MCP Integration

BIOS is available as an MCP (Model Context Protocol) server. Connect it directly to AI coding assistants like Cursor, Claude Desktop, Windsurf, or any MCP-compatible client — and run scientific deep research from your editor.

Prerequisites

You'll need a BIOS API key. If you don't have one yet:

1. Go to Account Settings → API Keys
2. Click Create API Key
3. Copy the key — it starts with bio_sk_

See the BIOS API docs for detailed instructions.

Claude Desktop (Recommended)

In Claude Desktop, connect BIOS from the UI:

1. Open Settings
2. Open Connectors
3. Click Add custom connector
4. Enter these values:

5. Click Add

Claude will open a browser page for MCP authorization. Enter your BIOS API key and click Authorize.

After authorization, return to Claude Desktop and start using BIOS tools.

Legacy Claude Desktop Config (claude_desktop_config.json)

For older Claude Desktop setups that still use local config files, use mcp-remote:

{
  "mcpServers": {
    "BIOS": {
      "command": "npx",
      "args": ["-y", "mcp-remote", "https://api.ai.bio.xyz/mcp"]
    }
  }
}

Authentication Model (Current)

BIOS MCP uses OAuth + API-key consent:

1. MCP client connects to https://api.ai.bio.xyz/mcp
2. Client discovers OAuth metadata from BIOS (/.well-known/...)
3. Browser consent page opens (/authorize/consent)
4. You enter BIOS API key once
5. Client uses OAuth tokens for subsequent calls

Other MCP Clients

Cursor IDE

Add BIOS MCP server URL in .cursor/mcp.json:

{
  "mcpServers": {
    "BIOS": {
      "url": "https://api.ai.bio.xyz/mcp"
    }
  }
}

Windsurf

Add BIOS MCP server URL in Windsurf MCP config:

{
  "mcpServers": {
    "BIOS": {
      "serverUrl": "https://api.ai.bio.xyz/mcp"
    }
  }
}

For any MCP-compatible client, use these connection details:

Available Tools

BIOS MCP currently exposes 15 tools:

Workflow

Here's how to use BIOS through MCP in your AI assistant:

1. Start a research session

Ask your AI assistant something like:

"Use BIOS to research what compounds show senolytic activity in human clinical trials"

The assistant will call start_deep_research and receive a conversation ID immediately while research runs in the background.

2. Poll for results

The assistant will call get_conversation to check progress. The status field shows in_progress while research is running and completed when done.

3. Continue or refine

Ask a follow-up question to continue the same session:

"Now focus on dasatinib and quercetin combination therapy and their clinical outcomes"

The assistant will call start_deep_research with the same conversationId and your new message.

4. Run standalone subagent tasks

For standalone work, ask for:

• query_literature / get_literature_job
• run_data_analysis / get_data_analysis_task
• list_literature_tasks / list_analysis_tasks

Research Modes

You can specify a research mode when starting a session:

Troubleshooting

"Tool not found" or no BIOS tools available

• Verify your MCP config file is saved and the JSON is valid
• Restart your AI assistant after editing the config
• Complete the OAuth consent flow in the browser prompt

"Authentication failed"

• Reconnect and complete OAuth consent again
• Make sure your API key is active on the API Keys page
• Confirm https://api.ai.bio.xyz is reachable from your network

Research seems stuck at "in_progress"

• Deep research can take 20 minutes to 8+ hours depending on the mode
• Ask your assistant to poll get_conversation again to check the latest status