AI-MCP-Bio

AI-MCP-Bio Platform

A fullstack application with frontend and backend running in separate Docker containers. The platform bridges artificial intelligence with specialized bioinformatics tools through a secure Model Context Protocol framework.

Features

• Modern Frontend: React-inspired landing page with authentication modals
• Secure Backend: Node.js/Express API with JWT authentication and SQLite database
• Docker Containerized: Separate containers for frontend and backend
• User Authentication: Email-based registration and login system
• Responsive Design: Mobile-first design with modern UI/UX
• Production Ready: Optimized for VPS deployment

Quick Start

Prerequisites

• Docker and Docker Compose installed
• Ports 8000 and 8001 available

Development Setup

1. Clone the repository

   git clone <repository-url>
   cd AI-MCP-Bio
   

2. Set up environment variables

   cp env.example .env
   # Edit .env with your secure JWT secret
   

3. Build and run the containers

   docker-compose up --build
   

4. Access the application

   • Frontend: http://localhost:8000
   • Backend API: http://localhost:8001

Production Deployment

For production deployment on a VPS:

1. Set up environment variables

   # Generate a secure JWT secret
   openssl rand -base64 32
   # Add this to your .env file
   

2. Build and deploy

   docker-compose -f docker-compose.yml up -d --build
   

3. Configure reverse proxy (optional)
   Set up nginx or another reverse proxy to handle SSL and domain routing.

Architecture

Frontend (Port 8000)

• Technology: Vanilla HTML/CSS/JavaScript
• Container: Nginx Alpine
• Features:
  • Responsive design
  • Authentication modals
  • JWT token management
  • Modern UI with animations

Backend (Port 8001)

• Technology: Node.js/Express
• Database: SQLite
• Container: Node.js Alpine
• Features:
  • JWT authentication
  • Password hashing (bcrypt)
  • Rate limiting
  • Input validation
  • Security headers

API Endpoints

Authentication

• POST /api/auth/register - User registration
• POST /api/auth/login - User login
• GET /api/auth/profile - Get user profile (protected)
• POST /api/auth/logout - User logout

System

• GET /health - Health check
• GET /api/protected - Protected route example

Environment Variables

Variable	Description	Default
JWT_SECRET	Secret key for JWT tokens	your-super-secret-jwt-key-change-this-in-production
NODE_ENV	Node environment	production
PORT	Backend server port	3001
DB_PATH	SQLite database path	/app/data/database.sqlite
CORS_ORIGIN	Allowed CORS origin	http://localhost:8000

Security Features

• JWT Authentication: Secure token-based authentication
• Password Hashing: bcrypt with salt rounds
• Rate Limiting: Protection against brute force attacks
• Input Validation: Server-side validation with express-validator
• Security Headers: Helmet.js for security headers
• CORS Protection: Configured CORS policy
• SQL Injection Protection: Parameterized queries

Database Schema

Users Table

CREATE TABLE users (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    email TEXT UNIQUE NOT NULL,
    password TEXT NOT NULL,
    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
    last_login DATETIME,
    is_active BOOLEAN DEFAULT 1
);

Development

Adding New Features

1. Backend: Add routes in backend/server.js
2. Frontend: Add functionality in frontend/ files
3. Database: Modify schema in backend/server.js

Testing

# Test backend health
curl http://localhost:8001/health

# Test frontend
curl http://localhost:8000

Troubleshooting

Common Issues

1. Port conflicts: Ensure ports 8000 and 8001 are available
2. Docker issues: Try docker-compose down and rebuild
3. Authentication issues: Check JWT_SECRET is set correctly
4. Database issues: Check volume permissions and SQLite file access

Logs

# View all logs
docker-compose logs

# View specific service logs
docker-compose logs backend
docker-compose logs frontend

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Test thoroughly
5. Submit a pull request

License

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

Support

For issues and questions, please create an issue in the repository or contact the development team.