diff --git a/Curated/Bhalla1999_Fig2B.json b/Curated/Bhalla1999_Fig2B.json index 1abc915..5b958b6 100644 --- a/Curated/Bhalla1999_Fig2B.json +++ b/Curated/Bhalla1999_Fig2B.json @@ -1,5 +1,5 @@ { - "ContentType": "Findsim", + "FileType": "Findsim", "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", @@ -27,22 +27,20 @@ { "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 @@ -56,26 +54,14 @@ ] }, "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"}, @@ -83,32 +69,92 @@ {"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" diff --git a/Curated/Bhalla1999_Fig4C.json b/Curated/Bhalla1999_Fig4C.json index 826ec51..907cb6d 100644 --- a/Curated/Bhalla1999_Fig4C.json +++ b/Curated/Bhalla1999_Fig4C.json @@ -1,5 +1,5 @@ { - "ContentType": "Findsim", + "FileType": "Findsim", "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", @@ -26,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity": { - "name": "Ca", - "alias": "Ca" - }, + "entity": {"name": "Ca"}, "field": "conc", "data": [ [1000,10], @@ -101,10 +98,7 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "uM", - "entity": { - "name": "MAPKpq", - "alias": "MAPKpp" - }, + "entity": {"name": "MAPKpq"}, "field": "conc", "data": [ [600, 0.0001, 0], @@ -120,169 +114,205 @@ }, "Modifications": { "subset": [ - {"name":"Ca_g","alias":"Ca_g"},{"name":"Phosphatase_g","alias":"Phosphatase_g"},{"name":"Gprotein_g","alias":"Gprotein_g"},{"name":"mGluR_g","alias":"mGluR_g"},{"name":"AC_g","alias":"AC_g"},{"name":"PKA_g","alias":"PKA_g"},{"name":"PP2B_g","alias":"PP2B_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"Ras_g","alias":"Ras_g"},{"name":"MAPK_g","alias":"MAPK_g"},{"name":"PP1_g","alias":"PP1_g"},{"name":"CaM_g","alias":"CaM_g"},{"name":"CaMKII_g","alias":"CaMKII_g"},{"name":"mGluRAntag_g","alias":"mGluRAntag_g"},{"name":"PLCb_g","alias":"PLCb_g"},{"name":"PLA2_g","alias":"PLA2_g"},{"name":"PKC_g","alias":"PKC_g"},{"name":"PIP2","alias":"PIP2"},{"name":"temp_PIP2","alias":"temp_PIP2"},{"name":"IP3","alias":"IP3"},{"name":"EGFR_g","alias":"EGFR_g"},{"name":"Sos_g","alias":"Sos_g"} + {"name": "Ca_g"},{"name": "Phosphatase_g"},{"name": "Gprotein_g"},{"name": "mGluR_g"},{"name": "AC_g"},{"name": "PKA_g"},{"name": "PP2B_g"},{"name": "PLCg_g"},{"name": "Ras_g"},{"name": "MAPK_g"},{"name": "PP1_g"},{"name": "CaM_g"},{"name": "CaMKII_g"},{"name": "mGluRAntag_g"},{"name": "PLCb_g"},{"name": "PLA2_g"},{"name": "PKC_g"},{"name": "PIP2"},{"name": "temp_PIP2"},{"name": "IP3"},{"name": "EGFR_g"},{"name": "Sos_g"} ], "itemsToDelete": [ - {"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"Gab1","alias":"Gab1"},{"name":"bPI3K","alias":"bPI3K"},{"name":"PI3K","alias":"PI3K"},{"name":"PIP3","alias":"PIP3"},{"name":"PTEN","alias":"PTEN"},{"name":"SHCpGrb2Gab1_PI3K","alias":"SHCpGrb2Gab1_PI3K"},{"name":"bPLCg","alias":"bPLCg"},{"name":"ebGEF+Ras","alias":"bGEF_act"},{"name":"RasGTP_PI3K","alias":"RasGTP_PI3K"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"SHCpGrb2_Gab1","alias":"SHCpGrb2_Gab1"},{"name":"SHCpGrb2Gab1+PI3K","alias":"PI3K_act"},{"name":"bPI3K_act","alias":"bPI3K_act"},{"name":"PI3K+RasGTP","alias":"PI3K_bind_RasGTP"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"aCaMKIII","alias":"aCaMKIII"},{"name":"PLCgp_deph","alias":"PLCgp_deph"},{"name":"SHCp+Grb2","alias":"Grb2_bind_SHC"},{"name":"PDK1_act_S6K","alias":"PDK1_act_S6K"},{"name":"ePI3K+AKT","alias":"phospho_AKTpT308"},{"name":"ePDK2+AKTp","alias":"phospho_AKTpS473"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"},{"name":"ecraf+MAPKK","alias":"MEK_phospho"},{"name":"ecraf+MAPKKp","alias":"MEKp_phospho"},{"name":"aAKT","alias":"AKTpT308S473"},{"name":"craf1+barr2","alias":"mGluR_barr2_Raf"},{"name":"mGluR_deph","alias":"mGluR_deph"} + {"name": "ePP2A+S6Kpq","alias": "clus_S6K_deph"}, + {"name": "ePP2A+S6Kpqrs","alias": "S6K_dephosp"}, + {"name": "Gab1"}, + {"name": "bPI3K"}, + {"name": "PI3K"}, + {"name": "PIP3"}, + {"name": "PTEN"}, + {"name": "SHCpGrb2Gab1_PI3K"}, + {"name": "bPLCg"}, + {"name": "ebGEF+Ras","alias": "bGEF_act"}, + {"name": "RasGTP_PI3K"}, + {"name": "ePP2A+S6Kpqr","alias": "S6K_deph"}, + {"name": "SHCpGrb2_Gab1"}, + {"name": "SHCpGrb2Gab1+PI3K","alias": "PI3K_act"}, + {"name": "bPI3K_act"}, + {"name": "PI3K+RasGTP","alias": "PI3K_bind_RasGTP"}, + {"name": "ePP2A+AKTpq","alias": "AKTpS473_deph"}, + {"name": "ePP2A+AKTp","alias": "AKTpT308_deph"}, + {"name": "ePP2A+eEF2p","alias": "eEF2p_deph"}, + {"name": "ePP2A+4EBPpqr","alias": "PP2A_4EBPpp"}, + {"name": "ePP2A+4EBPpq","alias": "PP2A_4EBPp"}, + {"name": "ePP2A+eIF4EBPpqr","alias": "PP2A_eIF4EBPpp"}, + {"name": "ePP2A+eIF4EBPpq","alias": "PP2A_eIF4EBPp"}, + {"name": "aCaMKIII"}, + {"name": "PLCgp_deph"}, + {"name": "SHCp+Grb2","alias": "Grb2_bind_SHC"}, + {"name": "PDK1_act_S6K"}, + {"name": "ePI3K+AKT","alias": "phospho_AKTpT308"}, + {"name": "ePDK2+AKTp","alias": "phospho_AKTpS473"}, + {"name": "eMAPK+S6K","alias": "clus_S6K_phospho"}, + {"name": "eMAPK+4EBPpq","alias": "MAPK_4EBPpp"}, + {"name": "eMAPK+eIF4EBPpq","alias": "MAPK_4EBP_phospho"}, + {"name": "ecraf+MAPKK","alias": "MEK_phospho"}, + {"name": "ecraf+MAPKKp","alias": "MEKp_phospho"}, + {"name": "aAKT","alias": "AKTpT308S473"}, + {"name": "craf1+barr2","alias": "mGluR_barr2_Raf"}, + {"name": "mGluR_deph" + } ], "parameterChange": [ - { - "entity": {"name": "Ca"}, - "field": "concInit", - "value": 8e-05, - "units": "mM"}, - { - "entity": {"name": "Ca"}, - "field": "isBuffered", - "value": 1, - "units": "none"}, - { - "entity": {"name": "MKP1","alias": "MKP1"}, + { "entity": {"name": "Ca"}, + "field": "concInit", + "value": 8e-05, + "units": "mM" + }, + { "entity": {"name": "Ca"}, + "field": "isBuffered", + "value": 1, + "units": "none" + }, + { "entity": {"name": "MKP1","alias": "MKP1"}, "field": "concInit", "value": 2e-06, - "units": "mM"}, - { - "entity": {"name": "Ras+craf","alias": "Ras_act_craf"}, + "units": "mM" + }, + { "entity": {"name": "Ras+craf","alias": "Ras_act_craf"}, "field": "Kf", "value": 24000, - "units": "none"}, - { - "entity": {"name": "CaMCa4+GEF","alias": "CaM_bind_GEF"}, + "units": "none" + }, + { "entity": {"name": "CaMCa4+GEF","alias": "CaM_bind_GEF"}, "field": "Kf", "value": 60000, - "units": "none"}, - { - "entity": {"name": "MAPK","alias": "MAPK"}, + "units": "none" + }, + { "entity": {"name": "MAPK","alias": "MAPK"}, "field": "concInit", "value": 0.00036, - "units": "mM"}, - { - "entity": {"name": "eMAPKK+MAPKp","alias": "MAPKKthr"}, + "units": "mM" + }, + { "entity": {"name": "eMAPKK+MAPKp","alias": "MAPKKthr"}, "field": "kcat", "value": 0.15, - "units": "none"}, - { - "entity": {"name": "eMAPKK+MAPK","alias": "MAPKKtyr"}, + "units": "none" + }, + { "entity": {"name": "eMAPKK+MAPK","alias": "MAPKKtyr"}, "field": "kcat", "value": 0.15, - "units": "none"}, - { - "entity": {"name": "eRas+MAPKK1","alias": "Rafp_RasGTP1"}, + "units": "none" + }, + { "entity": {"name": "eRas+MAPKK1","alias": "Rafp_RasGTP1"}, "field": "kcat", "value": 0.105, - "units": "none"}, - { - "entity": {"name": "eRas+MAPKK2","alias": "Rafp_RasGTP2"}, + "units": "none" + }, + { "entity": {"name": "eRas+MAPKK2","alias": "Rafp_RasGTP2"}, "field": "kcat", "value": 0.105, - "units": "none"}, - { - "entity": {"name": "eMKP1+MAPKpq","alias": "MKP1pT424_deph"}, + "units": "none" + }, + { "entity": {"name": "eMKP1+MAPKpq","alias": "MKP1pT424_deph"}, "field": "kcat", "value": 1, - "units": "none"}, - { - "entity": {"name": "eMKP1+MAPKp","alias": "MKP1pY421_deph"}, + "units": "none" + }, + { "entity": {"name": "eMKP1+MAPKp","alias": "MKP1pY421_deph"}, "field": "kcat", "value": 1, - "units": "none"}, - { - "entity": {"name": "eMKP1+MAPKpq"}, + "units": "none" + }, + { "entity": {"name": "eMKP1+MAPKpq"}, "field": "Km", "value": 6.97e-05, - "units": "none"}, - { - "entity": {"name": "eMKP1+MAPKp"}, + "units": "none" + }, + { "entity": {"name": "eMKP1+MAPKp"}, "field": "Km", "value": 6.97e-05, - "units": "none"}, - { - "entity": {"name": "eEGFR+SHC","alias": "EGFR_act_SHC"}, + "units": "none" + }, + { "entity": {"name": "eEGFR+SHC","alias": "EGFR_act_SHC"}, "field": "Km", "value": 0.000871, - "units": "none"}, - { - "entity": {"name": "SHCp_deph","alias": "SHCp_deph"}, + "units": "none" + }, + { "entity": {"name": "SHCp_deph","alias": "SHCp_deph"}, "field": "Kf", "value": 0.00167, - "units": "none"}, - { - "entity": {"name": "eSHCpSosGrb2+Ras","alias": "Sos_Ras_GEF"}, + "units": "none" + }, + { "entity": {"name": "eSHCpSosGrb2+Ras","alias": "Sos_Ras_GEF"}, "field": "kcat", "value": 0.02, - "units": "none"}, - { - "entity": {"name": "ePKC+craf","alias": "PKC_act_raf"}, + "units": "none" + }, + { "entity": {"name": "ePKC+craf","alias": "PKC_act_raf"}, "field": "Km", "value": 0.0697, - "units": "none"}, - { - "entity": {"name": "eCaMGEF+Ras","alias": "CaMGEF_actRas"}, + "units": "none" + }, + { "entity": {"name": "eCaMGEF+Ras","alias": "CaMGEF_actRas"}, "field": "kcat", "value": 0.02, - "units": "none"}, - { - "entity": {"name": "bPKC","alias": "bPKCp"}, + "units": "none" + }, + { "entity": {"name": "bPKC","alias": "bPKCp"}, "field": "concInit", "value": 0, - "units": "mM"}, - { - "entity": {"name": "craf1","alias": "craf1"}, + "units": "mM" + }, + { "entity": {"name": "craf1","alias": "craf1"}, "field": "concInit", "value": 0.0002, - "units": "mM"}, - { - "entity": {"name": "MAPKK","alias": "MAPKK"}, + "units": "mM" + }, + { "entity": {"name": "MAPKK","alias": "MAPKK"}, "field": "concInit", "value": 0.00018, - "units": "mM"}, - { - "entity": {"name": "PP2A","alias": "PP2A"}, + "units": "mM" + }, + { "entity": {"name": "PP2A","alias": "PP2A"}, "field": "concInit", "value": 0.00012, - "units": "mM"}, - { - "entity": {"name": "PPhosphatase2A","alias": "PPhosphatase2A"}, + "units": "mM" + }, + { "entity": {"name": "PPhosphatase2A","alias": "PPhosphatase2A"}, "field": "concInit", "value": 0.000224, - "units": "mM"}, - { - "entity": {"name": "PIP2","alias": "PIP2"}, + "units": "mM" + }, + { "entity": {"name": "PIP2","alias": "PIP2"}, "field": "concInit", "value": 0.01, - "units": "mM"}, - { - "entity": {"name": "DAG","alias": "DAG"}, + "units": "mM" + }, + { "entity": {"name": "DAG","alias": "DAG"}, "field": "isBuffered", "value": 0, - "units": "none"}, - { - "entity": {"name": "AA","alias": "AA"}, + "units": "none" + }, + { "entity": {"name": "AA","alias": "AA"}, "field": "isBuffered", "value": 0, - "units": "none"}, - { - "entity": {"name": "AA"}, + "units": "none" + }, + { "entity": {"name": "AA"}, "field": "concInit", "value": 0, - "units": "mM"}, - { - "entity": {"name": "DAG"}, + "units": "mM" + }, + { "entity": {"name": "DAG"}, "field": "concInit", "value": 0, - "units": "mM"}, - { - "entity": {"name": "PLCg","alias": "PLCg"}, + "units": "mM" + }, + { "entity": {"name": "PLCg","alias": "PLCg"}, "field": "concInit", "value": 0.00082, - "units": "mM"}, - { - "entity": {"name": "GAP","alias": "GAP"}, + "units": "mM" + }, + { "entity": {"name": "GAP","alias": "GAP"}, "field": "concInit", "value": 2e-06, - "units": "mM"}, - { - "entity": {"name": "RasGDP","alias": "RasGDP"}, + "units": "mM" + }, + { "entity": {"name": "RasGDP","alias": "RasGDP"}, "field": "concInit", "value": 0.0002, "units": "mM" diff --git a/Curated/Gu2004_fig3B.json b/Curated/Gu2004_fig3B.json index 524f8c7..71981cf 100644 --- a/Curated/Gu2004_fig3B.json +++ b/Curated/Gu2004_fig3B.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "National Centre for Biological Sciences", @@ -24,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "EGF", - "alias": "EGF" - }, + "entity": {"name": "EGF","alias": "EGF"}, "field": "conc", "data": [ [3600,1.0] @@ -37,16 +36,10 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "aMAPK", - "alias": "aMAPK" - }, + "entity": {"name": "aMAPK","alias": "aMAPK"}, "field": "conc", "normalization": { - "entity" : { - "name": "aMAPK", - "alias": "aMAPK" - }, + "entity": {"name": "aMAPK"}, "sampling": "start" }, "data": [ @@ -59,121 +52,104 @@ ] }, "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"} ], "itemsToDelete": [ - {"name":"PP2A","alias":"PP2A"},{"name":"phosph_AC2","alias":"phosph_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":"mGluR_barr2_Raf_scaffolding","alias":"mGluR_barr2_Raf_scaffolding"},{"name":"MAPK_p_p/cluster_phospho_S6K","alias":"MAPK_p_p/cluster_phospho_S6K"},{"name":"MAPK_p_p/MAPK_4E_BP_p_p","alias":"MAPK_p_p/MAPK_4E_BP_p_p"},{"name":"MAPK_p_p/MAPK_4E_BP_phospho","alias":"MAPK_p_p/MAPK_4E_BP_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_phosph_neurogranin","alias":"PKC_phosph_neurogranin"},{"name":"PKC_phosph_ng_CaM","alias":"PKC_phosph_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_bind_Ras_GTP","alias":"PI3K_bind_Ras_GTP"},{"name":"PIP2_phospho_Ras_GTP","alias":"PIP2_phospho_Ras_GTP"} + {"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": "PLC_Ca+Gq","alias": "Act_PLC_by_Gq"}, + {"name": "Inact_PLC_Gq"}, + {"name": "PLC_bind_Gq"}, + {"name": "PKC_phosph_neurogranin"}, + {"name": "PKC_phosph_ng_CaM"}, + {"name": "PIP2_PLA2_act"}, + {"name": "PIP2_Ca_PLA2_act"}, + {"name": "CaMCa4+GEF","alias": "CaM_bind_GEF"}, + {"name": "PI3K_bind_Ras_GTP"}, + {"name": "PIP2_phospho_Ras_GTP" + } ], "parameterChange": [ - { - "name": "EGF", - "alias": "EGF", + { "entity": {"name": "EGF"}, "field": "concInit", "value": 0.0, "units": "mM" }, - { - "name": "bPKC", - "alias": "bPKCp", + { "entity": {"name": "bPKC","alias": "bPKCp"}, "field": "concInit", "value": 2e-05, "units": "mM" }, - { - "name": "GAP", - "alias": "GAP", + { "entity": {"name": "GAP","alias": "GAP"}, "field": "concInit", "value": 2e-05, "units": "mM" }, - { - "name": "PIP2", - "alias": "PIP2", + { "entity": {"name": "PIP2","alias": "PIP2"}, "field": "concInit", "value": 0.007, "units": "mM" }, - { - "name": "enolase", - "alias": "enolase", + { "entity": {"name": "enolase","alias": "enolase"}, "field": "concInit", "value": 0.0005, "units": "mM" }, - { - "name": "SHCp_deph", - "alias": "SHCp_deph", + { "entity": {"name": "SHCp_deph","alias": "SHCp_deph"}, "field": "Kf", "value": 0.2, "units": "none" }, - { - "name": "Ras+craf", - "alias": "Ras_act_craf", + { "entity": {"name": "Ras+craf","alias": "Ras_act_craf"}, "field": "Kf", "value": 9999.26668, "units": "none" }, - { - "name": "ePKC+craf", - "alias": "PKC_act_raf", + { "entity": {"name": "ePKC+craf","alias": "PKC_act_raf"}, "field": "Km", "value": 0.02098, "units": "none" }, - { - "name": "eMKP1+MAPKp", - "alias": "MKP1pY421_deph", + { "entity": {"name": "eMKP1+MAPKp","alias": "MKP1pY421_deph"}, "field": "Km", "value": 0.00734, "units": "none" }, - { - "name": "eMKP1+MAPKpq", - "alias": "MKP1pT424_deph", + { "entity": {"name": "eMKP1+MAPKpq","alias": "MKP1pT424_deph"}, "field": "Km", "value": 0.00734, "units": "none" }, - { - "name": "eMKP1+MAPKpq", - "alias": "MKP1pT424_deph", + { "entity": {"name": "eMKP1+MAPKpq"}, "field": "kcat", "value": 4, "units": "none" }, - { - "name": "eMKP1+MAPKp", - "alias": "MKP1pY421_deph", + { "entity": {"name": "eMKP1+MAPKp"}, "field": "kcat", "value": 4, "units": "none" }, - { - "name": "eRas+MAPKK1", - "alias": "Rafp_RasGTP1", + { "entity": {"name": "eRas+MAPKK1","alias": "Rafp_RasGTP1"}, "field": "kcat", "value": 0.3, "units": "none" }, - { - "name": "eRas+MAPKK2", - "alias": "Rafp_RasGTP2", + { "entity": {"name": "eRas+MAPKK2","alias": "Rafp_RasGTP2"}, "field": "kcat", "value": 0.3, "units": "none" }, - { - "name": "eCaMGEF+Ras", - "alias": "CaMGEF_actRas", + { "entity": {"name": "eCaMGEF+Ras","alias": "CaMGEF_actRas"}, "field": "kcat", "value": 0.2, "units": "none" }, - { - "name": "eSHCpSosGrb2+Ras", - "alias": "Sos_Ras_GEF", + { "entity": {"name": "eSHCpSosGrb2+Ras","alias": "Sos_Ras_GEF"}, "field": "kcat", "value": 0.2, "units": "none" diff --git a/Curated/Jain2009_Fig2B.json b/Curated/Jain2009_Fig2B.json index fdc339d..7a982e9 100644 --- a/Curated/Jain2009_Fig2B.json +++ b/Curated/Jain2009_Fig2B.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +27,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "BDNF", - "alias": "BDNF" - }, + "entity": {"name": "BDNF","alias": "BDNF"}, "field": "conc", "data": [ [0,7.3] @@ -38,10 +37,7 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "BDNF_act_TrKB", - "alias": "BDNF_act_TrKB" - }, + "entity": { "name": "BDNF_act_TrKB","alias": "BDNF_act_TrKB"}, "field": "conc", "data": [ [0, 0, 0], @@ -53,10 +49,11 @@ }, "Modifications": { "subset": [ - {"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"} + {"name": "BDNF_g"},{"name": "TrKB_g"} ], "itemsToDelete": [ - {"name":"eTrKB+PLCg","alias":"TrKB_act_PLCg"},{"name":"eTrKB+SHC","alias":"TrKB_act_SHC"} + {"name": "eTrKB+PLCg","alias": "TrKB_act_PLCg"}, + {"name": "eTrKB+SHC", "alias": "TrKB_act_SHC" } ], "notes": "Jain2009_Fig2B" } diff --git a/Curated/Jain2009_Fig2F.json b/Curated/Jain2009_Fig2F.json index 124b3d5..262ce24 100644 --- a/Curated/Jain2009_Fig2F.json +++ b/Curated/Jain2009_Fig2F.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +27,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "PDK1", - "alias": "PDK1" - }, + "entity": {"name": "PDK1","alias": "PDK1"}, "field": "conc", "data": [ [0,3.5] @@ -38,10 +37,7 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "AKTp", - "alias": "AKTpT308" - }, + "entity": {"name": "AKTp","alias": "AKTpT308"}, "field": "conc", "data": [ [0, 0, 0], @@ -54,22 +50,32 @@ }, "Modifications": { "subset": [ - {"name":"AKT_g","alias":"AKT_g"},{"name":"PI3K_g","alias":"PI3K_g"} + {"name": "AKT_g"},{"name": "PI3K_g"} ], "itemsToDelete": [ - {"name":"PTEN","alias":"PTEN"},{"name":"RasGTP_PI3K","alias":"RasGTP_PI3K"},{"name":"SHCp_Grb2+Gab1","alias":"bind_Gab1"},{"name":"temp_PIP2","alias":"temp_PIP2"},{"name":"SHCpGrb2Gab1_PI3K","alias":"SHCpGrb2Gab1_PI3K"},{"name":"PI3K","alias":"PI3K"},{"name":"Gab1","alias":"Gab1"},{"name":"bPI3K","alias":"bPI3K"},{"name":"SHCpGrb2_Gab1","alias":"SHCpGrb2_Gab1"},{"name":"SHCpGrb2Gab1+PI3K","alias":"PI3K_act"},{"name":"bPI3K_act","alias":"bPI3K_act"},{"name":"PI3K+RasGTP","alias":"PI3K_bind_RasGTP"},{"name":"PIP3_PDK2","alias":"PIP3_PDK2"},{"name":"aAKT","alias":"AKTpT308S473"},{"name":"PDK1_act_S6K","alias":"PDK1_act_S6K"} + {"name": "PTEN"}, + {"name": "RasGTP_PI3K"}, + {"name": "SHCp_Grb2+Gab1","alias": "bind_Gab1"}, + {"name": "temp_PIP2"}, + {"name": "SHCpGrb2Gab1_PI3K"}, + {"name": "PI3K"}, + {"name": "Gab1"}, + {"name": "bPI3K"}, + {"name": "SHCpGrb2_Gab1"}, + {"name": "SHCpGrb2Gab1+PI3K","alias": "PI3K_act"}, + {"name": "bPI3K_act"}, + {"name": "PI3K+RasGTP","alias": "PI3K_bind_RasGTP"}, + {"name": "PIP3_PDK2"}, + {"name": "aAKT","alias": "AKTpT308S473"}, + {"name": "PDK1_act_S6K"} ], "parameterChange": [ - { - "name": "PIP3", - "alias": "PIP3", + { "entity": {"name": "PIP3","alias": "PIP3"}, "field": "concInit", "value": 0.00025, "units": "mM" }, - { - "name": "AKT", - "alias": "AKT", + { "entity": {"name": "AKT","alias": "AKT"}, "field": "concInit", "value": 0.0005, "units": "mM" diff --git a/Curated/Jain2009_Fig3F.json b/Curated/Jain2009_Fig3F.json index f65dfbd..feeb101 100644 --- a/Curated/Jain2009_Fig3F.json +++ b/Curated/Jain2009_Fig3F.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,20 +27,14 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity" : { - "name": "eIF4E", - "alias": "eIF4E" - }, + "entity": {"name": "eIF4E","alias": "eIF4E"}, "field": "conc" } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "uM", - "entity" : { - "name": "eIF4E_4EBP", - "alias": "eIF4E_4EBP" - }, + "entity": { "name": "eIF4E_4EBP","alias": "eIF4E_4EBP"}, "field": "conc", "data": [ [0, 0, 0], @@ -53,40 +49,32 @@ }, "Modifications": { "subset": [ - {"name":"eIF4E_4EBP","alias":"eIF4E_4EBP"},{"name":"eIF4E+4EBP","alias":"eIF4E_bind_BP2"},{"name":"4EBP","alias":"4EBP"},{"name":"eIF4E","alias":"eIF4E"} + {"name": "eIF4E_4EBP"},{"name": "eIF4E+4EBP","alias": "eIF4E_bind_BP2"},{"name": "4EBP"},{"name": "eIF4E"} ], "parameterChange": [ - { - "name": "eIF4E", - "alias": "eIF4E", - "field": "concInit", + {"entity": {"name": "eIF4E"},"field": "concInit", "value": 0.0016, "units": "mM" }, - { - "name": "eIF4E", - "alias": "eIF4E", + {"entity": {"name": "eIF4E" + }, "field": "isBuffered", "value": 1, "units": "none" }, - { - "name": "eIF4E_4EBP", - "alias": "eIF4E_4EBP", - "field": "concInit", + {"entity": {"name": "eIF4E_4EBP" + },"field": "concInit", "value": 0, "units": "mM" }, - { - "name": "4EBP", - "alias": "4EBP", + {"entity": {"name": "4EBP","alias": "4EBP" + }, "field": "concInit", "value": 0.00027, "units": "mM" }, - { - "name": "4EBP", - "alias": "4EBP", + {"entity": {"name": "4EBP" + }, "field": "isBuffered", "value": 1, "units": "none" diff --git a/Curated/Jain2009_Fig4C.json b/Curated/Jain2009_Fig4C.json index 9e7d9b8..a5384a9 100644 --- a/Curated/Jain2009_Fig4C.json +++ b/Curated/Jain2009_Fig4C.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,9 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity" : { - "name": "S6Kpqrs", - "alias": "S6KpT229" + "entity": {"name": "S6Kpqrs","alias": "S6KpT229" }, "field": "conc", "data": [ @@ -37,10 +37,10 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { + "entity": { "name": "bCaMKIII", "alias": "CaMKIIIp" - }, + }, "field": "conc", "data": [ [60, 8, 0], @@ -52,29 +52,27 @@ }, "Modifications": { "subset": [ - {"name":"CaMKIII_g","alias":"CaMKIII_g"},{"name":"S6K_g","alias":"S6K_g"} + {"name": "CaMKIII_g"},{"name": "S6K_g"} ], "itemsToDelete": [ - {"name":"eS6Kpqr+40S","alias":"S6_phos"},{"name":"eS6Kpqrs+40S","alias":"S6_phospho"},{"name":"CaMKIII_CaM_Ca4[0]/phospho","alias":"CaMKIII_CaM_Ca4[0]/phospho"},{"name":"eEF2thr56_basal","alias":"eEF2thr56_basal"} + {"name": "eS6Kpqr+40S","alias": "S6_phos" }, + {"name": "eS6Kpqrs+40S","alias": "S6_phospho"}, + {"name": "S6_dephosph"}, + {"name": "CaMKIII_CaM_Ca4[0]/phospho"}, + {"name": "eEF2thr56_basal"} ], "parameterChange": [ - { - "name": "bS6K", - "alias": "bS6K", + { "entity": {"name": "bS6K","alias": "bS6K"}, "field": "concInit", "value": 0, "units": "mM" }, - { - "name": "CaMKIII", - "alias": "CaMKIII", + { "entity": {"name": "CaMKIII","alias": "CaMKIII"}, "field": "concInit", "value": 6.8e-05, "units": "mM" }, - { - "name": "CaMKIIIp_deph", - "alias": "CaMKIII_deph", + { "entity": {"name": "CaMKIIIp_deph","alias": "CaMKIII_deph"}, "field": "Kf", "value": 0, "units": "none" diff --git a/Curated/Jain2009_Fig4D.json b/Curated/Jain2009_Fig4D.json index 659a9aa..17bf31c 100644 --- a/Curated/Jain2009_Fig4D.json +++ b/Curated/Jain2009_Fig4D.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,20 +27,17 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity" : { - "name": "eEF2p", - "alias": "eEF2p" - }, + "entity": {"name": "eEF2p","alias": "eEF2p"}, "field": "conc" } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { + "entity": { "name": "eEF2", "alias": "eEF2" - }, + }, "field": "conc", "data": [ [0, 0, 0], @@ -52,29 +51,34 @@ }, "Modifications": { "subset": [ - {"name":"PP2A","alias":"PP2A"},{"name":"eEF2","alias":"eEF2"},{"name":"eEF2p","alias":"eEF2p"} + {"name": "PP2A"},{"name": "eEF2"},{"name": "eEF2p"} ], "itemsToDelete": [ - {"name":"PP2A_dephospho_I1","alias":"PP2A_dephospho_I1"},{"name":"PP2A_dephospho_PP1_I_p","alias":"PP2A_dephospho_PP1_I_p"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"mGluR_deph","alias":"mGluR_deph"} + {"name": "PP2A_dephospho_I1"}, + {"name": "PP2A_dephospho_PP1_I_p"}, + {"name": "ePP2A+S6Kpq","alias": "clus_S6K_deph"}, + {"name": "ePP2A+S6Kpqrs","alias": "S6K_dephosp"}, + {"name": "ePP2A+S6Kpqr","alias": "S6K_deph"}, + {"name": "ePP2A+AKTpq","alias": "AKTpS473_deph"}, + {"name": "ePP2A+AKTp","alias": "AKTpT308_deph"}, + {"name": "ePP2A+4EBPpqr","alias": "PP2A_4EBPpp"}, + {"name": "ePP2A+4EBPpq","alias": "PP2A_4EBPp"}, + {"name": "ePP2A+eIF4EBPpqr","alias": "PP2A_eIF4EBPpp"}, + {"name": "ePP2A+eIF4EBPpq","alias": "PP2A_eIF4EBPp"}, + {"name": "mGluR_deph"} ], "parameterChange": [ - { - "name": "PP2A", - "alias": "PP2A", + { "entity": {"name": "PP2A","alias": "PP2A"}, "field": "concInit", "value": 6.5e-07, "units": "mM" }, - { - "name": "eEF2", - "alias": "eEF2", + { "entity": {"name": "eEF2"}, "field": "concInit", "value": 0, "units": "mM" }, - { - "name": "eEF2p", - "alias": "eEF2p", + { "entity": {"name": "eEF2p"}, "field": "concInit", "value": 2.2e-05, "units": "mM" diff --git a/Curated/Jain2009_Fig4F.json b/Curated/Jain2009_Fig4F.json index b86502b..16160a2 100644 --- a/Curated/Jain2009_Fig4F.json +++ b/Curated/Jain2009_Fig4F.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "aS6", - "alias": "S6p" - }, + "entity": {"name": "aS6","alias": "S6p"}, "field": "conc", "isBuffered": 0 } @@ -36,10 +35,7 @@ "timeUnits": "sec", "settleTime": 2400, "quantityUnits": "nM", - "entity" : { - "name": "43S", - "alias": "43S" - }, + "entity": {"name": "43S","alias": "43S"}, "field": "conc", "data": [ [6.8, 3.61, 0], @@ -51,19 +47,15 @@ }, "Modifications": { "subset": [ - {"name":"Transl_init_g","alias":"Transl_init_g"},{"name":"_40S_g","alias":"40S_g"},{"name":"_43S_g","alias":"43S_g"} + {"name": "Transl_init_g"},{"name": "_40S_g","alias": "40S_g"},{"name": "_43S_g","alias": "43S_g"} ], "parameterChange": [ - { - "name": "M_clx", - "alias": "M_clx", + { "entity": {"name": "M_clx","alias": "M_clx"}, "field": "concInit", "value": 0.0015, "units": "mM" }, - { - "name": "Q_clx", - "alias": "Q_clx", + { "entity": {"name": "Q_clx","alias": "Q_clx"}, "field": "concInit", "value": 4.97e-05, "units": "mM" diff --git a/Curated/Jain2009_Fig5B.json b/Curated/Jain2009_Fig5B.json index 0d537d1..e558b48 100644 --- a/Curated/Jain2009_Fig5B.json +++ b/Curated/Jain2009_Fig5B.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +27,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "BDNF", - "alias": "BDNF" - }, + "entity": {"name": "BDNF","alias": "BDNF"}, "field": "conc", "data": [ [900,2] @@ -38,10 +37,7 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "uM", - "entity" : { - "name": "aAKT", - "alias": "aAKT" - }, + "entity": {"name": "aAKT","alias": "aAKT"}, "field": "conc", "data": [ [900, 0.005, 0], @@ -54,26 +50,19 @@ }, "Modifications": { "subset": [ - {"name":"Phosphatase_g","alias":"Phosphatase_g"},{"name":"Ca_g","alias":"Ca_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"Sos_g","alias":"Sos_g"},{"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"},{"name":"AKT_g","alias":"AKT_g"},{"name":"PI3K_g","alias":"PI3K_g"},{"name":"PIP2","alias":"PIP2"},{"name":"PIP3","alias":"PIP3"},{"name":"MAPK_g","alias":"MAPK_g"},{"name":"Ras_g","alias":"Ras_g"},{"name":"PKC_g","alias":"PKC_g"} + {"name": "Phosphatase_g"},{"name": "Ca_g"},{"name": "PLCg_g"},{"name": "Sos_g"},{"name": "BDNF_g"},{"name": "TrKB_g"},{"name": "AKT_g"}, {"name": "PI3K_g"},{"name": "PIP2"},{"name": "PIP3"},{"name": "MAPK_g"},{"name": "Ras_g"},{"name": "PKC_g"} ], "parameterChange": [ - { - "name": "AKT", - "alias": "AKT", + {"entity": {"name": "AKT","alias": "AKT"}, "field": "concInit", "value": 0.00017, "units": "mM" }, - { - "name": "BDNF", - "alias": "BDNF", - "field": "concInit", + {"entity": {"name": "BDNF"},"field": "concInit", "value": 0, "units": "mM" }, - { - "name": "SHCp_deph", - "alias": "SHCp_deph", + {"entity": {"name": "SHCp_deph","alias": "SHCp_deph"}, "field": "Kf", "value": 0.2, "units": "none" diff --git a/Curated/Ji2010_fig1C_ERK_acute.json b/Curated/Ji2010_fig1C_ERK_acute.json index 6d30d44..6a8af03 100644 --- a/Curated/Ji2010_fig1C_ERK_acute.json +++ b/Curated/Ji2010_fig1C_ERK_acute.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,7 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { + "entity": { "name": "BDNF", "alias": "BDNF" }, @@ -37,16 +39,16 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { + "entity": { "name": "pERK", "alias": "pERK" - }, + }, "field": "conc", "normalization": { - "entity" : { - "name": "pERK", - "alias": "pERK" + "entity": { + "name": "pERK" }, + "dose": 0, "sampling": "presetTime", "sampTime": 1800 }, @@ -62,127 +64,348 @@ }, "Modifications": { "subset": [ - {"name":"Ca_g","alias":"Ca_g"},{"name":"Phosphatase_g","alias":"Phosphatase_g"},{"name":"Sos_g","alias":"Sos_g"},{"name":"Ras_g","alias":"Ras_g"},{"name":"MAPK_g","alias":"MAPK_g"},{"name":"CaM_g","alias":"CaM_g"},{"name":"PKC_g","alias":"PKC_g"},{"name":"PI3K_g","alias":"PI3K_g"},{"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"},{"name":"PLA2_g","alias":"PLA2_g"},{"name":"PLCb_g","alias":"PLCb_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"PC","alias":"PC"} + { + "name": "Ca_g" + }, + { + "name": "Phosphatase_g" + }, + { + "name": "Sos_g" + }, + { + "name": "Ras_g" + }, + { + "name": "MAPK_g" + }, + { + "name": "CaM_g" + }, + { + "name": "PKC_g" + }, + { + "name": "PI3K_g" + }, + { + "name": "BDNF_g" + }, + { + "name": "TrKB_g" + }, + { + "name": "PLA2_g" + }, + { + "name": "PLCb_g" + }, + { + "name": "PLCg_g" + }, + { + "name": "PC" + } ], "itemsToDelete": [ - {"name":"eMAPK+PLA2","alias":"MAPKpp_act_PLA2"},{"name":"dephosph_inhib1","alias":"dephosph_inhib1"},{"name":"ecraf+MAPKK","alias":"MEK_phospho"},{"name":"ecraf+MAPKKp","alias":"MEKp_phospho"},{"name":"PIP3_AKT_t308_s473","alias":"PIP3_AKT_t308_s473"},{"name":"phosph_AC2","alias":"phosph_AC2"},{"name":"bg_act_GEF","alias":"bg_act_GEF"},{"name":"dephosph_inact_GEF_p","alias":"dephosph_inact_GEF_p"},{"name":"dephosph_PLC_g","alias":"dephosph_PLC_g"},{"name":"ng+CaM","alias":"ng_bind_CaM"},{"name":"eCaM+ngp","alias":"CaM_ng_deph"},{"name":"PKC_phospho_ng","alias":"PKC_phospho_ng"},{"name":"PKC_phospho_ng_CaM","alias":"PKC_phospho_ng_CaM"},{"name":"GEF_Gprot_bg","alias":"GEF_Gprot_bg"},{"name":"aCaM_CaN","alias":"tCaM_CaN"},{"name":"craf1+barr2","alias":"mGluR_barr2_Raf"},{"name":"eCaN+I1p","alias":"CaN_deph_I1p"},{"name":"PP2A_dephospho_I1","alias":"PP2A_dephospho_I1"},{"name":"mGluR_deph","alias":"mGluR_deph"},{"name":"CaMCa4+CaMKIII","alias":"CaMKIII_bind_CaMCa4"},{"name":"bS6K","alias":"bS6K"},{"name":"eS6Kpqrs+CaMKIII","alias":"S6Kp_act_CaMKIII"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"},{"name":"PP2A_dephospho_PP1_Ip","alias":"PP2A_dephospho_PP1_Ip"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"PP2A_4EBP","alias":"PP2A_4EBP"},{"name":"SHCpGrb2Gab1PI3K_phospho","alias":"SHCpGrb2Gab1PI3K_phospho"},{"name":"ebPI3K+PIP2","alias":"bPIP2_phospho"},{"name":"ePTEN+PIP3","alias":"PIP3_deph"},{"name":"eRas+PIP2","alias":"PIP2_phospho_RasGTP"},{"name":"ePDK2+AKTp","alias":"phospho_AKTpS473"},{"name":"emTORC1+4EBP","alias":"TOR_4EBPp"},{"name":"eS6Kpqr+40S","alias":"S6_phos"},{"name":"eS6Kpqrs+40S","alias":"S6_phospho"},{"name":"S6_deph","alias":"S6_deph"},{"name":"PLC_bind_Gq","alias":"PLC_bind_Gq"},{"name":"Inact_PLC_Gq","alias":"Inact_PLC_Gq"},{"name":"PLC_Ca+Gq","alias":"Act_PLC_by_Gq"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"PDK1_act_S6K","alias":"PDK1_act_S6K"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"} + { + "name": "eMAPK+PLA2", + "alias": "MAPKpp_act_PLA2" + }, + { + "name": "dephosph_inhib1" + }, + { + "name": "ecraf+MAPKK", + "alias": "MEK_phospho" + }, + { + "name": "ecraf+MAPKKp", + "alias": "MEKp_phospho" + }, + { + "name": "PIP3_AKT_t308_s473" + }, + { + "name": "phosph_AC2" + }, + { + "name": "bg_act_GEF" + }, + { + "name": "dephosph_inact_GEF_p" + }, + { + "name": "dephosph_PLC_g" + }, + { + "name": "ng+CaM", + "alias": "ng_bind_CaM" + }, + { + "name": "eCaM+ngp", + "alias": "CaM_ng_deph" + }, + { + "name": "PKC_phospho_ng" + }, + { + "name": "PKC_phospho_ng_CaM" + }, + { + "name": "GEF_Gprot_bg" + }, + { + "name": "aCaM_CaN", + "alias": "tCaM_CaN" + }, + { + "name": "craf1+barr2", + "alias": "mGluR_barr2_Raf" + }, + { + "name": "eCaN+I1p", + "alias": "CaN_deph_I1p" + }, + { + "name": "PP2A_dephospho_I1" + }, + { + "name": "mGluR_deph" + }, + { + "name": "CaMCa4+CaMKIII", + "alias": "CaMKIII_bind_CaMCa4" + }, + { + "name": "bS6K" + }, + { + "name": "eS6Kpqrs+CaMKIII", + "alias": "S6Kp_act_CaMKIII" + }, + { + "name": "eMAPK+4EBPpq", + "alias": "MAPK_4EBPpp" + }, + { + "name": "eMAPK+eIF4EBPpq", + "alias": "MAPK_4EBP_phospho" + }, + { + "name": "PP2A_dephospho_PP1_Ip" + }, + { + "name": "ePP2A+AKTpq", + "alias": "AKTpS473_deph" + }, + { + "name": "ePP2A+eEF2p", + "alias": "eEF2p_deph" + }, + { + "name": "ePP2A+4EBPpqr", + "alias": "PP2A_4EBPpp" + }, + { + "name": "ePP2A+4EBPpq", + "alias": "PP2A_4EBPp" + }, + { + "name": "ePP2A+eIF4EBPpqr", + "alias": "PP2A_eIF4EBPpp" + }, + { + "name": "PP2A_4EBP" + }, + { + "name": "SHCpGrb2Gab1PI3K_phospho" + }, + { + "name": "ebPI3K+PIP2", + "alias": "bPIP2_phospho" + }, + { + "name": "ePTEN+PIP3", + "alias": "PIP3_deph" + }, + { + "name": "eRas+PIP2", + "alias": "PIP2_phospho_RasGTP" + }, + { + "name": "ePDK2+AKTp", + "alias": "phospho_AKTpS473" + }, + { + "name": "emTORC1+4EBPhospho", + "alias": "TOR_4EBP_phospho" + }, + { + "name": "emTORC1+4EBP", + "alias": "TOR_4EBPp" + }, + { + "name": "eS6Kpqr+40S", + "alias": "S6_phos" + }, + { + "name": "eS6Kpqrs+40S", + "alias": "S6_phospho" + }, + { + "name": "S6_deph" + }, + { + "name": "PLC_bind_Gq" + }, + { + "name": "Inact_PLC_Gq" + }, + { + "name": "PLC_Ca+Gq", + "alias": "Act_PLC_by_Gq" + }, + { + "name": "ePP2A+AKTp", + "alias": "AKTpT308_deph" + }, + { + "name": "PDK1_act_S6K" + }, + { + "name": "ePP2A+S6Kpqrs", + "alias": "S6K_dephosp" + }, + { + "name": "ePP2A+S6Kpqr", + "alias": "S6K_deph" + }, + { + "name": "ePP2A+S6Kpq", + "alias": "clus_S6K_deph" + }, + { + "name": "eMAPK+S6K", + "alias": "clus_S6K_phospho" + } ], "parameterChange": [ { - "name": "BDNF", - "alias": "BDNF", + "entity": {"name": "BDNF" + }, "field": "concInit", "value": 0, "units": "mM" }, { - "name": "bPKC", - "alias": "bPKCp", + "entity": {"name": "bPKC","alias": "bPKCp" + }, "field": "concInit", "value": 2e-05, "units": "mM" }, { - "name": "PPhosphatase2A", - "alias": "PPhosphatase2A", + "entity": {"name": "PPhosphatase2A","alias": "PPhosphatase2A" + }, "field": "concInit", "value": 0.001, "units": "mM" }, { - "name": "Ras+craf", - "alias": "Ras_act_craf", + "entity": {"name": "Ras+craf","alias": "Ras_act_craf" + }, "field": "Kf", "value": 9999.6668, "units": "none" }, { - "name": "SHCp_deph", - "alias": "SHCp_deph", + "entity": {"name": "SHCp_deph","alias": "SHCp_deph" + }, "field": "Kf", "value": 0.2, "units": "none" }, { - "name": "ePKC+craf", - "alias": "PKC_act_raf", + "entity": {"name": "ePKC+craf","alias": "PKC_act_raf" + }, "field": "Km", "value": 0.0209818384, "units": "none" }, { - "name": "eMAPKK+MAPK", - "alias": "MAPKKtyr", + "entity": {"name": "eMAPKK+MAPK","alias": "MAPKKtyr" + }, "field": "kcat", "value": 0.3, "units": "none" }, { - "name": "eMAPKK+MAPKp", - "alias": "MAPKKthr", + "entity": {"name": "eMAPKK+MAPKp","alias": "MAPKKthr" + }, "field": "kcat", "value": 0.3, "units": "none" }, { - "name": "eRas+MAPKK1", - "alias": "Rafp_RasGTP1", + "entity": {"name": "eRas+MAPKK1","alias": "Rafp_RasGTP1" + }, "field": "kcat", "value": 0.3, "units": "none" }, { - "name": "eRas+MAPKK2", - "alias": "Rafp_RasGTP2", + "entity": {"name": "eRas+MAPKK2","alias": "Rafp_RasGTP2" + }, "field": "kcat", "value": 0.3, "units": "none" }, { - "name": "eSHCpSosGrb2+Ras", - "alias": "Sos_Ras_GEF", + "entity": {"name": "eSHCpSosGrb2+Ras","alias": "Sos_Ras_GEF" + }, "field": "kcat", "value": 0.2, "units": "none" }, { - "name": "eMKP1+MAPKp", - "alias": "MKP1pY421_deph", + "entity": {"name": "eMKP1+MAPKp","alias": "MKP1pY421_deph" + }, "field": "kcat", "value": 4, "units": "none" }, { - "name": "eMKP1+MAPKpq", - "alias": "MKP1pT424_deph", + "entity": {"name": "eMKP1+MAPKpq","alias": "MKP1pT424_deph" + }, "field": "kcat", "value": 4, "units": "none" }, { - "name": "eMKP1+MAPKpq", - "alias": "MKP1pT424_deph", + "entity": {"name": "eMKP1+MAPKpq" + }, "field": "Km", "value": 0.00734, "units": "none" }, { - "name": "eMKP1+MAPKp", - "alias": "MKP1pY421_deph", + "entity": {"name": "eMKP1+MAPKp" + }, "field": "Km", "value": 0.00734, "units": "none" }, { - "name": "PI3K+RasGTP", - "alias": "PI3K_bind_RasGTP", + "entity": {"name": "PI3K+RasGTP","alias": "PI3K_bind_RasGTP" + }, "field": "Kf", "value": 3600, "units": "none" }, { - "name": "PI3K+RasGTP", - "alias": "PI3K_bind_RasGTP", + "entity": {"name": "PI3K+RasGTP" + }, "field": "Kb", "value": 0.2, "units": "none" diff --git a/Curated/Mundell2001_Fig3B.json b/Curated/Mundell2001_Fig3B.json index 703ba67..8e7753c 100644 --- a/Curated/Mundell2001_Fig3B.json +++ b/Curated/Mundell2001_Fig3B.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,7 +27,7 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity" : { + "entity": { "name": "Glutamate", "alias": "Glutamate" }, @@ -38,15 +40,14 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { + "entity": { "name": "tot_surface_mGluR_with_barr2", "alias": "tot_surface_mGluR_with_barr2" - }, + }, "field": "conc", "normalization": { - "entity" : { - "name": "tot_surface_mGluR_with_barr2", - "alias": "tot_surface_mGluR_with_barr2" + "entity": { + "name": "tot_surface_mGluR_with_barr2" }, "sampling": "start" }, @@ -60,10 +61,78 @@ }, "Modifications": { "subset": [ - {"name":"mGluR_g","alias":"mGluR_g"},{"name":"barr2_g","alias":"barr2_g"},{"name":"PP2A","alias":"PP2A"} + { + "name": "mGluR_g" + }, + { + "name": "barr2_g" + }, + { + "name": "PP2A" + } ], "itemsToDelete": [ - {"name":"mGluR_Gq","alias":"mGluR_Gq"},{"name":"amGluR","alias":"Glu_mGluR_Gq"},{"name":"Glu_mGluR+Gq","alias":"Glu_mGluR_bind_Gq"},{"name":"Glu+mGluR_Gq","alias":"Glu_bind_mGluR_Gq"},{"name":"Act_Gq","alias":"Act_Gq"},{"name":"mGluR_bind_Gq","alias":"mGluR_bind_Gq"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"} + { + "name": "mGluR_Gq" + }, + { + "name": "amGluR", + "alias": "Glu_mGluR_Gq" + }, + { + "name": "Glu_mGluR+Gq", + "alias": "Glu_mGluR_bind_Gq" + }, + { + "name": "Act_Gq" + }, + { + "name": "ePP2A+S6Kpq", + "alias": "clus_S6K_deph" + }, + { + "name": "ePP2A+S6Kpqrs", + "alias": "S6K_dephosp" + }, + { + "name": "ePP2A+S6Kpqr", + "alias": "S6K_deph" + }, + { + "name": "ePP2A+AKTpq", + "alias": "AKTpS473_deph" + }, + { + "name": "ePP2A+AKTp", + "alias": "AKTpT308_deph" + }, + { + "name": "ePP2A+eEF2p", + "alias": "eEF2p_deph" + }, + { + "name": "ePP2A+4EBPpqr", + "alias": "PP2A_4EBPpp" + }, + { + "name": "ePP2A+4EBPpq", + "alias": "PP2A_4EBPp" + }, + { + "name": "ePP2A+eIF4EBPpqr", + "alias": "PP2A_eIF4EBPpp" + }, + { + "name": "ePP2A+eIF4EBPpq", + "alias": "PP2A_eIF4EBPp" + }, + { + "name": "ePP2A+I1p", + "alias": "PP2A_dephos_I1" + }, + { + "name": "PP2A_dephos_PP1_Ip" + } ] } } diff --git a/Curated/Tran2007_Fig2A.json b/Curated/Tran2007_Fig2A.json index d8ec792..49d1896 100644 --- a/Curated/Tran2007_Fig2A.json +++ b/Curated/Tran2007_Fig2A.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +27,7 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity" : { - "name": "Glutamate", - "alias": "Glutamate" - }, + "entity": {"name": "Glutamate","alias": "Glutamate"}, "field": "conc", "data": [ [300,0.0] @@ -38,16 +37,10 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "beta2ARp", - "alias": "beta2ARp" - }, + "entity": {"name": "beta2ARp","alias": "beta2ARp"}, "field": "conc", "normalization": { - "entity" : { - "name": "beta2ARp", - "alias": "beta2ARp" - }, + "entity": {"name": "beta2ARp"}, "sampling": "start" }, "data": [ @@ -63,15 +56,37 @@ }, "Modifications": { "subset": [ - {"name":"mGluR_g","alias":"mGluR_g"},{"name":"barr2_g","alias":"barr2_g"},{"name":"PP2A","alias":"PP2A"},{"name":"MAPK_g","alias":"MAPK_g"} + {"name": "mGluR_g"},{"name": "barr2_g"},{"name": "PP2A"},{"name": "MAPK_g"} ], "itemsToDelete": [ - {"name":"mGluR_Gq","alias":"mGluR_Gq"},{"name":"amGluR","alias":"Glu_mGluR_Gq"},{"name":"Glu_mGluR+Gq","alias":"Glu_mGluR_bind_Gq"},{"name":"Glu+mGluR_Gq","alias":"Glu_bind_mGluR_Gq"},{"name":"Act_Gq","alias":"Act_Gq"},{"name":"mGluR_bind_Gq","alias":"mGluR_bind_Gq"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"},{"name":"eMAPK+crafp","alias":"MAPKpp_feedback"},{"name":"eMAPK+PLA2","alias":"MAPKpp_act_PLA2"},{"name":"Sos_phospho","alias":"Sos_phospho"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"} + {"name": "mGluR_Gq"}, + {"name": "amGluR","alias": "Glu_mGluR_Gq"}, + {"name": "Glu_mGluR+Gq","alias": "Glu_mGluR_bind_Gq"}, + {"name": "Glu+mGluR_Gq","alias": "Glu_bind_mGluR_Gq"}, + {"name": "Act_Gq"}, + {"name": "mGluR_bind_Gq"}, + {"name": "ePP2A+S6Kpq","alias": "clus_S6K_deph"}, + {"name": "ePP2A+S6Kpqrs","alias": "S6K_dephosp"}, + {"name": "ePP2A+S6Kpqr","alias": "S6K_deph"}, + {"name": "ePP2A+AKTpq","alias": "AKTpS473_deph"}, + {"name": "ePP2A+AKTp","alias": "AKTpT308_deph"}, + {"name": "ePP2A+eEF2p","alias": "eEF2p_deph"}, + {"name": "ePP2A+4EBPpqr","alias": "PP2A_4EBPpp"}, + {"name": "ePP2A+4EBPpq","alias": "PP2A_4EBPp"}, + {"name": "ePP2A+eIF4EBPpqr","alias": "PP2A_eIF4EBPpp"}, + {"name": "ePP2A+eIF4EBPpq","alias": "PP2A_eIF4EBPp"}, + {"name": "ePP2A+I1p","alias": "PP2A_dephos_I1"}, + {"name": "PP2A_dephos_PP1_Ip"}, + {"name": "eMAPK+S6K","alias": "clus_S6K_phospho"}, + {"name": "eMAPK+crafp","alias": "MAPKpp_feedback"}, + {"name": "eMAPK+PLA2","alias": "MAPKpp_act_PLA2"}, + {"name": "Sos_phospho"}, + {"name": "eMAPK+4EBPpq","alias": "MAPK_4EBPpp"}, + {"name": "eMAPK+eIF4EBPpq","alias": "MAPK_4EBP_phospho"} + ], "parameterChange": [ - { - "name": "Glutamate", - "alias": "Glutamate", + {"entity": {"name": "Glutamate"}, "field": "concInit", "value": 0.1, "units": "mM" diff --git a/FindSim-Schema.json b/FindSim-Schema.json index 0201b1e..d1b90db 100644 --- a/FindSim-Schema.json +++ b/FindSim-Schema.json @@ -19,7 +19,7 @@ }, "type": "object", "properties": { - "ContentType":{"type": "string"}, + "FileType":{"type": "string"}, "Version": {"type": "string"}, "Metadata": { "type": "object", @@ -83,7 +83,8 @@ {"properties": { "sourceType": {"const": "other"}, "doi": { "type": "string" }, - "year": {"type": "number"} + "year": {"type": "number"}, + "journal":{"type":"string"} }, "required": ["doi","year"] } @@ -306,7 +307,7 @@ "enum": ["nM", "uM", "mM", "M", "#", "s", "sec", "1/s", "1/sec", "uV", "mV", "V", "pA", "nA", "uA", "none"] } }, - "required": [ "field", "value", "units"] + "required": [ "entity","field", "value", "units"] } }, "notes": {"type": "string" } @@ -319,7 +320,7 @@ "additionalProperties": false } }, - "required": ["Metadata", "Experiment", "Readouts"], + "required": ["FileType","Version","Metadata", "Experiment", "Readouts"], "additionalProperties": false, "if": { "required": [ "Experiment" ], diff --git a/Non-Curated/Bhalla1999_Fig2C.json b/Non-Curated/Bhalla1999_Fig2C.json index 983524f..e2726c0 100644 --- a/Non-Curated/Bhalla1999_Fig2C.json +++ b/Non-Curated/Bhalla1999_Fig2C.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity" : { - "name": "Ca", - "alias": "Ca" - }, + "entity" : {"name": "Ca","alias": "Ca"}, "field": "conc" } ], @@ -36,16 +34,10 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "ratio", - "entity" : { - "name": "aPLCg", - "alias": "CaPLCgp" - }, + "entity" : {"name": "aPLCg","alias": "CaPLCgp"}, "field": "conc", "normalization": { - "entity" : { - "name": "aPLCg", - "alias": "CaPLCgp" - }, + "entity" : {"name": "aPLCg","alias": "CaPLCgp"}, "dose": 100, "sampling": "dose" }, @@ -73,22 +65,17 @@ ], "parameterChange": [ { - "name": "EGF", - "alias": "EGF", + "entity" : {"name": "EGF","alias": "EGF"}, "field": "concInit", "value": 0.0001, "units": "mM" }, - { - "name": "PLCg", - "alias": "PLCg", + { "entity" : {"name": "PLCg","alias": "PLCg"}, "field": "concInit", "value": 0.00082, "units": "mM" }, - { - "name": "Ca", - "alias": "Ca", + { "entity" : {"name": "Ca","alias": "Ca"}, "field": "isBuffered", "value": 1, "units": "none" diff --git a/Non-Curated/HH_Fig13.json b/Non-Curated/HH_Fig13.json index 841dafe..a469b76 100644 --- a/Non-Curated/HH_Fig13.json +++ b/Non-Curated/HH_Fig13.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -24,10 +25,7 @@ { "timeUnits": "msec", "quantityUnits": "nA", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "inject", "data": [ [0,2000], @@ -38,10 +36,7 @@ "Readouts": { "timeUnits": "msec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma", "alias": "soma"}, "field": "Vm", "data": [ [0, -45.0], diff --git a/Non-Curated/HH_vclamp4.json b/Non-Curated/HH_vclamp4.json index 017d2b5..a4243a5 100644 --- a/Non-Curated/HH_vclamp4.json +++ b/Non-Curated/HH_vclamp4.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -24,10 +25,7 @@ { "timeUnits": "msec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "Vclamp", "data": [ [0,-65.0], @@ -40,10 +38,7 @@ "Readouts": { "timeUnits": "msec", "quantityUnits": "uA", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "current", "data": [ [0, 0], diff --git a/Non-Curated/Jain2009_Fig2C.json b/Non-Curated/Jain2009_Fig2C.json index b808ffd..5a610dc 100644 --- a/Non-Curated/Jain2009_Fig2C.json +++ b/Non-Curated/Jain2009_Fig2C.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "BDNF", - "alias": "BDNF" - }, + "entity" : { "name": "BDNF", "alias": "BDNF" }, "field": "conc" } ], @@ -36,10 +34,7 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "nM", - "entity" : { - "name": "aSHC", - "alias": "SHCp" - }, + "entity" : {"name": "aSHC","alias": "SHCp"}, "field": "conc", "data": [ [0, 0, 0], diff --git a/Non-Curated/Jain2009_Fig2D.json b/Non-Curated/Jain2009_Fig2D.json index 538dc25..3bebdc4 100644 --- a/Non-Curated/Jain2009_Fig2D.json +++ b/Non-Curated/Jain2009_Fig2D.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "BDNF", - "alias": "BDNF" - }, + "entity" : {"name": "BDNF", "alias": "BDNF"}, "field": "conc" } ], @@ -36,10 +34,7 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "nM", - "entity" : { - "name": "PLCgp", - "alias": "PLCgp" - }, + "entity" : {"name": "PLCgp", "alias": "PLCgp"}, "field": "conc", "data": [ [0, 3, 0], @@ -58,8 +53,7 @@ ], "parameterChange": [ { - "name": "PLCg", - "alias": "PLCg", + "entity":{"name": "PLCg","alias": "PLCg"}, "field": "concInit", "value": 0.0001, "units": "mM" diff --git a/Non-Curated/Jain2009_Fig3B.json b/Non-Curated/Jain2009_Fig3B.json index 8edc8d6..233e557 100644 --- a/Non-Curated/Jain2009_Fig3B.json +++ b/Non-Curated/Jain2009_Fig3B.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "mTOR", - "alias": "mTOR" - }, + "entity" : {"name": "mTOR","alias": "mTOR" }, "field": "conc" } ], @@ -36,10 +34,7 @@ "timeUnits": "sec", "settleTime": 3600, "quantityUnits": "uM", - "entity" : { - "name": "S6Kpqr", - "alias": "S6KpT412" - }, + "entity" : {"name": "S6Kpqr", "alias": "S6KpT412"}, "field": "conc", "data": [ [0.45, 0.01, 0], @@ -58,9 +53,7 @@ {"name":"eS6Kpqr+40S","alias":"S6_phos"},{"name":"eS6Kpqrs+40S","alias":"S6_phospho"},{"name":"eS6Kpqrs+CaMKIII","alias":"S6Kp_act_CaMKIII"},{"name":"bS6K","alias":"bS6K"},{"name":"emTORC1+4EBP","alias":"TOR_4EBPp"},{"name":"emTORC1+4EBPhospho","alias":"TOR_4EBP_phospho"},{"name":"S6_dephosph","alias":"S6_dephosph"} ], "parameterChange": [ - { - "name": "S6K", - "alias": "S6K", + { "entity":{ "name": "S6K","alias": "S6K"}, "field": "concInit", "value": 0.0009, "units": "mM" diff --git a/Non-Curated/Jain2009_Fig4B.json b/Non-Curated/Jain2009_Fig4B.json index 75979d2..2f8bc18 100644 --- a/Non-Curated/Jain2009_Fig4B.json +++ b/Non-Curated/Jain2009_Fig4B.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -25,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "M", - "entity" : { - "name": "CaMCa4", - "alias": "CaMCa4" - }, + "entity" : {"name": "CaMCa4","alias": "CaMCa4"}, "field": "conc" } ], @@ -36,10 +34,7 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "uM", - "entity" : { - "name": "eEF2p", - "alias": "eEF2p" - }, + "entity" : {"name": "eEF2p", "alias": "eEF2p" }, "field": "conc", "display": { "useXlog": true, @@ -67,15 +62,12 @@ ], "parameterChange": [ { - "name": "eEF2", - "alias": "eEF2", + "entity":{"name": "eEF2","alias": "eEF2"}, "field": "concInit", "value": 0.00054555, "units": "mM" }, - { - "name": "CaMKIII", - "alias": "CaMKIII", + { "entity":{"name": "CaMKIII","alias": "CaMKIII"}, "field": "concInit", "value": 3.65e-05, "units": "mM" diff --git a/Non-Curated/Jain2009_Fig4F.json b/Non-Curated/Jain2009_Fig4F.json index 18e27d0..ced4005 100644 --- a/Non-Curated/Jain2009_Fig4F.json +++ b/Non-Curated/Jain2009_Fig4F.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,10 +25,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "aS6", - "alias": "S6p" - }, + "entity" : {"name": "aS6","alias": "S6p"}, "field": "conc" } ], @@ -35,10 +33,7 @@ "timeUnits": "sec", "settleTime": 2400, "quantityUnits": "nM", - "entity" : { - "name": "43S", - "alias": "43S" - }, + "entity" : {"name": "43S","alias": "43S"}, "field": "conc", "data": [ [6.8, 3.61, 0], @@ -53,16 +48,12 @@ {"name":"Transl_init_g","alias":"Transl_init_g"},{"name":"_40S_g","alias":"40S_g"},{"name":"_43S_g","alias":"43S_g"} ], "parameterChange": [ - { - "name": "M_clx", - "alias": "M_clx", + { "entity":{"name": "M_clx","alias": "M_clx"}, "field": "concInit", "value": 0.0015, "units": "mM" }, - { - "name": "Q_clx", - "alias": "Q_clx", + { "entity":{"name": "Q_clx","alias": "Q_clx"}, "field": "concInit", "value": 4.97e-05, "units": "mM" diff --git a/Non-Curated/PKC_SB_Fig7.json b/Non-Curated/PKC_SB_Fig7.json index 219d98d..e576cc3 100644 --- a/Non-Curated/PKC_SB_Fig7.json +++ b/Non-Curated/PKC_SB_Fig7.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upi Bhalla", "organization": "National Centre for Biological Sciences", @@ -25,30 +26,21 @@ "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "Ca", - "alias": "Ca" - }, + "entity" : {"name": "Ca","alias": "Ca" }, "value": 1.0 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "DAG", - "alias": "DAG" - }, + "entity" : {"name": "DAG", "alias": "DAG"}, "value": 50 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "AA", - "alias": "AA" - }, + "entity" : {"name": "AA","alias": "AA"}, "value": 50 } ], @@ -56,16 +48,10 @@ "timeUnits": "sec", "settleTime": 15, "quantityUnits": "ratio", - "entity" : { - "name": "aPKC", - "alias": "aPKC" - }, + "entity" : {"name": "aPKC","alias": "aPKC"}, "field": "conc", "normalization": { - "entity" : { - "name": "aPKC", - "alias": "aPKC" - }, + "entity" : { "name": "aPKC","alias": "aPKC" }, "sampling": "start" }, "bardata": [ @@ -109,44 +95,36 @@ {"name":"ePKC+craf","alias":"PKC_act_raf"},{"name":"PKC_inact_GAP","alias":"PKC_inact_GAP"},{"name":"PKC_act_GEF","alias":"PKC_act_GEF"},{"name":"PKC_phosph_neurogranin","alias":"PKC_phosph_neurogranin"},{"name":"PKC_phosph_ng_CaM","alias":"PKC_phosph_ng_CaM"},{"name":"phosph_AC2","alias":"phosph_AC2"} ], "parameterChange": [ - { - "name": "Ca", - "alias": "Ca", + { "entity" :{"name": "Ca","alias": "Ca"}, "field": "concInit", "value": 0.0001, "units": "mM" }, - { - "name": "Ca", - "alias": "Ca", + { "entity" :{"name": "Ca","alias": "Ca"}, "field": "isBuffered", "value": 1, "units": "none" }, { - "name": "DAG", - "alias": "DAG", + "entity" :{"name": "DAG","alias": "DAG"}, "field": "concInit", "value": 0, "units": "mM" }, { - "name": "DAG", - "alias": "DAG", + "entity" :{"name": "DAG","alias": "DAG"}, "field": "isBuffered", "value": 1, "units": "none" }, { - "name": "AA", - "alias": "AA", + "entity" :{"name": "AA","alias": "AA"}, "field": "concInit", "value": 0, "units": "mM" }, { - "name": "AA", - "alias": "AA", + "entity" :{"name": "AA","alias": "AA"}, "field": "isBuffered", "value": 1, "units": "none" diff --git a/Non-Curated/PKC_SB_Fig8.json b/Non-Curated/PKC_SB_Fig8.json index b00f3b3..51621a1 100644 --- a/Non-Curated/PKC_SB_Fig8.json +++ b/Non-Curated/PKC_SB_Fig8.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upi Bhalla", "organization": "National Centre for Biological Sciences", @@ -25,30 +26,21 @@ "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "Ca", - "alias": "Ca" - }, + "entity" : {"name": "Ca","alias": "Ca"}, "value": 1.0 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "DAG", - "alias": "DAG" - }, + "entity" : {"name": "DAG","alias": "DAG"}, "value": 100 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "AA", - "alias": "AA" - }, + "entity" : {"name": "AA","alias": "AA"}, "value": 50 } ], @@ -62,10 +54,7 @@ }, "field": "conc", "normalization": { - "entity" : { - "name": "aPKC", - "alias": "aPKC" - }, + "entity" : {"name": "aPKC","alias": "aPKC"}, "sampling": "start" }, "bardata": [ @@ -119,44 +108,32 @@ {"name":"ePKC+craf","alias":"PKC_act_raf"},{"name":"PKC_inact_GAP","alias":"PKC_inact_GAP"},{"name":"PKC_act_GEF","alias":"PKC_act_GEF"},{"name":"PKC_phosph_neurogranin","alias":"PKC_phosph_neurogranin"},{"name":"PKC_phosph_ng_CaM","alias":"PKC_phosph_ng_CaM"},{"name":"phosph_AC2","alias":"phosph_AC2"} ], "parameterChange": [ - { - "name": "Ca", - "alias": "Ca", + {"entity":{"name": "Ca","alias": "Ca"}, "field": "concInit", "value": 0.0001, "units": "mM" }, - { - "name": "Ca", - "alias": "Ca", + {"entity":{"name": "Ca","alias": "Ca"}, "field": "isBuffered", "value": 1, "units": "none" }, - { - "name": "DAG", - "alias": "DAG", + {"entity":{"name": "DAG","alias": "DAG"}, "field": "concInit", "value": 0, "units": "mM" }, - { - "name": "DAG", - "alias": "DAG", + {"entity":{"name": "DAG","alias": "DAG"}, "field": "isBuffered", "value": 1, "units": "none" }, - { - "name": "AA", - "alias": "AA", + {"entity":{"name": "AA","alias": "AA"}, "field": "concInit", "value": 0, "units": "mM" }, - { - "name": "AA", - "alias": "AA", + {"entity":{"name": "AA","alias": "AA"}, "field": "isBuffered", "value": 1, "units": "none" diff --git a/Non-Curated/directParamsDemo.json b/Non-Curated/directParamsDemo.json index c451cb4..9cbac27 100644 --- a/Non-Curated/directParamsDemo.json +++ b/Non-Curated/directParamsDemo.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -22,41 +23,25 @@ }, "Readouts": { "paramdata": [ - { - "entity" : { - "name": "MAPK_phosph_PLA2", - "alias": "MAPK_phosph_PLA2" - }, + { "entity" : {"name": "MAPK_phosph_PLA2","alias": "MAPK_phosph_PLA2"}, "field": "kcat", "units": "1/sec", "value": 20, "stderr": 0 }, - { - "entity" : { - "name": "MAPK_phosph_4EBP", - "alias": "MAPK_phosph_4EBP" - }, + { "entity" : {"name": "MAPK_phosph_4EBP","alias": "MAPK_phosph_4EBP"}, "field": "kcat", "units": "1/sec", "value": 0.1, "stderr": 0 }, - { - "entity" : { - "name": "MAPK_phosph_PLA2", - "alias": "MAPK_phosph_PLA2" - }, + { "entity" : {"name": "MAPK_phosph_PLA2","alias": "MAPK_phosph_PLA2"}, "field": "Km", "units": "uM", "value": 27, "stderr": 0 }, - { - "entity" : { - "name": "MAPK_phosph_4EBP", - "alias": "MAPK_phosph_4EBP" - }, + { "entity" : {"name": "MAPK_phosph_4EBP","alias": "MAPK_phosph_4EBP"}, "field": "Km", "units": "uM", "value": 20, diff --git a/TestJson/Non-Curated/dr_j2c.json b/TestJson/Non-Curated/dr_j2c.json index 82c583a..edd030d 100644 --- a/TestJson/Non-Curated/dr_j2c.json +++ b/TestJson/Non-Curated/dr_j2c.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,10 +25,7 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "BDNF", - "alias": "BDNF" - }, + "entity" : {"name": "BDNF","alias": "BDNF"}, "field": "conc" } ], @@ -35,10 +33,7 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "nM", - "entity" : { - "name": "aSHC", - "alias": "SHCp" - }, + "entity" : {"name": "aSHC","alias": "SHCp"}, "field": "conc", "data": [ [0, 0, 0], @@ -56,9 +51,7 @@ {"name":"eTrKB+PLCg","alias":"TrKB_act_PLCg"} ], "parameterChange": [ - { - "name": "SHCp_deph", - "alias": "SHCp_deph", + { "entity":{ "name": "SHCp_deph", "alias": "SHCp_deph"}, "field": "Kf", "value": 0.2, "units": "none" diff --git a/TestJson/bc_ratio_sb8.json b/TestJson/bc_ratio_sb8.json index b00f3b3..d15df4f 100644 --- a/TestJson/bc_ratio_sb8.json +++ b/TestJson/bc_ratio_sb8.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upi Bhalla", "organization": "National Centre for Biological Sciences", @@ -25,30 +27,21 @@ "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "Ca", - "alias": "Ca" - }, + "entity": {"name": "Ca","alias": "Ca"}, "value": 1.0 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "DAG", - "alias": "DAG" - }, + "entity": {"name": "DAG","alias": "DAG"}, "value": 100 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity" : { - "name": "AA", - "alias": "AA" - }, + "entity": {"name": "AA","alias": "AA"}, "value": 50 } ], @@ -56,16 +49,10 @@ "timeUnits": "sec", "settleTime": 150, "quantityUnits": "ratio", - "entity" : { - "name": "aPKC", - "alias": "aPKC" - }, + "entity": { "name": "aPKC","alias": "aPKC"}, "field": "conc", "normalization": { - "entity" : { - "name": "aPKC", - "alias": "aPKC" - }, + "entity": {"name": "aPKC"}, "sampling": "start" }, "bardata": [ @@ -113,50 +100,43 @@ }, "Modifications": { "subset": [ - {"name":"Ca","alias":"Ca"},{"name":"AA","alias":"AA"},{"name":"PKC_g","alias":"PKC_g"},{"name":"DAG","alias":"DAG"} + {"name": "Ca"},{"name": "AA"},{"name": "PKC_g"},{"name": "DAG"} ], "itemsToDelete": [ - {"name":"ePKC+craf","alias":"PKC_act_raf"},{"name":"PKC_inact_GAP","alias":"PKC_inact_GAP"},{"name":"PKC_act_GEF","alias":"PKC_act_GEF"},{"name":"PKC_phosph_neurogranin","alias":"PKC_phosph_neurogranin"},{"name":"PKC_phosph_ng_CaM","alias":"PKC_phosph_ng_CaM"},{"name":"phosph_AC2","alias":"phosph_AC2"} + {"name": "ePKC+craf","alias": "PKC_act_raf"}, + {"name": "PKC_inact_GAP"}, + {"name": "PKC_act_GEF"}, + {"name": "PKC_phosph_neurogranin"}, + {"name": "PKC_phosph_ng_CaM"}, + {"name": "phosph_AC2"} ], "parameterChange": [ - { - "name": "Ca", - "alias": "Ca", + { "entity": {"name": "Ca"}, "field": "concInit", "value": 0.0001, "units": "mM" }, - { - "name": "Ca", - "alias": "Ca", + { "entity": {"name": "Ca"}, "field": "isBuffered", "value": 1, "units": "none" }, - { - "name": "DAG", - "alias": "DAG", + { "entity": {"name": "DAG"}, "field": "concInit", "value": 0, "units": "mM" }, - { - "name": "DAG", - "alias": "DAG", + { "entity": {"name": "DAG"}, "field": "isBuffered", "value": 1, "units": "none" }, - { - "name": "AA", - "alias": "AA", + { "entity": {"name": "AA"}, "field": "concInit", "value": 0, "units": "mM" }, - { - "name": "AA", - "alias": "AA", + { "entity": {"name": "AA"}, "field": "isBuffered", "value": 1, "units": "none" diff --git a/TestJson/dp.json b/TestJson/dp.json index 5d7482e..fdf0cc5 100644 --- a/TestJson/dp.json +++ b/TestJson/dp.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -23,40 +25,28 @@ "Readouts": { "paramdata": [ { - "entity" : { - "name": "eMAPK+PLA2", - "alias": "MAPKpp_act_PLA2" - }, + "entity": {"name": "eMAPK+PLA2","alias": "MAPKpp_act_PLA2"}, "field": "kcat", "units": "1/sec", "value": 20, "stderr": 50 }, { - "entity" : { - "name": "eMAPK+eIF4EBPpq", - "alias": "MAPK_4EBP_phospho" - }, + "entity": {"name": "eMAPK+eIF4EBPpq","alias": "MAPK_4EBP_phospho"}, "field": "kcat", "units": "1/sec", "value": 0.1, "stderr": 0.05 }, { - "entity" : { - "name": "eMAPK+PLA2", - "alias": "MAPKpp_act_PLA2" - }, + "entity": {"name": "eMAPK+PLA2"}, "field": "Km", "units": "uM", "value": 27, "stderr": 5 }, { - "entity" : { - "name": "eMAPK+eIF4EBPpq", - "alias": "MAPK_4EBP_phospho" - }, + "entity": {"name": "eMAPK+eIF4EBPpq"}, "field": "Km", "units": "uM", "value": 20, @@ -66,7 +56,7 @@ }, "Modifications": { "subset": [ - {"name":"all"} + {"name": "all"} ] } } diff --git a/TestJson/dp_Kd_tau.json b/TestJson/dp_Kd_tau.json index 650aac0..4c57436 100644 --- a/TestJson/dp_Kd_tau.json +++ b/TestJson/dp_Kd_tau.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -23,40 +25,28 @@ "Readouts": { "paramdata": [ { - "entity" : { - "name": "RecLigandBinding", - "alias": "RecLigandBinding" - }, + "entity": {"name": "RecLigandBinding","alias": "RecLigandBinding"}, "field": "tau", "units": "sec", "value": 0.04, "stderr": 0.01 }, { - "entity" : { - "name": "makeTernary", - "alias": "makeTernary" - }, + "entity": {"name": "makeTernary","alias": "makeTernary"}, "field": "tau", "units": "sec", "value": 160, "stderr": 50 }, { - "entity" : { - "name": "RecLigandBinding", - "alias": "RecLigandBinding" - }, + "entity": {"name": "RecLigandBinding"}, "field": "Kd", "units": "uM", "value": 0.6, "stderr": 0.1 }, { - "entity" : { - "name": "makeTernary", - "alias": "makeTernary" - }, + "entity": {"name": "makeTernary"}, "field": "Kd", "units": "uM", "value": 0.015, @@ -66,10 +56,10 @@ }, "Modifications": { "subset": [ - {"name":"mGluR_g","alias":"mGluR_g"},{"name":"Gq_GDP","alias":"G_GDP"} + {"name": "mGluR_g"},{"name": "Gq_GDP","alias": "G_GDP"} ], "itemsToDelete": [ - {"name":"Activate_Gq","alias":"Activate_Gq"} + {"name": "Activate_Gq"} ] } } diff --git a/TestJson/dr_ratio_b2c.json b/TestJson/dr_ratio_b2c.json index 05234a2..3dd4333 100644 --- a/TestJson/dr_ratio_b2c.json +++ b/TestJson/dr_ratio_b2c.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity" : { - "name": "Ca", - "alias": "Ca" - }, + "entity": {"name": "Ca","alias": "Ca"}, "field": "conc" } ], @@ -35,16 +34,10 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "ratio", - "entity" : { - "name": "aPLCg", - "alias": "CaPLCgp" - }, + "entity": {"name": "aPLCg","alias": "CaPLCgp"}, "field": "conc", "normalization": { - "entity" : { - "name": "aPLCg", - "alias": "CaPLCgp" - }, + "entity": {"name": "aPLCg"}, "dose": 100, "sampling": "dose" }, @@ -65,29 +58,26 @@ }, "Modifications": { "subset": [ - {"name":"Ca_g","alias":"Ca_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"EGFR_g","alias":"EGFR_g"} + {"name": "Ca_g"},{"name": "PLCg_g"},{"name": "EGFR_g"} ], "itemsToDelete": [ - {"name":"PLCgp_deph","alias":"PLCgp_deph"},{"name":"eEGFR+SHC","alias":"EGFR_act_SHC"},{"name":"eCaPLCg+PIP2","alias":"CaPLCg_PIP2hydr"},{"name":"EGF_act_PLCg","alias":"EGF_act_PLCg"} + {"name": "PLCgp_deph"}, + {"name": "eEGFR+SHC","alias": "EGFR_act_SHC"}, + {"name": "eCaPLCg+PIP2","alias": "CaPLCg_PIP2hydr"}, + {"name": "EGF_act_PLCg"} ], "parameterChange": [ - { - "name": "EGF", - "alias": "EGF", + { "entity": {"name": "EGF","alias": "EGF"}, "field": "concInit", "value": 0.0001, "units": "mM" }, - { - "name": "PLCg", - "alias": "PLCg", + { "entity": {"name": "PLCg","alias": "PLCg"}, "field": "concInit", "value": 0.00082, "units": "mM" }, - { - "name": "Ca", - "alias": "Ca", + { "entity": {"name": "Ca"}, "field": "isBuffered", "value": 1, "units": "none" diff --git a/TestJson/epsc.json b/TestJson/epsc.json index 991ae90..535d769 100644 --- a/TestJson/epsc.json +++ b/TestJson/epsc.json @@ -1,15 +1,14 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upi", "organization": "NCBS", "email": "bhalla@ncbs.res.in", "source": { - "sourceType": "other", - "doi": "0", - "authors": "None", + "sourceType": "inhouse", "journal": "None. This is a purely fictional _experiment_ for the purposes of testing findSim", - "year": 0, - "figure": "" + "url": "www.ncbs.res.in" }, "testModel": "models/plastic8.py", "testMap": "models/plastic8.json" @@ -24,7 +23,7 @@ { "timeUnits": "sec", "quantityUnits": "Hz", - "entity" : { + "entity": { "name": "synInput", "alias": "synInput" }, @@ -36,7 +35,7 @@ { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { + "entity": { "name": "synapse", "alias": "synapse" }, @@ -49,7 +48,7 @@ { "timeUnits": "sec", "quantityUnits": "mV", - "entity" : { + "entity": { "name": "soma", "alias": "soma" }, @@ -64,10 +63,10 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "pA", - "entity" : { + "entity": { "name": "vclamp", "alias": "vclamp" - }, + }, "field": "EPSC_peak", "data": [ [4, 40, 0], @@ -78,7 +77,9 @@ }, "Modifications": { "subset": [ - {"name":"all"} + { + "name": "all" + } ] } } diff --git a/TestJson/epsc_ratio.json b/TestJson/epsc_ratio.json index 1cbb8a1..67a4bf8 100644 --- a/TestJson/epsc_ratio.json +++ b/TestJson/epsc_ratio.json @@ -1,14 +1,14 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", "email": "bhalla@ncbs.res.in", "source": { "sourceType": "other", - "authors": "Bhalla", "year": 2019, - "doi": "0", - "figure": "synthetic" + "doi": "0" }, "testModel": "models/plastic8.py", "testMap": "models/plastic8.json" @@ -24,10 +24,7 @@ { "timeUnits": "sec", "quantityUnits": "Hz", - "entity" : { - "name": "synInput", - "alias": "synInput" - }, + "entity": { "name": "synInput","alias": "synInput" }, "field": "rate", "data": [ [0,0] @@ -36,10 +33,7 @@ { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "synapse", - "alias": "synapse" - }, + "entity": {"name": "synapse","alias": "synapse"}, "field": "weight", "data": [ [0,0.4], @@ -51,10 +45,7 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity": {"name": "soma","alias": "soma"}, "field": "EPSP_peak", "data": [ [4, 2], diff --git a/TestJson/epsc_window_baseline_norm.json b/TestJson/epsc_window_baseline_norm.json index 51e1cb9..f8a181a 100644 --- a/TestJson/epsc_window_baseline_norm.json +++ b/TestJson/epsc_window_baseline_norm.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upi", "organization": "NCBS", @@ -24,10 +25,7 @@ { "timeUnits": "sec", "quantityUnits": "Hz", - "entity" : { - "name": "synInput", - "alias": "synInput" - }, + "entity" : {"name": "synInput", "alias": "synInput"}, "field": "rate", "data": [ [0,5] @@ -36,10 +34,7 @@ { "timeUnits": "sec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "Vclamp", "data": [ [0,-65.0], @@ -51,19 +46,13 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "vclamp", - "alias": "vclamp" - }, + "entity" : {"name": "vclamp","alias": "vclamp"}, "field": "current", "window": {"startt": -0.010, "endt": 0.005, "dt": 0.0005, "operation": "max", "baseline": "min" }, "normalization": { - "entity" : { - "name": "vclamp", - "alias": "vclamp" - }, + "entity" : {"name": "vclamp","alias": "vclamp"}, "sampling": "start" }, "data": [ diff --git a/TestJson/epsp.json b/TestJson/epsp.json index 809058b..b44afdf 100644 --- a/TestJson/epsp.json +++ b/TestJson/epsp.json @@ -1,15 +1,15 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upi", "organization": "NCBS", "email": "bhalla@ncbs.res.in", "source": { "sourceType": "inhouse", - "url": "www.ncbs.res.in", - "authors": "None", - "journal": "None. This is a purely fictional _experiment_ for the purposes of testing findSim", - "year": 0, - "figure": "" + "url":"www.ncbs.res.in", + "journal": "None. This is a purely fictional _experiment_ for the purposes of testing findSim" + }, "testModel": "models/plastic8.py", "testMap": "models/plastic8.json" @@ -24,10 +24,7 @@ { "timeUnits": "sec", "quantityUnits": "Hz", - "entity" : { - "name": "synInput", - "alias": "synInput" - }, + "entity": { "name": "synInput", "alias": "synInput" }, "field": "rate", "data": [ [0,0], @@ -38,10 +35,7 @@ { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "synapse", - "alias": "synapse" - }, + "entity": {"name": "synapse","alias": "synapse"}, "field": "weight", "data": [ [0,0.4], @@ -53,10 +47,7 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity": {"name": "soma","alias": "soma"}, "field": "EPSP_peak", "data": [ [4, 2, 0], @@ -67,7 +58,7 @@ }, "Modifications": { "subset": [ - {"name":"all"} + {"name": "all"} ] } } diff --git a/TestJson/epsp_ratio.json b/TestJson/epsp_ratio.json index 298be39..ce0cfee 100644 --- a/TestJson/epsp_ratio.json +++ b/TestJson/epsp_ratio.json @@ -1,15 +1,14 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", "email": "bhalla@ncbs.res.in", "source": { "sourceType": "other", - "doi": "www.ncbs.res.in", - "authors": "None", "year": 2019, - "PMID": 0, - "figure": "synthetic" + "doi": "0" }, "testModel": "models/plastic8.py", "testMap": "models/plastic8.json" @@ -25,10 +24,7 @@ { "timeUnits": "sec", "quantityUnits": "Hz", - "entity" : { - "name": "synInput", - "alias": "synInput" - }, + "entity": {"name": "synInput","alias": "synInput"}, "field": "rate", "data": [ [0,0], @@ -39,10 +35,7 @@ { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "synapse", - "alias": "synapse" - }, + "entity": {"name": "synapse","alias": "synapse"}, "field": "weight", "data": [ [0,0.4], @@ -54,17 +47,11 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity": {"name": "soma","alias": "soma"}, "field": "EPSP_peak", "normalization": { "sampling": "start", - "entity" : { - "name": "soma", - "alias": "soma" - } + "entity": {"name": "soma"} }, "data": [ [4, 1], diff --git a/TestJson/iclamp_hh13.json b/TestJson/iclamp_hh13.json index e7c07b2..7531e94 100644 --- a/TestJson/iclamp_hh13.json +++ b/TestJson/iclamp_hh13.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -24,10 +26,7 @@ { "timeUnits": "msec", "quantityUnits": "nA", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity": {"name": "soma","alias": "soma"}, "field": "inject", "data": [ [0,2000], @@ -38,10 +37,7 @@ "Readouts": { "timeUnits": "msec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity": {"name": "soma"}, "field": "Vm", "data": [ [0, -45.0], @@ -56,7 +52,7 @@ }, "Modifications": { "subset": [ - {"name":"all"} + {"name": "all"} ] } } diff --git a/TestJson/iclamp_hh_window.json b/TestJson/iclamp_hh_window.json index bbb36c3..ea161cf 100644 --- a/TestJson/iclamp_hh_window.json +++ b/TestJson/iclamp_hh_window.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -24,10 +25,7 @@ { "timeUnits": "msec", "quantityUnits": "nA", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "inject", "data": [ [0,0], @@ -39,10 +37,7 @@ "Readouts": { "timeUnits": "msec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "Vm", "window": {"startt": -2, "endt": 5, "dt": 0.2, "operation": "oscPk" diff --git a/TestJson/iclamp_hh_window_baseline.json b/TestJson/iclamp_hh_window_baseline.json index c2be427..f76ebc5 100644 --- a/TestJson/iclamp_hh_window_baseline.json +++ b/TestJson/iclamp_hh_window_baseline.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -24,10 +25,7 @@ { "timeUnits": "msec", "quantityUnits": "nA", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "inject", "data": [ [0,0], @@ -39,10 +37,7 @@ "Readouts": { "timeUnits": "msec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "Vm", "window": {"startt": -2, "endt": 5, "dt": 0.2, "operation": "max", "baseline": "min" diff --git a/TestJson/iclamp_hh_window_baseline_norm.json b/TestJson/iclamp_hh_window_baseline_norm.json index 8c07f32..726c128 100644 --- a/TestJson/iclamp_hh_window_baseline_norm.json +++ b/TestJson/iclamp_hh_window_baseline_norm.json @@ -1,4 +1,5 @@ -{ +{ "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -24,10 +25,7 @@ { "timeUnits": "msec", "quantityUnits": "nA", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "inject", "data": [ [0,0], @@ -39,19 +37,13 @@ "Readouts": { "timeUnits": "msec", "quantityUnits": "ratio", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "field": "Vm", "window": {"startt": -2, "endt": 5, "dt": 0.2, "operation": "max", "baseline": "min" }, "normalization": { - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity" : {"name": "soma","alias": "soma"}, "sampling": "start" }, "data": [ diff --git a/TestJson/ts_j4d.json b/TestJson/ts_j4d.json index a991fba..2148a54 100644 --- a/TestJson/ts_j4d.json +++ b/TestJson/ts_j4d.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,20 +26,14 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity" : { - "name": "eEF2p", - "alias": "eEF2p" - }, + "entity": {"name": "eEF2p","alias": "eEF2p"}, "field": "conc" } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entity" : { - "name": "eEF2", - "alias": "eEF2" - }, + "entity": {"name": "eEF2","alias": "eEF2"}, "field": "conc", "data": [ [0, 0, 0], @@ -50,30 +46,35 @@ ] }, "Modifications": { - "subset": [ - {"name":"PP2A","alias":"PP2A"},{"name":"eEF2","alias":"eEF2"},{"name":"eEF2p","alias":"eEF2p"} + "subset": [ + {"name": "PP2A"},{"name": "eEF2"},{"name": "eEF2p"} ], "itemsToDelete": [ - {"name":"PP2A_dephospho_I1","alias":"PP2A_dephospho_I1"},{"name":"PP2A_dephospho_PP1_I_p","alias":"PP2A_dephospho_PP1_I_p"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"mGluR_deph","alias":"mGluR_deph"} + {"name": "PP2A_dephospho_I1"}, + {"name": "PP2A_dephospho_PP1_I_p"}, + {"name": "ePP2A+S6Kpq","alias": "clus_S6K_deph"}, + {"name": "ePP2A+S6Kpqrs","alias": "S6K_dephosp"}, + {"name": "ePP2A+S6Kpqr","alias": "S6K_deph"}, + {"name": "ePP2A+AKTpq","alias": "AKTpS473_deph"}, + {"name": "ePP2A+AKTp","alias": "AKTpT308_deph"}, + {"name": "ePP2A+4EBPpqr","alias": "PP2A_4EBPpp"}, + {"name": "ePP2A+4EBPpq","alias": "PP2A_4EBPp"}, + {"name": "ePP2A+eIF4EBPpqr","alias": "PP2A_eIF4EBPpp"}, + {"name": "ePP2A+eIF4EBPpq","alias": "PP2A_eIF4EBPp"}, + {"name": "mGluR_deph"} ], "parameterChange": [ - { - "name": "PP2A", - "alias": "PP2A", + { "entity": {"name": "PP2A","alias": "PP2A"}, "field": "concInit", "value": 6.5e-07, "units": "mM" }, - { - "name": "eEF2", - "alias": "eEF2", + { "entity": {"name": "eEF2"}, "field": "concInit", "value": 0, "units": "mM" }, - { - "name": "eEF2p", - "alias": "eEF2p", + { "entity": {"name": "eEF2p"}, "field": "concInit", "value": 2.2e-05, "units": "mM" diff --git a/TestJson/ts_norm_m3b.json b/TestJson/ts_norm_m3b.json index 66f6f78..287b5e2 100644 --- a/TestJson/ts_norm_m3b.json +++ b/TestJson/ts_norm_m3b.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity" : { - "name": "Glutamate", - "alias": "Glutamate" - }, + "entity": {"name": "Glutamate", "alias": "Glutamate"}, "field": "conc", "data": [ [0,100.0] @@ -37,16 +36,10 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "tot_surface_mGluR_with_barr2", - "alias": "tot_surface_mGluR_with_barr2" - }, + "entity": {"name": "tot_surface_mGluR_with_barr2","alias": "tot_surface_mGluR_with_barr2"}, "field": "conc", "normalization": { - "entity" : { - "name": "tot_surface_mGluR_with_barr2", - "alias": "tot_surface_mGluR_with_barr2" - }, + "entity": {"name": "tot_surface_mGluR_with_barr2"}, "sampling": "start" }, "data": [ @@ -59,10 +52,27 @@ }, "Modifications": { "subset": [ - {"name":"mGluR_g","alias":"mGluR_g"},{"name":"barr2_g","alias":"barr2_g"},{"name":"PP2A","alias":"PP2A"} + {"name": "mGluR_g"},{"name": "barr2_g"},{"name": "PP2A"} ], "itemsToDelete": [ - {"name":"mGluR_Gq","alias":"mGluR_Gq"},{"name":"amGluR","alias":"Glu_mGluR_Gq"},{"name":"Glu_mGluR+Gq","alias":"Glu_mGluR_bind_Gq"},{"name":"Glu+mGluR_Gq","alias":"Glu_bind_mGluR_Gq"},{"name":"Act_Gq","alias":"Act_Gq"},{"name":"mGluR_bind_Gq","alias":"mGluR_bind_Gq"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"} + {"name": "mGluR_Gq"}, + {"name": "amGluR","alias": "Glu_mGluR_Gq"}, + {"name": "Glu_mGluR+Gq","alias": "Glu_mGluR_bind_Gq"}, + {"name": "Glu+mGluR_Gq","alias": "Glu_bind_mGluR_Gq"}, + {"name": "Act_Gq"}, + {"name": "mGluR_bind_Gq"}, + {"name": "ePP2A+S6Kpq","alias": "clus_S6K_deph"}, + {"name": "ePP2A+S6Kpqrs","alias": "S6K_dephosp"}, + {"name": "ePP2A+S6Kpqr","alias": "S6K_deph"}, + {"name": "ePP2A+AKTpq","alias": "AKTpS473_deph"}, + {"name": "ePP2A+AKTp","alias": "AKTpT308_deph"}, + {"name": "ePP2A+eEF2p","alias": "eEF2p_deph"}, + {"name": "ePP2A+4EBPpqr","alias": "PP2A_4EBPpp"}, + {"name": "ePP2A+4EBPpq","alias": "PP2A_4EBPp"}, + {"name": "ePP2A+eIF4EBPpqr","alias": "PP2A_eIF4EBPpp"}, + {"name": "ePP2A+eIF4EBPpq","alias": "PP2A_eIF4EBPp"}, + {"name": "ePP2A+I1p","alias": "PP2A_dephos_I1"}, + {"name": "PP2A_dephos_PP1_Ip"} ] } } diff --git a/TestJson/ts_ratio_t2a.json b/TestJson/ts_ratio_t2a.json index 5d85bf0..7f664e5 100644 --- a/TestJson/ts_ratio_t2a.json +++ b/TestJson/ts_ratio_t2a.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Nisha Ann Viswan", "organization": "NCBS", @@ -24,10 +26,7 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity" : { - "name": "Glutamate", - "alias": "Glutamate" - }, + "entity": {"name": "Glutamate","alias": "Glutamate"}, "field": "conc", "data": [ [300,0.0] @@ -37,16 +36,10 @@ "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entity" : { - "name": "beta2ARp", - "alias": "beta2ARp" - }, + "entity": {"name": "beta2ARp","alias": "beta2ARp"}, "field": "conc", "normalization": { - "entity" : { - "name": "beta2ARp", - "alias": "beta2ARp" - }, + "entity": {"name": "beta2ARp"}, "sampling": "start" }, "data": [ @@ -62,15 +55,36 @@ }, "Modifications": { "subset": [ - {"name":"mGluR_g","alias":"mGluR_g"},{"name":"barr2_g","alias":"barr2_g"},{"name":"PP2A","alias":"PP2A"},{"name":"MAPK_g","alias":"MAPK_g"} + {"name": "mGluR_g"},{"name": "barr2_g"},{"name": "PP2A"},{"name": "MAPK_g"} ], "itemsToDelete": [ - {"name":"mGluR_Gq","alias":"mGluR_Gq"},{"name":"amGluR","alias":"Glu_mGluR_Gq"},{"name":"Glu_mGluR+Gq","alias":"Glu_mGluR_bind_Gq"},{"name":"Glu+mGluR_Gq","alias":"Glu_bind_mGluR_Gq"},{"name":"Act_Gq","alias":"Act_Gq"},{"name":"mGluR_bind_Gq","alias":"mGluR_bind_Gq"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"},{"name":"eMAPK+crafp","alias":"MAPKpp_feedback"},{"name":"eMAPK+PLA2","alias":"MAPKpp_act_PLA2"},{"name":"Sos_phospho","alias":"Sos_phospho"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"} + {"name": "mGluR_Gq"}, + {"name": "amGluR","alias": "Glu_mGluR_Gq"}, + {"name": "Glu_mGluR+Gq","alias": "Glu_mGluR_bind_Gq"}, + {"name": "Glu+mGluR_Gq","alias": "Glu_bind_mGluR_Gq"}, + {"name": "Act_Gq"}, + {"name": "mGluR_bind_Gq"}, + {"name": "ePP2A+S6Kpq","alias": "clus_S6K_deph"}, + {"name": "ePP2A+S6Kpqrs","alias": "S6K_dephosp"}, + {"name": "ePP2A+S6Kpqr","alias": "S6K_deph"}, + {"name": "ePP2A+AKTpq","alias": "AKTpS473_deph"}, + {"name": "ePP2A+AKTp","alias": "AKTpT308_deph"}, + {"name": "ePP2A+eEF2p","alias": "eEF2p_deph"}, + {"name": "ePP2A+4EBPpqr","alias": "PP2A_4EBPpp"}, + {"name": "ePP2A+4EBPpq","alias": "PP2A_4EBPp"}, + {"name": "ePP2A+eIF4EBPpqr","alias": "PP2A_eIF4EBPpp"}, + {"name": "ePP2A+eIF4EBPpq","alias": "PP2A_eIF4EBPp"}, + {"name": "ePP2A+I1p","alias": "PP2A_dephos_I1"}, + {"name": "PP2A_dephos_PP1_Ip"}, + {"name": "eMAPK+S6K","alias": "clus_S6K_phospho"}, + {"name": "eMAPK+crafp","alias": "MAPKpp_feedback"}, + {"name": "eMAPK+PLA2","alias": "MAPKpp_act_PLA2"}, + {"name": "Sos_phospho"}, + {"name": "eMAPK+4EBPpq","alias": "MAPK_4EBPpp"}, + {"name": "eMAPK+eIF4EBPpq","alias": "MAPK_4EBP_phospho"} ], "parameterChange": [ - { - "name": "Glutamate", - "alias": "Glutamate", + { "entity": {"name": "Glutamate"}, "field": "concInit", "value": 0.1, "units": "mM" diff --git a/TestJson/vclamp_hh.json b/TestJson/vclamp_hh.json index 4b43ee3..bc71224 100644 --- a/TestJson/vclamp_hh.json +++ b/TestJson/vclamp_hh.json @@ -1,4 +1,6 @@ { + "FileType": "Findsim", + "Version": "2.0", "Metadata": { "transcriber": "Upinder S. Bhalla", "organization": "NCBS", @@ -24,10 +26,7 @@ { "timeUnits": "msec", "quantityUnits": "mV", - "entity" : { - "name": "soma", - "alias": "soma" - }, + "entity": {"name": "soma","alias": "soma" }, "field": "Vclamp", "data": [ [0,-65.0], @@ -40,10 +39,7 @@ "Readouts": { "timeUnits": "msec", "quantityUnits": "uA", - "entity" : { - "name": "vclamp", - "alias": "vclamp" - }, + "entity": {"name": "vclamp","alias": "vclamp"}, "field": "current", "data": [ [0, 0, 0], @@ -64,7 +60,7 @@ }, "Modifications": { "subset": [ - {"name":"all"} + {"name": "all"} ] } } diff --git a/test.sh b/test.sh index 581a2fd..2808a20 100755 --- a/test.sh +++ b/test.sh @@ -10,3 +10,10 @@ $PYTHON findSim.py ./Curated/Jain2009_Fig3F.json --model models/synSynth7.g --ma $PYTHON findSim.py ./Curated/Bhalla1999_Fig2B.json --model models/synSynth7.g --map models/synSynth7_map.json --solver LSODA $PYTHON findSim.py ./Curated/Gu2004_fig3B.json --model models/synSynth7.g --map models/synSynth7_map.json --solver LSODA $PYTHON findSim.py ./Curated/Bhalla1999_Fig4C.json --model models/synSynth7.g --map models/synSynth7_map.json --solver LSODA +$PYTHON findSim.py ./Non-Curated/PKC_SB_Fig7.json --model models/synSynth7.g --map models/synSynth7_map.json --solver LSODA +$PYTHON findSim.py ./Non-Curated/HH_Fig13.json +$PYTHON findSim.py ./TestJson/iclamp_hh13.json +$PYTHON findSim.py ./TestJson/iclamp_hh_window_baseline_norm.json +$PYTHON findSim.py ./TestJson/epsc_window_baseline_norm.json +$PYTHON findSim.py ./TestJson/epsc.json +