Python embedded Examples

Example #1

"""
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()

Example #2

File: fig5d.py Project: zhwycsz/pysb

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')

Example #3

File: fig5d.py Project: Adityaparmar2903/pysb

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__))