Tier 0 · open
Data & licensing
The corpus is a versioned artifact, not a moving target. Each release carries a content hash computed over every live model, so a published result can be traced to the exact corpus that produced it.
Current release
- Versionv0.3.0
- Content hash3574ed92836e…
- Released2026-08-03
- Models15,717
- Redistributable10,276
- Zenodo DOIpending — use the version + hash above until a DOI is issued
Licensing is stated, not assumed
Models come from many sources under different licences. The table below is the licence as understood from the source repository or publication at the time of ingestion; it is stored per-model in the corpus DB so the right answer is always derivable, not guessed. Nothing that cannot be lawfully redistributed is ever re-served — reports will tell you which sources to obtain directly.
Openly redistributable (10,276 models)
These may be included in derivative datasets with attribution. Cite the original source publication, not just the Syntropa corpus.
| Source | Models | Licence |
|---|---|---|
| embl_gems (CarveMe RefSeq, Machado 2018) | 5,573 | CC-BY 4.0 |
| CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome | 4,326 | CC-BY 4.0 (our reconstruction; tool Apache-2.0) |
| APOLLO-595 | 366 | CC0 1.0 |
| SysBioChalmers | 9 | CC-BY 4.0 |
| biomass composition | 1 | CC-BY 4.0 (Syntropa original) |
| embl_gems (CarveMe RefSeq) | 1 | CC-BY 4.0 |
Link-only (5,441 models)
These are held locally for discovery runs but are not included in the redistributable corpus dump. Obtain them from the original source; the discovery reports always name which source each hit came from.
| Source | Models | Licence status |
|---|---|---|
| AGORA2 v2.01 (Heinken 2023) | 4,672 | Unconfirmed (repo MIT; vmh.life data license not confirmed, preprint noted CC-BY-NC 4.0) |
| AGORA v1.03 (Magnusdottir 2017) | 601 | Unconfirmed (no repo license file; vmh.life data license not confirmed) |
| BiGG | 91 | Per-publication (BiGG requests citation) |
| PARADIGM | 77 | No license (all rights reserved) |
How to cite
Until a Zenodo DOI is issued, cite by corpus version and content hash. In a methods section:
Syntropa microbial metabolic corpus v0.3.0 Content hash (SHA-256, first 12 chars): 3574ed92836e… Released: 2026-08-03 https://syntropa.org/data
Each discovery report embeds its own provenance stamp (corpus version, hash, tool version, and git commit), so individual results are reproducible independently of the full corpus release.
Model source links
- EMBL-GEMs — github.com/cdanielmachado/embl_gems
- AGORA2 — vmh.life (Heinken et al. 2023)
- CarveMe reconstructions — github.com/cdanielmachado/carveme
- APOLLO-595 — doi.org/10.7910/DVN/PIZCBI
- BiGG Models — bigg.ucsd.edu
- SysBioChalmers — github.com/SysBioChalmers