(* Generated by JWS Online *)

(* This is an experimental feature of JWS Online. Please report any mistakes.*)

(* Note that the following notable SBML entities or features are not supported in notebook outputyet: *)
    (* Events *)
    (* Constraints *)
    (* Units and UnitDefinitions *)
    (* AlgebraicRules *)
    (* conversionFactors *)

variables = {
ACE[t], AMP[t], ATP[t], BPG[t], F16P[t], F6P[t], G3P[t], G6P[t], GLCi[t], NADH[t], P2G[t], P3G[t], PEP[t], PYR[t], TRIO[t]
};

initialValues = {
ACE[0] == 0.020961620573545, AMP[0] == 0.735086409252821, ATP[0] == 1.71151931449073, BPG[0] == 8.59865417775755*^-05, F16P[0] == 8.44097120440662, F6P[0] == 0.578946953777943, G3P[0] == 0.85406872398333, G6P[0] == 2.83285776994039, GLCi[0] == 0.0363872606459786, NADH[0] == 0.298484471521169, P2G[0] == 0.0145743573339282, P3G[0] == 0.134803835263793, PEP[0] == 0.0170684820602329, PYR[0] == 4.00163453632936, TRIO[0] == 3.13659774869995
};

rates = {
v\[LetterSpace]ADH, v\[LetterSpace]AK, v\[LetterSpace]ALD, v\[LetterSpace]ATP, v\[LetterSpace]ENO, v\[LetterSpace]G3PA, v\[LetterSpace]G3PDH, v\[LetterSpace]GAPDH, v\[LetterSpace]GLK, v\[LetterSpace]GLT, v\[LetterSpace]GLYCO, v\[LetterSpace]PDC, v\[LetterSpace]PFK, v\[LetterSpace]PGI, v\[LetterSpace]PGK, v\[LetterSpace]PGM, v\[LetterSpace]PYK, v\[LetterSpace]SUC, v\[LetterSpace]Treha
};

rateEquations = {
v\[LetterSpace]ADH -> -((VmADH*(ETOH*NAD - (ACE[t]*NADH[t])/KeqADH))/(KiADHNAD*KmADHETOH*(1 + (ETOH*KmADHNAD)/(KiADHNAD*KmADHETOH) + NAD/KiADHNAD + (ETOH*NAD)/(KiADHNAD*KmADHETOH) + (KmADHNADH*ACE[t])/(KiADHNADH*KmADHACE) + (ETOH*NAD*ACE[t])/(KiADHACE*KiADHNAD*KmADHETOH) + (KmADHNADH*NAD*ACE[t])/(KiADHNAD*KiADHNADH*KmADHACE) + NADH[t]/KiADHNADH + (ETOH*KmADHNAD*NADH[t])/(KiADHNAD*KiADHNADH*KmADHETOH) + (ACE[t]*NADH[t])/(KiADHNADH*KmADHACE) + (ETOH*ACE[t]*NADH[t])/(KiADHETOH*KiADHNADH*KmADHACE)))), v\[LetterSpace]AK -> 133.333*AKopt*(ADP^2 - (AMP[t]*ATP[t])/KeqAK), v\[LetterSpace]ALD -> (VmALD*(F16P[t] - (KeqTPI*TRIO[t]^2)/(KeqALD*(1 + KeqTPI)^2)))/(KmALDF16P*(1 + F16P[t]/KmALDF16P + TRIO[t]/((1 + KeqTPI)*KmALDDHAP) + (KeqTPI*TRIO[t])/((1 + KeqTPI)*KmALDGAP) + (KeqTPI*F16P[t]*TRIO[t])/((1 + KeqTPI)*KmALDF16P*KmALDGAPi) + (KeqTPI*TRIO[t]^2)/((1 + KeqTPI)^2*KmALDDHAP*KmALDGAP))), v\[LetterSpace]ATP -> (KATPASE*ATP[t]^nATP)/(KmATP^nATP + ATP[t]^nATP), v\[LetterSpace]ENO -> (VmENO*(P2G[t] - PEP[t]/KeqENO))/(KmENOP2G*(1 + P2G[t]/KmENOP2G + PEP[t]/KmENOPEP)), v\[LetterSpace]G3PA -> (VmG3PA*G3P[t])/(KmG3PAG3P*(1 + Phi/KmG3PAPhi)*(1 + G3P[t]/KmG3PAG3P)), v\[LetterSpace]G3PDH -> (VmG3PDH*(-((NAD*G3P[t])/KeqG3PDH) + (NADH[t]*TRIO[t])/(1 + KeqTPI)))/(KmG3PDHDHAP*KmG3PDHNADH*(1 + ADP/KmG3PDHADP + ATP[t]/KmG3PDHATP + F16P[t]/KmG3PDHF16P)*(1 + NAD/KmG3PDHNAD + NADH[t]/KmG3PDHNADH)*(1 + G3P[t]/KmG3PDHG3P + TRIO[t]/((1 + KeqTPI)*KmG3PDHDHAP))), v\[LetterSpace]GAPDH -> (-((VmGAPDHf*BPG[t]*NADH[t])/(KeqGAPDH*KmGAPDHGAP*KmGAPDHNAD)) + (KeqTPI*NAD*VmGAPDHf*TRIO[t])/((1 + KeqTPI)*KmGAPDHGAP*KmGAPDHNAD))/((1 + NAD/KmGAPDHNAD + NADH[t]/KmGAPDHNADH)*(1 + BPG[t]/KmGAPDHBPG + (KeqTPI*TRIO[t])/((1 + KeqTPI)*KmGAPDHGAP))), v\[LetterSpace]GLK -> (VmGLK*(-((ADP*G6P[t])/KeqGLK) + ATP[t]*GLCi[t]))/(KmGLKATP*KmGLKGLCi*(1 + ADP/KmGLKADP + ATP[t]/KmGLKATP)*(1 + G6P[t]/KmGLKG6P + GLCi[t]/KmGLKGLCi)), v\[LetterSpace]GLT -> (VmGLT*(GLCo - GLCi[t]/KeqGLT))/(KmGLTGLCo*(1 + GLCo/KmGLTGLCo + GLCi[t]/KmGLTGLCi + (alpha*GLCo*GLCi[t])/(KmGLTGLCi*KmGLTGLCo))), v\[LetterSpace]GLYCO -> KGLYCOGEN*ATP[t]*G6P[t], v\[LetterSpace]PDC -> (VmPDC*PYR[t]^nPDC)/(KmPDCPYR^nPDC*(1 + PYR[t]^nPDC/KmPDCPYR^nPDC)), v\[LetterSpace]PFK -> (gR*VmPFK*ATP[t]*F6P[t]*(1 + ATP[t]/KmPFKATP + F6P[t]/KmPFKF6P + (gR*ATP[t]*F6P[t])/(KmPFKATP*KmPFKF6P)))/(KmPFKATP*KmPFKF6P*((L0*(1 + (CPFKAMP*AMP[t])/KPFKAMP)^2*(1 + (CiPFKATP*ATP[t])/KiPFKATP)^2*(1 + (CPFKATP*ATP[t])/KmPFKATP)^2*(1 + (CPFKF26BP*F26BP)/KPFKF26BP + (CPFKF16BP*F16P[t])/KPFKF16BP)^2)/((1 + AMP[t]/KPFKAMP)^2*(1 + ATP[t]/KiPFKATP)^2*(1 + F26BP/KPFKF26BP + F16P[t]/KPFKF16BP)^2) + (1 + ATP[t]/KmPFKATP + F6P[t]/KmPFKF6P + (gR*ATP[t]*F6P[t])/(KmPFKATP*KmPFKF6P))^2)), v\[LetterSpace]PGI -> (VmPGI*(-(F6P[t]/KeqPGI) + G6P[t]))/(KmPGIG6P*(1 + F6P[t]/KmPGIF6P + G6P[t]/KmPGIG6P)), v\[LetterSpace]PGK -> (VmPGK*(ADP*KeqPGK*BPG[t] - ATP[t]*P3G[t]))/(KmPGKATP*KmPGKP3G*(1 + ADP/KmPGKADP + ATP[t]/KmPGKATP)*(1 + BPG[t]/KmPGKBPG + P3G[t]/KmPGKP3G)), v\[LetterSpace]PGM -> (VmPGM*(-(P2G[t]/KeqPGM) + P3G[t]))/(KmPGMP3G*(1 + P2G[t]/KmPGMP2G + P3G[t]/KmPGMP3G)), v\[LetterSpace]PYK -> (VmPYK*(ADP*PEP[t] - (ATP[t]*PYR[t])/KeqPYK))/(KmPYKADP*KmPYKPEP*(1 + ADP/KmPYKADP + ATP[t]/KmPYKATP)*(1 + PEP[t]/KmPYKPEP + PYR[t]/KmPYKPYR)), v\[LetterSpace]SUC -> KSUCC*ACE[t], v\[LetterSpace]Treha -> KTREHALOSE*ATP[t]*G6P[t]
};

parameters = {
AKopt -> 0.669027384631504, AXPsum -> 4.1, CPFKAMP -> 0.0703733354872318, CPFKATP -> 3.92007230818607, CPFKF16BP -> 0.497287747227918, CPFKF26BP -> 0.0169045870014536, CiPFKATP -> 129.944855330581, ETOH -> 50.0, EXTERNAL -> 0.0, F26BP -> 0.02, GLCo -> 20.0, KATPASE -> 42.0705769854329, KGLYCOGEN -> 0.977472520682727, KPFKAMP -> 0.0953464313885568, KPFKF16BP -> 0.0910578202022938, KPFKF26BP -> 0.000788204396870689, KSUCC -> 16.68508899926, KTREHALOSE -> 0.500616814711998, KeqADH -> 6.9*^-05, KeqAK -> 0.45, KeqALD -> 0.069, KeqENO -> 6.7, KeqG3PDH -> 4300.0, KeqGAPDH -> 0.00562639062770364, KeqGLK -> 3800.0, KeqGLT -> 1.0, KeqPGI -> 0.314, KeqPGK -> 3200.0, KeqPGM -> 0.19, KeqPYK -> 6500.0, KeqTPI -> 0.045, KiADHACE -> 1.06069180458452, KiADHETOH -> 86.6964879095848, KiADHNAD -> 0.929334305364439, KiADHNADH -> 0.0281954142935579, KiPFKATP -> 0.629349743346242, KmADHACE -> 1.07248685047976, KmADHETOH -> 17.2456286627476, KmADHNAD -> 0.166769639219937, KmADHNADH -> 0.105656811657223, KmALDDHAP -> 2.31373624578339, KmALDF16P -> 0.290710055001503, KmALDGAP -> 1.92661390756668, KmALDGAPi -> 9.63179022883364, KmATP -> 0.235555853813508, KmENOP2G -> 0.0366500838590152, KmENOPEP -> 0.485374038512661, KmG3PAG3P -> 4.19774181864929, KmG3PAPhi -> 0.752086905478373, KmG3PDHADP -> 1.45931578303823, KmG3PDHATP -> 0.520892324585364, KmG3PDHDHAP -> 0.417843988956108, KmG3PDHF16P -> 4.42804700123956, KmG3PDHG3P -> 1.014284409772, KmG3PDHNAD -> 0.855229911902209, KmG3PDHNADH -> 0.0244080593501774, KmGAPDHBPG -> 0.0103571131911046, KmGAPDHGAP -> 0.169036456827137, KmGAPDHNAD -> 0.0836010430272397, KmGAPDHNADH -> 0.060976295368858, KmGLKADP -> 0.253545174984255, KmGLKATP -> 0.123817018291608, KmGLKG6P -> 29.0056944225839, KmGLKGLCi -> 0.0697345487083755, KmGLTGLCi -> 1.25861629411934, KmGLTGLCo -> 1.11844371774078, KmPDCPYR -> 4.24956584535036, KmPFKATP -> 0.66667696421218, KmPFKF6P -> 0.128662486563679, KmPGIF6P -> 0.2794876594961, KmPGIG6P -> 1.35840250049127, KmPGKADP -> 0.193439959393382, KmPGKATP -> 0.28803020122741, KmPGKBPG -> 0.00290885157187471, KmPGKP3G -> 0.495134254954938, KmPGMP2G -> 0.0779767804899997, KmPGMP3G -> 1.11080591289804, KmPYKADP -> 0.475697546620804, KmPYKATP -> 1.51813362449153, KmPYKPEP -> 0.127016742234385, KmPYKPYR -> 20.4730221085492, L0 -> 0.739254244885314, NADSUM -> 1.0, Phi -> 1.20470265921072, VmADH -> 479.951176287046, VmALD -> 150.282822785562, VmENO -> 350.467207519718, VmG3PA -> 36.0054380978204, VmG3PDH -> 25.2034727708702, VmGAPDHf -> 324.941804213337, VmGLK -> 286.092955831363, VmGLT -> 63.4244580249427, VmPDC -> 169.130966780205, VmPFK -> 136.836946410547, VmPGI -> 315.470814576513, VmPGK -> 1030.09847797527, VmPGM -> 2007.9381605905, VmPYK -> 1329.62417575784, alpha -> 0.91, biomassFac -> 0.720903608283592, gR -> 3.5972036851668, nATP -> 1.0, nPDC -> 1.88297482037065, default\[LetterSpace]compartment -> 1.0
};

assignments = {
ADP -> AXPsum - AMP[t] - ATP[t], NAD -> NADSUM - NADH[t]
};

events = {

};

speciesAnnotations = {
ACE[t]->"urn:miriam:obo.chebi:CHEBI15343", ACE[t]->"urn:miriam:kegg.compound:C00084", AMP[t]->"urn:miriam:obo.chebi:CHEBI16027", AMP[t]->"urn:miriam:kegg.compound:C00020", ATP[t]->"urn:miriam:obo.chebi:CHEBI15422", ATP[t]->"urn:miriam:kegg.compound:C00002", BPG[t]->"urn:miriam:obo.chebi:28907", BPG[t]->"urn:miriam:kegg.compound:C00236", F16P[t]->"urn:miriam:obo.chebi:16905", F16P[t]->"urn:miriam:kegg.compound:C00354", F6P[t]->"urn:miriam:kegg.compound:C00085", F6P[t]->"urn:miriam:obo.chebi:15946", G3P[t]->"urn:miriam:kegg.compound:C00093", G3P[t]->"urn:miriam:obo.chebi:CHEBI15978", G6P[t]->"urn:miriam:kegg.compound:C00092", G6P[t]->"urn:miriam:obo.chebi:17665", GLCi[t]->"urn:miriam:kegg.compound:C00293", GLCi[t]->"urn:miriam:obo.chebi:CHEBI17234", NADH[t]->"urn:miriam:obo.chebi:16908", NADH[t]->"urn:miriam:kegg.compound:C00004", P2G[t]->"urn:miriam:kegg.compound:C00631", P2G[t]->"urn:miriam:obo.chebi:17835", P3G[t]->"urn:miriam:kegg.compound:C00197", P3G[t]->"urn:miriam:obo.chebi:17794", PEP[t]->"urn:miriam:obo.chebi:18021", PEP[t]->"urn:miriam:kegg.compound:C00074", PYR[t]->"urn:miriam:obo.chebi:15361", PYR[t]->"urn:miriam:kegg.compound:C00022", TRIO[t]->"urn:miriam:obo.chebi:CHEBI15978", TRIO[t]->"urn:miriam:obo.chebi:CHEBI17138", TRIO[t]->"urn:miriam:kegg.compound:C00093", TRIO[t]->"urn:miriam:kegg.compound:C00661"
};

reactionAnnotations = {
v\[LetterSpace]ADH->"urn:miriam:kegg.reaction:R00754", v\[LetterSpace]ALD->"urn:miriam:kegg.reaction:R01068", v\[LetterSpace]ATP->"urn:miriam:obo.go:0006200", v\[LetterSpace]ENO->"urn:miriam:kegg.reaction:R00658", v\[LetterSpace]GAPDH->"urn:miriam:kegg.reaction:R01061", v\[LetterSpace]GLK->"urn:miriam:kegg.reaction:R00299", v\[LetterSpace]GLT->"urn:miriam:obo.go:0015758", v\[LetterSpace]PDC->"urn:miriam:kegg.reaction:R00224", v\[LetterSpace]PFK->"urn:miriam:kegg.reaction:R04779", v\[LetterSpace]PGI->"urn:miriam:kegg.reaction:R02740", v\[LetterSpace]PGK->"urn:miriam:kegg.reaction:R01512", v\[LetterSpace]PGM->"urn:miriam:kegg.reaction:R01518"
};

units = {
{"time" -> "min", "metabolite" -> "mmol/L", "extent" -> "mM"}
};

(* Time evolution *)
odes = {
ACE'[t] == 1.0*v\[LetterSpace]PDC -1.0*v\[LetterSpace]ADH -2.0*v\[LetterSpace]SUC, AMP'[t] == 1.0*v\[LetterSpace]AK , ATP'[t] == 1.0*v\[LetterSpace]AK +1.0*v\[LetterSpace]PGK +1.0*v\[LetterSpace]PYK -1.0*v\[LetterSpace]PFK -1.0*v\[LetterSpace]ATP -1.0*v\[LetterSpace]GLYCO -4.0*v\[LetterSpace]SUC -1.0*v\[LetterSpace]GLK -1.0*v\[LetterSpace]Treha, BPG'[t] == 1.0*v\[LetterSpace]GAPDH -1.0*v\[LetterSpace]PGK, F16P'[t] == 1.0*v\[LetterSpace]PFK -1.0*v\[LetterSpace]ALD, F6P'[t] == 1.0*v\[LetterSpace]PGI -1.0*v\[LetterSpace]PFK, G3P'[t] == 1.0*v\[LetterSpace]G3PDH -1.0*v\[LetterSpace]G3PA, G6P'[t] == 1.0*v\[LetterSpace]GLK -1.0*v\[LetterSpace]PGI -1.0*v\[LetterSpace]GLYCO -2.0*v\[LetterSpace]Treha, GLCi'[t] == 1.0*v\[LetterSpace]GLT -1.0*v\[LetterSpace]GLK, NADH'[t] == 1.0*v\[LetterSpace]GAPDH +3.0*v\[LetterSpace]SUC -1.0*v\[LetterSpace]G3PDH -1.0*v\[LetterSpace]ADH, P2G'[t] == 1.0*v\[LetterSpace]PGM -1.0*v\[LetterSpace]ENO, P3G'[t] == 1.0*v\[LetterSpace]PGK -1.0*v\[LetterSpace]PGM, PEP'[t] == 1.0*v\[LetterSpace]ENO -1.0*v\[LetterSpace]PYK, PYR'[t] == 1.0*v\[LetterSpace]PYK -1.0*v\[LetterSpace]PDC, TRIO'[t] == 2.0*v\[LetterSpace]ALD -1.0*v\[LetterSpace]G3PDH -1.0*v\[LetterSpace]GAPDH
};
timeCourse = NDSolve[Join[odes, initialValues]//.rateEquations//.assignments//.parameters, variables, {t, 0, 100}];

(* Steady-state solution initialized with result of time evolution *)
findRootEquations = odes /.D[_[t],t]->0;
findRootVariables = Partition[Flatten[{#, #/.timeCourse/.t->100} &/@variables],2];
steadyStateVariables = FindRoot[findRootEquations//.rateEquations//.assignments//.parameters, findRootVariables, MaxIterations->100]
fluxes = #//.assignments//.parameters/.steadyStateVariables&/@rateEquations

(* Plot the time evolution of the variables *)
plotTable=Table[Plot[variables[[i]]/.parameters/.timeCourse,{t,0,100},PlotLegends->variables[[i]],PlotRange->Full],{i,Length[variables]}]