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-001This uses a public PRIDE processed peak list (5.98 MB), an Erwinia-and-spikes UniProt database (2.14 MB in the verified run), and a pinned Sage binary (about 6.6 MB on Apple silicon). Downloads are cached and Sage is installed automatically. All four selected deposited reference peptides were recovered at the configured 1% spectrum q-value threshold. This checks interoperability and reference-result consistency, not overall search accuracy. See the first experiment for verified sizes and outputs.
The same inputs can also run through Comet and MS Amanda, with unfiltered reference-peptide recovery. See compare search engines for commands, prerequisites and evaluation scope.
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.
Every experiment selects an evaluator. Runs use new output directories and share downloaded resources. Components preserve native formats; interoperability failures remain visible rather than being silently converted.
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.