23  MCP Setup Guide

Model Context Protocol (MCP) servers extend Claude Code’s capabilities by providing access to external services and data sources.

23.1 What Are MCPs?

MCPs are plugins that give Claude Code additional tools: - PubMed MCP: Search scientific literature - File system MCP: Enhanced file operations - Database MCPs: Query databases directly - Custom MCPs: Build your own

23.2 Installing MCPs

MCPs are typically npm packages or standalone servers.

23.2.1 General Installation Pattern

# Install globally
npm install -g @some-org/mcp-server-name

# Or in a project
npm install @some-org/mcp-server-name

23.2.2 Configuration

MCPs are configured in Claude Code’s config file:

Location: - Mac/Linux: ~/.claude/config.json - Windows: %USERPROFILE%\.claude\config.json

Example configuration:

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": ["@some-org/mcp-pubmed"]
    },
    "filesystem": {
      "command": "npx",
      "args": ["@some-org/mcp-filesystem", "/path/to/allowed/directory"]
    }
  }
}

23.3 PubMed MCP

For searching scientific literature.

23.3.1 Installation

npm install -g @anthropic-ai/mcp-pubmed

23.3.2 Configuration

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": ["@anthropic-ai/mcp-pubmed"],
      "env": {
        "NCBI_API_KEY": "your-api-key"
      }
    }
  }
}

23.3.3 Getting an NCBI API Key

1. Go to ncbi.nlm.nih.gov
2. Create/sign in to your NCBI account
3. Go to Settings → API Key Management
4. Generate a new key

23.3.4 Usage

> Use the PubMed MCP to search for papers about single-cell RNA sequencing published in 2024

Claude will use the MCP to search and return results.

23.4 File System MCP

Enhanced file operations with better safety.

23.4.1 Configuration

{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "@anthropic-ai/mcp-filesystem",
        "/Users/you/Projects"
      ]
    }
  }
}

The path argument restricts access to that directory.

23.5 Database MCPs

23.5.1 SQLite

{
  "mcpServers": {
    "sqlite": {
      "command": "npx",
      "args": ["@anthropic-ai/mcp-sqlite", "path/to/database.db"]
    }
  }
}

23.5.2 PostgreSQL

{
  "mcpServers": {
    "postgres": {
      "command": "npx",
      "args": ["@anthropic-ai/mcp-postgres"],
      "env": {
        "DATABASE_URL": "postgresql://user:pass@localhost:5432/dbname"
      }
    }
  }
}

23.6 Custom MCPs

You can build MCPs for your specific needs.

23.6.1 MCP Server Structure

An MCP server implements the MCP protocol:

// Simple MCP server example
import { Server } from "@modelcontextprotocol/sdk/server";

const server = new Server({
  name: "my-mcp",
  version: "1.0.0"
});

server.setRequestHandler("tools/list", async () => {
  return {
    tools: [{
      name: "my_tool",
      description: "Does something useful",
      inputSchema: {
        type: "object",
        properties: {
          query: { type: "string" }
        }
      }
    }]
  };
});

server.setRequestHandler("tools/call", async (request) => {
  if (request.params.name === "my_tool") {
    // Implement your tool logic
    return { result: "..." };
  }
});

server.listen();

23.6.2 Useful for Academics

Consider building MCPs for: - Internal databases - Lab equipment APIs - Custom data sources - Institution-specific services

23.7 Troubleshooting MCPs

23.7.1 MCP Not Loading

1. Check the config JSON is valid
2. Verify the package is installed
3. Check Claude Code logs

23.7.2 MCP Commands Fail

1. Test the MCP server standalone
2. Check environment variables
3. Verify API keys/credentials

23.7.3 Finding Available MCPs

Check: - github.com/anthropics for official MCPs - npm for community MCPs: npm search mcp-server

23.8 Security Considerations

MCPs can access external services. Consider:

• API keys: Keep them secure, use environment variables
• Network access: MCPs may make external requests
• Data privacy: Be careful what data goes through MCPs
• Permissions: MCPs have the permissions of the user running Claude Code

23.9 Summary

MCPs extend Claude Code with: - External data sources (literature, databases) - Enhanced capabilities - Custom integrations

Set them up in ~/.claude/config.json and use them naturally in conversation.