docs/getting-started/mcp-integration.md

MCP Integration

The DETERMINATOR exposes a Model Context Protocol (MCP) server, allowing you to use its search tools directly from Claude Desktop or other MCP clients.

What is MCP?

The Model Context Protocol (MCP) is a standard for connecting AI assistants to external tools and data sources. The DETERMINATOR implements an MCP server that exposes its search capabilities as MCP tools.

MCP Server URL

When running locally:

http://localhost:7860/gradio_api/mcp/

Claude Desktop Configuration

1. Locate 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 The DETERMINATOR Server

Edit claude_desktop_config.json and add:

{
  "mcpServers": {
    "determinator": {
      "url": "http://localhost:7860/gradio_api/mcp/"
    }
  }
}

3. Restart Claude Desktop

Close and restart Claude Desktop for changes to take effect.

4. Verify Connection

In Claude Desktop, you should see The DETERMINATOR tools available:

• search_pubmed
• search_clinical_trials
• search_biorxiv
• search_all
• analyze_hypothesis

Available Tools

search_pubmed

Search peer-reviewed biomedical literature from PubMed.

Parameters:

• query (string): Search query
• max_results (integer, optional): Maximum number of results (default: 10)

Example:

Search PubMed for "metformin diabetes"

search_clinical_trials

Search ClinicalTrials.gov for interventional studies.

Parameters:

• query (string): Search query
• max_results (integer, optional): Maximum number of results (default: 10)

Example:

Search clinical trials for "Alzheimer's disease treatment"

search_biorxiv

Search bioRxiv/medRxiv preprints via Europe PMC.

Parameters:

• query (string): Search query
• max_results (integer, optional): Maximum number of results (default: 10)

Example:

Search bioRxiv for "CRISPR gene editing"

search_all

Search all sources simultaneously (PubMed, ClinicalTrials.gov, Europe PMC).

Parameters:

• query (string): Search query
• max_results (integer, optional): Maximum number of results per source (default: 10)

Example:

Search all sources for "COVID-19 vaccine efficacy"

analyze_hypothesis

Perform secure statistical analysis using Modal sandboxes.

Parameters:

• hypothesis (string): Hypothesis to analyze
• data (string, optional): Data description or code

Example:

Analyze the hypothesis that metformin reduces cancer risk

Using Tools in Claude Desktop

Once configured, you can ask Claude to use DeepCritical tools:

Use DeepCritical to search PubMed for recent papers on Alzheimer's disease treatments.

Claude will automatically:

1. Call the appropriate DeepCritical tool
2. Retrieve results
3. Use the results in its response

Troubleshooting

Connection Issues

Server Not Found:

• Ensure DeepCritical is running (uv run gradio run src/app.py)
• Verify the URL in claude_desktop_config.json is correct
• Check that port 7860 is not blocked by firewall

Tools Not Appearing:

• Restart Claude Desktop after configuration changes
• Check Claude Desktop logs for errors
• Verify MCP server is accessible at the configured URL

Authentication

If DeepCritical requires authentication:

• Configure API keys in DeepCritical settings
• Use HuggingFace OAuth login
• Ensure API keys are valid

Advanced Configuration

Custom Port

If running on a different port, update the URL:

{
  "mcpServers": {
    "deepcritical": {
      "url": "http://localhost:8080/gradio_api/mcp/"
    }
  }
}

Multiple Instances

You can configure multiple DeepCritical instances:

{
  "mcpServers": {
    "deepcritical-local": {
      "url": "http://localhost:7860/gradio_api/mcp/"
    },
    "deepcritical-remote": {
      "url": "https://your-server.com/gradio_api/mcp/"
    }
  }
}

Next Steps

• Learn about Configuration for advanced settings
• Explore Examples for use cases
• Read the Architecture Documentation