Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add instructions/k-dense-ai/scientific-agent-skills/agents-mdgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsWhat 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 | $0.04326 | $0.04326 |
| Opus 5 | $0.02163 | $0.02163 |
| Sonnet 5 | $0.00865 | $0.00865 |
| Haiku 4.5 | $0.00433 | $0.00433 |
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 yesterday.
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 — 373 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 (docx, pdf, pptx,
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.
- yesterday 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 (40,390 stars, last pushed yesterday), licensed MIT. It adds 4,326 tokens to every session, about $0.0216 per session on Opus 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.
Other instructions, from other repositories
bioinformatics-agent-skills AGENTS.md
Instructions for YuliaNuzhnenko/bioinformatics-agent-skills, covering agent integration & specification guide 🤖, 📌 supported agent host architectures, 🧪 skill frontmatter specification and 🔒 security & sandboxing.
bioinformatics-agent-skills CLAUDE.md
Instructions for YuliaNuzhnenko/bioinformatics-agent-skills, covering claude code project guidelines, project overview, development & validation commands and skill conventions.
precision-medicine-mcp CLAUDE.md
Instructions for lynnlangit/precision-medicine-mcp, covering claude.md — project context for claude code, git workflow, session management, what this project is and repository structure.
asb-skill-collections copilot-instructions.md
Instructions for HolobiomicsLab/asb-skill-collections: This repository publishes the ASB Metabolomics Skill Collection (collections/metabolomics/v2/): 5,859 evidence-grounded skills over 909 software tools for computational LC-MS/MS metabolomics, each derived from a peer-reviewed method paper.
mgi-link CLAUDE.md
Claude Code instructions for berntpopp/mgi-link, covering claude.md, tl;dr, common commands and layout.
gnomad-genetics-mcp-server CLAUDE.md
Claude Code instructions for cyanheads/gnomad-genetics-mcp-server, covering developer protocol, core rules, patterns, server config (src/config/server-config.ts) and server identity and instructions.