Protocols.io MCP Server

A Model Context Protocol (MCP) server that enables MCP clients like Claude Desktop to interact with protocols.io, a popular platform for sharing scientific protocols and methods.

Available Tools

The server provides the following tools that can be used by MCP clients:

Search and Retrieval

• search_public_protocols - Search for public protocols by keyword
• get_protocol - Get basic protocol information by ID
• get_protocol_steps - Get detailed steps for a specific protocol
• get_my_protocols - Retrieve all protocols from your account

Protocol Creation and Management

• create_protocol - Create a new protocol with title and description
• update_protocol_title - Update the title of an existing protocol
• update_protocol_description - Update the description of an existing protocol

Step Management

• set_protocol_steps - Replace all steps in a protocol
• add_protocol_step - Add a single step to the end of a protocol
• delete_protocol_step - Delete a specific step from a protocol

Requirements

• Python 3.10 or higher
• protocols.io account with API access token
• MCP client (such as Claude Desktop)

Installation

Quick Start with Docker

docker run -d -p 8000:8000 -e PROTOCOLS_IO_CLIENT_ACCESS_TOKEN="your_access_token_here" --name protocols-io-mcp --restart always ghcr.io/hqn21/protocols-io-mcp:latest

Install the package using pip

pip install protocols-io-mcp

Configuration

Environment Variables

Before running the server or tests, you must set your protocols.io API access token:

export PROTOCOLS_IO_CLIENT_ACCESS_TOKEN="your_client_access_token"

To obtain an API token:

1. Visit protocols.io/developer
2. Sign in to your account
3. Go to API clients section and add a new client
4. Copy the generated client access token and set it in your environment

Usage

Command Line Interface

Run the MCP server with various transport options:

# Default: stdio transport (recommended for MCP clients)
protocols-io-mcp

# HTTP transport
protocols-io-mcp --transport http --host 127.0.0.1 --port 8000

# Server-Sent Events transport
protocols-io-mcp --transport sse --host 127.0.0.1 --port 8000

CLI Options

Usage: protocols-io-mcp [OPTIONS]

  Run the protocols.io MCP server.
    
Options:
  --transport [stdio|http|sse]  Transport protocol to use [default: stdio]
  --host TEXT                   Host to bind to when using http and sse
                                transport [default: 127.0.0.1]
  --port INTEGER                Port to bind to when using http and sse
                                transport [default: 8000]
  --help                        Show this message and exit.

Integration with Claude Desktop

To use this server with Claude Desktop, add the following configuration to your claude_desktop_config.json:

{
  "mcpServers": {
    "protocols-io": {
      "command": "protocols-io-mcp",
      "env": {
        "PROTOCOLS_IO_CLIENT_ACCESS_TOKEN": "your_client_access_token"
      }
    }
  }
}

Troubleshooting

MCP protocols-io: spawn protocols-io-mcp ENOENT

This error indicates that Claude Desktop cannot find the protocols-io-mcp command. To resolve this:

1. Make sure you have installed the protocols-io-mcp package globally using pip.
2. Change the command field in your claude_desktop_config.json to the full path of the protocols-io-mcp executable. You can find the path by running:

   which protocols-io-mcp

3. Your final configuration should look like:

   {
     "mcpServers": {
       "protocols-io": {
         "command": "/full/path/to/protocols-io-mcp",
         "env": {
           "PROTOCOLS_IO_CLIENT_ACCESS_TOKEN": "your_client_access_token"
         }
       }
     }
   }

Development

Running Tests

Ensure you have set the PROTOCOLS_IO_CLIENT_ACCESS_TOKEN environment variable, then run:

pytest

License

This project is licensed under the MIT License. See the LICENSE file for details.