Model M13b: "Direct 1" MOMP model from Cui et al. (2008) PLoS One.
Cui, J., Chen, C., Lu, H., Sun, T., & Shen, P. (2008). Two independent positive
feedbacks and bistability in the Bcl-2 apoptotic switch. PLoS ONE, 3(1), e1469.
:doi:`10.1371/journal.pone.0001469` :pmid:`18213378`.
"""
from pysb import *
from earm import shen_modules
Model()
shen_modules.momp_monomers()
# The specific MOMP model to use
shen_modules.cui_direct1()
# Observables
Observable('AcBax_', Bax(bf=None, state='A'))
#Observable('Bax4_', MatchOnce(Bax(bf=None, s1=1, s2=4) %
# Bax(bf=None, s1=2, s2=1) %
# Bax(bf=None, s1=3, s2=2) %
# Bax(bf=None, s1=4, s2=3)))
Observable('Bid_', Bid(bf=None))
Observable('Bad_', Bad(bf=None))
Observable('Bcl2_', Bcl2(bf=None))
Observable('Bcl2_Bad_', Bcl2(bf=1) % Bad(bf=1))
Observable('Bcl2_Bid_', Bcl2(bf=1) % Bid(bf=1))
Observable('Bcl2_Bax_', Bcl2(bf=1) % Bax(bf=1))
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.cui_direct1(do_pore_transport=True)
# Set initial condition for uncleaved Bid to 20nM, per the paper
Initial(Bid(state="U", bf=None), Parameter("Bid_0", 20e-9 * N_A * V))
albeck_modules.rec_to_bid()
albeck_modules.pore_to_parp()
# Declare common observables
shared.observables()
# Additional observables
Observable("aBax_", Bax(state="A", 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))
"""
Model M13b: "Direct 1" MOMP model from [Cui2008]_.
"""
from pysb import *
from earm import shen_modules
Model()
shen_modules.momp_monomers()
# The specific MOMP model to use
shen_modules.cui_direct1()
# Observables
Observable('AcBax_', Bax(bf=None, state='A'))
#Observable('Bax4_', MatchOnce(Bax(bf=None, s1=1, s2=4) %
# Bax(bf=None, s1=2, s2=1) %
# Bax(bf=None, s1=3, s2=2) %
# Bax(bf=None, s1=4, s2=3)))
Observable('Bid_', Bid(bf=None))
Observable('Bad_', Bad(bf=None))
Observable('Bcl2_', Bcl2(bf=None))
Observable('Bcl2_Bad_', Bcl2(bf=1) % Bad(bf=1))
Observable('Bcl2_Bid_', Bcl2(bf=1) % Bid(bf=1))
Observable('Bcl2_Bax_', Bcl2(bf=1) % Bax(bf=1))
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.cui_direct1(do_pore_transport=True)
# Set initial condition for uncleaved Bid to 20nM, per the paper
Initial(Bid(state='U', bf=None), Parameter('Bid_0', 20e-9 * N_A * V))
albeck_modules.rec_to_bid()
albeck_modules.pore_to_parp()
# Declare common observables
shared.observables()
# Additional observables
Observable('aBax_', Bax(state='A', 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))
