The Waldron Lab's AI agent-compatible scientific protocols. This repository is a content node in
the protocol federation: it holds protocols and nothing else. The standard they conform to, the
tooling that validates them, and the registry that makes them discoverable all live in
waldronlab/agent-protocol-standard.
Each protocol is a single self-contained file at protocols/<name>/protocol.md,
combining machine-readable YAML frontmatter (provenance, DOIs, dependencies, human reviews) with
human-readable instructions.
For the current list with descriptions, versions, and review status, read
PROTOCOLS.yaml or browse protocols/. PROTOCOLS.yaml is the
machine-readable index agents fetch, and it is generated by CI from the protocols themselves —
never edit it by hand, and do not expect a hand-written list anywhere to be authoritative.
We welcome new protocols! Your primary concern as a contributor should be clarity and scientific correctness. Don't worry too much about formatting syntax—our continuous integration (CI) tools will automatically check that for you when you open a pull request.
To get started:
- Find an idea: Check our Issues tab and look for the
good-first-protocollabel to find a protocol that needs writing. - Read the guide: Follow the step-by-step instructions in CONTRIBUTING.md to claim an issue, set up your file from a template, and submit your work.
Agents find these protocols by fetching
registry.yaml
from the standard repository, following this repository's index_url to
PROTOCOLS.yaml,
and then following each protocol's protocol_url. Those are raw URLs, not the HTML views: an agent
following the documented URL must receive parseable YAML.
- Scientific Protocols & Documentation (the contents of
protocols/, unless otherwise specified in a protocol's YAML frontmatter): Creative Commons Attribution 4.0 International (CC-BY-4.0) - Anything else in this repository: MIT License