def pore_transport(subunit, size, csource, cdest, ktable):
"""Alias for pysb.macros.pore_transport with default arguments.
- Uses the default binding site names for the binding site on the pore
and on the cargo
- Uses the default pore site names for subunit-subunit binding
- Uses only a single size (not a min and max size) for the size of
transport-competent pores
"""
return macros.pore_transport(subunit, 's1', 's2', 'bf', size, size,
csource, 'bf', cdest, ktable)
def pore_transport(subunit, size, csource, cdest, ktable):
"""Alias for pysb.macros.pore_transport with default arguments.
- Uses the default binding site names for the binding site on the pore
and on the cargo
- Uses the default pore site names for subunit-subunit binding
- Uses only a single size (not a min and max size) for the size of
transport-competent pores
"""
return macros.pore_transport(subunit, 's1', 's2', 'bf',
size, size, csource, 'bf', cdest, ktable)
Initial(Smac(loc='m', t=None), Smac_0)
# Maximum number of subunits in a pore
max_size = 6
# Size at which pores are "competent" to transport cargo
min_transport_size = 4
# Build handy rate "sets" (in this formulation, rates don't vary with pore size)
assembly_rates = [[2e-4, 1e-3]] * (max_size - 1)
transport_rates = [[3e-5, 1e-3, 1e1]] * (max_size - min_transport_size + 1)
# Assemble the pore
# (specify t=None so the pore can't fall apart while it's bound to cargo)
assemble_pore_sequential(Bax(t=None), 's1', 's2', max_size, assembly_rates)
# Transport Smac
pore_transport(Bax, 's1', 's2', 't', min_transport_size, max_size,
Smac(loc='m'), 't', Smac(loc='c'), transport_rates)
# Add an observable for each pore size
for size in range(1, max_size + 1):
Observable('Bax%d' % size, pore_species(Bax, 's1', 's2', size))
# Observe unbound Smac in each compartment
Observable('mSmac', Smac(loc='m', t=None))
Observable('cSmac', Smac(loc='c'))
if __name__ == '__main__':
print __doc__, "\n", model
print "\nNOTE: This model code is designed to be imported and programatically " \
"manipulated,\nnot executed directly. The above output is merely a " \
"diagnostic aid. Please see\n" \
"run_bax_pore_sequential.py for example usage."
Initial(Smac(loc='m', t=None), Smac_0)
# Maximum number of subunits in a pore
max_size = 6
# Size at which pores are "competent" to transport cargo
min_transport_size = 4
# Build handy rate "sets" (in this formulation, rates don't vary with pore size)
assembly_rates = [[2e-4, 1e-3]] * (max_size - 1)
transport_rates = [[3e-5, 1e-3, 1e1]] * (max_size - min_transport_size + 1)
# Assemble the pore
# (specify t=None so the pore can't fall apart while it's bound to cargo)
assemble_pore_sequential(Bax(t=None), 's1', 's2', max_size, assembly_rates)
# Transport Smac
pore_transport(Bax, 's1', 's2', 't', min_transport_size, max_size,
Smac(loc='m'), 't', Smac(loc='c'), transport_rates)
# Add an observable for each pore size
for size in range(1, max_size + 1):
Observable('Bax%d' % size, pore_species(Bax, 's1', 's2', size))
# Observe unbound Smac in each compartment
Observable('mSmac', Smac(loc='m', t=None))
Observable('cSmac', Smac(loc='c'))
if __name__ == '__main__':
print __doc__, "\n", model
print "\nNOTE: This model code is designed to be imported and programatically " \
"manipulated,\nnot executed directly. The above output is merely a " \
"diagnostic aid. Please see\n" \
"run_bax_pore_sequential.py for example usage."
