(* 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 = {
ACA[t], ACA0[t], ADP[t], AMP[t], ATP[t], DHAP[t], DHAPCN[t], DPG[t], EtOH[t], EtOH0[t], F6P[t], FBP[t], G6P[t], GAP[t], Glc[t], Glc0[t], Glyc[t], Glyc0[t], HCN[t], HCN0[t], NAD[t], NADH[t], OAc[t], OAc0[t], PEP[t], Pyr[t], PyrCN[t], glycogen[t], lacto[t]
};

initialValues = {
ACA[0] == 0.0, ACA0[0] == 0.0, ADP[0] == 1.5, AMP[0] == 0.33, ATP[0] == 2.1, DHAP[0] == 0.0, DHAPCN[0] == 0.0, DPG[0] == 0.0, EtOH[0] == 0.0, EtOH0[0] == 0.0, F6P[0] == 0.0, FBP[0] == 0.0, G6P[0] == 0.0, GAP[0] == 0.0, Glc[0] == 0.0, Glc0[0] == 24.0, Glyc[0] == 0.0, Glyc0[0] == 0.0, HCN[0] == 0.0, HCN0[0] == 5.0, NAD[0] == 0.75, NADH[0] == 0.23, OAc[0] == 0.0, OAc0[0] == 0.0, PEP[0] == 0.0, Pyr[0] == 0.0, PyrCN[0] == 0.0, glycogen[0] == 0.0, lacto[0] == 0.0
};

rates = {
v\[LetterSpace]ACAvap, v\[LetterSpace]ADH1, v\[LetterSpace]AK, v\[LetterSpace]ALD, v\[LetterSpace]ALDH, v\[LetterSpace]ATPcon, v\[LetterSpace]DHAPCN, v\[LetterSpace]GAPDH, v\[LetterSpace]Glctr, v\[LetterSpace]HCNvap, v\[LetterSpace]HK, v\[LetterSpace]LACTO, v\[LetterSpace]PDC, v\[LetterSpace]PFK, v\[LetterSpace]PGI, v\[LetterSpace]PK, v\[LetterSpace]PYRCN, v\[LetterSpace]PYRdrain, v\[LetterSpace]Storage, v\[LetterSpace]TIM, v\[LetterSpace]diACA, v\[LetterSpace]diEtOH, v\[LetterSpace]diGlyc, v\[LetterSpace]diHCN, v\[LetterSpace]diOAc, v\[LetterSpace]lpGlyc, v\[LetterSpace]lpPEP
};

rateEquations = {
v\[LetterSpace]ACAvap -> 0.5*kVap*ACA0[t], v\[LetterSpace]ADH1 -> (2*sc*V1adh1*V2adh1*(EtOH[t]*NAD[t] - (ACA[t]*NADH[t])/Keq))/(Kadh1EtOH*Kiadh1NAD*V2adh1 + (Kadh1NADH*V1adh1*ACA[t])/Keq + Kadh1NAD*V2adh1*EtOH[t] + Kadh1EtOH*V2adh1*NAD[t] + (Kadh1NADH*V1adh1*ACA[t]*NAD[t])/(Keq*Kiadh1NAD) + V2adh1*EtOH[t]*NAD[t] + (V2adh1*ACA[t]*EtOH[t]*NAD[t])/Kiadh1ACA + (Kadh1ACA*V1adh1*NADH[t])/Keq + (V1adh1*ACA[t]*NADH[t])/Keq + (Kadh1NAD*V2adh1*EtOH[t]*NADH[t])/Kiadh1NADH + (V1adh1*ACA[t]*EtOH[t]*NADH[t])/(Keq*Kiadh1EtOH)), v\[LetterSpace]AK -> sc*(-(kakr*ADP[t]^2) + kakf*AMP[t]*ATP[t]), v\[LetterSpace]ALD -> sc*((Valdf*FBP[t])/(KaldFBP + (KaldGAP*Valdf*DHAP[t])/(Kaldeq*Valdr) + FBP[t] + (KaldDHAP*Valdf*GAP[t])/(Kaldeq*Valdr) + (Valdf*DHAP[t]*GAP[t])/(Kaldeq*Valdr) + (FBP[t]*GAP[t])/KaldIGAP) - (Valdf*DHAP[t]*GAP[t])/(Kaldeq*(KaldFBP + (KaldGAP*Valdf*DHAP[t])/(Kaldeq*Valdr) + FBP[t] + (KaldDHAP*Valdf*GAP[t])/(Kaldeq*Valdr) + (Valdf*DHAP[t]*GAP[t])/(Kaldeq*Valdr) + (FBP[t]*GAP[t])/KaldIGAP))), v\[LetterSpace]ALDH -> kOAc*sc*ACA[t]*NAD[t], v\[LetterSpace]ATPcon -> (0.832*sc*Vatpconm*ATP[t])/(KatpconATP + ATP[t]), v\[LetterSpace]DHAPCN -> -(kdhapb*DHAPCN[t]) + kdhapf*DHAP[t]*HCN[t], v\[LetterSpace]GAPDH -> sc*((Vgapdh*GAP[t]*NAD[t])/(KgapdhGAP*KgapdhNAD*(1 + DPG[t]/KgapdhDPG + GAP[t]/KgapdhGAP)*(1 + NAD[t]/KgapdhNAD + NADH[t]/KgapdhNADH)) - (Vgapdh*DPG[t]*NADH[t])/(Kgapdheq*KgapdhGAP*KgapdhNAD*(1 + DPG[t]/KgapdhDPG + GAP[t]/KgapdhGAP)*(1 + NAD[t]/KgapdhNAD + NADH[t]/KgapdhNADH))), v\[LetterSpace]Glctr -> sc*(-((Vglctr*Glc[t])/(KglctrGlc*Vratio*(1 + G6P[t]/KglctrIG6P + Glc[t]/KglctrGlc + (G6P[t]*Glc[t])/(KglctrGlc*KglctrIIG6P) + ((1 + (Pglctr*Glc[t])/KglctrGlc)*(1 + Glc0[t]/KglctrGlc))/(1 + (Pglctr*Glc0[t])/KglctrGlc)))) + (Vglctr*Glc0[t])/(KglctrGlc*Vratio*(1 + Glc0[t]/KglctrGlc + ((1 + G6P[t]/KglctrIG6P + Glc[t]/KglctrGlc + (G6P[t]*Glc[t])/(KglctrGlc*KglctrIIG6P))*(1 + (Pglctr*Glc0[t])/KglctrGlc))/(1 + (Pglctr*Glc[t])/KglctrGlc)))), v\[LetterSpace]HCNvap -> kVap*HCN0[t], v\[LetterSpace]HK -> (sc*Vhkm*ATP[t]*Glc[t])/(KhkATP*KhkDGlc + KhkGlc*ATP[t] + KhkATP*Glc[t] + ATP[t]*Glc[t]), v\[LetterSpace]LACTO -> kacaf*ACA0[t]*HCN0[t] - kacab*lacto[t], v\[LetterSpace]PDC -> (0.7*sc*V1PDC*Pyr[t])/((KaPDC*(1 + G6P[t]/KxPDC))/(1 + (bet*G6P[t])/(alp*KxPDC)) + ((1 + G6P[t]/(alp*KxPDC))*Pyr[t])/(1 + (bet*G6P[t])/(alp*KxPDC))), v\[LetterSpace]PFK -> (sc*Vpfkm*ATP[t]*F6P[t]^2)/((KpfkmATP + ATP[t])*(Kpfk*(1 + (kappapfk*ATP[t]^2)/AMP[t]^2) + F6P[t]^2)), v\[LetterSpace]PGI -> sc*(-((Vpgi*F6P[t])/(Kpgieq*(KpgiG6P + (KpgiG6P*F6P[t])/KpgiF6P + G6P[t]))) + (Vpgi*G6P[t])/(KpgiG6P + (KpgiG6P*F6P[t])/KpgiF6P + G6P[t])), v\[LetterSpace]PK -> (sc*Vpkm*ADP[t]*PEP[t])/((KpkADP + ADP[t])*(KpkPEP + PEP[t])), v\[LetterSpace]PYRCN -> kpyrf*HCN[t]*Pyr[t] - kpyrb*PyrCN[t], v\[LetterSpace]PYRdrain -> (1.15*sc*VPYRd*Pyr[t])/(KmPYRd + Pyr[t]), v\[LetterSpace]Storage -> kg6pst*sc*ATP[t]*G6P[t], v\[LetterSpace]TIM -> sc*((Vtimm*DHAP[t])/(KtimDHAP + DHAP[t] + (KtimDHAP*GAP[t])/KtimGAP) - (Vtimm*GAP[t])/(Ktimeq*(KtimDHAP + DHAP[t] + (KtimDHAP*GAP[t])/KtimGAP))), v\[LetterSpace]diACA -> sc*((dACA*ACA[t])/Vratio - (dACA*ACA0[t])/Vratio), v\[LetterSpace]diEtOH -> sc*((dEtOH*EtOH[t])/Vratio - (dEtOH*EtOH0[t])/Vratio), v\[LetterSpace]diGlyc -> sc*((dGlyc*Glyc[t])/Vratio - (dGlyc*Glyc0[t])/Vratio), v\[LetterSpace]diHCN -> sc*((dHCN*HCN[t])/Vratio - (dHCN*HCN0[t])/Vratio), v\[LetterSpace]diOAc -> sc*((dOAc*OAc[t])/Vratio - (dOAc*OAc0[t])/Vratio), v\[LetterSpace]lpGlyc -> (sc*Vlpglycm*DHAP[t])/(KlpglycDHAP*(1 + (KlpglycINADH*(1 + NAD[t]/KlpglycINAD))/NADH[t]) + DHAP[t]*(1 + (KlpglycNADH*(1 + NAD[t]/KlpglycINAD))/NADH[t])), v\[LetterSpace]lpPEP -> sc*(klppepf*ADP[t]*DPG[t] - klppepr*ATP[t]*PEP[t])
};

parameters = {
Atot -> 3.93, Etotadh1 -> 0.0045, KG6Pactiv -> 3.1, KaPDC -> 8.8888889, Kadh1ACA -> 1.1, Kadh1EtOH -> 17.0, Kadh1NAD -> 0.17, Kadh1NADH -> 0.11, KaldDHAP -> 2.0, KaldFBP -> 0.3, KaldGAP -> 4.0, KaldIGAP -> 10.0, Kaldeq -> 0.081, KatpconATP -> 10000000000.0, Keq -> 5.0476587558*^-05, KgapdhDPG -> 0.01, KgapdhGAP -> 0.6, KgapdhNAD -> 0.1, KgapdhNADH -> 0.06, Kgapdheq -> 0.0055, KglctrGlc -> 1.7, KglctrIG6P -> 1.2, KglctrIIG6P -> 7.2, KhkATP -> 0.1, KhkDGlc -> 0.37, KhkGlc -> 0.0, Kiadh1ACA -> 1.1, Kiadh1EtOH -> 90.0, Kiadh1NAD -> 0.92, Kiadh1NADH -> 0.031, KlpglycDHAP -> 25.0, KlpglycINAD -> 0.13, KlpglycINADH -> 0.034, KlpglycNADH -> 0.13, KmPYRd -> 0.5, Kpdc -> 0.8, Kpfk -> 0.021, KpfkmATP -> 0.0, KpgiF6P -> 0.15, KpgiG6P -> 0.8, Kpgieq -> 0.13, KpkADP -> 0.17, KpkDPEP -> 0.2, KpkPEP -> 0.2, KtimDHAP -> 1.23, KtimGAP -> 1.27, Ktimeq -> 0.055, KxPDC -> 9.0, Ntot -> 0.98, Pglctr -> 1.0, V1PDC -> 0.9558, V1adh1 -> 110.16, V2adh1 -> 550.8, VPYRd -> 1.96, Valdf -> 2207.82, Valdr -> 11039.1, Vatpconm -> 128000000000.0, Vgapdh -> 833.858, Vglctr -> 142.0944, Vhkm -> 41.40376, Vlpglycm -> 81.4797, Vpdcm -> 95.58, Vpfkm -> 38.163468, Vpgi -> 496.042, Vpkm -> 343.096, Vratio -> 59.0, Vtimm -> 116.365, alp -> 0.09, bet -> 100.0, dACA -> 24.7, dEtOH -> 16.72, dGlyc -> 1.9, dHCN -> 34.2, dOAc -> 16.72, kOAc -> 0.5, kVap -> 0.00287219, kacab -> 2.03*^-06, kacaf -> 0.036, kakf -> 432.9, kakr -> 133.333, kappapfk -> 0.15, kdhapb -> 0.012, kdhapf -> 0.037, kg6pst -> 2.598218, klppepf -> 443866.0, klppepr -> 1528.62, kpyrb -> 0.0037, kpyrf -> 0.034, sc -> 2.0, X -> 0.0, drain -> 0.0, default -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

units = {
{"time" -> "", "metabolite" -> "", "extent" -> ""}
};

(* Time evolution *)
odes = {
ACA'[t] == 1.0*v\[LetterSpace]PDC +1.0*v\[LetterSpace]ADH1 -1.0*v\[LetterSpace]ALDH -59.0*v\[LetterSpace]diACA, ACA0'[t] == 1.0*v\[LetterSpace]diACA -1.0*v\[LetterSpace]LACTO -1.0*v\[LetterSpace]ACAvap, ADP'[t] == 1.0*v\[LetterSpace]ATPcon +1.0*v\[LetterSpace]PFK +1.0*v\[LetterSpace]HK +1.0*v\[LetterSpace]Storage +2.0*v\[LetterSpace]AK -1.0*v\[LetterSpace]lpPEP -1.0*v\[LetterSpace]PK, AMP'[t] ==  -1.0*v\[LetterSpace]AK, ATP'[t] == 1.0*v\[LetterSpace]lpPEP +1.0*v\[LetterSpace]PK -1.0*v\[LetterSpace]ATPcon -1.0*v\[LetterSpace]PFK -1.0*v\[LetterSpace]HK -1.0*v\[LetterSpace]Storage -1.0*v\[LetterSpace]AK, DHAP'[t] == 1.0*v\[LetterSpace]ALD -1.0*v\[LetterSpace]lpGlyc -1.0*v\[LetterSpace]TIM -1.0*v\[LetterSpace]DHAPCN, DHAPCN'[t] == 1.0*v\[LetterSpace]DHAPCN , DPG'[t] == 1.0*v\[LetterSpace]GAPDH -1.0*v\[LetterSpace]lpPEP, EtOH'[t] ==  -59.0*v\[LetterSpace]diEtOH -1.0*v\[LetterSpace]ADH1, EtOH0'[t] == 1.0*v\[LetterSpace]diEtOH , F6P'[t] == 1.0*v\[LetterSpace]PGI -1.0*v\[LetterSpace]PFK, FBP'[t] == 1.0*v\[LetterSpace]PFK -1.0*v\[LetterSpace]ALD, G6P'[t] == 1.0*v\[LetterSpace]HK -1.0*v\[LetterSpace]PGI -1.0*v\[LetterSpace]Storage, GAP'[t] == 1.0*v\[LetterSpace]TIM +1.0*v\[LetterSpace]ALD -1.0*v\[LetterSpace]GAPDH, Glc'[t] == 59.0*v\[LetterSpace]Glctr -1.0*v\[LetterSpace]HK, Glc0'[t] ==  -1.0*v\[LetterSpace]Glctr, Glyc'[t] == 1.0*v\[LetterSpace]lpGlyc -59.0*v\[LetterSpace]diGlyc, Glyc0'[t] == 1.0*v\[LetterSpace]diGlyc , HCN'[t] ==  -59.0*v\[LetterSpace]diHCN -1.0*v\[LetterSpace]PYRCN -1.0*v\[LetterSpace]DHAPCN, HCN0'[t] == 1.0*v\[LetterSpace]diHCN -1.0*v\[LetterSpace]LACTO -1.0*v\[LetterSpace]HCNvap, NAD'[t] == 1.0*v\[LetterSpace]lpGlyc -1.0*v\[LetterSpace]ALDH -1.0*v\[LetterSpace]GAPDH -1.0*v\[LetterSpace]ADH1, NADH'[t] == 1.0*v\[LetterSpace]ALDH +1.0*v\[LetterSpace]GAPDH +1.0*v\[LetterSpace]ADH1 -1.0*v\[LetterSpace]lpGlyc, OAc'[t] == 1.0*v\[LetterSpace]ALDH -59.0*v\[LetterSpace]diOAc, OAc0'[t] == 1.0*v\[LetterSpace]diOAc , PEP'[t] == 1.0*v\[LetterSpace]lpPEP -1.0*v\[LetterSpace]PK, Pyr'[t] == 1.0*v\[LetterSpace]PK -1.0*v\[LetterSpace]PYRdrain -1.0*v\[LetterSpace]PDC -1.0*v\[LetterSpace]PYRCN, PyrCN'[t] == 1.0*v\[LetterSpace]PYRCN , glycogen'[t] == 1.0*v\[LetterSpace]Storage , lacto'[t] == 1.0*v\[LetterSpace]LACTO 
};
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]}]