Protocols.io MCP server for AI agents

The protocols.io MCP server enables Claude Desktop and other MCP clients to interact with protocols.io, a platform for sharing scientific protocols and methods. This integration allows you to search, retrieve, create, and manage scientific protocols directly through your MCP client.

Requirements

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

Installation Options

Using 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

Using pip

pip install protocols-io-mcp

Configuration

Setting Up Your API Token

Before using the server, you need to set up your protocols.io API access token:

export PROTOCOLS_IO_CLIENT_ACCESS_TOKEN="your_client_access_token"

How to Obtain an API Token

Visit protocols.io/developer
Sign in to your account
Go to API clients section and add a new client
Copy the generated client access token

Running the Server

Command Line 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

Available 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 connect 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"
      }
    }
  }
}

Available Tools

The MCP server provides several tools that Claude can access:

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

Troubleshooting

Common Errors

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

This error means Claude Desktop cannot find the protocols-io-mcp command. To fix it:

Make sure you've installed the package globally with pip
Find the full path to the executable:
```
which protocols-io-mcp
```

Update your Claude Desktop configuration with the full path:

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

How to install this MCP server

For Claude Code

To add this MCP server to Claude Code, run this command in your terminal:

claude mcp add-json "protocols-io" '{"command":"protocols-io-mcp","env":{"PROTOCOLS_IO_CLIENT_ACCESS_TOKEN":"your_client_access_token"}}'

See the official Claude Code MCP documentation for more details.

For Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > Tools & Integrations and click "New MCP Server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

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

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explicitly ask the agent to use the tool by mentioning the tool name and describing what the function does.

For Claude Desktop

To add this MCP server to Claude Desktop:

1. Find your configuration file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: %APPDATA%\Claude\claude_desktop_config.json
Linux: ~/.config/Claude/claude_desktop_config.json

2. Add this to your configuration file:

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

3. Restart Claude Desktop for the changes to take effect