:doi:`10.1016/j.jtbi.2010.11.040` :pmid:`21130780`.
"""
from pysb import *
from earm import shared
from earm.shared import V
from scipy.constants import N_A
from earm import albeck_modules
from earm import shen_modules
import re
Model()
# Declare monomers
albeck_modules.ligand_to_c8_monomers()
shen_modules.momp_monomers()
albeck_modules.apaf1_to_parp_monomers()
# The specific MOMP model to use
shen_modules.howells(do_pore_assembly=True, do_pore_transport=True)
# Set initial condition for uncleaved Bid to 0.1uM, per the paper
Initial(Bid(state='U', bf=None), Parameter('Bid_0', 0.1e-6 * N_A * V))
albeck_modules.rec_to_bid()
albeck_modules.pore_to_parp()
# Declare common observables
shared.observables()
# Additional observables
"""
Model M9b: MOMP model from [Chen2007biophysj]_.
"""
from pysb import *
from earm import shen_modules
from pysb.integrate import odesolve
from pylab import linspace, plot, figure, ion, legend
from pysb.bng import generate_equations
import re
Model()
shen_modules.momp_monomers()
#shen_modules.momp_initial_conditions(bid_state='T')
# The specific MOMP model to use
shen_modules.chen_biophys_j(do_pore_assembly=True)
Observable('aBax_', Bax(state='A', bf=None))
#Observable('aBax_', Bax(state='A', bf=None, s1=None, s2=None))
#Observable('aBax_', Bax(state='A'))
Observable('Bid_', Bid(bf=None))
Observable('Bcl2_', Bcl2(bf=None))
Observable('Bcl2_Bid_', Bcl2(bf=1) % Bid(bf=1))
Observable('Bcl2_Bax_', Bcl2(bf=1) % Bax(bf=1))
def simulate(f2=0.5, tmax=3000):
t = linspace(0, tmax, 100)
ion()