(* 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 = {
E1[t], E2[t], T1[t], T2[t], Tstar1[t], Tstar2[t], Ttot[t], VI[t], VNI[t]
};

initialValues = {
E1[0] == 0.0682, E2[0] == 0.691, T1[0] == 79.5, T2[0] == 289.0, Tstar1[0] == 58.2, Tstar2[0] == 0.0654, Ttot[0] == 426.7654, VI[0] == 150000.0, VNI[0] == 3570.0
};

rates = {
v1, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v2, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v3, v30, v31, v32, v33, v34, v35, v36, v37, v38, v4, v5, v6, v7, v8, v9
};

rateEquations = {
v1 -> d1*T1[t], v10 -> (aTS*pT*Tstar2[t]*VI[t])/(KV + VI[t]), v11 -> aAS*pT*Tstar2[t], v12 -> (KS*lambdaT)/(KS + VI[t]), v13 -> gammaT*T1[t], v14 -> d2*T2[t], v15 -> k2*T2[t]*VI[t], v16 -> f*k2*zeta1*T2[t]*VI[t], v17 -> (aT*T2[t]*VI[t])/(KV + VI[t]), v18 -> aA*T2[t], v19 -> d2*Tstar2[t], v2 -> k1*T1[t]*VI[t], v20 -> (aTS*Tstar2[t]*VI[t])/(KV + VI[t]), v21 -> aAS*Tstar2[t], v22 -> 1000*delta*NT*Tstar1[t], v23 -> 1000*delta*NT*zeta2*Tstar1[t], v24 -> c*VI[t], v25 -> 1000*k1*rho1*T1[t]*VI[t], v26 -> 1000*k1*rho1*zeta1*T1[t]*VI[t], v27 -> 1000*k2*rho2*T2[t]*VI[t], v28 -> 1000*f*k2*rho2*zeta1*T2[t]*VI[t], v29 -> c*VNI[t], v3 -> k1*zeta1*T1[t]*VI[t], v30 -> lambdaE, v31 -> (bE1*E1[t]*Tstar1[t])/(Kb1 + Tstar1[t]), v32 -> (dE*E1[t]*Tstar1[t])/(Kd + Tstar1[t]), v33 -> deltaE1*E1[t], v34 -> (gammaE*E1[t]*(T1[t] + Tstar1[t]))/(Kgamma + T1[t] + Tstar1[t]), v35 -> (aE*pE*E2[t]*VI[t])/(KV + VI[t]), v36 -> (bE2*Kb2*E2[t])/(Kb2 + E2[t]), v37 -> deltaE2*E2[t], v38 -> (aE*E2[t]*VI[t])/(KV + VI[t]), v4 -> gammaT*T1[t], v5 -> (aT*pT*T2[t]*VI[t])/(KV + VI[t]), v6 -> aA*pT*T2[t], v7 -> delta*Tstar1[t], v8 -> m*E1[t]*Tstar1[t], v9 -> gammaTS*Tstar1[t]
};

parameters = {
KS -> 27900.0, KV -> 1060.0, Kb1 -> 0.0249, Kb2 -> 87.0, Kd -> 0.12, Kgamma -> 1.36, NT -> 11.7, aA -> 0.00407, aAS -> 9.58*^-05, aE -> 0.0168, aT -> 0.00985, aTS -> 0.000449, bE1 -> 0.0693, bE2 -> 0.0061, c -> 12.7, d1 -> 0.0912, d2 -> 0.0031, dE -> 0.0472, delta -> 0.171, deltaE1 -> 0.0597, deltaE2 -> 0.00145, f -> 0.507, gammaE -> 0.000689, gammaT -> 0.000646, gammaTS -> 7.98*^-06, k1 -> 7.97*^-06, k2 -> 1.05*^-08, lambdaE -> 0.000488, lambdaT -> 8.66, m -> 1.1, pE -> 0.395, pT -> 9.85, rho1 -> 1.0, rho2 -> 1.0, zeta1 -> 0.524, zeta2 -> 0.16, default -> 1.0
};

assignments = {
viruscopiesperml -> VI[t] + VNI[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
E1'[t] == 1.0*v31 +1.0*v30 +1.0*v35 -1.0*v33 -1.0*v32 -1.0*v34, E2'[t] == 1.0*v34 +1.0*v36 -1.0*v37 -1.0*v38, T1'[t] == 1.0*v6 +1.0*v5 +1.0*v3 -1.0*v1 -1.0*v2 -1.0*v4, T2'[t] == 1.0*v13 +1.0*v12 +1.0*v16 -1.0*v15 -1.0*v18 -1.0*v17 -1.0*v14, Tstar1'[t] == 1.0*v10 +1.0*v2 +1.0*v11 -1.0*v9 -1.0*v8 -1.0*v3 -1.0*v7, Tstar2'[t] == 1.0*v15 +1.0*v9 -1.0*v21 -1.0*v19 -1.0*v16 -1.0*v20, Ttot'[t] == 1.0*v13 +1.0*v12 +1.0*v6 +1.0*v10 +1.0*v11 +1.0*v5 -1.0*v18 -1.0*v1 -1.0*v21 -1.0*v17 -1.0*v19 -1.0*v8 -1.0*v14 -1.0*v4 -1.0*v20 -1.0*v7, VI'[t] == 1.0*v22 +1.0*v28 +1.0*v26 -1.0*v25 -1.0*v24 -1.0*v27 -1.0*v23, VNI'[t] == 1.0*v23 -1.0*v29
};
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]}]