(* 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 = {
AA[t], AAp[t], B[t], Bp[t], SetYp[t], TT[t], TTAA[t], TTAAp[t], TTW[t], TTWAA[t], TTWAAp[t], TTWW[t], TTWWAA[t], TTWWAAp[t], W[t], WAA[t], WAAp[t], WWAA[t], WWAAp[t], Y[t], Yp[t], Z[t]
};

initialValues = {
AA[0] == 2.5*^-06, AAp[0] == 0.0, B[0] == 2*^-06, Bp[0] == 0.0, SetYp[0] == 1.63*^-06, TT[0] == 2.5*^-06, TTAA[0] == 0.0, TTAAp[0] == 0.0, TTW[0] == 0.0, TTWAA[0] == 0.0, TTWAAp[0] == 0.0, TTWW[0] == 0.0, TTWWAA[0] == 0.0, TTWWAAp[0] == 0.0, W[0] == 5*^-06, WAA[0] == 0.0, WAAp[0] == 0.0, WWAA[0] == 0.0, WWAAp[0] == 0.0, Y[0] == 1*^-05, Yp[0] == 0.0, Z[0] == 2*^-05
};

rates = {
complex\[LetterSpace]r1, complex\[LetterSpace]r10, complex\[LetterSpace]r11, complex\[LetterSpace]r12, complex\[LetterSpace]r2, complex\[LetterSpace]r3, complex\[LetterSpace]r4, complex\[LetterSpace]r5, complex\[LetterSpace]r6, complex\[LetterSpace]r7, complex\[LetterSpace]r8, complex\[LetterSpace]r9, phosphorylation\[LetterSpace]r1, phosphorylation\[LetterSpace]r10, phosphorylation\[LetterSpace]r2, phosphorylation\[LetterSpace]r3, phosphorylation\[LetterSpace]r4, phosphorylation\[LetterSpace]r5, phosphorylation\[LetterSpace]r6, phosphorylation\[LetterSpace]r7, phosphorylation\[LetterSpace]r8, phosphorylation\[LetterSpace]r9, phosphotransfer\[LetterSpace]r1, phosphotransfer\[LetterSpace]r10, phosphotransfer\[LetterSpace]r11, phosphotransfer\[LetterSpace]r12, phosphotransfer\[LetterSpace]r2, phosphotransfer\[LetterSpace]r3, phosphotransfer\[LetterSpace]r4, phosphotransfer\[LetterSpace]r5, phosphotransfer\[LetterSpace]r6, phosphotransfer\[LetterSpace]r7, phosphotransfer\[LetterSpace]r8, phosphotransfer\[LetterSpace]r9
};

rateEquations = {
complex\[LetterSpace]r1 -> cell*(complex\[LetterSpace]r1\[LetterSpace]k1*TTW[t] - complex\[LetterSpace]r1\[LetterSpace]k2*TT[t]*W[t]), complex\[LetterSpace]r10 -> cell*(complex\[LetterSpace]r10\[LetterSpace]k1*TTWW[t] - complex\[LetterSpace]r10\[LetterSpace]k2*TTW[t]*W[t]), complex\[LetterSpace]r11 -> cell*(-(complex\[LetterSpace]r11\[LetterSpace]k2*W[t]*WAA[t]) + complex\[LetterSpace]r11\[LetterSpace]k1*WWAA[t]), complex\[LetterSpace]r12 -> cell*(complex\[LetterSpace]r12\[LetterSpace]k1*TTWAA[t] - complex\[LetterSpace]r12\[LetterSpace]k2*TTAA[t]*W[t]), complex\[LetterSpace]r2 -> cell*(-(complex\[LetterSpace]r2\[LetterSpace]k2*AA[t]*W[t]) + complex\[LetterSpace]r2\[LetterSpace]k1*WAA[t]), complex\[LetterSpace]r3 -> cell*(complex\[LetterSpace]r3\[LetterSpace]k1*TTWAA[t] - complex\[LetterSpace]r3\[LetterSpace]k2*TT[t]*WAA[t]), complex\[LetterSpace]r4 -> cell*(complex\[LetterSpace]r4\[LetterSpace]k1*TTWWAA[t] - complex\[LetterSpace]r4\[LetterSpace]k2*TTW[t]*WAA[t]), complex\[LetterSpace]r5 -> cell*(-(complex\[LetterSpace]r5\[LetterSpace]k2*AA[t]*TTWW[t]) + complex\[LetterSpace]r5\[LetterSpace]k1*TTWWAA[t]), complex\[LetterSpace]r6 -> cell*(complex\[LetterSpace]r6\[LetterSpace]k1*TTWWAA[t] - complex\[LetterSpace]r6\[LetterSpace]k2*TT[t]*WWAA[t]), complex\[LetterSpace]r7 -> cell*(-(complex\[LetterSpace]r7\[LetterSpace]k2*AA[t]*TT[t]) + complex\[LetterSpace]r7\[LetterSpace]k1*TTAA[t]), complex\[LetterSpace]r8 -> cell*(-(complex\[LetterSpace]r8\[LetterSpace]k2*AA[t]*TTW[t]) + complex\[LetterSpace]r8\[LetterSpace]k1*TTWAA[t]), complex\[LetterSpace]r9 -> cell*(complex\[LetterSpace]r9\[LetterSpace]k1*TTWWAA[t] - complex\[LetterSpace]r9\[LetterSpace]k2*TTWAA[t]*W[t]), phosphorylation\[LetterSpace]r1 -> cell*phosphorylation\[LetterSpace]r1\[LetterSpace]k1*TTWWAA[t], phosphorylation\[LetterSpace]r10 -> cell*phosphorylation\[LetterSpace]r10\[LetterSpace]k1*Bp[t], phosphorylation\[LetterSpace]r2 -> cell*phosphorylation\[LetterSpace]r2\[LetterSpace]k1*AA[t], phosphorylation\[LetterSpace]r3 -> cell*phosphorylation\[LetterSpace]r3\[LetterSpace]k1*WAA[t], phosphorylation\[LetterSpace]r4 -> cell*phosphorylation\[LetterSpace]r4\[LetterSpace]k1*WWAA[t], phosphorylation\[LetterSpace]r5 -> cell*phosphorylation\[LetterSpace]r5\[LetterSpace]k1*TTAA[t], phosphorylation\[LetterSpace]r6 -> cell*phosphorylation\[LetterSpace]r6\[LetterSpace]k1*TTWAA[t], phosphorylation\[LetterSpace]r7 -> cell*phosphorylation\[LetterSpace]r7\[LetterSpace]k1*Y[t], phosphorylation\[LetterSpace]r8 -> cell*phosphorylation\[LetterSpace]r8\[LetterSpace]k1*Yp[t], phosphorylation\[LetterSpace]r9 -> cell*phosphorylation\[LetterSpace]r9\[LetterSpace]k1*Yp[t]*Z[t], phosphotransfer\[LetterSpace]r1 -> cell*phosphotransfer\[LetterSpace]r1\[LetterSpace]k1*AAp[t]*B[t], phosphotransfer\[LetterSpace]r10 -> cell*phosphotransfer\[LetterSpace]r10\[LetterSpace]k1*TTAAp[t]*Y[t], phosphotransfer\[LetterSpace]r11 -> cell*phosphotransfer\[LetterSpace]r11\[LetterSpace]k1*TTWAAp[t]*Y[t], phosphotransfer\[LetterSpace]r12 -> cell*phosphotransfer\[LetterSpace]r12\[LetterSpace]k1*TTWWAAp[t]*Y[t], phosphotransfer\[LetterSpace]r2 -> cell*phosphotransfer\[LetterSpace]r2\[LetterSpace]k1*B[t]*WAAp[t], phosphotransfer\[LetterSpace]r3 -> cell*phosphotransfer\[LetterSpace]r3\[LetterSpace]k1*B[t]*WWAAp[t], phosphotransfer\[LetterSpace]r4 -> cell*phosphotransfer\[LetterSpace]r4\[LetterSpace]k1*B[t]*TTAAp[t], phosphotransfer\[LetterSpace]r5 -> cell*phosphotransfer\[LetterSpace]r5\[LetterSpace]k1*B[t]*TTWAAp[t], phosphotransfer\[LetterSpace]r6 -> cell*phosphotransfer\[LetterSpace]r6\[LetterSpace]k1*B[t]*TTWWAAp[t], phosphotransfer\[LetterSpace]r7 -> cell*phosphotransfer\[LetterSpace]r7\[LetterSpace]k1*AAp[t]*Y[t], phosphotransfer\[LetterSpace]r8 -> cell*phosphotransfer\[LetterSpace]r8\[LetterSpace]k1*WAAp[t]*Y[t], phosphotransfer\[LetterSpace]r9 -> cell*phosphotransfer\[LetterSpace]r9\[LetterSpace]k1*WWAAp[t]*Y[t]
};

parameters = {
Hill -> 4.0, complex\[LetterSpace]r1\[LetterSpace]k1 -> 0.00365, complex\[LetterSpace]r1\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r2\[LetterSpace]k1 -> 0.00894, complex\[LetterSpace]r2\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r3\[LetterSpace]k1 -> 297.0, complex\[LetterSpace]r3\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r4\[LetterSpace]k1 -> 0.64, complex\[LetterSpace]r4\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r5\[LetterSpace]k1 -> 0.112, complex\[LetterSpace]r5\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r6\[LetterSpace]k1 -> 0.0229, complex\[LetterSpace]r6\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r7\[LetterSpace]k1 -> 39.3, complex\[LetterSpace]r7\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r8\[LetterSpace]k1 -> 727.0, complex\[LetterSpace]r8\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r9\[LetterSpace]k1 -> 7.87*^-06, complex\[LetterSpace]r9\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r10\[LetterSpace]k1 -> 0.0511, complex\[LetterSpace]r10\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r11\[LetterSpace]k1 -> 0.102, complex\[LetterSpace]r11\[LetterSpace]k2 -> 1000000.0, complex\[LetterSpace]r12\[LetterSpace]k1 -> 0.0676, complex\[LetterSpace]r12\[LetterSpace]k2 -> 1000000.0, phosphorylation\[LetterSpace]r1\[LetterSpace]k1 -> 15.5, phosphorylation\[LetterSpace]r2\[LetterSpace]k1 -> 0.0227, phosphorylation\[LetterSpace]r3\[LetterSpace]k1 -> 0.0227, phosphorylation\[LetterSpace]r4\[LetterSpace]k1 -> 0.0227, phosphorylation\[LetterSpace]r5\[LetterSpace]k1 -> 0.0227, phosphorylation\[LetterSpace]r6\[LetterSpace]k1 -> 0.0227, phosphorylation\[LetterSpace]r7\[LetterSpace]k1 -> 0.00124, phosphorylation\[LetterSpace]r8\[LetterSpace]k1 -> 0.037, phosphorylation\[LetterSpace]r9\[LetterSpace]k1 -> 500000.0, phosphorylation\[LetterSpace]r10\[LetterSpace]k1 -> 0.35, phosphotransfer\[LetterSpace]r1\[LetterSpace]k1 -> 6000000.0, phosphotransfer\[LetterSpace]r2\[LetterSpace]k1 -> 6000000.0, phosphotransfer\[LetterSpace]r3\[LetterSpace]k1 -> 6000000.0, phosphotransfer\[LetterSpace]r4\[LetterSpace]k1 -> 6000000.0, phosphotransfer\[LetterSpace]r5\[LetterSpace]k1 -> 6000000.0, phosphotransfer\[LetterSpace]r6\[LetterSpace]k1 -> 6000000.0, phosphotransfer\[LetterSpace]r7\[LetterSpace]k1 -> 30000000.0, phosphotransfer\[LetterSpace]r8\[LetterSpace]k1 -> 30000000.0, phosphotransfer\[LetterSpace]r9\[LetterSpace]k1 -> 30000000.0, phosphotransfer\[LetterSpace]r10\[LetterSpace]k1 -> 30000000.0, phosphotransfer\[LetterSpace]r11\[LetterSpace]k1 -> 30000000.0, phosphotransfer\[LetterSpace]r12\[LetterSpace]k1 -> 30000000.0, cell -> 1.41
};

assignments = {
Bias -> 1 - Yp[t]^Hill/(2.333*SetYp[t]^Hill + Yp[t]^Hill)
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
AA'[t] == 1.0*complex\[LetterSpace]r2 +1.0*complex\[LetterSpace]r5 +1.0*complex\[LetterSpace]r7 +1.0*complex\[LetterSpace]r8 +1.0*phosphotransfer\[LetterSpace]r1 +1.0*phosphotransfer\[LetterSpace]r7 -1.0*phosphorylation\[LetterSpace]r2, AAp'[t] == 1.0*phosphorylation\[LetterSpace]r2 -1.0*phosphotransfer\[LetterSpace]r1 -1.0*phosphotransfer\[LetterSpace]r7, B'[t] == 1.0*phosphorylation\[LetterSpace]r10 -1.0*phosphotransfer\[LetterSpace]r1 -1.0*phosphotransfer\[LetterSpace]r2 -1.0*phosphotransfer\[LetterSpace]r3 -1.0*phosphotransfer\[LetterSpace]r4 -1.0*phosphotransfer\[LetterSpace]r5 -1.0*phosphotransfer\[LetterSpace]r6, Bp'[t] == 1.0*phosphotransfer\[LetterSpace]r1 +1.0*phosphotransfer\[LetterSpace]r2 +1.0*phosphotransfer\[LetterSpace]r3 +1.0*phosphotransfer\[LetterSpace]r4 +1.0*phosphotransfer\[LetterSpace]r5 +1.0*phosphotransfer\[LetterSpace]r6 -1.0*phosphorylation\[LetterSpace]r10, SetYp'[t] == 0.0 , TT'[t] == 1.0*complex\[LetterSpace]r1 +1.0*complex\[LetterSpace]r3 +1.0*complex\[LetterSpace]r6 +1.0*complex\[LetterSpace]r7 , TTAA'[t] == 1.0*complex\[LetterSpace]r12 +1.0*phosphotransfer\[LetterSpace]r4 +1.0*phosphotransfer\[LetterSpace]r10 -1.0*complex\[LetterSpace]r7 -1.0*phosphorylation\[LetterSpace]r5, TTAAp'[t] == 1.0*phosphorylation\[LetterSpace]r5 -1.0*phosphotransfer\[LetterSpace]r4 -1.0*phosphotransfer\[LetterSpace]r10, TTW'[t] == 1.0*complex\[LetterSpace]r4 +1.0*complex\[LetterSpace]r8 +1.0*complex\[LetterSpace]r10 -1.0*complex\[LetterSpace]r1, TTWAA'[t] == 1.0*complex\[LetterSpace]r9 +1.0*phosphotransfer\[LetterSpace]r5 +1.0*phosphotransfer\[LetterSpace]r11 -1.0*complex\[LetterSpace]r3 -1.0*complex\[LetterSpace]r8 -1.0*complex\[LetterSpace]r12 -1.0*phosphorylation\[LetterSpace]r6, TTWAAp'[t] == 1.0*phosphorylation\[LetterSpace]r6 -1.0*phosphotransfer\[LetterSpace]r5 -1.0*phosphotransfer\[LetterSpace]r11, TTWW'[t] == 1.0*complex\[LetterSpace]r5 -1.0*complex\[LetterSpace]r10, TTWWAA'[t] == 1.0*phosphotransfer\[LetterSpace]r6 +1.0*phosphotransfer\[LetterSpace]r12 -1.0*complex\[LetterSpace]r4 -1.0*complex\[LetterSpace]r5 -1.0*complex\[LetterSpace]r6 -1.0*complex\[LetterSpace]r9 -1.0*phosphorylation\[LetterSpace]r1, TTWWAAp'[t] == 1.0*phosphorylation\[LetterSpace]r1 -1.0*phosphotransfer\[LetterSpace]r6 -1.0*phosphotransfer\[LetterSpace]r12, W'[t] == 1.0*complex\[LetterSpace]r1 +1.0*complex\[LetterSpace]r2 +1.0*complex\[LetterSpace]r9 +1.0*complex\[LetterSpace]r10 +1.0*complex\[LetterSpace]r11 +1.0*complex\[LetterSpace]r12 , WAA'[t] == 1.0*complex\[LetterSpace]r3 +1.0*complex\[LetterSpace]r4 +1.0*complex\[LetterSpace]r11 +1.0*phosphotransfer\[LetterSpace]r2 +1.0*phosphotransfer\[LetterSpace]r8 -1.0*complex\[LetterSpace]r2 -1.0*phosphorylation\[LetterSpace]r3, WAAp'[t] == 1.0*phosphorylation\[LetterSpace]r3 -1.0*phosphotransfer\[LetterSpace]r2 -1.0*phosphotransfer\[LetterSpace]r8, WWAA'[t] == 1.0*complex\[LetterSpace]r6 +1.0*phosphotransfer\[LetterSpace]r3 +1.0*phosphotransfer\[LetterSpace]r9 -1.0*complex\[LetterSpace]r11 -1.0*phosphorylation\[LetterSpace]r4, WWAAp'[t] == 1.0*phosphorylation\[LetterSpace]r4 -1.0*phosphotransfer\[LetterSpace]r3 -1.0*phosphotransfer\[LetterSpace]r9, Y'[t] == 1.0*phosphorylation\[LetterSpace]r8 +1.0*phosphorylation\[LetterSpace]r9 -1.0*phosphorylation\[LetterSpace]r7 -1.0*phosphotransfer\[LetterSpace]r7 -1.0*phosphotransfer\[LetterSpace]r8 -1.0*phosphotransfer\[LetterSpace]r9 -1.0*phosphotransfer\[LetterSpace]r10 -1.0*phosphotransfer\[LetterSpace]r11 -1.0*phosphotransfer\[LetterSpace]r12, Yp'[t] == 1.0*phosphorylation\[LetterSpace]r7 +1.0*phosphotransfer\[LetterSpace]r7 +1.0*phosphotransfer\[LetterSpace]r8 +1.0*phosphotransfer\[LetterSpace]r9 +1.0*phosphotransfer\[LetterSpace]r10 +1.0*phosphotransfer\[LetterSpace]r11 +1.0*phosphotransfer\[LetterSpace]r12 -1.0*phosphorylation\[LetterSpace]r8 -1.0*phosphorylation\[LetterSpace]r9, Z'[t] == 1.0*phosphorylation\[LetterSpace]r9 -1.0*phosphorylation\[LetterSpace]r9
};
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]}]