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Jadwin_model_pulse.bngl
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Jadwin_model_pulse.bngl
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###
#@notes:'This is an atomized translation of an SBML model created on 02/04/2018. The original model has 9 molecules and 5 reactions. The translated model has 5 molecules and 5 rules'
###
begin model
begin parameters
EGF_uM 0 #4e-4
Kinase_uM 0.81
YA_uM 8.1 #0.81
GRB2_uM 0.24 #5.4 #0
Shc_uM 0.24
Kf_r4 1.0 #units:s_1_uM_1
Kr_r4 1 #units:s_1
Kf_r7 0.54 #units:s_1_uM_1
Kf_r6 63.0 #units:s_1_uM_1
Kr_r6 0.16 #units:s_1
Km_PTP 3.3
Km_r0 Km_PTP*(6.022e23*1e-6) #units:uM
Vmax_PTP 4.6
Vmax_r0 Vmax_PTP*(6.022e23*1e-6) #units:uM_s_1
Kf_r1 1.0 #units:s_1_uM_1
Kr_r1 1.5 #units:s_1
Kr_r7 0
end parameters
begin compartments
#volume units:
extracellular 3 4e+12*1e-15
membrane 2 205.0*1e-15 extracellular
cytoplasm 3 2590.0*1e-15 membrane
end compartments
begin molecule types
SH2A(ya)
SH2B(ya)
Kinase(egf,kinase~kinase~0)
EGF(kinase)
YA(p~P~0,sh2a,sh2b)
end molecule types
begin seed species
@cytoplasm:SH2A(ya) GRB2_uM*1e-6*6.022e23*2.59e3*1e-15 #3.7360488e+26*1e-6*1e-15 # 0.24mol/L * 6.022e23/mol *2585.0L #SH2A #SH2A
@cytoplasm:SH2B(ya) Shc_uM*1e-6*6.022e23*2.59e3*1e-15 #3.7360488e+26*1e-6*1e-15 # 0.24mol/L * 6.022e23/mol *2585.0L #SH2A #SH2A
@membrane:YA(p~0,sh2a,sh2b) YA_uM*1e-6*6.022e23*2.05e2*1e-15 #9.999531e+26*1e-6*1e-15 #original 8.1/ #YA #YA
@membrane:Kinase(egf,kinase~kinase) Kinase_uM*1e-6*6.022e23*2.05e2*1e-15 #9.999531e+25*1e-6*1e-15 #original 0.81/ #kinase #kinase
@extracellular:EGF(kinase) EGF_uM*1e-6*6.022e23*4e12*1e-15 #9.6352e+33*1e-6*1e-15 #original 0.0004/ #EGF #EGF
end seed species
begin observables
Species SH2A_cytoplasm @cytoplasm:SH2A(ya) #SH2A
Species pYA_membrane @membrane:YA(p~P,sh2a,sh2b) #pYA
Species YA_membrane @membrane:YA(p~0,sh2a,sh2b) #YA
Species pYASH2A_membrane @membrane:YA(p~P,sh2a!1,sh2b).SH2A(ya!1) #pYASH2A
Species pYASH2B_membrane @membrane:YA(p~P,sh2a,sh2b!2).SH2B(ya!2) #pYASH2B
Species SH2B_cytoplasm @cytoplasm:SH2B(ya) #SH2B
Species Kinase_EGF_membrane @membrane:Kinase(egf!0,kinase~0).EGF(kinase!0) #Kinase_EGF
Species kinase_membrane @membrane:Kinase(egf,kinase~kinase) #kinase
Species EGF_extracellular @extracellular:EGF(kinase) #EGF
end observables
begin functions
functionRate3() = if(Vmax_r0 * (1 / (Km_r0 + pYA_membrane)) >= 0, Vmax_r0 * (1 / (Km_r0 + pYA_membrane)), 0)
functionRate3m() = if(if(YA_membrane>0, Vmax_r0 * pYA_membrane * (1 / (Km_r0 + pYA_membrane))/YA_membrane,0) < 0, -(if(YA_membrane>0, Vmax_r0 * pYA_membrane * (1 / (Km_r0 + pYA_membrane))/YA_membrane,0)), 0)
end functions
begin reaction rules
r4: YA(p~P,sh2a,sh2b)@membrane + SH2A(ya)@cytoplasm <-> YA(p~P,sh2a!1,sh2b)@membrane.SH2A(ya!1)@membrane Kf_r4/(6.022e23*1e-6),Kr_r4
r7: YA(p~0,sh2a,sh2b)@membrane + Kinase(egf!0,kinase~0)@membrane.EGF(kinase!0)@membrane <-> YA(p~P,sh2a,sh2b)@membrane + Kinase(egf!0,kinase~0)@membrane.EGF(kinase!0)@membrane Kf_r7/(6.022e23*1e-6),Kr_r7
r6: Kinase(egf,kinase~kinase)@membrane + EGF(kinase)@extracellular <-> Kinase(egf!0,kinase~0)@membrane.EGF(kinase!0)@membrane Kf_r6/(6.022e23*1e-6),Kr_r6
r0: YA(p~P,sh2a,sh2b)@membrane <-> YA(p~0,sh2a,sh2b)@membrane functionRate3(),functionRate3m()
r1: YA(p~P,sh2a,sh2b)@membrane + SH2B(ya)@cytoplasm <-> YA(p~P,sh2a,sh2b!2)@membrane.SH2B(ya!2)@membrane Kf_r1/(6.022e23*1e-6),Kr_r1
end reaction rules
end model
generate_network({overwrite=>1})
simulate({method=>"ode",t_start=>0,t_end=>0,n_steps=>100})
setConcentration("EGF(kinase)@extracellular", 4e-4*1e-6*6.022e23*4e12*1e-15)
simulate({method=>"ode",continue=>1,t_start=>0,t_end=>10,n_steps=>10})
setConcentration("EGF(kinase)@extracellular", 0)
simulate({method=>"ode",continue=>1,t_start=>10,t_end=>100,n_steps=>90})
#parameter_scan({parameter=>"EGF_uM",par_min=>4e-5,par_max=>4e-2,n_scan_pts=>4,\
# method=>"ode",t_end=>100,log_scale=>1})
#parameter_scan({parameter=>"GRB2_uM",par_min=>0,par_max=>5.5,n_scan_pts=>276,\
# method=>"ode",t_end=>100,log_scale=>0})
#parameter_scan({parameter=>"Shc_uM",par_min=>0,par_max=>6,n_scan_pts=>61,\
# method=>"ode",t_end=>100,log_scale=>0})