pl.ps2.parscan2

Module Contents

class pl.ps2.parscan2.ParScan2(models_folder="Models", working_folder="Results", sim_data_folder="double_param_scan_data", sim_plots_folder="double_param_scan_plots")[source]

This module provides the user with a complete pipeline of scripts for computing double parameter scans.

__init__(models_folder="Models", working_folder="Results", sim_data_folder="double_param_scan_data", sim_plots_folder="double_param_scan_plots")[source]
run(config_file)[source]
generate_data(simulator, model, sim_length, inputdir, outputdir, cluster, local_cpus, runs)[source]

The first pipeline step: data generation.

Parameters:
  • simulator – the name of the simulator (e.g. Copasi)
  • model – the model to process
  • sim_length – the length of the simulation
  • inputdir – the directory containing the model
  • outputdir – the directory to store the results
  • cluster – local, lsf for Load Sharing Facility, sge for Sun Grid Engine.
  • local_cpus – the number of CPU.
  • runs – the number of model simulation
Returns:

True if the task was completed successfully, False otherwise.
analyse_data(model, scanned_par1, scanned_par2, inputdir, outputdir, cluster="local", local_cpus=1, runs=1)[source]

The second pipeline step: data analysis.

Parameters:
  • model – the model name
  • scanned_par1 – the first scanned parameter
  • scanned_par2 – the second scanned parameter
  • inputdir – the directory containing the simulated data sets to process
  • outputdir – the directory to store the performed analysis
  • cluster – local, lsf for Load Sharing Facility, sge for Sun Grid Engine.
  • local_cpus – the number of CPU.
  • runs – the number of model simulation
Returns:

True if the task was completed successfully, False otherwise.
generate_report(model, scanned_par1, scanned_par2, outputdir, sim_plots_folder)[source]

The third pipeline step: report generation.

Parameters:
  • model – the model name
  • scanned_par1 – the first scanned parameter
  • scanned_par2 – the second scanned parameter
  • outputdir – the directory containing the report
  • sim_plots_folder – the folder containing the plots.
Returns:

True if the task was completed successfully, False otherwise.
parse(my_dict)[source]