def albeck_as_matlab():
"""Loads model as stated in Albeck's 2008 paper."""
from earm import albeck_modules
model = Model()
# Declare monomers
albeck_modules.all_monomers()
# Generate the upstream and downstream sections
albeck_modules.rec_to_bid()
albeck_modules.pore_to_parp()
# The specific MOMP model to use
albeck_modules.albeck_11e()
# Add citoplasmic Bcl2 as it was in Albeck's model because it's absent in
# EARM implementation.
Monomer("Bcl2c", ["b"])
Parameter("Bcl2c_0", 2e4)
alias_model_components()
Initial(Bcl2c(b=None), Bcl2c_0)
bind(Bid(bf=None, state="T"), "bf", Bcl2c(b=None), "b", [1e-6, 0.001])
# There is another discrepancy in C8A and Bid kf
model.parameters["bind_C8A_BidU_to_C8ABidU_kf"].value = 1e-7
return model
def albeck_apoptosome_corrected(stimuli="extrinsic"):
"""to_deprecate: Loads model as stated in Albeck's 2008 paper and modifies
apoptosome dyanmics."""
from earm import albeck_modules
model = Model()
# Declare monomers
albeck_modules.all_monomers()
# Generate the upstream and downstream sections
albeck_modules.rec_to_bid()
pore_to_parp_double_apop()
# The specific MOMP model to use
albeck_modules.albeck_11e()
# Add citoplasmic Bcl2 as it was in Albeck's model because it's absent in
# EARM implementation.
Monomer("Bcl2c", ["b"])
Parameter("Bcl2c_0", 2e4)
alias_model_components()
Initial(Bcl2c(b=None), Bcl2c_0)
bind(Bid(bf=None, state="T"), "bf", Bcl2c(b=None), "b", [1e-6, 0.001])
# There is another discrepancy in C8A and Bid kf
model.parameters["bind_C8A_BidU_to_C8ABidU_kf"].value = 1e-7
return choose_stimuli(model, stimuli)
def arm(stimuli="extrinsic", add_CASPAM=True):
"""Returns the new apoptotic reaction model. stimuli can be extrinsic
(default) or intrinsic.
Parameters
----------
stimuli: string (default: extrinsic)
Either intrinsic or extrinsic to choose stimuli
add_CASPAM: bool (default: True)
if True, CASPAM biosensors are added to the model
"""
from earm import albeck_modules
model = Model()
# Declare monomers
albeck_modules.all_monomers()
# Generate the upstream and downstream sections
albeck_modules.rec_to_bid()
pore_to_parp_double_apop()
# The specific MOMP model to use
albeck_modules.albeck_11e()
# Add citoplasmic Bcl2 as it was in Albeck's model because it's absent in
# EARM implementation.
Monomer("Bcl2c", ["b"])
Parameter("Bcl2c_0", 2e4)
alias_model_components()
Initial(Bcl2c(b=None), Bcl2c_0)
bind(Bid(bf=None, state="T"), "bf", Bcl2c(b=None), "b", [1e-6, 0.001])
# There is another discrepancy in C8A and Bid kf
model.parameters["bind_C8A_BidU_to_C8ABidU_kf"].value = 1e-7
if add_CASPAM:
# Add biosensors and their perturbation
add_biosensors()
model.parameters["dsCas3_0"].value = 7.5e5
model.parameters["dsCas8_0"].value = 7.5e5
model.parameters["dsCas9_0"].value = 7.5e5
model.parameters["bind_sCas3sCas3_C3A_kf"].value = 2.8e-07
model.parameters["bind_sCas8sCas8_C8A_kf"].value = 5.4e-08
model.parameters["bind_sCas9sCas9_Apop_kf"].value = 2.8e-07
# Add interaction between single activation
add_apaf_biosensor_cleavage()
# Other parameters that need to be corrected
model.parameters["L_0"].value = 1e3
model.parameters["Smac_0"].value = 1e5
model.parameters["CytoC_0"].value = 1e5
return choose_stimuli(model, stimuli)
def load_pysb_model(func, pore: bool):
"""Load an Albeck model.
func: Callable
Specific Albeck model function, such as albeck_11b.
pore: bool
If True, do pore transport in the model.
"""
model = Model() # noqa: F405
# Declare monomers
albeck_modules.all_monomers()
# Generate the upstream and downstream sections
albeck_modules.rec_to_bid()
albeck_modules.pore_to_parp()
# The specific MOMP model to use
func(do_pore_transport=pore)
return model
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))
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.cui_direct2(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))
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))