From BioNetWiki
begin model
begin parameters
# Physical and geometric constants
NA 6.0e23 #Avogadro’s num
f 0.01 #scaling factor
Vo f*1e-10 # L
V f*3e-12 # L
# Initial concentrations
EGF_conc 2e-9 # nM
EGF0 EGF_conc*NA*Vo #nM
EGFR0 f*1.8e5 #copy per cell
# Rate constants
kp1 9.0e7/(NA*Vo) #input /M/sec
km1 0.06 #/sec
end parameters
begin molecule types
EGF(R)
EGFR(L,CR1,Y1068~U~P)
end molecule types
begin seed species
EGF(R) EGF0
EGFR(L,CR1,Y1068~U) EGFR0
end seed species
begin reaction rules
EGF(R) + EGFR(L) <-> EGF(R!1).EGFR(L!1) kp1, km1
end reaction rules
begin observables
# Species LR EGF(R!1).EGFR(L!1)
Molecules Lbound EGF(R!+)
end observables
end model
begin actions
generate_network({overwrite=>1});
saveConcentrations();
simulate_ode({suffix=>ode,n_steps=>20,t_end=>100});
# resetConcentrations();
# simulate_nf({suffix=>ssa,n_steps=>20,t_end=>100});
end actions