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 # 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`) 
+
+Simulation-ready GEMs can be integrated into community modeling frameworks of various flavors:<br>
+ [![COBRApy](https://img.shields.io/badge/-COBRApy-028?&logo=GitHub)](https://github.com/opencobra/cobrapy)&nbsp; standard Flux-Balance Analysis (FBA), Flux-Variability Analysis (FVA) 
+ <br>
+[![COMETSpy](https://img.shields.io/badge/-COMETSpy-028?&logo=GitHub)](https://github.com/segrelab/cometspy)&nbsp; dynamic FBA, spatiotemporal simulations
+<br>
+[![MICOM](https://img.shields.io/badge/-MICOM-028?&logo=GitHub)](https://github.com/micom-dev)&nbsp; community trade-offs, growth rate estimation
+
+
+more organisms to come soon!