Exemple #1
0
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()


Exemple #4
0
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()
Exemple #5
0
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))

Exemple #6
0
## 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'))