(* 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], Z[t]
};

initialValues = {
X[0] == 0.1, Y[0] == 1.5, Z[0] == 0.1
};

rates = {
R1, R2, R3, R4, R5, R6, R7
};

rateEquations = {
R1 -> compartment*vin, R2 -> compartment*kout*X[t], R3 -> (4*ER*k\[LetterSpace]CaA^n*vM3*X[t]^n*(-X[t] + Y[t])*Z[t]^m)/((k\[LetterSpace]CaA^n + X[t]^n)*(k\[LetterSpace]CaI^n + X[t]^n)*(kip3^m + Z[t]^m)), R4 -> (compartment*vM2*X[t]^2)/(k2^2 + X[t]^2), R5 -> ER*kf*(-X[t] + Y[t]), R6 -> (compartment*vp*X[t]^2)/(kp^2 + X[t]^2), R7 -> compartment*kdeg*Z[t]
};

parameters = {
k2 -> 0.1, k\[LetterSpace]CaA -> 0.15, k\[LetterSpace]CaI -> 0.15, kdeg -> 0.08, kf -> 0.5, kip3 -> 0.1, kout -> 0.5, kp -> 0.3, m -> 2.2, n -> 2.02, vM2 -> 15.0, vM3 -> 40.0, vin -> 0.05, vp -> 0.05, ER -> 1.0, compartment -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
X[t]->"http://identifiers.org/obo.chebi/CHEBI:29108", X[t]->"http://identifiers.org/kegg.compound/C00076", Y[t]->"http://identifiers.org/obo.chebi/CHEBI:29108", Y[t]->"http://identifiers.org/kegg.compound/C00076", Z[t]->"http://identifiers.org/obo.chebi/CHEBI:16595", Z[t]->"http://identifiers.org/kegg.compound/C01245"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
X'[t] == 1.0*R1 +1.0*R3 +1.0*R5 -1.0*R2 -1.0*R4, Y'[t] == 1.0*R4 -1.0*R3 -1.0*R5, Z'[t] == 1.0*R6 -1.0*R7
};
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]}]