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PhysiBoSS

README.md

PhysiBoSS Building Block

This package provides the PhysiBoSS Building Block (BB).

Table of Contents

Description

This building block is used to perform a multiscale simulation of a population of cells using PhysiBoSS. The tool uses the different Boolean models personalised by the Personalise patient building block and with the mutants selected by the High-throughput mutant analysis building block. More information on this tool can be found in Ponce-de-Leon et al. (2022) and the PhysiBoSS GitHub repository.

User instructions

Requirements

  • Python >= 3.6
  • Singularity
  • permedcoe base package: python3 -m pip install permedcoe

In addition to the dependencies, it is necessary to generate the associated singularity image (PhysiCell-COVID19.singularity), located in the Resources folder of this repository.

They MUST be available and exported in the following environment variable before its usage:

export PERMEDCOE_IMAGES="/path/to/images/"

Installation

This package provides an automatic installation script:

./install.sh

Usage

The PhysiBoSS package provides a clear interface that allows it to be used with multiple workflow managers (e.g. PyCOMPSs, NextFlow and Snakemake).

It can be imported from python and invoked directly from a PyCOMPSs application, or through the command line for other workflow managers (e.g. Snakemake and NextFlow).

Supports 3 different operations modes:

  • default
  • physiboss_model
  • analyse_replicates

Default

The command line is:

PhysiBoSS_BB -d \
    --tmpdir <working_directory> \
    default \
    --sample <sample> \
    --repetition <repetition> \
    --prefix <prefix> \
    --bnd_file <bnd_file> \
    --cfg_file <cfg_file> \
    --out_file <out_file> \
    --err_file <err_file> \
    --results_file <results_file> \
    --parallel <parallel> \
    --max_time <max_time>

Where the parameters are:

Flag Parameter Type Description
--tmpdir <working_directory> Folder Working directory (temporary files)
Input --sample <sample> String Patient's identifier
Input --repetition <repetition> Integer Number of repetition to be performed
Input --prefix <prefix> String Name of the model
Input --bnd_file <bnd_file> File Name of the model's BND file
Input --cfg_file <cfg_file> File Name of the model's CFG file
Input --parallel <parallel> Integer Internal parallelism
Input --max_time <max_time> Integer PhysiBoSS simulation maximum time
Output --out_file <out_file> File Main output of the PhysiBoSS run
Output --err_file <err_file> File Error output of the PhysiBoSS run
Output --results_dir <results_dir> Folder Results directory

physiboss_model

The command line is:

PhysiBoSS_BB -d \
    --tmpdir PhysiBoSS_wd \
    physiboss_model \
    --sample <sample> \
    --repetition <repetition> \
    --prefix <prefix> \
    --model_dir <model_dir> \
    --out_file <out_file> \
    --err_file <err_file> \
    --results_file <results_file> \
    --parallel <parallel> \
    --max_time <max_time>

Where the parameters are:

Flag Parameter Type Description
--tmpdir <working_directory> Folder Working directory (temporary files)
Input --sample <sample> String Patient's identifier
Input --repetition <repetition> Integer Number of repetition to be performed
Input --prefix <prefix> String Name of the model
Input --model_dir <model_dir> Folder Model directory
Output --out_file <out_file> File Main output of the PhysiBoSS run
Output --err_file <err_file> File Error output of the PhysiBoSS run
Output --results_dir <results_dir> Folder Results directory
Input --parallel <parallel> Integer Internal parallelism
Input --max_time <max_time> Integer PhysiBoSS simulation maximum time

analyse_replicates

The command line is:

PhysiBoSS_BB -d \
    --tmpdir PhysiBoSS_wd \
    analyse_replicates \
    --replicates <replicates> \
    --replicates_folder <replicates_folder> \
    --prefix <prefix> \
    --out_file <out_file> \
    --err_file <err_file> \
    --results_dir <results_dir> \
    --parallel <parallel>

Where the parameters are:

Flag Parameter Type Description
--tmpdir <working_directory> Folder Working directory (temporary files)
Input --replicates <replicates> Integer Number of replicates
Input --replicates_folder <replicates_folder> Folder Replicates folder
Input --prefix <prefix> String Name of the model
Output --out_file <out_file> File Main output of the PhysiBoSS run
Output --err_file <err_file> File Error output of the PhysiBoSS run
Output --results_dir <results_dir> Folder Results directory
Input --parallel <parallel> Integer Internal parallelism

Uninstall

Uninstall can be achieved by executing the following scripts:

./uninstall.sh
./clean.sh

License

Apache 2.0

Contact

https://permedcoe.eu/contact/

This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).