examples/sbtab/jiang_model.multi.csv
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='Compartment',,,,,,,,,,,,,,,,
!ID,!Name,!Size,,,,,,,,,,,,,,
CYTOPLASM,cytoplasm,1,,,,,,,,,,,,,,
MT_IMS,mitochondrial intermembrane space,1,,,,,,,,,,,,,,
MT_IM,mitochondrial inner membrane,1,,,,,,,,,,,,,,
MATRIX,mitochondrial matrix,1,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='Compound',,,,,,,,,,,,,,,,
!ID,!Name,!Location,!Charge,!IsConstant,!InitialConcentration,!hasOnlySubstanceUnits,!Identifiers:kegg.compound,,,,,,,,,
GLC,glucose,CYTOPLASM,0,FALSE,0,FALSE,C00267,,,,,,,,,
F6P,fructose-6-phosphate,CYTOPLASM,0,FALSE,0,FALSE,C00085,,,,,,,,,
FBP,"fructose-1,6-bisphosphate",CYTOPLASM,0,FALSE,0,FALSE,C00354,,,,,,,,,
GAP,glyceraldehyde 3-phosphate,CYTOPLASM,0,FALSE,0,FALSE,C00118,,,,,,,,,
DPG,"1,2-bisphospho-D-glycerate",CYTOPLASM,0,FALSE,0,FALSE,C00236,,,,,,,,,
PEP,phosphoenolpyruvate,CYTOPLASM,0,FALSE,0,FALSE,C00074,,,,,,,,,
PYR_cyt,pyruvate,CYTOPLASM,0,FALSE,0,FALSE,C00022,,,,,,,,,
AMP,adenine monophosphate,CYTOPLASM,0,FALSE,0,FALSE,C00020,,,,,,,,,
LAC,lactate,CYTOPLASM,0,FALSE,0,FALSE,C00186,,,,,,,,,
G3P,glycerol-3-phosphate,CYTOPLASM,0,FALSE,0,FALSE,C00093,,,,,,,,,
DHAP,dihydrohxyacetone-phosphate,CYTOPLASM,0,FALSE,0,FALSE,C00111,,,,,,,,,
OXA_cyt,oxaloacetate,CYTOPLASM,0,FALSE,0,FALSE,C00036,,,,,,,,,
Asp_cyt,aspartate,CYTOPLASM,0,FALSE,0,FALSE,C00049,,,,,,,,,
Glu_cyt,glutamate,CYTOPLASM,0,FALSE,0,FALSE,C00025,,,,,,,,,
OG_cyt,oxoglutarate,CYTOPLASM,0,FALSE,0,FALSE,C00026,,,,,,,,,
Mal_cyt,malate,CYTOPLASM,0,FALSE,0,FALSE,C00149,,,,,,,,,
Acetyl_CoA_cyt,acetyl CoA,CYTOPLASM,0,FALSE,0,FALSE,C00024,,,,,,,,,
CoA_cyt,coenzyme A,CYTOPLASM,0,FALSE,0,FALSE,C00010,,,,,,,,,
IsoCitcyt,isocitrate,CYTOPLASM,0,FALSE,0,FALSE,C00311,,,,,,,,,
Cit_cyt,citrate,CYTOPLASM,0,FALSE,0,FALSE,C00158,,,,,,,,,
ATP_cyt,adenine triphosphate,CYTOPLASM,0,FALSE,0,FALSE,C0002,,,,,,,,,
ADP_cyt,adenine diphosphate,CYTOPLASM,0,FALSE,0,FALSE,C0008,,,,,,,,,
NAD,NAD,CYTOPLASM,0,FALSE,0,FALSE,C00003,,,,,,,,,
NADH_cyt,NADH,CYTOPLASM,0,FALSE,0,FALSE,C00004,,,,,,,,,
NADP_cyt,NADP,CYTOPLASM,0,FALSE,0,FALSE,C00006,,,,,,,,,
NADPH_cyt,NADPH,CYTOPLASM,0,FALSE,0,FALSE,C00005,,,,,,,,,
Pyr,pyruvate,MATRIX,0,FALSE,0,FALSE,C00022,,,,,,,,,
CO2,carbon dioxide,MATRIX,0,FALSE,0,FALSE,C00011,,,,,,,,,
CoA,coenzyme A,MATRIX,0,FALSE,0,FALSE,C00010,,,,,,,,,
Acetyl_CoA,acetyl CoA,MATRIX,0,FALSE,0,FALSE,C00024,,,,,,,,,
Pi,phosphate,MATRIX,0,FALSE,0,FALSE,C00009,,,,,,,,,
Fum,fumarate,MATRIX,0,FALSE,0,FALSE,C00122,,,,,,,,,
SCoA,succinyl-CoA,MATRIX,0,FALSE,0,FALSE,C00091,,,,,,,,,
Suc,succinate,MATRIX,0,FALSE,0,FALSE,C00042,,,,,,,,,
GTP,guanosine triphosphate,MATRIX,0,FALSE,0,FALSE,C00044,,,,,,,,,
GDP,guanosine diphosphate,MATRIX,0,FALSE,0,FALSE,C00035,,,,,,,,,
Ala,slanine,MATRIX,0,FALSE,0,FALSE,C00041,,,,,,,,,
Asp,aspartate,MATRIX,0,FALSE,0,FALSE,C00049,,,,,,,,,
Glu,glutamate,MATRIX,0,FALSE,0,FALSE,C00025,,,,,,,,,
H2O,water,MATRIX,0,FALSE,0,FALSE,C00001,,,,,,,,,
ETFred,electron transfer flavoprotein (reduced form),MATRIX,0,FALSE,0,FALSE,C04570,,,,,,,,,
ETFox,electron transfer flavoprotein (oxidised form),MATRIX,0,FALSE,0,FALSE,C04253,,,,,,,,,
FADH2,FADH2,MATRIX,0,FALSE,0,FALSE,C01352,,,,,,,,,
FAD,FAD,MATRIX,0,FALSE,0,FALSE,C00016,,,,,,,,,
OG,oxoglutarate,MATRIX,0,FALSE,0,FALSE,C00026,,,,,,,,,
Mal,malate,MATRIX,0,FALSE,0,FALSE,C00149,,,,,,,,,
OXA,oxaloacetate,MATRIX,0,FALSE,0,FALSE,C00036,,,,,,,,,
Cit,citrate,MATRIX,0,FALSE,0,FALSE,C00158,,,,,,,,,
IsoCit,isocitrate,MATRIX,0,FALSE,0,FALSE,C00311,,,,,,,,,
ATP,adenine triphosphate,MATRIX,0,FALSE,0,FALSE,C0002,,,,,,,,,
ADP,adenine diphosphate,MATRIX,0,FALSE,0,FALSE,C0008,,,,,,,,,
NADP_p,NADP+,MATRIX,0,FALSE,0,FALSE,C00006,,,,,,,,,
NADPH,NADPH,MATRIX,0,FALSE,0,FALSE,C00005,,,,,,,,,
NAD_p,NAD+,MATRIX,0,FALSE,0,FALSE,C00003,,,,,,,,,
NADH,NADH,MATRIX,0,FALSE,0,FALSE,C00004,,,,,,,,,
Q,ubiquinone,MT_IMS,0,FALSE,0,FALSE,C00399,,,,,,,,,
QH2,ubiquinol,MT_IMS,0,FALSE,0,FALSE,C00390,,,,,,,,,
Cytc3p,ferrocytochrome c,MT_IMS,0,FALSE,0,FALSE,C00126,,,,,,,,,
Cytc2p,ferricytochrome c,MT_IMS,0,FALSE,0,FALSE,C00125,,,,,,,,,
,,,,,,,,,,,,,,,,
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='Reaction',,,,,,,,,,,,,,,,
!ID,!Name,!ReactionFormula,!Regulator,!KineticLaw,!IsReversible,!Identifiers:ec-code,,,,,,,,,,
GLCflow,, <=> GLC,,"CYTOPLASM * (Glc_F * pow(10, -3) - GLC) * flow",TRUE,,,,,,,,,,,
LACflow,,LAC <=>,,CYTOPLASM * LAC * flow,FALSE,,,,,,,,,,,
GAPflow,,GAP <=>,,CYTOPLASM * GAP * flow,FALSE,,,,,,,,,,,
v1,glucokinase,GLC + ATP_cyt <=> F6P + ADP_cyt,,CYTOPLASM * (V1 * ATP_cyt * GLC / ((K1GLC + GLC) * (K1ATP + ATP_cyt))),FALSE,2.7.1.2,,,,,,,,,,
v2,6-phosphofructokinase,F6P + ATP_cyt <=> FBP + ADP_cyt,AMP,"CYTOPLASM * (V2 * ATP_cyt * pow(F6P, 2) / ((K2 * (1 + k2 * pow(ATP_cyt / AMP, 2)) + pow(F6P, 2)) * (K2ATP + ATP_cyt)))",FALSE,2.7.1.11,,,,,,,,,,
v3,fructose-bisphosphate aldolase,FBP <=> 2.0 GAP,,"CYTOPLASM * (k3f * FBP - k3b * pow(GAP, 2))",TRUE,4.1.2.13,,,,,,,,,,
v4,glyceraldehyde 3-phosphate dehydrogenase,GAP + NAD <=> DPG + NADH_cyt,,CYTOPLASM * (V4 * NAD * GAP / ((K4GAP + GAP) * (K4NAD + NAD))),FALSE,1.2.1.12,,,,,,,,,,
v5,bisphosphoglycerate phosphotase (1/2),DPG + ADP_cyt <=> PEP + ATP_cyt,,CYTOPLASM * (k5f * DPG * ADP_cyt - k5b * PEP * ATP_cyt),TRUE,5.4.2.4,,,,,,,,,,
v6,pyruvate kinase,PEP + ADP_cyt <=> PYR_cyt + ATP_cyt,,CYTOPLASM * (V6 * ADP_cyt * PEP / ((K6PEP + PEP) * (K6ADP + ADP_cyt))),FALSE,2.7.1.40,,,,,,,,,,
v7,lactate dehydrogenase,PYR_cyt + NADH_cyt <=> LAC + NAD,,CYTOPLASM * (k8f * NADH_cyt * PYR_cyt - k8b * NAD * LAC),TRUE,1.1.1.27,,,,,,,,,,
hidden_1,,AMP + ATP_cyt <=> 2.0 ADP_cyt,,"CYTOPLASM * (k9f * AMP * ATP_cyt - k9b * pow(ADP_cyt, 2))",TRUE,,,,,,,,,,,
v8,pyruvate carrier,PYR_cyt <=> Pyr,,MATRIX * (V * PYR_cyt * v8_PYC / (K + PYR_cyt)),TRUE,,,,,,,,,,,
v9,pyruvate dehydrogenase complex,Pyr + CoA + NAD_p <=> CO2 + Acetyl_CoA + NADH,,MATRIX * (KcF * v9_PDC * Pyr * CoA * NAD_p / (KmC * Pyr * CoA + KmB * Pyr * NAD_p + KmA * CoA * NAD_p + Pyr * CoA * NAD_p + KmA * KmP * Kib * Kic / KmR / Kip / Kiq * Acetyl_CoA * NADH + KmC / Kir * Pyr * CoA * NADH + KmB / Kiq * Pyr * NAD_p * Acetyl_CoA + KmA * KmP * Kib * Kic / KmR / Kip / Kia / Kiq * Pyr * Acetyl_CoA * NADH)),FALSE,1.2.4.1,,,,,,,,,,
v10,citrate synthase,OXA + Acetyl_CoA <=> Cit + CoA,,MATRIX * (V * Acetyl_CoA * OXA * v10_CS / (Acetyl_CoA * OXA + Ka * OXA + Kb * Acetyl_CoA + Kia * Kib)),TRUE,2.3.3.3,,,,,,,,,,
v11,aconitase,Cit <=> IsoCit,,MATRIX * ((KcF * Kp * Cit - KcR * Ks * IsoCit) * v11_ACO / (Ks * IsoCit + Kp * Cit + Ks * Kp)),TRUE,4.2.1.3,,,,,,,,,,
v12,isocitrate dehydrogenase (NAD+) (alpha/beta/gamma),IsoCit + NAD_p <=> OG + NADH,ADP,MATRIX * (KcF * v12_IDHa * (IsoCit * IsoCit + b * ADP * IsoCit) / (IsoCit * IsoCit + c * IsoCit + d * ADP + e * ADP * IsoCit + f)),FALSE,1.1.1.41,,,,,,,,,,
v14,oxoglutarate dehydrogenase complex,OG + CoA + NAD_p <=> CO2 + SCoA + NADH,,MATRIX * (KcF * v14_OGDC * OG * CoA * NAD_p / (KmC * OG * CoA + KmB * OG * NAD_p + KmA * CoA * NAD_p + OG * CoA * NAD_p + KmA * KmP * Kib * Kic / KmR / Kip / Kiq * SCoA * NADH + KmC / Kir * OG * CoA * NADH + KmB / Kiq * OG * NAD_p * SCoA + KmA * KmP * Kib * Kic / KmR / Kip / Kia / Kiq * OG * SCoA * NADH)),FALSE,1.2.4.2,,,,,,,,,,
v15,succinyl-CoA synthetase,GDP + SCoA + Pi <=> Suc + GTP + CoA,,MATRIX * ((GDP * SCoA * pi - Suc * GTP * CoA / Keq) * (Kc1 * v15_SCS + Kc2 * v15_SCS * (KmC * Suc / KmC2 * Kip + pi / KmC2)) / (Kia * KmB * pi + KmB * GDP * pi + KmA * SCoA * pi + KmC * GDP * SCoA + GDP * SCoA * pi + GDP * SCoA * pi * pi / KmC2 + Kia * KmB * KmC * Suc / Kip + Kia * KmB * KmC * Suc * GTP / Kip / Kiq + Kia * KmB * KmC * Suc * CoA / Kip / Kir + Kia * KmB * Kic * GTP * CoA / KmQ / Kir + Kia * KmB * KmC * Suc * GTP * CoA / Kip / KmQ / Kir + Kia * KmB * KmC * Suc * Suc * GTP * CoA / Kip / KmP2 / KmQ / Kir + Kia * KmB * pi * GTP / Kiq + Kia * KmB * pi * CoA / Kir + Kia * KmB * pi * GTP * CoA / KmQ / Kir + Kia * KmB * pi * Suc * GTP * CoA / KmP2 / KmQ / Kir + KmB * KmC * GDP * Suc / Kip + KmA * KmC * SCoA * Suc / Kip + KmC * GDP * SCoA * Suc / Kip + KmC * GDP * SCoA * pi * Suc / KmC2 / Kip + KmA * SCoA * pi * GTP / Kiq + KmB * GDP * pi * CoA / Kir + KmA * KmC * SCoA * Suc * GTP / Kip / Kiq + KmB * KmC * GDP * Suc * CoA / Kip / Kir)),TRUE,6.2.1.4,,,,,,,,,,
v16,succinate dehydrogenase,Suc + Q <=> Fum + QH2,,MATRIX * (KcF * KcR * v16_SDH * (Suc * Q - Fum * QH2 / Keq) / (KcR * KmS2 * Suc + KcR * KmS1 * Q + KcF * KmP2 * Fum / Keq + KcF * KmP1 * QH2 / Keq + KcR * Suc * Q + KcF * KmP2 * Suc * Fum / (Keq * KiS1) + KcF * Fum * QH2 / Keq + KcR * KmS1 * Q * QH2 / KiP2)),TRUE,1.3.5.1,,,,,,,,,,
v17,fumarase,Fum <=> Mal,,MATRIX * ((KcF * Kp * Fum - KcR * Ks * Mal) * v17_FM / (Ks * Mal + Kp * Fum + Ks * Kp)),TRUE,4.2.1.2,,,,,,,,,,
v18,malate dehydrogenase (mitochondrion),Mal + NAD_p <=> NADH + OXA,,MATRIX * ((KcF * Mal * NAD_p / KiS1 / KmS2 - KcR * OXA * NADH / KmP1 / KiP2) * v18_MDH / (1 + Mal / KiS1 + KmS1 * NAD_p / KiS1 / KmS2 + KmP2 * OXA / KmP1 / KiP2 + NADH / KiP2 + Mal * NAD_p / KiS1 / KmS2 + KmP2 * Mal * OXA / KiS1 / KmP1 / KiP2 + KmS1 * NAD_p * NADH / KiS1 / KmS2 / KiP2 + OXA * NADH / KmP1 * KiP2 + Mal * NAD_p * OXA / KiS1 / KmS2 / KiP1 + NAD_p * OXA * NADH / KiS2 / KmP1 / KiP2)),TRUE,1.1.1.37,,,,,,,,,,
v20,alanine transaminase,Ala + OG <=> Glu + Pyr,,MATRIX * (KcF * KcR * v20_AlaTA * (Ala * OG - Glu * Pyr / Keq) / (KcR * KmS2 * Ala + KcR * KmS1 * OG + KcF * KmP2 * Glu / Keq + KcF * KmP1 * Pyr / Keq + KcR * Ala * OG + KcF * KmP2 * Ala * Glu / (Keq * KiS1) + KcF * Glu * Pyr / Keq + KcR * KmS1 * OG * Pyr / KiP2)),TRUE,2.6.1.2,,,,,,,,,,
v21,aspartate transaminase,OXA + Glu <=> Asp + OG,,MATRIX * (KcF * KcR * v21_AspTA * (OXA * Glu - Asp * OG / Keq) / (KcR * KmS2 * OXA + KcR * KmS1 * Glu + KcF * KmP2 * Asp / Keq + KcF * KmP1 * OG / Keq + KcR * OXA * Glu + KcF * KmP2 * OXA * Asp / (Keq * KiS1) + KcF * Asp * OG / Keq + KcR * KmS1 * Glu * OG / KiP2)),TRUE,2.6.1.1,,,,,,,,,,
v22,aspartate/glutamate carrier,Glu_cyt + Asp <=> Asp_cyt + Glu,,MATRIX * ((Asp * Glu_cyt / alpha / KiS1 / KiS2 * KcF - Glu * Asp_cyt / beta / KiP1 / KiP2 * KcR) * v22_AGC / (1 + Asp / KiS1 + Glu_cyt / KiS2 + Glu / KiP1 + Asp_cyt / KiP2 + Asp * Glu_cyt / alpha / KiS1 / KiS2 + Glu * Asp_cyt / beta / KiP1 / KiP2 + Glu_cyt * Asp_cyt / gamma / KiS2 / KiP2 + Asp * Glu / delta / KiS1 / KiP1)),TRUE,,,,,,,,,,,
v24,NADH:ubiquinone oxidoreductase,NADH + Q <=> NAD_p + QH2,,MATRIX * (KcF * KcR * v24_Complex_I * (NADH * Q - NAD_p * QH2 / Keq) / (KcR * KmS2 * NADH + KcR * KmS1 * Q + KcF * KmP2 * NAD_p / Keq + KcF * KmP1 * QH2 / Keq + KcR * NADH * Q + KcF * KmP2 * NADH * NAD_p / (Keq * KiS1) + KcF * NAD_p * QH2 / Keq + KcR * KmS1 * Q * QH2 / KiP2)),TRUE,2.7.4.6,,,,,,,,,,
v25,ubiquinol:cytochrome c oxidoreductase,QH2 + 2.0 Cytc3p <=> Q + 2.0 Cytc2p,,MT_IMS * (KcF * v25_Complex_III * QH2 * Cytc3p / ((KmA * Kq2 * Kb2 + KmA * Kq2 * Cytc3p + KcF / k8 * Kq1 * QH2 * Kb1 + KcF / k8 * Kq1 * QH2 * Cytc3p) * Cytc2p + KmA * Cytc3p + KmB * QH2 + QH2 * Cytc3p)),FALSE,1.10.2.2,,,,,,,,,,
v26,cytochrome c oxidase,Cytc2p <=> Cytc3p,,MT_IMS * (KcF * v26_Complex_IV * Cytc2p / (Ks + Cytc2p)),FALSE,1.9.3.1,,,,,,,,,,
v27,citrate synthase,Cit_cyt + CoA_cyt <=> OXA_cyt + Acetyl_CoA_cyt,,CYTOPLASM * Kid * Kc * (V * Acetyl_CoA_cyt * OXA_cyt * v10_CS / (Acetyl_CoA_cyt * OXA_cyt + Ka * OXA_cyt + Kb * Acetyl_CoA_cyt + Kia * Kib)) / (Keq * Kia * Kb),TRUE,2.3.3.3,,,,,,,,,,
v28,ATPase complex,ADP + Pi <=> ATP + H2O,,MATRIX * v28_Complex_V * V * ADP / (Km + ADP + ADP * ADP / Ki),TRUE,3.6.1.5,,,,,,,,,,
v29,aconitase,Cit_cyt <=> IsoCitcyt,,CYTOPLASM * ((KcF * Kp * Cit_cyt - KcR * Ks * IsoCitcyt) * v29_ACO / (Ks * IsoCitcyt + Kp * Cit_cyt + Ks * Kp)),TRUE,4.2.1.3,,,,,,,,,,
v30,oxoglutarate carrier,Mal_cyt + OG <=> OG_cyt + Mal,,MATRIX * ((OG * Mal_cyt / alpha / KiS1 / KiS2 * KcF - Mal * OG_cyt / beta / KiP1 / KiP2 * KcR) * v30_OGC / (1 + OG / KiS1 + Mal_cyt / KiS2 + Mal / KiP1 + OG_cyt / KiP2 + OG * Mal_cyt / alpha / KiS1 / KiS2 + Mal * OG_cyt / beta / KiP1 / KiP2 + Mal_cyt * OG_cyt / gamma / KiS2 / KiP2 + OG * Mal / delta / KiS1 / KiP1)),TRUE,,,,,,,,,,,
v31,malate dehydrogenase (cytosol),NADH_cyt + OXA_cyt <=> Mal_cyt + NAD,,CYTOPLASM * (v31_MDH * (k1 * k2 * k3 * k4 * NADH_cyt * OXA_cyt - kminus1 * kminus2 * kminus3 * kminus4 * Mal_cyt * NAD) / (kminus1 * (kminus2 + k3) * k4 + k1 * (kminus2 + k3) * k4 * NADH_cyt + kminus1 * (kminus2 + k3) * kminus4 * NAD + k2 * k3 * k4 * OXA_cyt + kminus1 * kminus2 * kminus3 * Mal_cyt + k1 * k2 * (k3 + k4) * NADH_cyt * OXA_cyt + (kminus1 + kminus2) * kminus3 * kminus4 * Mal_cyt * NAD + k1 + kminus2 + kminus3 * NADH_cyt * Mal_cyt + k1 * k2 * kminus3 * NADH_cyt * OXA_cyt * Mal_cyt + k2 * k3 * kminus4 * OXA_cyt * NAD + k2 * kminus3 * kminus4 * OXA_cyt * Mal_cyt * NAD)),FALSE,1.1.1.37,,,,,,,,,,
v32,aspartate transaminase,Asp_cyt + OG_cyt <=> OXA_cyt + Glu_cyt,,CYTOPLASM * (KcF * KcR * v32_AspTA * (Asp_cyt * OG_cyt - OXA_cyt * Glu_cyt / Keq) / (KcR * KmS2 * Asp_cyt + KcR * KmS1 * OG_cyt + KcF * KmP2 * OXA_cyt / Keq + KcF * KmP1 * Glu_cyt / Keq + KcR * Asp_cyt * OG_cyt + KcF * KmP2 * Asp_cyt * OXA_cyt / (Keq * KiS1) + KcF * OXA_cyt * Glu_cyt / Keq + KcR * KmS1 * OG_cyt * Glu_cyt / KiP2)),TRUE,2.6.1.1,,,,,,,,,,
v33,citrate carrier,Cit_cyt + Mal <=> Mal_cyt + Cit,,MATRIX * ((Cit_cyt * Mal / alpha / KiS1 / KiS2 * KcF - Mal_cyt * Cit / beta / KiP1 / KiP2 * KcR) * v33_CIC / (1 + Cit_cyt / KiS1 + Mal / KiS2 + Mal_cyt / KiP1 + Cit / KiP2 + Cit_cyt * Mal / alpha / KiS1 / KiS2 + Mal_cyt * Cit / beta / KiP1 / KiP2 + Mal * Cit / gamma / KiS2 / KiP2 + Cit_cyt * Mal_cyt / delta / KiS1 / KiP1)),TRUE,,,,,,,,,,,
v34,ETF:Q oxidoreductase,ETFred + Q <=> ETFox + QH2,,MATRIX * (KcF * KcR * v34_ETF_QO * (ETFred * Q - ETFox * QH2 / Keq) / (KcR * KmS2 * ETFred + KcR * KmS1 * Q + KcF * KmP2 * ETFox / Keq + KcF * KmP1 * QH2 / Keq + KcR * ETFred * Q + KcF * KmP2 * ETFred * ETFox / (Keq * KiS1) + KcF * ETFox * QH2 / Keq + KcR * KmS1 * Q * QH2 / KiP2)),TRUE,1.5.5.1,,,,,,,,,,
v35,glutathione reductase,FADH2 + ETFox <=> ETFred + FAD,,MATRIX * (KcF * KcR * v35_ACD * (FADH2 * ETFox - ETFred * FAD / Keq) / (KcR * KiS1 * KmS2 + KcR * KmS2 * FADH2 + KcR * KmS1 * ETFox + KcF * KmP2 * ETFred / Keq + KcF * KmP1 * FAD / Keq + KcR * FADH2 * ETFox + KcF * KmP2 * FADH2 * ETFred / (Keq * KiS1) + KcF * ETFred * FAD / Keq + KcR * KmS1 * ETFox * FAD / KiP2 + KcR * FADH2 * ETFox * ETFred / KiP1 + KcF * ETFox * ETFred * FAD / (KiS2 * Keq))),TRUE,1.8.1.7,,,,,,,,,,
v36,pyruvate decarboxylase,ATP + CO2 + Pyr <=> Pi + ADP + OXA,,MATRIX * (KcF * KcR * v36_PC * (ATP * CO2 * Pyr - pi * ADP * OXA / Keq) / (Kia * KmB * KcR * Pyr + KmC * KcR * ATP * CO2 + KmA * KcR * CO2 * Pyr + KmB * KcR * ATP * Pyr + KcR * ATP * CO2 * Pyr + Kip * KmQ * KcF * OXA / Keq + KmQ * KcF * pi * OXA / Keq + KmP * KcF * ADP * OXA / Keq + KmR * KcF * pi * ADP / Keq + KcF * pi * ADP * OXA / Keq + Kia * KmB * KcR * Pyr * pi / Kip + Kia * KmB * KcR * Pyr * ADP / Kia + Kiq * KmP * KcF * CO2 * OXA / Kib / Keq + Kia * KmP * KcF * ATP * OXA / Kia / Keq + KmA * KcR * ATP * CO2 * OXA / Kir + KmR * KcF * Pyr * pi * ADP / Kic / Keq + KmA * KcR * CO2 * Pyr * ADP / Kiq + KmA * KcR * CO2 * Pyr * pi / Kip + KmP * KcF * CO2 * ADP * OXA / Kib / Keq + KmQ * KcF * CO2 * pi * OXA / Kib / Keq)),TRUE,6.4.1.1,,,,,,,,,,
v37,glycerol-3-phosphate dehydrogenase (FAD dependent),G3P + FAD <=> FADH2 + DHAP,,CYTOPLASM * (V * v37_GUT2P * G3P / (K + G3P)),FALSE,1.1.99.5,,,,,,,,,,
v38,glycerol-3-phosphate dehydrogenase (NAD+ dependent),NADH_cyt + DHAP <=> G3P + NAD,,CYTOPLASM * (V * v38_GUT2P * NADH_cyt / (K + NADH_cyt)),FALSE,1.1.1.8,,,,,,,,,,
v40,ATP/ADP carrier,ADP_cyt <=> ADP,,MATRIX * (V * v40_AAC * ADP_cyt / (K + ADP_cyt)),FALSE,,,,,,,,,,,
v41,cytosolic isocitrate dehydrogenase,IsoCitcyt + NADP_cyt <=> OG_cyt + NADPH_cyt,CO2,CYTOPLASM * v41_IDHc * (IsoCitcyt * NADP_cyt / (phi0 * IsoCitcyt * NADP_cyt + phi1 * NADP_cyt + phi2 * IsoCitcyt + phi12) - OG_cyt * NADPH_cyt * CO2 / (phir0 * OG_cyt * NADPH_cyt * CO2 + phir1 * NADPH_cyt * CO2 + phir2 * OG_cyt * CO2 + phir3 * OG_cyt * NADPH_cyt + phir12 * CO2 + phir13 * NADPH_cyt + phir23 * OG_cyt + phir123)),TRUE,1.1.1.42,,,,,,,,,,
v42,citrate carrier,IsoCitcyt + Mal <=> Mal_cyt + IsoCit,,MATRIX * ((IsoCitcyt * Mal / alpha / KiS1 / KiS2 * KcF - Mal_cyt * IsoCit / beta / KiP1 / KiP2 * KcR) * v42_CIC / (1 + IsoCitcyt / KiS1 + Mal / KiS2 + Mal_cyt / KiP1 + IsoCit / KiP2 + IsoCitcyt * Mal / alpha / KiS1 / KiS2 + Mal_cyt * IsoCit / beta / KiP1 / KiP2 + Mal * IsoCit / gamma / KiS2 / KiP2 + IsoCitcyt * Mal_cyt / delta / KiS1 / KiP1)),TRUE,,,,,,,,,,,
v43,ATP/ADP carrier,ATP <=> ATP_cyt,,MATRIX * (V * v43_AAC * ATP / (K + ATP)),FALSE,,,,,,,,,,,
v39,malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+),Mal_cyt + NADP_cyt <=> NADPH_cyt + PYR_cyt,,CYTOPLASM * (v39_MDH * Kcat * Mal_cyt * NADP_cyt / ((Kmal + Mal_cyt) * (Knadp + NADP_cyt))),TRUE,1.1.1.40,,,,,,,,,,
v44,malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+),Mal + NADP_p <=> NADPH + Pyr,,MATRIX * (v44_MDH * Kcat * Mal / (Km + Mal)),TRUE,1.1.1.40,,,,,,,,,,
,,,,,,,,,,,,,,,,
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='Quantity' description='Parameter prior',,,,,,,,,,,,,,,,
!QuantityType,!Unit,!BiologicalElement,!MathematicalType,!PriorMedian,!PriorStd,!PriorGeometricStd,!LowerBound,!UpperBound,!DataStd,!Symbol,!PhysicalType,!Dependence,!UseAsPriorInformation,!SBMLElement,!Abbreviation,!MatrixInfo
standard chemical potential,kJ/mol,Species,Additive,-880,1500,,-3000,2000,10,mu0,Thermodynamic,Basic,1,Global parameter ,scp,"[I_species, 0, 0, 0, 0, 0, 0, 0]"
catalytic rate constant geometric mean,1/s,Reaction,Multiplicative,10,,100,0.0000001,10000,100,KV,Kinetic,Basic,1,Local parameter,kcrg,"[0, I_reaction, 0, 0, 0, 0, 0, 0]"
Michaelis constant,mM,Reaction/Species,Multiplicative,0.1,,10,0.000001,1000,1,KM,Kinetic,Basic,1,Local parameter,kmc,"[0, 0, I_KM, 0, 0, 0, 0, 0]"
activation constant,mM,Reaction/Species,Multiplicative,0.1,,10,0.0001,100,1,KA,Kinetic,Basic,1,Local parameter,kac,"[0, 0, 0, I_KA, 0, 0, 0, 0]"
inhibitory constant,mM,Reaction/Species,Multiplicative,0.1,,10,0.0001,100,1,KI,Kinetic,Basic,1,Local parameter,kic,"[0, 0, 0, 0, I_KI, 0, 0, 0]"
concentration,mM,Species,Multiplicative,0.1,,10,0.000001,1000,1,c,Dynamic,Basic,1,Species (conc.),c,"[0, 0, 0, 0, 0, I_species, 0, 0]"
concentration of enzyme,mM,Reaction,Multiplicative,0.001,,100,0.000001,0.5,0.05,u,Dynamic,Basic,1,Local parameter,eco,"[0, 0, 0, 0, 0, 0, I_reaction, 0]"
pH,dimensionless,None,Additive,7,1,,0,14,1,pH,Dynamic,Basic,1,Global parameter,ph,"[0, 0, 0, 0, 0, 0, 0, 1]"
standard Gibbs energy of reaction,kJ/mol,Reaction,Additive,0,1500,,-1000,1000,10,dmu0,Thermodynamic,Derived,0,Global parameter ,dscp,"[Nt, 0, 0, 0, 0, 0, 0, 0]"
equilibrium constant,dimensionless,Reaction,Multiplicative,1,,100,1.00E-10,100000000,100,Keq,Thermodynamic,Derived,1,Local parameter,keq,"[[-1/RT * Nt], 0, 0, 0, 0, 0, 0, 0]"
substrate catalytic rate constant,1/s,Reaction,Multiplicative,10,,100,0.01,10000000,100,Kcatf,Kinetic,Derived,1,Local parameter ,kcrf,"[[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, 0, 0]"
product catalytic rate constant,1/s,Reaction,Multiplicative,10,,100,0.000000001,10000000,100,Kcatr,Kinetic,Derived,1,Local parameter ,kcrr,"[[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, 0, 0]"
chemical potential,kJ/mol,Species,Additive,-880,1500,,-3000,2000,20,mu,Dynamic,Derived,0,,cp,"[I_species, 0, 0, 0, 0, [RT * I_species], 0, 0]"
reaction affinity,kJ/mol,Reaction,Additive,0,10,,-60,60,10,A,Dynamic,Derived,0,,raf,"[[-1 * Nt], 0, 0, 0, 0, [-RT * Nt], 0, 0]"
forward maximal velocity,mM/s,Reaction,Multiplicative,0.01,,100,0.00000001,1000000,0.1,Vmaxf,Dynamic,Derived,0,Local parameter,vmaf,"[[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, I_reaction, 0]"
reverse maximal velocity,mM/s,Reaction,Multiplicative,0.01,,100,0.00000001,1000000,0.1,Vmaxr,Dynamic,Derived,0,Local parameter,vmar,"[[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, I_reaction, 0]"
forward mass action term,1/s,Reaction,Multiplicative,1,,1000,0.0000001,10000000,1,thetaf,Dynamic,Derived,0,,thtf,"[[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, 0, 0]"
reverse mass action term,1/s,Reaction,Multiplicative,1,,1000,0.0000001,10000000,1,thetar,Dynamic,Derived,0,,thtr,"[[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, 0, 0]"
forward enzyme mass action term,mM/s,Reaction,Multiplicative,1,,1000,0.0000001,10000000,1,tauf,Dynamic,Derived,0,,tauf,"[[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, I_reaction, 0]"
reverse enzyme mass action term,mM/s,Reaction,Multiplicative,1,,1000,0.0000001,10000000,1,taur,Dynamic,Derived,0,,taur,"[[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, I_reaction, 0]"
Michaelis constant product,mM,Reaction,Multiplicative,1,,1000,0.001,1000,1,KMprod,Kinetic,Derived,0,Local parameter,kmprod,"[0, 0, Nkm, 0, 0, 0, 0, 0]"
,,,,,,,,,,,,,,,,
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='PbConfig' description='Parameter balancing configuration file',,,,,,,,,,,,,,,,
!Option,!Value,,,,,,,,,,,,,,,
use_pseudo_values,TRUE,,,,,,,,,,,,,,,
ph,7,,,,,,,,,,,,,,,
temperature,298.15,,,,,,,,,,,,,,,
overwrite_kinetics,TRUE,,,,,,,,,,,,,,,
cell_volume,43,,,,,,,,,,,,,,,
parametrisation,hal,,,,,,,,,,,,,,,
enzyme_prefactor,TRUE,,,,,,,,,,,,,,,
default_inhibition,complete,,,,,,,,,,,,,,,
default_activation,complete,,,,,,,,,,,,,,,
model_name,outputname,,,,,,,,,,,,,,,
boundary_values,ignore,,,,,,,,,,,,,,,