BioReactLab

BioReactLab is a comprehensive web application for managing and analyzing metabolic reactions in biological systems. The platform provides researchers and scientists with tools for chemical formula manipulation, metabolic pathway analysis, and reaction balancing.

Overview

The application combines a React-based frontend with a Django backend to provide:

• Chemical formula management with auto-completion and validation
• Metabolic reaction analysis and balancing
• Interactive molecular structure visualization
• Real-time formula validation and preview

The application is deployed on Netlify and can be accessed at: https://shimmering-alfajores-f7f968.netlify.app/

Prerequisites

• Python 3.11+
• Node.js 18.x+
• Conda (recommended for RDKit installation)

Installation

Backend Setup

# Create and activate conda environment
conda create -n bioreactlab python=3.11
conda activate bioreactlab

# Install RDKit
conda install -c conda-forge rdkit

# Install Python dependencies
cd backend
pip install -r requirements.txt

# Run migrations
python manage.py migrate

# Start the server
python manage.py runserver

Frontend Setup

cd frontend
npm install
npm run dev

Project Structure

bioreactlab/
├── frontend/ # React frontend application
│ ├── src/
│ │ ├── components/ # Reusable UI components
│ │ ├── pages/ # Page components
│ │ ├── services/ # API services
│ │ └── styles/ # Global styles
│ └── public/ # Static assets
├── backend/ # Django backend application
│ ├── api/ # REST API endpoints
│ ├── metabolic/ # Metabolic processing logic
│ └── reactions/ # Reaction management
└── docs/ # Documentation

Technology Stack

Frontend

• React 18
• TypeScript
• Material-UI
• Vite
• OpenChemLib

Backend

• Django 4.2
• Django REST Framework
• RDKit
• SQLite/PostgreSQL

Development

Running Tests

Backend Tests:

cd backend
python manage.py test

Frontend Tests:

cd frontend
npm run test

Local Development

1. Start the backend server:

cd backend
python manage.py runserver

2. Start the frontend development server:

cd frontend
npm run dev

Deployment

The application uses GitHub Actions for CI/CD:

• Frontend is deployed to Netlify
• Backend is deployed to Railway

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contributing

1. Fork the repository
2. Create your feature branch (git checkout -b feature/AmazingFeature)
3. Commit your changes (git commit -m 'Add some AmazingFeature')
4. Push to the branch (git push origin feature/AmazingFeature)
5. Open a Pull Request