standard-GEM validation

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.

Cite us

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

Using the validation data

The generated JSON files and avatars are published through GitHub Pages so that they can be consumed by other services. They are available at:

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

Each JSON file contains metadata about the repository, release history, and test results for the model.

A minimal redirect page gh-pages-index.html points to the interactive overview on metabolicatlas.org. That site uses the data published from this repository to display up‑to‑date information about standard‑GEM models.