(* 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 = {
D\[LetterSpace]1[t], E\[LetterSpace]1[t], RS\[LetterSpace]1[t], R\[LetterSpace]1[t], X\[LetterSpace]1[t], theta\[LetterSpace]1[t]
};

initialValues = {
D\[LetterSpace]1[0] == 0.0, E\[LetterSpace]1[0] == 0.0, RS\[LetterSpace]1[0] == 0.0, R\[LetterSpace]1[0] == 0.0, X\[LetterSpace]1[0] == 0.0, theta\[LetterSpace]1[0] == 0.0
};

rates = {
E2Fdegradationviacellcycleprogression\[LetterSpace]1, \[LetterSpace]1, \[LetterSpace]2, cellcycleprogression\[LetterSpace]1, cellcycleprogressionslow\[LetterSpace]1, cyclinD\[LetterSpace]1, cyclinEdegradation\[LetterSpace]1, cyclinEsynthesis\[LetterSpace]1, null2\[LetterSpace]1, null3\[LetterSpace]1, pRBdeplation\[LetterSpace]1, pRBsynthesis\[LetterSpace]1
};

rateEquations = {
E2Fdegradationviacellcycleprogression\[LetterSpace]1 -> (cell*dtheta\[LetterSpace]1*theta\[LetterSpace]1[t]*X\[LetterSpace]1[t])/(qtheta\[LetterSpace]1 + X\[LetterSpace]1[t]), \[LetterSpace]1 -> (aD\[LetterSpace]1*cell*GF\[LetterSpace]1)/(GF\[LetterSpace]1 + k1\[LetterSpace]1^(-1)), \[LetterSpace]2 -> (cell*pD\[LetterSpace]1*D\[LetterSpace]1[t]*RS\[LetterSpace]1[t])/(qD\[LetterSpace]1 + D\[LetterSpace]1[t] + RS\[LetterSpace]1[t]), cellcycleprogression\[LetterSpace]1 -> cell*(aX\[LetterSpace]1*E\[LetterSpace]1[t] + f\[LetterSpace]1*theta\[LetterSpace]1[t] + g\[LetterSpace]1*E\[LetterSpace]1[t]*X\[LetterSpace]1[t]^2), cellcycleprogressionslow\[LetterSpace]1 -> cell*dX\[LetterSpace]1*X\[LetterSpace]1[t], cyclinD\[LetterSpace]1 -> cell*dD\[LetterSpace]1*D\[LetterSpace]1[t]*E\[LetterSpace]1[t], cyclinEdegradation\[LetterSpace]1 -> cell*dE\[LetterSpace]1*E\[LetterSpace]1[t]*X\[LetterSpace]1[t], cyclinEsynthesis\[LetterSpace]1 -> aE\[LetterSpace]1*cell*(GF\[LetterSpace]1/(GF\[LetterSpace]1 + k2\[LetterSpace]1^(-1)) + aF\[LetterSpace]1*theta\[LetterSpace]1[t]), null2\[LetterSpace]1 -> (cell*pE\[LetterSpace]1*E\[LetterSpace]1[t]*RS\[LetterSpace]1[t])/(qE\[LetterSpace]1 + E\[LetterSpace]1[t] + RS\[LetterSpace]1[t]), null3\[LetterSpace]1 -> atheta\[LetterSpace]1*cell*(GF\[LetterSpace]1/(GF\[LetterSpace]1 + k3\[LetterSpace]1^(-1)) + fC\[LetterSpace]1\[LetterSpace]1*theta\[LetterSpace]1[t]), pRBdeplation\[LetterSpace]1 -> cell*Mass\[LetterSpace]Action\[LetterSpace]2\[LetterSpace]1[pS\[LetterSpace]1, R\[LetterSpace]1[t], theta\[LetterSpace]1[t]], pRBsynthesis\[LetterSpace]1 -> (cell*pX\[LetterSpace]1*(RT\[LetterSpace]1 - RS\[LetterSpace]1[t] - R\[LetterSpace]1[t])*X\[LetterSpace]1[t])/(qX\[LetterSpace]1 + RT\[LetterSpace]1 - RS\[LetterSpace]1[t] - R\[LetterSpace]1[t] + X\[LetterSpace]1[t])
};

parameters = {
GF\[LetterSpace]1 -> 6.3, RT\[LetterSpace]1 -> 2.5, aD\[LetterSpace]1 -> 0.4, aE\[LetterSpace]1 -> 0.16, aF\[LetterSpace]1 -> 0.9, aX\[LetterSpace]1 -> 0.08, atheta\[LetterSpace]1 -> 0.05, dD\[LetterSpace]1 -> 0.4, dE\[LetterSpace]1 -> 0.2, dX\[LetterSpace]1 -> 1.04, dtheta\[LetterSpace]1 -> 0.12, fC\[LetterSpace]1\[LetterSpace]1 -> 0.003, f\[LetterSpace]1 -> 0.35, g\[LetterSpace]1 -> 0.528, k1\[LetterSpace]1 -> 0.05, k2\[LetterSpace]1 -> 1000.0, k3\[LetterSpace]1 -> 1.5, pD\[LetterSpace]1 -> 0.48, pE\[LetterSpace]1 -> 0.096, pS\[LetterSpace]1 -> 0.6, pX\[LetterSpace]1 -> 0.48, qD\[LetterSpace]1 -> 0.6, qE\[LetterSpace]1 -> 0.6, qX\[LetterSpace]1 -> 0.8, qtheta\[LetterSpace]1 -> 0.3, cell -> 1.0
};

assignments = {
Mass\[LetterSpace]Action\[LetterSpace]2\[LetterSpace]1[k1_,S1_,S2_] -> k1*S1*S2, Rb\[LetterSpace]phos -> RT\[LetterSpace]1 - RS\[LetterSpace]1[t] - R\[LetterSpace]1[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
D\[LetterSpace]1'[t] == 1.0*\[LetterSpace]1 -1.0*cyclinD\[LetterSpace]1, E\[LetterSpace]1'[t] == 1.0*cyclinEsynthesis\[LetterSpace]1 -1.0*cyclinEdegradation\[LetterSpace]1, RS\[LetterSpace]1'[t] == 1.0*pRBdeplation\[LetterSpace]1 -1.0*\[LetterSpace]2 -1.0*null2\[LetterSpace]1, R\[LetterSpace]1'[t] == 1.0*pRBsynthesis\[LetterSpace]1 -1.0*pRBdeplation\[LetterSpace]1, X\[LetterSpace]1'[t] == 1.0*cellcycleprogression\[LetterSpace]1 -1.0*cellcycleprogressionslow\[LetterSpace]1, theta\[LetterSpace]1'[t] == 1.0*\[LetterSpace]2 +1.0*null2\[LetterSpace]1 +1.0*null3\[LetterSpace]1 -1.0*pRBdeplation\[LetterSpace]1 -1.0*E2Fdegradationviacellcycleprogression\[LetterSpace]1
};
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]}]