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

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

SUBMITTER: Dupont Thibert C 

PROVIDER: S-EPMC11891441 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature