pl.ps1.parscan1

Module Contents

class pl.ps1.parscan1.ParScan1(models_folder="Models", working_folder="Results", sim_data_folder="single_param_scan_data", sim_plots_folder="single_param_scan_plots")[source]

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

__init__(models_folder="Models", working_folder="Results", sim_data_folder="single_param_scan_data", sim_plots_folder="single_param_scan_plots")[source]
run(config_file)[source]
generate_data(simulator, model, scanned_par, cluster, local_cpus, runs, simulate_intervals, single_param_scan_intervals, inputdir, outputdir)[source]

The first pipeline step: data generation.

Parameters:
  • simulator – the name of the simulator (e.g. Copasi)
  • model – the model to process
  • scanned_par – the scanned parameter
  • cluster – local, lsf for Load Sharing Facility, sge for Sun Grid Engine.
  • local_cpus – the number of CPU.
  • runs – the number of model simulation
  • simulate_intervals – the time step of each simulation
  • single_param_scan_intervals – the number of scans to perform
  • inputdir – the directory containing the model
  • outputdir – the directory to store the results
Returns:

True if the task was completed successfully, False otherwise.

analyse_data(model, knock_down_only, outputdir, sim_data_folder, sim_plots_folder, runs, local_cpus, percent_levels, min_level, max_level, levels_number, homogeneous_lines, cluster="local", xaxis_label="", yaxis_label="")[source]

The second pipeline step: data analysis.

Parameters:
  • model – the model name
  • knock_down_only – True for knock down simulation, false if also scanning over expression.
  • outputdir – the directory containing the results
  • sim_data_folder – the folder containing the simulated data sets
  • sim_plots_folder – the folder containing the generated plots
  • runs – the number of simulations
  • local_cpus – the number of cpus
  • percent_levels – True if the levels are percents.
  • min_level – the minimum level
  • max_level – the maximum level
  • levels_number – the number of levels
  • homogeneous_lines – True if generated line style should be homogeneous
  • cluster – local, lsf for Load Sharing Facility, sge for Sun Grid Engine.
  • xaxis_label – the name of the x axis (e.g. Time [min])
  • yaxis_label – the name of the y axis (e.g. Level [a.u.])
Returns:

True if the task was completed successfully, False otherwise.

generate_report(model, scanned_par, outputdir, sim_plots_folder)[source]

The third pipeline step: report generation.

Parameters:
  • model – the model name
  • scanned_par – the 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]