(* 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 = {
L[t], T[t], T1[t], V[t], Vi[t], Vni[t]
};

initialValues = {
L[0] == 2.0, T[0] == 600000.0, T1[0] == 0.3, V[0] == 50000.0, Vi[0] == 50000.0, Vni[0] == 0.0
};

rates = {
v1, v10, v11, v12, v13, v2, v3, v4, v5, v6, v7, v8, v9
};

rateEquations = {
v1 -> lambda, v10 -> alphaL*k*T[t]*Vi[t], v11 -> alphaL*epsilonRT*k*T[t]*Vi[t], v12 -> delta*NN*T1[t], v13 -> delta*epsilonPI*NN*T1[t], v2 -> dT*T[t], v3 -> k*T[t]*Vi[t], v4 -> dL*L[t], v5 -> a*L[t], v6 -> delta*T1[t], v7 -> c*Vi[t], v8 -> c*Vni[t], v9 -> epsilonRT*k*T[t]*Vi[t]
};

parameters = {
NN -> 4000.0, a -> 0.1, alphaL -> 0.001, c -> 23.0, dL -> 0.004, dT -> 0.01, delta -> 1.0, epsilonPI -> 0.65, epsilonRT -> 0.0, k -> 2.4*^-08, lambda -> 10000.0, default -> 1.0
};

assignments = {
ratio -> Log[Vni[t]/Vi[t]]/Log[10]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
L'[t] == 1.0*v10 -1.0*v4 -1.0*v11 -1.0*v5, T'[t] == 1.0*v1 +1.0*v9 -1.0*v3 -1.0*v2, T1'[t] == 1.0*v11 +1.0*v5 +1.0*v3 -1.0*v9 -1.0*v10 -1.0*v6, V'[t] == 1.0*v12 -1.0*v7 -1.0*v8, Vi'[t] == 1.0*v12 -1.0*v7 -1.0*v13, Vni'[t] == 1.0*v13 -1.0*v8
};
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]}]