Detalle de: GALLANT: a standardized workflow for multi strain genome-scale metabolic modeling.

Genome-scale metabolic models (GEMs) of bacteria are one of the most important drivers of recent advances in metabolic engineering and systems biology. However, single strain GEMs define the metabolic capabilities of the strain in question, thus limiting the ability to perform metabolic studies at the species level. To overcome this, here we present GALLANT, a standardized and reproducible workflow that returns multi-strain GEMs to analyze the unique capabilities of individual strains, but with the added value that it is also able to group GEMs according to their pan-genome to perform studies of metabolic potential at the species level. The main goal of GALLANT is to deliver output GEMs to the highest standards. To this end, GALLANT uses a high-quality, customized GEM database as a template and it combines it with other databases like BIGG and KEGG to return final GEM drafts. To reduce the need for subsequent manual curation, it features an optimized automatic gap-filling module for multi- strain modeling, while built-in GEM quality assurance tools such as MEMOTE guide the user in the process of refining final results. GALLANT’s robust modular design supports parallel delivery of single strain GEMs and it is fully geared up to be run on high performance servers in order to scale up the process and reduce execution times considerably. We demonstrate that GALLANT provides a standardized, fast and accurate process to build multi-strain GEMs and, in doing so, it improves the current understanding of potential metabolisms.