(* 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 = {
DPGA[t], GAP[t], PGA[t], Ru5P[t], RuBP[t]
};

initialValues = {
DPGA[0] == 0.0011, GAP[0] == 0.02, PGA[0] == 2.4, Ru5P[0] == 0.0501, RuBP[0] == 2.0
};

rates = {
GAP2Ru5P, GAP2sink, GAP\[LetterSpace]DH, PGA2sink, PGA\[LetterSpace]K, Ru5P\[LetterSpace]K, RuBisCO
};

rateEquations = {
GAP2Ru5P -> chloroplast*function\[LetterSpace]1[GAP[t], GAP2Ru5P\[LetterSpace]Km, GAP2Ru5P\[LetterSpace]V], GAP2sink -> chloroplast*function\[LetterSpace]1[GAP[t], GAP2sink\[LetterSpace]Km, GAP2sink\[LetterSpace]V], GAP\[LetterSpace]DH -> chloroplast*function\[LetterSpace]1[DPGA[t], GAP\[LetterSpace]DH\[LetterSpace]Km, GAP\[LetterSpace]DH\[LetterSpace]V], PGA2sink -> chloroplast*function\[LetterSpace]1[PGA[t], PGA2sink\[LetterSpace]Km, PGA2sink\[LetterSpace]V], PGA\[LetterSpace]K -> chloroplast*function\[LetterSpace]2[PGA\[LetterSpace]K\[LetterSpace]Vm, PGA[t], ATP, PGA\[LetterSpace]K\[LetterSpace]K1, PGA\[LetterSpace]K\[LetterSpace]K2], Ru5P\[LetterSpace]K -> chloroplast*function\[LetterSpace]2[Ru5P\[LetterSpace]K\[LetterSpace]Vm, Ru5P[t], ATP, Ru5P\[LetterSpace]K\[LetterSpace]K1, Ru5P\[LetterSpace]K\[LetterSpace]K2], RuBisCO -> chloroplast*function\[LetterSpace]1[RuBP[t], RuBisCO\[LetterSpace]Km, RuBisCO\[LetterSpace]V]
};

parameters = {
ADP -> 0.82, ATP -> 0.68, RuBisCO\[LetterSpace]Km -> 1.0, RuBisCO\[LetterSpace]V -> 3.78, PGA\[LetterSpace]K\[LetterSpace]Vm -> 11.75, PGA\[LetterSpace]K\[LetterSpace]K1 -> 0.24, PGA\[LetterSpace]K\[LetterSpace]K2 -> 0.39, GAP\[LetterSpace]DH\[LetterSpace]Km -> 0.5, GAP\[LetterSpace]DH\[LetterSpace]V -> 5.04, GAP2Ru5P\[LetterSpace]Km -> 0.84, GAP2Ru5P\[LetterSpace]V -> 3.05, Ru5P\[LetterSpace]K\[LetterSpace]Vm -> 8.0, Ru5P\[LetterSpace]K\[LetterSpace]K1 -> 0.15, Ru5P\[LetterSpace]K\[LetterSpace]K2 -> 0.059, PGA2sink\[LetterSpace]Km -> 0.75, PGA2sink\[LetterSpace]V -> 3.0, GAP2sink\[LetterSpace]Km -> 5.0, GAP2sink\[LetterSpace]V -> 0.1, chloroplast -> 1.0
};

assignments = {
function\[LetterSpace]2[Vm_,s1_,s2_,K1_,K2_] -> (s1*s2*Vm)/((K1 + s1)*(K2 + s2)), function\[LetterSpace]1[substrate_,Km_,V_] -> (substrate*V)/(Km + substrate), Pi -> 15 - ADP - GAP[t] - PGA[t] - Ru5P[t] - 2*(ATP + DPGA[t] + RuBP[t])
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
DPGA'[t] == 1.0*PGA\[LetterSpace]K -1.0*GAP\[LetterSpace]DH, GAP'[t] == 1.0*GAP\[LetterSpace]DH -1.0*GAP2Ru5P -1.0*GAP2sink, PGA'[t] == 2.0*RuBisCO -1.0*PGA\[LetterSpace]K -1.0*PGA2sink, Ru5P'[t] == 0.6*GAP2Ru5P -1.0*Ru5P\[LetterSpace]K, RuBP'[t] == 1.0*Ru5P\[LetterSpace]K -1.0*RuBisCO
};
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]}]