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
"""
Model M7a: Extrinsic apoptosis model incorporating the MOMP model "Current
model" (Figure 11e) from [Albeck2008]_.
"""
from pysb import *
from earm import albeck_modules
from earm import shared
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()
# Declare shared observables
shared.observables()
# Additional observables
Observable('aBax_', Bax(bf=None, state='A'))