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PySB implementation of the ErbB related MAPK and AKT signaling
pathways originally published in [Chen2009]_.
This file containst functions that implement the ErbB execution
pathway in three modules:
- Receptor layer events, taking into account all ErbB1-4 interactions with ligand.
- AKT pathway
- MAPK pathway
from pysb import *
from pysb.util import alias_model_components
from egfr.shared import * # modified model aliases
# Receptor Layer
# Default rates?
# Monomer declarations
# ====================
def erbb_reclayer_monomers():
""" Declares the ErbB receptor interactions.
'bf' is the default site to be used for all binding/catalysis reactions.
Monomer('EGF', ['bf']) # Epidermal Growth Factor ligand
Monomer('HRG', ['bf']) # Heregulin ligand
Monomer('erbb1', ['bf'])
Monomer('erbb2', ['bf'])
Monomer('erbb3', ['bf'])
Monomer('erbb4', ['bf'])
Monomer('DEP1', ['bf'])
Monomer('DEP2', ['bf'])
Monomer('DEP3', ['bf'])
Monomer('DEP4', ['bf'])
def rec_events():
# binding to receptors
bind_table([[ EGF, HRG],
[erbb1, (1.0,1.0), None],
[erbb3, None, (1.0,1.0)],
[erbb4, None, (1.0,1.0)],
# erbb dimerization
bind_table([[ erbb1, erbb2, erbb3, erbb4],
[erbb1, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)],
[erbb2, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)],
[erbb3, (kdimf, kdimr), (kdimf, kdimr), None, (kdimf, kdimr)],
[erbb4, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)]
# ATP binding
bind_table([[ ATP],
[erbb1, (kf, kr)],
[erbb2, (kf, kr)],
[erbb4, (kf, kr)]
# Receptor cross phosphorylation
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