Dataset Open Access
This repository hosts artifacts for use with q2-micom and MICOM. In particular it provides summarized metabolic model databases and growth media.
Model databases are provided for family, genus and species ranks. AGORA is a manually curated database of 818 high quality metabolic reconstructions. Raw data was obtained from https://www.vmh.life/.
CarveME is an automatically reconstructed database but offers much more organisms (>5K strains). Raw data was obtained from https://github.com/cdanielmachado/embl_gems.
We currently only provide an average western diet which is only compatible with AGORA.
Diener et. al. Additional data related to https://doi.org/10.1101/361907.