(* 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 = {
ain[t], c[t], ca[t], cap[t], n[t]
};

initialValues = {
ain[0] == 0.0, c[0] == 0.1, ca[0] == 0.0, cap[0] == 0.0, n[0] == 0.001
};

rates = {
v1, v2, v3, v4, v5, v6, v7, v8, v9
};

rateEquations = {
v1 -> (k1*c[t])/(V1 + c[t]), v2 -> kf*ain[t]*c[t], v3 -> ku*c[t], v4 -> kb*ca[t], v5 -> kin*Piecewise[{{a0, aStart < t < aStart + d}}, 0], v6 -> kout*ain[t], v7 -> kr*cap[t], v8 -> kd*ca[t], v9 -> (mu0*c[t]*n[t]*(1 - n[t]/nm))/(V + c[t])
};

parameters = {
V -> 1.5, V1 -> 0.2, Vc -> 1*^-09, Vm -> 0.0001, a0 -> 20.62, aStart -> 0.0, d -> 120.0, k1 -> 0.2, kb -> 1.5, kd -> 0.1, kf -> 2.5, kin -> 0.007, kout -> 0.01, kr -> 0.02, ku -> 0.1, mu0 -> 0.05, nm -> 1.0, default -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
ain'[t] == 1.0*v5 +1.0*v4 +1.0*v7 -1.0*v2 -1.0*v6, c'[t] == 1.0*v1 +1.0*v4 -1.0*v2 -1.0*v3, ca'[t] == 1.0*v2 -1.0*v8 -1.0*v4, cap'[t] == 1.0*v8 -1.0*v7, n'[t] == 1.0*v9 
};
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]}]