""" Model M10b: "Direct" MOMP model from Chen et al. (2007) FEBS Letters. Chen, C., Cui, J., Zhang, W., & Shen, P. (2007). Robustness analysis identifies the plausible model of the Bcl-2 apoptotic switch. FEBS letters, 581(26), 5143-5150. :doi:`10.1016/j.febslet.2007.09.063` :pmid:`17936275`. """ from pysb import * from earm import shen_modules Model() shen_modules.momp_monomers() # The specific MOMP model to use shen_modules.chen_febs_direct() # 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))
""" Model M10b: "Direct" MOMP model from [Chen2007febs]_. """ from pysb import * from earm import shen_modules Model() shen_modules.momp_monomers() # The specific MOMP model to use shen_modules.chen_febs_direct() # 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.chen_febs_direct(do_pore_assembly=True, 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)) # Now that we've converted the original parameters to numbers, we can load # the rest of the model 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))
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.chen_febs_direct(do_pore_assembly=True, 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)) # Now that we've converted the original parameters to numbers, we can load # the rest of the model 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))