begin name
hoffmann2
end name

begin reactions
v1 {1.0}NFkB + {1.0}IkBalpha = {1.0}IkBalphaNFkB
v10 {1.0}IkBalphaNFkB = {1.0}NFkB
v11 {1.0}IkBbetaNFkB = {1.0}NFkB
v12 {1.0}IkBepsNFkB = {1.0}NFkB
v13 {1.0}NFkB = {1.0}NFkBnuc
v14 {1.0}NFkBnuc + {1.0}IkBalphanuc = {1.0}IkBalphanucNFkBnuc
v15 {1.0}NFkBnuc + {1.0}IkBbetanuc = {1.0}IkBbetanucNFkBnuc
v16 {1.0}NFkBnuc + {1.0}IkBepsnuc = {1.0}IkBepsnucNFkBnuc
v17 {1.0}$EXTERNAL = {1.0}IkBalphatranscript
v18 {1.0}$EXTERNAL = {1.0}IkBalphatranscript
v19 {1.0}IkBalphatranscript = {1.0}$EXTERNAL
v2 {1.0}NFkB + {1.0}IkBbeta = {1.0}IkBbetaNFkB
v20 {1.0}$EXTERNAL = {1.0}IkBbetatranscript
v21 {1.0}IkBbetatranscript = {1.0}$EXTERNAL
v22 {1.0}$EXTERNAL = {1.0}IkBepstranscript
v23 {1.0}IkBepstranscript = {1.0}$EXTERNAL
v24 {1.0}IKK + {1.0}IkBalpha = {1.0}IKKIkBalpha
v25 {1.0}$EXTERNAL = {1.0}IkBalpha
v26 {1.0}IkBalpha = {1.0}$EXTERNAL
v27 {1.0}IkBalpha = {1.0}IkBalphanuc
v28 {1.0}IKK + {1.0}IkBbeta = {1.0}IKKIkBbeta
v29 {1.0}$EXTERNAL = {1.0}IkBbeta
v3 {1.0}NFkB + {1.0}IkBeps = {1.0}IkBepsNFkB
v30 {1.0}IkBbeta = {1.0}$EXTERNAL
v31 {1.0}IkBbeta = {1.0}IkBbetanuc
v32 {1.0}IKK + {1.0}IkBeps = {1.0}IKKIkBeps
v33 {1.0}$EXTERNAL = {1.0}IkBeps
v34 {1.0}IkBeps = {1.0}$EXTERNAL
v35 {1.0}IkBeps = {1.0}IkBepsnuc
v36 {1.0}IKK + {1.0}IkBalphaNFkB = {1.0}IKKIkBalphaNFkB
v37 {1.0}IkBalphanucNFkBnuc = {1.0}IkBalphaNFkB
v38 {1.0}IKK + {1.0}IkBbetaNFkB = {1.0}IKKIkBbetaNFkB
v39 {1.0}IkBbetanucNFkBnuc = {1.0}IkBbetaNFkB
v4 {1.0}NFkB + {1.0}IKKIkBalpha = {1.0}IKKIkBalphaNFkB
v40 {1.0}IKK + {1.0}IkBepsNFkB = {1.0}IKKIkBepsNFkB
v41 {1.0}IkBepsnucNFkBnuc = {1.0}IkBepsNFkB
v42 {1.0}IKKIkBalpha = {1.0}IKK
v43 {1.0}IKKIkBbeta = {1.0}IKK
v44 {1.0}IKKIkBeps = {1.0}IKK
v45 {1.0}IKK = {1.0}$EXTERNAL
v5 {1.0}IKKIkBalphaNFkB = {1.0}NFkB + {1.0}IKK
v6 {1.0}NFkB + {1.0}IKKIkBbeta = {1.0}IKKIkBbetaNFkB
v7 {1.0}IKKIkBbetaNFkB = {1.0}NFkB + {1.0}IKK
v8 {1.0}NFkB + {1.0}IKKIkBeps = {1.0}IKKIkBepsNFkB
v9 {1.0}IKKIkBepsNFkB = {1.0}NFkB + {1.0}IKK
end reactions

begin rate equations
v1 = cytoplasm*(-(d4*IkBalphaNFkB[t]) + a4*IkBalpha[t]*NFkB[t])
v10 = cytoplasm*deg4*IkBalphaNFkB[t]
v11 = cytoplasm*deg4*IkBbetaNFkB[t]
v12 = cytoplasm*deg4*IkBepsNFkB[t]
v13 = cytoplasm*k1*NFkB[t] - k01*nucleus*NFkBnuc[t]
v14 = nucleus*(-(d4*IkBalphanucNFkBnuc[t]) + a4*IkBalphanuc[t]*NFkBnuc[t])
v15 = nucleus*(-(d5*IkBbetanucNFkBnuc[t]) + a5*IkBbetanuc[t]*NFkBnuc[t])
v16 = nucleus*(-(d6*IkBepsnucNFkBnuc[t]) + a6*IkBepsnuc[t]*NFkBnuc[t])
v17 = nucleus*tr2a
v18 = nucleus*tr2*NFkBnuc[t]^2
v19 = nucleus*tr3*IkBalphatranscript[t]
v2 = cytoplasm*(-(d5*IkBbetaNFkB[t]) + a5*IkBbeta[t]*NFkB[t])
v20 = nucleus*tr2b
v21 = nucleus*tr3*IkBbetatranscript[t]
v22 = nucleus*tr2e
v23 = nucleus*tr3*IkBepstranscript[t]
v24 = cytoplasm*(a1*IkBalpha[t]*IKK[t] - d1*IKKIkBalpha[t])
v25 = nucleus*tr1*IkBalphatranscript[t]
v26 = cytoplasm*deg1*IkBalpha[t]
v27 = cytoplasm*tp1*IkBalpha[t] - nucleus*tp2*IkBalphanuc[t]
v28 = cytoplasm*(a2*IkBbeta[t]*IKK[t] - d2*IKKIkBbeta[t])
v29 = nucleus*tr1*IkBbetatranscript[t]
v3 = cytoplasm*(-(d6*IkBepsNFkB[t]) + a6*IkBeps[t]*NFkB[t])
v30 = cytoplasm*deg1*IkBbeta[t]
v31 = 0.5*cytoplasm*tp1*IkBbeta[t] - 0.5*nucleus*tp2*IkBbetanuc[t]
v32 = cytoplasm*(a3*IkBeps[t]*IKK[t] - d3*IKKIkBeps[t])
v33 = nucleus*tr1*IkBepstranscript[t]
v34 = cytoplasm*deg1*IkBeps[t]
v35 = 0.5*cytoplasm*tp1*IkBeps[t] - 0.5*nucleus*tp2*IkBepsnuc[t]
v36 = cytoplasm*(a7*IkBalphaNFkB[t]*IKK[t] - d1*IKKIkBalphaNFkB[t])
v37 = k2*nucleus*IkBalphanucNFkBnuc[t]
v38 = cytoplasm*(a8*IkBbetaNFkB[t]*IKK[t] - d2*IKKIkBbetaNFkB[t])
v39 = nucleus*v39k2IkBbetanucNFkBnuc*(flagforaftertrigger + fraftertrigger[t])*IkBbetanucNFkBnuc[t]
v4 = cytoplasm*(-(d4*IKKIkBalphaNFkB[t]) + a4*IKKIkBalpha[t]*NFkB[t])
v40 = cytoplasm*(a9*IkBepsNFkB[t]*IKK[t] - d3*IKKIkBepsNFkB[t])
v41 = 0.5*k2eps*nucleus*IkBepsnucNFkBnuc[t]
v42 = cytoplasm*r1*IKKIkBalpha[t]
v43 = cytoplasm*r2*IKKIkBbeta[t]
v44 = cytoplasm*r3*IKKIkBeps[t]
v45 = cytoplasm*k02*IKK[t]
v5 = cytoplasm*r4*IKKIkBalphaNFkB[t]
v6 = cytoplasm*(-(d5*IKKIkBbetaNFkB[t]) + a5*IKKIkBbeta[t]*NFkB[t])
v7 = cytoplasm*r5*IKKIkBbetaNFkB[t]
v8 = cytoplasm*(-(d6*IKKIkBepsNFkB[t]) + a6*IKKIkBeps[t]*NFkB[t])
v9 = cytoplasm*r6*IKKIkBepsNFkB[t]
end rate equations

begin parameters
a1 = 1.35
a2 = 0.36
a3 = 0.54
a4 = 30.0
a5 = 30.0
a6 = 30.0
a7 = 11.1
a8 = 2.88
a9 = 4.2
d1 = 0.075
d2 = 0.105
d3 = 0.105
d4 = 0.03
d5 = 0.03
d6 = 0.03
deg1 = 0.00678
deg4 = 0.00135
flagforaftertrigger = 0.5
fr = 1.0
k01 = 0.0048
k02 = 0.0072
k1 = 5.4
k2 = 0.828
k2beta = 0.624
k2eps = 0.624
r1 = 0.2442
r2 = 0.09
r3 = 0.132
r4 = 1.224
r5 = 0.45
r6 = 0.66
tp1 = 0.018
tp2 = 0.012
tr1 = 0.2448
tr2 = 0.99
tr2a = "9.25e-05"
tr2b = "1.068e-05"
tr2e = "7.62e-06"
tr3 = 0.0168
triggervalue = 0.0
v39k2IkBbetanucNFkBnuc = 0.0069
cytoplasm = 1.0
nucleus = 1.0
end parameters

begin initial conditions
IKK[0] = IKKi
IKKIkBalpha[0] = IKKIkBalphai
IKKIkBalphaNFkB[0] = IKKIkBalphaNFkBi
IKKIkBbeta[0] = IKKIkBbetai
IKKIkBbetaNFkB[0] = IKKIkBbetaNFkBi
IKKIkBeps[0] = IKKIkBepsi
IKKIkBepsNFkB[0] = IKKIkBepsNFkBi
IkBalpha[0] = IkBalphai
IkBalphaNFkB[0] = IkBalphaNFkBi
IkBalphanuc[0] = IkBalphanuci
IkBalphanucNFkBnuc[0] = IkBalphanucNFkBnuci
IkBalphatranscript[0] = IkBalphatranscripti
IkBbeta[0] = IkBbetai
IkBbetaNFkB[0] = IkBbetaNFkBi
IkBbetanuc[0] = IkBbetanuci
IkBbetanucNFkBnuc[0] = IkBbetanucNFkBnuci
IkBbetatranscript[0] = IkBbetatranscripti
IkBeps[0] = IkBepsi
IkBepsNFkB[0] = IkBepsNFkBi
IkBepsnuc[0] = IkBepsnuci
IkBepsnucNFkBnuc[0] = IkBepsnucNFkBnuci
IkBepstranscript[0] = IkBepstranscripti
NFkB[0] = NFkBi
NFkBnuc[0] = NFkBnuci
fraftertrigger[0] = fraftertriggeri
end initial conditions

begin initial values
IKKi = 0.0
IKKIkBalphai = 0.0
IKKIkBalphaNFkBi = 0.0
IKKIkBbetai = 0.0
IKKIkBbetaNFkBi = 0.0
IKKIkBepsi = 0.0
IKKIkBepsNFkBi = 0.0
IkBalphai = 0.1
IkBalphaNFkBi = 0.0
IkBalphanuci = 0.0
IkBalphanucNFkBnuci = 0.0
IkBalphatranscripti = 0.0
IkBbetai = 0.0
IkBbetaNFkBi = 0.0
IkBbetanuci = 0.0
IkBbetanucNFkBnuci = 0.0
IkBbetatranscripti = 0.0
IkBepsi = 0.0
IkBepsNFkBi = 0.0
IkBepsnuci = 0.0
IkBepsnucNFkBnuci = 0.0
IkBepstranscripti = 0.0
NFkBi = 0.1
NFkBnuci = 0.001
fraftertriggeri = 0.5
end initial values

begin assignment rules
TotalNFkBn := IkBbetanucNFkBnuc[t] + NFkBnuc[t]
TotalIkBalpha := IkBalpha[t] + IkBalphaNFkB[t] + IKKIkBalpha[t] + IKKIkBalphaNFkB[t]
TotalIkBeps := IkBeps[t] + IkBepsNFkB[t] + IKKIkBeps[t] + IKKIkBepsNFkB[t]
TotalIkBbeta := IkBbeta[t] + IkBbetaNFkB[t] + IKKIkBbeta[t] + IKKIkBbetaNFkB[t]
end assignment rules

begin function definitions
end function definitions

begin events
event_0000001 = (t >= 2000 && triggervalue == 0, {IKK[t] -> 0.1, triggervalue -> 1, flagforaftertrigger -> 0}, 0)
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units