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OpenBio supports Model Context Protocol (MCP), allowing you to connect external tool servers and extend the AI’s capabilities beyond built-in biology tools. Connect documentation search, code repositories, web search, and other services directly to your research workflow.
What is MCP?Model Context Protocol (MCP) is a standard for connecting AI assistants to external tools and data sources. By connecting MCP servers, you can give OpenBio access to additional capabilities like documentation search, GitHub integration, database queries, and more.
Watch a demo of MCP integration with BioRender:

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Overview

MCP servers extend OpenBio’s capabilities by providing:
  • External tool access: Connect to services beyond biology tools
  • Documentation search: Search code libraries, frameworks, and documentation
  • API integrations: Connect to external APIs and services
  • Custom workflows: Build specialized integrations for your needs

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Setting Up MCP Servers

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Accessing MCP Settings

Location: Profile Settings → MCP Servers tab
  1. Click your profile icon in the top right
  2. Select “Settings” or “Profile”
  3. Navigate to the “MCP Servers” tab
  4. View and manage your connected servers

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Adding an MCP Server

1

Open MCP Settings

Navigate to Profile → Settings → MCP Servers
2

Click Add Server

Click the ”+” button
3

Configure Server

Fill in the required information:
  • Name: A friendly name for your server (e.g., “GitHub”, “Documentation”)
  • URL: The MCP server endpoint URL (must use HTTPS)
  • Transport: Choose “http” or “sse” based on server requirements
  • Headers: Add authentication headers if required (e.g., Authorization: Bearer TOKEN)
  • Timeout: Set request timeout (1-300 seconds)
OpenBio only support hosted MCP servers.
4

Save Server

Click “Add Server” to add the server to your list
5

Check connection

If the connection is successful, you will see the the number and list of tools available from the server. If it is not successful, you will see an error message. You can try to reload the tools after clicking the refresh button.

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Authentication Methods

MCP servers support two authentication methods: Headers Authentication:
  • Add API keys or tokens in the Headers field
  • Format: {"Authorization": "Bearer YOUR_TOKEN"}
  • Headers are encrypted and stored securely
OAuth Authentication:
  • Some servers support OAuth flow
  • Click “Connect” to initiate OAuth
  • Complete authorization in the popup window
  • Credentials are stored securely
No Authentication:
  • Some servers do not require authentication
  • Turn the “no headers” switch to enable this
  • Proceed with the connection and the server will be enabled

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Managing MCP Servers

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Enabling and Disabling

  • Enable: Toggle the switch to activate a server
  • Disable: Turn off to temporarily disable without deleting
  • Limit: Up to 3 servers can be enabled simultaneously
It is important to enable the servers that you would be using in your work, as they can pollute the agent’s memory and slow down the response time if not used.
Only 3 MCP servers can be enabled at once. Disable one before enabling another.

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Editing Servers

  1. Click the “Edit” button on any server
  2. Modify configuration settings
  3. Click “Update Server” to save the changes

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Deleting Servers

  1. Click “Delete” on the server
  2. Confirm deletion
  3. Server is removed from your list

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Refreshing Tools

After adding or updating servers:
  1. Click “Refresh MCP Tools” button
  2. This ensures the latest tools are available in the chat conversations

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Using MCP Tools

When MCP servers are enabled openbio will automatically discover the tools available and make use of them in the chat conversations. You can also hint the agent to use the tools by mentioning the tool name in the chat.

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Using in Chat

Simply ask OpenBio to use MCP tools: 
Search the React documentation for useState hook
Create a GitHub issue titled "Bug fix needed"
Search the web for latest CRISPR research
OpenBio will automatically:
  1. Identify relevant MCP tools
  2. Execute the tools with appropriate parameters
  3. Return results in the conversation

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Common MCP Server Examples

You can find MCP servers here: https://github.com/modelcontextprotocol/servers

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Security and Best Practices

Always use HTTPS URLs for MCP servers. HTTP connections are not allowed for security.
API keys and tokens are encrypted before storage. Never share your credentials.
Keep track of which MCP servers are enabled and their purposes.

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Troubleshooting

Solutions:
  • Ensure server is enabled (green toggle)
  • Click “Refresh MCP Tools” button
  • Verify server connection is working
  • Check server supports tool discovery
Solutions:
  • Disable one of the 3 enabled servers
  • Enable the new server
  • Maximum 3 servers can be active simultaneously
Solutions:
  • Check popup blockers are disabled
  • Verify OAuth callback URL is configured
  • Try reconnecting the server
  • Check server OAuth documentation

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Limitations

  • Server limit: Maximum 3 enabled servers at once
  • HTTPS required: All server URLs must use HTTPS
  • Rate limits: Subject to individual server rate limits
  • Timeout limits: Maximum 300 seconds per request

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Next Steps

Chat Guide

Learn how to use MCP tools in conversations

Profile Settings

Manage your account settings

Tools Reference

Explore built-in OpenBio tools
Pro Tip: Start with one MCP server that matches your workflow. Once comfortable, add more servers to extend capabilities. Remember you can enable up to 3 at once!