(* 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 = {
MAPK[t], MAPKMEKpp[t], MAPKPH[t], MAPKp[t], MAPKpMAPKPH[t], MAPKpMEKpp[t], MAPKpp[t], MAPKppMAPKPH[t], MEK[t], MEKPH[t], MEKRAFp[t], MEKp[t], MEKpMEKPH[t], MEKpRAFp[t], MEKpp[t], MEKppMEKPH[t], RAF[t], RAFK[t], RAFPH[t], RAFRAFK[t], RAFp[t], RAFpRAFPH[t]
};

initialValues = {
MAPK[0] == 0.4, MAPKMEKpp[0] == 0.0, MAPKPH[0] == 0.3, MAPKp[0] == 0.0, MAPKpMAPKPH[0] == 0.0, MAPKpMEKpp[0] == 0.0, MAPKpp[0] == 0.0, MAPKppMAPKPH[0] == 0.0, MEK[0] == 0.2, MEKPH[0] == 0.2, MEKRAFp[0] == 0.0, MEKp[0] == 0.0, MEKpMEKPH[0] == 0.0, MEKpRAFp[0] == 0.0, MEKpp[0] == 0.0, MEKppMEKPH[0] == 0.0, RAF[0] == 0.3, RAFK[0] == 0.2, RAFPH[0] == 0.3, RAFRAFK[0] == 0.0, RAFp[0] == 0.0, RAFpRAFPH[0] == 0.0
};

rates = {
Reaction1, Reaction10, Reaction11, Reaction12, Reaction13, Reaction14, Reaction15, Reaction16, Reaction17, Reaction18, Reaction19, Reaction2, Reaction20, Reaction21, Reaction22, Reaction23, Reaction24, Reaction25, Reaction26, Reaction27, Reaction28, Reaction29, Reaction3, Reaction30, Reaction4, Reaction5, Reaction6, Reaction7, Reaction8, Reaction9
};

rateEquations = {
Reaction1 -> Reaction1\[LetterSpace]a1*RAF[t]*RAFK[t], Reaction10 -> Reaction10\[LetterSpace]a4*MEKp[t]*MEKPH[t], Reaction11 -> Reaction11\[LetterSpace]d4*MEKpMEKPH[t], Reaction12 -> Reaction12\[LetterSpace]k4*MEKpMEKPH[t], Reaction13 -> Reaction13\[LetterSpace]a5*MEKp[t]*RAFp[t], Reaction14 -> Reaction14\[LetterSpace]d5*MEKpRAFp[t], Reaction15 -> Reaction15\[LetterSpace]k5*MEKpRAFp[t], Reaction16 -> Reaction16\[LetterSpace]a6*MEKPH[t]*MEKpp[t], Reaction17 -> Reaction17\[LetterSpace]d6*MEKppMEKPH[t], Reaction18 -> Reaction18\[LetterSpace]k6*MEKppMEKPH[t], Reaction19 -> Reaction19\[LetterSpace]a7*MAPK[t]*MEKpp[t], Reaction2 -> Reaction2\[LetterSpace]d1*RAFRAFK[t], Reaction20 -> Reaction20\[LetterSpace]d7*MAPKMEKpp[t], Reaction21 -> Reaction21\[LetterSpace]k7*MAPKMEKpp[t], Reaction22 -> Reaction22\[LetterSpace]a8*MAPKp[t]*MAPKPH[t], Reaction23 -> Reaction23\[LetterSpace]d8*MAPKpMAPKPH[t], Reaction24 -> Reaction24\[LetterSpace]k8*MAPKpMAPKPH[t], Reaction25 -> Reaction25\[LetterSpace]a9*MAPKp[t]*MEKpp[t], Reaction26 -> Reaction26\[LetterSpace]d9*MAPKpMEKpp[t], Reaction27 -> Reaction27\[LetterSpace]k9*MAPKpMEKpp[t], Reaction28 -> Reaction28\[LetterSpace]a10*MAPKPH[t]*MAPKpp[t], Reaction29 -> Reaction29\[LetterSpace]d10*MAPKppMAPKPH[t], Reaction3 -> Reaction3\[LetterSpace]k1*RAFRAFK[t], Reaction30 -> Reaction30\[LetterSpace]k10*MAPKppMAPKPH[t], Reaction4 -> Reaction4\[LetterSpace]a2*RAFp[t]*RAFPH[t], Reaction5 -> Reaction5\[LetterSpace]d2*RAFpRAFPH[t], Reaction6 -> Reaction6\[LetterSpace]k2*RAFpRAFPH[t], Reaction7 -> Reaction7\[LetterSpace]a3*MEK[t]*RAFp[t], Reaction8 -> Reaction8\[LetterSpace]d3*MEKRAFp[t], Reaction9 -> Reaction9\[LetterSpace]k3*MEKRAFp[t]
};

parameters = {
Reaction1\[LetterSpace]a1 -> 1.0, Reaction2\[LetterSpace]d1 -> 0.4, Reaction3\[LetterSpace]k1 -> 0.1, Reaction4\[LetterSpace]a2 -> 0.5, Reaction5\[LetterSpace]d2 -> 0.5, Reaction6\[LetterSpace]k2 -> 0.1, Reaction7\[LetterSpace]a3 -> 3.3, Reaction8\[LetterSpace]d3 -> 0.42, Reaction9\[LetterSpace]k3 -> 0.1, Reaction10\[LetterSpace]a4 -> 10.0, Reaction11\[LetterSpace]d4 -> 0.8, Reaction12\[LetterSpace]k4 -> 0.1, Reaction13\[LetterSpace]a5 -> 3.3, Reaction14\[LetterSpace]d5 -> 0.4, Reaction15\[LetterSpace]k5 -> 0.1, Reaction16\[LetterSpace]a6 -> 10.0, Reaction17\[LetterSpace]d6 -> 0.8, Reaction18\[LetterSpace]k6 -> 0.1, Reaction19\[LetterSpace]a7 -> 20.0, Reaction20\[LetterSpace]d7 -> 0.6, Reaction21\[LetterSpace]k7 -> 0.1, Reaction22\[LetterSpace]a8 -> 5.0, Reaction23\[LetterSpace]d8 -> 0.4, Reaction24\[LetterSpace]k8 -> 0.1, Reaction25\[LetterSpace]a9 -> 20.0, Reaction26\[LetterSpace]d9 -> 0.6, Reaction27\[LetterSpace]k9 -> 0.1, Reaction28\[LetterSpace]a10 -> 5.0, Reaction29\[LetterSpace]d10 -> 0.4, Reaction30\[LetterSpace]k10 -> 0.1, Cytoplasm -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
MAPKPH[t]->"http://identifiers.org/uniprot/Q90W58"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
MAPK'[t] == 1.0*Reaction20 +1.0*Reaction24 -1.0*Reaction19, MAPKMEKpp'[t] == 1.0*Reaction19 -1.0*Reaction20 -1.0*Reaction21, MAPKPH'[t] == 1.0*Reaction23 +1.0*Reaction24 +1.0*Reaction29 +1.0*Reaction30 -1.0*Reaction22 -1.0*Reaction28, MAPKp'[t] == 1.0*Reaction21 +1.0*Reaction23 +1.0*Reaction26 +1.0*Reaction30 -1.0*Reaction22 -1.0*Reaction25, MAPKpMAPKPH'[t] == 1.0*Reaction22 -1.0*Reaction23 -1.0*Reaction24, MAPKpMEKpp'[t] == 1.0*Reaction25 -1.0*Reaction26 -1.0*Reaction27, MAPKpp'[t] == 1.0*Reaction27 +1.0*Reaction29 -1.0*Reaction28, MAPKppMAPKPH'[t] == 1.0*Reaction28 -1.0*Reaction29 -1.0*Reaction30, MEK'[t] == 1.0*Reaction8 +1.0*Reaction12 -1.0*Reaction7, MEKPH'[t] == 1.0*Reaction11 +1.0*Reaction12 +1.0*Reaction17 +1.0*Reaction18 -1.0*Reaction10 -1.0*Reaction16, MEKRAFp'[t] == 1.0*Reaction7 -1.0*Reaction8 -1.0*Reaction9, MEKp'[t] == 1.0*Reaction9 +1.0*Reaction11 +1.0*Reaction14 +1.0*Reaction18 -1.0*Reaction10 -1.0*Reaction13, MEKpMEKPH'[t] == 1.0*Reaction10 -1.0*Reaction11 -1.0*Reaction12, MEKpRAFp'[t] == 1.0*Reaction13 -1.0*Reaction14 -1.0*Reaction15, MEKpp'[t] == 1.0*Reaction15 +1.0*Reaction17 +1.0*Reaction20 +1.0*Reaction21 +1.0*Reaction26 +1.0*Reaction27 -1.0*Reaction16 -1.0*Reaction19 -1.0*Reaction25, MEKppMEKPH'[t] == 1.0*Reaction16 -1.0*Reaction17 -1.0*Reaction18, RAF'[t] == 1.0*Reaction6 +1.0*Reaction2 -1.0*Reaction1, RAFK'[t] == 1.0*Reaction2 +1.0*Reaction3 -1.0*Reaction1, RAFPH'[t] == 1.0*Reaction6 +1.0*Reaction5 -1.0*Reaction4, RAFRAFK'[t] == 1.0*Reaction1 -1.0*Reaction2 -1.0*Reaction3, RAFp'[t] == 1.0*Reaction8 +1.0*Reaction3 +1.0*Reaction5 +1.0*Reaction9 +1.0*Reaction14 +1.0*Reaction15 -1.0*Reaction4 -1.0*Reaction7 -1.0*Reaction13, RAFpRAFPH'[t] == 1.0*Reaction4 -1.0*Reaction5 -1.0*Reaction6
};
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]}]