pl.ps2.parscan2
¶
Module Contents¶
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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.
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__init__
(models_folder="Models", working_folder="Results", sim_data_folder="double_param_scan_data", sim_plots_folder="double_param_scan_plots")[source]¶
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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.
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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.
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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.
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