Recombyne is an advanced web-based plasmid design application that combines the power of AI with intuitive DNA sequence visualization. It serves as a conversational interface for molecular biologists and genetic engineers to design custom plasmids through natural language interactions.

• Conversational Interface: Interact with the AI copilot using natural language to design and modify plasmids
• Real-time Sequence Visualization: Utilizes @teselagen/ove for interactive DNA sequence viewing and editing
• Smart Backbone Selection: Browse and insert pre-built plasmid backbones with category-based organization
• GenBank Integration: Search and import sequences directly from NCBI GenBank
• Context-Aware AI: Maintains conversation history for consistent and accurate assistance
• Modern UI: Clean, responsive design with intuitive split-pane layout

Recombyne acts as a "cursor" for plasmid design by:

1. Understanding user intent through natural language processing
2. Providing context-aware suggestions and modifications
3. Visualizing changes in real-time with interactive sequence views
4. Maintaining conversation history for consistent guidance
5. Integrating with external databases for comprehensive sequence information

This project leverages several powerful open-source tools:

• @teselagen/ove: For advanced DNA sequence visualization and editing capabilities
• DNAChisel: For sequence optimization and design functionality

We are grateful to the maintainers and contributors of these projects for making this application possible.

• Node.js (v18 or higher)
• npm or yarn package manager
• OpenAI API key (for AI functionality)
• NCBI API key (for GenBank integration)

1. Clone the repository:

git clone https://github.com/yourusername/recombyne.git
cd recombyne-18

2. Install dependencies:

npm install
# or
yarn install

3. Set up environment variables: Copy the .env.example file to .env in the root directory and update the values:

cp .env.example .env

4. Build the application:

• To build only the frontend:

  npm run build:frontend

• To build only the backend:

  npm run build:backend

5. Start the servers:

• To start the backend server:

  npm run start:backend

• To start the frontend (development mode):

  npm start
  # or
  yarn start

The application will be available at:

• Frontend: http://localhost:3000 (or the next available port, e.g., 3010)
• Backend API: http://localhost:3001 (or as set in your .env)

Note: If ports 3000/3001 are in use, Vite and the backend will select the next available port and display it in the terminal.

The application requires several environment variables to function properly. Here's what each variable is used for:

• Server Configuration

  • SERVER_PORT: Port for the Express server (default: 3001)
  • PYTHONPATH: Path to Python executable for DNA optimization (default: /usr/local/bin/python3)

• OpenAI Configuration

  • REACT_APP_OPENAI_API_KEY: Your OpenAI API key for AI features
    • Get your key from: https://platform.openai.com/api-keys

• NCBI Configuration

  • REACT_APP_NCBI_EMAIL: Your email for NCBI API requests
  • REACT_APP_NCBI_TOOL_NAME: Name of your tool for NCBI API (default: recombyne-plasmid-editor)
  • REACT_APP_NCBI_API_KEY: Your NCBI API key for enhanced access
    • Get your key from: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

• Development Configuration

  • REACT_APP_USE_MOCK_API: Set to false for production

The application uses a dual-server setup:

• Frontend: Vite development server (default port 3000, but will increment if busy)
• Backend: Express server (default port 3001, configurable via .env)

You can start each server independently using the scripts above. This modular approach allows you to work on frontend or backend in isolation, or both together.

1. If you encounter dependency conflicts during installation, you can try:

npm install --legacy-peer-deps

2. If the application fails to start, check:

   • All required environment variables are set correctly
   • Ports 3000 and 3001 (or your specified ports) are not in use
   • You have the correct Node.js version installed

3. If the backend server fails to start or DNA optimization fails:

   • Ensure Python 3 and all required Python dependencies (see src/server/python/requirements.txt) are installed:

     pip install -r src/server/python/requirements.txt

   • Check for errors in the backend server terminal for Python or API issues.

4. For NCBI API issues:

   • Ensure your NCBI API key is valid
   • Check your email is correctly set
   • Verify your tool name is properly configured

5. For OpenAI API issues:

   • Verify your API key is valid and has sufficient credits
   • Check your network connection to OpenAI's servers

To stop the application, press Ctrl+C in the terminal. This will gracefully shut down both the frontend and backend servers.