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FceRI_viz.bngl
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FceRI_viz.bngl
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## title: FceRI_viz.bngl
# description: A
begin model
begin parameters
IgE_tot 2
FcR_tot 4.0e2
Lyn_tot 2.8e1
Syk_tot 4.0e2
Lat_tot 4.0e2
kp1 1.7e-6
km1 0.01
kp2 4.0e-1
km2 km1
kpL 5e-2
kmL 20
kpLs 5e-2
kmLs 0.12
kpS 6e-2
kmS 0.13
kpSs 6e-2
kmSs 0.13
pLb 30
pLbs 100
pLg 1
pLgs 3
pLS 30
pLSs 100
pSS 100
pSSs 200
dm 20
dc 20
kpMM 5e-3
kmMM 20
pMM 200
end parameters
begin molecule types
FcR(alpha,beta~0~P,gamma~0~P)
IgE(Fc,Fc)
Lat(Y136~0~P)
Lyn(U,SH2)
Syk(tSH2,PTK~0~P)
end molecule types
begin observables
Molecules pLat Lat(Y136~P!?)
Molecules LynFree Lyn(U,SH2)
Molecules FcRMon FcR(alpha) FcR(alpha!1).IgE(Fc!1,Fc)
Molecules FcRDim FcR().FcR()
Molecules FcRPbeta FcR(beta~P!?)
Molecules FcRPgamma FcR(gamma~P) FcR(gamma~P!+)
Molecules FcRSyk FcR(gamma~P!1).Syk(tSH2!1)
Molecules FcRSykPS FcR(gamma~P!1).Syk(tSH2!1,PTK~P)
Molecules SykTest Syk()
Molecules LynTest Lyn()
Molecules FcRTest FcR()
end observables
begin functions
Pb() = FcRPbeta/FcRDim
Pg() = FcRPgamma/FcRDim
SykP() = FcRSykPS/FcRDim
end functions
begin species
IgE(Fc,Fc) IgE_tot
Lyn(SH2,U) Lyn_tot
Syk(PTK~0,tSH2) Syk_tot
FcR(alpha,beta~0,gamma~0) FcR_tot
Lat(Y136~0) Lat_tot
end species
begin reaction rules
R1: FcR(alpha) + IgE(Fc,Fc) <-> FcR(alpha!1).IgE(Fc!1,Fc) kp1, km1
R2: FcR(alpha) + IgE(Fc,Fc!+) <-> FcR(alpha!1).IgE(Fc!1,Fc!+) kp2, km2
R3: FcR(beta~0) + Lyn(U,SH2) <-> FcR(beta~0!1).Lyn(U!1,SH2) kpL, kmL
R4: IgE(Fc!1,Fc!2).Lyn(U!3,SH2).FcR(alpha!2,beta~0!3).FcR(alpha!1,beta~0) -> \
IgE(Fc!1,Fc!2).Lyn(U!3,SH2).FcR(alpha!2,beta~0!3).FcR(alpha!1,beta~P) pLb
R5: IgE(Fc!1,Fc!2).Lyn(U!3,SH2).FcR(alpha!2,beta~0!3).FcR(alpha!1,gamma~0) -> \
IgE(Fc!1,Fc!2).Lyn(U!3,SH2).FcR(alpha!2,beta~0!3).FcR(alpha!1,gamma~P) pLg
R6: IgE(Fc!1,Fc!2).Lyn(U,SH2!3).FcR(alpha!2,beta~P!3).FcR(alpha!1,beta~0) -> \
IgE(Fc!1,Fc!2).Lyn(U,SH2!3).FcR(alpha!2,beta~P!3).FcR(alpha!1,beta~P) pLbs
R7: IgE(Fc!1,Fc!2).Lyn(U,SH2!3).FcR(alpha!2,beta~P!3).FcR(alpha!1,gamma~0) -> \
IgE(Fc!1,Fc!2).Lyn(U,SH2!3).FcR(alpha!2,beta~P!3).FcR(alpha!1,gamma~P) pLgs
R8: FcR(beta~P) + Lyn(U,SH2) <-> FcR(beta~P!1).Lyn(U,SH2!1) kpLs, kmLs
R9: FcR(gamma~P) + Syk(tSH2) <-> FcR(gamma~P!1).Syk(tSH2!1) kpS, kmS
R10: IgE(Fc!1,Fc!2).Syk(tSH2!3,PTK~0).FcR(alpha!2,gamma~P!3).FcR(alpha!1,gamma~P!4).Syk(tSH2!4,PTK~0) -> \
IgE(Fc!1,Fc!2).Syk(tSH2!3,PTK~0).FcR(alpha!2,gamma~P!3).FcR(alpha!1,gamma~P!4).Syk(tSH2!4,PTK~P) pSS
R11: IgE(Fc!1,Fc!2).Syk(tSH2!3,PTK~P).FcR(alpha!2,gamma~P!3).FcR(alpha!1,gamma~P!4).Syk(tSH2!4,PTK~0) -> \
IgE(Fc!1,Fc!2).Syk(tSH2!3,PTK~P).FcR(alpha!2,gamma~P!3).FcR(alpha!1,gamma~P!4).Syk(tSH2!4,PTK~P) pSSs
R12: Syk(tSH2!+,PTK~P) + Lat(Y136~0) -> Syk(tSH2!+,PTK~P!1).Lat(Y136~0!1) kpMM
R13: Syk(PTK~P!1).Lat(Y136~0!1) -> Syk(PTK~P) + Lat(Y136~0) kmMM
R14: Syk(PTK~P!1).Lat(Y136~0!1) -> Syk(PTK~P) + Lat(Y136~P) pMM
R15: Lat(Y136~P) -> Lat(Y136~0) dm
R16: FcR(beta~P) -> FcR(beta~0) dm
R17: FcR(gamma~P) -> FcR(gamma~0) dm
R18: Syk(tSH2!+,PTK~P) -> Syk(tSH2!+,PTK~0) dm
R19: Syk(tSH2,PTK~P) -> Syk(tSH2,PTK~0) dc
end reaction rules
end model
# 1. Generate the network for the model and simulate for 10 minutes.
# generate_network()
simulate({method=>"ode",t_end=>600,n_steps=>500})
# 2. Uncomment this line and rerun the model.
#visualize({type=>"opts"})
# 3. Navigate to the appropriate folder in the results directory and move the file with suffix _opts.txt back
# to the main project folder. Then uncomment the subsequent lines to produce a compressed atom-rule
# graph.
#visualize({type=>"regulatory",background=>0,opts=>["../../../FceRI_viz_opts.txt"]})