(* 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 = {
Aktt32D[t], BaF3Epo[t], EpoR32D[t], Erkt32D[t], GTPRas[t], IntpS6[t], Intpakt[t], Intperk[t], Mekt32D[t], PDK1t32D[t], PI3Kt32D[t], PI45P232D[t], PIP3[t], PIP3Akt[t], PIP3PDK1[t], PTEN32D[t], Phosphataset32D[t], Proliferation[t], RSKa[t], RSKtd[t], Raft32D[t], Raptord[t], Rast32D[t], Rictord[t], RpSHIP1[t], RpSos[t], S6t32D[t], SHIP1t32D[t], TORC1[t], TORC2[t], actPhosphatase[t], mTORa[t], mTORt[t], pAkt[t], pEpoR[t], pErk[t], pMek[t], pRaf[t], pS6[t], pSos[t], phos2[t], ppErk[t], ppMek[t]
};

initialValues = {
Aktt32D[0] == 0.60774, BaF3Epo[0] == 0.02, EpoR32D[0] == 0.016766, Erkt32D[0] == 2.3261, GTPRas[0] == 0.14735982220783525, IntpS6[0] == 0.0, Intpakt[0] == 0.0, Intperk[0] == 0.0, Mekt32D[0] == 4.7439, PDK1t32D[0] == 1.5545, PI3Kt32D[0] == 0.0124, PI45P232D[0] == 10, PIP3[0] == 0.0015820688561687386, PIP3Akt[0] == 0.3654172114157491, PIP3PDK1[0] == 0.00979331927840607, PTEN32D[0] == 0.096799, Phosphataset32D[0] == 0.0415, Proliferation[0] == 0.0, RSKa[0] == 0.09656086787310815, RSKtd[0] == 1.6972, Raft32D[0] == 7.8073, Raptord[0] == 0.1, Rast32D[0] == 7.8554, Rictord[0] == 0.099259, RpSHIP1[0] == 0.0, RpSos[0] == 0.0, S6t32D[0] == 4.5318, SHIP1t32D[0] == 0.12778, TORC1[0] == 0.0, TORC2[0] == 0.0, actPhosphatase[0] == 0.0, mTORa[0] == 0.0, mTORt[0] == 0.1, pAkt[0] == 0.007108053543974432, pEpoR[0] == 0.0, pErk[0] == 0.024884819917878956, pMek[0] == 4.687884851008414, pRaf[0] == 0.0005320136586637678, pS6[0] == 0.0008491959467671434, pSos[0] == 0.0, phos2[0] == 0.0, ppErk[0] == 0.014762189034818775, ppMek[0] == 0.018664442030427147
};

rates = {
v1, 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, v53, v54, v55, v56, v57, v58, v59, v6, v60, v61, v62, v63, v64, v65, v66, v67, v68, v69, v7, v70, v71
};

rateEquations = {
v1 -> Epodegradation*BaF3Epo[t], v18 -> kSHIP1*(pEpoR[t] - RpSHIP1[t])*(-RpSHIP1[t] + SHIP1t32D[t]), v19 -> lSHIP1*RpSHIP1[t], v2 -> (EpoRactivation1*BaF3Epo[t]^nb*(EpoR32D[t] - (1 + kPI3K/(1 + kPI3K + kPI3K*kPI3Kras) + (kPI3K*kPI3Kras)/(1 + kPI3K + kPI3K*kPI3Kras))*pEpoR[t]))/((ksatb^nb + BaF3Epo[t]^nb)*(1 + phos2[t]/Ki1)), v20 -> (kPI3K*vPIP3*pEpoR[t]*PI45P232D[t])/(1 + kPI3K + kPI3K*kPI3Kras), v21 -> (kPI3K*kPI3Kras*main1*vPIP3*pEpoR[t]*PI45P232D[t])/(1 + kPI3K + kPI3K*kPI3Kras), v22 -> kshbasal*PIP3[t]*(-RpSHIP1[t] + SHIP1t32D[t]), v23 -> vPI45P2*PIP3[t]*PTEN32D[t], v24 -> vPI34P2*PIP3[t]*RpSHIP1[t], v25 -> kPDK1*PIP3[t]*(PDK1t32D[t] - PIP3PDK1[t]), v26 -> lPDK1*PIP3PDK1[t], v27 -> kAkt*PIP3[t]*(Aktt32D[t] - pAkt[t] - PIP3Akt[t]), v28 -> lAkt*PIP3Akt[t], v29 -> vpAkt*PIP3Akt[t]*PIP3PDK1[t], v3 -> Phosphataseactivation1*pEpoR[t]*(-actPhosphatase[t] + Phosphataset32D[t]), v30 -> vpAkt*PIP3Akt[t]*PIP3PDK1[t], v31 -> (vpAkt*PIP3Akt[t]*PIP3PDK1[t])/(1 + Aktin*kaktind), v32 -> dpAkt*pAkt[t], v33 -> vPIP3basal*(-((kPI3K*pEpoR[t])/(1 + kPI3K + kPI3K*kPI3Kras)) - (kPI3K*kPI3Kras*pEpoR[t])/(1 + kPI3K + kPI3K*kPI3Kras) + PI3Kt32D[t])*PI45P232D[t], v34 -> main1*vPIP3basal*PI45P232D[t], v35 -> kpes*ppErk[t]*(Sostb - pSos[t] - RpSos[t]), v36 -> kdpes*pSos[t], v37 -> kSos*(pEpoR[t] - RpSos[t])*(Sostb - pSos[t] - RpSos[t]), v38 -> lSos*RpSos[t], v39 -> kpes*ppErk[t]*RpSos[t], v4 -> Phosphatasedeactivation1*actPhosphatase[t], v40 -> kbackRas*(-GTPRas[t] - (kPI3K*kPI3Kras*pEpoR[t])/(1 + kPI3K + kPI3K*kPI3Kras) + Rast32D[t]), v41 -> kaRas*(-GTPRas[t] - (kPI3K*kPI3Kras*pEpoR[t])/(1 + kPI3K + kPI3K*kPI3Kras) + Rast32D[t])*RpSos[t], v42 -> kdRas*GTPRas[t], v43 -> kpRaf*(GTPRas[t] + (kPI3K*kPI3Kras*pEpoR[t])/(1 + kPI3K + kPI3K*kPI3Kras))*(-pRaf[t] + Raft32D[t]), v44 -> lpRaf*pRaf[t], v45 -> kpMek*(Mekt32D[t] - pMek[t] - ppMek[t])*pRaf[t], v46 -> lpMek*pMek[t], v47 -> kppMek*pMek[t]*pRaf[t], v48 -> lppMek*ppMek[t], v49 -> kpErk*(Erkt32D[t] - pErk[t] - ppErk[t])*ppMek[t], v5 -> pEpoRdeactivation1*actPhosphatase[t]*pEpoR[t], v50 -> dDUSP3*lpErk*pErk[t], v51 -> (kppErk*pErk[t]*ppMek[t])/(1 + kmekind*Mekin), v52 -> dDUSP3*lppErk*ppErk[t], v53 -> ppErk[t], v54 -> pAkt[t], v55 -> kvpakt*pAkt[t]*(-mTORa[t] + mTORt[t] - TORC1[t] - TORC2[t]), v56 -> (kvppErk*RSKa[t]*(-mTORa[t] + mTORt[t] - TORC1[t] - TORC2[t]))/(1 + kinrskb*RSKin), v57 -> kdactm*mTORa[t], v58 -> (kst1*(Raptord[t] - TORC1[t])*(mTORa[t] - TORC1[t] - TORC2[t]))/(1 + kinrapab*Rapamycin), v59 -> kdt1*TORC1[t], v6 -> (Phosact1*pEpoR[t]^n1)/(Ji1^n1 + pEpoR[t]^n1), v60 -> kdactm*TORC1[t], v61 -> kst2*(Rictord[t] - TORC2[t])*(mTORa[t] - TORC1[t] - TORC2[t]), v62 -> kdt2*TORC2[t], v63 -> kdactm*TORC2[t], v64 -> (karsk*ppErk[t]*(-RSKa[t] + RSKtd[t]))/(1 + kinrskb*RSKin), v65 -> kdrsk*RSKa[t], v66 -> kas6t*(-pS6[t] + S6t32D[t])*TORC1[t], v67 -> kas6r*RSKa[t]*(-pS6[t] + S6t32D[t]), v68 -> kbacks6*(-pS6[t] + S6t32D[t]), v69 -> kdphoss6*pS6[t], v7 -> Phosdeact1*phos2[t], v70 -> pdoffcorrect/60 + (pdk2correct*(cycleaktind*pAkt[t] + cyclemekind*ppErk[t]))/maxccd, v71 -> pS6[t]
};

parameters = {
Aktin -> 0.0, EpoRactivation1 -> 0.140964, Epodegradation -> 0.0173287, Ji1 -> 0.220505, Ki1 -> 0.0272784, Mekin -> 0.0, Phosact1 -> 341.317, Phosdeact1 -> 1*^-05, Phosphataseactivation1 -> 144.425, Phosphatasedeactivation1 -> 1*^-05, RSKin -> 0.0, Rapamycin -> 0.0, Sostb -> 4.46181*^-05, cycleaktind -> 0.551765, cyclemekind -> 0.0331257, dDUSP3 -> 96.7609, dpAkt -> 3.4739, initAktt32D -> 0.60774, initErkt32D -> 2.3261, initMekt32D -> 4.7439, initPDK1t32D -> 1.5545, initPI3Kt32D -> 0.0124, initPI45P232D -> 10.0, initPTEN32D -> 0.096799, initRSKtd -> 1.6972, initRaft32D -> 7.8073, initRast32D -> 7.8554, initRpGab2PI3K -> 0.0, initRpPI3K -> 0.0, initRpSHIP1 -> 0.0, initS6t32D -> 4.5318, initSHIP1t32D -> 0.12778, initTORC1 -> 0.0, kAkt -> 9984.96, kPDK1 -> 9439.5, kPI3K -> 0.000104741, kPI3Kras -> 10000.0, kSHIP1 -> 0.0745937, kSos -> 59.4049, kaRas -> 2981.53, kaktind -> 2.054443007, karsk -> 1.26435, kas6r -> 0.000533083, kas6t -> 2180.44, kbackRas -> 0.0103384, kbacks6 -> 1.00003*^-05, kdRas -> 0.540777, kdactm -> 0.0617342, kdpes -> 0.0270729, kdphoss6 -> 0.328006, kdrsk -> 0.677229, kdt1 -> 1588.13, kdt2 -> 1*^-05, kinrapab -> 2.778901656, kinrskb -> 0.552054462, kmekind -> 0.500416844, kpErk -> 9999.08, kpMek -> 9774.26, kpRaf -> 1.17959, kpes -> 0.583255, kppErk -> 9999.96, kppMek -> 9999.77, ksatb -> 0.0024577, kshbasal -> 1*^-05, kst1 -> 20.0908, kst2 -> 0.0619403, kvpakt -> 0.000174996, kvppErk -> 0.000282332, lAkt -> 10.1007, lPDK1 -> 2355.54, lSHIP1 -> 0.000650697, lSos -> 0.39616, lpErk -> 177.216, lpMek -> 0.0414313, lpRaf -> 2549.69, lppErk -> 3.2516, lppMek -> 1336.21, main1 -> 0.000224787, maxccd -> 0.88, n1 -> 4.0, nb -> 2.03939, pEpoRdeactivation1 -> 3.20488, pdk2correct -> 0.264415, pdoffcorrect -> 0.641853, vPI34P2 -> 9996.96, vPI45P2 -> 84.5564, vPIP3 -> 10000.0, vPIP3basal -> 0.104429, vpAkt -> 6.9, cyt -> 1.0
};

assignments = {
pS6plot -> 532.9197*pS6[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
Aktt32D'[t] == 0.0 , BaF3Epo'[t] ==  -1.0*v1, EpoR32D'[t] == 0.0 , Erkt32D'[t] == 0.0 , GTPRas'[t] == 1.0*v40 +1.0*v41 -1.0*v42, IntpS6'[t] == 1.0*v71 , Intpakt'[t] == 1.0*v54 , Intperk'[t] == 1.0*v53 , Mekt32D'[t] == 0.0 , PDK1t32D'[t] == 0.0 , PI3Kt32D'[t] == 0.0 , PI45P232D'[t] == 0.0 , PIP3'[t] == 1.0*v20 +1.0*v21 +1.0*v26 +1.0*v28 +1.0*v30 +1.0*v33 +1.0*v34 -1.0*v22 -1.0*v23 -1.0*v24 -1.0*v25 -1.0*v27, PIP3Akt'[t] == 1.0*v27 -1.0*v28 -1.0*v29, PIP3PDK1'[t] == 1.0*v25 -1.0*v26, PTEN32D'[t] == 0.0 , Phosphataset32D'[t] == 0.0 , Proliferation'[t] == 1.0*v70 , RSKa'[t] == 1.0*v64 -1.0*v65, RSKtd'[t] == 0.0 , Raft32D'[t] == 0.0 , Raptord'[t] == 0.0 , Rast32D'[t] == 0.0 , Rictord'[t] == 0.0 , RpSHIP1'[t] == 1.0*v18 -1.0*v19, RpSos'[t] == 1.0*v37 -1.0*v38 -1.0*v39, S6t32D'[t] == 0.0 , SHIP1t32D'[t] == 0.0 , TORC1'[t] == 1.0*v58 -1.0*v59 -1.0*v60, TORC2'[t] == 1.0*v61 -1.0*v62 -1.0*v63, actPhosphatase'[t] == 1.0*v3 -1.0*v4, mTORa'[t] == 1.0*v55 +1.0*v56 +1.0*v59 +1.0*v62 -1.0*v57 -1.0*v58 -1.0*v61, mTORt'[t] == 0.0 , pAkt'[t] == 1.0*v31 -1.0*v32, pEpoR'[t] == 1.0*v2 -1.0*v5, pErk'[t] == 1.0*v49 +1.0*v52 -1.0*v50 -1.0*v51, pMek'[t] == 1.0*v45 +1.0*v48 -1.0*v46 -1.0*v47, pRaf'[t] == 1.0*v43 -1.0*v44, pS6'[t] == 1.0*v66 +1.0*v67 +1.0*v68 -1.0*v69, pSos'[t] == 1.0*v35 +1.0*v39 -1.0*v36, phos2'[t] == 1.0*v6 -1.0*v7, ppErk'[t] == 1.0*v51 -1.0*v52, ppMek'[t] == 1.0*v47 -1.0*v48
};
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]}]