(* 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 = {
x1[t], x2[t], z[t]
};

initialValues = {
x1[0] == 5.08098, x2[0] == 1397.73, z[0] == 90.0
};

rates = {
R1, R2, R3, R4, R5, R6
};

rateEquations = {
R1 -> Ratex1appearance + alpha1*(1 - Fig7AR1alphaOnOff + Fig7AR1alphaOnOff*x1[t]^g11*x2[t]^g21), R2 -> beta1*x1[t], R3 -> alpha2*x1[t]^g12*x2[t]^g22, R4 -> beta2*x2[t], R5 -> k1*y1, R6 -> k2*y2
};

parameters = {
Fig7AR1alphaOnOff -> 1.0, Ratex1appearanceOnOff -> 0.0, Ratex1appearanceOnOffPiecewise -> 0.0, Ratex1appearanceduration -> 1.0, Ratex1appearancemagnitude -> 7.0, Ratex1appearancetimefirst -> 10.0, Ratex1appearancetimesecond -> 150.0, alpha1 -> 7.0, alpha2 -> 7.0, beta1basalvalue -> 0.2, beta1increaseOnOff -> 1.0, beta1increaseOntime -> 500.0, beta1increasevalue -> 0.0, beta1increasevalue2 -> 0.03, beta2 -> 0.02, flagformation -> 1.0, flagresorption -> 1.0, g11 -> 1.09, g12 -> 1.0, g21 -> -0.5, g22 -> 0.09, initialvaluex1 -> 5.08098, initialvaluex2 -> 1397.73, initialvaluez -> 90.0, k1 -> 0.26, k2 -> 0.0008, plotzyaxisdenominator -> 113.749, default -> 1.0
};

assignments = {
y1 -> flagresorption*(-x1bar + x1[t]), x2bar -> (beta1/alpha1)^(g12/gamma)*(beta2/alpha2)^((1 - g11)/gamma), x1variable -> x1[t], Ratex1appearance -> Ratex1appearancemagnitude*Ratex1appearanceOnOff*Ratex1appearanceOnOffPiecewise, y2 -> flagformation*(-x2bar + x2[t]), x2variable -> x2[t], gamma -> g12*g21 - (1 - g11)*(1 - g22), beta1 -> beta1basalvalue + beta1increaseOnOff*beta1increasevalue, plotzyaxis -> (100*z[t])/plotzyaxisdenominator, x1bar -> (beta1/alpha1)^((1 - g22)/gamma)*(beta2/alpha2)^(g21/gamma), plotx2yaxis -> -initialvaluex2 + y2 + x2[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {
R5->"http://identifiers.org/go/GO:0045453"
};

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

(* Time evolution *)
odes = {
x1'[t] == 1.0*R1 -1.0*R2, x2'[t] == 1.0*R3 -1.0*R4, z'[t] == 1.0*R6 -1.0*R5
};
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]}]