Test interoperability between bioinformatics datasets, databases, workflows and benchmarks. Explicit configurations select combinations; each run records sources, settings, native outputs and failures. Proteomics is the first application.
With Python 3.12+ and Poetry installed, from a source checkout:
poetry install
poetry run interop-trace run erwinia_sage --output results/simple-001
poetry run interop-trace classify results/simple-001This uses a small public PRIDE peak list, a UniProt database and Sage, installed automatically. Downloads are cached. Classification checks recovery of four reference peptides; passing does not establish overall scientific accuracy. See the first experiment for sizes and outputs.
For a local browser interface:
poetry install --extras ui
poetry run interop-trace uiOpen http://127.0.0.1:8080/ to select experiments, monitor runs and inspect results. See the interface guide.
| Layer | Component |
|---|---|
| datasets | pride |
| databases | uniprot |
| workflows | comet |
| workflows | msamanda |
| workflows | sage |
| benchmarks | expected_peptides |
| benchmarks | proteobench_dda |
Generated from the registries. See parameters and scope.
- Users: first experiment, configuration, CLI and cache.
- Developers: development guide, API reference, documentation builds.
poetry install --all-extras
poetry run pre-commit installSee the developer guide for checks and CONTRIBUTING.md for review policy.
Cite using CITATION.cff. Licensed under Apache-2.0.