BioModTool

BioModTool generates biomass objective functions for genome-scale metabolic models from user-provided biomass composition data.

Key Features:

• Data Loading: BioModTool loads biomass composition data from a structured Excel file completed by the user.
• Data Normalization: BioModTool normalizes biomass composition data into model-compatible units (mmol.gDW-1).
• Biomass Objective Function Generation: BioModTool creates a structured biomass objective function to update a metabolic model.
• COBRApy Compatibility: BioModTool runs as a Python module compatible with COBRApy.

Scientific Applications:

• Genome-Scale Metabolic Reconstruction: BioModTool accelerates new genome-scale metabolic reconstructions by enabling easy definition of new biomass objective functions.
• Model Improvement: BioModTool improves existing genome-scale metabolic reconstructions through updated biomass objective functions.
• Experimental Data Analysis: BioModTool facilitates biomass-specific experimental datasets analyses with genome-scale models.

Methodology:

BioModTool loads biomass composition data from a structured Excel file, normalizes the data into model-compatible units (mmol.gDW-1), and creates a structured biomass objective function to update a metabolic model.