(* 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 = {
CP[t], CP2[t], M[t], TF[t]
};

initialValues = {
CP[0] == 0.039, CP2[0] == 0.088, M[0] == 1.35, TF[0] == 0.06
};

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

rateEquations = {
r1 -> function\[LetterSpace]4\[LetterSpace]r1*system, r10 -> IC*kicd*system, r11 -> kcp2d*system*CP2[t], r12 -> kica*system*CP2[t]*TF[t], r13 -> function\[LetterSpace]4\[LetterSpace]r13*system, r14 -> chk2*system*CP2[t], r15 -> IC*kcp2d*system, r16 -> chk2c*IC*system, r17 -> function\[LetterSpace]4\[LetterSpace]r17*system, r2 -> function\[LetterSpace]4\[LetterSpace]r2*system, r3 -> kmd*system*M[t], r4 -> function\[LetterSpace]1*system, r5 -> kcpd*system*CP[t], r6 -> ka*system*CP[t]^2, r7 -> kd*system*CP2[t], r8 -> function\[LetterSpace]4\[LetterSpace]r8*system, r9 -> chk2*system*CP[t]
};

parameters = {
Dex -> 0.0, ICtot -> 1.0, IR\[LetterSpace]pulse\[LetterSpace]duration -> 2.0, J -> 0.3, Jp -> 0.05, TFtot -> 0.5, chk2ToggleOnOff -> 1.0, chk2\[LetterSpace]value -> 0.25, chk2c\[LetterSpace]value -> 0.1, chk2pulseactive -> 1.0, chk2pulseactive\[LetterSpace]elim -> 1.0, chk2pulseactive\[LetterSpace]elim\[LetterSpace]elim -> 0.0, initialValue\[LetterSpace]CP -> 0.039, initialValue\[LetterSpace]CP2 -> 0.088, initialValue\[LetterSpace]M -> 1.35, initialValue\[LetterSpace]TF -> 0.06, ka -> 100.0, kcp2d -> 0.0525, kcpd -> 0.525, kcps -> 0.5, kd -> 0.01, kica -> 20.0, kicd -> 0.01, kmd -> 0.1, kms -> 1.0, kp1 -> 10.0, kp2 -> 0.1, n -> 2.0, trigONtime -> 4.0, system -> 1.0
};

assignments = {
IC -> TFtot - TF[t], function\[LetterSpace]1 -> kcps*M[t], function\[LetterSpace]4\[LetterSpace]r17 -> (IC*kp2)/(system*(2*IC + Jp + CP[t] + 2*CP2[t])), function\[LetterSpace]4\[LetterSpace]r2 -> (kms*TF[t]^n)/(system*(J^n + TF[t]^n)), chk2pulseonoff -> chk2pulseactive - chk2pulseactive\[LetterSpace]elim - chk2pulseactive\[LetterSpace]elim\[LetterSpace]elim, function\[LetterSpace]4\[LetterSpace]r8 -> (kp1*CP[t])/(system*(2*IC + Jp + CP[t] + 2*CP2[t])), function\[LetterSpace]4\[LetterSpace]r13 -> (kp2*CP2[t])/(system*(2*IC + Jp + CP[t] + 2*CP2[t])), function\[LetterSpace]4\[LetterSpace]r1 -> Dex/system, CPtot -> 2*IC + CP[t] + 2*CP2[t], trigOFFtime -> IR\[LetterSpace]pulse\[LetterSpace]duration + trigONtime, chk2c -> (chk2c\[LetterSpace]value*chk2pulseonoff*chk2ToggleOnOff)/IR\[LetterSpace]pulse\[LetterSpace]duration, chk2 -> (chk2pulseonoff*chk2ToggleOnOff*chk2\[LetterSpace]value)/IR\[LetterSpace]pulse\[LetterSpace]duration
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
CP'[t] == 1.0*r4 +2.0*r7 -1.0*r5 -2.0*r6 -1.0*r8 -1.0*r9, CP2'[t] == 1.0*r10 +1.0*r6 -1.0*r11 -1.0*r12 -1.0*r13 -1.0*r14 -1.0*r7, M'[t] == 1.0*r1 +1.0*r2 -1.0*r3, TF'[t] == 1.0*r10 +1.0*r15 +1.0*r16 +1.0*r17 -1.0*r12
};
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]}]