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COBREXA

README.md

COBREXA FVA Building Block

This package provides the COBREXA Flux Variability Analysis (FVA) Building Block (BB). Use this BB to analyze the viable feasibility and optimality ranges of your metabolic models.

Table of Contents

Description

COBREXA is a toolkit for working with large constraint-based metabolic models, and running very large numbers of analysis tasks on these models in parallel. Its main purpose is to make the methods of Constraint-based Reconstruction and Analysis (COBRA) scale to problem sizes that require the use of huge computer clusters and HPC environments, which allows them to be realistically applied to pre-exascale-sized models.

This building block runs Flux Variability Analysis (FVA) on a given model. The analysis computes a feasible range of fluxes that may go through each reaction in the model while the model is in near-optimal state (in particular, constrained to the minimum of 99% of the flux through the objective function). This gives a relatively good overview of what the model is capable of, in particular allowing to enumerate the under-definedness and redundancy present in the main model pathways.

User instructions

Requirements

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

In addition to the dependencies, it is necessary to download the cobrexa.jl_latest.sif singularity image. It can be downloaded with:

singularity pull oras://ghcr.io/lcsb-biocore/apptainer/cobrexa.jl:latest

or running the cobrexa.jl_latest.sif script, located in the Resources folder of this repository.

It 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 COBREXA 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:

COBREXA_FVA -d \
    --verbose <verbose> \
    --input_sbml <input_sbml> \
    --output_txt <output_txt>

Where the parameters are:

Flag Parameter Type Description
Input --verbose <verbose> Boolean Enable or disable debug mode (true
Input --input_sbml <input_sbml> File Input SBML file (internally XML-formatted)
Output --output_txt <output_txt> File Output text file

Uninstall

Uninstall can be achieved by executing the following scripts:

./uninstall.sh
./clean.sh

Contact

https://permedcoe.eu/contact/

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