protocols.io
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.
What is protocols.io?
protocols.io is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to 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.
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.
This server falls under the Search & Data Extraction category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- A Model Context Protocol (MCP) server that enables MCP clien
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx protocols-ioConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use protocols.io
The protocols.io MCP server connects AI assistants to protocols.io, a platform used by researchers worldwide to share and discover scientific laboratory protocols and methods. It allows Claude and other MCP clients to search public protocols, retrieve detailed protocol steps by ID, list protocols in your account, and create or edit protocols directly from a conversation. This makes it a practical tool for life scientists and research teams who want to query, reuse, or draft experimental workflows without leaving their AI assistant.
Prerequisites
- Python 3.9 or later installed
- pip or uv for Python package management
- A protocols.io account (free registration at protocols.io)
- A protocols.io Client Access Token (for STDIO) or Client ID and Secret (for HTTP/SSE transport)
- An MCP-compatible client such as Claude Desktop
Install the package via pip
Install the protocols-io-mcp package from PyPI. This is the official distribution for the server.
pip install protocols-io-mcpGenerate a protocols.io access token
Log in to protocols.io, go to Settings > Developer access, and create a new Client Access Token. Copy the token value — you will need it in the next step.
Test the server from the command line
Run the server directly to verify your token works before adding it to Claude Desktop.
PROTOCOLS_IO_CLIENT_ACCESS_TOKEN=your_token_here protocols-io-mcpAdd the server to Claude Desktop config
Edit your Claude Desktop configuration file and add the protocols-io server with your access token as an environment variable.
{
"mcpServers": {
"protocols-io": {
"command": "protocols-io-mcp",
"env": {
"PROTOCOLS_IO_CLIENT_ACCESS_TOKEN": "your_token_here"
}
}
}
}Restart Claude Desktop and verify
Restart Claude Desktop and ask it to search for a known protocol to confirm the connection is working.
protocols.io Examples
Client configuration
Claude Desktop config for protocols.io using the STDIO transport with a Client Access Token.
{
"mcpServers": {
"protocols-io": {
"command": "protocols-io-mcp",
"env": {
"PROTOCOLS_IO_CLIENT_ACCESS_TOKEN": "your_token_here"
}
}
}
}Prompts to try
Example prompts for searching, retrieving, and creating scientific protocols.
- "Search protocols.io for CRISPR-Cas9 gene editing protocols and summarize the top 3 results"
- "Retrieve the full steps for protocol ID 12345"
- "List all protocols in my protocols.io account"
- "Create a new protocol titled 'Western Blot for HER2 Detection' with a brief description"
- "Find RNA extraction protocols that mention TRIzol reagent"Troubleshooting protocols.io
Authentication error or 401 when the server starts
Verify that PROTOCOLS_IO_CLIENT_ACCESS_TOKEN is set correctly and has not expired. Regenerate the token in your protocols.io account settings if needed. Ensure there are no extra whitespace characters around the token value.
Search returns no results for known protocols
The search tool queries public protocols by keyword. Ensure your search terms match the protocol title or description. For private protocols, make sure your token has the correct scopes — private protocol access requires additional permissions in your protocols.io account.
The 'protocols-io-mcp' command is not found after pip install
Ensure pip's script directory is in your PATH. On macOS/Linux run 'python -m site --user-base' to find the base path and add '/bin' to your PATH. Alternatively use 'python -m protocols_io_mcp' to run the server module directly.
Frequently Asked Questions about protocols.io
What is protocols.io?
protocols.io is a Model Context Protocol (MCP) server that 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. It connects AI assistants to external tools and data sources through a standardized interface.
How do I install protocols.io?
Follow the installation instructions on the protocols.io GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.
Which AI clients work with protocols.io?
protocols.io works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is protocols.io free to use?
Yes, protocols.io is open source and available under the MIT License license. You can use it freely in both personal and commercial projects.
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Quick Config Preview
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