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

## TL;DR

BioModTool is a Python tool that helps users create biomass objective functions for metabolic models using their own data, making it easier for both experts and non-experts.

## Contribution

BioModTool introduces a user-friendly tool for generating biomass objective functions from user data, supporting both modelers and non-modelers.

## Key findings

- BioModTool normalizes biomass composition data into model-compatible units.
- The tool supports both Python module and interface-based usage for different user types.
- It accelerates genome-scale metabolic model reconstructions and analyses.

## Abstract

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.

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.