Python howells 예제들

예제 #1

파일: howells.py 프로젝트: rouxery/earm

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.howells(do_pore_assembly=True, do_pore_transport=True)

# Set initial condition for uncleaved Bid to 0.1uM, per the paper
Initial(Bid(state='U', bf=None), Parameter('Bid_0', 0.1e-6 * 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))

예제 #2

파일: howells.py 프로젝트: LoLab-VU/earm

"""
Model M15b: MOMP model from [Howells2011]_.
"""

from pysb import *
from earm import shen_modules

Model()

shen_modules.momp_monomers()

# The specific MOMP model to use
shen_modules.howells()

# 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('Bad_Bcl2_', Bcl2(bf=1) % Bad(bf=1))
Observable('Bid_Bcl2_', Bcl2(bf=1) % Bid(bf=1))
Observable('Bax_Bcl2_', Bcl2(bf=1) % Bax(bf=1))
Observable('pBad1433_', Bad(bf=None, state='C', serine='B'))

예제 #3

"""
Model M15b: MOMP model from [Howells2011]_.
"""

from pysb import *
from earm import shen_modules

Model()

shen_modules.momp_monomers()

# The specific MOMP model to use
shen_modules.howells()

# 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('Bad_Bcl2_', Bcl2(bf=1) % Bad(bf=1))
Observable('Bid_Bcl2_', Bcl2(bf=1) % Bid(bf=1))
Observable('Bax_Bcl2_', Bcl2(bf=1) % Bax(bf=1))
Observable('pBad1433_', Bad(bf=None, state='C', serine='B'))

예제 #4

파일: howells.py 프로젝트: radamthompson/earm

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.howells(do_pore_assembly=True, do_pore_transport=True)

# Set initial condition for uncleaved Bid to 0.1uM, per the paper
Initial(Bid(state='U', bf=None), Parameter('Bid_0', 0.1e-6 * 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))