(* 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 = {
CD[t], CE[t], EF[t], MC[t], RB[t], RE[t], RP[t]
};

initialValues = {
CD[0] == 0.0, CE[0] == 0.0, EF[0] == 0.0, MC[0] == 0.0, RB[0] == 0.0, RE[0] == 0.55, RP[0] == 0.0
};

rates = {
r1, r10, r11, r12, r13, r14, r15, r16, r17, r2, r3, r4, r5, r6, r7, r8, r9
};

rateEquations = {
r1 -> (cell*r1\[LetterSpace]kM*S)/(r1\[LetterSpace]KS + S), r10 -> (cell*r10\[LetterSpace]kkRBUP*RP[t])/(r10\[LetterSpace]Kp + RP[t]), r11 -> cell*r11\[LetterSpace]dMC*MC[t], r12 -> cell*r12\[LetterSpace]dEF*EF[t], r13 -> cell*r13\[LetterSpace]dCE*CE[t], r14 -> cell*r14\[LetterSpace]dCD*CD[t], r15 -> cell*r15\[LetterSpace]dRB*RB[t], r16 -> cell*r16\[LetterSpace]dRP*RP[t], r17 -> cell*r17\[LetterSpace]dRE*RE[t], r2 -> (cell*r2\[LetterSpace]kkCDS*S)/(r2\[LetterSpace]KS + S), r3 -> cell*((r3\[LetterSpace]kkb*MC[t])/(r3\[LetterSpace]KMC + MC[t]) + (r3\[LetterSpace]kkEF*EF[t]*MC[t])/((r3\[LetterSpace]KEF + EF[t])*(r3\[LetterSpace]KMC + MC[t]))), r4 -> (cell*r4\[LetterSpace]kkCE*EF[t])/(r4\[LetterSpace]KEF + EF[t]), r5 -> (cell*r5\[LetterSpace]kkCD*MC[t])/(r5\[LetterSpace]KMC + MC[t]), r6 -> cell*r6\[LetterSpace]kkRB, r7 -> cell*((r7\[LetterSpace]kkRBPP*CD[t]*RE[t])/(r7\[LetterSpace]KD + RE[t]) + (r7\[LetterSpace]kkRBPP*CE[t]*RE[t])/(r7\[LetterSpace]KE + RE[t])), r8 -> cell*r8\[LetterSpace]kkRE*EF[t]*RB[t], r9 -> cell*((r9\[LetterSpace]kkRBP*CD[t]*RB[t])/(r9\[LetterSpace]KD + RB[t]) + (r9\[LetterSpace]kkRBP2*CE[t]*RB[t])/(r9\[LetterSpace]KE + RB[t]))
};

parameters = {
S -> 1.0, r1\[LetterSpace]KS -> 0.5, r1\[LetterSpace]kM -> 1.0, r2\[LetterSpace]KS -> 0.5, r2\[LetterSpace]kkCDS -> 0.45, r3\[LetterSpace]KEF -> 0.15, r3\[LetterSpace]KMC -> 0.15, r3\[LetterSpace]kkEF -> 0.4, r3\[LetterSpace]kkb -> 0.003, r4\[LetterSpace]KEF -> 0.15, r4\[LetterSpace]kkCE -> 0.35, r5\[LetterSpace]KMC -> 0.15, r5\[LetterSpace]kkCD -> 0.03, r6\[LetterSpace]kkRB -> 0.18, r7\[LetterSpace]KD -> 0.92, r7\[LetterSpace]KE -> 0.92, r7\[LetterSpace]kkRBPP -> 18.0, r8\[LetterSpace]kkRE -> 180.0, r9\[LetterSpace]KD -> 0.92, r9\[LetterSpace]KE -> 0.92, r9\[LetterSpace]kkRBP -> 18.0, r9\[LetterSpace]kkRBP2 -> 18.0, r10\[LetterSpace]Kp -> 0.01, r10\[LetterSpace]kkRBUP -> 3.6, r11\[LetterSpace]dMC -> 0.7, r12\[LetterSpace]dEF -> 0.25, r13\[LetterSpace]dCE -> 1.5, r14\[LetterSpace]dCD -> 1.5, r15\[LetterSpace]dRB -> 0.06, r16\[LetterSpace]dRP -> 0.06, r17\[LetterSpace]dRE -> 0.03, cell -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
CD'[t] == 1.0*r2 +1.0*r5 -1.0*r14, CE'[t] == 1.0*r4 -1.0*r13, EF'[t] == 1.0*r3 +1.0*r7 -1.0*r8 -1.0*r12, MC'[t] == 1.0*r1 -1.0*r11, RB'[t] == 1.0*r6 +1.0*r10 -1.0*r8 -1.0*r9 -1.0*r15, RE'[t] == 1.0*r8 -1.0*r7 -1.0*r17, RP'[t] == 1.0*r7 +1.0*r9 -1.0*r10 -1.0*r16
};
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]}]