(* 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 = {
CA[t], CD[t], CDc20[t], CDc20T[t], CDh1[t], CE[t], CYCA[t], CYCB[t], CYCD[t], CYCE[t], DRG[t], E2F[t], ERG[t], GM[t], IEP[t], MASS[t], P27[t], PPX[t]
};

initialValues = {
CA[0] == 0.0434486, CD[0] == 0.0488772, CDc20[0] == 1*^-07, CDc20T[0] == 0.006466, CDh1[0] == 0.98702, CE[0] == 0.1380924, CYCA[0] == 0.3411, CYCB[0] == 0.00514, CYCD[0] == 0.401389, CYCE[0] == 1.09959, DRG[0] == 0.9005328, E2F[0] == 4.25991, ERG[0] == 0.0121808, GM[0] == 1.032033, IEP[0] == 1.98*^-05, MASS[0] == 1.28486, P27[0] == 0.011877, PPX[0] == 1.0
};

rates = {
v\[LetterSpace]1, v\[LetterSpace]10, v\[LetterSpace]11, v\[LetterSpace]12, v\[LetterSpace]13, v\[LetterSpace]14, v\[LetterSpace]15, v\[LetterSpace]16, v\[LetterSpace]17, v\[LetterSpace]18, v\[LetterSpace]19, v\[LetterSpace]2, v\[LetterSpace]20, v\[LetterSpace]21, v\[LetterSpace]22, v\[LetterSpace]23, v\[LetterSpace]24, v\[LetterSpace]25, v\[LetterSpace]26, v\[LetterSpace]27, v\[LetterSpace]28, v\[LetterSpace]29, v\[LetterSpace]3, v\[LetterSpace]30, v\[LetterSpace]31, v\[LetterSpace]32, v\[LetterSpace]33, v\[LetterSpace]34, v\[LetterSpace]35, v\[LetterSpace]36, v\[LetterSpace]37, v\[LetterSpace]38, v\[LetterSpace]39, v\[LetterSpace]4, v\[LetterSpace]40, v\[LetterSpace]41, v\[LetterSpace]42, v\[LetterSpace]5, v\[LetterSpace]6, v\[LetterSpace]7, v\[LetterSpace]8, v\[LetterSpace]9
};

rateEquations = {
v\[LetterSpace]1 -> k16*ERG[t], v\[LetterSpace]10 -> K30*CA[t]*CDc20[t], v\[LetterSpace]11 -> K25R*CE[t], v\[LetterSpace]12 -> K25R*CA[t], v\[LetterSpace]13 -> v\[LetterSpace]8*CE[t], v\[LetterSpace]14 -> v\[LetterSpace]8*CYCE[t], v\[LetterSpace]15 -> v\[LetterSpace]6*P27[t], v\[LetterSpace]16 -> v\[LetterSpace]6*CE[t], v\[LetterSpace]17 -> v\[LetterSpace]6*CD[t], v\[LetterSpace]18 -> v\[LetterSpace]6*CA[t], v\[LetterSpace]19 -> v\[LetterSpace]2*CYCB[t], v\[LetterSpace]2 -> k18*DRG[t], v\[LetterSpace]20 -> ((K3a + K3*CDc20[t])*(1 - CDh1[t]))/(1 + J3 - CDh1[t]), v\[LetterSpace]21 -> (v\[LetterSpace]4*CDh1[t])/(J4 + CDh1[t]), v\[LetterSpace]22 -> K34*PPX[t], v\[LetterSpace]23 -> (K31*CYCB[t]*(1 - IEP[t]))/(1 + J31 - IEP[t]), v\[LetterSpace]24 -> (K32*IEP[t]*PPX[t])/(J32 + IEP[t]), v\[LetterSpace]25 -> K12*CDc20T[t], v\[LetterSpace]26 -> (K13*(-CDc20[t] + CDc20T[t])*IEP[t])/(J13 - CDc20[t] + CDc20T[t]), v\[LetterSpace]27 -> (K14*CDc20[t])/(J14 + CDc20[t]), v\[LetterSpace]28 -> K12*CDc20[t], v\[LetterSpace]29 -> K22*(E2FT - E2F[t]), v\[LetterSpace]3 -> K10*CD[t], v\[LetterSpace]30 -> (K23a + K23*(CYCA[t] + CYCB[t]))*E2F[t], v\[LetterSpace]31 -> K27*MASS[t]*Piecewise[{{0, RBH/RBT > 0.8}}, 1], v\[LetterSpace]32 -> K28*GM[t], v\[LetterSpace]33 -> eps*MU*GM[t], v\[LetterSpace]34 -> (eps*k15)/(1 + DRG[t]^2/J15^2), v\[LetterSpace]35 -> eps*(K11a + K11*CYCB[t]), v\[LetterSpace]36 -> E2FA*eps*K29*MASS[t], v\[LetterSpace]37 -> eps*K33, v\[LetterSpace]38 -> eps*(E2FA*K7 + K7a), v\[LetterSpace]39 -> eps*K9*DRG[t], v\[LetterSpace]4 -> K10*CYCD[t], v\[LetterSpace]40 -> eps*K5, v\[LetterSpace]41 -> eps*((k17*DRG[t]^2)/(J17^2*(1 + DRG[t]^2/J17^2)) + k17a*ERG[t]), v\[LetterSpace]42 -> eps*(K1a + (K1*CYCB[t]^2)/(J1^2*(1 + CYCB[t]^2/J1^2))), v\[LetterSpace]5 -> K25*CYCE[t]*P27[t], v\[LetterSpace]6 -> K25*CYCA[t]*P27[t], v\[LetterSpace]7 -> k24*CYCD[t]*P27[t], v\[LetterSpace]8 -> k24r*CD[t], v\[LetterSpace]9 -> K30*CDc20[t]*CYCA[t]
};

parameters = {
E2FA -> 0.0, E2FT -> 5.0, FB -> 2.0, FE -> 25.0, GA -> 0.3, GB -> 1.0, GE -> 0.0, HA -> 0.5, HB -> 1.0, HE -> 0.5, J1 -> 0.1, J13 -> 0.005, J14 -> 0.005, J15 -> 0.1, J17 -> 0.3, J3 -> 0.01, J31 -> 0.01, J32 -> 0.01, J4 -> 0.01, J8 -> 0.1, K1 -> 0.06, K10 -> 0.5, K11 -> 0.15, K11a -> 0.0, K12 -> 0.15, K13 -> 0.5, K14 -> 0.25, K19 -> 2.0, K19a -> 0.0, K1a -> 0.01, K2 -> 2.0, K20 -> 1.0, K21 -> 1.0, K22 -> 0.1, K23 -> 0.1, K23a -> 0.0005, K25 -> 100.0, K25R -> 1.0, K26 -> 1000.0, K26R -> 20.0, K27 -> 0.02, K28 -> 0.02, K29 -> 0.005, K2a -> 0.005, K2aa -> 0.1, K3 -> 14.0, K30 -> 2.0, K31 -> 0.07, K32 -> 0.18, K33 -> 0.005, K34 -> 0.005, K3a -> 0.75, K4 -> 4.0, K5 -> 2.0, K6 -> 10.0, K6a -> 1.0, K7 -> 0.06, K7a -> 0.0, K8 -> 0.2, K8a -> 0.01, K9 -> 0.25, LA -> 3.0, LB -> 5.0, LD -> 3.3, LE -> 5.0, MU -> 0.0061, PP1T -> 1.0, RBT -> 10.0, YB -> 0.05, YE -> 1.0, eps -> 1.0, k15 -> 0.025, k16 -> 0.025, k17 -> 1.0, k17a -> 0.035, k18 -> 1.0, k24 -> 100.0, k24r -> 1.0, p -> 1.0, s -> 1.0, default\[LetterSpace]compartment -> 1.0
};

assignments = {
L -> (K26R + K20*(LA*CYCA[t] + LB*CYCB[t] + LD*CYCD[t] + LE*CYCE[t]))/K26, E2RBC -> (2*E2FT*RBH)/(E2FT + L + RBH + (-4*E2FT*RBH + (E2FT + L + RBH)^2)^0.5), RBH -> RBT/(1 + (K20*(LA*CYCA[t] + LB*CYCB[t] + LD*CYCD[t] + LE*CYCE[t]))/(K19*PP1A + K19a*(-PP1A + PP1T))), PP1A -> PP1T/(1 + K21*(FB*CYCB[t] + FE*(CYCA[t] + CYCE[t])))
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
CA'[t] == 1.0*v\[LetterSpace]6 -1.0*v\[LetterSpace]18 -1.0*v\[LetterSpace]10 -1.0*v\[LetterSpace]12, CD'[t] == 1.0*v\[LetterSpace]7 -1.0*v\[LetterSpace]8 -1.0*v\[LetterSpace]17 -1.0*v\[LetterSpace]3, CDc20'[t] == 1.0*v\[LetterSpace]26 -1.0*v\[LetterSpace]27 -1.0*v\[LetterSpace]28, CDc20T'[t] == 1.0*v\[LetterSpace]35 -1.0*v\[LetterSpace]25, CDh1'[t] == 1.0*v\[LetterSpace]20 -1.0*v\[LetterSpace]21, CE'[t] == 1.0*v\[LetterSpace]5 -1.0*v\[LetterSpace]16 -1.0*v\[LetterSpace]13 -1.0*v\[LetterSpace]11, CYCA'[t] == 1.0*v\[LetterSpace]36 +1.0*v\[LetterSpace]18 +1.0*v\[LetterSpace]12 -1.0*v\[LetterSpace]6 -1.0*v\[LetterSpace]9, CYCB'[t] == 1.0*v\[LetterSpace]42 -1.0*v\[LetterSpace]19, CYCD'[t] == 1.0*v\[LetterSpace]8 +1.0*v\[LetterSpace]17 +1.0*v\[LetterSpace]39 -1.0*v\[LetterSpace]4 -1.0*v\[LetterSpace]7, CYCE'[t] == 1.0*v\[LetterSpace]38 +1.0*v\[LetterSpace]16 +1.0*v\[LetterSpace]11 -1.0*v\[LetterSpace]14 -1.0*v\[LetterSpace]5, DRG'[t] == 1.0*v\[LetterSpace]41 -1.0*v\[LetterSpace]2, E2F'[t] == 1.0*v\[LetterSpace]29 -1.0*v\[LetterSpace]30, ERG'[t] == 1.0*v\[LetterSpace]34 -1.0*v\[LetterSpace]1, GM'[t] == 1.0*v\[LetterSpace]31 -1.0*v\[LetterSpace]32, IEP'[t] == 1.0*v\[LetterSpace]23 -1.0*v\[LetterSpace]24, MASS'[t] == 1.0*v\[LetterSpace]33 , P27'[t] == 1.0*v\[LetterSpace]8 +1.0*v\[LetterSpace]13 +1.0*v\[LetterSpace]11 +1.0*v\[LetterSpace]40 +1.0*v\[LetterSpace]10 +1.0*v\[LetterSpace]12 +1.0*v\[LetterSpace]3 -1.0*v\[LetterSpace]6 -1.0*v\[LetterSpace]15 -1.0*v\[LetterSpace]5 -1.0*v\[LetterSpace]7, PPX'[t] == 1.0*v\[LetterSpace]37 -1.0*v\[LetterSpace]22
};
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]}]