Python chen_biophys_j Examples

Example #1

File: chen_biophys_j.py Project: radamthompson/earm

"""

from pysb import *
from earm import shen_modules
from pysb.integrate import odesolve
from pylab import linspace, plot, figure, ion, legend
from pysb.bng import generate_equations
import re

Model()

shen_modules.momp_monomers()
#shen_modules.momp_initial_conditions(bid_state='T')

# The specific MOMP model to use
shen_modules.chen_biophys_j(do_pore_assembly=True)

Observable('aBax_', Bax(state='A', bf=None))
#Observable('aBax_', Bax(state='A', bf=None, s1=None, s2=None))
#Observable('aBax_', Bax(state='A'))
Observable('Bid_', Bid(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))


def simulate(f2=0.5, tmax=3000):
    t = linspace(0, tmax, 100)
    ion()
    figure()
    model.parameters['Bid_0'].value = f2 * 1e-1

Example #2

File: chen_biophys_j.py Project: 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_biophys_j(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))

Example #3

File: chen_biophys_j.py Project: LoLab-VU/earm

"""

from pysb import *
from earm import shen_modules
from pysb.integrate import odesolve
from pylab import linspace, plot, figure, ion, legend
from pysb.bng import generate_equations
import re

Model()

shen_modules.momp_monomers()
#shen_modules.momp_initial_conditions(bid_state='T')

# The specific MOMP model to use
shen_modules.chen_biophys_j(do_pore_assembly=True)

Observable('aBax_', Bax(state='A', bf=None))
#Observable('aBax_', Bax(state='A', bf=None, s1=None, s2=None))
#Observable('aBax_', Bax(state='A'))
Observable('Bid_', Bid(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))

def simulate(f2=0.5, tmax=3000):
    t = linspace(0, tmax, 100)  
    ion()
    figure()
    model.parameters['Bid_0'].value = f2 * 1e-1
    x = odesolve(model, t)

Example #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_biophys_j(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))