README.md

metadata

title: DeepCritical
emoji: 🧬
colorFrom: blue
colorTo: purple
sdk: gradio
sdk_version: 5.0.0
python_version: '3.11'
app_file: src/app.py
pinned: false
license: mit
tags:
  - mcp-in-action-track-enterprise
  - mcp-hackathon
  - drug-repurposing
  - biomedical-ai
  - pydantic-ai
  - llamaindex
  - modal

DeepCritical

AI-Powered Drug Repurposing Research Agent

Features

• Multi-Source Search: PubMed, ClinicalTrials.gov, bioRxiv/medRxiv
• MCP Integration: Use our tools from Claude Desktop or any MCP client
• Modal Sandbox: Secure execution of AI-generated statistical code
• LlamaIndex RAG: Semantic search and evidence synthesis

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.
• analyze_hypothesis: Secure statistical analysis using Modal sandboxes.

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.
• Modal: For secure code execution.

Team

• The-Obstacle-Is-The-Way
• MarioAderman
• Josephrp

Links

• GitHub Repository