# Bench Beacon

> Bench Beacon is Papers with Code for the lab sciences, built for AI agents. It maps biology and chemistry research code to papers, assays, instruments, file formats and deposited datasets (GEO, SRA, PRIDE, Zenodo), and verifies each link. Status: early access (waitlist). The API is not public yet.

Bench Beacon indexes metadata about public research repositories: what method, instrument or file format the code targets, which papers it belongs to, whether the promised code is actually present, which data accessions it links, its license and maintenance status. It returns descriptions and pointers (URLs), never file contents. Every tool is read-only and idempotent; the same tools are planned over MCP (streamable HTTP) and REST.

Conventions every response follows:

- Inferred fields have the form {"v": value, "src": "rule" | "llm" | "pending", "conf": 0-1}. "pending" means not extracted yet, not absent.
- code_present: "yes" | "partial" | "no" — whether code a paper or README promises is actually in the repository.
- handles_format: whether the repository verifiably reads or writes a given file format, with the evidence in "why".
- License verdicts: {"spdx", "reusable": "yes" | "conditional" | "unknown", "why", "caveat"?}. Informational, not legal advice. No license means all rights reserved.
- Repositories flagged for secrets or personal data are excluded.

## Tools

- find_tools(format | instrument | assay): repositories that verifiably handle a file format, instrument or assay
- find_by_paper(identifier): repositories for a DOI, arXiv ID or bioRxiv DOI, with code_present and linked accessions
- check_paper_code(identifier): reproducibility verdict for one paper
- search(query, assay, instrument, format, discipline, license_reusable, has_paper, limit): ranked results with the reason each matched
- get_repo_record(full_name): full record with provenance, readiness breakdown, paper and data links, file pointers

## Access

- [Join the waitlist](https://benchbeacon.org/#waitlist): early access for agent builders and research teams
- Contact: support@benchbeacon.org
- Repository owners can request correction or removal of a record at support@benchbeacon.org

## Optional

- [Operator](https://tangentworks.info): Bench Beacon is a Tangent Works project