My MCP Configuration

Centralized config for all my bioinformatics MCP servers.

Setup on a new machine

Prerequisites

• uv (Python MCP servers)
• Node.js 18+ (for medical-mcp)
• VS Code with GitHub Copilot

Installation

macOS/Linux:

git clone <this-repo-url> ~/my-mcp-config
cd ~/my-mcp-config
chmod +x scripts/install.sh
./scripts/install.sh

Windows (PowerShell):

git clone <this-repo-url> $env:USERPROFILE\my-mcp-config
cd $env:USERPROFILE\my-mcp-config
.\scripts\install.ps1

This will:

1. Copy mcp.vscode.json → VS Code user config location
2. Restart VS Code to pick up the new servers

First run

VS Code will prompt for API keys when each server first starts. Leave blank if you don't have keys (most work without them, just with lower rate limits).

Updating

git pull
./scripts/install.sh  # re-copy config

To upgrade server versions, edit the version pins in mcp.vscode.json and commit.

Servers included

| Server | Purpose | Docs | |--------|---------|------| | biothings-mcp | BioThings APIs (genes, drugs) | GitHub | | biomcp | cBioPortal, NCI, AlphaGenome | biomcp.org | | alex-mcp | OpenAlex academic search | GitHub | | semantic-scholar-fastmcp | Semantic Scholar papers | GitHub | | academic-search-mcp | Multi-source academic search | GitHub | | medical-mcp | PubMed, FDA, WHO, RxNorm | GitHub |

Troubleshooting

"No servers found"

Run MCP: List Servers in VS Code command palette. If empty, check that:

• The config file was copied to the correct location (check install script output)
• VS Code was restarted after installation
• GitHub Copilot extension is installed and enabled

"Server failed to start"

Check VS Code Output panel → select the server from dropdown. Common issues:

• Missing uv or node in PATH
• Network issues downloading packages (first run only)
• Invalid API keys (most servers work without keys, just slower)

"Module not found" errors

The first time each server starts, uvx/npx will download it. This can take 10-30 seconds. Check the Output panel for progress.

Project structure

my-mcp-config/
├── README.md                    # This file
├── mcp.vscode.json             # VS Code MCP config (single source of truth)
├── .env.example                # Template for secrets
└── scripts/
    ├── install.sh              # macOS/Linux setup
    └── install.ps1             # Windows setup

Why this approach

| Old way | This meta-repo way | |---------|-------------------| | Clone 6 repos individually | Clone 1 config repo | | Hard-code 6 absolute paths in JSON | Zero paths, uvx/npx resolve everything | | npm install && npm run build × 6 | No builds, registry packages auto-installed | | Manual git pull in each repo to update | git pull meta-repo + restart VS Code | | Per-machine JSON edits | Single versioned mcp.vscode.json | | Secrets scattered | VS Code ${input:...} prompts once per machine |