standard-GEM validation 0.1

standard-GEM-validation 0.1

First public release of standard-GEM-validation, the automated validation pipeline for repositories adopting the standard-GEM format.

This release establishes a reproducible, machine-readable validation layer for standard-GEM repositories. The pipeline discovers model repositories, validates their standard-GEM structure and model files, and publishes results that can be reused by downstream services, including the standard-GEM overview in Metabolic Atlas.

Highlights

• Automated discovery of standard-GEM repositories across GitHub and GitLab.
• Daily GitHub Actions workflow for validating discovered repositories.
• Repository metadata collection, including release history, latest commit information, contributor counts, and owner avatars.
• Validation of standard-GEM adherence through comparison of .standard-GEM.md files against the current standard-GEM release.
• Model loading checks with cobrapy for YAML, SBML, MATLAB, and JSON model formats.
• SBML validation using cobrapy.
• YAML formatting validation with yamllint.
• MEMOTE-based scoring of selected model consistency and annotation checks.
• Versioned JSON outputs for each validated model repository.
• GitHub Pages deployment of the generated validation data for reuse by websites and other services.

Published validation data

The release provides machine-readable validation outputs through GitHub Pages at metabolicatlas.github.io/standard-GEM-validation:

• index.json: provider-keyed index of discovered standard-GEM repositories.
• results/<model>.json: metadata, release information, standard-GEM adherence, and validation results for each model.
• avatars/<avatar>.png: cached repository owner avatars for downstream display.

These files are intended to support transparent monitoring of standard-GEM adoption and validation status without requiring each GEM repository to maintain a separate validation pipeline.

Known limitations

• Validation currently depends on public repository metadata and available release/model files.
• The pipeline validates the current standard-GEM release only.
• Some validation checks depend on model file availability and compatibility with the underlying tools.
• The validation suite is intentionally modular; additional tests should be added as the standard and community needs mature.

Citation

If you use standard-GEM or this validation pipeline in scientific work, please cite:

Anton, M. et al. standard-GEM: standardization of open-source genome-scale metabolic models. bioRxiv. doi:10.1101/2023.03.21.512712

Contributors

Thanks to all contributors to standard-GEM and standard-GEM-validation, and to the GEM community members whose repositories helped define the first validation targets.

Changelog: https://github.com/MetabolicAtlas/standard-GEM-validation/commits/0.1