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 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
irvin.FADD_to_C8() irvin.NFkB_cFlip_interaction() #3 irvin.cFLIP_L_Bid_interaction() #4 irvin.RIP1_Hypothesis_1()#5 irvin.ComplexI_to_NFkB() irvin.ComplexII_Hypothesis_1() #5 irvin.RIP1_deubiqutination_Hypothesis_1()#5 irvin.RIP1_to_SecondaryComplex() irvin.RIP1_truncation() irvin.Bid_Hypothesis() #6 irvin.C8_catalyzed_truncations() irvin.rip1_to_MLKL() irvin.C3_inhibits_MLKL()#7 # From lopez_modules lopez.declare_initial_conditions() lopez.translocate_tBid_Bax_BclxL() lopez.tBid_activates_Bax_and_Bak() lopez.tBid_binds_all_anti_apoptotics() lopez.sensitizers_bind_anti_apoptotics() lopez.effectors_bind_anti_apoptotics() lopez.lopez_pore_formation(do_pore_transport=True) # From albeck_modules albeck.pore_to_parp() # Observables irvin.observables()
irvin.FADD_to_C8() irvin.cFlip_competitive_inhibition() #2 irvin.NFkB_cFlip_interaction() #3 irvin.cFLIP_L_Bid_interaction() #4 irvin.RIP1_Hypothesis_2() #5 irvin.ComplexI_to_NFkB() irvin.ComplexII_Hypothesis_2() #5 irvin.TRADD_RIP1unmod_Hypothesis_2() #5a irvin.RIP1_deubiqutination_Hypothesis_1() #5a irvin.RIP1_to_SecondaryComplex() irvin.RIP1_truncation() irvin.Bid_Hypothesis() #6 irvin.C8_catalyzed_truncations() irvin.rip1_to_MLKL() irvin.C3_inhibits_MLKL() #7 # From lopez_modules lopez.declare_initial_conditions() lopez.translocate_tBid_Bax_BclxL() lopez.tBid_activates_Bax_and_Bak() lopez.tBid_binds_all_anti_apoptotics() lopez.sensitizers_bind_anti_apoptotics() lopez.effectors_bind_anti_apoptotics() lopez.lopez_pore_formation(do_pore_transport=True) # From albeck_modules albeck.pore_to_parp() # Observables irvin.observables()
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))
## Apoptotic signaling
albeck_modules.ligand_to_c8_monomers()
apoptosis_modules.apoptosis_monomers()
apoptosis_modules.apoptosis_initial()
albeck_modules.apaf1_to_parp_monomers()
lopez_modules.translocate_tBid_Bax_BclxL()
lopez_modules.tBid_activates_Bax_and_Bak()
lopez_modules.effector_auto_activation()
lopez_modules.tBid_binds_all_anti_apoptotics()
lopez_modules.effectors_bind_anti_apoptotics()
lopez_modules.sensitizers_bind_anti_apoptotics()
lopez_modules.lopez_pore_formation()
apoptosis_modules.apoptosis_sensitizer_translocation()
apoptosis_modules.apoptosis_bim_and_puma_bind_anti_apoptotics()
apoptosis_modules.apoptosis_bim_activate_bax()
albeck_modules.pore_to_parp()
## Crosstalk between MAPK and AKT pathways
crosstalk_modules.crosstalk_mapk_akt_monomers()
crosstalk_modules.crosstalk_mapk_akt_initial()
crosstalk_modules.crosstalk_mapk_akt_events()
#
## Crosstalk between ErbB signaling and apoptotic signaling
crosstalk_modules.crosstalk_erbb_apoptosis_monomers()
crosstalk_modules.crosstalk_erbb_apoptosis_initial()
crosstalk_modules.crosstalk_erbb_apoptosis_events()
#
## Observables
#Observable('obsAKTPP', AKT(bpip3=None, bpdk1=None, S='PP'))
#Observable('obsErbB1_P_CE', erbb(ty='1', st='P'))
#Observable('obsERKPP', ERK(st='PP'))