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Tooling radar

Last reviewed: 2026-08-30

This radar tracks promising public tools and data sources that are not yet adopted by GeneCluster. A listing is not an endorsement or integration claim.

Admission criteria

A candidate should have:

  • a public source and clear license or access terms;
  • a versioned installation or service interface;
  • a plausible GeneCluster input and output contract;
  • a public or synthetic fixture;
  • manageable compute, storage, and redistribution requirements;
  • a clear claim boundary.

Near-term candidates

Candidate Current public state Potential use Integration requirement
Ensembl Plants release 63 plant assemblies, annotations, orthology Normalize stable accessions and checksums into source ledgers
ATTED-II v13 plant coexpression support Keep correlation evidence separate from physical clustering
Rhea release 141 curated biochemical reactions Map reaction identifiers without inferring gene function from reaction membership alone
RetroRules 3.0.0 reaction-rule expansion Record rule diameter, release, and uncertainty
HIT-EC public source repository EC prediction with abstention Add immutable code/model versions and a public protein fixture
Proto public Git repository sequence-design experimentation Keep planned until a public toy fixture and stable install contract exist

Sources: Ensembl Plants data, ATTED-II, Rhea, RetroRules, HIT-EC, and Proto.

Later candidates

  • workflow portability through Nextflow, Snakemake, or another reproducible engine;
  • provenance packaging with RO-Crate profiles;
  • additional public synteny and coexpression sources;
  • static review surfaces for large cluster comparisons;
  • provider-neutral artifact transfer with explicit allowlists and hashes.

These remain planned until a concrete public fixture and maintainer need justify the extra dependency surface.

Promotion path

  1. select one public or synthetic fixture;
  2. record the official source, version, license, and access date;
  3. define exact inputs, outputs, failure states, and resource limits;
  4. run the fixture outside the public source tree when it creates heavy data;
  5. retain compact outputs, versions, commands, and hashes;
  6. add a quickstart or wrapper;
  7. update the canonical tooling status.

Do not record private tracker IDs, credentials, local paths, provider payloads, raw data, unpublished sequences, or private output locations.