(* 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 = {
AcCoA[t], AcP[t], Acs[t], HOAc[t], LacI[t], OAc[t], Pta[t]
};

initialValues = {
AcCoA[0] == 0.0, AcP[0] == 0.0, Acs[0] == 0.0, HOAc[0] == 0.0, LacI[0] == 0.0, OAc[0] == 0.0, Pta[0] == 0.0
};

rates = {
R\[LetterSpace]Acs, R\[LetterSpace]LacI, R\[LetterSpace]Pta, R\[LetterSpace]dAcs, R\[LetterSpace]dLacI, R\[LetterSpace]dPta, V\[LetterSpace]Ace, V\[LetterSpace]Ack, V\[LetterSpace]Acs, V\[LetterSpace]Pta, V\[LetterSpace]TCA, V\[LetterSpace]gly, V\[LetterSpace]out
};

rateEquations = {
R\[LetterSpace]Acs -> compartment*(alpha0 + (alpha2*(AcP[t]/Kg2)^n)/(1 + (AcP[t]/Kg2)^n)), R\[LetterSpace]LacI -> compartment*(alpha0 + (alpha1*(AcP[t]/Kg1)^n)/(1 + (AcP[t]/Kg1)^n)), R\[LetterSpace]Pta -> alpha0 + alpha3/(1 + (LacI[t]/Kg3)^n), R\[LetterSpace]dAcs -> compartment*kd*Acs[t], R\[LetterSpace]dLacI -> compartment*kd*LacI[t], R\[LetterSpace]dPta -> compartment*kd*Pta[t], V\[LetterSpace]Ace -> C*compartment*(-(Keq*HOAc[t]) + H*OAc[t]), V\[LetterSpace]Ack -> compartment*(kAck\[LetterSpace]f*AcP[t] - kAck\[LetterSpace]r*OAc[t]), V\[LetterSpace]Acs -> (compartment*k2*Acs[t]*OAc[t])/(KM2 + OAc[t]), V\[LetterSpace]Pta -> (compartment*k1*AcCoA[t]*Pta[t])/(KM1 + AcCoA[t]), V\[LetterSpace]TCA -> compartment*kTCA*AcCoA[t], V\[LetterSpace]gly -> compartment*S0, V\[LetterSpace]out -> compartment*k3*(-HOAc\[LetterSpace]E + HOAc[t])
};

parameters = {
C -> 100.0, H -> 1*^-07, KM1 -> 0.06, KM2 -> 0.1, Keq -> 0.0005, Kg1 -> 10.0, Kg2 -> 10.0, Kg3 -> 0.001, S0 -> 0.5, alpha0 -> 0.0, alpha1 -> 0.1, alpha2 -> 2.0, alpha3 -> 2.0, k1 -> 80.0, k2 -> 0.8, k3 -> 0.01, kAck\[LetterSpace]f -> 1.0, kAck\[LetterSpace]r -> 1.0, kTCA -> 10.0, kd -> 0.06, n -> 2.0, HOAc\[LetterSpace]E -> 0.0, compartment -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
AcCoA[t]->"http://identifiers.org/obo.chebi/CHEBI:15351", AcCoA[t]->"http://identifiers.org/kegg.compound/C00024", AcP[t]->"http://identifiers.org/obo.chebi/CHEBI:15350", AcP[t]->"http://identifiers.org/kegg.compound/C00227", Acs[t]->"http://identifiers.org/uniprot/P27550", OAc[t]->"http://identifiers.org/obo.chebi/CHEBI:30089", OAc[t]->"http://identifiers.org/kegg.compound/C00033", Pta[t]->"http://identifiers.org/uniprot/P0A9M8"
};

reactionAnnotations = {
V\[LetterSpace]Pta->"http://identifiers.org/ec-code/2.3.1.8", V\[LetterSpace]Pta->"http://identifiers.org/kegg.reaction/R00230"
};

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

(* Time evolution *)
odes = {
AcCoA'[t] == 1.0*V\[LetterSpace]gly +1.0*V\[LetterSpace]Acs -1.0*V\[LetterSpace]TCA -1.0*V\[LetterSpace]Pta, AcP'[t] == 1.0*V\[LetterSpace]Pta -1.0*V\[LetterSpace]Ack, Acs'[t] == 1.0*R\[LetterSpace]Acs -1.0*R\[LetterSpace]dAcs, HOAc'[t] == 1.0*V\[LetterSpace]Ace -1.0*V\[LetterSpace]out, LacI'[t] == 1.0*R\[LetterSpace]LacI -1.0*R\[LetterSpace]dLacI, OAc'[t] == 1.0*V\[LetterSpace]Ack -1.0*V\[LetterSpace]Acs -1.0*V\[LetterSpace]Ace, Pta'[t] == 1.0*R\[LetterSpace]Pta -1.0*R\[LetterSpace]dPta
};
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]}]