build_model_from_species

Build Model From Genes Building Block

This package provides the Build Model From Genes Building Block (BB).

Table of Contents

• Build Model From Genes Building Block
  • Table of Contents
  • Description
  • User instructions
    • Requirements
    • Installation
    • Usage
    • Uninstall
  • License
  • Contact

Description

This building block performs automatic network construction using OmniPath and pypath. This enables the generation of a Boolean model in MaBoSS format. It takes a list of genes of interest and returns either a simple network as a SIF file or a MaBoSS network as a BND and CFG files.

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 (FromSpeciesToMaBoSSModel.singularity), located in the Resources folder of this repository.

They MUST be available and exported respectively 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 build_model_from_species 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).

The command line is:

build_model_from_species_BB -d \
    --tmpdir <working_directory> \
    --build_model_from <genes | sif> \
    --input_file <input_file> \
    --output_bnd_file <output_bnd_file> \
    --output_cfg_file <output_cfg_file>

Where the parameters are:

	Flag	Parameter	Type	Description
	--tmpdir	<working_directory>	Folder	Working directory (temporary files)
Input	--build_model_from	<genes	sif>	String
Input	--input_file	<input_file>	File	List of genes as a CSV file
Output	--output_bnd_file	<output_bnd_file>	File	BND file of the generated MaBoSS model
Output	--output_cfg_file	<output_cfg_file>	File	CFG file of the generated MaBoSS model

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).