(* 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], C[t], I[t], R[t], X[t]
};

initialValues = {
A[0] == 0.0, C[0] == 0.0, I[0] == 1.0, R[0] == 1.0, X[0] == 0.0
};

rates = {
A\[LetterSpace]degradation, C\[LetterSpace]I\[LetterSpace]binding, C\[LetterSpace]degradation, I\[LetterSpace]activation, I\[LetterSpace]degradation, I\[LetterSpace]expression, R\[LetterSpace]L\[LetterSpace]binding, R\[LetterSpace]degradation, R\[LetterSpace]expression, X\[LetterSpace]degradation
};

rateEquations = {
A\[LetterSpace]degradation -> cell*kdegA*A[t], C\[LetterSpace]I\[LetterSpace]binding -> cell*(k1*C[t]*I[t] - k2*X[t]), C\[LetterSpace]degradation -> cell*kdegC*C[t], I\[LetterSpace]activation -> cell*k3*X[t], I\[LetterSpace]degradation -> cell*kdegI*I[t], I\[LetterSpace]expression -> cell*(BI + (TFs*A[t])/(KD + A[t])), R\[LetterSpace]L\[LetterSpace]binding -> cell*(-(koff*C[t]) + kon*L*R[t]), R\[LetterSpace]degradation -> cell*kdegR*R[t], R\[LetterSpace]expression -> cell*(BR + (Rs*A[t])/(KD + A[t])), X\[LetterSpace]degradation -> cell*kdegX*X[t]
};

parameters = {
BI -> 0.005, BR -> 0.005, KD -> 200.0, Rs -> 3.0, TFs -> 3.0, k1 -> 1.0, k2 -> 5.0, k3 -> 45.0, kdegA -> 0.005, kdegC -> 0.01, kdegI -> 0.005, kdegR -> 0.005, kdegX -> 0.005, koff -> 0.05, kon -> 0.001, L -> 0.1, cell -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
A'[t] == 1.0*I\[LetterSpace]activation -1.0*A\[LetterSpace]degradation, C'[t] == 1.0*R\[LetterSpace]L\[LetterSpace]binding +1.0*I\[LetterSpace]activation -1.0*C\[LetterSpace]degradation -1.0*C\[LetterSpace]I\[LetterSpace]binding, I'[t] == 1.0*I\[LetterSpace]expression -1.0*C\[LetterSpace]I\[LetterSpace]binding -1.0*I\[LetterSpace]degradation, R'[t] == 1.0*R\[LetterSpace]expression -1.0*R\[LetterSpace]degradation -1.0*R\[LetterSpace]L\[LetterSpace]binding, X'[t] == 1.0*C\[LetterSpace]I\[LetterSpace]binding -1.0*I\[LetterSpace]activation -1.0*X\[LetterSpace]degradation
};
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]}]