begin name
schliemann1
end name

begin reactions
J1 {1.0}TNFR = {1.0}TNFRE
J10 {1.0}TNFRC1 = {1.0}$EXTERNAL
J11 {1.0}TNFRC2 = {1.0}$EXTERNAL
J12 {1.0}TNFRC2FLIP = {1.0}$EXTERNAL
J13 {1.0}TNFRC2FLIPFLIP = {1.0}$EXTERNAL
J14 {1.0}TNFRC2pCasp8 = {1.0}$EXTERNAL
J15 {1.0}TNFRC2pCasp8pCasp8 = {1.0}$EXTERNAL
J16 {1.0}TNFRC2FLIPpCasp8 = {1.0}$EXTERNAL
J17 {1.0}TNFRC2FLIPpCasp8RIPTRAF2 = {1.0}$EXTERNAL
J18 {1.0}TNFRE + {1.0}TNFE = {1.0}TNFTNFRE
J19 {1.0}TNFTNFRE + {1.0}TRADD = {1.0}TNFTNFRTRADD
J2 {1.0}$EXTERNAL = {1.0}TNFR
J20 {1.0}RIP + {1.0}TRAF2 + {1.0}TNFTNFRTRADD = {1.0}TNFRC1
J21 {1.0}TNFRC1 = {1.0}TNFRCint1
J22 {1.0}TNFRCint1 = {1.0}RIP + {1.0}TRAF2 + {1.0}TNFRCint2
J23 {2.0}FADD + {1.0}TNFRCint2 = {1.0}TNFRCint3
J24 {1.0}TNFRCint3 = {1.0}TNFRC2
J25 {1.0}TNFRC2 + {1.0}FLIP = {1.0}TNFRC2FLIP
J26 {1.0}FLIP + {1.0}TNFRC2FLIP = {1.0}TNFRC2FLIPFLIP
J27 {1.0}TNFRC2 + {1.0}pCasp8 = {1.0}TNFRC2pCasp8
J28 {1.0}TNFRC2pCasp8 + {1.0}pCasp8 = {1.0}TNFRC2pCasp8pCasp8
J29 {1.0}TNFRC2pCasp8pCasp8 = {1.0}TNFRC2 + {1.0}Casp8
J3 {1.0}TNFRE = {1.0}$EXTERNAL
J30 {1.0}FLIP + {1.0}TNFRC2pCasp8 = {1.0}TNFRC2FLIPpCasp8
J31 {1.0}TNFRC2FLIP + {1.0}pCasp8 = {1.0}TNFRC2FLIPpCasp8
J32 {1.0}TNFRC2FLIPpCasp8 = {1.0}TNFRC2 + {1.0}Casp8
J33 {1.0}RIP + {1.0}TRAF2 + {1.0}TNFRC2FLIPpCasp8 = {1.0}TNFRC2FLIPpCasp8RIPTRAF2
J34 {1.0}IKK = {1.0}IKKa
J35 {1.0}$EXTERNAL = {1.0}IKK
J36 {1.0}$EXTERNAL = {1.0}NFkB
J37 {1.0}$EXTERNAL = {1.0}FLIP
J38 {1.0}$EXTERNAL = {1.0}XIAP
J39 {1.0}$EXTERNAL = {1.0}A20
J4 {1.0}$EXTERNAL = {1.0}RIP
J40 {1.0}IKKa = {1.0}$EXTERNAL
J41 {1.0}IkBaNFkB = {1.0}$EXTERNAL
J42 {1.0}NFkBN = {1.0}$EXTERNAL
J43 {1.0}IkBamRNA = {1.0}$EXTERNAL
J44 {1.0}IkBa = {1.0}$EXTERNAL
J45 {1.0}IkBaN = {1.0}$EXTERNAL
J46 {1.0}IkBaNFkBN = {1.0}$EXTERNAL
J47 {1.0}PIkBa = {1.0}$EXTERNAL
J48 {1.0}A20mRNA = {1.0}$EXTERNAL
J49 {1.0}XIAPmRNA = {1.0}$EXTERNAL
J5 {1.0}$EXTERNAL = {1.0}TRADD
J50 {1.0}FLIPmRNA = {1.0}$EXTERNAL
J51 {1.0}IKK = {1.0}IKKa
J52 {1.0}IKKa = {1.0}IKK
J53 {1.0}TNFRC1 = {1.0}TRAF2 + {1.0}TNFTNFRTRADD
J54 {1.0}NFkB + {1.0}IkBa = {1.0}IkBaNFkB
J55 {1.0}IkBaNFkB = {1.0}NFkB + {1.0}PIkBa
J56 {1.0}NFkB = {1.0}NFkBN
J57 {1.0}$EXTERNAL = {1.0}IkBamRNA
J58 {1.0}$EXTERNAL = {1.0}IkBa
J59 {1.0}IkBa = {1.0}IkBaN
J6 {1.0}$EXTERNAL = {1.0}TRAF2
J60 {1.0}NFkBN + {1.0}IkBaN = {1.0}IkBaNFkBN
J61 {1.0}IkBaNFkBN = {1.0}IkBaNFkB
J62 {1.0}$EXTERNAL = {1.0}A20mRNA
J63 {1.0}$EXTERNAL = {1.0}A20
J64 {1.0}$EXTERNAL = {1.0}XIAPmRNA
J65 {1.0}$EXTERNAL = {1.0}XIAP
J66 {1.0}$EXTERNAL = {1.0}FLIPmRNA
J67 {1.0}$EXTERNAL = {1.0}FLIP
J68 {1.0}$EXTERNAL = {1.0}pCasp8
J69 {1.0}$EXTERNAL = {1.0}pCasp3
J7 {1.0}$EXTERNAL = {1.0}FADD
J70 {1.0}$EXTERNAL = {1.0}pCasp6
J71 {1.0}Casp8 = {1.0}$EXTERNAL
J72 {1.0}Casp3 = {1.0}$EXTERNAL
J73 {1.0}Casp6 = {1.0}$EXTERNAL
J74 {1.0}XIAPCasp3 = {1.0}$EXTERNAL
J75 {1.0}$EXTERNAL = {1.0}BAR
J76 {1.0}BARCasp8 = {1.0}$EXTERNAL
J77 {1.0}PARP = {1.0}$EXTERNAL
J78 {1.0}cPARP = {1.0}$EXTERNAL
J79 {1.0}pCasp3 = {1.0}Casp3
J8 {1.0}TNFTNFRE = {1.0}$EXTERNAL
J80 {1.0}pCasp6 = {1.0}Casp6
J81 {1.0}pCasp8 = {1.0}Casp8
J82 {1.0}XIAP + {1.0}Casp3 = {1.0}XIAPCasp3
J83 {1.0}XIAP = {1.0}$EXTERNAL
J84 {1.0}XIAPCasp3 = {1.0}XIAP
J85 {1.0}RIP = {1.0}$EXTERNAL
J86 {1.0}FLIP = {1.0}$EXTERNAL
J87 {1.0}PARP = {1.0}cPARP
J88 {1.0}BAR + {1.0}Casp8 = {1.0}BARCasp8
J9 {1.0}TNFTNFRTRADD = {1.0}$EXTERNAL
end reactions

begin rate equations
J1 = J1ka1*TNFR[t]
J10 = J10ka10*TNFRC1[t]
J11 = J11ka11*TNFRC2[t]
J12 = J12ka12*TNFRC2FLIP[t]
J13 = J13ka13*TNFRC2FLIPFLIP[t]
J14 = J14ka14*TNFRC2pCasp8[t]
J15 = J15ka15*TNFRC2pCasp8pCasp8[t]
J16 = J16ka16*TNFRC2FLIPpCasp8[t]
J17 = J17ka17*TNFRC2FLIPpCasp8RIPTRAF2[t]
J18 = J18ka18*TNFRE[t]*TNFE[t] - J18kd18*TNFTNFRE[t]
J19 = J19ka19*TNFTNFRE[t]*TRADD[t]
J2 = J2ka2
J20 = J20ka20*RIP[t]*TNFTNFRTRADD[t]*TRAF2[t]
J21 = J21ka21*TNFRC1[t]
J22 = J22ka22*TNFRCint1[t]
J23 = J23ka23*FADD[t]^2*TNFRCint2[t]
J24 = J24ka24*TNFRCint3[t]
J25 = J25ka25*FLIP[t]*TNFRC2[t]
J26 = J26ka26*FLIP[t]*TNFRC2FLIP[t]
J27 = J27ka27*pCasp8[t]*TNFRC2[t]
J28 = J28ka28*pCasp8[t]*TNFRC2pCasp8[t]
J29 = J29ka29*TNFRC2pCasp8pCasp8[t]
J3 = J3ka3*TNFRE[t]
J30 = J30ka30*FLIP[t]*TNFRC2pCasp8[t]
J31 = J31ka31*pCasp8[t]*TNFRC2FLIP[t]
J32 = J32ka32*TNFRC2FLIPpCasp8[t]
J33 = J33ka33*RIP[t]*TNFRC2FLIPpCasp8[t]*TRAF2[t]
J34 = J34ka34*IKK[t]*TNFRC2FLIPpCasp8RIPTRAF2[t]
J35 = J35ka35 - J35kd35*IKK[t]
J36 = J36ka36 - J36kd36*NFkB[t]
J37 = J37ka37 - J37kd37*FLIP[t]
J38 = J38ka38 - J38kd38*XIAP[t]
J39 = J39ka39 - J39kd39*A20[t]
J4 = J4ka4 - J4kd4*RIP[t]
J40 = J40ka40*IKKa[t]
J41 = J41ka41*IkBaNFkB[t]
J42 = J42ka42*NFkBN[t]
J43 = J43ka43*IkBamRNA[t]
J44 = J44ka44*IkBa[t]
J45 = J45ka45*IkBaN[t]
J46 = J46ka46*IkBaNFkBN[t]
J47 = J47ka47*PIkBa[t]
J48 = J48ka48*A20mRNA[t]
J49 = J49ka49*XIAPmRNA[t]
J5 = J5ka5 - J5kd5*TRADD[t]
J50 = J50ka50*FLIPmRNA[t]
J51 = J51ka51*IKK[t]*TNFRC1[t]
J52 = J52ka52*IKKa[t]
J53 = J53ka53*A20[t]*TNFRC1[t]
J54 = J54ka54*IkBa[t]*NFkB[t]
J55 = J55ka55*IkBaNFkB[t]*IKKa[t]
J56 = J56ka56*NFkB[t]
J57 = J57ka57*NFkBN[t]
J58 = J58ka58*IkBamRNA[t]
J59 = J59ka59*IkBa[t] - J59kd59*IkBaN[t]
J6 = J6ka6 - J6kd6*TRAF2[t]
J60 = J60ka60*IkBaN[t]*NFkBN[t]
J61 = J61ka61*IkBaNFkBN[t]
J62 = J62ka62*NFkBN[t]
J63 = J63ka63*A20mRNA[t]
J64 = J64ka64*NFkBN[t]
J65 = J65ka65*XIAPmRNA[t]
J66 = J66ka66*NFkBN[t]
J67 = J67ka67*FLIPmRNA[t]
J68 = J68ka68 - J68kd68*pCasp8[t]
J69 = J69ka69 - J69kd69*pCasp3[t]
J7 = J7ka7 - J7kd7*FADD[t]
J70 = J70ka70 - J70kd70*pCasp6[t]
J71 = J71ka71*Casp8[t]
J72 = J72ka72*Casp3[t]
J73 = J73ka73*Casp6[t]
J74 = J74ka74*XIAPCasp3[t]
J75 = J75ka75 - J75kd75*BAR[t]
J76 = J76ka76*BARCasp8[t]
J77 = -J77kd77 + J77ka77*PARP[t]
J78 = J78ka78*cPARP[t]
J79 = J79ka79*Casp8[t]*pCasp3[t]
J8 = J8ka8*TNFTNFRE[t]
J80 = J80ka80*Casp3[t]*pCasp6[t]
J81 = J81ka81*Casp6[t]*pCasp8[t]
J82 = J82ka82*Casp3[t]*XIAP[t] - J82kd82*XIAPCasp3[t]
J83 = J83ka83*Casp3[t]*XIAP[t]
J84 = J84ka84*XIAPCasp3[t]
J85 = J85ka85*Casp3[t]*RIP[t]
J86 = J86ka86*Casp3[t]*FLIP[t]
J87 = J87ka87*Casp3[t]*PARP[t]
J88 = -(J88kd88*BARCasp8[t]) + J88ka88*BAR[t]*Casp8[t]
J9 = J9ka9*TNFTNFRTRADD[t]
end rate equations

begin parameters
J1ka1 = 0.001
J2ka2 = "2.8e-07"
J3ka3 = "5.6e-05"
J4ka4 = "2.0256e-05"
J4kd4 = 0.0001
J5ka5 = "2.9344e-05"
J5kd5 = 0.0001
J6ka6 = "3.3056e-05"
J6kd6 = 0.0001
J7ka7 = "3.0944e-05"
J7kd7 = 0.0001
J8ka8 = "5.6e-05"
J9ka9 = 0.02352
J10ka10 = "5.6e-05"
J11ka11 = "5.6e-05"
J12ka12 = "5.6e-05"
J13ka13 = "5.6e-05"
J14ka14 = "5.6e-05"
J15ka15 = "5.6e-05"
J16ka16 = "5.6e-05"
J17ka17 = "5.6e-05"
J18ka18 = 0.00953471
J18kd18 = "6.60377e-05"
J19ka19 = 0.00427827
J20ka20 = 0.0976562
J21ka21 = 0.001135
J22ka22 = 0.001135
J23ka23 = 0.0118534
J24ka24 = 0.1135
J25ka25 = 0.3125
J26ka26 = 0.3125
J27ka27 = 0.03125
J28ka28 = 0.03125
J29ka29 = 0.45
J30ka30 = 0.3125
J31ka31 = 0.3125
J32ka32 = 0.3
J33ka33 = 0.00976562
J34ka34 = 0.03125
J35ka35 = "6.4e-05"
J35kd35 = 0.0001
J36ka36 = "1.6e-06"
J36kd36 = 0.0001
J37ka37 = "2.24902e-06"
J37kd37 = 0.0001
J38ka38 = 0.000772256
J38kd38 = 0.0001
J39ka39 = "9.6e-06"
J39kd39 = 0.0001
J40ka40 = 0.0001
J41ka41 = 0.0001
J42ka42 = 0.0001
J43ka43 = 0.000394201
J44ka44 = 0.00154022
J45ka45 = 0.0001
J46ka46 = 0.0001
J47ka47 = 0.0115517
J48ka48 = 0.000470498
J49ka49 = 0.000104931
J50ka50 = 0.000165744
J51ka51 = 93.75
J52ka52 = 0.1
J53ka53 = 0.00625
J54ka54 = 1.25
J55ka55 = 0.104167
J56ka56 = 0.0125
J57ka57 = "3.0303e-05"
J58ka58 = 0.0606061
J59ka59 = 0.005
J59kd59 = 0.00257576
J60ka60 = 1.4348
J61ka61 = 0.0151515
J62ka62 = "3.78788e-05"
J63ka63 = 0.0151515
J64ka64 = "3.33333e-05"
J65ka65 = 0.0506061
J66ka66 = "3.33333e-05"
J67ka67 = 0.00687273
J68ka68 = 0.000197531
J68kd68 = "6.17284e-05"
J69ka69 = "4.93827e-05"
J69kd69 = "6.17284e-05"
J70ka70 = "3.95062e-06"
J70kd70 = "6.17284e-05"
J71ka71 = "5.78704e-05"
J72ka72 = "5.78704e-05"
J73ka73 = "5.78704e-05"
J74ka74 = "5.78704e-05"
J75ka75 = "1.66603e-06"
J75kd75 = "5.78704e-06"
J76ka76 = "5.78704e-05"
J77ka77 = "5.78704e-06"
J77kd77 = "9.64506e-06"
J78ka78 = "5.78704e-06"
J79ka79 = 0.015625
J80ka80 = 0.009375
J81ka81 = 0.0015625
J82ka82 = 0.625
J82kd82 = 0.001
J83ka83 = 1.875
J84ka84 = "5e-05"
J85ka85 = 0.15625
J86ka86 = 0.15625
J87ka87 = 0.1875
J88ka88 = 0.520833
J88kd88 = 0.001
cytoplasm = 3.2
extracellular = 1344.0
nucleus = 1.056
end parameters

begin initial conditions
A20[0] = A20i
A20mRNA[0] = A20mRNAi
BAR[0] = BARi
BARCasp8[0] = BARCasp8i
Casp3[0] = Casp3i
Casp6[0] = Casp6i
Casp8[0] = Casp8i
FADD[0] = FADDi
FLIP[0] = FLIPi
FLIPmRNA[0] = FLIPmRNAi
IKK[0] = IKKi
IKKa[0] = IKKai
IkBa[0] = IkBai
IkBaN[0] = IkBaNi
IkBaNFkB[0] = IkBaNFkBi
IkBaNFkBN[0] = IkBaNFkBNi
IkBamRNA[0] = IkBamRNAi
NFkB[0] = NFkBi
NFkBN[0] = NFkBNi
PARP[0] = PARPi
PIkBa[0] = PIkBai
RIP[0] = RIPi
TNFR[0] = TNFRi
TNFRC1[0] = TNFRC1i
TNFRC2[0] = TNFRC2i
TNFRC2FLIP[0] = TNFRC2FLIPi
TNFRC2FLIPFLIP[0] = TNFRC2FLIPFLIPi
TNFRC2FLIPpCasp8[0] = TNFRC2FLIPpCasp8i
TNFRC2FLIPpCasp8RIPTRAF2[0] = TNFRC2FLIPpCasp8RIPTRAF2i
TNFRC2pCasp8[0] = TNFRC2pCasp8i
TNFRC2pCasp8pCasp8[0] = TNFRC2pCasp8pCasp8i
TNFRCint1[0] = TNFRCint1i
TNFRCint2[0] = TNFRCint2i
TNFRCint3[0] = TNFRCint3i
TNFRE[0] = TNFREi
TNFE[0] = TNFEi
TNFTNFRE[0] = TNFTNFREi
TNFTNFRTRADD[0] = TNFTNFRTRADDi
TRADD[0] = TRADDi
TRAF2[0] = TRAF2i
XIAP[0] = XIAPi
XIAPCasp3[0] = XIAPCasp3i
XIAPmRNA[0] = XIAPmRNAi
cPARP[0] = cPARPi
pCasp3[0] = pCasp3i
pCasp6[0] = pCasp6i
pCasp8[0] = pCasp8i
end initial conditions

begin initial values
A20i = 0.104434
A20mRNAi = 5.56657e-05
BARi = 0.28789
BARCasp8i = 0.0
Casp3i = 0.0
Casp6i = 0.0
Casp8i = 0.0
FADDi = 0.30944
FLIPi = 0.0320472
FLIPmRNAi = 0.000139056
IKKi = 0.64
IKKai = 0.0
IkBai = 0.00101518
IkBaNi = 0.0013839
IkBaNFkBi = 0.0151032
IkBaNFkBNi = 9.00189e-05
IkBamRNAi = 5.31517e-05
NFkBi = 0.000115365
NFkBNi = 0.000691431
PARPi = 1.66667
PIkBai = 0.0
RIPi = 0.20256
TNFRi = 0.00028
TNFRC1i = 0.0
TNFRC2i = 0.0
TNFRC2FLIPi = 0.0
TNFRC2FLIPFLIPi = 0.0
TNFRC2FLIPpCasp8i = 0.0
TNFRC2FLIPpCasp8RIPTRAF2i = 0.0
TNFRC2pCasp8i = 0.0
TNFRC2pCasp8pCasp8i = 0.0
TNFRCint1i = 0.0
TNFRCint2i = 0.0
TNFRCint3i = 0.0
TNFREi = 0.005
TNFEi = 0.2688
TNFTNFREi = 0.0
TNFTNFRTRADDi = 0.0
TRADDi = 0.29344
TRAF2i = 0.33056
XIAPi = 7.83371
XIAPCasp3i = 0.0
XIAPmRNAi = 0.000219646
cPARPi = 0.0
pCasp3i = 0.8
pCasp6i = 0.064
pCasp8i = 3.2
end initial values

begin assignment rules
end assignment rules

begin function definitions
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units