def generate_processes(self, config):
agent_id = config.get('agent_id',
'0') # TODO -- configure the agent_id
# Transport
# load the kinetic parameters
transport = ConvenienceKinetics(config.get('transport', {}))
# Metabolism
# get target fluxes from transport, and update constrained_reaction_ids
metabolism_config = config.get('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.get('expression', {}))
# Division
division_config = dict(config.get('division', {}),
daughter_path=self.daughter_path,
agent_id=agent_id,
compartment=self)
# initial_mass = metabolism.initial_mass
# division_config.update({'constrained_reaction_ids': target_fluxes})
# TODO -- configure metadivision
division = MetaDivision(division_config)
return {
'transport': transport,
'metabolism': metabolism,
'expression': expression,
'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):
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):
# Transport
transport = ConvenienceKinetics(config.get('transport'))
# Metabolism
# add target fluxes from transport
target_fluxes = transport.kinetic_rate_laws.reaction_ids
config['metabolism']['constrained_reaction_ids'] = target_fluxes
metabolism = Metabolism(config['metabolism'])
# flagella expression
transcription = Transcription(config['transcription'])
translation = Translation(config['translation'])
degradation = RnaDegradation(config['degradation'])
complexation = Complexation(config['complexation'])
# chemotaxis -- flagella activity, receptor activity, and PMF
receptor = ReceptorCluster(config['receptor'])
flagella = FlagellaActivity(config['flagella'])
PMF = MembranePotential(config['PMF'])
# Division
# get initial volume from metabolism
if 'division' not in config:
config['division'] = {}
config['division']['initial_state'] = metabolism.initial_state
division = DivisionVolume(config['division'])
return {
'metabolism': metabolism,
'transport': transport,
'transcription': transcription,
'translation': translation,
'degradation': degradation,
'complexation': complexation,
'receptor': receptor,
'flagella': flagella,
'PMF': PMF,
'division': division,
}
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,
compartment=self)
division = MetaDivision(division_config)
return {
'transport': transport,
'growth': growth,
'expression': expression,
'mass_deriver': mass_deriver,
'division': division,
}
def generate_processes(self, config):
# Transport
transport_config = config.get('transport')
transport = ConvenienceKinetics(transport_config)
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)
# Expression
transcription_config = config.get('transcription', {})
translation_config = config.get('translation', {})
degradation_config = config.get('degradation', {})
transcription = Transcription(transcription_config)
translation = Translation(translation_config)
degradation = RnaDegradation(degradation_config)
complexation = Complexation(config.get('complexation', {}))
# Division
# get initial volume from metabolism
division_config = config.get('division', {})
division_config.update({'initial_state': metabolism.initial_state})
division = DivisionVolume(division_config)
return {
'transport': transport,
'transcription': transcription,
'translation': translation,
'degradation': degradation,
'complexation': complexation,
'metabolism': metabolism,
'division': division
}
def generate_processes(self, config):
process = ConvenienceKinetics(config['process'])
return {'process': process}