The standard-GEM initiative provides a community-driven, git-based template that streamlines the creation, curation, and long-term maintenance of genome-scale metabolic models (GEMs). By embedding FAIR principles directly into the model development workflow, standard-GEM ensures transparency, provenance tracking, and reproducibility at every stage. It defines a clear repository structure, enforces best practices in documentation, and integrates with automated validation pipelines, lowering the cost of model upkeep while raising quality and openness. Already adopted by multiple high-profile GEMs, standard-GEM transforms models from static research outputs into evolving digital infrastructure, enabling reliable reuse across platforms and fostering collaborative, community-driven systems biology research.
For an up-to-date listing of GEMs as result of this validation, see metabolicatlas.org/gems/standard-gems.
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
The project homepage renders this README automatically.
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, model metrics (reaction and metabolite counts) for each validated release, 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.