Bioresearcher Onboard

BioMCP Project-Local Onboarding

This skill sets up a self-contained, project-local BioMCP runtime in your working directory under .bioresearcher-runtime/.

What it does

• Checks if the host has Node.js >= 22.13. If missing, downloads a pinned, cryptographically verified portable Node.js LTS binary into .bioresearcher-runtime/node/ (zero global installation, does not touch ~ or /usr/local).
• Auto-detects network conditions (official distribution vs. fast npmmirror in mainland China).
• Installs biomcp locally into .bioresearcher-runtime/node_modules/ with sub-100ms startup latency and offline resilience.
• Configures optional features (R analysis, Biowasm genomics, SQLite database) and registers the server in your harness configuration (opencode.json, .mcp.json, etc.) without overwriting existing settings.
• Verifies the configuration using the built-in diagnostic doctor.

Steps

Follow the steps below in order.

Step 1: Run Stage 0 Bootstrap

Execute the bootstrap script corresponding to your operating system.

For Unix-like shells (Linux, macOS, Git Bash):

bash skills/bioresearcher-onboard/scripts/bootstrap.sh

For Windows (PowerShell):

powershell -NoProfile -ExecutionPolicy Bypass -File skills\bioresearcher-onboard\scripts\bootstrap.ps1

The script automatically:

1. Reuses your host Node.js if version >= 22.13 is available.
2. If missing, downloads and verifies the official portable Node.js archive into .bioresearcher-runtime/node/.
3. Installs biomcp@1.4.0 into .bioresearcher-runtime/node_modules/.
4. Updates your harness configuration (opencode.json or .mcp.json) with absolute executable paths.

Step 2: Configure Optional Features (Optional)

By default, the core biomedical tools (PubMed/literature, clinical trials, genes, variants, drugs, diseases, patents) and built-in SQLite are installed.

If the user needs specialized capabilities, pass the corresponding flags to the bootstrap script or set environment variables before running:

• R / Bioconductor Analysis (DESeq2, edgeR, limma; requires ~2 GB RAM): Pass --with-r to install the webr@0.6 peer dependency and enable R analysis in .biomcp.json.
• Biowasm Analysis (SAM/BAM/BED/BCF genomics tools): Pass --with-biowasm to enable Biowasm in .biomcp.json.
• Local SQLite Database: Pass --sqlite-path=<path_to_db> (e.g. --sqlite-path=data/research.db).
• Client Override: Pass --client=opencode, --client=claude-code, --client=cursor, --client=zcode, --client=pi, --client=codebuddy, or --client=workbuddy if auto-detection should be overridden.

Example with R analysis and SQLite enabled:

bash skills/bioresearcher-onboard/scripts/bootstrap.sh --with-r --sqlite-path=data/research.db

Step 3: In-Session Feature Reconfiguration

Once BioMCP is registered and running, you do not need to hand-edit configuration files. Use the built-in biomcp_configure tool to inspect or adjust features dynamically:

• Inspect feature status: biomcp_configure(action="status")
• Enable or disable features: biomcp_configure(action="set", values={"features.analysis_r.enabled": true})
• Configure SQLite database: biomcp_configure(action="set", values={"features.database.enabled": true, "features.database.type": "sqlite", "features.database.sqlite_path": "data/research.db"}, confirm_sensitive=true)

Step 4: Restart the Harness

MCP servers are spawned at client startup. Instruct the user to restart their agent session or IDE to activate the newly connected BioMCP tools:

• OpenCode: Restart the session or open a new terminal session.
• Claude Code: Start a new session (claude).
• Cursor / VS Code: Reload the window or restart the application.
• ZCode: Reload the workspace or start a new ADE session.
• Pi Coding Agent: Start a new agent session (pi).
• CodeBuddy: Reload the window or restart the CLI session.
• WorkBuddy: Restart the application or switch workspace.

After restarting, verify connectivity by asking the agent to search for a gene or article (e.g., gene_search(query="BRAF")).