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Converted all Json experiment file to support newschema,update map fi…
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…le for the new naming and small chages in findsim.py and simWrapMoose.py to accodomate the changes
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@hrani
hrani committed Apr 9, 2024
1 parent fd34817 commit e8ad517
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Showing 17 changed files with 1,704 additions and 1,674 deletions.
260 changes: 128 additions & 132 deletions Curated/Bhalla1999_Fig2B.json
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Original file line number Diff line number Diff line change
Expand Up @@ -25,158 +25,154 @@
{
"timeUnits": "sec",
"quantityUnits": "mM",
"entity": "EGF",
"entity" : {
"name": "EGF",
"alias": "EGF"
},
"field": "conc",
"data": [
[
2100,
0.0001
]
[2100,0.0001]
]
}
],
"Readouts": {
"timeUnits": "sec",
"quantityUnits": "ratio",
"entities": [
"aMAPK"
],
"entity" : {
"name": "aMAPK",
"alias": "aMAPK"
},
"field": "conc",
"normalization": {
"time": 2400,
"entities": [
"aMAPK"
],
"entity" : {
"name": "aMAPK",
"alias": "aMAPK"
},
"dose": 0,
"sampling": "presetTime"
"sampling": "presetTime",
"sampTime": 2400
},
"data": [
[
2100,
0.02,
0.06
],
[
2400,
1,
0
],
[
3900,
0.12,
0.17
],
[
5700,
0.1,
0.1
],
[
9300,
0.08,
0.08
]
[2100, 0.02, 0.06],
[2400, 1, 0],
[3900, 0.12, 0.17],
[5700, 0.1, 0.1],
[9300, 0.08, 0.08]
]
},
"Modifications": {
"subset": [
"EGFR_g",
"Sos_g",
"Ras_g",
"MAPK_g",
"Ca_g",
"PKC_g",
"Phosphatase_g",
"PLCg_g",
"PLCb_g",
"PLA2_g",
"PC",
"IP3",
"PIP2"
{"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"}
],
"itemsToDelete": [
"PP2A",
"phospho_AC2",
"GEF_Gprot_bg",
"bg_act_GEF",
"MEK_phospho",
"MEKp_phospho",
"mGluR_barr2_Raf",
"clus_S6K_phospho",
"MAPK_4EBPpp",
"MAPK_4EBP_phospho",
"Act_PLC_by_Gq",
"Inact_PLC_Gq",
"PLC_bind_Gq",
"PKC_phospho_ng",
"PKC_phospho_ng_CaM",
"PIP2_PLA2_act",
"PIP2_Ca_PLA2_act",
"CaM_bind_GEF",
"PI3K_bind_RasGTP",
"PIP2_phospho_Ras_GTP"
{"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":"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":"CaMCa4+GEF","alias":"CaM_bind_GEF"},{"name":"PI3K+RasGTP","alias":"PI3K_bind_RasGTP"},{"name":"PIP2_phospho_Ras_GTP","alias":"PIP2_phospho_Ras_GTP"}
],
"parameterChange" :
[{"entity": "bPKCp",
"field": "concInit",
"value" :2.00E-05,
"units" :"mM"},
{"entity": "GAP",
"field": "concInit",
"value" :2.0E-5,
"units" :"mM"},
{"entity": "PIP2",
"field": "concInit",
"value" :0.007,
"units" :"mM"},
{"entity": "RasGDP",
"field": "concInit",
"value" :0.0005,
"units" :"mM"},
{"entity": "SHCp_deph",
"field": "Kf",
"value" :0.2,
"units" :"none"},
{"entity": "Ras_act_craf",
"field": "Kf",
"value" :9999.2668,
"units" :"none"},
{"entity": "PKC_act_raf",
"field": "Km",
"value" :0.02098,
"units" :"none"},
{"entity": "MKP1pY421_deph",
"field": "Km",
"value" :0.00734,
"units" :"none"},
{"entity": "MKP1pT424_deph",
"field": "Km",
"value" :0.00734,
"units" :"none"},
{"entity": "MKP1pT424_deph",
"field": "kcat",
"value" :4,
"units" :"none"},
{"entity": "MKP1pY421_deph",
"field": "kcat",
"value" :4,
"units" :"none"},
{"entity": "Rafp_RasGTP1",
"field": "kcat",
"value" :0.3,
"units" :"none"},
{"entity": "Rafp_RasGTP2",
"field": "kcat",
"value" :0.3,
"units" :"none"},
{"entity": "CaMGEF_actRas",
"field": "kcat",
"value" :0.02,
"units" :"none"},
{"entity": "Sos_Ras_GEF",
"field": "kcat",
"value" :0.2,
"units" :"none"}
"parameterChange": [
{
"name": "bPKC",
"alias": "bPKCp",
"field": "concInit",
"value": 2e-05,
"units": "mM"
},
{
"name": "GAP",
"alias": "GAP",
"field": "concInit",
"value": 2e-05,
"units": "mM"
},
{
"name": "PIP2",
"alias": "PIP2",
"field": "concInit",
"value": 0.007,
"units": "mM"
},
{
"name": "RasGDP",
"alias": "RasGDP",
"field": "concInit",
"value": 0.0005,
"units": "mM"
},
{
"name": "SHCp_deph",
"alias": "SHCp_deph",
"field": "Kf",
"value": 0.2,
"units": "none"
},
{
"name": "Ras+craf",
"alias": "Ras_act_craf",
"field": "Kf",
"value": 9999.2668,
"units": "none"
},
{
"name": "ePKC+craf",
"alias": "PKC_act_raf",
"field": "Km",
"value": 0.02098,
"units": "none"
},
{
"name": "eMKP1+MAPKp",
"alias": "MKP1pY421_deph",
"field": "Km",
"value": 0.00734,
"units": "none"
},
{
"name": "eMKP1+MAPKpq",
"alias": "MKP1pT424_deph",
"field": "Km",
"value": 0.00734,
"units": "none"
},
{
"name": "eMKP1+MAPKpq",
"alias": "MKP1pT424_deph",
"field": "kcat",
"value": 4,
"units": "none"
},
{
"name": "eMKP1+MAPKp",
"alias": "MKP1pY421_deph",
"field": "kcat",
"value": 4,
"units": "none"
},
{
"name": "eRas+MAPKK1",
"alias": "Rafp_RasGTP1",
"field": "kcat",
"value": 0.3,
"units": "none"
},
{
"name": "eRas+MAPKK2",
"alias": "Rafp_RasGTP2",
"field": "kcat",
"value": 0.3,
"units": "none"
},
{
"name": "eCaMGEF+Ras",
"alias": "CaMGEF_actRas",
"field": "kcat",
"value": 0.02,
"units": "none"
},
{
"name": "eSHCpSosGrb2+Ras",
"alias": "Sos_Ras_GEF",
"field": "kcat",
"value": 0.2,
"units": "none"
}
],
"notes": "Bhalla1999_Fig2B"
}
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