This server enables MCP clients like Claude Desktop to interact with protocols.io for searching, retrieving, creating, and managing scientific protocols.
Search & Discovery
Search public protocols by keyword with paginated results (3 per page)
Retrieve all protocols from your account
Get protocol information by ID (title, description, URL, dates, DOI, publication status)
View detailed protocol steps including materials, quantities, and reference protocols
Protocol Creation & Editing
Create new protocols with title and description (requires searching at least 2 reference protocols first for credibility)
Update protocol titles and descriptions
Step Management
Replace all steps in a protocol at once
Add individual steps to the end of protocols with descriptions, materials (name, quantity, unit), and references to other protocol IDs
Delete specific steps by step ID
Key Features
Material tracking with quantities and units (mL, g, μL, etc.)
Protocol referencing system for credibility
Date filtering recommendations (avoids pre-2015 protocols)
Multiple authentication methods: client access tokens (STDIO) and OAuth 2.0 (HTTP/SSE)
Multiple transport options: STDIO, HTTP, and SSE for different deployment scenarios
Error handling with descriptive messages
Enables searching, retrieving, creating, and managing scientific protocols and their steps on the protocols.io platform, including protocol metadata management and step-by-step procedure handling.
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@protocols-io-mcp-serversearch for CRISPR protocols"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
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 keywordget_protocol- Get basic protocol information by IDget_protocol_steps- Get detailed steps for a specific protocolget_my_protocols- Retrieve all protocols from your account
Protocol Creation and Management
create_protocol- Create a new protocol with title and descriptionupdate_protocol_title- Update the title of an existing protocolupdate_protocol_description- Update the description of an existing protocol
Step Management
set_protocol_steps- Replace all steps in a protocoladd_protocol_step- Add a single step to the end of a protocoldelete_protocol_step- Delete a specific step from a protocol
Related MCP server: Calculator MCP Server
Requirements
Python 3.10 or higher
protocols.io account with API credentials
MCP client (such as Claude Desktop)
Obtain Protocols.io API Credentials
Visit protocols.io/developers
Sign in to your account
Navigate to the API Clients section
Click ADD CLIENT to create a new application
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/callbackCopy the Client ID and Client Secret
Installation
Quick Start with Docker
The server will be accessible at http://0.0.0.0:8000/mcp with HTTP transport
Install via pip
Set Environment Variables
STDIO Transport
HTTP/SSE Transport
Usage
Command Line Interface
Run the MCP server with various transport options:
CLI Options
Integration with Claude Desktop
To use this server with Claude Desktop, add the following configuration to your claude_desktop_config.json:
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:
Make sure you have installed the
protocols-io-mcppackage globally using pip.Change the
commandfield in yourclaude_desktop_config.jsonto the full path of theprotocols-io-mcpexecutable. You can find the path by running:which protocols-io-mcpYour 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:
License
This project is licensed under the MIT License. See the LICENSE file for details.