Python chen_febs_directの例

コード例 #1

ファイル: chen_febs_direct.py プロジェクト: rouxery/earm

"""
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))

コード例 #2

ファイル: chen_febs_direct.py プロジェクト: radamthompson/earm

"""
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))

コード例 #3

ファイル: chen_febs_direct.py プロジェクト: 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.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))

コード例 #4

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))