def get_iAF1260b_environment(
time_step=TIME_STEP,
bounds=[20,20],
n_bins=[10, 10],
jitter_force=1e-4,
depth=3000.0,
scale_concentration=1, # scales minimal media
diffusion=5e-3,
override_initial={},
keep_fields_emit=[],
):
# get external state from iAF1260b metabolism
config = get_iAF1260b_config()
metabolism = Metabolism(config)
molecules = {
mol_id: conc * scale_concentration
for mol_id, conc in metabolism.initial_state['external'].items()
}
for mol_id, conc in override_initial.items():
molecules[mol_id] = conc
gradient = {
'type': 'uniform',
'molecules': molecules}
return get_lattice_config(
time_step=time_step,
bounds=bounds,
molecules=list(molecules.keys()),
n_bins=n_bins,
jitter_force=jitter_force,
depth=depth,
diffusion=diffusion,
gradient=gradient,
keep_fields_emit=keep_fields_emit,
)
def default_metabolism_config():
metabolism_config = get_iAF1260b_config()
metabolism_config.update({
'moma': False,
'tolerance': {
'EX_glc__D_e': [1.05, 1.0],
'EX_lcts_e': [1.05, 1.0]
}
})
return metabolism_config
def default_metabolism_config():
metabolism_config = get_iAF1260b_config()
metabolism_config.update({
'initial_mass': 1339.0, # fg of metabolite pools
'time_step': COMPARTMENT_TIMESTEP,
'tolerance': {
'EX_glc__D_e': [1.05, 1.0],
'EX_lcts_e': [1.05, 1.0],
}})
return metabolism_config
def get_metabolism_initial_state(scale_concentration=1, override={}):
# get external state from iAF1260b metabolism
config = get_iAF1260b_config()
metabolism = Metabolism(config)
molecules = {
mol_id: conc * scale_concentration
for mol_id, conc in metabolism.initial_state['external'].items()
}
for mol_id, conc in override.items():
molecules[mol_id] = conc
return molecules
def default_metabolism_config():
config = get_iAF1260b_config()
# set flux bond tolerance for reactions in ode_expression's lacy_config
metabolism_config = {
'moma': False,
'tolerance': {
'EX_glc__D_e': [1.05, 1.0],
'EX_lcts_e': [1.05, 1.0]
}
}
config.update(metabolism_config)
return config
def default_metabolism_config():
config = get_iAF1260b_config()
# set flux bond tolerance for reactions in ode_expression's lacy_config
metabolism_config = {
'time_step': TIMESTEP,
'initial_mass': 1339.0, # fg of metabolite pools
'tolerance': {
'EX_glc__D_e': [1.05, 1.0],
'EX_lcts_e': [1.05, 1.0]
}
}
config.update(metabolism_config)
return config