(* 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 = {
LRC\[LetterSpace]Cave[t], LRC\[LetterSpace]EE[t], LRC\[LetterSpace]Surf[t], Smad2c[t], Smad2n[t], Smad4c[t], Smad4n[t], Smads\[LetterSpace]Complex\[LetterSpace]c[t], Smads\[LetterSpace]Complex\[LetterSpace]n[t], T1R\[LetterSpace]Cave[t], T1R\[LetterSpace]EE[t], T1R\[LetterSpace]Surf[t], T2R\[LetterSpace]Cave[t], T2R\[LetterSpace]EE[t], T2R\[LetterSpace]Surf[t], TGF\[LetterSpace]beta[t]
};

initialValues = {
LRC\[LetterSpace]Cave[0] == 0.0, LRC\[LetterSpace]EE[0] == 0.0, LRC\[LetterSpace]Surf[0] == 0.0, Smad2c[0] == 492.61, Smad2n[0] == 236.45, Smad4c[0] == 1149.4, Smad4n[0] == 551.72, Smads\[LetterSpace]Complex\[LetterSpace]c[0] == 0.0, Smads\[LetterSpace]Complex\[LetterSpace]n[0] == 0.0, T1R\[LetterSpace]Cave[0] == 2.092, T1R\[LetterSpace]EE[0] == 2.06, T1R\[LetterSpace]Surf[0] == 0.237, T2R\[LetterSpace]Cave[0] == 1.778, T2R\[LetterSpace]EE[0] == 1.148, T2R\[LetterSpace]Surf[0] == 0.202, TGF\[LetterSpace]beta[0] == 0.08
};

rates = {
R10\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]degradation, R11\[LetterSpace]T2R\[LetterSpace]production, R12\[LetterSpace]T2R\[LetterSpace]Cave\[LetterSpace]formation, R13\[LetterSpace]T2R\[LetterSpace]Cave\[LetterSpace]recycling, R14\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]formation, R15\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]recycling, R16\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]degradation, R17\[LetterSpace]LRC\[LetterSpace]formation, R18\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]formation, R19\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]recycling, R1\[LetterSpace]Smad2\[LetterSpace]import, R20\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]formation, R21\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]recycling, R22\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]degradation, R23\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]formation, R24\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]import, R25\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]Dissociation, R26\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]degradation, R2\[LetterSpace]Smad2\[LetterSpace]export, R3\[LetterSpace]Smad4\[LetterSpace]import, R4\[LetterSpace]Smad4\[LetterSpace]export, R5\[LetterSpace]T1R\[LetterSpace]production, R6\[LetterSpace]T1R\[LetterSpace]Cave\[LetterSpace]formation, R7\[LetterSpace]T1R\[LetterSpace]Cave\[LetterSpace]recycling, R8\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]formation, R9\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]recycling
};

rateEquations = {
R10\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]degradation -> Kdeg\[LetterSpace]T1R\[LetterSpace]EE*V\[LetterSpace]cyt*T1R\[LetterSpace]EE[t], R11\[LetterSpace]T2R\[LetterSpace]production -> V\[LetterSpace]cyt*v\[LetterSpace]T2R, R12\[LetterSpace]T2R\[LetterSpace]Cave\[LetterSpace]formation -> ki\[LetterSpace]Cave*V\[LetterSpace]cyt*T2R\[LetterSpace]Surf[t], R13\[LetterSpace]T2R\[LetterSpace]Cave\[LetterSpace]recycling -> kr\[LetterSpace]Cave*V\[LetterSpace]cyt*T2R\[LetterSpace]Cave[t], R14\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]formation -> ki\[LetterSpace]EE*V\[LetterSpace]cyt*T2R\[LetterSpace]Surf[t], R15\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]recycling -> kr\[LetterSpace]EE*V\[LetterSpace]cyt*T2R\[LetterSpace]EE[t], R16\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]degradation -> Kdeg\[LetterSpace]T2R\[LetterSpace]EE*V\[LetterSpace]cyt*T2R\[LetterSpace]EE[t], R17\[LetterSpace]LRC\[LetterSpace]formation -> k\[LetterSpace]LRC*V\[LetterSpace]cyt*T1R\[LetterSpace]Surf[t]*T2R\[LetterSpace]Surf[t]*TGF\[LetterSpace]beta[t], R18\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]formation -> ki\[LetterSpace]Cave*V\[LetterSpace]cyt*LRC\[LetterSpace]Surf[t], R19\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]recycling -> kr\[LetterSpace]Cave*V\[LetterSpace]cyt*LRC\[LetterSpace]Cave[t], R1\[LetterSpace]Smad2\[LetterSpace]import -> Kimp\[LetterSpace]Smad2c*V\[LetterSpace]cyt*Smad2c[t], R20\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]formation -> ki\[LetterSpace]EE*V\[LetterSpace]cyt*LRC\[LetterSpace]Surf[t], R21\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]recycling -> kr\[LetterSpace]EE*V\[LetterSpace]cyt*LRC\[LetterSpace]EE[t], R22\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]degradation -> Kcd*V\[LetterSpace]cyt*LRC\[LetterSpace]EE[t], R23\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]formation -> k\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]c*V\[LetterSpace]cyt*LRC\[LetterSpace]EE[t]*Smad2c[t]*Smad4c[t], R24\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]import -> Kimp\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]c*V\[LetterSpace]cyt*Smads\[LetterSpace]Complex\[LetterSpace]c[t], R25\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]Dissociation -> Kdiss\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]n*V\[LetterSpace]nuc*Smads\[LetterSpace]Complex\[LetterSpace]n[t], R26\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]degradation -> Klid*V\[LetterSpace]cyt*LRC\[LetterSpace]Cave[t]*Smads\[LetterSpace]Complex\[LetterSpace]n[t], R2\[LetterSpace]Smad2\[LetterSpace]export -> Kexp\[LetterSpace]Smad2n*V\[LetterSpace]nuc*Smad2n[t], R3\[LetterSpace]Smad4\[LetterSpace]import -> Kimp\[LetterSpace]Smad4c*V\[LetterSpace]cyt*Smad4c[t], R4\[LetterSpace]Smad4\[LetterSpace]export -> Kexp\[LetterSpace]Smad4n*V\[LetterSpace]nuc*Smad4n[t], R5\[LetterSpace]T1R\[LetterSpace]production -> V\[LetterSpace]cyt*v\[LetterSpace]T1R, R6\[LetterSpace]T1R\[LetterSpace]Cave\[LetterSpace]formation -> ki\[LetterSpace]Cave*V\[LetterSpace]cyt*T1R\[LetterSpace]Surf[t], R7\[LetterSpace]T1R\[LetterSpace]Cave\[LetterSpace]recycling -> kr\[LetterSpace]Cave*V\[LetterSpace]cyt*T1R\[LetterSpace]Cave[t], R8\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]formation -> ki\[LetterSpace]EE*V\[LetterSpace]cyt*T1R\[LetterSpace]Surf[t], R9\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]recycling -> kr\[LetterSpace]EE*V\[LetterSpace]cyt*T1R\[LetterSpace]EE[t]
};

parameters = {
Kcd -> 0.005, Kdeg\[LetterSpace]T1R\[LetterSpace]EE -> 0.005, Kdeg\[LetterSpace]T2R\[LetterSpace]EE -> 0.025, Kdiss\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]n -> 0.1174, Kexp\[LetterSpace]Smad2n -> 1.0, Kexp\[LetterSpace]Smad4n -> 0.5, Kimp\[LetterSpace]Smad2c -> 0.16, Kimp\[LetterSpace]Smad4c -> 0.08, Kimp\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]c -> 0.16, Klid -> 0.02609, k\[LetterSpace]LRC -> 2197.0, k\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]c -> 6.85*^-05, ki\[LetterSpace]Cave -> 0.33, ki\[LetterSpace]EE -> 0.33, kr\[LetterSpace]Cave -> 0.03742, kr\[LetterSpace]EE -> 0.033, v\[LetterSpace]T1R -> 0.0103, v\[LetterSpace]T2R -> 0.02869, V\[LetterSpace]cyt -> 0.00105, V\[LetterSpace]medium -> 1.0, V\[LetterSpace]nuc -> 0.00035
};

assignments = {
Total\[LetterSpace]Smad2c -> Smad2c[t] + Smads\[LetterSpace]Complex\[LetterSpace]c[t], Total\[LetterSpace]Smad2n -> Smad2n[t] + Smads\[LetterSpace]Complex\[LetterSpace]n[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {
R1\[LetterSpace]Smad2\[LetterSpace]import->"http://identifiers.org/obo.go/GO:0007184", R23\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]formation->"http://identifiers.org/obo.go/GO:0007184", R3\[LetterSpace]Smad4\[LetterSpace]import->"http://identifiers.org/obo.go/GO:0007184"
};

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

(* Time evolution *)
odes = {
LRC\[LetterSpace]Cave'[t] == 1.0*R18\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]formation -1.0*R19\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]recycling -1.0*R26\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]degradation, LRC\[LetterSpace]EE'[t] == 1.0*R20\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]formation -1.0*R21\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]recycling -1.0*R22\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]degradation, LRC\[LetterSpace]Surf'[t] == 1.0*R17\[LetterSpace]LRC\[LetterSpace]formation -1.0*R18\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]formation -1.0*R20\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]formation, Smad2c'[t] == 1.0*R2\[LetterSpace]Smad2\[LetterSpace]export -1.0*R1\[LetterSpace]Smad2\[LetterSpace]import -1.0*R23\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]formation, Smad2n'[t] == 1.0*R1\[LetterSpace]Smad2\[LetterSpace]import +1.0*R25\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]Dissociation -1.0*R2\[LetterSpace]Smad2\[LetterSpace]export, Smad4c'[t] == 1.0*R4\[LetterSpace]Smad4\[LetterSpace]export -1.0*R3\[LetterSpace]Smad4\[LetterSpace]import -1.0*R23\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]formation, Smad4n'[t] == 1.0*R3\[LetterSpace]Smad4\[LetterSpace]import +1.0*R25\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]Dissociation -1.0*R4\[LetterSpace]Smad4\[LetterSpace]export, Smads\[LetterSpace]Complex\[LetterSpace]c'[t] == 1.0*R23\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]formation -1.0*R24\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]import, Smads\[LetterSpace]Complex\[LetterSpace]n'[t] == 1.0*R24\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]import -1.0*R25\[LetterSpace]Smads\[LetterSpace]Complex\[LetterSpace]Dissociation, T1R\[LetterSpace]Cave'[t] == 1.0*R6\[LetterSpace]T1R\[LetterSpace]Cave\[LetterSpace]formation -1.0*R7\[LetterSpace]T1R\[LetterSpace]Cave\[LetterSpace]recycling, T1R\[LetterSpace]EE'[t] == 1.0*R8\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]formation -1.0*R9\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]recycling -1.0*R10\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]degradation, T1R\[LetterSpace]Surf'[t] == 1.0*R5\[LetterSpace]T1R\[LetterSpace]production +1.0*R7\[LetterSpace]T1R\[LetterSpace]Cave\[LetterSpace]recycling +1.0*R9\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]recycling +1.0*R19\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]recycling +1.0*R21\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]recycling -1.0*R6\[LetterSpace]T1R\[LetterSpace]Cave\[LetterSpace]formation -1.0*R8\[LetterSpace]T1R\[LetterSpace]EE\[LetterSpace]formation -1.0*R17\[LetterSpace]LRC\[LetterSpace]formation, T2R\[LetterSpace]Cave'[t] == 1.0*R12\[LetterSpace]T2R\[LetterSpace]Cave\[LetterSpace]formation -1.0*R13\[LetterSpace]T2R\[LetterSpace]Cave\[LetterSpace]recycling, T2R\[LetterSpace]EE'[t] == 1.0*R14\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]formation -1.0*R15\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]recycling -1.0*R16\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]degradation, T2R\[LetterSpace]Surf'[t] == 1.0*R11\[LetterSpace]T2R\[LetterSpace]production +1.0*R13\[LetterSpace]T2R\[LetterSpace]Cave\[LetterSpace]recycling +1.0*R15\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]recycling +1.0*R19\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]recycling +1.0*R21\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]recycling -1.0*R12\[LetterSpace]T2R\[LetterSpace]Cave\[LetterSpace]formation -1.0*R14\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]formation -1.0*R17\[LetterSpace]LRC\[LetterSpace]formation, TGF\[LetterSpace]beta'[t] == 1.0*R15\[LetterSpace]T2R\[LetterSpace]EE\[LetterSpace]recycling +1.0*R19\[LetterSpace]LRC\[LetterSpace]Cave\[LetterSpace]recycling +1.0*R21\[LetterSpace]LRC\[LetterSpace]EE\[LetterSpace]recycling -1.0*R17\[LetterSpace]LRC\[LetterSpace]formation
};
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]}]