docs/index.md

DeepCritical Documentation

Medical Drug Repurposing Research Agent

AI-powered deep research system for accelerating drug repurposing discovery.

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Quick Links

Architecture

• Overview - Project overview, use case, architecture
• Design Patterns - Technical patterns, data models

Implementation

• Roadmap - Phased execution plan with TDD
• Phase 1: Foundation ✅ - Tooling, config, first tests
• Phase 2: Search ✅ - PubMed search
• Phase 3: Judge ✅ - LLM evidence assessment
• Phase 4: UI ✅ - Orchestrator + Gradio
• Phase 5: Magentic ✅ - Multi-agent orchestration
• Phase 6: Embeddings ✅ - Semantic search + dedup
• Phase 7: Hypothesis ✅ - Mechanistic reasoning
• Phase 8: Report ✅ - Structured scientific reports
• Phase 9: Source Cleanup ✅ - Remove DuckDuckGo
• Phase 10: ClinicalTrials ✅ - Clinical trials API
• Phase 11: bioRxiv ✅ - Preprint search
• Phase 12: MCP Server ✅ - Claude Desktop integration
• Phase 13: Modal Integration ✅ - Secure code execution
• Phase 14: Demo Submission ✅ - Hackathon submission

Guides

• Deployment Guide - Gradio, MCP, and Modal launch steps

Development

• Testing Strategy - Unit, Integration, and E2E testing patterns

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What We're Building

One-liner: AI agent that searches medical literature to find existing drugs that might treat new diseases.

Example Query:

"What existing drugs might help treat long COVID fatigue?"

Output: Research report with drug candidates, mechanisms, evidence quality, and citations.

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Architecture Summary

User Question → Research Agent (Orchestrator)
                      ↓
              Search Loop:
                → Tools (PubMed, ClinicalTrials, bioRxiv)
                → Judge (Quality + Budget)
                → Repeat or Synthesize
                      ↓
              Research Report with Citations

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Features

Feature	Status	Description
Gradio UI	✅ Complete	Streaming chat interface
MCP Server	✅ Complete	Tools accessible from Claude Desktop
Modal Sandbox	✅ Complete	Secure statistical analysis
Multi-Source Search	✅ Complete	PubMed, ClinicalTrials, bioRxiv

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Team

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

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Status

Phase	Status
Phases 1-14	✅ COMPLETE

Test Coverage: 65% (96 tests passing) Architecture Review: PASSED (98-99/100)