(* 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 = {
X[t], Y[t], Z[t]
};

initialValues = {
X[0] == 15.0, Y[0] == 0.0, Z[0] == 0.25
};

rates = {
Calcium\[LetterSpace]Influx, Calcium\[LetterSpace]Influx\[LetterSpace]stimulation, Calcium\[LetterSpace]into\[LetterSpace]cytoplasm, Calcium\[LetterSpace]into\[LetterSpace]store, Leakage, Leakage\[LetterSpace]from\[LetterSpace]cytoplasm, TF\[LetterSpace]degradation, TF\[LetterSpace]synthesis, TF\[LetterSpace]synthesis\[LetterSpace]basal
};

rateEquations = {
Calcium\[LetterSpace]Influx -> Calcium\[LetterSpace]Influx\[LetterSpace]v0, Calcium\[LetterSpace]Influx\[LetterSpace]stimulation -> Calcium\[LetterSpace]Influx\[LetterSpace]stimulation\[LetterSpace]beta*Calcium\[LetterSpace]Influx\[LetterSpace]stimulation\[LetterSpace]v1, Calcium\[LetterSpace]into\[LetterSpace]cytoplasm -> (Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]Vm3*Y[t]^Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]m*Z[t]^Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]p)/((Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]Kr^Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]m + Y[t]^Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]m)*(Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]K\[LetterSpace]A^Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]p + Z[t]^Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]p)), Calcium\[LetterSpace]into\[LetterSpace]store -> (Calcium\[LetterSpace]into\[LetterSpace]store\[LetterSpace]Vm2*Z[t]^Calcium\[LetterSpace]into\[LetterSpace]store\[LetterSpace]n)/(Calcium\[LetterSpace]into\[LetterSpace]store\[LetterSpace]K2^Calcium\[LetterSpace]into\[LetterSpace]store\[LetterSpace]n + Z[t]^Calcium\[LetterSpace]into\[LetterSpace]store\[LetterSpace]n), Leakage -> Leakage\[LetterSpace]k1*Y[t], Leakage\[LetterSpace]from\[LetterSpace]cytoplasm -> Leakage\[LetterSpace]from\[LetterSpace]cytoplasm\[LetterSpace]k*Z[t], TF\[LetterSpace]degradation -> TF\[LetterSpace]degradation\[LetterSpace]kd*X[t], TF\[LetterSpace]synthesis -> (kf*X[t]^2)/(Kd + X[t]^2), TF\[LetterSpace]synthesis\[LetterSpace]basal -> TF\[LetterSpace]synthesis\[LetterSpace]basal\[LetterSpace]Rbas
};

parameters = {
Ka -> 0.5, Kb -> 0.5, Kd0 -> 10.0, gamma -> 9.0, kf0 -> 6.0, TF\[LetterSpace]degradation\[LetterSpace]kd -> 1.0, TF\[LetterSpace]synthesis\[LetterSpace]basal\[LetterSpace]Rbas -> 0.1, Calcium\[LetterSpace]Influx\[LetterSpace]v0 -> 1.0, Calcium\[LetterSpace]Influx\[LetterSpace]stimulation\[LetterSpace]v1 -> 5.7, Calcium\[LetterSpace]Influx\[LetterSpace]stimulation\[LetterSpace]beta -> 0.3, Calcium\[LetterSpace]into\[LetterSpace]store\[LetterSpace]Vm2 -> 30.0, Calcium\[LetterSpace]into\[LetterSpace]store\[LetterSpace]K2 -> 0.5, Calcium\[LetterSpace]into\[LetterSpace]store\[LetterSpace]n -> 2.0, Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]Vm3 -> 325.0, Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]Kr -> 1.7, Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]K\[LetterSpace]A -> 0.46, Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]m -> 2.0, Calcium\[LetterSpace]into\[LetterSpace]cytoplasm\[LetterSpace]p -> 4.0, Leakage\[LetterSpace]k1 -> 0.7, Leakage\[LetterSpace]from\[LetterSpace]cytoplasm\[LetterSpace]k -> 10.0, cytoplasm -> 1.0, store -> 1.0
};

assignments = {
Kd -> Kd0/(1 + Z[t]^4/Kb^4), kf -> kf0*(1 + (gamma*Z[t]^4)/(Ka^4 + Z[t]^4))
};

events = {

};

speciesAnnotations = {
Y[t]->"http://identifiers.org/chebi/CHEBI:22984", Y[t]->"http://identifiers.org/kegg.compound/C00076", Z[t]->"http://identifiers.org/chebi/CHEBI:22984", Z[t]->"http://identifiers.org/kegg.compound/C00076"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
X'[t] == 1.0*TF\[LetterSpace]synthesis +1.0*TF\[LetterSpace]synthesis\[LetterSpace]basal -1.0*TF\[LetterSpace]degradation, Y'[t] == 1.0*Calcium\[LetterSpace]into\[LetterSpace]store -1.0*Calcium\[LetterSpace]into\[LetterSpace]cytoplasm -1.0*Leakage, Z'[t] == 1.0*Calcium\[LetterSpace]Influx +1.0*Calcium\[LetterSpace]Influx\[LetterSpace]stimulation +1.0*Calcium\[LetterSpace]into\[LetterSpace]cytoplasm +1.0*Leakage -1.0*Calcium\[LetterSpace]into\[LetterSpace]store -1.0*Leakage\[LetterSpace]from\[LetterSpace]cytoplasm
};
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]}]