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 albeck_apoptosome_corrected(stimuli="extrinsic"): """to_deprecate: Loads model as stated in Albeck's 2008 paper and modifies apoptosome dyanmics.""" from earm import albeck_modules model = Model() # Declare monomers albeck_modules.all_monomers() # Generate the upstream and downstream sections albeck_modules.rec_to_bid() pore_to_parp_double_apop() # 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 choose_stimuli(model, stimuli)
def arm(stimuli="extrinsic", add_CASPAM=True): """Returns the new apoptotic reaction model. stimuli can be extrinsic (default) or intrinsic. Parameters ---------- stimuli: string (default: extrinsic) Either intrinsic or extrinsic to choose stimuli add_CASPAM: bool (default: True) if True, CASPAM biosensors are added to the model """ from earm import albeck_modules model = Model() # Declare monomers albeck_modules.all_monomers() # Generate the upstream and downstream sections albeck_modules.rec_to_bid() pore_to_parp_double_apop() # 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 if add_CASPAM: # Add biosensors and their perturbation add_biosensors() model.parameters["dsCas3_0"].value = 7.5e5 model.parameters["dsCas8_0"].value = 7.5e5 model.parameters["dsCas9_0"].value = 7.5e5 model.parameters["bind_sCas3sCas3_C3A_kf"].value = 2.8e-07 model.parameters["bind_sCas8sCas8_C8A_kf"].value = 5.4e-08 model.parameters["bind_sCas9sCas9_Apop_kf"].value = 2.8e-07 # Add interaction between single activation add_apaf_biosensor_cleavage() # Other parameters that need to be corrected model.parameters["L_0"].value = 1e3 model.parameters["Smac_0"].value = 1e5 model.parameters["CytoC_0"].value = 1e5 return choose_stimuli(model, stimuli)
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
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))
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.cui_direct2(do_pore_transport=True) # Set initial condition for uncleaved Bid to 20nM, per the paper Initial(Bid(state='U', bf=None), Parameter('Bid_0', 20e-9 * 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))