""" Model M1a: Extrinsic apoptosis model with expanded, "embedded together" model of MOMP. """ from pysb import * from earm import shared from earm import lopez_modules from earm import albeck_modules Model() # Declare monomers albeck_modules.ligand_to_c8_monomers() lopez_modules.momp_monomers() albeck_modules.apaf1_to_parp_monomers() # Generate the upstream and downstream sections albeck_modules.rec_to_bid() albeck_modules.pore_to_parp() # The specific MOMP model to use lopez_modules.embedded() # Declare observables shared.observables()
from pysb import *
from earm import lopez_modules
from earm import albeck_modules
from pysb.kappa import contact_map
import os
# A variant version of Lopez embedded with no Smac/CytoC
Model()
lopez_modules.momp_monomers()
Observable('aBax', Bax(state='A'))
Observable('cSmac', Smac(state='C'))
# The specific MOMP model to use
lopez_modules.embedded(do_pore_transport=False)
# Set Bid initial condition to be tBid
model.update_initial_condition_pattern(Bid(state='U', bf=None),
Bid(state='T', bf=None))
# Get rid of CytoC and Smac
model.parameters['Smac_0'].value = 0
model.parameters['CytoC_0'].value = 0
# Put some Noxa at the membrane
Initial(Noxa(state='M', bf=None), Parameter('mNoxa_0', 1))
Initial(Bad(state='M', bf=None), Parameter('mBad_0', 1))
# Generate the contact map
output_dir = os.path.abspath(os.path.dirname(__file__))
contact_map(model, output_dir, 'fig5d')
from pysb import *
from earm import lopez_modules
from earm import albeck_modules
from pysb.kappa import contact_map
import os
# A variant version of Lopez embedded with no Smac/CytoC
Model()
lopez_modules.momp_monomers()
Observable('aBax', Bax(state='A'))
Observable('cSmac', Smac(state='C'))
# The specific MOMP model to use
lopez_modules.embedded(do_pore_transport=False)
# Set Bid initial condition to be tBid
model.update_initial_condition_pattern(Bid(state='U', bf=None),
Bid(state='T', bf=None))
# Get rid of CytoC and Smac
model.parameters['Smac_0'].value = 0
model.parameters['CytoC_0'].value = 0
# Put some Noxa at the membrane
Initial(Noxa(state='M', bf=None), Parameter('mNoxa_0', 1))
Initial(Bad(state='M', bf=None), Parameter('mBad_0', 1))
# Generate the contact map
output_dir = os.path.abspath(os.path.dirname(__file__))