(* 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 = {
AMPK[t], AMPK\[LetterSpace]pT172[t], Akt[t], Akt\[LetterSpace]pS473[t], CDKN1A[t], CDKN1B[t], DNA\[LetterSpace]damage[t], FoxO3a[t], FoxO3a\[LetterSpace]pS253[t], IKKbeta[t], JNK[t], JNK\[LetterSpace]pT183[t], Mito\[LetterSpace]mass\[LetterSpace]new[t], Mito\[LetterSpace]mass\[LetterSpace]old[t], Mito\[LetterSpace]mass\[LetterSpace]turnover[t], Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new[t], Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old[t], Mitophagy[t], Nil[t], ROS[t], SA\[LetterSpace]beta\[LetterSpace]gal[t], mTORC1[t], mTORC1\[LetterSpace]pS2448[t]
};

initialValues = {
AMPK[0] == 10.0, AMPK\[LetterSpace]pT172[0] == 10.0, Akt[0] == 10.0, Akt\[LetterSpace]pS473[0] == 10.0, CDKN1A[0] == 10.0, CDKN1B[0] == 10.0, DNA\[LetterSpace]damage[0] == 1.0, FoxO3a[0] == 10.0, FoxO3a\[LetterSpace]pS253[0] == 10.0, IKKbeta[0] == 10.0, JNK[0] == 25.0, JNK\[LetterSpace]pT183[0] == 10.0, Mito\[LetterSpace]mass\[LetterSpace]new[0] == 1.0, Mito\[LetterSpace]mass\[LetterSpace]old[0] == 0.0, Mito\[LetterSpace]mass\[LetterSpace]turnover[0] == 25.0, Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new[0] == 12.12, Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old[0] == 0.0, Mitophagy[0] == 10.0, Nil[0] == 0.0, ROS[0] == 10.0, SA\[LetterSpace]beta\[LetterSpace]gal[0] == 0.81, mTORC1[0] == 10.0, mTORC1\[LetterSpace]pS2448[0] == 10.0
};

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

rateEquations = {
reaction\[LetterSpace]1 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]1\[LetterSpace]1[Akt[t], Akt\[LetterSpace]S473\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]insulin, Insulin], reaction\[LetterSpace]10 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]10\[LetterSpace]1[Mitophagy[t], mTORC1\[LetterSpace]pS2448[t], mitophagy\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448], reaction\[LetterSpace]11 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]11\[LetterSpace]1[Akt\[LetterSpace]pS473[t], FoxO3a[t], FoxO3a\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473], reaction\[LetterSpace]12 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]12\[LetterSpace]1[FoxO3a\[LetterSpace]pS253[t], FoxO3a\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]JNK\[LetterSpace]pT183, JNK\[LetterSpace]pT183[t]], reaction\[LetterSpace]13 -> Cell*FoxO3a\[LetterSpace]pS253\[LetterSpace]degrad*FoxO3a\[LetterSpace]pS253[t], reaction\[LetterSpace]14 -> Cell*function\[LetterSpace]2[FoxO3a\[LetterSpace]synthesis], reaction\[LetterSpace]15 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]15\[LetterSpace]1[CDKN1A\[LetterSpace]transcr\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]DNA\[LetterSpace]damage, DNA\[LetterSpace]damage[t], FoxO3a[t]], reaction\[LetterSpace]16 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]16\[LetterSpace]1[Akt\[LetterSpace]pS473[t], CDKN1A[t], CDKN1A\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473], reaction\[LetterSpace]17 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]17\[LetterSpace]1[CDKN1B\[LetterSpace]transcr\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]DNA\[LetterSpace]damage, DNA\[LetterSpace]damage[t], FoxO3a[t]], reaction\[LetterSpace]18 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]18\[LetterSpace]1[Akt\[LetterSpace]pS473[t], CDKN1B[t], CDKN1B\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473], reaction\[LetterSpace]19 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]19\[LetterSpace]1[DNA\[LetterSpace]damaged\[LetterSpace]by\[LetterSpace]irradiation, Irradiation], reaction\[LetterSpace]2 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]2\[LetterSpace]1[Akt\[LetterSpace]pS473[t], Akt\[LetterSpace]pS473\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448, mTORC1\[LetterSpace]pS2448[t]], reaction\[LetterSpace]20 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]20\[LetterSpace]1[DNA\[LetterSpace]damaged\[LetterSpace]by\[LetterSpace]ROS, ROS[t]], reaction\[LetterSpace]21 -> Cell*DNA\[LetterSpace]repair*DNA\[LetterSpace]damage[t], reaction\[LetterSpace]22 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]22\[LetterSpace]1[Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new[t], ROS\[LetterSpace]prod\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new], reaction\[LetterSpace]23 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]23\[LetterSpace]1[Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old[t], ROS\[LetterSpace]prod\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old], reaction\[LetterSpace]24 -> Cell*ROS\[LetterSpace]turnover*ROS[t], reaction\[LetterSpace]25 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]25\[LetterSpace]1[JNK[t], JNK\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]ROS, ROS[t]], reaction\[LetterSpace]26 -> Cell*JNK\[LetterSpace]pT183\[LetterSpace]inactiv*JNK\[LetterSpace]pT183[t], reaction\[LetterSpace]27 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]27\[LetterSpace]1[ROS[t], sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]inc\[LetterSpace]by\[LetterSpace]ROS], reaction\[LetterSpace]28 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]28\[LetterSpace]1[Mitophagy[t], sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]inc\[LetterSpace]by\[LetterSpace]Mitophagy], reaction\[LetterSpace]29 -> Cell*sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]dec*SA\[LetterSpace]beta\[LetterSpace]gal[t], reaction\[LetterSpace]3 -> AMPK\[LetterSpace]T172\[LetterSpace]phos*Cell*AMPK[t], reaction\[LetterSpace]30 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]30\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]turnover[t], mTORC1\[LetterSpace]pS2448[t], mito\[LetterSpace]biogenesis\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448], reaction\[LetterSpace]31 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]31\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]turnover[t], mTORC1\[LetterSpace]pS2448[t], mito\[LetterSpace]biogenesis\[LetterSpace]by\[LetterSpace]AMPK\[LetterSpace]pT172], reaction\[LetterSpace]32 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]32\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]new[t], Mitophagy[t], mitophagy\[LetterSpace]new], reaction\[LetterSpace]33 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]33\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]old[t], Mitophagy[t], mitophagy\[LetterSpace]old], reaction\[LetterSpace]34 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]34\[LetterSpace]1[CDKN1A[t], Mito\[LetterSpace]mass\[LetterSpace]new[t], mito\[LetterSpace]dysfunction], reaction\[LetterSpace]35 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]35\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]new[t], mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new\[LetterSpace]inc], reaction\[LetterSpace]36 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]36\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]old[t], mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old\[LetterSpace]inc], reaction\[LetterSpace]37 -> Cell*mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new\[LetterSpace]dec*Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new[t], reaction\[LetterSpace]38 -> Cell*mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old\[LetterSpace]dec*Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old[t], reaction\[LetterSpace]39 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]39\[LetterSpace]1[IKKbeta\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]ROS, ROS[t]], reaction\[LetterSpace]4 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]4\[LetterSpace]1[AMPK\[LetterSpace]pT172[t], AMPK\[LetterSpace]pT172\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new, Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new[t]], reaction\[LetterSpace]40 -> Cell*IKKbeta\[LetterSpace]inactiv*IKKbeta[t], reaction\[LetterSpace]41 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]41\[LetterSpace]1[Amino\[LetterSpace]Acids, IKKbeta[t], mTORC1[t], mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA\[LetterSpace]n\[LetterSpace]IKKbeta], reaction\[LetterSpace]5 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]5\[LetterSpace]1[AMPK\[LetterSpace]pT172[t], AMPK\[LetterSpace]pT172\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old, Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old[t]], reaction\[LetterSpace]6 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]6\[LetterSpace]1[Amino\[LetterSpace]Acids, mTORC1[t], mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA], reaction\[LetterSpace]7 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]7\[LetterSpace]1[Akt\[LetterSpace]pS473[t], Amino\[LetterSpace]Acids, mTORC1[t], mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA\[LetterSpace]n\[LetterSpace]Akt\[LetterSpace]pS473], reaction\[LetterSpace]8 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]8\[LetterSpace]1[AMPK\[LetterSpace]pT172[t], mTORC1\[LetterSpace]pS2448[t], mTORC1\[LetterSpace]pS2448\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]AMPK\[LetterSpace]pT172], reaction\[LetterSpace]9 -> Cell*function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]9\[LetterSpace]1[AMPK\[LetterSpace]pT172[t], FoxO3a[t], mitophagy\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]AMPK\[LetterSpace]pT172]
};

parameters = {
AMPK\[LetterSpace]T172\[LetterSpace]phos -> 0.355183987378767, AMPK\[LetterSpace]pT172\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new -> 0.117744691539618, AMPK\[LetterSpace]pT172\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old -> 1.00000000000003*^-06, Akt\[LetterSpace]S473\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]insulin -> 0.588783148144923, Akt\[LetterSpace]pS473\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448 -> 0.114598191621279, CDKN1A\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473 -> 0.0667971061916905, CDKN1A\[LetterSpace]transcr\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]DNA\[LetterSpace]damage -> 0.0852182335681166, CDKN1B\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473 -> 0.0596841598127919, CDKN1B\[LetterSpace]transcr\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]DNA\[LetterSpace]damage -> 0.0920526565951487, DNA\[LetterSpace]damaged\[LetterSpace]by\[LetterSpace]ROS -> 0.118873655169353, DNA\[LetterSpace]damaged\[LetterSpace]by\[LetterSpace]irradiation -> 9237.72311545872, DNA\[LetterSpace]repair -> 0.325724769122274, FoxO3a\[LetterSpace]pS253\[LetterSpace]degrad -> 39.4068609318082, FoxO3a\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473 -> 6.83511123229576, FoxO3a\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]JNK\[LetterSpace]pT183 -> 0.112877630496044, FoxO3a\[LetterSpace]synthesis -> 407.307409980937, IKKbeta\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]ROS -> 1.0, IKKbeta\[LetterSpace]inactiv -> 1.0, JNK\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]ROS -> 0.00502329152478409, JNK\[LetterSpace]pT183\[LetterSpace]inactiv -> 0.0718429173444438, ROS\[LetterSpace]prod\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new -> 4.55464788075885, ROS\[LetterSpace]prod\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old -> 772.829490967078, ROS\[LetterSpace]turnover -> 3.23082321168464, mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA -> 1.00008999860285*^-06, mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA\[LetterSpace]n\[LetterSpace]Akt\[LetterSpace]pS473 -> 162.471039450073, mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA\[LetterSpace]n\[LetterSpace]IKKbeta -> 1.00008996727694*^-05, mTORC1\[LetterSpace]pS2448\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]AMPK\[LetterSpace]pT172 -> 191.297262771509, mito\[LetterSpace]biogenesis\[LetterSpace]by\[LetterSpace]AMPK\[LetterSpace]pT172 -> 5.8915457309741*^-05, mito\[LetterSpace]biogenesis\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448 -> 0.0133620123598202, mito\[LetterSpace]dysfunction -> 0.0270695257507146, mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new\[LetterSpace]dec -> 1094.58423149719, mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new\[LetterSpace]inc -> 9882.02736076158, mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old\[LetterSpace]dec -> 0.954903499913184, mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old\[LetterSpace]inc -> 0.00586017882122243, mitophagy\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]AMPK\[LetterSpace]pT172 -> 1319.84219165251, mitophagy\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448 -> 645.999307230137, mitophagy\[LetterSpace]new -> 0.22465992989378, mitophagy\[LetterSpace]old -> 0.00122607614891116, scale\[LetterSpace]AMPK\[LetterSpace]pT172\[LetterSpace]obs -> 1.0, scale\[LetterSpace]Akt\[LetterSpace]pS473\[LetterSpace]obs -> 1.0, scale\[LetterSpace]CDKN1A\[LetterSpace]obs -> 1.0, scale\[LetterSpace]CDKN1B\[LetterSpace]obs -> 1.0, scale\[LetterSpace]DNA\[LetterSpace]damage\[LetterSpace]gammaH2AX\[LetterSpace]obs -> 1.0, scale\[LetterSpace]FoxO3a\[LetterSpace]pS253\[LetterSpace]obs -> 1.0, scale\[LetterSpace]FoxO3a\[LetterSpace]total\[LetterSpace]obs -> 1.0, scale\[LetterSpace]JNK\[LetterSpace]pT183\[LetterSpace]obs -> 1.0, scale\[LetterSpace]Mito\[LetterSpace]Mass\[LetterSpace]obs -> 1.0, scale\[LetterSpace]Mito\[LetterSpace]Membr\[LetterSpace]Pot\[LetterSpace]obs -> 1.0, scale\[LetterSpace]Mitophagy\[LetterSpace]obs -> 1.0, scale\[LetterSpace]ROS\[LetterSpace]obs -> 1.0, scale\[LetterSpace]SA\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]obs -> 1.0, scale\[LetterSpace]mTOR\[LetterSpace]pS2448\[LetterSpace]obs -> 1.0, sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]dec -> 0.154821166783837, sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]inc\[LetterSpace]by\[LetterSpace]Mitophagy -> 1.00000000000011*^-06, sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]inc\[LetterSpace]by\[LetterSpace]ROS -> 0.0701139988718817, Cell -> 1.0
};

assignments = {
function\[LetterSpace]2[v_] -> v, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]1\[LetterSpace]1[Akt_,Akt\[LetterSpace]S473\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]insulin_,Insulin_] -> Akt*Akt\[LetterSpace]S473\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]insulin*Insulin, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]2\[LetterSpace]1[Akt\[LetterSpace]pS473_,Akt\[LetterSpace]pS473\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448_,mTORC1\[LetterSpace]pS2448_] -> Akt\[LetterSpace]pS473*Akt\[LetterSpace]pS473\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448*mTORC1\[LetterSpace]pS2448, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]4\[LetterSpace]1[AMPK\[LetterSpace]pT172_,AMPK\[LetterSpace]pT172\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new_,Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new_] -> AMPK\[LetterSpace]pT172*AMPK\[LetterSpace]pT172\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new*Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]6\[LetterSpace]1[Amino\[LetterSpace]Acids_,mTORC1_,mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA_] -> Amino\[LetterSpace]Acids*mTORC1*mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]8\[LetterSpace]1[AMPK\[LetterSpace]pT172_,mTORC1\[LetterSpace]pS2448_,mTORC1\[LetterSpace]pS2448\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]AMPK\[LetterSpace]pT172_] -> AMPK\[LetterSpace]pT172*mTORC1\[LetterSpace]pS2448*mTORC1\[LetterSpace]pS2448\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]AMPK\[LetterSpace]pT172, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]10\[LetterSpace]1[Mitophagy_,mTORC1\[LetterSpace]pS2448_,mitophagy\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448_] -> Mitophagy*mitophagy\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448*mTORC1\[LetterSpace]pS2448, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]11\[LetterSpace]1[Akt\[LetterSpace]pS473_,FoxO3a_,FoxO3a\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473_] -> Akt\[LetterSpace]pS473*FoxO3a*FoxO3a\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]15\[LetterSpace]1[CDKN1A\[LetterSpace]transcr\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]DNA\[LetterSpace]damage_,DNA\[LetterSpace]damage_,FoxO3a_] -> CDKN1A\[LetterSpace]transcr\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]DNA\[LetterSpace]damage*DNA\[LetterSpace]damage*FoxO3a, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]17\[LetterSpace]1[CDKN1B\[LetterSpace]transcr\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]DNA\[LetterSpace]damage_,DNA\[LetterSpace]damage_,FoxO3a_] -> CDKN1B\[LetterSpace]transcr\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]DNA\[LetterSpace]damage*DNA\[LetterSpace]damage*FoxO3a, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]19\[LetterSpace]1[DNA\[LetterSpace]damaged\[LetterSpace]by\[LetterSpace]irradiation_,Irradiation_] -> DNA\[LetterSpace]damaged\[LetterSpace]by\[LetterSpace]irradiation*Irradiation, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]20\[LetterSpace]1[DNA\[LetterSpace]damaged\[LetterSpace]by\[LetterSpace]ROS_,ROS_] -> DNA\[LetterSpace]damaged\[LetterSpace]by\[LetterSpace]ROS*ROS, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]22\[LetterSpace]1[Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new_,ROS\[LetterSpace]prod\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new_] -> Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new*ROS\[LetterSpace]prod\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]25\[LetterSpace]1[JNK_,JNK\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]ROS_,ROS_] -> JNK*JNK\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]ROS*ROS, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]28\[LetterSpace]1[Mitophagy_,sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]inc\[LetterSpace]by\[LetterSpace]Mitophagy_] -> Mitophagy*sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]inc\[LetterSpace]by\[LetterSpace]Mitophagy, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]30\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]turnover_,mTORC1\[LetterSpace]pS2448_,mito\[LetterSpace]biogenesis\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448_] -> mito\[LetterSpace]biogenesis\[LetterSpace]by\[LetterSpace]mTORC1\[LetterSpace]pS2448*Mito\[LetterSpace]mass\[LetterSpace]turnover*mTORC1\[LetterSpace]pS2448, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]32\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]new_,Mitophagy_,mitophagy\[LetterSpace]new_] -> Mitophagy*mitophagy\[LetterSpace]new*Mito\[LetterSpace]mass\[LetterSpace]new, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]33\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]old_,Mitophagy_,mitophagy\[LetterSpace]old_] -> Mitophagy*mitophagy\[LetterSpace]old*Mito\[LetterSpace]mass\[LetterSpace]old, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]41\[LetterSpace]1[Amino\[LetterSpace]Acids_,IKKbeta_,mTORC1_,mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA\[LetterSpace]n\[LetterSpace]IKKbeta_] -> Amino\[LetterSpace]Acids*IKKbeta*mTORC1*mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA\[LetterSpace]n\[LetterSpace]IKKbeta, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]39\[LetterSpace]1[IKKbeta\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]ROS_,ROS_] -> IKKbeta\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]ROS*ROS, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]36\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]old_,mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old\[LetterSpace]inc_] -> Mito\[LetterSpace]mass\[LetterSpace]old*mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old\[LetterSpace]inc, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]35\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]new_,mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new\[LetterSpace]inc_] -> Mito\[LetterSpace]mass\[LetterSpace]new*mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new\[LetterSpace]inc, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]34\[LetterSpace]1[CDKN1A_,Mito\[LetterSpace]mass\[LetterSpace]new_,mito\[LetterSpace]dysfunction_] -> CDKN1A*mito\[LetterSpace]dysfunction*Mito\[LetterSpace]mass\[LetterSpace]new, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]31\[LetterSpace]1[Mito\[LetterSpace]mass\[LetterSpace]turnover_,mTORC1\[LetterSpace]pS2448_,mito\[LetterSpace]biogenesis\[LetterSpace]by\[LetterSpace]AMPK\[LetterSpace]pT172_] -> mito\[LetterSpace]biogenesis\[LetterSpace]by\[LetterSpace]AMPK\[LetterSpace]pT172*Mito\[LetterSpace]mass\[LetterSpace]turnover*mTORC1\[LetterSpace]pS2448, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]27\[LetterSpace]1[ROS_,sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]inc\[LetterSpace]by\[LetterSpace]ROS_] -> ROS*sen\[LetterSpace]ass\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]inc\[LetterSpace]by\[LetterSpace]ROS, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]23\[LetterSpace]1[Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old_,ROS\[LetterSpace]prod\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old_] -> Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old*ROS\[LetterSpace]prod\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]18\[LetterSpace]1[Akt\[LetterSpace]pS473_,CDKN1B_,CDKN1B\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473_] -> Akt\[LetterSpace]pS473*CDKN1B*CDKN1B\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]16\[LetterSpace]1[Akt\[LetterSpace]pS473_,CDKN1A_,CDKN1A\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473_] -> Akt\[LetterSpace]pS473*CDKN1A*CDKN1A\[LetterSpace]inactiv\[LetterSpace]by\[LetterSpace]Akt\[LetterSpace]pS473, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]12\[LetterSpace]1[FoxO3a\[LetterSpace]pS253_,FoxO3a\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]JNK\[LetterSpace]pT183_,JNK\[LetterSpace]pT183_] -> FoxO3a\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]JNK\[LetterSpace]pT183*FoxO3a\[LetterSpace]pS253*JNK\[LetterSpace]pT183, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]9\[LetterSpace]1[AMPK\[LetterSpace]pT172_,FoxO3a_,mitophagy\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]AMPK\[LetterSpace]pT172_] -> AMPK\[LetterSpace]pT172*FoxO3a*mitophagy\[LetterSpace]activ\[LetterSpace]by\[LetterSpace]FoxO3a\[LetterSpace]n\[LetterSpace]AMPK\[LetterSpace]pT172, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]7\[LetterSpace]1[Akt\[LetterSpace]pS473_,Amino\[LetterSpace]Acids_,mTORC1_,mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA\[LetterSpace]n\[LetterSpace]Akt\[LetterSpace]pS473_] -> Akt\[LetterSpace]pS473*Amino\[LetterSpace]Acids*mTORC1*mTORC1\[LetterSpace]S2448\[LetterSpace]phos\[LetterSpace]by\[LetterSpace]AA\[LetterSpace]n\[LetterSpace]Akt\[LetterSpace]pS473, function\[LetterSpace]4\[LetterSpace]reaction\[LetterSpace]5\[LetterSpace]1[AMPK\[LetterSpace]pT172_,AMPK\[LetterSpace]pT172\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old_,Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old_] -> AMPK\[LetterSpace]pT172*AMPK\[LetterSpace]pT172\[LetterSpace]dephos\[LetterSpace]by\[LetterSpace]Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old*Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old, Akt\[LetterSpace]pS473\[LetterSpace]obs -> scale\[LetterSpace]Akt\[LetterSpace]pS473\[LetterSpace]obs*Akt\[LetterSpace]pS473[t], Irradiation -> Piecewise[{{0, t < -1}}, Piecewise[{{0, t < 0}}, Piecewise[{{1, t < 0.003472}}, 0]]], Amino\[LetterSpace]Acids -> 1, Insulin -> 1, DNA\[LetterSpace]damage\[LetterSpace]gammaH2AX\[LetterSpace]obs -> scale\[LetterSpace]DNA\[LetterSpace]damage\[LetterSpace]gammaH2AX\[LetterSpace]obs*DNA\[LetterSpace]damage[t], mTOR\[LetterSpace]pS2448\[LetterSpace]obs -> scale\[LetterSpace]mTOR\[LetterSpace]pS2448\[LetterSpace]obs*mTORC1\[LetterSpace]pS2448[t], FoxO3a\[LetterSpace]pS253\[LetterSpace]obs -> scale\[LetterSpace]FoxO3a\[LetterSpace]pS253\[LetterSpace]obs*FoxO3a\[LetterSpace]pS253[t], AMPK\[LetterSpace]pT172\[LetterSpace]obs -> scale\[LetterSpace]AMPK\[LetterSpace]pT172\[LetterSpace]obs*AMPK\[LetterSpace]pT172[t], Mito\[LetterSpace]Mass\[LetterSpace]obs -> scale\[LetterSpace]Mito\[LetterSpace]Mass\[LetterSpace]obs*(Mito\[LetterSpace]mass\[LetterSpace]new[t] + Mito\[LetterSpace]mass\[LetterSpace]old[t]), CDKN1A\[LetterSpace]obs -> scale\[LetterSpace]CDKN1A\[LetterSpace]obs*CDKN1A[t], CDKN1B\[LetterSpace]obs -> scale\[LetterSpace]CDKN1B\[LetterSpace]obs*CDKN1B[t], Mito\[LetterSpace]Membr\[LetterSpace]Pot\[LetterSpace]obs -> scale\[LetterSpace]Mito\[LetterSpace]Membr\[LetterSpace]Pot\[LetterSpace]obs*(Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new[t] + Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old[t]), Mitophagy\[LetterSpace]obs -> scale\[LetterSpace]Mitophagy\[LetterSpace]obs*Mitophagy[t], FoxO3a\[LetterSpace]total\[LetterSpace]obs -> scale\[LetterSpace]FoxO3a\[LetterSpace]total\[LetterSpace]obs*(FoxO3a[t] + FoxO3a\[LetterSpace]pS253[t]), ROS\[LetterSpace]obs -> scale\[LetterSpace]ROS\[LetterSpace]obs*ROS[t], JNK\[LetterSpace]pT183\[LetterSpace]obs -> scale\[LetterSpace]JNK\[LetterSpace]pT183\[LetterSpace]obs*JNK\[LetterSpace]pT183[t], SA\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]obs -> scale\[LetterSpace]SA\[LetterSpace]beta\[LetterSpace]gal\[LetterSpace]obs*SA\[LetterSpace]beta\[LetterSpace]gal[t]
};

events = {

};

speciesAnnotations = {
Insulin[t]->"http://identifiers.org/chebi/CHEBI:5931", Nil[t]->"http://identifiers.org/biomodels.sbo/SBO:0000291", ROS[t]->"http://identifiers.org/chebi/CHEBI:26523"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
AMPK'[t] == 1.0*reaction\[LetterSpace]4 +1.0*reaction\[LetterSpace]5 -1.0*reaction\[LetterSpace]3, AMPK\[LetterSpace]pT172'[t] == 1.0*reaction\[LetterSpace]3 -1.0*reaction\[LetterSpace]4 -1.0*reaction\[LetterSpace]5, Akt'[t] == 1.0*reaction\[LetterSpace]2 -1.0*reaction\[LetterSpace]1, Akt\[LetterSpace]pS473'[t] == 1.0*reaction\[LetterSpace]1 -1.0*reaction\[LetterSpace]2, CDKN1A'[t] == 1.0*reaction\[LetterSpace]15 -1.0*reaction\[LetterSpace]16, CDKN1B'[t] == 1.0*reaction\[LetterSpace]17 -1.0*reaction\[LetterSpace]18, DNA\[LetterSpace]damage'[t] == 1.0*reaction\[LetterSpace]19 +1.0*reaction\[LetterSpace]20 -1.0*reaction\[LetterSpace]21, FoxO3a'[t] == 1.0*reaction\[LetterSpace]12 +1.0*reaction\[LetterSpace]14 -1.0*reaction\[LetterSpace]11, FoxO3a\[LetterSpace]pS253'[t] == 1.0*reaction\[LetterSpace]11 -1.0*reaction\[LetterSpace]12 -1.0*reaction\[LetterSpace]13, IKKbeta'[t] == 1.0*reaction\[LetterSpace]39 -1.0*reaction\[LetterSpace]40, JNK'[t] == 1.0*reaction\[LetterSpace]26 -1.0*reaction\[LetterSpace]25, JNK\[LetterSpace]pT183'[t] == 1.0*reaction\[LetterSpace]25 -1.0*reaction\[LetterSpace]26, Mito\[LetterSpace]mass\[LetterSpace]new'[t] == 1.0*reaction\[LetterSpace]30 +1.0*reaction\[LetterSpace]31 -1.0*reaction\[LetterSpace]32 -1.0*reaction\[LetterSpace]34, Mito\[LetterSpace]mass\[LetterSpace]old'[t] == 1.0*reaction\[LetterSpace]34 -1.0*reaction\[LetterSpace]33, Mito\[LetterSpace]mass\[LetterSpace]turnover'[t] == 1.0*reaction\[LetterSpace]32 +1.0*reaction\[LetterSpace]33 -1.0*reaction\[LetterSpace]30 -1.0*reaction\[LetterSpace]31, Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]new'[t] == 1.0*reaction\[LetterSpace]35 -1.0*reaction\[LetterSpace]37, Mito\[LetterSpace]membr\[LetterSpace]pot\[LetterSpace]old'[t] == 1.0*reaction\[LetterSpace]36 -1.0*reaction\[LetterSpace]38, Mitophagy'[t] == 1.0*reaction\[LetterSpace]9 -1.0*reaction\[LetterSpace]10, Nil'[t] == 1.0*reaction\[LetterSpace]10 +1.0*reaction\[LetterSpace]13 +1.0*reaction\[LetterSpace]16 +1.0*reaction\[LetterSpace]18 +1.0*reaction\[LetterSpace]21 +1.0*reaction\[LetterSpace]24 +1.0*reaction\[LetterSpace]37 +1.0*reaction\[LetterSpace]38 +1.0*reaction\[LetterSpace]40 , ROS'[t] == 1.0*reaction\[LetterSpace]22 +1.0*reaction\[LetterSpace]23 -1.0*reaction\[LetterSpace]24, SA\[LetterSpace]beta\[LetterSpace]gal'[t] == 1.0*reaction\[LetterSpace]27 +1.0*reaction\[LetterSpace]28 -1.0*reaction\[LetterSpace]29, mTORC1'[t] == 1.0*reaction\[LetterSpace]8 -1.0*reaction\[LetterSpace]6 -1.0*reaction\[LetterSpace]7 -1.0*reaction\[LetterSpace]41, mTORC1\[LetterSpace]pS2448'[t] == 1.0*reaction\[LetterSpace]6 +1.0*reaction\[LetterSpace]7 +1.0*reaction\[LetterSpace]41 -1.0*reaction\[LetterSpace]8
};
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]}]