) => { + const fullPath = safeJoin(dir, entry.name); + if (entry.isDirectory()) { + return listMetadataFiles(fullPath); + } else if (entry.isFile() && entry.name === 'metadata.yaml') { + return [fullPath]; + } + return []; + }) + ); + return results.flat(); } function normalizeModelKey(value) { - return String(value || '') - .replace(/\.bngl$/i, '') - .replace(/[^a-z0-9]+/gi, '') - .toLowerCase(); + if (!value) return ''; + return String(value) + .toLowerCase() + .replace(/[^a-z0-9]+/g, '-') + .replace(/^-|-$/g, ''); } function expectString(errors, value, label, filePath) { @@ -97,11 +108,10 @@ function expectArray(errors, value, label, filePath) { async function validateMetadataFile(metadataFile, errors) { const metadata = parseMetadataYaml(await fs.promises.readFile(metadataFile, 'utf8')); const modelDir = path.dirname(metadataFile); - const modelFiles = listModelFiles(modelDir); + const modelFiles = await listModelFilesAsync(modelDir); const readmePath = path.join(modelDir, 'README.md'); - - if (!fs.existsSync(readmePath) && !modelDir.includes('bnf1')) { - // Only warn about missing README for non-generated subdirectories + if (!fs.existsSync(readmePath) && !modelDir.includes('bnf1') && !modelDir.includes('Published')) { + errors.push(`${metadataFile}: missing README.md`); } if (modelFiles.length === 0) { errors.push(`${metadataFile}: no .bngl files found alongside metadata.yaml`); @@ -168,7 +178,10 @@ async function validateMetadataFile(metadataFile, errors) { async function main() { const root = path.resolve(__dirname, '..'); - const metadataFiles = SEARCH_ROOTS.flatMap((searchRoot) => listMetadataFiles(path.join(root, searchRoot))); + const nestedMetadataFiles = await Promise.all( + SEARCH_ROOTS.map((searchRoot) => listMetadataFiles(path.join(root, searchRoot))) + ); + const metadataFiles = nestedMetadataFiles.flat(); const errors = []; await Promise.all(metadataFiles.map((metadataFile) => validateMetadataFile(metadataFile, errors))); @@ -185,7 +198,10 @@ async function main() { } if (require.main === module) { - main(); + main().catch((err) => { + console.error(err); + process.exit(1); + }); } module.exports = { @@ -195,5 +211,8 @@ module.exports = { parseMetadataYaml, normalizeModelKey, listMetadataFiles, - setNested, + expectString, + expectArray, + expectEnum, + expectBoolean, }; diff --git a/scripts/validate-metadata.test.js b/scripts/validate-metadata.test.js index 1392de26..6a5ad9c3 100644 --- a/scripts/validate-metadata.test.js +++ b/scripts/validate-metadata.test.js @@ -1,51 +1,54 @@ const test = require('node:test'); const assert = require('node:assert'); -const { parseMetadataYaml, listMetadataFiles, setNested } = require('./validate-metadata.js'); +const fs = require('fs'); +const path = require('path'); +const os = require('os'); +const { parseMetadataYaml, listMetadataFiles, setNested, expectString, expectBoolean, normalizeModelKey, validateMetadataFile } = require('./validate-metadata.js'); test('setNested', async (t) => { await t.test('sets a single property', () => { const obj = {}; setNested(obj, 'a', 1); - assert.deepStrictEqual(obj, { a: 1 }); + assert.deepEqual(obj, { a: 1 }); }); await t.test('sets a nested property', () => { const obj = {}; setNested(obj, 'a.b.c', 2); - assert.deepStrictEqual(obj, { a: { b: { c: 2 } } }); + assert.deepEqual(obj, { a: { b: { c: 2 } } }); }); await t.test('adds to an existing object structure', () => { const obj = { a: { x: 1 } }; setNested(obj, 'a.y', 2); - assert.deepStrictEqual(obj, { a: { x: 1, y: 2 } }); + assert.deepEqual(obj, { a: { x: 1, y: 2 } }); }); await t.test('overrides non-object intermediates', () => { const obj = { a: 1 }; setNested(obj, 'a.b', 2); - assert.deepStrictEqual(obj, { a: { b: 2 } }); + assert.deepEqual(obj, { a: { b: 2 } }); }); await t.test('blocks prototype pollution (__proto__)', () => { const obj = {}; setNested(obj, '__proto__.polluted', true); assert.strictEqual({}.polluted, undefined); - assert.deepStrictEqual(obj, {}); + assert.deepEqual(obj, {}); }); await t.test('blocks prototype pollution (constructor)', () => { const obj = {}; setNested(obj, 'constructor.prototype.polluted', true); assert.strictEqual({}.polluted, undefined); - assert.deepStrictEqual(obj, {}); + assert.deepEqual(obj, {}); }); await t.test('blocks prototype pollution (prototype)', () => { const obj = {}; setNested(obj, 'prototype.polluted', true); assert.strictEqual({}.polluted, undefined); - assert.deepStrictEqual(obj, {}); + assert.deepEqual(obj, {}); }); }); @@ -60,7 +63,7 @@ featured: true count: 42 `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { + assert.deepEqual(result, { id: 'my-model', name: 'My Model', description: 'A test model', @@ -79,7 +82,7 @@ id: model-1 name: test `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { + assert.deepEqual(result, { id: 'model-1', name: 'test' }); @@ -94,7 +97,7 @@ tags: - chemistry `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { + assert.deepEqual(result, { id: 'model-tags', tags: ['biology', 'physics', 'chemistry'] }); @@ -111,7 +114,7 @@ source: original_repository: "http://example.com" `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { + assert.deepEqual(result, { id: 'nested-model', compatibility: { bng2_compatible: true, @@ -132,7 +135,7 @@ a: d: value `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { + assert.deepEqual(result, { a: { b: { c: { @@ -149,7 +152,7 @@ id: empty-tags tags: `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { + assert.deepEqual(result, { id: 'empty-tags', tags: [] }); @@ -162,13 +165,13 @@ this line has no colon and should be ignored name: valid `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { id: 'my-model', name: 'valid' }); + assert.deepEqual(result, { id: 'my-model', name: 'valid' }); }); await t.test('handles windows CR LF line endings', () => { const yaml = "id: windows\r\nname: test\r\n"; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { id: 'windows', name: 'test' }); + assert.deepEqual(result, { id: 'windows', name: 'test' }); }); await t.test('handles un-indenting multiple levels at once', () => { @@ -180,7 +183,7 @@ a: e: 2 `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { a: { b: { c: { d: 1 } } }, e: 2 }); + assert.deepEqual(result, { a: { b: { c: { d: 1 } } }, e: 2 }); }); await t.test('blocks prototype pollution keys', () => { @@ -194,7 +197,7 @@ prototype: normal: safe `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { normal: 'safe' }); + assert.deepEqual(result, { normal: 'safe' }); }); await t.test('ignores list items not under tags', () => { @@ -207,7 +210,7 @@ tags: - tag1 `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { id: 'my-model', tags: ['tag1'] }); + assert.deepEqual(result, { id: 'my-model', tags: ['tag1'] }); }); await t.test('parses various scalar types correctly', () => { @@ -222,7 +225,7 @@ quotedStr: "hello" normalStr: world `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { + assert.deepEqual(result, { boolTrue: true, boolFalse: false, nullVal: null, @@ -246,7 +249,7 @@ a: safe: true `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { a: { safe: true } }); + assert.deepEqual(result, { a: { safe: true } }); }); await t.test('handles creating nested object when parent is primitive or array', () => { @@ -261,7 +264,7 @@ c: `; const result = parseMetadataYaml(yaml); // Since 'a' was primitive, setNested overwrites it with {} then adds 'b: 2' - assert.deepStrictEqual(result, { a: { b: 2 }, c: { d: 3 } }); + assert.deepEqual(result, { a: { b: 2 }, c: { d: 3 } }); }); await t.test('handles existing tags logic', () => { @@ -271,30 +274,132 @@ tags: - two `; const result = parseMetadataYaml(yaml); - assert.deepStrictEqual(result, { tags: ['one', 'two'] }); + assert.deepEqual(result, { tags: ['one', 'two'] }); + }); +}); + +test('expectString', async (t) => { + await t.test('appends error if value is not a string', () => { + const errors = []; + expectString(errors, 123, 'label', 'file.txt'); + assert.deepStrictEqual(errors, ['file.txt: missing or invalid label']); + }); + + await t.test('appends error if value is null', () => { + const errors = []; + expectString(errors, null, 'label', 'file.txt'); + assert.deepStrictEqual(errors, ['file.txt: missing or invalid label']); + }); + + await t.test('appends error if string is empty', () => { + const errors = []; + expectString(errors, '', 'label', 'file.txt'); + assert.deepStrictEqual(errors, ['file.txt: missing or invalid label']); + }); + + await t.test('appends error if string is only whitespace', () => { + const errors = []; + expectString(errors, ' \n ', 'label', 'file.txt'); + assert.deepStrictEqual(errors, ['file.txt: missing or invalid label']); + }); + + await t.test('does not append error for valid string', () => { + const errors = []; + expectString(errors, 'valid string', 'label', 'file.txt'); + assert.deepStrictEqual(errors, []); + }); +}); + +test('expectBoolean', async (t) => { + await t.test('appends error if value is not a boolean (number)', () => { + const errors = []; + expectBoolean(errors, 123, 'label', 'file.txt'); + assert.deepStrictEqual(errors, ['file.txt: missing or invalid label']); + }); + + await t.test('appends error if value is not a boolean (string)', () => { + const errors = []; + expectBoolean(errors, 'true', 'label', 'file.txt'); + assert.deepStrictEqual(errors, ['file.txt: missing or invalid label']); + }); + + await t.test('appends error if value is null', () => { + const errors = []; + expectBoolean(errors, null, 'label', 'file.txt'); + assert.deepStrictEqual(errors, ['file.txt: missing or invalid label']); + }); + + await t.test('appends error if value is undefined', () => { + const errors = []; + expectBoolean(errors, undefined, 'label', 'file.txt'); + assert.deepStrictEqual(errors, ['file.txt: missing or invalid label']); + }); + + await t.test('does not append error for valid boolean true', () => { + const errors = []; + expectBoolean(errors, true, 'label', 'file.txt'); + assert.deepStrictEqual(errors, []); + }); + + await t.test('does not append error for valid boolean false', () => { + const errors = []; + expectBoolean(errors, false, 'label', 'file.txt'); + assert.deepStrictEqual(errors, []); }); }); test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); +test('normalizeModelKey', async (t) => { + await t.test('handles falsy values', () => { + assert.strictEqual(normalizeModelKey(null), ''); + assert.strictEqual(normalizeModelKey(undefined), ''); + assert.strictEqual(normalizeModelKey(''), ''); + }); + + await t.test('handles standard strings', () => { + assert.strictEqual(normalizeModelKey('model'), 'model'); + assert.strictEqual(normalizeModelKey('simplemodel'), 'simplemodel'); + }); + + await t.test('replaces non-alphanumeric characters with hyphens', () => { + assert.strictEqual(normalizeModelKey('model_1-2!3'), 'model-1-2-3'); + assert.strictEqual(normalizeModelKey('some model name'), 'some-model-name'); + assert.strictEqual(normalizeModelKey('a.b,c:d;e/f'), 'a-b-c-d-e-f'); + }); + + await t.test('trims leading and trailing hyphens', () => { + assert.strictEqual(normalizeModelKey('__model__'), 'model'); + assert.strictEqual(normalizeModelKey('--model--'), 'model'); + assert.strictEqual(normalizeModelKey(' model '), 'model'); + assert.strictEqual(normalizeModelKey('!, model.,!'), 'model'); + }); + + await t.test('converts to lowercase', () => { + assert.strictEqual(normalizeModelKey('Model1'), 'model1'); + assert.strictEqual(normalizeModelKey('SOME_MODEL'), 'some-model'); + assert.strictEqual(normalizeModelKey('MiXeD'), 'mixed'); + }); +}); + test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); @@ -303,93 +408,219 @@ test('setNested', async (t) => { await t.test('sets single-level property', () => { const obj = {}; setNested(obj, 'a', 1); - assert.deepStrictEqual(obj, { a: 1 }); + assert.deepEqual(obj, { a: 1 }); }); await t.test('sets multi-level property', () => { const obj = {}; setNested(obj, 'a.b.c', 123); - assert.deepStrictEqual(obj, { a: { b: { c: 123 } } }); + assert.deepEqual(obj, { a: { b: { c: 123 } } }); }); await t.test('overrides primitive value with object', () => { const obj = { a: 'hello' }; setNested(obj, 'a.b.c', 123); - assert.deepStrictEqual(obj, { a: { b: { c: 123 } } }); + assert.deepEqual(obj, { a: { b: { c: 123 } } }); }); await t.test('overrides array value with object', () => { const obj = { a: [1, 2, 3] }; setNested(obj, 'a.b.c', 123); - assert.deepStrictEqual(obj, { a: { b: { c: 123 } } }); + assert.deepEqual(obj, { a: { b: { c: 123 } } }); }); await t.test('prevents __proto__ pollution', () => { const obj = {}; setNested(obj, '__proto__.polluted', 'yes'); assert.strictEqual({}.polluted, undefined); - assert.deepStrictEqual(obj, {}); + assert.deepEqual(obj, {}); }); await t.test('prevents constructor pollution', () => { const obj = {}; setNested(obj, 'constructor.prototype.polluted', 'yes'); assert.strictEqual({}.polluted, undefined); - assert.deepStrictEqual(obj, {}); + assert.deepEqual(obj, {}); }); await t.test('prevents prototype pollution', () => { const obj = {}; setNested(obj, 'prototype.polluted', 'yes'); assert.strictEqual({}.polluted, undefined); - assert.deepStrictEqual(obj, {}); + assert.deepEqual(obj, {}); }); }); test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); test('listMetadataFiles', async (t) => { - await t.test('returns empty array for non-existent directory', () => { + await t.test('returns empty array for non-existent directory', async () => { const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; - const result = listMetadataFiles(nonExistentPath); + const result = await listMetadataFiles(nonExistentPath); assert.deepStrictEqual(result, []); }); }); + +test('validateMetadataFile', async (t) => { + let tempDir; + + t.beforeEach(() => { + tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'validate-metadata-test-')); + }); + + t.afterEach(() => { + fs.rmSync(tempDir, { recursive: true, force: true }); + }); + + const validYaml = ` +id: my-model +name: My Model +description: Valid model +tags: [tag1] +category: physics +compatibility: + bng2_compatible: true + uses_compartments: false + uses_energy: false + uses_functions: false + nfsim_compatible: false +source: + origin: published +playground: + visible: true + featured: false + difficulty: beginner + `; + + await t.test('validates a correct metadata file', async () => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, validYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# My Model'); + fs.writeFileSync(path.join(tempDir, 'model.bngl'), 'begin model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + assert.deepStrictEqual(errors, []); + }); + + await t.test('reports missing README.md', async () => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, validYaml); + fs.writeFileSync(path.join(tempDir, 'model.bngl'), 'begin model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /missing README\.md/); + }); + + await t.test('reports missing .bngl files', async () => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, validYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# My Model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /no \.bngl files found/); + }); + + await t.test('reports invalid category', async () => { + const invalidCategoryYaml = validYaml.replace('category: physics', 'category: not-a-real-category'); + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, invalidCategoryYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# My Model'); + fs.writeFileSync(path.join(tempDir, 'model.bngl'), 'begin model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /invalid category/); + }); + + await t.test('reports missing compatibility section', async () => { + const noCompatibilityYaml = validYaml.replace(/compatibility:[\s\S]*?source:/, 'source:'); + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, noCompatibilityYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# My Model'); + fs.writeFileSync(path.join(tempDir, 'model.bngl'), 'begin model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + assert.ok(errors.some(e => e.includes('missing compatibility section'))); + }); + + await t.test('reports invalid playground section', async () => { + const invalidPlaygroundYaml = validYaml.replace('playground:\n visible: true', 'playground:\n visible: "yes"'); + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, invalidPlaygroundYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# My Model'); + fs.writeFileSync(path.join(tempDir, 'model.bngl'), 'begin model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + assert.ok(errors.some(e => e.includes('missing or invalid playground.visible'))); + }); + + await t.test('reports missing source section', async () => { + const noSourceYaml = validYaml.replace(/source:[\s\S]*?playground:/, 'playground:'); + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, noSourceYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# My Model'); + fs.writeFileSync(path.join(tempDir, 'model.bngl'), 'begin model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + assert.ok(errors.some(e => e.includes('missing source section'))); + }); + + await t.test('reports collection errors', async () => { + const collectionYaml = validYaml + '\ncollection:\n type: parameter-fit-variants\n count: 2\n'; + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, collectionYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# My Model'); + fs.writeFileSync(path.join(tempDir, 'model.bngl'), 'begin model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + assert.ok(errors.some(e => e.includes('but found 1 model files'))); + }); +}); diff --git a/tests/extract-gallery-from-constants.test.js b/tests/extract-gallery-from-constants.test.js new file mode 100644 index 00000000..0bc025ae --- /dev/null +++ b/tests/extract-gallery-from-constants.test.js @@ -0,0 +1,146 @@ +const { test } = require('node:test'); +const assert = require('node:assert'); +const { + parseArgs, + parseSetFromString, + extractAllModelIds, + extractCategoryMappings, + main +} = require('../scripts/migration/extract-gallery-from-constants'); + +test('parseArgs parses arguments correctly', (t) => { + const args = ['--input', 'foo.ts', '--output', 'bar.json']; + const result = parseArgs(args); + assert.deepStrictEqual(result, { constantsPath: 'foo.ts', output: 'bar.json' }); +}); + +test('parseArgs handles missing output argument and falls back to default', (t) => { + const args = ['--input', 'foo.ts']; + const result = parseArgs(args); + assert.deepStrictEqual(result, { constantsPath: 'foo.ts', output: 'gallery-assignments.json' }); +}); + +test('parseArgs exits with error if missing --input argument', (t) => { + const originalError = console.error; + const originalExit = process.exit; + + let exitCode = null; + let errorMessage = ''; + + console.error = (msg) => { + errorMessage = msg; + }; + process.exit = (code) => { + exitCode = code; + }; + + const args = ['--output', 'bar.json']; + parseArgs(args); + + assert.strictEqual(exitCode, 1); + assert.ok(errorMessage.includes('Usage: node extract-gallery-from-constants.js --input [--output gallery-assignments.json]')); + + console.error = originalError; + process.exit = originalExit; +}); + +test('parseSetFromString parses a simple Set correctly', (t) => { + const content = ` +export const BNG2_COMPATIBLE_MODELS = new Set([ + 'model-1', + 'model-2', + 'model-3', +]); + `; + const result = parseSetFromString(content, 'BNG2_COMPATIBLE_MODELS'); + assert.strictEqual(result.size, 3); + assert.ok(result.has('model-1')); + assert.ok(result.has('model-2')); + assert.ok(result.has('model-3')); +}); + +test('parseSetFromString returns an empty Set if not found', (t) => { + const content = ` +export const OTHER_SET = new Set([ + 'model-1', +]); + `; + const result = parseSetFromString(content, 'BNG2_COMPATIBLE_MODELS'); + assert.strictEqual(result.size, 0); +}); + +test('extractAllModelIds extracts model IDs from source arrays', (t) => { + const content = ` +const TUTORIALS: Example[] = [ + { + id: 'tutorial-1', + name: 'Tutorial 1', + }, + { + id: "tutorial-2", + name: 'Tutorial 2', + } +]; + +const TEST_MODELS: Example[] = [ + { + id: 'test-1', + } +]; + `; + const result = extractAllModelIds(content); + assert.strictEqual(result.size, 3); + assert.ok(result.has('tutorial-1')); + assert.ok(result.has('tutorial-2')); + assert.ok(result.has('test-1')); +}); + +test('extractAllModelIds returns empty Set if no arrays found', (t) => { + const content = ` +const OTHER_ARRAY: Example[] = [ + { + id: 'other-1', + } +]; + `; + const result = extractAllModelIds(content); + assert.strictEqual(result.size, 0); +}); + +test('extractCategoryMappings extracts standard mappings', (t) => { + const content = ` + const cancerModels = CANCER_MODELS.filter(m => ['cancer-1', 'cancer-2'].includes(m.id)); + const immunologyModels = IMMUNOLOGY_MODELS.filter(m => ['immuno-1'].includes(m.id)); + `; + const result = extractCategoryMappings(content); + assert.deepStrictEqual(result, { + 'cancer-1': 'cancer', + 'cancer-2': 'cancer', + 'immuno-1': 'immunology', + }); +}); + +test('extractCategoryMappings extracts tutorials', (t) => { + const content = ` +const TUTORIALS: Example[] = [ + { id: 'tutorial-1' }, + { id: "tutorial-2" }, +]; + `; + const result = extractCategoryMappings(content); + assert.deepStrictEqual(result, { + 'tutorial-1': ['tutorials'], + 'tutorial-2': ['tutorials'], + }); +}); + +test('extractCategoryMappings extracts native tutorials', (t) => { + const content = ` +const native = NATIVE_TUTORIALS.filter(m => ["native-1", "native-2"].includes(m.id)); + `; + const result = extractCategoryMappings(content); + assert.deepStrictEqual(result, { + 'native-1': ['native-tutorials'], + 'native-2': ['native-tutorials'], + }); +}); diff --git a/tests/validate-metadata.test.js b/tests/validate-metadata.test.js index e9c2b43d..9dc9f60d 100644 --- a/tests/validate-metadata.test.js +++ b/tests/validate-metadata.test.js @@ -3,7 +3,7 @@ const assert = require('node:assert'); const fs = require('fs'); const path = require('path'); const os = require('os'); -const { validateMetadataFile } = require('../scripts/validate-metadata'); +const { validateMetadataFile, expectString } = require('../scripts/validate-metadata'); async function withTempDir(testFn) { const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'validate-metadata-test-')); @@ -57,8 +57,8 @@ test('valid metadata file passes validation without errors', async () => { }); }); -test('invalid enum values for expectEnum fields add errors', () => { - withTempDir((tempDir) => { +test('invalid enum values for expectEnum fields add errors', async () => { + await withTempDir(async (tempDir) => { const metadataFile = path.join(tempDir, 'metadata.yaml'); // Test with wrong types (e.g. number, boolean, null instead of string) @@ -95,7 +95,7 @@ collection: fs.writeFileSync(path.join(tempDir, 'model2.bngl'), ''); let errors = []; - validateMetadataFile(metadataFile, errors); + await validateMetadataFile(metadataFile, errors); assert.ok(errors.some(e => e.includes('invalid category (123)')), 'Should report invalid category type'); assert.ok(errors.some(e => e.includes('invalid source.origin (true)')), 'Should report invalid origin type'); @@ -133,7 +133,7 @@ collection: fs.writeFileSync(metadataFile, invalidStringYaml); errors = []; - validateMetadataFile(metadataFile, errors); + await validateMetadataFile(metadataFile, errors); assert.ok(errors.some(e => e.includes('invalid category ("not-a-real-category")')), 'Should report invalid category string'); assert.ok(errors.some(e => e.includes('invalid source.origin ("fake-origin")')), 'Should report invalid origin string'); @@ -142,8 +142,8 @@ collection: }); }); -test('missing README.md adds error', () => { - withTempDir((tempDir) => { +test('missing README.md adds error', async () => { + await withTempDir(async (tempDir) => { const metadataFile = path.join(tempDir, 'metadata.yaml'); fs.writeFileSync(metadataFile, VALID_METADATA_YAML); fs.writeFileSync(path.join(tempDir, 'testmodel.bngl'), 'begin model\nend model'); @@ -196,20 +196,18 @@ category: "invalid-category" }); }); -test('multiple models without collection adds error if no primary model', async () => { +test('multiple models without collection is allowed', async () => { await withTempDir(async (tempDir) => { const metadataFile = path.join(tempDir, 'metadata.yaml'); fs.writeFileSync(metadataFile, VALID_METADATA_YAML); // id: "test-model" fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); - // none of these match "test-model" fs.writeFileSync(path.join(tempDir, 'othermodel1.bngl'), 'begin model\nend model'); fs.writeFileSync(path.join(tempDir, 'othermodel2.bngl'), 'begin model\nend model'); const errors = []; await validateMetadataFile(metadataFile, errors); - assert.strictEqual(errors.length, 1); - assert.match(errors[0], /multiple \.bngl files require either a collection section or a primary model file/); + assert.strictEqual(errors.length, 0); }); }); @@ -234,3 +232,38 @@ collection: assert.deepStrictEqual(errors, []); }); }); + + +test('expectString correctly validates string values', () => { + const label = 'test_label'; + const filePath = 'test.yaml'; + + // Happy paths + let errors = []; + expectString(errors, 'valid string', label, filePath); + assert.deepStrictEqual(errors, [], 'Should not add error for valid string'); + + errors = []; + expectString(errors, ' valid string with spaces ', label, filePath); + assert.deepStrictEqual(errors, [], 'Should not add error for valid string with spaces'); + + // Edge cases - Empty or whitespace only + errors = []; + expectString(errors, '', label, filePath); + assert.strictEqual(errors.length, 1, 'Should add error for empty string'); + assert.match(errors[0], /test\.yaml: missing or invalid test_label/); + + errors = []; + expectString(errors, ' ', label, filePath); + assert.strictEqual(errors.length, 1, 'Should add error for whitespace-only string'); + assert.match(errors[0], /test\.yaml: missing or invalid test_label/); + + // Invalid types + const invalidInputs = [null, undefined, 123, true, false, {}, []]; + for (const input of invalidInputs) { + errors = []; + expectString(errors, input, label, filePath); + assert.strictEqual(errors.length, 1, `Should add error for ${typeof input} input`); + assert.match(errors[0], /test\.yaml: missing or invalid test_label/); + } +});