This repository stores the validation results for genome‑scale metabolic models (GEMs) that adopt the standard-GEM format. A small utility in runner.py running daily with GitHub Actions discovers repositories tagged with standard-gem, runs a suite of tests from the tests package, and writes the outcomes to JSON files in results. Avatars of repository owners are cached in avatars.
If you use standard-GEM or this validation pipeline in your scientific work, please cite:
Anton, M., et al (2023). standard-GEM: standardization of open-source genome-scale metabolic models. bioRxiv, 2023-03 doi:10.1101/2023.03.21.512712
Documentation source lives in docs/index.md and is published as a single page at /docs/. Each JSON file contains metadata about the repository, release history, and test results for the model.
The generated JSON files, and avatars are published through GitHub Pages so that they can be read by people and consumed by other services:
https://metabolicatlas.github.io/standard-GEM-validation/index.json
https://metabolicatlas.github.io/standard-GEM-validation/results/<model>.json
https://metabolicatlas.github.io/standard-GEM-validation/avatars/<avatar>.png
The interactive overview on metabolicatlas.org uses the data published from this repository to display up-to-date information about standard-GEM models.