Scientific Agent Skills is a collection of reusable procedures that give AI agents capabilities for scientific research across areas such as biology, chemistry, medicine, and drug discovery. It is used by researchers and by people building AI scientist workflows with compatible coding agents. The catalogue contains many of the project's skills and supporting instructions.
Borrowing it
Nothing to install: this file belongs to K-Dense-AI/scientific-agent-skills. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/main/AGENTS.mdgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/k-dense-ai/scientific-agent-skills/agents-md)<a href="https://agentmods.dev/instructions/k-dense-ai/scientific-agent-skills/agents-md"><img src="https://agentmods.dev/badge/instructions/k-dense-ai/scientific-agent-skills/agents-md/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/instructions/k-dense-ai/scientific-agent-skills/agents-md"><img src="https://agentmods.dev/badge/instructions/k-dense-ai/scientific-agent-skills/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.04440 | $0.04440 |
| Opus 5.5 | $0.01776 | $0.01776 |
| Sonnet 5.5 | $0.00888 | $0.00888 |
| Haiku 4.5 | $0.00444 | $0.00444 |
Grade A, and why
scientific-agent-skills AGENTS.md scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
local links resolve, scripts parse, no `eval`/`exec`/`os.system`, no standard-library shadowing, How it starts
The opening of the file, as written. The whole thing — 381 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Repository Guidance
This repository is a collection of Agent Skills for science and research. Every skill lives in its
own directory under skills/ and must conform to the open
Agent Skills specification.
Read this file before creating or changing a skill. CONTRIBUTING.md covers the same ground at
more length, plus the pull-request process.
What belongs here
In scope: a narrow skill for one scientific package, database, platform, or research workflow —
scanpy, depmap, benchling-integration, experimental-design.
Out of scope, and routinely declined:
- General software-engineering or coding-judgment skills — they compete for selection on every task.
- General infrastructure with a scientific example bolted on (a vector database, a cloud SDK) — accepting one implies carrying every competitor.
- Broad "orchestrator" skills that route to other skills — they overlap every specialist by design.
- A second provider for a service an existing skill already reaches.
The general-purpose skills that do exist are narrow output-format helpers (generate-image,
markdown-mermaid-writing). They are not precedent for broadening scope.
Layout
The repository root is an Agent Plugins 1.0.0 package: plugin.json
plus the portable skills/ tree. Keep plugin.json valid against the Agent Plugins manifest
schema, and keep its version identical to pyproject.toml [project].version. Do not add
non-portable top-level fields to plugin.json (no inline MCP, hooks, or client-only keys — use
mcp.json or a reverse-domain extensions namespace if those are ever needed).
plugin.json # Agent Plugins manifest (repo root)
skills/<skill-name>/
├── SKILL.md # required
├── references/ # optional: long documentation, loaded only when needed
├── scripts/ # optional: executable helpers
└── assets/ # optional: templates and static resources
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago Changed · +4 lines · +40 tokens per session d608ab4e9f30
- 1mo ago Changed · +2 lines · +37 tokens per session 4f4782ca1955
- 1mo ago Changed · +2 lines · +37 tokens per session 7f128536bef1
- 2mo ago First seen · 373 lines · 4,326 tokens per session scan A f3a422683149
scientific-agent-skills AGENTS.md is an instructions file published in the GitHub repository K-Dense-AI/scientific-agent-skills (56,220 stars, last pushed 4d ago), licensed MIT. It adds 4,440 tokens to every session, about $0.0178 per session on Opus 5.5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
scientific-agent-skills AGENTS.md compared with instructions from other repositories
| Mod | Type | Stars | Last push | Licence | Scan | Tokens | Works with |
|---|---|---|---|---|---|---|---|
| scientific-agent-skills AGENTS.mdK-Dense-AI/scientific-agent-skills | Instructions file | 56k | 4d ago | MIT | A | 4,440 | Codex, OpenCode |
| vscode buildNext.instructions.mdmicrosoft/vscode | Instructions file | 195k | today | MIT | A | 9,719 | GitHub Copilot |
| next.js AGENTS.mdvercel/next.js | Instructions file | 143k | today | MIT | A | 7,461 | Codex, OpenCode |
| vscode oss-third-party-notices.instructions.mdmicrosoft/vscode | Instructions file | 195k | today | MIT | A | 5,516 | GitHub Copilot |
| langchain AGENTS.mdlangchain-ai/langchain | Instructions file | 149k | today | MIT | A | 4,680 | Codex, OpenCode |
| vscode copilot-instructions.mdmicrosoft/vscode | Instructions file | 195k | today | MIT | A | 3,093 | GitHub Copilot |
| deepseek-harness AGENTS.mddeepseek-ai/deepseek-harness | Instructions file | 274k | 2d ago | MIT | A | 4,313 | Codex, OpenCode |