def main():
out_dir = os.path.join(TEST_OUT_DIR, NAME)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
timeseries = run_injector()
plot_settings = {}
plot_simulation_output(timeseries, plot_settings, out_dir)
save_timeseries(timeseries, out_dir)
def main():
out_dir = os.path.join(COMPARTMENT_OUT_DIR, Antibiotics.name)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
plot_settings = {
'max_rows': 25,
}
timeseries = run_antibiotics_composite()
plot_simulation_output(timeseries, plot_settings, out_dir)
save_timeseries(timeseries, out_dir)
'total_time': end_time
}
return simulate_process_in_experiment(kinetic_process, settings)
def test_convenience_kinetics_correlated_to_reference():
timeseries = test_convenience_kinetics()
flattened = flatten_timeseries(timeseries)
reference_timeseries = load_timeseries(
os.path.join(REFERENCE_DATA_DIR, NAME + '.csv'))
assert_timeseries_close(flattened,
reference_timeseries,
tolerances={
'internal_pyr_c': 9,
'internal_pep_c': 9,
'internal_g6p_c': 9,
})
if __name__ == '__main__':
out_dir = os.path.join(PROCESS_OUT_DIR, NAME)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
timeseries = test_convenience_kinetics()
plot_settings = {}
plot_simulation_output(timeseries, plot_settings, out_dir)
save_timeseries(timeseries, out_dir)