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.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
"""Produce contact map for Figure 5D from the PySB publication""" from __future__ import print_function from pysb import * from earm import lopez_modules from earm import albeck_modules from pysb.kappa import contact_map import os # A variant version of Lopez embedded with no Smac/CytoC Model() lopez_modules.momp_monomers() Observable('aBax', Bax(state='A')) Observable('cSmac', Smac(state='C')) # The specific MOMP model to use lopez_modules.embedded(do_pore_transport=False) # Set Bid initial condition to be tBid model.update_initial_condition_pattern(Bid(state='U', bf=None), Bid(state='T', bf=None)) # Get rid of CytoC and Smac model.parameters['Smac_0'].value = 0 model.parameters['CytoC_0'].value = 0 # Put some Noxa at the membrane Initial(Noxa(state='M', bf=None), Parameter('mNoxa_0', 1)) Initial(Bad(state='M', bf=None), Parameter('mBad_0', 1))
""" Model M3a: Extrinsic apoptosis model with "indirect" model of MOMP. """ from pysb import * from earm import shared from earm import lopez_modules from earm import albeck_modules Model() # Declare monomers albeck_modules.ligand_to_c8_monomers() lopez_modules.momp_monomers() albeck_modules.apaf1_to_parp_monomers() # Generate the upstream and downstream sections albeck_modules.rec_to_bid() albeck_modules.pore_to_parp() # The specific MOMP model to use lopez_modules.indirect() # Declare observables shared.observables()
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() """ 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()