(* 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 = {
A[t], Ap[t], B[t], Bp[t], M[t], MYp[t], MYpYp[t], MYpYpYp[t], MYpYpYpYp[t], T[t], TA[t], TW[t], TWA[t], Tasp[t], Tasp\[LetterSpace]A[t], Tasp\[LetterSpace]W[t], Tasp\[LetterSpace]WA[t], Tni[t], Tni\[LetterSpace]A[t], Tni\[LetterSpace]W[t], Tni\[LetterSpace]WA[t], W[t], WA[t], Y[t], Yp[t], Z[t]
};

initialValues = {
A[0] == 3*^-06, Ap[0] == 3.48*^-08, B[0] == 1.93*^-06, Bp[0] == 6.87*^-08, M[0] == 6.24*^-09, MYp[0] == 7.77*^-10, MYpYp[0] == 2.99*^-10, MYpYpYp[0] == 3.78*^-10, MYpYpYpYp[0] == 2.31*^-09, T[0] == 3.12*^-06, TA[0] == 4.44*^-07, TW[0] == 5.91*^-07, TWA[0] == 8.47*^-07, Tasp[0] == 0.0, Tasp\[LetterSpace]A[0] == 0.0, Tasp\[LetterSpace]W[0] == 0.0, Tasp\[LetterSpace]WA[0] == 0.0, Tni[0] == 0.0, Tni\[LetterSpace]A[0] == 0.0, Tni\[LetterSpace]W[0] == 0.0, Tni\[LetterSpace]WA[0] == 0.0, W[0] == 2.89*^-06, WA[0] == 6.78*^-07, Y[0] == 9.9*^-06, Yp[0] == 7*^-09, Z[0] == 2*^-05
};

rates = {
motor\[LetterSpace]r1, motor\[LetterSpace]r2, motor\[LetterSpace]r3, motor\[LetterSpace]r4, 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, reaction\[LetterSpace]1, reaction\[LetterSpace]2, reaction\[LetterSpace]3, regulatory\[LetterSpace]r1, regulatory\[LetterSpace]r10, regulatory\[LetterSpace]r11, regulatory\[LetterSpace]r12, regulatory\[LetterSpace]r13, regulatory\[LetterSpace]r14, regulatory\[LetterSpace]r15, regulatory\[LetterSpace]r16, regulatory\[LetterSpace]r17, regulatory\[LetterSpace]r18, regulatory\[LetterSpace]r2, regulatory\[LetterSpace]r3, regulatory\[LetterSpace]r4, regulatory\[LetterSpace]r5, regulatory\[LetterSpace]r6, regulatory\[LetterSpace]r7, regulatory\[LetterSpace]r8, regulatory\[LetterSpace]r9
};

rateEquations = {
motor\[LetterSpace]r1 -> cell*function\[LetterSpace]4\[LetterSpace]motor\[LetterSpace]r1[M[t], MYp[t], Yp[t], cell, ka, kappa], motor\[LetterSpace]r2 -> cell*function\[LetterSpace]4\[LetterSpace]motor\[LetterSpace]r2[MYp[t], MYpYp[t], Yp[t], alpha, cell, ka, kappa], motor\[LetterSpace]r3 -> cell*function\[LetterSpace]4\[LetterSpace]motor\[LetterSpace]r3[MYpYp[t], MYpYpYp[t], Yp[t], alpha, cell, ka, kappa], motor\[LetterSpace]r4 -> cell*function\[LetterSpace]4\[LetterSpace]motor\[LetterSpace]r4[MYpYpYp[t], MYpYpYpYp[t], Yp[t], alpha, cell, ka, kappa], phosphorylation\[LetterSpace]r1 -> cell*Autophosphorylation[phosphorylation\[LetterSpace]r1\[LetterSpace]kcat, parameter\[LetterSpace]2, A[t]], phosphorylation\[LetterSpace]r10 -> cell*phosphorylation\[LetterSpace]r10\[LetterSpace]k1*Bp[t], phosphorylation\[LetterSpace]r2 -> cell*ModAutophosphorylation[TWA[t], A[t], phosphorylation\[LetterSpace]r2\[LetterSpace]kcat, parameter\[LetterSpace]2], phosphorylation\[LetterSpace]r3 -> cell*ModAutophosphorylation[Tni\[LetterSpace]WA[t], A[t], phosphorylation\[LetterSpace]r3\[LetterSpace]kcat, parameter\[LetterSpace]2], phosphorylation\[LetterSpace]r4 -> cell*phosphorylation\[LetterSpace]r4\[LetterSpace]k1*Tasp\[LetterSpace]WA[t]*Yp[t], phosphorylation\[LetterSpace]r5 -> cell*phosphorylation\[LetterSpace]r5\[LetterSpace]k1*Ap[t]*Y[t], phosphorylation\[LetterSpace]r6 -> cell*Autophosphorylation[phosphorylation\[LetterSpace]r6\[LetterSpace]kcat, parameter\[LetterSpace]2, Y[t]], phosphorylation\[LetterSpace]r7 -> cell*phosphorylation\[LetterSpace]r7\[LetterSpace]k1*Yp[t], phosphorylation\[LetterSpace]r8 -> cell*phosphorylation\[LetterSpace]r8\[LetterSpace]k1*Yp[t]*Z[t], phosphorylation\[LetterSpace]r9 -> cell*phosphorylation\[LetterSpace]r9\[LetterSpace]k1*Ap[t]*B[t], reaction\[LetterSpace]1 -> cell*(asp*reaction\[LetterSpace]1\[LetterSpace]k1*TA[t] - reaction\[LetterSpace]1\[LetterSpace]k2*Tasp\[LetterSpace]A[t]), reaction\[LetterSpace]2 -> cell*(-(reaction\[LetterSpace]2\[LetterSpace]k2*Tasp\[LetterSpace]W[t]) + asp*reaction\[LetterSpace]2\[LetterSpace]k1*TW[t]), reaction\[LetterSpace]3 -> cell*(-(reaction\[LetterSpace]3\[LetterSpace]k2*Tasp\[LetterSpace]WA[t]) + asp*reaction\[LetterSpace]3\[LetterSpace]k1*TWA[t]), regulatory\[LetterSpace]r1 -> cell*(asp*regulatory\[LetterSpace]r1\[LetterSpace]k1*T[t] - regulatory\[LetterSpace]r1\[LetterSpace]k2*Tasp[t]), regulatory\[LetterSpace]r10 -> cell*(regulatory\[LetterSpace]r10\[LetterSpace]k1*A[t]*Tasp[t] - regulatory\[LetterSpace]r10\[LetterSpace]k2*Tasp\[LetterSpace]A[t]), regulatory\[LetterSpace]r11 -> cell*(regulatory\[LetterSpace]r11\[LetterSpace]k1*A[t]*Tasp\[LetterSpace]W[t] - regulatory\[LetterSpace]r11\[LetterSpace]k2*Tasp\[LetterSpace]WA[t]), regulatory\[LetterSpace]r12 -> cell*(-(regulatory\[LetterSpace]r12\[LetterSpace]k2*Tasp\[LetterSpace]WA[t]) + regulatory\[LetterSpace]r12\[LetterSpace]k1*Tasp\[LetterSpace]A[t]*W[t]), regulatory\[LetterSpace]r13 -> cell*(-(regulatory\[LetterSpace]r13\[LetterSpace]k2*Tasp\[LetterSpace]WA[t]) + regulatory\[LetterSpace]r13\[LetterSpace]k1*Tasp[t]*WA[t]), regulatory\[LetterSpace]r14 -> cell*(-(regulatory\[LetterSpace]r14\[LetterSpace]k2*Tni\[LetterSpace]W[t]) + regulatory\[LetterSpace]r14\[LetterSpace]k1*Tni[t]*W[t]), regulatory\[LetterSpace]r15 -> cell*(regulatory\[LetterSpace]r15\[LetterSpace]k1*A[t]*Tni[t] - regulatory\[LetterSpace]r15\[LetterSpace]k2*Tni\[LetterSpace]A[t]), regulatory\[LetterSpace]r16 -> cell*(regulatory\[LetterSpace]r16\[LetterSpace]k1*A[t]*Tni\[LetterSpace]W[t] - regulatory\[LetterSpace]r16\[LetterSpace]k2*Tni\[LetterSpace]WA[t]), regulatory\[LetterSpace]r17 -> cell*(-(regulatory\[LetterSpace]r17\[LetterSpace]k2*Tni\[LetterSpace]WA[t]) + regulatory\[LetterSpace]r17\[LetterSpace]k1*Tni\[LetterSpace]A[t]*W[t]), regulatory\[LetterSpace]r18 -> cell*(-(regulatory\[LetterSpace]r18\[LetterSpace]k2*Tni\[LetterSpace]WA[t]) + regulatory\[LetterSpace]r18\[LetterSpace]k1*Tni[t]*WA[t]), regulatory\[LetterSpace]r2 -> cell*(ni*regulatory\[LetterSpace]r2\[LetterSpace]k1*T[t] - regulatory\[LetterSpace]r2\[LetterSpace]k2*Tni[t]), regulatory\[LetterSpace]r3 -> cell*(-(regulatory\[LetterSpace]r3\[LetterSpace]k2*TW[t]) + regulatory\[LetterSpace]r3\[LetterSpace]k1*T[t]*W[t]), regulatory\[LetterSpace]r4 -> cell*(regulatory\[LetterSpace]r4\[LetterSpace]k1*A[t]*T[t] - regulatory\[LetterSpace]r4\[LetterSpace]k2*TA[t]), regulatory\[LetterSpace]r5 -> cell*(regulatory\[LetterSpace]r5\[LetterSpace]k1*A[t]*W[t] - regulatory\[LetterSpace]r5\[LetterSpace]k2*WA[t]), regulatory\[LetterSpace]r6 -> cell*(regulatory\[LetterSpace]r6\[LetterSpace]k1*A[t]*TW[t] - regulatory\[LetterSpace]r6\[LetterSpace]k2*TWA[t]), regulatory\[LetterSpace]r7 -> cell*(-(regulatory\[LetterSpace]r7\[LetterSpace]k2*TWA[t]) + regulatory\[LetterSpace]r7\[LetterSpace]k1*TA[t]*W[t]), regulatory\[LetterSpace]r8 -> cell*(-(regulatory\[LetterSpace]r8\[LetterSpace]k2*TWA[t]) + regulatory\[LetterSpace]r8\[LetterSpace]k1*T[t]*WA[t]), regulatory\[LetterSpace]r9 -> cell*(-(regulatory\[LetterSpace]r9\[LetterSpace]k2*Tasp\[LetterSpace]W[t]) + regulatory\[LetterSpace]r9\[LetterSpace]k1*Tasp[t]*W[t])
};

parameters = {
alpha -> 0.14, ka -> 0.1, kappa -> 2.25*^-07, parameter\[LetterSpace]1 -> 1*^-07, parameter\[LetterSpace]3 -> 0.0003, asp -> 0.0, ni -> 0.0, species\[LetterSpace]1 -> 0.1, phosphorylation\[LetterSpace]r1\[LetterSpace]kcat -> 0.001, phosphorylation\[LetterSpace]r2\[LetterSpace]kcat -> 75000.0, phosphorylation\[LetterSpace]r3\[LetterSpace]kcat -> 200000.0, phosphorylation\[LetterSpace]r4\[LetterSpace]k1 -> 100000000.0, phosphorylation\[LetterSpace]r5\[LetterSpace]k1 -> 200000.0, phosphorylation\[LetterSpace]r6\[LetterSpace]kcat -> 0.0, phosphorylation\[LetterSpace]r7\[LetterSpace]k1 -> 0.037, phosphorylation\[LetterSpace]r8\[LetterSpace]k1 -> 500000.0, phosphorylation\[LetterSpace]r9\[LetterSpace]k1 -> 1000000.0, phosphorylation\[LetterSpace]r10\[LetterSpace]k1 -> 1.0, regulatory\[LetterSpace]r1\[LetterSpace]k1 -> 1000000.0, regulatory\[LetterSpace]r1\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r2\[LetterSpace]k1 -> 1000.0, regulatory\[LetterSpace]r2\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r3\[LetterSpace]k1 -> 100000.0, regulatory\[LetterSpace]r3\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r4\[LetterSpace]k1 -> 10000.0, regulatory\[LetterSpace]r4\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r5\[LetterSpace]k1 -> 100000.0, regulatory\[LetterSpace]r5\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r6\[LetterSpace]k1 -> 400000.0, regulatory\[LetterSpace]r6\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r7\[LetterSpace]k1 -> 400000.0, regulatory\[LetterSpace]r7\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r8\[LetterSpace]k1 -> 400000.0, regulatory\[LetterSpace]r8\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r9\[LetterSpace]k1 -> 100000.0, regulatory\[LetterSpace]r9\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r10\[LetterSpace]k1 -> 10000.0, regulatory\[LetterSpace]r10\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r11\[LetterSpace]k1 -> 400000.0, regulatory\[LetterSpace]r11\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r12\[LetterSpace]k1 -> 400000.0, regulatory\[LetterSpace]r12\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r13\[LetterSpace]k1 -> 400000.0, regulatory\[LetterSpace]r13\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r14\[LetterSpace]k1 -> 0.1, regulatory\[LetterSpace]r14\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r15\[LetterSpace]k1 -> 0.01, regulatory\[LetterSpace]r15\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r16\[LetterSpace]k1 -> 0.4, regulatory\[LetterSpace]r16\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r17\[LetterSpace]k1 -> 0.4, regulatory\[LetterSpace]r17\[LetterSpace]k2 -> 1.0, regulatory\[LetterSpace]r18\[LetterSpace]k1 -> 0.4, regulatory\[LetterSpace]r18\[LetterSpace]k2 -> 1.0, reaction\[LetterSpace]1\[LetterSpace]k1 -> 1000000.0, reaction\[LetterSpace]1\[LetterSpace]k2 -> 1.0, reaction\[LetterSpace]2\[LetterSpace]k1 -> 1000000.0, reaction\[LetterSpace]2\[LetterSpace]k2 -> 1.0, reaction\[LetterSpace]3\[LetterSpace]k1 -> 1000000.0, reaction\[LetterSpace]3\[LetterSpace]k2 -> 1.0, cell -> 1.41*^-15
};

assignments = {
ModAutophosphorylation[M_,S_,kcat_,correction_] -> correction*kcat*M*S, Autophosphorylation[kcat_,correction_,E_] -> correction*E*kcat, function\[LetterSpace]4\[LetterSpace]motor\[LetterSpace]r4[MYpYpYp_,MYpYpYpYp_,Yp_,alpha_,cell_,ka_,kappa_] -> (ka*(-4*alpha^3*kappa*MYpYpYpYp + MYpYpYp*Yp))/cell, function\[LetterSpace]4\[LetterSpace]motor\[LetterSpace]r3[MYpYp_,MYpYpYp_,Yp_,alpha_,cell_,ka_,kappa_] -> (ka*((-3*alpha^2*kappa*MYpYpYp)/2 + MYpYp*Yp))/cell, function\[LetterSpace]4\[LetterSpace]motor\[LetterSpace]r2[MYp_,MYpYp_,Yp_,alpha_,cell_,ka_,kappa_] -> (ka*((-2*alpha*kappa*MYpYp)/3 + MYp*Yp))/cell, function\[LetterSpace]4\[LetterSpace]motor\[LetterSpace]r1[M_,MYp_,Yp_,cell_,ka_,kappa_] -> (ka*(-(kappa*MYp)/4 + M*Yp))/cell, parameter\[LetterSpace]2 -> species\[LetterSpace]1/(parameter\[LetterSpace]3 + species\[LetterSpace]1), Bias -> (M[t] + MYp[t])/(M[t] + MYp[t] + MYpYp[t] + MYpYpYp[t] + MYpYpYpYp[t])
};

events = {

};

speciesAnnotations = {
M[t]->"http://identifiers.org/uniprot/P06974", T[t]->"http://identifiers.org/uniprot/P07017", W[t]->"http://identifiers.org/uniprot/P0A964", Z[t]->"http://identifiers.org/uniprot/P0A9H9", asp[t]->"http://identifiers.org/obo.chebi/CHEBI:35391", ni[t]->"http://identifiers.org/obo.chebi/CHEBI:49786", species\[LetterSpace]1[t]->"http://identifiers.org/obo.chebi/CHEBI:15422"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
A'[t] == 1.0*phosphorylation\[LetterSpace]r5 +1.0*phosphorylation\[LetterSpace]r9 -1.0*phosphorylation\[LetterSpace]r1 -1.0*phosphorylation\[LetterSpace]r2 -1.0*phosphorylation\[LetterSpace]r3 -1.0*regulatory\[LetterSpace]r4 -1.0*regulatory\[LetterSpace]r5 -1.0*regulatory\[LetterSpace]r6 -1.0*regulatory\[LetterSpace]r10 -1.0*regulatory\[LetterSpace]r11 -1.0*regulatory\[LetterSpace]r15 -1.0*regulatory\[LetterSpace]r16, Ap'[t] == 1.0*phosphorylation\[LetterSpace]r1 +1.0*phosphorylation\[LetterSpace]r2 +1.0*phosphorylation\[LetterSpace]r3 -1.0*phosphorylation\[LetterSpace]r5 -1.0*phosphorylation\[LetterSpace]r9, B'[t] == 1.0*phosphorylation\[LetterSpace]r10 -1.0*phosphorylation\[LetterSpace]r9, Bp'[t] == 1.0*phosphorylation\[LetterSpace]r9 -1.0*phosphorylation\[LetterSpace]r10, M'[t] ==  -1.0*motor\[LetterSpace]r1, MYp'[t] == 1.0*motor\[LetterSpace]r1 -1.0*motor\[LetterSpace]r2, MYpYp'[t] == 1.0*motor\[LetterSpace]r2 -1.0*motor\[LetterSpace]r3, MYpYpYp'[t] == 1.0*motor\[LetterSpace]r3 -1.0*motor\[LetterSpace]r4, MYpYpYpYp'[t] == 1.0*motor\[LetterSpace]r4 , T'[t] ==  -1.0*regulatory\[LetterSpace]r1 -1.0*regulatory\[LetterSpace]r2 -1.0*regulatory\[LetterSpace]r3 -1.0*regulatory\[LetterSpace]r4 -1.0*regulatory\[LetterSpace]r8, TA'[t] == 1.0*regulatory\[LetterSpace]r4 -1.0*regulatory\[LetterSpace]r7 -1.0*reaction\[LetterSpace]1, TW'[t] == 1.0*regulatory\[LetterSpace]r3 -1.0*regulatory\[LetterSpace]r6 -1.0*reaction\[LetterSpace]2, TWA'[t] == 1.0*regulatory\[LetterSpace]r6 +1.0*regulatory\[LetterSpace]r7 +1.0*regulatory\[LetterSpace]r8 -1.0*reaction\[LetterSpace]3, Tasp'[t] == 1.0*regulatory\[LetterSpace]r1 -1.0*regulatory\[LetterSpace]r9 -1.0*regulatory\[LetterSpace]r10 -1.0*regulatory\[LetterSpace]r13, Tasp\[LetterSpace]A'[t] == 1.0*regulatory\[LetterSpace]r10 +1.0*reaction\[LetterSpace]1 -1.0*regulatory\[LetterSpace]r12, Tasp\[LetterSpace]W'[t] == 1.0*regulatory\[LetterSpace]r9 +1.0*reaction\[LetterSpace]2 -1.0*regulatory\[LetterSpace]r11, Tasp\[LetterSpace]WA'[t] == 1.0*phosphorylation\[LetterSpace]r4 +1.0*regulatory\[LetterSpace]r11 +1.0*regulatory\[LetterSpace]r12 +1.0*regulatory\[LetterSpace]r13 +1.0*reaction\[LetterSpace]3 -1.0*phosphorylation\[LetterSpace]r4, Tni'[t] == 1.0*regulatory\[LetterSpace]r2 -1.0*regulatory\[LetterSpace]r14 -1.0*regulatory\[LetterSpace]r15 -1.0*regulatory\[LetterSpace]r18, Tni\[LetterSpace]A'[t] == 1.0*regulatory\[LetterSpace]r15 -1.0*regulatory\[LetterSpace]r17, Tni\[LetterSpace]W'[t] == 1.0*regulatory\[LetterSpace]r14 -1.0*regulatory\[LetterSpace]r16, Tni\[LetterSpace]WA'[t] == 1.0*regulatory\[LetterSpace]r16 +1.0*regulatory\[LetterSpace]r17 +1.0*regulatory\[LetterSpace]r18 , W'[t] ==  -1.0*regulatory\[LetterSpace]r3 -1.0*regulatory\[LetterSpace]r5 -1.0*regulatory\[LetterSpace]r7 -1.0*regulatory\[LetterSpace]r9 -1.0*regulatory\[LetterSpace]r12 -1.0*regulatory\[LetterSpace]r14 -1.0*regulatory\[LetterSpace]r17, WA'[t] == 1.0*regulatory\[LetterSpace]r5 -1.0*regulatory\[LetterSpace]r8 -1.0*regulatory\[LetterSpace]r13 -1.0*regulatory\[LetterSpace]r18, Y'[t] == 1.0*phosphorylation\[LetterSpace]r4 +1.0*phosphorylation\[LetterSpace]r7 +1.0*phosphorylation\[LetterSpace]r8 -1.0*phosphorylation\[LetterSpace]r5 -1.0*phosphorylation\[LetterSpace]r6, Yp'[t] == 1.0*phosphorylation\[LetterSpace]r5 +1.0*phosphorylation\[LetterSpace]r6 -1.0*phosphorylation\[LetterSpace]r4 -1.0*phosphorylation\[LetterSpace]r7 -1.0*phosphorylation\[LetterSpace]r8 -1.0*motor\[LetterSpace]r1 -1.0*motor\[LetterSpace]r2 -1.0*motor\[LetterSpace]r3 -1.0*motor\[LetterSpace]r4, Z'[t] == 1.0*phosphorylation\[LetterSpace]r8 -1.0*phosphorylation\[LetterSpace]r8
};
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]}]