DeepCritical / docs /getting-started /mcp-integration.md
Joseph Pollack
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MCP Integration

DeepCritical 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. DeepCritical 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 DeepCritical Server

Edit claude_desktop_config.json and add:

{
  "mcpServers": {
    "deepcritical": {
      "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 DeepCritical 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