(* 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], AB[t], AgB[t], B[t], gB[t], rB[t]
};

initialValues = {
A[0] == 40.0, AB[0] == 0.0, AgB[0] == 0.0, B[0] == 0.0, gB[0] == 1.0, rB[0] == 0.0
};

rates = {
A\[LetterSpace]binds\[LetterSpace]gB, basal\[LetterSpace]transcription\[LetterSpace]B, degradation\[LetterSpace]A, degradation\[LetterSpace]B, degradation\[LetterSpace]dimer, degradation\[LetterSpace]mRNA\[LetterSpace]B, formation\[LetterSpace]dimer, gB\[LetterSpace]releases\[LetterSpace]A, production\[LetterSpace]A, stim\[LetterSpace]transcription\[LetterSpace]B, translation\[LetterSpace]B
};

rateEquations = {
A\[LetterSpace]binds\[LetterSpace]gB -> alpha*cell*A[t]*gB[t], basal\[LetterSpace]transcription\[LetterSpace]B -> cell*transcription\[LetterSpace]and\[LetterSpace]translation[rhof, gB[t]], degradation\[LetterSpace]A -> cell*deltaA*A[t], degradation\[LetterSpace]B -> cell*deltaB*B[t], degradation\[LetterSpace]dimer -> cell*deltaAB*AB[t], degradation\[LetterSpace]mRNA\[LetterSpace]B -> cell*deltar*rB[t], formation\[LetterSpace]dimer -> cell*gamma*A[t]*B[t], gB\[LetterSpace]releases\[LetterSpace]A -> cell*theta*AgB[t], production\[LetterSpace]A -> cell*Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[rhoA], stim\[LetterSpace]transcription\[LetterSpace]B -> cell*transcription\[LetterSpace]and\[LetterSpace]translation[rhob, AgB[t]], translation\[LetterSpace]B -> cell*transcription\[LetterSpace]and\[LetterSpace]translation[beta, rB[t]]
};

parameters = {
alpha -> 0.001, beta -> 3.0, deltaA -> 0.01, deltaAB -> 0.01, deltaB -> 0.01, deltar -> 0.03, gamma -> 1.0, rhoA -> 100.0, rhob -> 5.0, rhof -> 0.1, theta -> 0.04, cell -> 1.0
};

assignments = {
transcription\[LetterSpace]and\[LetterSpace]translation[k_,X_] -> k*X, Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[v_] -> v
};

events = {

};

speciesAnnotations = {
A[t]->"http://identifiers.org/chebi/CHEBI:36080", AB[t]->"http://identifiers.org/go/GO:0043234", AgB[t]->"http://identifiers.org/so/SO:0000704", B[t]->"http://identifiers.org/chebi/CHEBI:36080", gB[t]->"http://identifiers.org/so/SO:0000704", rB[t]->"http://identifiers.org/chebi/CHEBI:33699"
};

reactionAnnotations = {

};

units = {
{"time" -> "time", "metabolite" -> "mole/litre", "extent" -> "substance"}
};

(* Time evolution *)
odes = {
A'[t] == 1.0*gB\[LetterSpace]releases\[LetterSpace]A +1.0*production\[LetterSpace]A -1.0*A\[LetterSpace]binds\[LetterSpace]gB -1.0*degradation\[LetterSpace]A -1.0*formation\[LetterSpace]dimer, AB'[t] == 1.0*formation\[LetterSpace]dimer -1.0*degradation\[LetterSpace]dimer, AgB'[t] == 1.0*A\[LetterSpace]binds\[LetterSpace]gB -1.0*gB\[LetterSpace]releases\[LetterSpace]A, B'[t] == 1.0*translation\[LetterSpace]B -1.0*degradation\[LetterSpace]B -1.0*formation\[LetterSpace]dimer, gB'[t] == 1.0*gB\[LetterSpace]releases\[LetterSpace]A -1.0*A\[LetterSpace]binds\[LetterSpace]gB, rB'[t] == 1.0*basal\[LetterSpace]transcription\[LetterSpace]B +1.0*stim\[LetterSpace]transcription\[LetterSpace]B -1.0*degradation\[LetterSpace]mRNA\[LetterSpace]B
};
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]}]