(* 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], ACEo[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] == 0.0204796335883082, ACEo[0] == 0.0199832348425703, AMP[0] == 0.815615549032524, ATP[0] == 1.60200361393713, BPG[0] == 8.04607071179563*^-05, F16P[0] == 7.88018175756601, F6P[0] == 0.494145977137238, G3P[0] == 0.898510944946246, G6P[0] == 2.26358698183118, GLCi[0] == 0.030050982468921, NADH[0] == 0.390801474565893, P2G[0] == 0.0132315645673044, P3G[0] == 0.126790594836765, PEP[0] == 0.0104013226052447, PYR[0] == 1.87974762229335, TRIO[0] == 3.03393493804436
};

rates = {
v\[LetterSpace]ACEt, 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]LACTO, 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]ACEt -> kACEt*optACEt*(ACE[t] - ACEo[t]), 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]LACTO -> CN*kLACTO*optLACTO*ACEo[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 -> 0.538823362397066, AXPsum -> 4.1, CN -> 5.0, CPFKAMP -> 0.0619066304454687, CPFKATP -> 4.11927102035743, CPFKF16BP -> 0.508729452985175, CPFKF26BP -> 0.0166446192764381, CiPFKATP -> 133.997614964125, ETOH -> 50.0, EXTERNAL -> 0.0, F26BP -> 0.02, GLCo -> 20.0, KATPASE -> 38.3151546531701, KGLYCOGEN -> 0.657952839162031, KPFKAMP -> 0.0908240053852103, KPFKF16BP -> 0.0867303342326532, KPFKF26BP -> 0.000809438316573068, KSUCC -> 15.5243973118548, KTREHALOSE -> 0.35532683402403, 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 -> 1.10269434597499, KiADHETOH -> 87.5197712783722, KiADHNAD -> 0.994086925030065, KiADHNADH -> 0.0266112112630811, KiPFKATP -> 0.672261990665842, KmADHACE -> 1.08640493765421, KmADHETOH -> 17.873472130943, KmADHNAD -> 0.173151837494663, KmADHNADH -> 0.106028057123405, KmALDDHAP -> 2.35279569817395, KmALDF16P -> 0.289978616714069, KmALDGAP -> 2.03507983684522, KmALDGAPi -> 10.1050124140839, KmATP -> 0.226775365195371, KmENOP2G -> 0.0384298786845413, KmENOPEP -> 0.48718115014322, KmG3PAG3P -> 4.36779649390928, KmG3PAPhi -> 0.784145076398265, KmG3PDHADP -> 1.66742704847041, KmG3PDHATP -> 0.477041600990239, KmG3PDHDHAP -> 0.434945788250048, KmG3PDHF16P -> 5.39383791442381, KmG3PDHG3P -> 0.989904702292856, KmG3PDHNAD -> 0.864230959749687, KmG3PDHNADH -> 0.024866434215201, KmGAPDHBPG -> 0.0105501300482522, KmGAPDHGAP -> 0.126014064354562, KmGAPDHNAD -> 0.0877156866078506, KmGAPDHNADH -> 0.0560916256777303, KmGLKADP -> 0.263092658044569, KmGLKATP -> 0.122952862202984, KmGLKG6P -> 29.9047243861895, KmGLKGLCi -> 0.070544843764403, KmGLTGLCi -> 1.2601958510505, KmGLTGLCo -> 1.14781100891666, KmPDCPYR -> 2.71686030412305, KmPFKATP -> 0.639382516791221, KmPFKF6P -> 0.136442544726107, KmPGIF6P -> 0.288898425005336, KmPGIG6P -> 1.31111953478591, KmPGKADP -> 0.195235190263297, KmPGKATP -> 0.307178610015771, KmPGKBPG -> 0.0030168048178011, KmPGKP3G -> 0.515383408435942, KmPGMP2G -> 0.0816972711677167, KmPGMP3G -> 1.1653123960473, KmPYKADP -> 0.423287756657824, KmPYKATP -> 1.67932644936778, KmPYKPEP -> 0.114687461199323, KmPYKPYR -> 21.2875778903632, L0 -> 0.744428179041052, NADSUM -> 1.0, Phi -> 1.20470265921072, VmADH -> 329.310550256221, VmALD -> 115.755229155784, VmENO -> 276.012216851944, VmG3PA -> 28.7585800442532, VmG3PDH -> 19.8677206272709, VmGAPDHf -> 279.717235797774, VmGLK -> 229.681980633949, VmGLT -> 43.9573369352783, VmPDC -> 209.10016696, VmPFK -> 127.540676183333, VmPGI -> 274.363965785613, VmPGK -> 797.96096752776, VmPGM -> 1591.55726747429, VmPYK -> 1223.18615050541, alpha -> 0.91, gR -> 3.47651271426468, kACEt -> 1431.0, kLACTO -> 0.09, nATP -> 1.0, nPDC -> 2.3801892387344, optACEt -> 0.566678504048252, optLACTO -> 0.566678504048252, yvol -> 50.0, default\[LetterSpace]compartment -> 1.0
};

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

events = {

};

speciesAnnotations = {
ACE[t]->"urn:miriam:kegg.compound:C00084", ACE[t]->"urn:miriam:obo.chebi:CHEBI:15343", ACEo[t]->"urn:miriam:kegg.compound:C00084", ACEo[t]->"urn:miriam:obo.chebi:CHEBI:15343", AMP[t]->"urn:miriam:kegg.compound:C00020", AMP[t]->"urn:miriam:obo.chebi:CHEBI:16027", ATP[t]->"urn:miriam:obo.chebi:CHEBI:15422", ATP[t]->"urn:miriam:kegg.compound:C00002", BPG[t]->"urn:miriam:obo.chebi:CHEBI:28907", BPG[t]->"urn:miriam:kegg.compound:C00236", F16P[t]->"urn:miriam:obo.chebi:CHEBI:16905", F16P[t]->"urn:miriam:kegg.compound:C00354", F6P[t]->"urn:miriam:obo.chebi:CHEBI:15946", F6P[t]->"urn:miriam:kegg.compound:C00085", G3P[t]->"urn:miriam:kegg.compound:C00093", G3P[t]->"urn:miriam:obo.chebi:CHEBI:15978", G6P[t]->"urn:miriam:kegg.compound:C00092", G6P[t]->"urn:miriam:obo.chebi:CHEBI:17665", GLCi[t]->"urn:miriam:kegg.compound:C00293", GLCi[t]->"urn:miriam:obo.chebi:CHEBI:17234", NADH[t]->"urn:miriam:obo.chebi:CHEBI:16908", NADH[t]->"urn:miriam:kegg.compound:C00004", P2G[t]->"urn:miriam:kegg.compound:C00631", P2G[t]->"urn:miriam:obo.chebi:CHEBI:17835", P3G[t]->"urn:miriam:kegg.compound:C00197", P3G[t]->"urn:miriam:obo.chebi:CHEBI:17794", PEP[t]->"urn:miriam:kegg.compound:C00074", PEP[t]->"urn:miriam:obo.chebi:CHEBI:18021", PYR[t]->"urn:miriam:obo.chebi:CHEBI:15361", PYR[t]->"urn:miriam:kegg.compound:C00022", TRIO[t]->"urn:miriam:kegg.compound:C00093", TRIO[t]->"urn:miriam:obo.chebi:CHEBI:15978", TRIO[t]->"urn:miriam:kegg.compound:C00661", TRIO[t]->"urn:miriam:obo.chebi:CHEBI:17138"
};

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]ACEt -2.0*v\[LetterSpace]SUC -1.0*v\[LetterSpace]ADH, ACEo'[t] == 0.02*v\[LetterSpace]ACEt -1.0*v\[LetterSpace]LACTO, AMP'[t] == 1.0*v\[LetterSpace]AK , ATP'[t] == 1.0*v\[LetterSpace]PGK +1.0*v\[LetterSpace]PYK +1.0*v\[LetterSpace]AK -1.0*v\[LetterSpace]PFK -1.0*v\[LetterSpace]ATP -4.0*v\[LetterSpace]SUC -1.0*v\[LetterSpace]GLYCO -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]}]