bioresearcher-skills

Agent Skills (agentskills.io open standard) for biomedical research with the biomcp-ts MCP server — deep multi-aspect research with citations, PubMed weekly update processing, uv Python environment bootstrap, and automated local runtime onboarding. Works in opencode, Claude Code, Codex, Cursor, Gemini CLI, and every harness that reads SKILL.md.

Skills

Skill	What it does
bioresearcher-onboard	Bootstraps a project-local biomcp MCP server runtime in .bioresearcher-runtime/: downloads portable Node.js 22 (if missing), vendors biomcp with fast mirror support (official or npmmirror), configures optional features (R, Biowasm, SQLite), and registers the server in OpenCode, Claude Code, Cursor, ZCode, Pi, CodeBuddy, or WorkBuddy.
bioresearcher-plot-making	Biomedical visualization router and plotting engine: classifies research data and produces publication-ready scientific figures (structural protein-binder complexes, conformational dynamics, literature method summaries, developmental case registers, and evidence tables) with built-in QA gates.
bioresearcher-deep-research	Orchestrates multi-aspect biomedical research (literature, trials, genes, variants, drugs, diseases, patents, omics) through biomcp-ts: interview → decompose → parallel-or-sequential research → cited Markdown + HTML report. 18 domain reference guides included.
bioresearcher-pubmed-weekly	Downloads the past week's PubMed updatefiles from NCBI and parses them (pure-Python streaming parser, handles <PubmedArticle> and <DeleteCitation>) into one Excel workbook.
bioresearcher-python-setup-uv	Bootstraps a project-local uv-managed Python environment (official or China mirror).

Install

Requires the biomcp-ts MCP server — either bootstrap it automatically with the bioresearcher-onboard skill, or see docs/biomcp-ts-setup.md for manual wiring.

Any harness (skills CLI):

npx skills add yeyuan98/bioresearcher-skills

To run onboarding immediately:

npx skills add yeyuan98/bioresearcher-skills --skill bioresearcher-onboard

Claude Code (plugin marketplace):

/plugin marketplace add yeyuan98/bioresearcher-skills
/plugin install bioresearcher@bioresearcher-skills

Installing the plugin also bundles the pinned core-only biomcp MCP server (.claude-plugin/mcp.json): it auto-starts with the plugin — no manual .mcp.json — and its tools surface as mcp__plugin_bioresearcher_biomcp__*. Requires Node.js >= 22.13 with npx on PATH (the first tool call pays the npx download). The plugin also ships the bioresearcher-dr-worker subagent used by the deep-research skill's parallel fan-out. Manual wiring is only needed for other harnesses or the all-features server variant — and a manual registration does not deduplicate against the bundled one (commands differ), so disable one of them via /mcp. See docs/biomcp-ts-setup.md for the permission model.

Plain git clone (pick the directory your harness reads): .opencode/skills/, .claude/skills/, .agents/skills/, .codex/skills/, or .gemini/skills/:

git clone https://github.com/yeyuan98/bioresearcher-skills .opencode/skills/bioresearcher-skills

Gemini CLI: gemini skills install https://github.com/yeyuan98/bioresearcher-skills (skills install is currently a preview-channel command).

WorkBuddy (connector market): the same server + skills ship as a WorkBuddy connector — see docs/connector-workbuddy.md. Releases from v1.3.0 on carry a bioresearcher-connector_workbuddy-v*.tar.gz bundle for market submission.

OpenCode (plugin / connector): the same server + skills + subagent ship as an OpenCode plugin — see docs/connector-opencode.md. Published to npm as opencode-bioresearcher ("plugin": ["opencode-bioresearcher"] in opencode.json or opencode plugin opencode-bioresearcher). Releases also carry a bioresearcher-connector_opencode-v*.tar.gz bundle for local or offline installation.

DeepSeek Harness (plugin / connector): the same server + skills + subagent ship as a DeepSeek Harness (dsh) plugin — see docs/connector-dsh.md. Releases carry a bioresearcher-connector_dsh-v*.tar.gz bundle for profile or overlay patch installation (dsh plugin --profile web add ./bioresearcher).

Development

node scripts/ci/lint-frontmatter.mjs   # strict-6 Agent Skills conformance
node scripts/ci/lint-agents.mjs        # plugin subagent frontmatter + manifest agreement
node scripts/ci/check-drift.mjs        # skills.json <-> metadata <-> CHANGELOG + VERSION slots
node scripts/ci/check-links.mjs        # links + duplicate headings
bash scripts/ci/check-bundle.sh        # <=1000 files / <=10 MiB per skill
bash scripts/ci/check-legacy-names.sh  # no retired biomcp-python tool names
node scripts/ci/check-tool-names.mjs   # biomcp tool refs match pinned registry
node scripts/ci/check-marketplace.mjs  # .claude-plugin validation
node scripts/ci/build-connector-workbuddy.mjs  # WorkBuddy connector bundle -> dist/
node scripts/ci/build-connector-opencode.mjs   # OpenCode connector bundle -> dist/
node scripts/ci/build-connector-dsh.mjs        # DeepSeek Harness connector bundle -> dist/

CI (.github/workflows/ci.yml) runs all of the above plus the official skills-ref validator and a local npx skills add ./ --list discovery smoke. Releases are cut automatically on push to main when VERSION changes (notes extracted from CHANGELOG.md).

Empirical agent tests

agent-test/ holds a unified, manually-run test suite that drives the real opencode CLI against these skills and a live keyless biomcp-ts MCP server (costs LLM tokens; never run in CI):

node agent-test/run.mjs --list
node agent-test/run.mjs --only skills-q01-discovery
node agent-test/run.mjs            # all cases

See agent-test/README.md for the case schema and the 12 mechanical check types. Sibling plugin test suites:

• Claude Code plugin tests
• OpenCode plugin tests
• DeepSeek Harness plugin tests

Docs

• biomcp-ts MCP setup — wiring, auth, rate limits
• Migration from the opencode plugin — tool-name map + openFDA downgrades
• Exposure checklist — directory submission mechanics
• Demos & partner docs — bilingual (zh/en) Agent + MCP publication documents with true-run demo artifacts and a self-contained replay runner (node demos/run-demo.mjs --list); the same material powers the GitHub Pages showroom (source: demos/website/, built by pages.yml — enable Pages → Source: GitHub Actions once)

License

Apache-2.0. Extracted and retargeted from opencode-bioresearcher-plugin v1.7.2 (personal project of the same author).