open-research-skills — agent and contributor guide

A curated collection of research-domain skills for AI agents. Authored by Pradyumna Jayaram, 2026.

This file is the entry point for AI agents and human contributors. It supersedes and replaces CONTRIBUTING.md (which is kept as a thin alias for the GitHub "Contribute" button).

What this repo is

open-research-skills (ORS) is a comprehensive skill library for AI agents working alongside researchers, academics, graduate students, postdocs, and R&D engineers. It covers the full lifecycle of research:

literature search → experimental design → analysis → writing → publication → grant writing → mentorship → ethics

Current status (v0.3.0)

19 categories, 123 skills — see INDEX.md for the per-skill table.

Layout

open-research-skills/
├── README.md                    # main readme
├── LICENSE                      # MIT
├── AGENTS.md                    # this file
├── CONTRIBUTING.md              # alias for GitHub "Contribute" button
├── CHANGELOG.md                 # release notes
├── ROADMAP.md                   # what's done, what's next
├── INDEX.md                     # per-skill table
├── SCHEMA.md                    # frontmatter spec (legacy, see spec/)
├── TAXONOMY.md                  # 18 categories (legacy, see spec/)
├── THIRD_PARTY_NOTICES.md       # upstream attributions
│
├── .claude-plugin/              # Claude Code plugin marketplace
│   └── marketplace.json
│
├── spec/                        # ORS specification
│   ├── README.md
│   ├── skill-format.md
│   └── category-taxonomy.md
│
├── template/                    # template for new skills
│   └── SKILL.md
│
├── examples/                    # worked examples
│   ├── README.md
│   ├── claude-code-installation.md
│   ├── api-integration.md
│   └── multi-skill-workflow.md
│
├── scripts/                     # repo automation
│   ├── README.md
│   ├── validate-skills.py
│   └── build-index.py
│
├── tests/                       # test suite
│   ├── test_frontmatter.py
│   ├── test_skill_structure.py
│   └── fixtures/
│
├── .github/workflows/           # CI
│   ├── validate.yml
│   └── release.yml
│
└── skills/                      # all 123 skills, organized in 19 categories
    ├── AGENTS.md                # skill-authoring guide
    ├── bioinformatics-sequence/ # 23 skills
    ├── chemoinformatics/        # 19 skills
    ├── research-grants/         # 9 skills
    └── ... (15 more categories)

Installation

As a Claude Code plugin (recommended)

/plugin marketplace add pradyumnasagar/open-research-skills
/plugin install ors-research@pradyumnasagar
/plugin install ors-bioinformatics@pradyumnasagar
/plugin install ors-career-ethics@pradyumnasagar

As a git clone

git clone https://github.com/pradyumnasagar/open-research-skills.git
cd open-research-skills
claude

In the chat, ask Claude to use a specific skill by name:

> Use the bwa-alignment skill to align these reads to GRCh38.

See examples/claude-code-installation.md for more.

Programmatically (API)

See examples/api-integration.md for Python, TypeScript, Bedrock, and Vertex examples.

Skill format

Every skill lives at skills/<category>/<slug>/SKILL.md and has the form:

---
name: <kebab-case-slug>
description: <one or two sentences — what & when>
license: MIT        # optional
---

<!-- metadata: ... (optional) -->

# Skill Title

> Tagline

## When to use
## Workflow
## Code patterns
## Pitfalls
## Validation
## References

The full spec is in spec/skill-format.md.

Adding a new skill

1. Read skills/AGENTS.md — the skill-authoring guide.
2. Copy template/SKILL.md to skills/<category>/<your-slug>/SKILL.md.
3. Fill in the frontmatter (name and description are required).
4. Fill in the body and the optional <!-- metadata: ... --> block.
5. Run python scripts/validate-skills.py skills/ to validate.
6. Run python scripts/build-index.py to regenerate INDEX.md.
7. Open a PR.

Adding a new category

See spec/category-taxonomy.md — the bar is high. Propose in an issue first.

License

MIT. All skills authored by Pradyumna Jayaram unless explicitly co-authored in a PR. See THIRD_PARTY_NOTICES.md for upstream attributions.

No AI co-authorship

This repo is authored by Pradyumna Jayaram. Commits must not include Co-Authored-By: lines for AI assistants.

Versioning

Semantic versioning:

• Major — break the frontmatter contract, remove/rename categories.
• Minor — add categories, add skills, backwards-compatible schema additions.
• Patch — fix typos, update tooling versions, add validation tests.

Current: v0.3.0 (restructure to match Anthropic skills pattern).