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Changes made to experiments w.r.t new schema
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@hrani
hrani committed Apr 17, 2024
1 parent 3baba25 commit e5311fc
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Showing 44 changed files with 1,017 additions and 893 deletions.
142 changes: 94 additions & 48 deletions Curated/Bhalla1999_Fig2B.json
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Original file line number Diff line number Diff line change
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{
"ContentType": "Findsim",
"FileType": "Findsim",
"Version": "2.0",
"Metadata": {
"transcriber": "Nisha Ann Viswan",
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{
"timeUnits": "sec",
"quantityUnits": "mM",
"entity": {"name": "EGF","alias": "EGF"},
"entity": {"name": "EGF"},
"field": "conc",
"data": [[2100,0.0001]
"data": [
[2100,0.0001]
]
}
],
"Readouts": {
"timeUnits": "sec",
"quantityUnits": "ratio",
"entity": {
"name": "aMAPK",
"alias": "aMAPK"
},
"entity": {"name": "aMAPK"},
"field": "conc",
"normalization": {
"entity": {"name": "aMAPK","alias": "aMAPK"},
"entity": {"name": "aMAPK"},
"dose": 0,
"sampling": "presetTime",
"sampTime": 2400
Expand All @@ -56,59 +54,107 @@
]
},
"Modifications": {
"subset": [
{"name": "EGFR_g","alias": "EGFR_g"},
{"name": "Sos_g","alias": "Sos_g"},
{"name": "Ras_g","alias": "Ras_g"},
{"name": "MAPK_g","alias": "MAPK_g"},
{"name": "Ca_g","alias": "Ca_g"},
{"name": "PKC_g","alias": "PKC_g"},
{"name": "Phosphatase_g","alias": "Phosphatase_g"},
{"name": "PLCg_g","alias": "PLCg_g"},
{"name": "PLCb_g","alias": "PLCb_g"},
{"name": "PLA2_g","alias": "PLA2_g"},
{"name": "PC","alias": "PC"},
{"name": "IP3","alias": "IP3"},
{"name": "PIP2","alias": "PIP2"}
"subset": [
{"name": "EGFR_g"},{"name": "Sos_g"},{"name": "Ras_g"},{"name": "MAPK_g"},{"name": "Ca_g"},{"name": "PKC_g"},{"name": "Phosphatase_g"},{"name": "PLCg_g"},{"name": "PLCb_g"},{"name": "PLA2_g"},{"name": "PC"},{"name": "IP3"},{"name": "PIP2"
}
],
"itemsToDelete": [
{"name": "PP2A","alias": "PP2A"},
{"name": "phospho_AC2","alias": "phospho_AC2"},
{"name": "GEF_Gprot_bg","alias": "GEF_Gprot_bg"},
{"name": "bg_act_GEF","alias": "bg_act_GEF"},
{"name": "PP2A"},{"name": "phospho_AC2"},
{"name": "GEF_Gprot_bg"},
{"name": "bg_act_GEF"},
{"name": "ecraf+MAPKK","alias": "MEK_phospho"},
{"name": "ecraf+MAPKKp","alias": "MEKp_phospho"},
{"name": "craf1+barr2","alias": "mGluR_barr2_Raf"},
{"name": "eMAPK+S6K","alias": "clus_S6K_phospho"},
{"name": "eMAPK+4EBPpq","alias": "MAPK_4EBPpp"},
{"name": "eMAPK+eIF4EBPpq","alias": "MAPK_4EBP_phospho"},
{"name": "PLC_Ca+Gq","alias": "Act_PLC_by_Gq"},
{"name": "Inact_PLC_Gq","alias": "Inact_PLC_Gq"},
{"name": "PLC_bind_Gq","alias": "PLC_bind_Gq"},
{"name": "PKC_phospho_ng","alias": "PKC_phospho_ng"},
{"name": "PKC_phospho_ng_CaM","alias": "PKC_phospho_ng_CaM"},
{"name": "PIP2_PLA2_act","alias": "PIP2_PLA2_act"},
{"name": "PIP2_Ca_PLA2_act","alias": "PIP2_Ca_PLA2_act"},
{"name": "Inact_PLC_Gq"},
{"name": "PLC_bind_Gq"},
{"name": "PKC_phospho_ng"},
{"name": "PKC_phospho_ng_CaM"},
{"name": "PIP2_PLA2_act"},
{"name": "PIP2_Ca_PLA2_act"},
{"name": "CaMCa4+GEF","alias": "CaM_bind_GEF"},
{"name": "PI3K+RasGTP","alias": "PI3K_bind_RasGTP"},
{"name": "PIP2_phospho_Ras_GTP","alias": "PIP2_phospho_Ras_GTP"}
{"name": "PIP2_phospho_Ras_GTP"
}
],
"parameterChange": [
{"entity": {"name": "bPKC","alias": "bPKCp"},"field": "concInit","value": 2e-05,"units": "mM"},
{"entity": {"name": "GAP","alias": "GAP"},"field": "concInit","value": 2e-05,"units": "mM"},
{"entity": {"name": "PIP2","alias": "PIP2"},"field": "concInit","value": 0.007,"units": "mM"},
{"entity": {"name": "RasGDP","alias": "RasGDP"},"field": "concInit","value": 0.0005,"units": "mM"},
{"entity": {"name": "SHCp_deph","alias": "SHCp_deph"},"field": "Kf","value": 0.2,"units": "none"},
{"entity": {"name": "Ras+craf","alias": "Ras_act_craf"},"field": "Kf","value": 9999.2668,"units": "none"},
{"entity": {"name": "ePKC+craf","alias": "PKC_act_raf"},"field": "Km","value": 0.02098,"units": "none"},
{"entity": {"name": "eMKP1+MAPKp","alias": "MKP1pY421_deph"},"field": "Km","value": 0.00734,"units": "none"},
{"entity": {"name": "eMKP1+MAPKpq","alias": "MKP1pT424_deph"},"field": "Km","value": 0.00734,"units": "none"},
{"entity": {"name": "eMKP1+MAPKpq"},"field": "kcat","value": 4,"units": "none"},
{"entity": {"name": "eMKP1+MAPKp"},"field": "kcat","value": 4,"units": "none"},
{"entity": {"name": "eRas+MAPKK1","alias": "Rafp_RasGTP1"},"field": "kcat","value": 0.3,"units": "none"},
{"entity": {"name": "eRas+MAPKK2","alias": "Rafp_RasGTP2"},"field": "kcat","value": 0.3,"units": "none"},
{"entity": {"name": "eCaMGEF+Ras","alias": "CaMGEF_actRas"},"field": "kcat","value": 0.02,"units": "none"},
{"entity": {"name": "eSHCpSosGrb2+Ras","alias": "Sos_Ras_GEF"},"field": "kcat","value": 0.2,"units": "none"
{ "entity": {"name": "bPKC","alias": "bPKCp"},
"field": "concInit",
"value": 2e-05,
"units": "mM"
},
{ "entity": {"name": "GAP","alias": "GAP"},
"field": "concInit",
"value": 2e-05,
"units": "mM"
},
{ "entity": {"name": "PIP2","alias": "PIP2"},
"field": "concInit",
"value": 0.007,
"units": "mM"
},
{ "entity": {"name": "RasGDP","alias": "RasGDP"},
"field": "concInit",
"value": 0.0005,
"units": "mM"
},
{ "entity": {"name": "SHCp_deph","alias": "SHCp_deph"},
"field": "Kf",
"value": 0.2,
"units": "none"
},
{ "entity": {"name": "Ras+craf","alias": "Ras_act_craf"},
"field": "Kf",
"value": 9999.2668,
"units": "none"
},
{ "entity": {"name": "ePKC+craf","alias": "PKC_act_raf"},
"field": "Km",
"value": 0.02098,
"units": "none"
},
{ "entity": {"name": "eMKP1+MAPKp","alias": "MKP1pY421_deph"},
"field": "Km",
"value": 0.00734,
"units": "none"
},
{ "entity": {"name": "eMKP1+MAPKpq","alias": "MKP1pT424_deph"},
"field": "Km",
"value": 0.00734,
"units": "none"
},
{ "entity": {"name": "eMKP1+MAPKpq"},
"field": "kcat",
"value": 4,
"units": "none"
},
{ "entity": {"name": "eMKP1+MAPKp"},
"field": "kcat",
"value": 4,
"units": "none"
},
{ "entity": {"name": "eRas+MAPKK1","alias": "Rafp_RasGTP1"},
"field": "kcat",
"value": 0.3,
"units": "none"
},
{ "entity": {"name": "eRas+MAPKK2","alias": "Rafp_RasGTP2"},
"field": "kcat",
"value": 0.3,
"units": "none"
},
{ "entity": {"name": "eCaMGEF+Ras","alias": "CaMGEF_actRas"},
"field": "kcat",
"value": 0.02,
"units": "none"
},
{ "entity": {"name": "eSHCpSosGrb2+Ras","alias": "Sos_Ras_GEF"},
"field": "kcat",
"value": 0.2,
"units": "none"
}
],
"notes": "Bhalla1999_Fig2B"
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