  Motivation: Manual curation of genome-scale reconstructions is laborious, yet
existing automated curation tools typically do not take species-specific
experimental data and manually refined genome annotations 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
available at https://github.com/opencobra/cobratoolbox.
