Scientific Agent Skills

# Scientific Agent Skills: setup notes

This kit holds setup notes written by Mindket. It does not contain the skills, their scripts or their reference files. Those install from K-Dense’s repository: https://github.com/K-Dense-AI/scientific-agent-skills

License: MIT, Copyright (c) 2025 K-Dense Inc. (the license file’s text). Full text: https://github.com/K-Dense-AI/scientific-agent-skills/blob/main/LICENSE.md

The repository’s own README adds that each skill has its own license in the license line of its SKILL.md, and that these can differ from the repository’s MIT license and carry extra terms. Mindket read the first 40 lines of every SKILL.md: most say MIT, BSD or Apache, and a few say something else, such as a noncommercial license (PolyForm Noncommercial for deepspot-m, CC BY-NC-SA 4.0 for what-if-oracle), GPL (bioservices, cobrapy, etetoolkit) or a proprietary service (rowan). Three say Unknown and four have no license line at all. Read the license line of each skill you install. The kit holds none of those skills, so it carries none of their terms.

Scientific Agent Skills is a community project by K-Dense. It is not made or endorsed by Anthropic.

The pages these notes came from: the README (https://github.com/K-Dense-AI/scientific-agent-skills/blob/main/README.md), the repository’s plugin.json and SECURITY.md, and the SKILL.md files of the skills named in these notes, under https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills. The GitHub CLI lines come from GitHub’s manual for gh skill install and gh skill update (https://cli.github.com/manual/gh_skill_install). Facts about where Claude Code loads skills come from Claude Code’s own skills page (https://code.claude.com/docs/en/skills). Mindket copied every command and ran none of them.

## What it is

A library of research skills for coding agents: more than 170 folders under skills/, each with a SKILL.md and, for many, reference files, scripts and templates. The README groups them by field: bioinformatics, drug discovery, proteomics, clinical research workflows, microscopy and medical imaging, neuroscience, machine learning, materials, engineering, geospatial work, laboratory automation, scientific writing and review, and database lookup across 80 sources.

The README says the agent can use any Python package on its own. A skill adds curated notes, examples and checks for one package, database or job, so the agent starts from written guidance. The README adds that community skills may have been reviewed less closely than K-Dense’s own.

## Who does what

- You: install only the skills you need, see that each skill’s Python packages are installed in their own environment (you, or the agent following the SKILL.md’s install lines), give any API key that skill asks for, and check what the agent produces.
- The installer, either npx skills or gh skill: puts skill folders where your agent reads them. npx skills can link them to one shared copy or copy them. It does not install what a skill needs to run.
- The agent (Claude, Codex or another): reads a skill when your request matches it, then runs the commands and scripts the skill names. The skills’ imperatives are written to the agent.
- The skills’ scripts: run on your machine, and some call web services. The README says skills can run code, install packages, make network requests and change files.

## Files in this kit

- setup/choose-skills.md: the README’s security advice, how to list and pick a few skills, and how to read each skill’s license and needs
- setup/claude-code.md: the npx and gh skill routes for Claude Code
- setup/codex.md: the same routes for Codex, and the README’s plugin line
- setup/cursor.md: the same routes for Cursor, and the README’s plugin symlink route
- setup/other-agents.md: Gemini CLI, Antigravity, and agents that scan ~/.agents/skills, with the README’s clone lines
- setup/python-and-keys.md: uv, separate environments, the system the README names, and example API keys

## What you need first

- An agent that reads Agent Skills. The README names Cursor, Claude Code, Codex, Google Antigravity, Gemini CLI and Claude Cowork.
- uv, a Python package manager. The README says it is required for installing skill dependencies.
- Python. The README asks for 3.13 or newer for the repository’s own tooling, and each skill states its own range.
- macOS, Linux, or Windows with WSL2. That is the README’s list.
- Node.js for the npx route (the skills installer’s README asks for 22.20 or newer), or the GitHub CLI version 2.90.0 or newer for the gh skill route.
- Whatever each skill says it needs. Some skills need no key, some take an optional one, and some need an account with a service.

## What installs where

- npx skills add: the skill folders, in the agent’s own skills folder, in the project or globally.
- gh skill install: the same, with a note about the source added to each SKILL.md’s header, which lets gh skill update find changes.
- Plugin route, for Cursor and Codex: the repository as one plugin, with every skill under skills/.
- Python packages, system tools and keys: nowhere. Each skill’s SKILL.md says what it needs, and installing the skill files installs none of it.

## Your data

The skill files are text and scripts. What a skill does depends on the skill: some work only on files on your computer, and others call public databases or services such as PubMed, ClinVar or OpenRouter. The README’s own advice is to read each SKILL.md first, since it says which external services the skill connects to. What you give your agent goes to your agent’s provider as in any other work.

## Update and remove

gh skill update (and its --all option) is in setup/claude-code.md. npx skills update and npx skills remove are in the skills installer’s README (https://github.com/vercel-labs/skills). The maker’s README gives no removal step. Claude Code’s skills page says a personal or project skill is removed by deleting its folder.

README.md  6 KB
setup/choose-skills.md  5 KB
setup/claude-code.md  4 KB
setup/codex.md  2 KB
setup/cursor.md  2 KB
setup/other-agents.md  3 KB
setup/python-and-keys.md  4 KB