Work

BioModTool: from biomass composition data to structured biomass objective functions for genome-scale metabolic models

Year: 2024

Type: article

Abstract: Summary BioModTool is a Python program allowing easy generation of biomass objective functions for genome-scale metabolic models from user data. BioModTool loads biomass composition data in the form of a structured Excel file completed by the user, normalizes these data into model-compatible units (mmol.gDW−1), and creates a structured biomass objective function to update a metabolic model. Aimed at a wide range of users, BioModTool can be run as a Python module compatible with COBRApy but also comes with an interface allowing its use by non-modelers. By providing an easy definition of new biomass objective functions, BioModTool can accelerate new genome-scale metabolic reconstructions, improve existing ones, and facilitate biomass-specific experimental datasets analyses with genome-scale models. Availability and implementation BioModTool is publicly available on PyPI (https://pypi.org/project/BioModTool/) under a GNU Lesser General Public License (LGPL). Installation instructions and source code are available on GitHub (https://github.com/Total-RD/BioModTool). BioModTool is compatible with Windows, Linux, and MacOS operating systems.

Source: Bioinformatics Advances

DOI: 10.1093/bioadv/vbaf036

Authors: Clémence Dupont Thibert, Sylvaine Roy, Gilles Curien, Maxime Durot

Institutions: Total (France), Laboratoire Physiologie Cellulaire & Végétale, Université Grenoble Alpes

Language: English

Topic: Microbial Metabolic Engineering and Bioproduction

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,917

Funders: Agence Nationale de la Recherche, Association Nationale de la Recherche et de la Technologie, Total