def compile_monomers():
Model('m')
# From irvin_modules
irvin.Momomers_FasL_to_DISC()
irvin.NFkB_cFlip_interaction_monomers()
irvin.TNFR1_to_ComplexII_monomers()
irvin.SecondaryComplex_to_Bid_monomers()
irvin.rip1_to_MLKL_monmers()
# From lopez_modules
lopez.momp_monomers()
# From albeck_modules
albeck.apaf1_to_parp_monomers()
return m.monomers
def compile_monomers():
Model('m')
# From irvin_modules
irvin.Momomers_FasL_to_DISC()
irvin.NFkB_cFlip_interaction_monomers()
irvin.TNFR1_to_ComplexII_monomers()
irvin.SecondaryComplex_to_Bid_monomers()
irvin.rip1_to_MLKL_monmers()
# From lopez_modules
lopez.momp_monomers()
# From albeck_modules
albeck.apaf1_to_parp_monomers()
return m.monomers
def compile_monomers():
Model('m')
# From irvin_modules
irvin.TNFa_to_ComplexI_Monomers()
irvin.ComplexII_to_Bid_Monomers()
irvin.NFkB_Activation_and_Signaling_monomers()
irvin.Bid_Hypothesis_monomers()
irvin.Momomers_zVad_to_C8()
# From lopez_modules
lopez.momp_monomers()
# From albeck_modules
albeck.apaf1_to_parp_monomers()
return m.monomers
def compile_monomers():
Model('m')
# From irvin_modules
irvin.TNFa_to_ComplexI_Monomers()
irvin.ComplexII_to_Bid_Monomers()
irvin.NFkB_Activation_and_Signaling_monomers()
irvin.Bid_Hypothesis_monomers()
irvin.Momomers_zVad_to_C8()
# From lopez_modules
lopez.momp_monomers()
# From albeck_modules
albeck.apaf1_to_parp_monomers()
return m.monomers
def compile_monomers():
Model('m')
# From irvin_modules
irvin.CD95_to_SecondaryComplex_monomers()
irvin.TNFR1_to_SecondaryComplex_monomers()
irvin.SecondaryComplex_to_Bid_monomers()
"""alias_model_components() was placed in on the line following declaration of a parameter. This function exports the Parameter as a global variable. And it appears to be required before any rules can use the Parameters
Line 69: Monomer('C8', ['bC8']) is changed to
Monomer('C8', ['bf', 'state'], {'state':['A']})
Line 104: Initial(C8(bC8=None), C8_0) is changed to
Initial(C8(bf=None, state = 'A'), C8_0)
Line 161: Rule('C8_activation' ...+ C8(bC8 = None...) is changed to
Rule ('C8_activation' ...+C8(bf = None, state = 'A')
Line 164: bind(Bar(bC8 = None), 'bC8', C8(bC8 = None), 'bC8', [kf7, kr7])
is changed to bind(Bar(bC8 = None), 'bC8', C8(bf = None, state = 'A'), 'bf', [kf7, kr7])
Line 293: Deleted. Monomer('Bid', ['bf', 'state'], {'state':['unmod', 'po4', 'trunc', 'M']})
Line 310: Deleted. Parameter('Bid_0' , 2.0e4)
Line 315: Deleted. Initial(Bid(bf = None, state = 'unmod'), Bid_0)
Line 382: Rule('RIP1_truncation_CIIA', RIP_CIIA_proC8 >> CIIA + C8(bC8 = None) + RIP1(bDD=None, bRHIM = None, state = 'trunc'), kc25) is changed to
Rule('RIP1_truncation_CIIA', RIP_CIIA_proC8 >> CIIA + C8(bf = None, state = 'A') + RIP1(bDD=None, bRHIM = None, state = 'trunc'), kc25)
Line 383: Rule('RIP1_truncation_CIIB', RIP_CIIB_proC8 >> FADD(bDD=None, bDED1=None, bDED2=None)+ C8(bC8=None) + RIP1(bDD=None, bRHIM = None, state = 'trunc'), kc25) is changed to
Line 384: catalyze_state(C8(bC8=None), 'bC8', RIP1(bDD=None), 'bRHIM', 'state', 'unmod', 'trunc', [kf26, kr26, kc26])
is changed to catalyze_state(C8(bf = None, state = 'A'), 'bf', RIP1(bDD=None), 'bRHIM', 'state', 'unmod', 'trunc', [kf26, kr26, kc26])
Line 403:catalyze_state(C8(bC8=None), 'bC8', RIP3(), 'bRHIM', 'state', 'unmod', 'trunc', [kf31, kr31, kc31])
is changed to catalyze_state(C8(bf = None, state = 'A'), 'bf', RIP3(), 'bRHIM', 'state', 'unmod', 'trunc', [kf31, kr31, kc31])
Line 406: catalyze_state(BidK(), 'bf', Bid(), 'bf', 'state', 'unmod', 'po4', [kf32, kr32, kc32]) is changed to
catalyze_state(BidK(), 'bf', Bid(), 'bf', 'state', 'U', 'po4', [kf32, kr32, kc32])
Line 407: catalyze_state(C8(bC8=None), 'bC8', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
is changed to catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
Line 407: catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
is changed to
catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'U', 'T', [kf33, kr33, kc33])
"""
# From lopez_modules
lopez.momp_monomers()
# From albeck_modules
albeck.apaf1_to_parp_monomers()
return m.monomers
"""
from pysb import *
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.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))
mtor_modules.mtorc1_signaling_monomers() mtor_modules.mtorc1_signaling_initial() mtor_modules.mtorc1_signaling() mtor_modules.mtorc2_signaling() mtor_modules.tsc2_monomers() mtor_modules.tsc2_initial() mtor_modules.tsc2_inhibition_by_akt() mtor_modules.tsc2_inhibition_by_erk() mtor_modules.tsc2_activation_by_erk() mtor_modules.tsc2_gap_function() # ## 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()
catalyze_state(BidK(), 'bf', Bid(), 'bf', 'state', 'U', 'po4', [kf32, kr32, kc32])
Line 407: catalyze_state(C8(bC8=None), 'bC8', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
is changed to catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
Line 407: catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
is changed to
catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'U', 'T', [kf33, kr33, kc33])
"""
# From lopez_modules
lopez.momp_monomers()
""" Line 99: Monomer('Bid', ['bf', 'state'], {'state':['U', 'T', 'M']})
is changed to Monomer('Bid', ['bf', 'state'], {'state':['U', 'T', 'M', 'po4']})
"""
# From albeck_modules
albeck.apaf1_to_parp_monomers()
""" Line 118: Monomer('C6', ['bf', 'state'], {'state':['pro', 'A']})
is changed to Monomer('C6', ['bf1','bf2', 'state'], {'state':['pro', 'A']})
Line 124: Monomer('PARP', ['bf', 'state'], {'state':['U', 'C']})
is chanbed to Monomer('PARP', ['bf', 'state'], {'state':['U', 'C', 'A']})"""
# Rules
irvin.CD95_to_SecondaryComplex()
irvin.TNFR1_to_SecondaryComplex()
irvin.SecondaryComplex_to_Bid()
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()
catalyze_state(BidK(), 'bf', Bid(), 'bf', 'state', 'U', 'po4', [kf32, kr32, kc32])
Line 407: catalyze_state(C8(bC8=None), 'bC8', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
is changed to catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
Line 407: catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'unmod', 'trunc', [kf33, kr33, kc33])
is changed to
catalyze_state(C8(bf = None, state = 'A'), 'bf', Bid(), 'bf', 'state', 'U', 'T', [kf33, kr33, kc33])
"""
# From lopez_modules
lopez.momp_monomers()
""" Line 99: Monomer('Bid', ['bf', 'state'], {'state':['U', 'T', 'M']})
is changed to Monomer('Bid', ['bf', 'state'], {'state':['U', 'T', 'M', 'po4']})
"""
# From albeck_modules
albeck.apaf1_to_parp_monomers()
""" Line 118: Monomer('C6', ['bf', 'state'], {'state':['pro', 'A']})
is changed to Monomer('C6', ['bf1','bf2', 'state'], {'state':['pro', 'A']})
Line 124: Monomer('PARP', ['bf', 'state'], {'state':['U', 'C']})
is chanbed to Monomer('PARP', ['bf', 'state'], {'state':['U', 'C', 'A']})"""
# Rules
irvin.CD95_to_SecondaryComplex()
irvin.TNFR1_to_SecondaryComplex()
irvin.SecondaryComplex_to_Bid()
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()