(* 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], ERG[t], GM[t], IEP[t], MASS[t], P27[t], PPX[t], var1[t], var2[t], var3[t], var4[t], var5[t], var6[t]
};

initialValues = {
CA[0] == 0.0356927, CD[0] == 0.010976, CDc20[0] == 0.00220177, CDc20T[0] == 2.36733, CDh1[0] == 0.000653278, CE[0] == 0.000542587, CYCA[0] == 1.4094, CYCB[0] == 2.72898, CYCD[0] == 0.43929, CYCE[0] == 0.0229112, DRG[0] == 0.900533, ERG[0] == 0.0121809, GM[0] == 1.35565, IEP[0] == 0.154655, MASS[0] == 1.68776, P27[0] == 0.00922806, PPX[0] == 1.0, var1[0] == 9.97574, var2[0] == 0.989986, var3[0] == 3.98594, var4[0] == 0.000190871, var5[0] == 0.00478911, var6[0] == 0.0192822
};

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, v39, v4, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v5, v50, v51, v52, v6, v7, v8, v9
};

rateEquations = {
v1 -> v1\[LetterSpace]k16*ERG[t], v10 -> K30*CA[t]*CDc20[t], v11 -> K25R*CE[t], v12 -> K25R*CA[t], v13 -> V8*CE[t], v14 -> V8*CYCE[t], v15 -> V6*P27[t], v16 -> V6*CE[t], v17 -> V6*CD[t], v18 -> V6*CA[t], v19 -> V2*CYCB[t], v2 -> v2\[LetterSpace]k18*DRG[t], v20 -> ((v20\[LetterSpace]K3a + v20\[LetterSpace]K3*CDc20[t])*(1 - CDh1[t]))/(1 + v20\[LetterSpace]J3 - CDh1[t]), v21 -> (V4*CDh1[t])/(v21\[LetterSpace]J4 + CDh1[t]), v22 -> v22\[LetterSpace]K34*PPX[t], v23 -> (v23\[LetterSpace]K31*CYCB[t]*(1 - IEP[t]))/(1 + v23\[LetterSpace]J31 - IEP[t]), v24 -> (v24\[LetterSpace]K32*IEP[t]*PPX[t])/(v24\[LetterSpace]J32 + IEP[t]), v25 -> K12*CDc20T[t], v26 -> (v26\[LetterSpace]K13*(-CDc20[t] + CDc20T[t])*IEP[t])/(v26\[LetterSpace]J13 - CDc20[t] + CDc20T[t]), v27 -> (v27\[LetterSpace]K14*CDc20[t])/(v27\[LetterSpace]J14 + CDc20[t]), v28 -> K12*CDc20[t], v29 -> K20*(LA*CYCA[t] + LB*CYCB[t] + LD*(CD[t] + CYCD[t]) + LE*CYCE[t])*var5[t], v3 -> K10*CD[t], v30 -> K20*(LA*CYCA[t] + LB*CYCB[t] + LD*(CD[t] + CYCD[t]) + LE*CYCE[t])*var6[t], v31 -> r31switch*v31\[LetterSpace]K27*MASS[t], v32 -> v32\[LetterSpace]K28*GM[t], v33 -> eps*v33\[LetterSpace]MU*GM[t], v34 -> (eps*v34\[LetterSpace]k15)/(1 + DRG[t]^2/v34\[LetterSpace]J15^2), v35 -> eps*(v35\[LetterSpace]K11a + v35\[LetterSpace]K11*CYCB[t]), v36 -> eps*v36\[LetterSpace]K29*MASS[t]*var2[t], v37 -> eps*v37\[LetterSpace]K33, v38 -> eps*(v38\[LetterSpace]K7a + v38\[LetterSpace]K7*var2[t]), v39 -> eps*v39\[LetterSpace]K9*DRG[t], v4 -> K10*CYCD[t], v40 -> eps*v40\[LetterSpace]K5, v41 -> eps*((v41\[LetterSpace]k17*DRG[t]^2)/(v41\[LetterSpace]J17^2*(1 + DRG[t]^2/v41\[LetterSpace]J17^2)) + v41\[LetterSpace]k17a*ERG[t]), v42 -> eps*(v42\[LetterSpace]K1a + (v42\[LetterSpace]K1*CYCB[t]^2)/(v42\[LetterSpace]J1^2*(1 + CYCB[t]^2/v42\[LetterSpace]J1^2))), v43 -> K20*(LA*CYCA[t] + LB*CYCB[t] + LD*(CD[t] + CYCD[t]) + LE*CYCE[t])*var4[t], v44 -> (PP1A*v44\[LetterSpace]K19 + (-PP1A + PP1T)*v44\[LetterSpace]K19a)*var1[t], v45 -> K26R*var5[t], v46 -> (K23a + K23*(CYCA[t] + CYCB[t]))*var2[t], v47 -> K22*var3[t], v48 -> K26*var2[t]*var4[t], v49 -> K26R*var6[t], v5 -> K25*CYCE[t]*P27[t], v50 -> K26*var3[t]*var4[t], v51 -> K22*var6[t], v52 -> (K23a + K23*(CYCA[t] + CYCB[t]))*var5[t], v6 -> K25*CYCA[t]*P27[t], v7 -> v7\[LetterSpace]k24*CYCD[t]*P27[t], v8 -> v8\[LetterSpace]k24r*CD[t], v9 -> K30*CDc20[t]*CYCA[t]
};

parameters = {
E2FT -> 5.0, FB -> 2.0, FE -> 25.0, Flag -> 1.0, GA -> 0.3, GB -> 1.0, GE -> 0.0, HA -> 0.5, HB -> 1.0, HE -> 0.5, J8 -> 0.1, K10 -> 5.0, K12 -> 1.5, K2 -> 20.0, K20 -> 10.0, K21 -> 1.0, K22 -> 1.0, K23 -> 1.0, K23a -> 0.005, K25 -> 1000.0, K25R -> 10.0, K26 -> 10000.0, K26R -> 200.0, K2a -> 0.05, K2aa -> 1.0, K30 -> 20.0, K4 -> 40.0, K6 -> 100.0, K6a -> 10.0, K8 -> 2.0, K8a -> 0.1, LA -> 3.0, LB -> 5.0, LD -> 3.3, LE -> 5.0, PP1T -> 1.0, RBT -> 10.0, YB -> 0.05, YE -> 1.0, eps -> 1.0, r31switch -> 1.0, v1\[LetterSpace]k16 -> 0.25, v2\[LetterSpace]k18 -> 10.0, v7\[LetterSpace]k24 -> 1000.0, v8\[LetterSpace]k24r -> 10.0, v20\[LetterSpace]J3 -> 0.01, v20\[LetterSpace]K3 -> 140.0, v20\[LetterSpace]K3a -> 7.5, v21\[LetterSpace]J4 -> 0.01, v22\[LetterSpace]K34 -> 0.05, v23\[LetterSpace]J31 -> 0.01, v23\[LetterSpace]K31 -> 0.7, v24\[LetterSpace]J32 -> 0.01, v24\[LetterSpace]K32 -> 1.8, v26\[LetterSpace]J13 -> 0.005, v26\[LetterSpace]K13 -> 5.0, v27\[LetterSpace]J14 -> 0.005, v27\[LetterSpace]K14 -> 2.5, v31\[LetterSpace]K27 -> 0.2, v32\[LetterSpace]K28 -> 0.2, v33\[LetterSpace]MU -> 0.061, v34\[LetterSpace]J15 -> 0.1, v34\[LetterSpace]k15 -> 0.25, v35\[LetterSpace]K11 -> 1.5, v35\[LetterSpace]K11a -> 0.0, v36\[LetterSpace]K29 -> 0.05, v37\[LetterSpace]K33 -> 0.05, v38\[LetterSpace]K7 -> 0.6, v38\[LetterSpace]K7a -> 0.0, v39\[LetterSpace]K9 -> 2.5, v40\[LetterSpace]K5 -> 20.0, v41\[LetterSpace]J17 -> 0.3, v41\[LetterSpace]k17 -> 10.0, v41\[LetterSpace]k17a -> 0.35, v42\[LetterSpace]J1 -> 0.1, v42\[LetterSpace]K1 -> 0.6, v42\[LetterSpace]K1a -> 0.1, v44\[LetterSpace]K19 -> 20.0, v44\[LetterSpace]K19a -> 0.0, cell -> 1.0
};

assignments = {
P27T -> CA[t] + CD[t] + CE[t] + P27[t], CYCAT -> CA[t] + CYCA[t], CYCDT -> CD[t] + CYCD[t], CYCET -> CE[t] + CYCE[t], V8 -> K8a + (K8*(YB*CYCB[t] + YE*(CYCA[t] + CYCE[t])))/(CYCET + J8), V6 -> K6a + K6*(HA*CYCA[t] + HB*CYCB[t] + HE*CYCE[t]), V4 -> K4*(GA*CYCA[t] + GB*CYCB[t] + GE*CYCE[t]), V2 -> K2aa*CDc20[t] + K2a*(1 - CDh1[t]) + K2*CDh1[t], PP1A -> PP1T/(1 + K21*(FB*CYCB[t] + FE*(CYCA[t] + CYCE[t])))
};

events = {

};

speciesAnnotations = {
CDc20[t]->"http://identifiers.org/uniprot/P26309", CDc20T[t]->"http://identifiers.org/uniprot/P26309", CDh1[t]->"http://identifiers.org/uniprot/P12830", IEP[t]->"http://identifiers.org/go/GO:0005680", MASS[t]->"http://identifiers.org/go/GO:0016049", P27[t]->"http://identifiers.org/uniprot/P46527", PPX[t]->"http://identifiers.org/uniprot/P38698", var1[t]->"http://identifiers.org/uniprot/P06400", var2[t]->"http://identifiers.org/uniprot/Q01094", var3[t]->"http://identifiers.org/uniprot/Q01094", var4[t]->"http://identifiers.org/uniprot/P06400"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
CA'[t] == 1.0*v6 -1.0*v10 -1.0*v12 -1.0*v18, CD'[t] == 1.0*v7 -1.0*v3 -1.0*v8 -1.0*v17, CDc20'[t] == 1.0*v26 -1.0*v27 -1.0*v28, CDc20T'[t] == 1.0*v35 -1.0*v25, CDh1'[t] == 1.0*v20 -1.0*v21, CE'[t] == 1.0*v5 -1.0*v11 -1.0*v13 -1.0*v16, CYCA'[t] == 1.0*v12 +1.0*v18 +1.0*v36 -1.0*v6 -1.0*v9, CYCB'[t] == 1.0*v42 -1.0*v19, CYCD'[t] == 1.0*v8 +1.0*v17 +1.0*v39 -1.0*v4 -1.0*v7, CYCE'[t] == 1.0*v11 +1.0*v16 +1.0*v38 -1.0*v5 -1.0*v14, DRG'[t] == 1.0*v41 -1.0*v2, ERG'[t] == 1.0*v34 -1.0*v1, GM'[t] == 1.0*v31 -1.0*v32, IEP'[t] == 1.0*v23 -1.0*v24, MASS'[t] == 1.0*v33 , P27'[t] == 1.0*v3 +1.0*v8 +1.0*v10 +1.0*v11 +1.0*v12 +1.0*v13 +1.0*v40 -1.0*v5 -1.0*v6 -1.0*v7 -1.0*v15, PPX'[t] == 1.0*v37 -1.0*v22, var1'[t] == 1.0*v29 +1.0*v30 +1.0*v43 -1.0*v44, var2'[t] == 1.0*v29 +1.0*v45 +1.0*v47 -1.0*v46 -1.0*v48, var3'[t] == 1.0*v30 +1.0*v46 +1.0*v49 -1.0*v47 -1.0*v50, var4'[t] == 1.0*v44 +1.0*v45 +1.0*v49 -1.0*v43 -1.0*v48 -1.0*v50, var5'[t] == 1.0*v48 +1.0*v51 -1.0*v29 -1.0*v45 -1.0*v52, var6'[t] == 1.0*v50 +1.0*v52 -1.0*v30 -1.0*v49 -1.0*v51
};
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]}]