BROOMM: Biomass Reaction Operations On Metabolic Models
An application to aid the curation of biomass reactions within metabolic models
Genome-scale metabolic models can now be automatically generated using various online databases and published software. However, such semi-automatically generated models contain generic biomass reactions with incorrect stoichiometries. Manual curation of these biomass reactions is required in order to obtain accurate results when carrying out quantitative analyses of these models, such as flux balance analysis (FBA), but manually editing models in the Systems Biology Markup Language (SBML) format often results in the introduction of errors. BROOMM is a desktop application that allows users to build or manipulate biomass reactions within genome-scale metabolic models without needing to access the XML files directly. There are two main modes of function: the ‘edit’ mode allows users to edit stoichiometries whilst the ‘transfer’ mode allows the user to transfer metabolite information from a curated model to the model needing curation.
The python implementation of BROOMM and associated documentation can be downloaded here.