def generate_processes(self, config):
transcription_config = config['transcription']
translation_config = config['translation']
degradation_config = config['degradation']
complexation_config = config['complexation']
# update timestep
transcription_config.update({'time_step': config['time_step']})
translation_config.update({'time_step': config['time_step']})
degradation_config.update({'time_step': config['time_step']})
complexation_config.update({'time_step': config['time_step']})
# make the processes
transcription = Transcription(transcription_config)
translation = Translation(translation_config)
degradation = RnaDegradation(degradation_config)
complexation = Complexation(complexation_config)
mass_deriver = TreeMass(
config.get('mass_deriver',
{'initial_mass': config['initial_mass']}))
division = DivisionVolume(config)
return {
'mass_deriver': mass_deriver,
'transcription': transcription,
'translation': translation,
'degradation': degradation,
'complexation': complexation,
'division': division
}
def generate_processes(self, config):
daughter_path = config['daughter_path']
agent_id = config['agent_id']
# get the configs
transcription_config = config['transcription']
translation_config = config['translation']
degradation_config = config['degradation']
complexation_config = config['complexation']
# update expression timestep
transcription_config.update({'time_step': config['time_step']})
translation_config.update({'time_step': config['time_step']})
degradation_config.update({'time_step': config['time_step']})
complexation_config.update({'time_step': config['time_step']})
# make the expression processes
transcription = Transcription(transcription_config)
translation = Translation(translation_config)
degradation = RnaDegradation(degradation_config)
complexation = Complexation(complexation_config)
mass_deriver = TreeMass(config.get('mass_deriver', {
'initial_mass': config['initial_mass']}))
# Transport
transport = ConvenienceKinetics(config['transport'])
target_fluxes = transport.kinetic_rate_laws.reaction_ids
# Metabolism
# add target fluxes from transport
metabolism_config = config.get('metabolism')
metabolism_config.update({'constrained_reaction_ids': target_fluxes})
metabolism = Metabolism(metabolism_config)
# Division condition
division_condition = DivisionVolume({})
processes = {
'metabolism': metabolism,
'transport': transport,
'mass_deriver': mass_deriver,
'transcription': transcription,
'translation': translation,
'degradation': degradation,
'complexation': complexation,
'division': division_condition
}
# divide process set to true, add meta-division processes
if config['divide']:
meta_division_config = dict(
{},
daughter_path=daughter_path,
agent_id=agent_id,
compartment=self)
meta_division = MetaDivision(meta_division_config)
processes['meta_division'] = meta_division
return processes
def generate_processes(self, config):
transcription = Transcription(config.get('transcription', self.config.get('transcription')))
translation = Translation(config.get('translation', self.config.get('translation')))
degradation = RnaDegradation(config.get('degradation', self.config.get('degradation')))
complexation = Complexation(config.get('complexation', self.config.get('complexation')))
mass_deriver = TreeMass(config.get('mass_deriver', {
'initial_mass': config.get('initial_mass', self.initial_mass)}))
division = DivisionVolume(config)
return {
'mass_deriver': mass_deriver,
'transcription': transcription,
'translation': translation,
'degradation': degradation,
'complexation': complexation,
'division': division}
def generate_processes(self, config):
cobra_process = COBRA_FBA(config['cobra'])
processes = {
'cobra': cobra_process,
'mass_deriver': TreeMass(),
'volume_deriver': Volume(),
}
if config['fields_on']:
initial_state_cobra = cobra_process.initial_state()
fields_config = config['field_deriver']
fields_config.update({
'initial_external': initial_state_cobra['external']
})
processes.update({
'field_deriver': LocalField(fields_config)
})
return processes
def generate_processes(self, config):
daughter_path = config['daughter_path']
agent_id = config['agent_id']
# Transport
transport = ConvenienceKinetics(config['transport'])
# Metabolism
# get target fluxes from transport, and update constrained_reaction_ids
metabolism_config = config['metabolism']
target_fluxes = transport.kinetic_rate_laws.reaction_ids
metabolism_config.update({'constrained_reaction_ids': target_fluxes})
metabolism = Metabolism(metabolism_config)
# Gene expression
expression = ODE_expression(config['expression'])
# Mass deriver
mass_deriver = TreeMass({})
# Division
division_condition = DivisionVolume({})
processes = {
'transport': transport,
'metabolism': metabolism,
'expression': expression,
'mass_deriver': mass_deriver,
'division': division_condition,
}
# divide process set to true, add meta-division processes
if config['divide']:
meta_division_config = dict({},
daughter_path=daughter_path,
agent_id=agent_id,
compartment=self)
meta_division = MetaDivision(meta_division_config)
processes['meta_division'] = meta_division
return processes
def generate_processes(self, config):
# division config
daughter_path = config['daughter_path']
agent_id = config['agent_id']
division_config = dict(
config.get('division', {}),
daughter_path=daughter_path,
agent_id=agent_id,
compartment=self)
return {
'receptor': ReceptorCluster(config['receptor']),
'flagella_activity': FlagellaActivity(config['flagella']),
'transcription': Transcription(config['transcription']),
'translation': Translation(config['translation']),
'degradation': RnaDegradation(config['degradation']),
'complexation': Complexation(config['complexation']),
'growth': GrowthProtein(config['growth']),
'division': MetaDivision(division_config),
'mass_deriver': TreeMass(config['mass_deriver']),
'global_deriver': DeriveGlobals(config['global_deriver']),
}
def generate_processes(self, config):
daughter_path = config['daughter_path']
agent_id = config['agent_id']
division_config = dict(config.get('division', {}),
daughter_path=daughter_path,
agent_id=agent_id,
compartment=self)
growth = GrowthProtein(config.get('growth', {}))
transport = ConvenienceKinetics(config.get('transport', {}))
division = MetaDivision(division_config)
expression = MinimalExpression(config.get('expression', {}))
mass = TreeMass(config.get('mass', {}))
return {
'transport': transport,
'growth': growth,
'expression': expression,
'division': division,
'mass': mass
}
def generate_processes(self, config):
daughter_path = config['daughter_path']
agent_id = config['agent_id']
growth = GrowthProtein(config['growth'])
transport = ConvenienceKinetics(config['transport'])
expression = MinimalExpression(config['expression'])
mass_deriver = TreeMass(config['mass'])
# configure division
division_config = dict(config.get('division', {}),
daughter_path=daughter_path,
agent_id=agent_id,
generator=self)
division = MetaDivision(division_config)
return {
'transport': transport,
'growth': growth,
'expression': expression,
'mass_deriver': mass_deriver,
'division': division,
}
def generate_processes(self, config):
receptor = ReceptorCluster(config['receptor'])
flagella = FlagellaActivity(config['flagella'])
# expression
transcription = Transcription(config['transcription'])
translation = Translation(config['translation'])
degradation = RnaDegradation(config['degradation'])
complexation = Complexation(config['complexation'])
mass_deriver = TreeMass(
config.get('mass_deriver', {
'initial_mass':
config.get('initial_mass', self.initial_mass)
}))
return {
'receptor': receptor,
'flagella': flagella,
'transcription': transcription,
'translation': translation,
'degradation': degradation,
'complexation': complexation,
'mass_deriver': mass_deriver,
}