def test_txp_mtb_ge():
default_test_setting = {
'environment': {
'volume': 1e-12 * units.L,
'ports': {
'exchange': (
'boundary',
'exchange',
),
'external': ('boundary', 'external'),
}
},
'timestep': 1,
'total_time': 10
}
compartment = TransportMetabolism({})
return simulate_compartment_in_experiment(compartment,
default_test_setting)
def test_txp_mtb_ge():
default_test_setting = {
'environment': {
'volume': 1e-12 * units.L,
'ports': {
'fields': ('fields', ),
'external': ('boundary', 'external'),
'dimensions': ('dimensions', ),
'global': ('boundary', ),
}
},
'timestep': 1,
'total_time': 10
}
agent_id = '0'
compartment = TransportMetabolism({'agent_id': agent_id})
return simulate_compartment_in_experiment(compartment,
default_test_setting)
def test_master():
# load the compartment
compartment_config = {
'external_path': ('external',),
'global_path': ('global',),
'agents_path': ('..', '..', 'cells',),
'transcription': {
'sequence': toy_chromosome_config['sequence'],
'templates': toy_chromosome_config['promoters'],
'genes': toy_chromosome_config['genes'],
'promoter_affinities': toy_chromosome_config['promoter_affinities'],
'transcription_factors': ['tfA', 'tfB'],
'elongation_rate': 10.0}}
compartment = Master(compartment_config)
# simulate
settings = {
'timestep': 1,
'total_time': 10}
return simulate_compartment_in_experiment(compartment, settings)
def test_expression_chemotaxis(
n_flagella=5,
total_time=10,
out_dir='out'
):
# make the compartment
config = get_baseline_config(n_flagella)
compartment = ChemotaxisExpressionFlagella(config)
# save the topology network
plot_compartment_topology(compartment, {}, out_dir)
# run experiment
initial_state = get_flagella_initial_state({
'molecules': 'internal'})
timeline = get_timeline(total_time=total_time)
experiment_settings = {
'initial_state': initial_state,
'timeline': {
'timeline': timeline,
'ports': {'external': ('boundary', 'external')}},
}
timeseries = simulate_compartment_in_experiment(
compartment,
experiment_settings)
print_growth(timeseries)
# plot
plot_timeseries(timeseries, out_dir)
# gene expression plot
plot_config = {
'ports': {
'transcripts': 'transcripts',
'proteins': 'proteins',
'molecules': 'internal'}}
plot_gene_expression_output(
timeseries,
plot_config,
out_dir)
def test_inclusion_body(total_time=1000):
agent_id = '0'
parameters = {
'agent_id': agent_id,
'inclusion_process': {
'damage_rate': 1e-4, # rapid damage
},
'growth_rate': {
'growth_rate': 0.001 # fast growth
},
}
compartment = InclusionBodyGrowth(parameters)
initial_state = compartment.initial_state()
# settings for simulation and plot
settings = {
'initial_state': {'agents': {agent_id: initial_state}},
'outer_path': ('agents', agent_id),
'return_raw_data': True,
'timestep': 1,
'total_time': total_time}
return simulate_compartment_in_experiment(compartment, settings)
def run_chemotaxis_master(out_dir):
total_time = 10
# make the compartment
compartment = ChemotaxisMaster({})
# save the topology network
settings = {'show_ports': True}
plot_compartment_topology(compartment, settings, out_dir)
# run an experinet
settings = {'timestep': 1, 'total_time': total_time}
timeseries = simulate_compartment_in_experiment(compartment, settings)
volume_ts = timeseries['boundary']['volume']
print('growth: {}'.format(volume_ts[-1] / volume_ts[0]))
# plots
# simulation output
plot_settings = {
'max_rows': 40,
'remove_zeros': True,
'skip_ports': ['reactions', 'prior_state', 'null']
}
plot_simulation_output(timeseries, plot_settings, out_dir)
# gene expression plot
gene_exp_plot_config = {
'name': 'flagella_expression',
'ports': {
'transcripts': 'transcripts',
'proteins': 'proteins',
'molecules': 'internal'
}
}
plot_gene_expression_output(timeseries, gene_exp_plot_config, out_dir)
def test_master():
master = load_master()
# simulate
settings = {'timestep': 1, 'total_time': 10}
return simulate_compartment_in_experiment(master, settings)
def test_chemotaxis_master(total_time=5):
compartment = ChemotaxisMaster({})
settings = {'timestep': 1, 'total_time': total_time}
return simulate_compartment_in_experiment(compartment, settings)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
agent_id = '0'
compartment = GrowthDivision({'agent_id': agent_id})
# settings for simulation and plot
settings = {
'environment': {
'volume': 1e-6 * units.L, # L
'ports': {
'fields': ('fields', ),
'external': (
'boundary',
'external',
),
'global': ('boundary', ),
'dimensions': ('dimensions', ),
},
},
'outer_path':
('agents', agent_id), # TODO -- need to set the agent_id through here?
'return_raw_data': True,
'timestep': 1,
'total_time': 500
}
output_data = simulate_compartment_in_experiment(compartment, settings)
plot_settings = {}
plot_agents_multigen(output_data, plot_settings, out_dir)
'external_path': environment_port
}
compartment = ChemotaxisMinimal(get_chemotaxis_config(config))
# run experiment
experiment_settings = {
'timeline': {
'timeline':
get_exponential_random_timeline(exponential_random_config),
'ports': {
'external': ('boundary', 'external')
}
},
'timestep': 0.01,
'total_time': 100
}
timeseries = simulate_compartment_in_experiment(compartment,
experiment_settings)
# plot settings for the simulations
plot_settings = {
'max_rows': 20,
'remove_zeros': True,
'overlay': {
'reactions': 'flux'
},
'skip_ports': ['prior_state', 'null', 'global']
}
plot_simulation_output(timeseries, plot_settings, out_dir,
'exponential_timeline')
def simulate_txp_mtb_ge(config={}, out_dir='out'):
end_time = 2520 # 2520 sec (42 min) is the expected doubling time in minimal media
environment_volume = 1e-14
timeline = [
(0, {
('external', 'glc__D_e'): 3.0,
('external', 'lcts_e'): 3.0,
}),
# (500, {
# ('external', 'glc__D_e'): 0.0,
# ('external', 'lcts_e'): 3.0,
# }),
(end_time, {})
]
sim_settings = {
'environment': {
'volume': environment_volume * units.L,
'ports': {
'external': ('boundary', 'external'),
'exchange': ('boundary', 'exchange'),
}
},
'timeline': {
'timeline': timeline,
'ports': {
'external': ('boundary', 'external')
}
}
}
# run simulation
compartment = TransportMetabolism({})
timeseries = simulate_compartment_in_experiment(compartment, sim_settings)
# calculate growth
volume_ts = timeseries['boundary']['volume']
try:
print('growth: {}'.format(volume_ts[-1] / volume_ts[0]))
except:
print('no volume!')
## plot
# diauxic plot
settings = {
'internal_path': ('cytoplasm', ),
'external_path': ('boundary', 'external'),
'global_path': ('boundary', ),
'exchange_path': ('boundary', 'exchange'),
'environment_volume': 1e-13, # L
# 'timeline': timeline
}
plot_diauxic_shift(timeseries, settings, out_dir)
# simulation plot
plot_settings = {
'max_rows': 30,
'remove_zeros': True,
'skip_ports': ['null', 'reactions'],
}
plot_simulation_output(timeseries, plot_settings, out_dir)