Biodiscovery Skills

Inspired by Intuition Pumps and Other Tools for Thinking by Daniel Dennett, this repo provides almost every thinking tool humanity has, adjusted for AI agents to make scientific breakthroughs.

Tools like Claude Science and others focus on exact methods and tool usage. No one addresses the problem of scientific thinking — which is the most important thing in doing science and making scientific discoveries.

Focused on the life sciences — the operators are domain-general, but the vocabulary, the worked failure modes and the literature tooling are aimed at biological discovery.

Contributions are welcome.

Just give this repo to your AI agent, and will set it up for you. Don't forget about paperclips registration.

Requirements

Paperclip — required. The discovery-director skill delegates literature search to it, and returns insights rather than reading lists. Install with:

curl -fsSL https://paperclip.gxl.ai/install.sh | bash

That installs to ~/.paperclip/, signs you in, and registers it with your agent. Alternatives: npx gxl-paperclip, or point your client at the hosted MCP server https://paperclip.gxl.ai/mcp. Non-interactive auth uses an API key from the keys dashboard:

export PAPERCLIP_API_KEY='gxl_...'

Everything else in both skills runs with no external dependencies.

Install

Claude Code — plugin (recommended)

/plugin marketplace add dekan-aleksandr/biodiscovery-skills
/plugin install biodiscovery-skills@biodiscovery-skills

Any agent — one command

curl -fsSL https://raw.githubusercontent.com/dekan-aleksandr/biodiscovery-skills/main/install.sh | bash

Copies both skills into ~/.claude/skills/. Pass a path to install elsewhere: ... | bash -s -- .claude/skills for project-level.

Manual

git clone https://github.com/dekan-aleksandr/biodiscovery-skills.git
cp -r biodiscovery-skills/skills/* ~/.claude/skills/

Or just point your agent here

Read https://raw.githubusercontent.com/dekan-aleksandr/biodiscovery-skills/main/skills/discovery-director/SKILL.md
and follow it. Load skills/discovery-toolbox/SKILL.md on demand when you hit its triggers.

Skills

discovery-director

The operating stance for an agent doing open-ended research: explore broadly → discriminate → go deep on exceptional leads → confirm independently.

Covers how to hold the research map while delegating work, how to treat literature (what humans tested, not what nature is doing), what counts as staying on the question versus drifting, how to read a detection floor as a property of the instrument rather than of reality, and seven discovery modes — orient, question, explore, discriminate, depth, confirm, accumulate.

Fires on: open-ended research, exploring a dataset for findings, hypothesis generation, screening a large candidate space, investigating an anomaly, deciding what to run next.

discovery-toolbox

~90 operators in nine routed sections, loaded on demand — never wholesale. Route to the smallest relevant section, activate 1–3 operators, return to the research loop.

Fires on: a null or weak screen, a result that looks too good, stalled search, a causal claim, an unexplained anomaly, a suspected pipeline bug, a lead about to be escalated.

docs/TOOL_INVENTORY.md — the long-form list of tools behind the toolbox, with sources.

License

MIT