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Releases: SysBioChalmers/raven-python

raven-python 0.1.0a1 — first alpha

30 May 21:07
@edkerk edkerk
v0.1.0a1
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raven-python 0.1.0a1 — first alpha Pre-release
Pre-release

First alpha release of raven-python — the Python counterpart of the RAVEN Toolbox 2, built on cobrapy. Released under the MIT license.

⚠️ Alpha software: APIs may change before 0.1.0.

What's included

  • De-novo reconstruction — KEGG and protein homology (BLAST / DIAMOND).
  • Context-specific modeling — tINIT / ftINIT, with task-aware gap-filling and the linear-merge MILP reduction.
  • Metabolic-task validation, connectivity gap-filling, HPA omics ingestion.
  • Sub-cellular localisation (MILP), N-model comparison, reporter metabolites, FSEOF, flux sampling.
  • I/O — cobra-standard YAML (+ GECKO ec-* fields), SIF, RAVEN-style Excel export.

Validated against MATLAB RAVEN on Human-GEM (5 Hart2015 cell lines, Jaccard 0.975–0.980).

Not yet implemented

  • Visualization (plotting/)
  • Metabolomics-based scoring in tINIT / ftINIT
  • Published binary release ZIPs (BLAST / DIAMOND / HMMER)
  • Published KEGG data-artefact releases

MetaCyc-based reconstruction and dynamic FBA are intentionally out of scope.

Install

pip install "git+https://github.com/SysBioChalmers/raven-python.git@v0.1.0a1"

Requires Python ≥ 3.11. Genome-scale (f)tINIT currently needs Gurobi; smaller work runs on GLPK.

See the README and docs/ for details.

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