# fceri_gamma2_hpp6.bngl # Created by BioNetGen 2.2.4 version("2.2.4+") begin model begin parameters NA 6.0221e23 PI 3.1415927 vol_cell 1e-12 cell_density 1e9 Rec_cell 4e5 Lyn_cell 3e4 Syk_cell 4e5 Lig_conc 10e-9 f 0.001 Vec (1/cell_density)*f Vcp vol_cell*f Lig_tot (Lig_conc*NA)*Vec Rec_tot Rec_cell*f Lyn_tot Lyn_cell*f Syk_tot Syk_cell*f kp1 (8e4/NA)/Vec km1 0 kp2 (1.51e8/NA)/Vcp km2 0 kpL (3.01e7/NA)/Vcp kmL 20.0 kpLs (3.01e7/NA)/Vcp kmLs 0.12 kpS (3.61e7/NA)/Vcp 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 k_lump 10000 kp1_1 2*((8e4/NA)/Vec) end parameters begin molecule types Lyn(U,SH2) Lig(l,l) Rec(a,b~Y~pY,g~Y~pY,g~Y~pY) X0002() population X0003() population X0001() population X0006() population X0004() population Syk(tSH2,l~Y~pY,a~Y~pY) X0005() population end molecule types begin observables Molecules LynFree Lyn(U,SH2) X0002() Molecules RecMon Rec(a) Rec(a!1).Lig(l!1,l) Molecules RecDim Rec(a!1).Lig(l!1,l!2).Rec(a!2) Molecules RecPbeta Rec(b~pY!?) Molecules RecPgamma Rec(g~pY!?) Molecules RecSyk Rec(g~pY!1).Syk(tSH2!1) Molecules RecSykPS Rec(g~pY!1).Syk(tSH2!1,a~pY) Molecules SykTest Syk() X0003() X0004() X0005() X0006() Molecules LynTest Lyn() X0002() Molecules RecTest Rec() Molecules LigTest Lig() X0001() end observables begin species X0001() Lig_tot X0002() Rec_tot X0003() Lyn_tot Rec(a,b~Y,g~Y,g~Y) Syk_tot X0004() 0 X0005() 0 X0006() 0 end species begin reaction rules Rule1_v1: Rec(a) + X0001() -> Lig(l!1,l).Rec(a!1) kp1_1 Rule1r_v1: Lig(l!1,l).Rec(a!1) -> Rec(a) + X0001() km1 DeleteMolecules Rule2_v1: Rec(a) + Lig(l!+,l) -> Lig(l!+,l!1).Rec(a!1) kp2 Rule2r_v1: Lig(l%T1!1,l!+).Rec(a!1) -> Rec(a) + Lig(l!+,l%T1) km2 Rule3_v1: Rec(b~Y) + X0002() -> Lyn(SH2,U!1).Rec(b~Y!1) kpL Rule3r_v1: Lyn(SH2,U!1).Rec(b~Y!1) -> Rec(b~Y) + X0002() kmL DeleteMolecules Rule4_v1: Lig(l!1,l!2).Lyn(SH2,U!3).Rec(a!2,b~Y!3).Rec(a!1,b~Y) -> Lig(l!1,l!2).Lyn(SH2,U!3).Rec(a!2,b~Y!3).Rec(a!1,b~pY) pLb Rule5_v1: Lig(l!1,l!2).Lyn(SH2,U!3).Rec(a!2,b~Y!3).Rec(a!1,g~Y) -> Lig(l!1,l!2).Lyn(SH2,U!3).Rec(a!2,b~Y!3).Rec(a!1,g~pY) pLg Rule6_v1: Rec(b~pY) + X0002() -> Lyn(SH2!1,U).Rec(b~pY!1) kpLs Rule6r_v1: Lyn(SH2!1,U).Rec(b~pY!1) -> Rec(b~pY) + X0002() kmLs DeleteMolecules Rule7_v1: Lig(l!1,l!2).Lyn(SH2!3,U).Rec%T6(a!1,b~Y).Rec(a!2,b~pY!3) -> Lig(l!1,l!2).Lyn(SH2!3,U).Rec(a!2,b~pY!3).Rec%T6(a!1,b~pY) pLbs Rule8_v1: Lig(l!1,l!2).Lyn(SH2!3,U).Rec(a!2,b~pY!3).Rec(a!1,g~Y) -> Lig(l!1,l!2).Lyn(SH2!3,U).Rec(a!2,b~pY!3).Rec(a!1,g~pY) pLgs Rule9_v1: Rec(g~pY) + Syk(tSH2) -> Rec(g~pY!1).Syk(tSH2!1) kpS Rule9_v2: Rec(g~pY) + X0003() -> Rec(g~pY!1).Syk(a~Y,l~Y,tSH2!1) kpS Rule9_v3: Rec(g~pY) + X0004() -> Rec(g~pY!1).Syk(a~pY,l~Y,tSH2!1) kpS Rule9_v4: Rec(g~pY) + X0005() -> Rec(g~pY!1).Syk(a~Y,l~pY,tSH2!1) kpS Rule9_v5: Rec(g~pY) + X0006() -> Rec(g~pY!1).Syk(a~pY,l~pY,tSH2!1) kpS Rule9r_v1: Rec(g~pY!1).Syk(tSH2!1) -> Rec(g~pY) + Syk(tSH2) kmS Rule10_v1: Lig(l!1,l!2).Lyn(SH2,U!3).Rec(a!2,b~Y!3).Rec(a!1,g~pY!4).Syk(l~Y,tSH2!4) -> Lig(l!1,l!2).Lyn(SH2,U!3).Rec(a!2,b~Y!3).Rec(a!1,g~pY!4).Syk(l~pY,tSH2!4) pLS Rule11_v1: Lig(l!1,l!2).Lyn(SH2!3,U).Rec(a!2,b~pY!3).Rec(a!1,g~pY!4).Syk(l~Y,tSH2!4) -> Lig(l!1,l!2).Lyn(SH2!3,U).Rec(a!2,b~pY!3).Rec(a!1,g~pY!4).Syk(l~pY,tSH2!4) pLSs Rule12_v1: Lig(l!1,l!2).Rec(a!2,g~pY!3).Rec(a!1,g~pY!4).Syk(a~Y,tSH2!3).Syk(a~Y,tSH2!4) -> Lig(l!1,l!2).Rec(a!2,g~pY!3).Rec(a!1,g~pY!4).Syk(a~Y,tSH2!3).Syk(a~pY,tSH2!4) pSS Rule13_v1: Lig(l!1,l!2).Rec(a!2,g~pY!3).Rec(a!1,g~pY!4).Syk(a~Y,tSH2!4).Syk(a~pY,tSH2!3) -> Lig(l!1,l!2).Rec(a!2,g~pY!3).Rec(a!1,g~pY!4).Syk(a~pY,tSH2!4).Syk(a~pY,tSH2!3) pSSs Rule14_v1: Rec(b~pY) -> Rec(b~Y) dm Rule15_v1: Rec(g~pY) -> Rec(g~Y) dm Rule16_v1: Syk(l~pY,tSH2!+) -> Syk(l~Y,tSH2!+) dm Rule17_v1: Syk(a~pY,tSH2!+) -> Syk(a~Y,tSH2!+) dm Rule18_v1: Syk(l~pY,tSH2) -> Syk(l~Y,tSH2) dc Rule18_v2: X0005() -> X0003() dc Rule18_v3: X0006() -> X0004() dc Rule19_v1: Syk(a~pY,tSH2) -> Syk(a~Y,tSH2) dc Rule19_v2: X0004() -> X0003() dc Rule19_v3: X0006() -> X0005() dc MapRule0: Lig(l,l) -> X0001() k_lump MapRule1: Lyn(SH2,U) -> X0002() k_lump MapRule2: Syk(a~Y,l~Y,tSH2) -> X0003() k_lump MapRule3: Syk(a~pY,l~Y,tSH2) -> X0004() k_lump MapRule4: Syk(a~Y,l~pY,tSH2) -> X0005() k_lump MapRule5: Syk(a~pY,l~pY,tSH2) -> X0006() k_lump end reaction rules end model ## model actions ## simulate_nf({ t_end=>1200, n_steps=>120 ,gml=>10000000, complex=>0 })