PBMCpedia-MCP

This subrepository contains an MCP server based on the Typescript MCP SDK, an Open Source project. The structure of this server was derived from the now-replaced tutorial for the SDK, licensed MIT by Anthropic.

It contains a single Typescript file representing an MCP interface for the respective webserver as well as a package.json containing dependencies. npm is required for dependency management.

Dependencies

Dependencies for the server can be installed globally for the user by running

npm install

in the server directory, or only for the server directory by running

npm install -D

in the same directory.

Running

The server can then be run using

npm tsx server.ts

or

npm start

in the server directory. This runs the local server in tsx, a wrapper for NodeJS which supports TypeScript. By default, the server binds to a default port, but this can be adjusted by setting the PORT environment variable to a desired port number. The server can also be run in stdIO mode by passing --transport stdio.

Adding the MCP Server

The following instructions assume that the server should appear as "SERVER_NAME", runs on port "PORT" (for HTTP transport) and the full file path of the cloned repository is "SERVER_PATH" (for stdIO transport). Replace these placeholders with your actual values (e.g. "PBMCpedia" and "3002").

Configuring the server with stdIO transport is recommended if you just want the server to always be available in your client. If you want more control over the server running, HTTP transport is the better option. This requires to start the server externally via the command when you want to use it.

This approach applies to clients providing a JSON configuration file to configure your MCP servers, including Gemini CLI ("settings.json") and LM Studio ("mcp.json"). You should be able to add this server by appending

"SERVER_NAME": {
    "command": "npm",
    "args": ["start", "--", "--transport", "stdio"],
    "cwd": "SERVER_PATH"
}

(for stdIO transport) or

    "SERVER_NAME": {
      "url": "http://localhost:PORT/mcp"
    }

(for HTTP transport) to your list of MCP server configurations, which is likely under

{
   "mcpServers":  {
    HERE
  }
}

For Claude Desktop and stdIO transport, the above instructions for stdIO transport apply as well. To access the JSON configuration file, you can follow these instructions: https://modelcontextprotocol.io/docs/develop/connect-local-servers

For Claude Desktop and HTTP transport, you can follow these instructions: https://modelcontextprotocol.io/docs/develop/connect-remote-servers Set the name as "SERVER_NAME" and the connector address as "http://localhost:PORT/mcp"

For Claude Code, run the command

claude mcp add --transport stdio SERVER_NAME -- npm start -- --transport stdio

and edit the JSON entry for the added server to contain "cwd": "SERVER_PATH" (see this documentation for reference) (stdIO transport)

or simply run

claude mcp add --transport http SERVER_NAME http://localhost:PORT/mcp

(HTTP transport)

Note

This server uses publicy available API and requires no API keys. Standard rate limits imposed by the webserver will apply and may cause tool invocation to fail if called too frequently.

PBMCpedia information:

• URL: https://web.ccb.uni-saarland.de/pbmcpedia/
• Publication DOI: https://doi.org/10.1093/nar/gkaf1245