pl.ps1.parscan1
¶
Module Contents¶
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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.
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__init__
(models_folder="Models", working_folder="Results", sim_data_folder="single_param_scan_data", sim_plots_folder="single_param_scan_plots")[source]¶
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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.
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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.
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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.
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