(* 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], ACAX[t], ADP[t], AMP[t], ATP[t], BPG[t], CNX[t], DHAP[t], EtOH[t], EtOHX[t], F6P[t], FBP[t], G6P[t], GAP[t], Glc[t], GlcX[t], Glyc[t], GlycX[t], NAD[t], NADH[t], PEP[t], Pyr[t]
};

initialValues = {
ACA[0] == 1.48153, ACAX[0] == 1.28836, ADP[0] == 1.5, AMP[0] == 0.33, ATP[0] == 2.1, BPG[0] == 0.00027, CNX[0] == 5.20358, DHAP[0] == 2.95, EtOH[0] == 19.2379, EtOHX[0] == 16.4514, F6P[0] == 0.49, FBP[0] == 4.64, G6P[0] == 4.2, GAP[0] == 0.115, Glc[0] == 0.573074, GlcX[0] == 1.55307, Glyc[0] == 4.196, GlycX[0] == 1.68478, NAD[0] == 0.65, NADH[0] == 0.33, PEP[0] == 0.04, Pyr[0] == 8.7
};

rates = {
v\[LetterSpace]1, v\[LetterSpace]10, v\[LetterSpace]11, v\[LetterSpace]12, v\[LetterSpace]13, v\[LetterSpace]14, v\[LetterSpace]15, v\[LetterSpace]16, v\[LetterSpace]17, v\[LetterSpace]18, v\[LetterSpace]19, v\[LetterSpace]2, v\[LetterSpace]20, v\[LetterSpace]21, v\[LetterSpace]22, v\[LetterSpace]23, v\[LetterSpace]24, v\[LetterSpace]3, v\[LetterSpace]4, v\[LetterSpace]5, v\[LetterSpace]6, v\[LetterSpace]7, v\[LetterSpace]8, v\[LetterSpace]9
};

rateEquations = {
v\[LetterSpace]1 -> k0*(GlcX0 - GlcX[t]), v\[LetterSpace]10 -> (V10m*ADP[t]*PEP[t])/((K10ADP + ADP[t])*(K10PEP + PEP[t])), v\[LetterSpace]11 -> (V11m*Pyr[t])/(K11 + Pyr[t]), v\[LetterSpace]12 -> (V12m*ACA[t]*NADH[t])/((K12ACA + ACA[t])*(K12NADH + NADH[t])), v\[LetterSpace]13 -> (k13*(EtOH[t] - EtOHX[t]))/Yvol, v\[LetterSpace]14 -> k0*EtOHX[t], v\[LetterSpace]15 -> (V15m*DHAP[t])/(K15DHAP*(1 + (K15INADH*(1 + NAD[t]/K15INAD))/NADH[t]) + DHAP[t]*(1 + (K15NADH*(1 + NAD[t]/K15INAD))/NADH[t])), v\[LetterSpace]16 -> (k16*(Glyc[t] - GlycX[t]))/Yvol, v\[LetterSpace]17 -> k0*GlycX[t], v\[LetterSpace]18 -> (k18*(ACA[t] - ACAX[t]))/Yvol, v\[LetterSpace]19 -> k0*ACAX[t], v\[LetterSpace]2 -> -((V2r*Glc[t])/(K2Glc*Yvol*(1 + G6P[t]/K2IG6P + Glc[t]/K2Glc + (G6P[t]*Glc[t])/(K2Glc*K2IIG6P) + ((1 + (P2*Glc[t])/K2Glc)*(1 + GlcX[t]/K2Glc))/(1 + (P2*GlcX[t])/K2Glc)))) + (V2f*GlcX[t])/(K2Glc*Yvol*(1 + GlcX[t]/K2Glc + ((1 + G6P[t]/K2IG6P + Glc[t]/K2Glc + (G6P[t]*Glc[t])/(K2Glc*K2IIG6P))*(1 + (P2*GlcX[t])/K2Glc))/(1 + (P2*Glc[t])/K2Glc))), v\[LetterSpace]20 -> k20*ACAX[t]*CNX[t], v\[LetterSpace]21 -> k0*(CNX0 - CNX[t]), v\[LetterSpace]22 -> k22*ATP[t]*G6P[t], v\[LetterSpace]23 -> k23*ATP[t], v\[LetterSpace]24 -> -(k24r*ADP[t]^2) + k24f*AMP[t]*ATP[t], v\[LetterSpace]3 -> (V3m*ATP[t]*Glc[t])/(K3ATP*K3DGlc + K3Glc*ATP[t] + K3ATP*Glc[t] + ATP[t]*Glc[t]), v\[LetterSpace]4 -> -((V4r*F6P[t])/(K4eq*(K4G6P + (K4G6P*F6P[t])/K4F6P + G6P[t]))) + (V4f*G6P[t])/(K4G6P + (K4G6P*F6P[t])/K4F6P + G6P[t]), v\[LetterSpace]5 -> (V5m*F6P[t]^2)/(K5*(1 + (kappa5*ATP[t]^2)/AMP[t]^2) + F6P[t]^2), v\[LetterSpace]6 -> (V6f*FBP[t])/(K6FBP + (K6GAP*DHAP[t])/(K6eq*ratio6) + FBP[t] + (K6DHAP*GAP[t])/(K6eq*ratio6) + (DHAP[t]*GAP[t])/(K6eq*ratio6) + (FBP[t]*GAP[t])/K6IGAP) - (V6f*DHAP[t]*GAP[t])/(K6eq*(K6FBP + (K6GAP*DHAP[t])/(K6eq*ratio6) + FBP[t] + (K6DHAP*GAP[t])/(K6eq*ratio6) + (DHAP[t]*GAP[t])/(K6eq*ratio6) + (FBP[t]*GAP[t])/K6IGAP)), v\[LetterSpace]7 -> (V7f*DHAP[t])/(K7DHAP + DHAP[t] + (K7DHAP*GAP[t])/K7GAP) - (V7r*GAP[t])/(K7eq*(K7DHAP + DHAP[t] + (K7DHAP*GAP[t])/K7GAP)), v\[LetterSpace]8 -> (V8f*GAP[t]*NAD[t])/(K8GAP*K8NAD*(1 + BPG[t]/K8BPG + GAP[t]/K8GAP)*(1 + NAD[t]/K8NAD + NADH[t]/K8NADH)) - (V8r*BPG[t]*NADH[t])/(K8eq*K8GAP*K8NAD*(1 + BPG[t]/K8BPG + GAP[t]/K8GAP)*(1 + NAD[t]/K8NAD + NADH[t]/K8NADH)), v\[LetterSpace]9 -> k9f*ADP[t]*BPG[t] - k9r*ATP[t]*PEP[t]
};

parameters = {
Atot -> 3.93, K10ADP -> 0.17, K10PEP -> 0.2, K11 -> 0.3, K12ACA -> 0.71, K12NADH -> 0.1, K15DHAP -> 25.0, K15INAD -> 0.13, K15INADH -> 0.034, K15NADH -> 0.13, K2Glc -> 1.7, K2IG6P -> 1.2, K2IIG6P -> 7.2, K3ATP -> 0.1, K3DGlc -> 0.37, K3Glc -> 0.0, K4F6P -> 0.15, K4G6P -> 0.8, K4eq -> 0.13, K5 -> 0.021, K6DHAP -> 2.0, K6FBP -> 0.3, K6GAP -> 4.0, K6IGAP -> 10.0, K6eq -> 0.081, K7DHAP -> 1.23, K7GAP -> 1.27, K7eq -> 0.055, K8BPG -> 0.01, K8GAP -> 0.6, K8NAD -> 0.1, K8NADH -> 0.06, K8eq -> 0.0055, Ntot -> 0.98, P2 -> 1.0, V10m -> 343.096, V11m -> 53.1328, V12m -> 89.8023, V15m -> 81.4797, V2f -> 1014.96, V2r -> 1014.96, V3m -> 51.7547, V4f -> 496.042, V4r -> 496.042, V5m -> 45.4327, V6f -> 2207.82, V7f -> 116.365, V7r -> 116.365, V8f -> 833.858, V8r -> 833.858, Yvol -> 59.0, k0 -> 0.048, k13 -> 16.72, k16 -> 1.9, k18 -> 24.7, k20 -> 0.00283828, k22 -> 2.25932, k23 -> 3.2076, k24f -> 432.9, k24r -> 133.333, k9f -> 443866.0, k9r -> 1528.62, kappa5 -> 0.15, ratio6 -> 5.0, CNX0 -> 5.6, GlcX0 -> 18.5, P -> 0.0, default\[LetterSpace]compartment -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
ACA[t]->"http://identifiers.org/kegg.compound/C00084", ACAX[t]->"http://identifiers.org/kegg.compound/C00084", ADP[t]->"http://identifiers.org/kegg.compound/C00008", AMP[t]->"http://identifiers.org/kegg.compound/C00020", ATP[t]->"http://identifiers.org/kegg.compound/C00002", BPG[t]->"http://identifiers.org/kegg.compound/C00236", CNX[t]->"http://identifiers.org/kegg.compound/C00042", CNX0[t]->"http://identifiers.org/kegg.compound/C00042", DHAP[t]->"http://identifiers.org/kegg.compound/C00111", EtOH[t]->"http://identifiers.org/kegg.compound/C00469", EtOHX[t]->"http://identifiers.org/kegg.compound/C00469", F6P[t]->"http://identifiers.org/kegg.compound/C00085", FBP[t]->"http://identifiers.org/kegg.compound/C00354", G6P[t]->"http://identifiers.org/kegg.compound/C00092", GAP[t]->"http://identifiers.org/kegg.compound/C00118", Glc[t]->"http://identifiers.org/kegg.compound/C00293", GlcX[t]->"http://identifiers.org/kegg.compound/C00293", GlcX0[t]->"http://identifiers.org/kegg.compound/C00293", Glyc[t]->"http://identifiers.org/kegg.compound/C00116", GlycX[t]->"http://identifiers.org/kegg.compound/C00116", NAD[t]->"http://identifiers.org/kegg.compound/C00003", NADH[t]->"http://identifiers.org/kegg.compound/C00004", P[t]->"http://identifiers.org/kegg.compound/C00009", PEP[t]->"http://identifiers.org/kegg.compound/C00074", Pyr[t]->"http://identifiers.org/kegg.compound/C00022"
};

reactionAnnotations = {
v\[LetterSpace]1->"http://identifiers.org/obo.go/GO%3A0015758", v\[LetterSpace]10->"http://identifiers.org/kegg.compound/C02601"
};

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

(* Time evolution *)
odes = {
ACA'[t] == 1.0*v\[LetterSpace]11 -59.0*v\[LetterSpace]18 -1.0*v\[LetterSpace]12, ACAX'[t] == 1.0*v\[LetterSpace]18 -1.0*v\[LetterSpace]20 -1.0*v\[LetterSpace]19, ADP'[t] == 1.0*v\[LetterSpace]3 +1.0*v\[LetterSpace]22 +2.0*v\[LetterSpace]24 +1.0*v\[LetterSpace]23 +1.0*v\[LetterSpace]5 -1.0*v\[LetterSpace]10 -1.0*v\[LetterSpace]9, AMP'[t] ==  -1.0*v\[LetterSpace]24, ATP'[t] == 1.0*v\[LetterSpace]10 +1.0*v\[LetterSpace]9 -1.0*v\[LetterSpace]3 -1.0*v\[LetterSpace]22 -1.0*v\[LetterSpace]24 -1.0*v\[LetterSpace]23 -1.0*v\[LetterSpace]5, BPG'[t] == 1.0*v\[LetterSpace]8 -1.0*v\[LetterSpace]9, CNX'[t] == 1.0*v\[LetterSpace]21 -1.0*v\[LetterSpace]20, DHAP'[t] == 1.0*v\[LetterSpace]6 -1.0*v\[LetterSpace]15 -1.0*v\[LetterSpace]7, EtOH'[t] == 1.0*v\[LetterSpace]12 -59.0*v\[LetterSpace]13, EtOHX'[t] == 1.0*v\[LetterSpace]13 -1.0*v\[LetterSpace]14, F6P'[t] == 1.0*v\[LetterSpace]4 -1.0*v\[LetterSpace]5, FBP'[t] == 1.0*v\[LetterSpace]5 -1.0*v\[LetterSpace]6, G6P'[t] == 1.0*v\[LetterSpace]3 -1.0*v\[LetterSpace]22 -1.0*v\[LetterSpace]4, GAP'[t] == 1.0*v\[LetterSpace]6 +1.0*v\[LetterSpace]7 -1.0*v\[LetterSpace]8, Glc'[t] == 59.0*v\[LetterSpace]2 -1.0*v\[LetterSpace]3, GlcX'[t] == 1.0*v\[LetterSpace]1 -1.0*v\[LetterSpace]2, Glyc'[t] == 1.0*v\[LetterSpace]15 -59.0*v\[LetterSpace]16, GlycX'[t] == 1.0*v\[LetterSpace]16 -1.0*v\[LetterSpace]17, NAD'[t] == 1.0*v\[LetterSpace]15 +1.0*v\[LetterSpace]12 -1.0*v\[LetterSpace]8, NADH'[t] == 1.0*v\[LetterSpace]8 -1.0*v\[LetterSpace]15 -1.0*v\[LetterSpace]12, PEP'[t] == 1.0*v\[LetterSpace]9 -1.0*v\[LetterSpace]10, Pyr'[t] == 1.0*v\[LetterSpace]10 -1.0*v\[LetterSpace]11
};
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]}]