Standard-GEM supports reproducible development of genome-scale metabolic models

Abstract

The field of metabolic modelling at the genome scale continues to expand, with increasing numbers of models being reconstructed, shared and curated. This expansion creates a need to adopt common principles regarding transparency and versioning, in addition to standardisation of file formats, annotations, and model testing. Here, we present a repository standard and template for Git-based genome-scale metabolic models (GEMs) supporting both newly reconstructed and actively curated models, following FAIR principles (findability, accessibility, interoperability, and reusability), and incorporating research software best practices. Standard-GEM exposes GEMs across web services and platforms in the metabolic modelling field and enables automatic validation of GEMs. The use of this template for new models and its adoption reduces the effort required to share, validate and reuse GEMs.