Where do the GEMs used in TrpNet come from?

TrpNet uses genome-scale metabolic models (GEMs) from two databases:

  • AGORA (assembly of gut organisms through reconstruction and analysis) and EMBL GEMs(European Molecular Biology Laboratory).Agora is a collection of GEMs for 818 human gut microbes, the detailed reconstruction method can be found here.
  • EMBL GEMs are built for all reference and representative bacterial genomes of NCBI RefSeq (release 84) using CarveMe, 1288 of which are annotated as human gut microbes.