(* 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 = {
Rp[t], X[t], Yp[t]
};

initialValues = {
Rp[0] == 0.0, X[0] == 0.0, Yp[0] == 0.0
};

rates = {
r1, r2, r3, r4, r5, r6
};

rateEquations = {
r1 -> env*(k0 + k1*S), r2 -> env*(k2 + k2\[LetterSpace]prime*Rp[t])*X[t], r3 -> (env*k3*X[t]*(Yt - Yp[t]))/(Km3 + Yt - Yp[t]), r4 -> (env*k4*Yp[t])/(Km4 + Yp[t]), r5 -> (env*k5*(Rt - Rp[t])*Yp[t])/(Km5 + Rt - Rp[t]), r6 -> (env*k6*Rp[t])/(Km6 + Rp[t])
};

parameters = {
Km3 -> 0.01, Km4 -> 0.01, Km5 -> 0.01, Km6 -> 0.01, Rt -> 1.0, Yt -> 1.0, k0 -> 0.0, k1 -> 1.0, k2 -> 0.01, k2\[LetterSpace]prime -> 10.0, k3 -> 0.1, k4 -> 0.2, k5 -> 0.1, k6 -> 0.05, S -> 0.0, env -> 1.0
};

assignments = {
R -> Rt - Rp[t], Y -> Yt - Yp[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
Rp'[t] == 1.0*r5 -1.0*r6, X'[t] == 1.0*r1 -1.0*r2, Yp'[t] == 1.0*r3 -1.0*r4
};
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]}]