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
"""
from pysb import *
from earm import shared
from anrm import irvin_modules_v2 as irvin
from earm import lopez_modules as lopez
from earm import albeck_modules as albeck
Model()
# -----Monomers-----
# 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
