README.md

metadata

title: DeepCritical
emoji: 🧬
colorFrom: blue
colorTo: purple
sdk: gradio
sdk_version: 5.0.0
app_file: src/app.py
pinned: false
license: mit

DeepCritical

AI-Powered Drug Repurposing Research Agent

Quick Start

1. Environment Setup

# Install uv if you haven't already
pip install uv

# Sync dependencies
uv sync

2. Run the UI

# Start the Gradio app
uv run python src/app.py

Open your browser to http://localhost:7860.

3. Connect via MCP

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

MCP Server URL: http://localhost:7860/gradio_api/mcp/

Claude Desktop Configuration: Add this to your claude_desktop_config.json:

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

Available Tools:

• search_pubmed: Search peer-reviewed biomedical literature.
• search_clinical_trials: Search ClinicalTrials.gov.
• search_biorxiv: Search bioRxiv/medRxiv preprints.
• search_all: Search all sources simultaneously.

Development

Run Tests

uv run pytest

Run Checks

make check

Architecture

DeepCritical uses a Vertical Slice Architecture:

1. Search Slice: Retrieving evidence from PubMed, ClinicalTrials.gov, and bioRxiv.
2. Judge Slice: Evaluating evidence quality using LLMs.
3. Orchestrator Slice: Managing the research loop and UI.

Built with:

• PydanticAI: For robust agent interactions.
• Gradio: For the streaming user interface.
• PubMed, ClinicalTrials.gov, bioRxiv: For biomedical data.
• MCP: For universal tool access.