A skill your agent uses when a skill fails for a missing tool or the environment needs checking.
$ npx skills add Aperivue/medsci-skills --skill setup-medsci -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install Aperivue/medsci-skills setup-medsci --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/setup-medsci .claude/skills/setup-medsci && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "setup-medsci" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/setup-medsci into .claude/skills/setup-medsci/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup-medsci", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/Aperivue/medsci-skills/tree/main/skills/setup-medsciType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add Aperivue/medsci-skills --skill setup-medsci -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install Aperivue/medsci-skills setup-medsci --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/setup-medsci .agents/skills/setup-medsci && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "setup-medsci" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/setup-medsci into .agents/skills/setup-medsci/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup-medsci", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add Aperivue/medsci-skills --skill setup-medsci -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install Aperivue/medsci-skills setup-medsci --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/setup-medsci .cursor/skills/setup-medsci && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "setup-medsci" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/setup-medsci into .cursor/skills/setup-medsci/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup-medsci", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/Aperivue/medsci-skills.git --path skills/setup-medsci--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add Aperivue/medsci-skills --skill setup-medsci -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install Aperivue/medsci-skills setup-medsci --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/setup-medsci .gemini/skills/setup-medsci && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "setup-medsci" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/setup-medsci into .gemini/skills/setup-medsci/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup-medsci", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install Aperivue/medsci-skills setup-medsciInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add Aperivue/medsci-skills --skill setup-medsci -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/setup-medsci .github/skills/setup-medsci && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "setup-medsci" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/setup-medsci into .github/skills/setup-medsci/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup-medsci", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add Aperivue/medsci-skills --skill setup-medsci -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install Aperivue/medsci-skills setup-medsci --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/setup-medsci .opencode/skills/setup-medsci && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "setup-medsci" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/setup-medsci into .opencode/skills/setup-medsci/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup-medsci", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
setup-medsciA skill your agent uses when a skill fails for a missing tool or the environment needs checking.
Setup Medsci is an agent skill from Aperivue/medsci-skills. Use when a skill fails for a missing tool or the environment needs checking. Diagnoses Python, R, Node, Claude Code, Git, Zotero and configured MCP servers and prints a pass/fail table with links to the setup docs. Read-only; installs nothing.
Its SKILL.md is about 960 tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files, including reference files (for example `references/setup-checklist.md` and `skill.yml`).
It sits in Research & Science, covering Citation management and MCP servers. It works with Model Context Protocol, Python, Git and Zotero. The repository describes itself as: Agent Skills for medical research — literature search, reporting-guideline & citation checks, statistics, publication figures, submission. Works with Claude Code, Codex, Cursor &… The licence is MIT.
4 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit 3b14ae2. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Shell commands in SKILL.md call:
claudepythonbrewwingetpipFrom the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Setup Medsci loads about 960 tokens when it runs, and up to ~1.9k if it reads all its reference files. Until then it costs about 64 tokens; SKILL.md has 403 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
The full file from Aperivue/medsci-skills at commit 3b14ae2, republished under its MIT licence (© Aperivue). 403 words, ~960 tokens.
.claude/skills/setup-medsci/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.Diagnose only. Never install, upgrade or configure anything — no brew install,
winget install, pip install, Rscript -e 'install.packages(...)', and no edits to
~/.claude.json or any MCP configuration (read claude mcp list only) — because auto-installers
for system Python and R are a support nightmare for non-developer users. If a tool is missing,
the user follows the setup doc themselves. Skill versions and content are out of scope
(validate_skills.sh, /manage-project status).
The diagnostic table is in English so it can be pasted into a GitHub issue. Remediation links
point to the docs/setup/ guides in the medsci-skills repository, and only these five exist:
docs/setup/README.md, docs/setup/mac.md, docs/setup/windows.md, docs/setup/mcp-setup.md,
docs/setup/common-issues.md.
uname -sDarwin → macOS → docs/setup/mac.mdLinux → Linux (similar tooling to Mac) → docs/setup/mac.mdMINGW*, MSYS*, CYGWIN*, or detection failure on Windows → docs/setup/windows.mdRead references/setup-checklist.md and run every check in it — R1-R5 required, O1-O5 optional —
with its detect command, version command, minimum version and status rule. Use command -v <tool>
first to detect presence without running it (avoids triggering long initialization). Capture the
version output and the exit code, and report the version exactly as printed: if a command fails,
report the failure verbatim rather than a version that is "probably" installed. If command -v
finds the tool but the version command or its parse fails, mark the row ❌ and report the failing
command — the install is broken, not just outdated. An MCP server is ✅ only when
claude mcp list shows it connected; configured-but-disconnected is ⚠️.
Print a single Markdown table to stdout in this exact format, one row per check, with the doc link from the reference for the detected OS:
## MedSci Skills Setup Diagnostic
OS detected: <macOS | Linux | Windows>
Date: <YYYY-MM-DD>
| Component | Status | Detected | Required | Action |
|---|:---:|---|---|---|
| Python 3.11+ | ✅ / ❌ | 3.11.9 | 3.11+ | OK / See docs/setup/mac.md Step 2 |
| MCP: zotero | ✅ / ❌ / ⚠️ | Connected | optional | OK / See docs/setup/mcp-setup.md |
Summary: <X required components passed, Y missing>
Next step: <one-sentence action>Status legend:
Use the reference's Summary Rules for the closing sentence.
cd ~/medsci-skills/demo/01_wisconsin_bc && claude '/orchestrate --e2e'.lit-sync, verify-refs and write-paper are smoother with Zotero MCP; link
docs/setup/mcp-setup.md.The diagnostic report goes to stdout. If the user asks for a copyable report (e.g. for a GitHub
issue), also write it to ~/.medsci-skills/diagnostic-YYYY-MM-DD.md and tell them where it is.
© Aperivue, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 2 other files (references) in skills/setup-medsci of Aperivue/medsci-skills.
Open the folder on GitHubat commit 3b14ae2
Setup Medsci next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Setup Medsci this skillAperivue/medsci-skills | 329 | — | ~960 | Automated safety check: Pass | MIT | |
| Literature Review Toolsbrycewang-stanford/Auto-Empirical-Research-Skills | 4.5k | — | ~2.5k | Automated safety check: Notes | Custom licence | |
| Annotate Paper54yyyu/zotero-mcp | 5.3k | — | ~1.5k | Automated safety check: Pass | MIT | |
| NSFC Literature Review WriterHuiyuLi-2000/Chinese-Grant-Writer-Skills | 432 | 1 repos | ~1.4k | Automated safety check: Notes | MIT | |
| Arxiv MCP Serverblazickjp/arxiv-mcp-server | 3.2k | — | ~353 | Automated safety check: Pass | Apache-2.0 | |
| CLI Anything ZoteroPiaoyangGuohai1/cli-anything-zotero | 137 | — | ~2.6k | Automated safety check: Pass | Apache-2.0 |
brycewang-stanford/Auto-Empirical-Research-Skills
Recommend AND run open-source AI tools, agents, Claude Code / Codex skills, and MCP servers for any stage of a literature review — searching, reading, extracting, synthesizing, screening…
54yyyu/zotero-mcp
Read the open paper and write study annotations into its PDF with zotero-cli - a context box on the title, a four-part summary on the abstract, role-coded abstract highlights, one box per figure…
HuiyuLi-2000/Chinese-Grant-Writer-Skills
Writes the research-status literature review and critique section of an NSFC grant proposal, backed by a bundled multi-source literature search.
blazickjp/arxiv-mcp-server
A skill your agent uses when finding, comparing, reading, or monitoring arXiv papers, including requests for abstracts, citation graphs, original LaTeX, section-level technical details, or…
PiaoyangGuohai1/cli-anything-zotero
Full-featured CLI for Zotero reference management. An agent skill from PiaoyangGuohai1/cli-anything-zotero.
Bubble-OoO/zotero-research-assistant-skill
Access and configure a user's local or cloud Zotero library without MCP by executing the bundled JSON CLI.
Aperivue/medsci-skills
A skill your agent uses when validating or evaluating a trained medical-imaging model.
Aperivue/medsci-skills
A skill your agent uses when turning a folder of research PDFs into Obsidian notes, even if Obsidian is not named.
Aperivue/medsci-skills
A skill your agent uses when building or auditing a radiomics or tabular clinical-ML prediction model with a classical learner (LASSO, SVM, random forest, XGBoost and similar).
Aperivue/medsci-skills
A skill your agent uses when checking whether a manuscript's references are real.
Aperivue/medsci-skills
A skill your agent uses when a clinical CSV/Excel dataset needs profiling and cleaning before analysis (missing values, outliers, duplicates, type mismatches).
Aperivue/medsci-skills
A skill your agent uses when checking a radiology or medical AI study design before drafting or submission.
Works with
Categories
A skill your agent uses when a skill fails for a missing tool or the environment needs checking. Setup Medsci is an agent skill from Aperivue/medsci-skills. Use when a skill fails for a missing tool or the environment needs checking.
Setup Medsci fits situations like: A skill fails for a missing tool; the environment needs checking.
Run `npx skills add Aperivue/medsci-skills --skill setup-medsci -a claude-code`. Or copy the skill folder (skills/setup-medsci in Aperivue/medsci-skills) into .claude/skills/setup-medsci in your project. Claude Code loads it when a task matches its description.
Run `npx skills add Aperivue/medsci-skills --skill setup-medsci -a codex`. Or copy the skill folder (skills/setup-medsci in Aperivue/medsci-skills) into .agents/skills/setup-medsci in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add Aperivue/medsci-skills --skill setup-medsci -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/setup-medsci, .gemini/skills/setup-medsci, .github/skills/setup-medsci and .opencode/skills/setup-medsci in your project.
Going by SKILL.md and its folder, Setup Medsci needs the command-line tools its instructions call (claude, python, brew, winget and pip). Our summary lists: Python 3.
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
Setup Medsci is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 960 tokens (SKILL.md is roughly 3.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 962 tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Setup Medsci: Literature Review Tools (brycewang-stanford/Auto-Empirical-Research-Skills, 4.5k stars), Annotate Paper (54yyyu/zotero-mcp, 5.3k stars), NSFC Literature Review Writer (HuiyuLi-2000/Chinese-Grant-Writer-Skills, 432 stars) and Arxiv MCP Server (blazickjp/arxiv-mcp-server, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Aperivue (a GitHub organization) maintains it in Aperivue/medsci-skills, which has 329 GitHub stars. The repository holds 54 skills in this directory. The repository was last updated on October 5, 2026.
Source: Aperivue/medsci-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.
