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 credentials
• MCP client (such as Claude Desktop)

Obtain Protocols.io API Credentials

1. Visit protocols.io/developers
2. Sign in to your account
3. Navigate to the API Clients section
4. Click ADD CLIENT to create a new application
5. Configure and copy the credentials based on your use case:

• Client Access Token: Copy the generated token for simple authentication (suitable for local STDIO transport)
• Client ID and Client Secret: For OAuth 2.0 authentication (suitable for remote HTTP/SSE transport):
• Set the redirect URL to {your_mcp_base_url}/auth/callback
• Copy the Client ID and Client Secret

Installation

Quick Start with Docker

docker run -d -p 8000:8000 -e PROTOCOLS_IO_CLIENT_ID="your_client_id" -e PROTOCOLS_IO_CLIENT_SECRET="your_client_secret" -e PROTOCOLS_IO_MCP_BASE_URL="https://example.com" --name protocols-io-mcp --restart always ghcr.io/hqn21/protocols-io-mcp:latest

The server will be accessible at http://0.0.0.0:8000/mcp with HTTP transport

Install via pip

pip install protocols-io-mcp

#### Set Environment Variables

##### STDIO Transport

export PROTOCOLS_IO_CLIENT_ACCESS_TOKEN="your_client_access_token"

##### HTTP/SSE Transport

export PROTOCOLS_IO_CLIENT_ID="your_client_id"
export PROTOCOLS_IO_CLIENT_SECRET="your_client_secret"
export PROTOCOLS_IO_MCP_BASE_URL="https://example.com"

Usage

Command Line Interface

Run the MCP server with various transport options:

# Default: STDIO transport
protocols-io-mcp

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

# SSE 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

1. 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.