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))