simul.copasi.copasi

Module Contents

class simul.copasi.copasi.Copasi

Copasi simulator.

__init__()

model_checking(model_filename, fileout, task_name="")

Check whether the Copasi model can be loaded and executed correctly.

Parameters:

• model_filename – the COPASI filename
• fileout – the file containing the model checking results
• task_name – the task to check

Returns:

boolean indicating whether the model could be loaded and executed successfully

sim(model, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False)

ps1(model, scanned_par, simulate_intervals, single_param_scan_intervals, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False)

ps2(model, sim_length, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False)

pe(model, inputdir, cluster, local_cpus, runs, outputdir, sim_data_dir, output_msg=False)

_run_par_comput(inputdir, model, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False)

_get_params_list(filein)

Return the list of parameter names from filein

Parameters:filein – a Copasi parameter estimation report file Returns:the list of parameter names

_write_best_fits(files, path_out, filename_out)

Write the final estimates to filename_out

Parameters:

• files – the list of Copasi parameter estimation reports
• path_out – the path to store the file combining the final (best) estimates (filename_out)
• filename_out – the file containing the final (best) estimates

_write_all_fits(files, path_out, filename_out)

Write all the estimates to filename_out

Parameters:

• files – the list of Copasi parameter estimation reports
• path_out – the path to store the file combining all the estimates
• filename_out – the file containing all the estimates