diff --git a/README.md b/README.md index 2def5ef..2daeb55 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,7 @@ # soil_microbe_GEMs 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`). - -Each GEMs have been evaluated for growth on various carbon substrates (`evaluate_carbon_usage.ipynb`) +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:
[![COBRApy](https://img.shields.io/badge/-COBRApy-028?&logo=GitHub)](https://github.com/opencobra/cobrapy)  standard Flux-Balance Analysis (FBA), Flux-Variability Analysis (FVA) @@ -12,5 +10,4 @@ Simulation-ready GEMs can be integrated into community modeling frameworks of va
[![MICOM](https://img.shields.io/badge/-MICOM-028?&logo=GitHub)](https://github.com/micom-dev)  community trade-offs, growth rate estimation - -more organisms to come soon! +60+ more GEMs to come soon!