(* 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 = {
KDX[t], KG[t], KGSA[t], LAC[t], NAD[t], PYR[t], XA[t], XLAC[t], XYL[t]
};

initialValues = {
KDX[0] == 0.0, KG[0] == 0.0, KGSA[0] == 0.0, LAC[0] == 0.0, NAD[0] == 8.0, PYR[0] == 0.0, XA[0] == 0.0, XLAC[0] == 0.0, XYL[0] == 5.0
};

rates = {
v1, v2, v3, v4, v5, v6, v7
};

rateEquations = {
v1 -> (Eb*VmXDH*NAD[t]*XYL[t])/(1000*KmXDHNAD*KmXDHXYL*(1 + (Ntot - NAD[t])/KmXDHNADH + NAD[t]/KmXDHNAD)*(1 + XLAC[t]/KmXDHXLAC + XYL[t]/KmXDHXYL)), v2 -> kXLA*XLAC[t], v3 -> (Ec*VmXLA*XLAC[t])/(1000*KmXLAXLAC*(1 + XA[t]/KmXLAXA + XLAC[t]/KmXLAXLAC)), v4 -> (Ed*VmXAD*XA[t])/(1000*KmXADXA*(1 + (Ntot - NAD[t])/KiXADNADH)*(1 + KDX[t]/KmXADKDX + XA[t]/KmXADXA)), v5 -> (Ex*fracX*VmKDXD*KDX[t])/(1000*KmKDXDKDX*(1 + KDX[t]/KmKDXDKDX + KGSA[t]/KmKDXDKGSA)*(1 + KG[t]/KiKDXDakg + LAC[t]/KiKDXDLAC + PYR[t]/KiKDXDPYR + XA[t]/KiKDXDxylonate)), v6 -> (Ea*VmKGSADH*KGSA[t]*NAD[t])/(1000*KmKGSADHKGSA*KmKGSADHNAD*((1 + KG[t]/KmKGSADHKG + KGSA[t]/KmKGSADHKGSA)*(1 + (Ntot - NAD[t])/KmKGSADHNADH + NAD[t]/KmKGSADHNAD) + (KDX[t]*(1 + (Ntot - NAD[t])/KmKGSADHNADH2 + NAD[t]/KmKGSADHNAD))/KmKGSADHKDX)), v7 -> kLDH*(Ntot - NAD[t])*PYR[t]
};

parameters = {
Ea -> 10.0, Eb -> 2.5, Ec -> 0.8, Ed -> 8.67, Ex -> 0.5, KiKDXDLAC -> 27.9762, KiKDXDPYR -> 17.9168, KiKDXDakg -> 14.7919, KiKDXDxylonate -> 18.3001, KiXADNADH -> 10.4629, KmKDXDKDX -> 0.207656, KmKDXDKGSA -> 0.288658, KmKGSADHKDX -> 0.2136, KmKGSADHKG -> 0.279059, KmKGSADHKGSA -> 0.0217501, KmKGSADHNAD -> 0.596286, KmKGSADHNADH -> 0.2674, KmKGSADHNADH2 -> 0.0241, KmXADKDX -> 0.862428, KmXADXA -> 0.793955, KmXDHNAD -> 0.161239, KmXDHNADH -> 0.0297091, KmXDHXLAC -> 0.535734, KmXDHXYL -> 0.19851, KmXLAXA -> 0.0381004, KmXLAXLAC -> 0.445269, Ntot -> 8.0, VmKDXD -> 107.075, VmKGSADH -> 49.3374, VmXAD -> 42.359, VmXDH -> 119.743, VmXLA -> 944.406, fracX -> 0.251104, kLDH -> 10.0, kXLA -> 0.00718272, default -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
KDX[t]->"http://identifiers.org/obo.chebi/CHEBI%3A1060", KDX[t]->"http://identifiers.org/kegg.compound/C03826", KG[t]->"http://identifiers.org/kegg.compound/C00026", KG[t]->"http://identifiers.org/obo.chebi/CHEBI%3A30915", KGSA[t]->"http://identifiers.org/kegg.compound/C00433", KGSA[t]->"http://identifiers.org/obo.chebi/CHEBI%3A17415", LAC[t]->"http://identifiers.org/obo.chebi/CHEBI%3A28358", LAC[t]->"http://identifiers.org/kegg.compound/C01432", NAD[t]->"http://identifiers.org/kegg.compound/C00003", NAD[t]->"http://identifiers.org/obo.chebi/CHEBI%3A15846", PYR[t]->"http://identifiers.org/obo.chebi/CHEBI%3A32816", PYR[t]->"http://identifiers.org/kegg.compound/C00022", XA[t]->"http://identifiers.org/obo.chebi/CHEBI%3A48093", XA[t]->"http://identifiers.org/kegg.compound/C00502", XLAC[t]->"http://identifiers.org/obo.chebi/CHEBI%3A15867", XLAC[t]->"http://identifiers.org/kegg.compound/C02266", XYL[t]->"http://identifiers.org/obo.chebi/CHEBI%3A15936", XYL[t]->"http://identifiers.org/kegg.compound/C00181"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
KDX'[t] == 1.0*v4 -1.0*v5, KG'[t] == 1.0*v6 , KGSA'[t] == 1.0*v5 -1.0*v6, LAC'[t] == 1.0*v7 , NAD'[t] == 1.0*v7 -1.0*v6 -1.0*v1, PYR'[t] ==  -1.0*v7, XA'[t] == 1.0*v2 +1.0*v3 -1.0*v4, XLAC'[t] == 1.0*v1 -1.0*v2 -1.0*v3, XYL'[t] ==  -1.0*v1
};
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]}]