(* 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 = {
x[t], y[t]
};

initialValues = {
x[0] == 1.0, y[0] == 1.0
};

rates = {
reaction\[LetterSpace]0000001, reaction\[LetterSpace]0000002, reaction\[LetterSpace]0000003, reaction\[LetterSpace]0000004
};

rateEquations = {
reaction\[LetterSpace]0000001 -> cytoplasm*gamma, reaction\[LetterSpace]0000002 -> cytoplasm*k*x[t] - ER*k1*y[t], reaction\[LetterSpace]0000003 -> beta*extracellular*y[t], reaction\[LetterSpace]0000004 -> alpha*cytoplasm*fy*x[t]
};

parameters = {
a -> 3.0, alpha -> 5.0, beta -> 1.0, gamma -> 1.0, k -> 0.01, k1 -> 2.0, n -> 4.0, ER -> 1.0, cytoplasm -> 1.0, extracellular -> 1.0
};

assignments = {
fy -> y[t]^n/(a^n + y[t]^n)
};

events = {

};

speciesAnnotations = {
x[t]->"http://identifiers.org/chebi/CHEBI:29108", x[t]->"http://identifiers.org/kegg.compound/C00076", y[t]->"http://identifiers.org/chebi/CHEBI:29108", y[t]->"http://identifiers.org/kegg.compound/C00076"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
x'[t] ==  -1.0*reaction\[LetterSpace]0000002 -1.0*reaction\[LetterSpace]0000004, y'[t] == 1.0*reaction\[LetterSpace]0000001 +1.0*reaction\[LetterSpace]0000002 +1.0*reaction\[LetterSpace]0000004 -1.0*reaction\[LetterSpace]0000003
};
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]}]