(* 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 = {
ADP[t], AMP[t], ATP[t], DHAP[t], F6P[t], FBP[t], G3P[t], G6P[t], NAD[t], NADH[t], PEP[t], acald[t], n13BPG[t], n2PG[t], n3PG[t], pyr[t]
};

initialValues = {
ADP[0] == 3.3, AMP[0] == 1.6, ATP[0] == 5.0, DHAP[0] == 1.15, F6P[0] == 1.1, FBP[0] == 0.43, G3P[0] == 0.36, G6P[0] == 6.2, NAD[0] == 1.5, NADH[0] == 0.05, PEP[0] == 1.0, acald[0] == 0.001, n13BPG[0] == 1.0, n2PG[0] == 1.0, n3PG[0] == 1.0, pyr[0] == 0.92
};

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]3, v\[LetterSpace]4, v\[LetterSpace]5, v\[LetterSpace]6, v\[LetterSpace]7, v\[LetterSpace]8, v\[LetterSpace]9
};

rateEquations = {
v\[LetterSpace]1 -> (HKrevparVmf*(Glu*ATP[t] - (ADP[t]*G6P[t])/HKrevparKeq))/(HKrevparalfa*HKrevparKa*HKrevparKb*(1 + Glu/HKrevparKa + ADP[t]/HKrevparKq + AMP[t]/HKrevparKi + (Glu*AMP[t])/(HKrevparbeta*HKrevparKa*HKrevparKi) + ATP[t]/HKrevparKb + (Glu*ATP[t])/(HKrevparalfa*HKrevparKa*HKrevparKb) + (AMP[t]*ATP[t])/(HKrevpargama*HKrevparKb*HKrevparKi) + G6P[t]/HKrevparKp + (ADP[t]*G6P[t])/(HKrevparalfa*HKrevparKp*HKrevparKq))), v\[LetterSpace]10 -> (n3PGDHparVm*n3PG[t]*NAD[t])/(n3PGDHparKa*n3PGDHparKb + n3PGDHparKb*NAD[t] + n3PG[t]*NAD[t]), v\[LetterSpace]11 -> (-((PGAMparVr*n2PG[t])/PGAMparKmp) + (PGAMparVf*n3PG[t])/PGAMparKms)/(1 + n2PG[t]/PGAMparKmp + n3PG[t]/PGAMparKms), v\[LetterSpace]12 -> ((ENOparVf*n2PG[t])/ENOparKms - (ENOparVr*PEP[t])/ENOparKmp)/(1 + n2PG[t]/ENOparKms + PEP[t]/ENOparKmp), v\[LetterSpace]13 -> ((PPDKparVmf*PPhi*AMP[t]*PEP[t])/(PPDKparalfa*PPDKparKa*PPDKparKb*PPDKparKc) - (Phi*PPDKparVmr*ATP[t]*pyr[t])/(PPDKparbeta*PPDKparKp*PPDKparKq*PPDKparKr))/(1 + Phi/PPDKparKr + (Phi*ATP[t])/(PPDKparalfa*PPDKparKq*PPDKparKr) + PEP[t]/PPDKparKa + (AMP[t]*PEP[t])/(PPDKparalfa*PPDKparKa*PPDKparKb) + (PPhi*AMP[t]*PEP[t])/(PPDKparalfa*PPDKparbeta*PPDKparKa*PPDKparKb*PPDKparKc) + (Phi*ATP[t]*pyr[t])/(PPDKparalfa*PPDKparbeta*PPDKparKp*PPDKparKq*PPDKparKr)), v\[LetterSpace]14 -> (-((PFORALDHparVmr*acald[t]*NAD[t])/(PFORALDHparbeta*PFORALDHparKp*PFORALDHparKq)) + (PFORALDHparVmf*NADH[t]*pyr[t])/(PFORALDHparalfa*PFORALDHparKa*PFORALDHparKb))/(1 + acald[t]/PFORALDHparKp + NAD[t]/PFORALDHparKq + (acald[t]*NAD[t])/(PFORALDHparbeta*PFORALDHparKp*PFORALDHparKq) + NADH[t]/PFORALDHparKa + pyr[t]/PFORALDHparKb + (NADH[t]*pyr[t])/(PFORALDHparalfa*PFORALDHparKa*PFORALDHparKb)), v\[LetterSpace]15 -> (ADHparVm*acald[t]*NADH[t])/(ADHparKa*ADHparKb + ADHparKb*NADH[t] + acald[t]*NADH[t]), v\[LetterSpace]16 -> AKpark1*ADP[t]^2 - AKpark2*AMP[t]*ATP[t], v\[LetterSpace]17 -> ATPasesparK*ATP[t], v\[LetterSpace]18 -> PPhisynthesispark*ATP[t], v\[LetterSpace]19 -> DHasespark1*NAD[t] - DHasespark2*NADH[t], v\[LetterSpace]2 -> glycogen*glycogendegradationpark*Phi, v\[LetterSpace]3 -> glycogensynthesispark*ATP[t]*G6P[t], v\[LetterSpace]4 -> (-((HPhiparVr*F6P[t])/HPhiparKmp) + (HPhiparVf*G6P[t])/HPhiparKms)/(1 + F6P[t]/HPhiparKmp + G6P[t]/HPhiparKms), v\[LetterSpace]5 -> ((PPhi*PPhiPFKparVmf*F6P[t])/(PPhiPFKparalfa*PPhiPFKparKa*PPhiPFKparKb) - (Phi*PPhiPFKparVmr*FBP[t])/(PPhiPFKparbeta*PPhiPFKparKp*PPhiPFKparKq))/(1 + PPhi/PPhiPFKparKb + Phi/PPhiPFKparKq + F6P[t]/PPhiPFKparKa + (PPhi*F6P[t])/(PPhiPFKparalfa*PPhiPFKparKa*PPhiPFKparKb) + FBP[t]/PPhiPFKparKp + (Phi*FBP[t])/(PPhiPFKparbeta*PPhiPFKparKp*PPhiPFKparKq)), v\[LetterSpace]6 -> ((ALDOparVmf*FBP[t])/ALDOparKs - (ALDOparVmr*DHAP[t]*G3P[t])/(ALDOparKp + ALDOparKq))/(1 + DHAP[t]/ALDOparKp + FBP[t]/ALDOparKs + G3P[t]/ALDOparKq + (DHAP[t]*G3P[t])/(ALDOparKp*ALDOparKq)), v\[LetterSpace]7 -> ((TPhiparVf*DHAP[t])/TPhiparKms - (TPhiparVr*G3P[t])/TPhiparKmp)/(1 + DHAP[t]/TPhiparKms + G3P[t]/TPhiparKmp), v\[LetterSpace]8 -> ((GAPDHparVmf*G3P[t]*NAD[t])/(GAPDHparalfa*GAPDHparKa*GAPDHparKb) - (GAPDHparVmr*n13BPG[t]*NADH[t])/(GAPDHparbeta*GAPDHparKp*GAPDHparKq))/(1 + G3P[t]/GAPDHparKb + n13BPG[t]/GAPDHparKp + NAD[t]/GAPDHparKa + (G3P[t]*NAD[t])/(GAPDHparalfa*GAPDHparKa*GAPDHparKb) + NADH[t]/GAPDHparKq + (n13BPG[t]*NADH[t])/(GAPDHparbeta*GAPDHparKp*GAPDHparKq)), v\[LetterSpace]9 -> ((PGKparVmf*ADP[t]*n13BPG[t])/(PGKparalfa*PGKparKa*PGKparKb) - (PGKparVmr*ATP[t]*n3PG[t])/(PGKparbeta*PGKparKp*PGKparKq))/(1 + ADP[t]/PGKparKb + ATP[t]/PGKparKq + n13BPG[t]/PGKparKa + (ADP[t]*n13BPG[t])/(PGKparalfa*PGKparKa*PGKparKb) + n3PG[t]/PGKparKp + (ATP[t]*n3PG[t])/(PGKparbeta*PGKparKp*PGKparKq))
};

parameters = {
ADHparKa -> 0.05, ADHparKb -> 0.15, ADHparVm -> 0.4, AKpark1 -> 2.26, AKpark2 -> 1.0, ALDOparKp -> 0.21, ALDOparKq -> 0.26, ALDOparKs -> 0.028, ALDOparVmf -> 0.16, ALDOparVmr -> 0.284, ATPasesparK -> 0.002, DHasespark1 -> 0.1, DHasespark2 -> 1.5, ENOparKmp -> 0.102, ENOparKms -> 0.06, ENOparVf -> 0.508, ENOparVr -> 0.103, GAPDHparKa -> 0.083, GAPDHparKb -> 0.043, GAPDHparKp -> 0.016, GAPDHparKq -> 0.06, GAPDHparVmf -> 0.405, GAPDHparVmr -> 3.68, GAPDHparalfa -> 1.0, GAPDHparbeta -> 1.0, HKrevparKa -> 0.025, HKrevparKb -> 0.121, HKrevparKeq -> 656.0, HKrevparKi -> 0.036, HKrevparKp -> 1.0, HKrevparKq -> 0.235, HKrevparVmf -> 0.095, HKrevparalfa -> 1.0, HKrevparbeta -> 1.0, HKrevpargama -> 1.0, HPhiparKmp -> 0.46, HPhiparKms -> 0.61, HPhiparVf -> 0.233, HPhiparVr -> 0.206, PFORALDHparKa -> 0.18, PFORALDHparKb -> 0.14, PFORALDHparKp -> 0.1, PFORALDHparKq -> 0.2, PFORALDHparVmf -> 0.3, PFORALDHparVmr -> 0.01, PFORALDHparalfa -> 1.0, PFORALDHparbeta -> 1.0, PGAMparKmp -> 0.106, PGAMparKms -> 0.83, PGAMparVf -> 0.116, PGAMparVr -> 0.104, PGKparKa -> 0.125, PGKparKb -> 0.04, PGKparKp -> 0.505, PGKparKq -> 0.061, PGKparVmf -> 3.182, PGKparVmr -> 1.742, PGKparalfa -> 1.0, PGKparbeta -> 1.0, PPDKparKa -> 0.03, PPDKparKb -> 0.002, PPDKparKc -> 0.091, PPDKparKp -> 0.3, PPDKparKq -> 0.28, PPDKparKr -> 1.0, PPDKparVmf -> 0.304, PPDKparVmr -> 0.019, PPDKparalfa -> 0.01, PPDKparbeta -> 2.0, PPhiPFKparKa -> 0.695, PPhiPFKparKb -> 0.38, PPhiPFKparKp -> 0.109, PPhiPFKparKq -> 2.3, PPhiPFKparVmf -> 0.213, PPhiPFKparVmr -> 0.346, PPhiPFKparalfa -> 0.5, PPhiPFKparbeta -> 2.0, PPhisynthesispark -> 0.0065, TPhiparKmp -> 0.32, TPhiparKms -> 0.445, TPhiparVf -> 4.366, TPhiparVr -> 6.098, glycogendegradationpark -> 0.0001, glycogensynthesispark -> 0.0015, n3PGDHparKa -> 0.087, n3PGDHparKb -> 0.212, n3PGDHparVm -> 0.01, Glu -> 5.0, PPhi -> 0.45, Phi -> 5.0, etoh -> 10.0, glycogen -> 1.0, n3POHpyr -> 1.0, default\[LetterSpace]compartment -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

units = {
{"time" -> "min", "metabolite" -> "mM/<compartment size units>", "extent" -> "mM"}
};

(* Time evolution *)
odes = {
ADP'[t] == 1.0*v\[LetterSpace]3 +1.0*v\[LetterSpace]1 +1.0*v\[LetterSpace]17 -1.0*v\[LetterSpace]9 -2.0*v\[LetterSpace]16, AMP'[t] == 1.0*v\[LetterSpace]18 +1.0*v\[LetterSpace]16 -1.0*v\[LetterSpace]13, ATP'[t] == 1.0*v\[LetterSpace]13 +1.0*v\[LetterSpace]9 +1.0*v\[LetterSpace]16 -1.0*v\[LetterSpace]3 -1.0*v\[LetterSpace]1 -1.0*v\[LetterSpace]17 -1.0*v\[LetterSpace]18, DHAP'[t] == 1.0*v\[LetterSpace]6 -1.0*v\[LetterSpace]7, F6P'[t] == 1.0*v\[LetterSpace]4 -1.0*v\[LetterSpace]5, FBP'[t] == 1.0*v\[LetterSpace]5 -1.0*v\[LetterSpace]6, G3P'[t] == 1.0*v\[LetterSpace]6 +1.0*v\[LetterSpace]7 -1.0*v\[LetterSpace]8, G6P'[t] == 1.0*v\[LetterSpace]1 +1.0*v\[LetterSpace]2 -1.0*v\[LetterSpace]3 -1.0*v\[LetterSpace]4, NAD'[t] == 1.0*v\[LetterSpace]14 +1.0*v\[LetterSpace]15 -1.0*v\[LetterSpace]19 -1.0*v\[LetterSpace]8 -1.0*v\[LetterSpace]10, NADH'[t] == 1.0*v\[LetterSpace]19 +1.0*v\[LetterSpace]8 +1.0*v\[LetterSpace]10 -1.0*v\[LetterSpace]14 -1.0*v\[LetterSpace]15, PEP'[t] == 1.0*v\[LetterSpace]12 -1.0*v\[LetterSpace]13, acald'[t] == 1.0*v\[LetterSpace]14 -1.0*v\[LetterSpace]15, n13BPG'[t] == 1.0*v\[LetterSpace]8 -1.0*v\[LetterSpace]9, n2PG'[t] == 1.0*v\[LetterSpace]11 -1.0*v\[LetterSpace]12, n3PG'[t] == 1.0*v\[LetterSpace]9 -1.0*v\[LetterSpace]11 -1.0*v\[LetterSpace]10, pyr'[t] == 1.0*v\[LetterSpace]13 -1.0*v\[LetterSpace]14
};
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]}]