(* 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 = {
IFNa\[LetterSpace]env[t], IFNa\[LetterSpace]mRNA[t], IFNb\[LetterSpace]env[t], IFNb\[LetterSpace]mRNA[t], IRF7Pn[t], IRF7m[t], SOCS1m[t], STAT[t], STATP2n[t], STATm[t], TNFam[t], TNFenv[t]
};

initialValues = {
IFNa\[LetterSpace]env[0] == 0.0, IFNa\[LetterSpace]mRNA[0] == 0.0, IFNb\[LetterSpace]env[0] == 0.0, IFNb\[LetterSpace]mRNA[0] == 0.0, IRF7Pn[0] == 0.0, IRF7m[0] == 0.0, SOCS1m[0] == 0.0, STAT[0] == 0.1, STATP2n[0] == 0.0, STATm[0] == 0.0, TNFam[0] == 0.0, TNFenv[0] == 0.0
};

rates = {
J1, J10, J11, J12, J2, J3, J4, J5, J6, J7, J8, J9
};

rateEquations = {
J1 -> IC2*(IC1*r0 + k15*IRF7Pn[t]) - (IFNb\[LetterSpace]mRNA[t]*Log[2])/tao1, J10 -> (1000000000*C*vmax19*TNFam[t])/(NA*(K19 + TNFam[t])), J11 -> -((Log[2]*STATm[t])/tao12) + IC2*(IC1*r4 + k26*STATP2n[t]), J12 -> -((Log[2]*STAT[t])/tao13) + k28*STATm[t], J2 -> (1000000000*C*vmax2*IFNb\[LetterSpace]mRNA[t])/(NA*(K2 + IFNb\[LetterSpace]mRNA[t])), J3 -> (K5*TJ*STAT[t])/(2*(K5 + STAT[t])) - (Log[2]*STATP2n[t])/tao3, J4 -> -((Log[2]*SOCS1m[t])/tao4) + IC2*(IC1*r3 + k8*STATP2n[t]), J5 -> -((IRF7m[t]*Log[2])/tao6) + IC2*(k14*IRF7Pn[t] + k11*STATP2n[t]), J6 -> IC1*k12*IRF7m[t], J7 -> IC2ifa*k16*IRF7Pn[t] - (IFNa\[LetterSpace]mRNA[t]*Log[2])/tao8, J8 -> (1000000000*C*vmax17*IFNa\[LetterSpace]mRNA[t])/(NA*(K17 + IFNa\[LetterSpace]mRNA[t])), J9 -> -((Log[2]*TNFam[t])/tao9) + IC2*(IC1*r1 + (rmax20*TNFenv[t])/(K20 + TNFenv[t]))
};

parameters = {
C -> 500000.0, K17 -> 0.002, K19 -> 0.004, K2 -> 72000.0, K20 -> 0.0006, K3 -> 0.0043, K5 -> 0.01, K9 -> 780.0, NA -> 6.023*^+23, TJtot -> 0.0001, bm -> 4.5, delta -> 0.0003, delta1 -> 0.1, delta2 -> 0.4, k11 -> 0.00036, k12 -> 3600.0, k14 -> 3.204*^-07, k15 -> 3.6*^-05, k16 -> 3600.0, k26 -> 0.360085, k28 -> 360.0, k8 -> 0.0036, n1 -> 5.0, n2 -> 5.0, n3 -> 8.0, r0 -> 0.003, r1 -> 0.00025, r3 -> 1*^-07, r4 -> 1*^-06, r5 -> 1.0, rmax20 -> 0.001, sp -> 0.1, sv -> 0.1, tao1 -> 2.5, tao12 -> 1.0, tao13 -> 15.0, tao3 -> 0.56, tao4 -> 0.46, tao6 -> 1.0, tao8 -> 2.0, tao9 -> 2.0, vmax17 -> 72000.0, vmax19 -> 154800.0, vmax2 -> 72000.0, w -> 0.0, c2 -> 1.0, compartment -> 1.0, default -> 1.0
};

assignments = {
NS -> (r5*t^n3)/(bm^n3 + t^n3), IC1 -> (1 + (NS/delta1)^n1*sp)/(1 + (NS/delta1)^n1), IC2 -> (1 + (NS/delta2)^n2*sv)/(1 + (NS/delta2)^n2), TJ -> (TJtot*(IFNa\[LetterSpace]env[t] + IFNb\[LetterSpace]env[t]))/((K3 + IFNa\[LetterSpace]env[t] + IFNb\[LetterSpace]env[t])*(1 + (K9*SOCS1m[t])/delta)), IC2ifa -> (1 + 3*(NS/delta2)^n2*sv)/(1 + (NS/delta2)^n2)
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

units = {
{"time" -> "", "metabolite" -> "<substance_units>/volume", "extent" -> "<substance_units>/volume"}
};

(* Time evolution *)
odes = {
IFNa\[LetterSpace]env'[t] == 1.0*J8 , IFNa\[LetterSpace]mRNA'[t] == 1.0*J7 , IFNb\[LetterSpace]env'[t] == 1.0*J2 , IFNb\[LetterSpace]mRNA'[t] == 1.0*J1 , IRF7Pn'[t] == 1.0*J6 , IRF7m'[t] == 1.0*J5 , SOCS1m'[t] == 1.0*J4 , STAT'[t] == 1.0*J12 , STATP2n'[t] == 1.0*J3 , STATm'[t] == 1.0*J11 , TNFam'[t] == 1.0*J9 , TNFenv'[t] == 1.0*J10 
};
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]}]