Compilation of published genome-scale metabolic models (GEMs) for constraint-based modeling of the soil microbiome
Each organism has its own directory. GEMs are uploaded in various formats depending on the original publication (usually XML/SBML). An R script was used to enforce a common nomenclature for all exchange metabolites (01_modify_metabolites.r). Python was used to verify COBRA compliance and ensure that growth rates match the rates described in publications. (/02_make_cobra_compliant.ipynb). GEMs have also been evaluated for growth on various carbon substrates (evaluate_carbon_usage.ipynb).
Simulation-ready GEMs can be integrated into community modeling frameworks of various flavors:
60+ more GEMs to come soon!