RatBat 2

A research data platform for OCD behavioral studies in rats

Team Members: Aidan Goodyer, Jeremy Orr, Leo Vugert, Nathan Perry, Timothy Pokanai
Project Start: September 13th, 2025

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Introduction

RatBat 2 is a comprehensive research data platform designed to support behavioral studies of rats with a focus on obsessive-compulsive disorder (OCD) research. The system enables researchers to explore, query, analyze, and visualize behavioral trial datasets in a flexible, secure, and reproducible environment.

Key Goals

Built as a capstone project in collaboration with Dr. Henry Szechtman and Dr. Anna Dvorkin-Gheva, this platform serves as a unified solution for:

• Easy data ingestion from multiple sources
• Metadata normalization and schema standardization
• Advanced querying and filtering capabilities
• Data visualization and analysis tools
• Secure access and reproducible workflows

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Project Structure

OCD-Rat-Infrastructure/
├── docs/              # Documentation and guides
├── refs/              # Reference materials and papers
├── src/
│   ├── ocd-rat-backend/    # FastAPI backend
│   └── ocd-rat-frontend/   # React frontend
├── test/              # Test cases
└── README.md          # This file

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Getting Started

Choose your setup method:

• Quick Start with Docker (Recommended) - No local installs required
• Manual Setup (Legacy) - For development without Docker

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Quick Start with Docker

The fastest way to get RatBat 2 running. This method requires only Docker and works on any platform.

Prerequisites

• Docker Desktop (includes Docker Compose)
  • Download for Mac
  • Download for Windows
  • Download for Linux

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Setup Steps

1. Clone the repository

   git clone https://github.com/OCD-Rats-Capstone/OCD-Rat-Infrastructure.git
   cd OCD-Rat-Infrastructure

2. Create environment file (optional)

   # Copy the example .env file
   cp .env.example .env
   
   # Or
   # just create a file called .env, this will contain keys, etc.
   
   
   # Edit if needed (defaults work fine)
   # Default password is "Gouda"

3. Start the application

   docker-compose up -d --build

4. Access the application

   • Frontend: http://localhost:80
   • Backend API: http://localhost:8000
   • API Docs: http://localhost:8000/docs
   • Database: localhost:5433 (if you need direct access)

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Common Commands

# View logs
docker-compose logs -f

# View logs for specific service
docker-compose logs -f backend

# Stop all services
docker-compose down

# Stop and remove all data (fresh start)
docker-compose down -v

# Rebuild after code changes
docker-compose build
docker-compose up -d

# Restart a specific service
docker-compose restart backend
docker-compose restart frontend

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What's Running?

Service	Container	Port	Purpose
Frontend	frontend	80	React UI
Backend	backend	8000	FastAPI server
Database	db	5433	PostgreSQL with data

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Sample .ENV File:

DB_HOST=localhost
DB_USER=postgres
DB_PASSWORD=Gouda
DB_NAME=postgres
DB_PORT=5432

# LLM Configuration (for cloud providers like OpenRouter)
OPENAI_API_KEY=your-api-key-here
LLM_BASE_URL=https://openrouter.ai/api/v1
LLM_MODEL=your-model-name

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Troubleshooting

Port conflicts: If ports 80, 8000, or 5433 are already in use, edit docker-compose.yml to change the port mappings.

Database not initializing: If the database seems empty, check the initialization logs:

docker-compose logs db

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Testing

Running Backend Tests

cd src/ocd-rat-backend
python3 -m pytest tests/ -v --tb=short

License

This project is licensed under the MIT License