DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.

Motivation Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools do not typically take species-specific experimental and curated genomic data into account. Results We developed DEMETER, a COBRA Toolbox extension, that enables the efficient, simultaneous refinement of thousands of draft genome-scale reconstructions, while ensuring adherence to the quality standards in the field, agreement with available experimental data, and refinement of pathways based on manually refined genome annotations. Availability DEMETER and tutorials are freely available at https://github.com/opencobra.