(* 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 = {
ATMA[t], ATMI[t], Abeta[t], AbetaDimer[t], AbetaDimer\[LetterSpace]antiAb[t], AbetaPlaque[t], AbetaPlaque\[LetterSpace]GliaA[t], Abeta\[LetterSpace]antiAb[t], AggAbeta\[LetterSpace]Proteasome[t], AggTau[t], AggTau\[LetterSpace]Proteasome[t], DUB[t], E1[t], E1\[LetterSpace]Ub[t], E2[t], E2\[LetterSpace]Ub[t], GSK3b[t], GSK3b\[LetterSpace]p53[t], GSK3b\[LetterSpace]p53\[LetterSpace]P[t], GliaA[t], GliaI[t], GliaM1[t], GliaM2[t], IR[t], MT\[LetterSpace]Tau[t], Mdm2[t], Mdm2DUB[t], Mdm2\[LetterSpace]P[t], Mdm2\[LetterSpace]P1\[LetterSpace]p53\[LetterSpace]Ub4[t], Mdm2\[LetterSpace]P\[LetterSpace]Ub[t], Mdm2\[LetterSpace]P\[LetterSpace]Ub2[t], Mdm2\[LetterSpace]P\[LetterSpace]Ub3[t], Mdm2\[LetterSpace]P\[LetterSpace]Ub4[t], Mdm2\[LetterSpace]P\[LetterSpace]Ub4\[LetterSpace]Proteasome[t], Mdm2\[LetterSpace]Ub[t], Mdm2\[LetterSpace]Ub2[t], Mdm2\[LetterSpace]Ub3[t], Mdm2\[LetterSpace]Ub4[t], Mdm2\[LetterSpace]Ub4\[LetterSpace]Proteasome[t], Mdm2\[LetterSpace]mRNA[t], Mdm2\[LetterSpace]p53[t], Mdm2\[LetterSpace]p53\[LetterSpace]Ub[t], Mdm2\[LetterSpace]p53\[LetterSpace]Ub2[t], Mdm2\[LetterSpace]p53\[LetterSpace]Ub3[t], Mdm2\[LetterSpace]p53\[LetterSpace]Ub4[t], NFT[t], PP1[t], Proteasome[t], Proteasome\[LetterSpace]Tau[t], ROS[t], Tau[t], Tau\[LetterSpace]P1[t], Tau\[LetterSpace]P2[t], Ub[t], antiAb[t], damDNA[t], degAbetaGlia[t], disaggPlaque1[t], disaggPlaque2[t], p53[t], p53DUB[t], p53\[LetterSpace]P[t], p53\[LetterSpace]Ub4\[LetterSpace]Proteasome[t], p53\[LetterSpace]mRNA[t]
};

initialValues = {
ATMA[0] == 0.0, ATMI[0] == 200.0, Abeta[0] == 0.0, AbetaDimer[0] == 0.0, AbetaDimer\[LetterSpace]antiAb[0] == 0.0, AbetaPlaque[0] == 0.0, AbetaPlaque\[LetterSpace]GliaA[0] == 0.0, Abeta\[LetterSpace]antiAb[0] == 0.0, AggAbeta\[LetterSpace]Proteasome[0] == 0.0, AggTau[0] == 0.0, AggTau\[LetterSpace]Proteasome[0] == 0.0, DUB[0] == 200.0, E1[0] == 100.0, E1\[LetterSpace]Ub[0] == 0.0, E2[0] == 100.0, E2\[LetterSpace]Ub[0] == 0.0, GSK3b[0] == 500.0, GSK3b\[LetterSpace]p53[0] == 0.0, GSK3b\[LetterSpace]p53\[LetterSpace]P[0] == 0.0, GliaA[0] == 0.0, GliaI[0] == 100.0, GliaM1[0] == 0.0, GliaM2[0] == 0.0, IR[0] == 0.0, MT\[LetterSpace]Tau[0] == 100.0, Mdm2[0] == 5.0, Mdm2DUB[0] == 200.0, Mdm2\[LetterSpace]P[0] == 0.0, Mdm2\[LetterSpace]P1\[LetterSpace]p53\[LetterSpace]Ub4[0] == 0.0, Mdm2\[LetterSpace]P\[LetterSpace]Ub[0] == 0.0, Mdm2\[LetterSpace]P\[LetterSpace]Ub2[0] == 0.0, Mdm2\[LetterSpace]P\[LetterSpace]Ub3[0] == 0.0, Mdm2\[LetterSpace]P\[LetterSpace]Ub4[0] == 0.0, Mdm2\[LetterSpace]P\[LetterSpace]Ub4\[LetterSpace]Proteasome[0] == 0.0, Mdm2\[LetterSpace]Ub[0] == 0.0, Mdm2\[LetterSpace]Ub2[0] == 0.0, Mdm2\[LetterSpace]Ub3[0] == 0.0, Mdm2\[LetterSpace]Ub4[0] == 0.0, Mdm2\[LetterSpace]Ub4\[LetterSpace]Proteasome[0] == 0.0, Mdm2\[LetterSpace]mRNA[0] == 10.0, Mdm2\[LetterSpace]p53[0] == 95.0, Mdm2\[LetterSpace]p53\[LetterSpace]Ub[0] == 0.0, Mdm2\[LetterSpace]p53\[LetterSpace]Ub2[0] == 0.0, Mdm2\[LetterSpace]p53\[LetterSpace]Ub3[0] == 0.0, Mdm2\[LetterSpace]p53\[LetterSpace]Ub4[0] == 0.0, NFT[0] == 0.0, PP1[0] == 50.0, Proteasome[0] == 500.0, Proteasome\[LetterSpace]Tau[0] == 0.0, ROS[0] == 0.0, Tau[0] == 0.0, Tau\[LetterSpace]P1[0] == 0.0, Tau\[LetterSpace]P2[0] == 0.0, Ub[0] == 4000.0, antiAb[0] == 0.0, damDNA[0] == 0.0, degAbetaGlia[0] == 0.0, disaggPlaque1[0] == 0.0, disaggPlaque2[0] == 0.0, p53[0] == 5.0, p53DUB[0] == 200.0, p53\[LetterSpace]P[0] == 0.0, p53\[LetterSpace]Ub4\[LetterSpace]Proteasome[0] == 0.0, p53\[LetterSpace]mRNA[0] == 10.0
};

rates = {
ATMInactivation, ATMactivation, AbetaAggregation1, AbetaBindingToGlia, AbetaDegradation, AbetaDimer\[LetterSpace]antiAbBinding, AbetaDimer\[LetterSpace]antiAbDegredation, AbetaDisaggregation1, AbetaDisaggregation3, AbetaDisaggregation4, AbetaPlaqueClearanceByGlia, AbetaPlaqueFormation1, AbetaPlaqueGrowth, AbetaROSproduction1, AbetaReleaseFromGlia, Abeta\[LetterSpace]antiAbBinding, Abeta\[LetterSpace]antiAbDegredation, Abetaproduction1, Abetaproduction2, Abetaproduction3, AggAbetaROSproduction2, DNAdamage, DNArepair, Degradationp53\[LetterSpace]Ub4, E1UbBinding, E2UbBinding, GSK3\[LetterSpace]p53PRelease, GSK3p53Binding, GSK3p53PBinding, GSK3p53Release, GliaActivationStep1, GliaActivationStep2, GliaActivationStep3, GliaInactivationStep1, GliaInactivationStep2, GliaInactivationStep3, Mdm2Degradation, Mdm2Deubiquitination1, Mdm2Deubiquitination2, Mdm2Deubiquitination3, Mdm2Deubiquitination4, Mdm2GSK3phosphorylation1, Mdm2GSK3phosphorylation2, Mdm2GSK3phosphorylation3, Mdm2PDegradation, Mdm2PDeubiquitination1, Mdm2PDeubiquitination2, Mdm2PDeubiquitination3, Mdm2PDeubiquitination4, Mdm2PProteasomeBinding1, Mdm2PUbiquitination, Mdm2PpolyUbiquitination1, Mdm2PpolyUbiquitination2, Mdm2PpolyUbiquitination3, Mdm2ProteasomeBinding1, Mdm2Synthesis, Mdm2Ubiquitination, Mdm2dephosphorylation, Mdm2mRNADegradation, Mdm2mRNASynthesis1, Mdm2mRNASynthesis2, Mdm2mRNASynthesis3, Mdm2mRNASynthesis4, Mdm2phosphorylation, Mdm2polyUbiquitination1, Mdm2polyUbiquitination2, Mdm2polyUbiquitination3, P53Mdm2Binding, P53Mdm2Release, PlaqueROSproduction, ProteasomeInhibitionAbeta, ProteasomeInhibitionAggTau, ROSDNAdamage, ROSgenerationByGlia, ROSremoval, TangleFormation1, TangleFormation2, Tau20SProteasomeDegradation, TauAggregation1, TauAggregation2, TauMTbinding, TauMTrelease, TauP1Aggregation1, TauP1Aggregation2, TauP2Aggregation1, TauP2Aggregation2, TauProteasomeBinding, TauSynthesis, Taudephosphorylation1, Taudephosphorylation2, Tauphosphorylation1, Tauphosphorylation2, Tauphosphorylation3, Tauphosphorylation4, Tauphosphorylation5, Tauphosphorylation6, antiAbRemoval, p53Deubiquitination1, p53Deubiquitination2, p53Deubiquitination3, p53Deubiqutination4, p53Monoubiquitination, p53Polyubiquitination1, p53Polyubiquitination2, p53Polyubiquitination3, p53ProteasomeBinding1, p53Synthesis, p53dephosphorylation, p53mRNADegradation, p53mRNASynthesis, p53phosphorylation, p53transcriptionViaAbeta
};

rateEquations = {
ATMInactivation -> kinactATM*ATMA[t], ATMactivation -> kactATM*ATMI[t]*damDNA[t], AbetaAggregation1 -> 0.5*kaggAbeta*Abeta[t]^2, AbetaBindingToGlia -> kbinAbetaGlia*AbetaPlaque[t]*GliaA[t], AbetaDegradation -> kdegAbeta*Abeta[t], AbetaDimer\[LetterSpace]antiAbBinding -> kbinAbantiAb*AbetaDimer[t]*antiAb[t], AbetaDimer\[LetterSpace]antiAbDegredation -> 10*kdegAbeta*AbetaDimer\[LetterSpace]antiAb[t], AbetaDisaggregation1 -> kdisaggAbeta*AbetaDimer[t], AbetaDisaggregation3 -> kdisaggAbeta1*AbetaPlaque[t], AbetaDisaggregation4 -> kdisaggAbeta2*AbetaPlaque[t]*antiAb[t], AbetaPlaqueClearanceByGlia -> kdegAbetaGlia*AbetaPlaque\[LetterSpace]GliaA[t], AbetaPlaqueFormation1 -> 0.5*kpf*AbetaDimer[t]^2, AbetaPlaqueGrowth -> (kpg*AbetaDimer[t]*AbetaPlaque[t]^2)/(kpghalf^2 + AbetaPlaque[t]^2), AbetaROSproduction1 -> kgenROSAbeta*Abeta[t], AbetaReleaseFromGlia -> krelAbetaGlia*AbetaPlaque\[LetterSpace]GliaA[t], Abeta\[LetterSpace]antiAbBinding -> kbinAbantiAb*Abeta[t]*antiAb[t], Abeta\[LetterSpace]antiAbDegredation -> 10*kdegAbeta*Abeta\[LetterSpace]antiAb[t], Abetaproduction1 -> kprodAbeta*Source, Abetaproduction2 -> kprodAbeta2*GSK3b\[LetterSpace]p53[t], Abetaproduction3 -> kprodAbeta2*GSK3b\[LetterSpace]p53\[LetterSpace]P[t], AggAbetaROSproduction2 -> kgenROSAbeta*AggAbeta\[LetterSpace]Proteasome[t], DNAdamage -> kdam*IR[t], DNArepair -> krepair*damDNA[t], Degradationp53\[LetterSpace]Ub4 -> (ATP*kdegp53*kproteff*p53\[LetterSpace]Ub4\[LetterSpace]Proteasome[t])/(5000 + ATP), E1UbBinding -> (ATP*kbinE1Ub*E1[t]*Ub[t])/(5000 + ATP), E2UbBinding -> kbinE2Ub*E1\[LetterSpace]Ub[t]*E2[t], GSK3\[LetterSpace]p53PRelease -> krelGSK3bp53*GSK3b\[LetterSpace]p53\[LetterSpace]P[t], GSK3p53Binding -> kbinGSK3bp53*GSK3b[t]*p53[t], GSK3p53PBinding -> kbinGSK3bp53*GSK3b[t]*p53\[LetterSpace]P[t], GSK3p53Release -> krelGSK3bp53*GSK3b\[LetterSpace]p53[t], GliaActivationStep1 -> kactglia1*AbetaPlaque[t]*GliaI[t], GliaActivationStep2 -> kactglia1*AbetaPlaque[t]*GliaM1[t], GliaActivationStep3 -> kactglia2*antiAb[t]*GliaM2[t], GliaInactivationStep1 -> kinactglia1*GliaA[t], GliaInactivationStep2 -> kinactglia2*GliaM2[t], GliaInactivationStep3 -> kinactglia2*GliaM1[t], Mdm2Degradation -> kdegMdm2*kproteff*Mdm2\[LetterSpace]Ub4\[LetterSpace]Proteasome[t], Mdm2Deubiquitination1 -> kactDUBMdm2*Mdm2DUB[t]*Mdm2\[LetterSpace]Ub[t], Mdm2Deubiquitination2 -> kactDUBMdm2*Mdm2DUB[t]*Mdm2\[LetterSpace]Ub2[t], Mdm2Deubiquitination3 -> kactDUBMdm2*Mdm2DUB[t]*Mdm2\[LetterSpace]Ub3[t], Mdm2Deubiquitination4 -> kactDUBMdm2*Mdm2DUB[t]*Mdm2\[LetterSpace]Ub4[t], Mdm2GSK3phosphorylation1 -> kphosMdm2GSK3b*GSK3b[t]*Mdm2\[LetterSpace]p53\[LetterSpace]Ub4[t], Mdm2GSK3phosphorylation2 -> kphosMdm2GSK3bp53*GSK3b\[LetterSpace]p53[t]*Mdm2\[LetterSpace]p53\[LetterSpace]Ub4[t], Mdm2GSK3phosphorylation3 -> kphosMdm2GSK3bp53*GSK3b\[LetterSpace]p53\[LetterSpace]P[t]*Mdm2\[LetterSpace]p53\[LetterSpace]Ub4[t], Mdm2PDegradation -> kdegMdm2*kproteff*Mdm2\[LetterSpace]P\[LetterSpace]Ub4\[LetterSpace]Proteasome[t], Mdm2PDeubiquitination1 -> kactDUBMdm2*Mdm2DUB[t]*Mdm2\[LetterSpace]P\[LetterSpace]Ub[t], Mdm2PDeubiquitination2 -> kactDUBMdm2*Mdm2DUB[t]*Mdm2\[LetterSpace]P\[LetterSpace]Ub2[t], Mdm2PDeubiquitination3 -> kactDUBMdm2*Mdm2DUB[t]*Mdm2\[LetterSpace]P\[LetterSpace]Ub3[t], Mdm2PDeubiquitination4 -> kactDUBMdm2*Mdm2DUB[t]*Mdm2\[LetterSpace]P\[LetterSpace]Ub4[t], Mdm2PProteasomeBinding1 -> kbinProt*Mdm2\[LetterSpace]P\[LetterSpace]Ub4[t]*Proteasome[t], Mdm2PUbiquitination -> kMdm2PUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]P[t], Mdm2PpolyUbiquitination1 -> kMdm2PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]P\[LetterSpace]Ub[t], Mdm2PpolyUbiquitination2 -> kMdm2PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]P\[LetterSpace]Ub2[t], Mdm2PpolyUbiquitination3 -> kMdm2PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]P\[LetterSpace]Ub3[t], Mdm2ProteasomeBinding1 -> kbinProt*Mdm2\[LetterSpace]Ub4[t]*Proteasome[t], Mdm2Synthesis -> ksynMdm2*Mdm2\[LetterSpace]mRNA[t], Mdm2Ubiquitination -> kMdm2Ub*E2\[LetterSpace]Ub[t]*Mdm2[t], Mdm2dephosphorylation -> kdephosMdm2*Mdm2\[LetterSpace]P[t], Mdm2mRNADegradation -> kdegMdm2mRNA*Mdm2\[LetterSpace]mRNA[t], Mdm2mRNASynthesis1 -> ksynMdm2mRNA*p53[t], Mdm2mRNASynthesis2 -> ksynMdm2mRNA*p53\[LetterSpace]P[t], Mdm2mRNASynthesis3 -> ksynMdm2mRNAGSK3bp53*GSK3b\[LetterSpace]p53[t], Mdm2mRNASynthesis4 -> ksynMdm2mRNAGSK3bp53*GSK3b\[LetterSpace]p53\[LetterSpace]P[t], Mdm2phosphorylation -> kphosMdm2*ATMA[t]*Mdm2[t], Mdm2polyUbiquitination1 -> kMdm2PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]Ub[t], Mdm2polyUbiquitination2 -> kMdm2PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]Ub2[t], Mdm2polyUbiquitination3 -> kMdm2PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]Ub3[t], P53Mdm2Binding -> kbinMdm2p53*Mdm2[t]*p53[t], P53Mdm2Release -> krelMdm2p53*Mdm2\[LetterSpace]p53[t], PlaqueROSproduction -> kgenROSPlaque*AbetaPlaque[t], ProteasomeInhibitionAbeta -> kinhibprot*AbetaDimer[t]*Proteasome[t], ProteasomeInhibitionAggTau -> kinhibprot*AggTau[t]*Proteasome[t], ROSDNAdamage -> kdamROS*ROS[t], ROSgenerationByGlia -> kgenROSGlia*AbetaPlaque\[LetterSpace]GliaA[t], ROSremoval -> kremROS*ROS[t], TangleFormation1 -> 0.5*ktangfor*AggTau[t]^2, TangleFormation2 -> ktangfor*AggTau[t]*NFT[t], Tau20SProteasomeDegradation -> kdegTau20SProt*Proteasome\[LetterSpace]Tau[t], TauAggregation1 -> 0.5*kaggTau*Tau[t]^2, TauAggregation2 -> kaggTau*AggTau[t]*Tau[t], TauMTbinding -> kbinMTTau*Tau[t], TauMTrelease -> krelMTTau*MT\[LetterSpace]Tau[t], TauP1Aggregation1 -> 0.5*kaggTauP1*Tau\[LetterSpace]P1[t]^2, TauP1Aggregation2 -> kaggTauP1*AggTau[t]*Tau\[LetterSpace]P1[t], TauP2Aggregation1 -> 0.5*kaggTauP2*Tau\[LetterSpace]P2[t]^2, TauP2Aggregation2 -> kaggTauP2*AggTau[t]*Tau\[LetterSpace]P2[t], TauProteasomeBinding -> kbinTauProt*Proteasome[t]*Tau[t], TauSynthesis -> ksynTau*Source, Taudephosphorylation1 -> kdephospTau*PP1[t]*Tau\[LetterSpace]P2[t], Taudephosphorylation2 -> kdephospTau*PP1[t]*Tau\[LetterSpace]P1[t], Tauphosphorylation1 -> kphospTauGSK3bp53*GSK3b\[LetterSpace]p53[t]*Tau[t], Tauphosphorylation2 -> kphospTauGSK3bp53*GSK3b\[LetterSpace]p53[t]*Tau\[LetterSpace]P1[t], Tauphosphorylation3 -> kphospTauGSK3bp53*GSK3b\[LetterSpace]p53\[LetterSpace]P[t]*Tau[t], Tauphosphorylation4 -> kphospTauGSK3bp53*GSK3b\[LetterSpace]p53\[LetterSpace]P[t]*Tau\[LetterSpace]P1[t], Tauphosphorylation5 -> kphospTauGSK3b*GSK3b[t]*Tau[t], Tauphosphorylation6 -> kphospTauGSK3b*GSK3b[t]*Tau\[LetterSpace]P1[t], antiAbRemoval -> kdegAntiAb*antiAb[t], p53Deubiquitination1 -> kactDUBp53*Mdm2\[LetterSpace]p53\[LetterSpace]Ub[t]*p53DUB[t], p53Deubiquitination2 -> kactDUBp53*Mdm2\[LetterSpace]p53\[LetterSpace]Ub2[t]*p53DUB[t], p53Deubiquitination3 -> kactDUBp53*Mdm2\[LetterSpace]p53\[LetterSpace]Ub3[t]*p53DUB[t], p53Deubiqutination4 -> kactDUBp53*Mdm2\[LetterSpace]p53\[LetterSpace]Ub4[t]*p53DUB[t], p53Monoubiquitination -> kp53Ub*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]p53[t], p53Polyubiquitination1 -> kp53PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]p53\[LetterSpace]Ub[t], p53Polyubiquitination2 -> kp53PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]p53\[LetterSpace]Ub2[t], p53Polyubiquitination3 -> kp53PolyUb*E2\[LetterSpace]Ub[t]*Mdm2\[LetterSpace]p53\[LetterSpace]Ub3[t], p53ProteasomeBinding1 -> kbinProt*Mdm2\[LetterSpace]P1\[LetterSpace]p53\[LetterSpace]Ub4[t]*Proteasome[t], p53Synthesis -> ksynp53*p53\[LetterSpace]mRNA[t], p53dephosphorylation -> kdephosp53*p53\[LetterSpace]P[t], p53mRNADegradation -> kdegp53mRNA*p53\[LetterSpace]mRNA[t], p53mRNASynthesis -> ksynp53mRNA*Source, p53phosphorylation -> kphosp53*ATMA[t]*p53[t], p53transcriptionViaAbeta -> ksynp53mRNAAbeta*Abeta[t]
};

parameters = {
kMdm2PUb -> 6.84*^-06, kMdm2PolyUb -> 0.00456, kMdm2Ub -> 4.56*^-06, kactATM -> 0.0001, kactDUBMdm2 -> 1*^-07, kactDUBProtp53 -> 0.0001, kactDUBp53 -> 1*^-07, kactglia1 -> 6*^-07, kactglia2 -> 6*^-07, kaggAbeta -> 3*^-06, kaggTau -> 1*^-08, kaggTauP1 -> 1*^-08, kaggTauP2 -> 1*^-07, kbinAbantiAb -> 1*^-06, kbinAbetaGlia -> 1*^-05, kbinE1Ub -> 0.0002, kbinE2Ub -> 0.001, kbinGSK3bp53 -> 2*^-06, kbinMTTau -> 0.1, kbinMdm2p53 -> 0.001155, kbinProt -> 2*^-06, kbinTauProt -> 1.925*^-07, kdam -> 0.08, kdamROS -> 1*^-05, kdegAbeta -> 1.5*^-05, kdegAbetaGlia -> 0.005, kdegAntiAb -> 2.75*^-06, kdegMdm2 -> 0.01, kdegMdm2mRNA -> 0.0005, kdegTau20SProt -> 0.01, kdegp53 -> 0.005, kdegp53mRNA -> 0.0001, kdephosMdm2 -> 0.5, kdephosp53 -> 0.5, kdephospTau -> 0.01, kdisaggAbeta -> 1*^-06, kdisaggAbeta1 -> 0.0002, kdisaggAbeta2 -> 1*^-06, kgenROSAbeta -> 2*^-05, kgenROSGlia -> 1*^-05, kgenROSPlaque -> 1*^-05, kinactATM -> 0.0005, kinactglia1 -> 5*^-06, kinactglia2 -> 5*^-06, kinhibprot -> 1*^-07, kp53PolyUb -> 0.01, kp53Ub -> 5*^-05, kpf -> 0.2, kpg -> 0.15, kpghalf -> 10.0, kphosMdm2 -> 2.0, kphosMdm2GSK3b -> 0.005, kphosMdm2GSK3bp53 -> 0.5, kphosp53 -> 0.0002, kphospTauGSK3b -> 0.0002, kphospTauGSK3bp53 -> 0.1, kprodAbeta -> 1.86*^-05, kprodAbeta2 -> 1.86*^-05, kproteff -> 1.0, krelAbetaGlia -> 5*^-05, krelGSK3bp53 -> 0.002, krelMTTau -> 0.0001, krelMdm2p53 -> 1.155*^-05, kremROS -> 7*^-05, krepair -> 2*^-05, ksynMdm2 -> 0.000495, ksynMdm2mRNA -> 0.0005, ksynMdm2mRNAGSK3bp53 -> 0.0007, ksynTau -> 8*^-05, ksynp53 -> 0.007, ksynp53mRNA -> 0.001, ksynp53mRNAAbeta -> 1*^-05, ktangfor -> 0.001, ADP -> 1000.0, AMP -> 1000.0, ATP -> 10000.0, Sink -> 1.0, Source -> 1.0, cell -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
ATMA'[t] == 1.0*ATMactivation +1.0*p53phosphorylation +1.0*Mdm2phosphorylation -1.0*p53phosphorylation -1.0*Mdm2phosphorylation -1.0*ATMInactivation, ATMI'[t] == 1.0*ATMInactivation -1.0*ATMactivation, Abeta'[t] == 1.0*Abetaproduction1 +1.0*Abetaproduction2 +1.0*Abetaproduction3 +1.0*p53transcriptionViaAbeta +1.0*AbetaROSproduction1 +2.0*AbetaDisaggregation1 -1.0*AbetaDegradation -1.0*p53transcriptionViaAbeta -1.0*AbetaROSproduction1 -2.0*AbetaAggregation1 -1.0*Abeta\[LetterSpace]antiAbBinding, AbetaDimer'[t] == 1.0*AbetaAggregation1 +1.0*AbetaDisaggregation3 +1.0*AbetaDisaggregation4 -1.0*ProteasomeInhibitionAbeta -2.0*AbetaPlaqueFormation1 -1.0*AbetaPlaqueGrowth -1.0*AbetaDisaggregation1 -1.0*AbetaDimer\[LetterSpace]antiAbBinding, AbetaDimer\[LetterSpace]antiAb'[t] == 1.0*AbetaDimer\[LetterSpace]antiAbBinding -1.0*AbetaDimer\[LetterSpace]antiAbDegredation, AbetaPlaque'[t] == 1.0*PlaqueROSproduction +1.0*AbetaPlaqueFormation1 +2.0*AbetaPlaqueGrowth +1.0*GliaActivationStep1 +1.0*GliaActivationStep2 +1.0*AbetaReleaseFromGlia -1.0*PlaqueROSproduction -1.0*AbetaPlaqueGrowth -1.0*AbetaDisaggregation3 -1.0*AbetaDisaggregation4 -1.0*GliaActivationStep1 -1.0*GliaActivationStep2 -1.0*AbetaBindingToGlia, AbetaPlaque\[LetterSpace]GliaA'[t] == 1.0*AbetaBindingToGlia +1.0*ROSgenerationByGlia -1.0*AbetaReleaseFromGlia -1.0*AbetaPlaqueClearanceByGlia -1.0*ROSgenerationByGlia, Abeta\[LetterSpace]antiAb'[t] == 1.0*Abeta\[LetterSpace]antiAbBinding -1.0*Abeta\[LetterSpace]antiAbDegredation, AggAbeta\[LetterSpace]Proteasome'[t] == 1.0*ProteasomeInhibitionAbeta +1.0*AggAbetaROSproduction2 -1.0*AggAbetaROSproduction2, AggTau'[t] == 2.0*TauP1Aggregation1 +2.0*TauP1Aggregation2 +2.0*TauP2Aggregation1 +2.0*TauP2Aggregation2 +2.0*TauAggregation1 +2.0*TauAggregation2 -1.0*TauP1Aggregation2 -1.0*TauP2Aggregation2 -1.0*TauAggregation2 -2.0*TangleFormation1 -1.0*TangleFormation2 -1.0*ProteasomeInhibitionAggTau, AggTau\[LetterSpace]Proteasome'[t] == 1.0*ProteasomeInhibitionAggTau , DUB'[t] == 0.0 , E1'[t] == 1.0*E2UbBinding -1.0*E1UbBinding, E1\[LetterSpace]Ub'[t] == 1.0*E1UbBinding -1.0*E2UbBinding, E2'[t] == 1.0*Mdm2Ubiquitination +1.0*Mdm2polyUbiquitination1 +1.0*Mdm2polyUbiquitination2 +1.0*Mdm2polyUbiquitination3 +1.0*p53Monoubiquitination +1.0*p53Polyubiquitination1 +1.0*p53Polyubiquitination2 +1.0*p53Polyubiquitination3 +1.0*Mdm2PUbiquitination +1.0*Mdm2PpolyUbiquitination1 +1.0*Mdm2PpolyUbiquitination2 +1.0*Mdm2PpolyUbiquitination3 -1.0*E2UbBinding, E2\[LetterSpace]Ub'[t] == 1.0*E2UbBinding -1.0*Mdm2Ubiquitination -1.0*Mdm2polyUbiquitination1 -1.0*Mdm2polyUbiquitination2 -1.0*Mdm2polyUbiquitination3 -1.0*p53Monoubiquitination -1.0*p53Polyubiquitination1 -1.0*p53Polyubiquitination2 -1.0*p53Polyubiquitination3 -1.0*Mdm2PUbiquitination -1.0*Mdm2PpolyUbiquitination1 -1.0*Mdm2PpolyUbiquitination2 -1.0*Mdm2PpolyUbiquitination3, GSK3b'[t] == 1.0*GSK3p53Release +1.0*GSK3\[LetterSpace]p53PRelease +1.0*Mdm2GSK3phosphorylation1 +1.0*Tauphosphorylation5 +1.0*Tauphosphorylation6 -1.0*GSK3p53Binding -1.0*GSK3p53PBinding -1.0*Mdm2GSK3phosphorylation1 -1.0*Tauphosphorylation5 -1.0*Tauphosphorylation6, GSK3b\[LetterSpace]p53'[t] == 1.0*Mdm2mRNASynthesis3 +1.0*GSK3p53Binding +1.0*Mdm2GSK3phosphorylation2 +1.0*Tauphosphorylation1 +1.0*Tauphosphorylation2 +1.0*Abetaproduction2 -1.0*Mdm2mRNASynthesis3 -1.0*GSK3p53Release -1.0*Mdm2GSK3phosphorylation2 -1.0*Tauphosphorylation1 -1.0*Tauphosphorylation2 -1.0*Abetaproduction2, GSK3b\[LetterSpace]p53\[LetterSpace]P'[t] == 1.0*Mdm2mRNASynthesis4 +1.0*GSK3p53PBinding +1.0*Mdm2GSK3phosphorylation3 +1.0*Tauphosphorylation3 +1.0*Tauphosphorylation4 +1.0*Abetaproduction3 -1.0*Mdm2mRNASynthesis4 -1.0*GSK3\[LetterSpace]p53PRelease -1.0*Mdm2GSK3phosphorylation3 -1.0*Tauphosphorylation3 -1.0*Tauphosphorylation4 -1.0*Abetaproduction3, GliaA'[t] == 1.0*GliaActivationStep3 +1.0*AbetaReleaseFromGlia +1.0*AbetaPlaqueClearanceByGlia -1.0*GliaInactivationStep1 -1.0*AbetaBindingToGlia, GliaI'[t] == 1.0*GliaInactivationStep3 -1.0*GliaActivationStep1, GliaM1'[t] == 1.0*GliaActivationStep1 +1.0*GliaInactivationStep2 -1.0*GliaActivationStep2 -1.0*GliaInactivationStep3, GliaM2'[t] == 1.0*GliaActivationStep2 +1.0*GliaInactivationStep1 -1.0*GliaActivationStep3 -1.0*GliaInactivationStep2, IR'[t] == 1.0*DNAdamage -1.0*DNAdamage, MT\[LetterSpace]Tau'[t] == 1.0*TauMTbinding -1.0*TauMTrelease, Mdm2'[t] == 1.0*Mdm2Synthesis +1.0*P53Mdm2Release +1.0*Mdm2Deubiquitination1 +1.0*p53ProteasomeBinding1 +1.0*Mdm2dephosphorylation -1.0*P53Mdm2Binding -1.0*Mdm2Ubiquitination -1.0*Mdm2phosphorylation, Mdm2DUB'[t] == 1.0*Mdm2Deubiquitination4 +1.0*Mdm2Deubiquitination3 +1.0*Mdm2Deubiquitination2 +1.0*Mdm2Deubiquitination1 +1.0*Mdm2PDeubiquitination4 +1.0*Mdm2PDeubiquitination3 +1.0*Mdm2PDeubiquitination2 +1.0*Mdm2PDeubiquitination1 -1.0*Mdm2Deubiquitination4 -1.0*Mdm2Deubiquitination3 -1.0*Mdm2Deubiquitination2 -1.0*Mdm2Deubiquitination1 -1.0*Mdm2PDeubiquitination4 -1.0*Mdm2PDeubiquitination3 -1.0*Mdm2PDeubiquitination2 -1.0*Mdm2PDeubiquitination1, Mdm2\[LetterSpace]P'[t] == 1.0*Mdm2phosphorylation +1.0*Mdm2PDeubiquitination1 -1.0*Mdm2dephosphorylation -1.0*Mdm2PUbiquitination, Mdm2\[LetterSpace]P1\[LetterSpace]p53\[LetterSpace]Ub4'[t] == 1.0*Mdm2GSK3phosphorylation1 +1.0*Mdm2GSK3phosphorylation2 +1.0*Mdm2GSK3phosphorylation3 -1.0*p53ProteasomeBinding1, Mdm2\[LetterSpace]P\[LetterSpace]Ub'[t] == 1.0*Mdm2PUbiquitination +1.0*Mdm2PDeubiquitination2 -1.0*Mdm2PpolyUbiquitination1 -1.0*Mdm2PDeubiquitination1, Mdm2\[LetterSpace]P\[LetterSpace]Ub2'[t] == 1.0*Mdm2PpolyUbiquitination1 +1.0*Mdm2PDeubiquitination3 -1.0*Mdm2PpolyUbiquitination2 -1.0*Mdm2PDeubiquitination2, Mdm2\[LetterSpace]P\[LetterSpace]Ub3'[t] == 1.0*Mdm2PpolyUbiquitination2 +1.0*Mdm2PDeubiquitination4 -1.0*Mdm2PpolyUbiquitination3 -1.0*Mdm2PDeubiquitination3, Mdm2\[LetterSpace]P\[LetterSpace]Ub4'[t] == 1.0*Mdm2PpolyUbiquitination3 -1.0*Mdm2PDeubiquitination4 -1.0*Mdm2PProteasomeBinding1, Mdm2\[LetterSpace]P\[LetterSpace]Ub4\[LetterSpace]Proteasome'[t] == 1.0*Mdm2PProteasomeBinding1 -1.0*Mdm2PDegradation, Mdm2\[LetterSpace]Ub'[t] == 1.0*Mdm2Ubiquitination +1.0*Mdm2Deubiquitination2 -1.0*Mdm2polyUbiquitination1 -1.0*Mdm2Deubiquitination1, Mdm2\[LetterSpace]Ub2'[t] == 1.0*Mdm2polyUbiquitination1 +1.0*Mdm2Deubiquitination3 -1.0*Mdm2polyUbiquitination2 -1.0*Mdm2Deubiquitination2, Mdm2\[LetterSpace]Ub3'[t] == 1.0*Mdm2polyUbiquitination2 +1.0*Mdm2Deubiquitination4 -1.0*Mdm2polyUbiquitination3 -1.0*Mdm2Deubiquitination3, Mdm2\[LetterSpace]Ub4'[t] == 1.0*Mdm2polyUbiquitination3 -1.0*Mdm2Deubiquitination4 -1.0*Mdm2ProteasomeBinding1, Mdm2\[LetterSpace]Ub4\[LetterSpace]Proteasome'[t] == 1.0*Mdm2ProteasomeBinding1 -1.0*Mdm2Degradation, Mdm2\[LetterSpace]mRNA'[t] == 1.0*Mdm2Synthesis +1.0*Mdm2mRNASynthesis1 +1.0*Mdm2mRNASynthesis2 +1.0*Mdm2mRNASynthesis3 +1.0*Mdm2mRNASynthesis4 -1.0*Mdm2Synthesis -1.0*Mdm2mRNADegradation, Mdm2\[LetterSpace]p53'[t] == 1.0*P53Mdm2Binding +1.0*p53Deubiquitination1 -1.0*P53Mdm2Release -1.0*p53Monoubiquitination, Mdm2\[LetterSpace]p53\[LetterSpace]Ub'[t] == 1.0*p53Monoubiquitination +1.0*p53Deubiquitination2 -1.0*p53Polyubiquitination1 -1.0*p53Deubiquitination1, Mdm2\[LetterSpace]p53\[LetterSpace]Ub2'[t] == 1.0*p53Polyubiquitination1 +1.0*p53Deubiquitination3 -1.0*p53Polyubiquitination2 -1.0*p53Deubiquitination2, Mdm2\[LetterSpace]p53\[LetterSpace]Ub3'[t] == 1.0*p53Polyubiquitination2 +1.0*p53Deubiqutination4 -1.0*p53Polyubiquitination3 -1.0*p53Deubiquitination3, Mdm2\[LetterSpace]p53\[LetterSpace]Ub4'[t] == 1.0*p53Polyubiquitination3 -1.0*p53Deubiqutination4 -1.0*Mdm2GSK3phosphorylation1 -1.0*Mdm2GSK3phosphorylation2 -1.0*Mdm2GSK3phosphorylation3, NFT'[t] == 2.0*TangleFormation1 +2.0*TangleFormation2 -1.0*TangleFormation2, PP1'[t] == 1.0*Taudephosphorylation1 +1.0*Taudephosphorylation2 -1.0*Taudephosphorylation1 -1.0*Taudephosphorylation2, Proteasome'[t] == 1.0*Mdm2Degradation +1.0*Degradationp53\[LetterSpace]Ub4 +1.0*Mdm2PDegradation +1.0*Tau20SProteasomeDegradation -1.0*Mdm2ProteasomeBinding1 -1.0*p53ProteasomeBinding1 -1.0*ProteasomeInhibitionAggTau -1.0*ProteasomeInhibitionAbeta -1.0*Mdm2PProteasomeBinding1 -1.0*TauProteasomeBinding, Proteasome\[LetterSpace]Tau'[t] == 1.0*TauProteasomeBinding -1.0*Tau20SProteasomeDegradation, ROS'[t] == 1.0*AbetaROSproduction1 +1.0*PlaqueROSproduction +1.0*AggAbetaROSproduction2 +1.0*ROSDNAdamage +1.0*ROSgenerationByGlia -1.0*ROSDNAdamage -1.0*ROSremoval, Tau'[t] == 1.0*TauMTrelease +1.0*Taudephosphorylation2 +1.0*TauSynthesis -1.0*TauMTbinding -1.0*Tauphosphorylation1 -1.0*Tauphosphorylation3 -1.0*Tauphosphorylation5 -2.0*TauAggregation1 -1.0*TauAggregation2 -1.0*TauProteasomeBinding, Tau\[LetterSpace]P1'[t] == 1.0*Tauphosphorylation1 +1.0*Tauphosphorylation3 +1.0*Tauphosphorylation5 +1.0*Taudephosphorylation1 -1.0*Tauphosphorylation2 -1.0*Tauphosphorylation4 -1.0*Tauphosphorylation6 -1.0*Taudephosphorylation2 -2.0*TauP1Aggregation1 -1.0*TauP1Aggregation2, Tau\[LetterSpace]P2'[t] == 1.0*Tauphosphorylation2 +1.0*Tauphosphorylation4 +1.0*Tauphosphorylation6 -1.0*Taudephosphorylation1 -2.0*TauP2Aggregation1 -1.0*TauP2Aggregation2, Ub'[t] == 1.0*Mdm2Deubiquitination4 +1.0*Mdm2Deubiquitination3 +1.0*Mdm2Deubiquitination2 +1.0*Mdm2Deubiquitination1 +4.0*Mdm2Degradation +1.0*p53Deubiqutination4 +1.0*p53Deubiquitination3 +1.0*p53Deubiquitination2 +1.0*p53Deubiquitination1 +4.0*Degradationp53\[LetterSpace]Ub4 +1.0*Mdm2PDeubiquitination4 +1.0*Mdm2PDeubiquitination3 +1.0*Mdm2PDeubiquitination2 +1.0*Mdm2PDeubiquitination1 +4.0*Mdm2PDegradation -1.0*E1UbBinding, antiAb'[t] == 1.0*AbetaDisaggregation4 +1.0*Abeta\[LetterSpace]antiAbDegredation +1.0*AbetaDimer\[LetterSpace]antiAbDegredation +1.0*GliaActivationStep3 -1.0*AbetaDisaggregation4 -1.0*Abeta\[LetterSpace]antiAbBinding -1.0*AbetaDimer\[LetterSpace]antiAbBinding -1.0*GliaActivationStep3 -1.0*antiAbRemoval, damDNA'[t] == 1.0*DNAdamage +1.0*ATMactivation +1.0*ROSDNAdamage -1.0*DNArepair -1.0*ATMactivation, degAbetaGlia'[t] == 1.0*AbetaPlaqueClearanceByGlia , disaggPlaque1'[t] == 1.0*AbetaDisaggregation3 , disaggPlaque2'[t] == 1.0*AbetaDisaggregation4 , p53'[t] == 1.0*Mdm2mRNASynthesis1 +1.0*P53Mdm2Release +1.0*GSK3p53Release +1.0*p53Synthesis +1.0*p53dephosphorylation -1.0*Mdm2mRNASynthesis1 -1.0*P53Mdm2Binding -1.0*GSK3p53Binding -1.0*p53phosphorylation, p53DUB'[t] == 1.0*p53Deubiqutination4 +1.0*p53Deubiquitination3 +1.0*p53Deubiquitination2 +1.0*p53Deubiquitination1 -1.0*p53Deubiqutination4 -1.0*p53Deubiquitination3 -1.0*p53Deubiquitination2 -1.0*p53Deubiquitination1, p53\[LetterSpace]P'[t] == 1.0*Mdm2mRNASynthesis2 +1.0*GSK3\[LetterSpace]p53PRelease +1.0*p53phosphorylation -1.0*Mdm2mRNASynthesis2 -1.0*GSK3p53PBinding -1.0*p53dephosphorylation, p53\[LetterSpace]Ub4\[LetterSpace]Proteasome'[t] == 1.0*p53ProteasomeBinding1 -1.0*Degradationp53\[LetterSpace]Ub4, p53\[LetterSpace]mRNA'[t] == 1.0*p53mRNASynthesis +1.0*p53Synthesis +1.0*p53transcriptionViaAbeta -1.0*p53mRNADegradation -1.0*p53Synthesis
};
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]}]