(* 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 = {
ATP[t], FDP[t], G6P[t], Glci[t], PEP[t]
};

initialValues = {
ATP[0] == 1.1278, FDP[0] == 9.144, G6P[0] == 1.011, Glci[0] == 0.0345, PEP[0] == 0.0095
};

rates = {
v\[LetterSpace]1, v\[LetterSpace]2, v\[LetterSpace]3, v\[LetterSpace]4, v\[LetterSpace]5, v\[LetterSpace]6, v\[LetterSpace]7, v\[LetterSpace]8
};

rateEquations = {
v\[LetterSpace]1 -> Vm1 - Ki1G6P*G6P[t], v\[LetterSpace]2 -> Vm2/(1 + Km2ATP/ATP[t] + Km2Glc/Glci[t] + (Km2ATP*Ks2Glc)/(ATP[t]*Glci[t])), v\[LetterSpace]3 -> (1.1*Vm3*G6P[t]^n3)/((1 + 1.4285714285714286*Km30*(1 + Km3G6P/G6P[t]))*(K3Gly^n3 + G6P[t]^n3)), v\[LetterSpace]4 -> (0.3*g4R*Vm4*ATP[t]*G6P[t]*(1 + ATP[t]/K4ATP + (0.3*G6P[t])/K4F6P + (0.3*g4R*ATP[t]*G6P[t])/(K4ATP*K4F6P)))/(K4ATP*K4F6P*((1 + ATP[t]/K4ATP + (0.3*G6P[t])/K4F6P + (0.3*g4R*ATP[t]*G6P[t])/(K4ATP*K4F6P))^2 + (L40*(1 + (c4AMP*(3 - ATP[t] - 0.5*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)))/K4AMP)^2*(1 + (c4ATP*ATP[t])/K4ATP + (0.3*c4F6P*G6P[t])/K4F6P + (0.3*c4ATP*c4F6P*gT*ATP[t]*G6P[t])/(K4ATP*K4F6P))^2)/(1 + (3 - ATP[t] - 0.5*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K4AMP)^2)), v\[LetterSpace]5 -> (0.5*Vm7*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t]*(g6R*(1 + (0.5*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K6ADP + PEP[t]/K6PEP + (0.5*g6R*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t])/(K6ADP*K6PEP)) + (0.5*c6ADP*c6PEP*g6T*L60*q6*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*(1 + (c6FDP*FDP[t])/K6FDP)^2*PEP[t]*(1 + (0.5*c6ADP*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K6ADP + (c6PEP*PEP[t])/K6PEP + (0.5*c6ADP*c6PEP*g6T*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t])/(K6ADP*K6PEP)))/(K6ADP*K6PEP*(1 + FDP[t]/K6FDP)^2)))/((1 + 9.550000000000001*^-9/h6)*K6ADP*K6PEP*((1 + (0.5*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K6ADP + PEP[t]/K6PEP + (0.5*g6R*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t])/(K6ADP*K6PEP))^2 + (L60*(1 + (c6FDP*FDP[t])/K6FDP)^2*(1 + (0.5*c6ADP*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K6ADP + (c6PEP*PEP[t])/K6PEP + (0.5*c6ADP*c6PEP*g6T*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t])/(K6ADP*K6PEP))^2)/(1 + FDP[t]/K6FDP)^2)), v\[LetterSpace]6 -> Vm5/(1 + (1 + ATP[t]/K5ATP + (0.5*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K5ADP + (3 - ATP[t] - 0.5*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K5AMP)*(K5NAD/NAD + (100.*K5G3P*K5NAD)/(NAD*FDP[t]) + (100.*K5G3P*K5NAD*NADH)/(K5NADH*NAD*FDP[t])) + (100.*K5G3P)/FDP[t]), v\[LetterSpace]7 -> (0.5*Vm6*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t]*(g6R*(1 + (0.5*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K6ADP + PEP[t]/K6PEP + (0.5*g6R*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t])/(K6ADP*K6PEP)) + (0.5*c6ADP*c6PEP*g6T*L60*q6*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*(1 + (c6FDP*FDP[t])/K6FDP)^2*PEP[t]*(1 + (0.5*c6ADP*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K6ADP + (c6PEP*PEP[t])/K6PEP + (0.5*c6ADP*c6PEP*g6T*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t])/(K6ADP*K6PEP)))/(K6ADP*K6PEP*(1 + FDP[t]/K6FDP)^2)))/((1 + 9.550000000000001*^-9/h6)*K6ADP*K6PEP*((1 + (0.5*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K6ADP + PEP[t]/K6PEP + (0.5*g6R*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t])/(K6ADP*K6PEP))^2 + (L60*(1 + (c6FDP*FDP[t])/K6FDP)^2*(1 + (0.5*c6ADP*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5))/K6ADP + (c6PEP*PEP[t])/K6PEP + (0.5*c6ADP*c6PEP*g6T*(-ATP[t] + (12*ATP[t] - 3*ATP[t]^2)^0.5)*PEP[t])/(K6ADP*K6PEP))^2)/(1 + FDP[t]/K6FDP)^2)), v\[LetterSpace]8 -> Vm8*ATP[t]
};

parameters = {
K3Gly -> 2.0, K4AMP -> 0.025, K4ATP -> 0.06, K4F6P -> 1.0, K5ADP -> 1.5, K5AMP -> 1.1, K5ATP -> 2.5, K5G3P -> 0.0025, K5NAD -> 0.18, K5NADH -> 0.0003, K6ADP -> 5.0, K6FDP -> 0.2, K6PEP -> 0.00793966, Ki1G6P -> 3.7, Km2ATP -> 0.1, Km2Glc -> 0.11, Km30 -> 1.0, Km3G6P -> 1.1, Ks2Glc -> 0.0062, L40 -> 3342.0, L60 -> 164.084, NAD -> 1.91939, NADH -> 0.0806142, Vm1 -> 19.7, Vm2 -> 68.5, Vm3 -> 14.31, Vm4 -> 31.7, Vm5 -> 49.9, Vm6 -> 3440.0, Vm7 -> 203.0, Vm8 -> 25.1, c4AMP -> 0.019, c4ATP -> 1.0, c4F6P -> 0.0005, c6ADP -> 1.0, c6FDP -> 0.01, c6PEP -> 0.000158793, g4R -> 10.0, g6R -> 0.1, g6T -> 1.0, gT -> 1.0, h6 -> 1.14815*^-07, n3 -> 8.25, q6 -> 1.0, Carbo -> 0.0, EtOH -> 0.0, Glco -> 1.0, Gly -> 0.0, X -> 0.0, default\[LetterSpace]compartment -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
ATP[t]->"http://identifiers.org/obo.chebi/CHEBI%3A15422", ATP[t]->"http://identifiers.org/kegg.compound/C00002", EtOH[t]->"http://identifiers.org/obo.chebi/CHEBI%3A16236", EtOH[t]->"http://identifiers.org/kegg.compound/C00469", FDP[t]->"http://identifiers.org/obo.chebi/CHEBI%3A16905", FDP[t]->"http://identifiers.org/kegg.compound/C00354", G6P[t]->"http://identifiers.org/obo.chebi/CHEBI%3A4170", G6P[t]->"http://identifiers.org/kegg.compound/C00092", PEP[t]->"http://identifiers.org/obo.chebi/CHEBI%3A44897", PEP[t]->"http://identifiers.org/kegg.compound/C00074"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
ATP'[t] == 1.0*v\[LetterSpace]7 +2.0*v\[LetterSpace]6 -1.0*v\[LetterSpace]8 -1.0*v\[LetterSpace]2 -1.0*v\[LetterSpace]4 -1.0*v\[LetterSpace]3, FDP'[t] == 1.0*v\[LetterSpace]4 -0.5*v\[LetterSpace]5 -1.0*v\[LetterSpace]6, G6P'[t] == 1.0*v\[LetterSpace]2 -1.0*v\[LetterSpace]4 -1.0*v\[LetterSpace]3, Glci'[t] == 1.0*v\[LetterSpace]1 -1.0*v\[LetterSpace]2, PEP'[t] == 2.0*v\[LetterSpace]6 -1.0*v\[LetterSpace]7
};
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]}]