CSE 487 Advanced Systems and Synthetic Biology

Summary for the DNA Fountain Project - DNA Digital Data Storage

This repository contains a Python script (see DNA_Fountain_Project_Code.py) for a project centered around DNA Fountain technology, which demonstrates the encoding and processing of digital data into DNA sequences for potential digital storage applications. The script performs the following tasks:

1. Data Encoding:

   • Encodes digital data into DNA sequences using a predefined encoding scheme.

2. Luby Transform Code:

   • Utilizes Luby Transform (LT) codes to encode the data into DNA droplets, providing robustness and error correction capabilities.

3. DNA Sequence Processing:

   • Processes the DNA droplets, handling different block indices and generating binary sequences.

4. Error Handling:

   • Includes error handling to manage unexpected bases and out-of-range indices during the droplet processing.

5. Output Generation:

   • Outputs the encoded DNA sequences and provides a final decoded message.

The script is designed to explore the potential of DNA as a medium for digital data storage, showcasing the feasibility and challenges of encoding and decoding digital information using biological molecules.

Usage

To run the script:

1. Ensure you have Python installed.
2. Navigate to the project directory.
3. Execute the script using Python:

   python DNA_Fountain_Project_1.py

Requirements

• Python 3.x
• Pygments (for syntax highlighting, if converting to HTML)
• Pandoc (for converting HTML to PDF, optional)
• MiKTeX (for pdflatex, optional)

File Structure

• DNA_Fountain_Project_1.py: Main script file containing the DNA Fountain encoding and processing logic.
• DNA_Fountain_Project_1.html: HTML file generated from the script (optional, for conversion to PDF).
• luby_blocks.csv: CSV file containing Luby Transform blocks data.

Conversion to PDF

For convenience, the script can be converted to a PDF file using Pandoc and pdflatex. Follow these steps:

1. Convert Python script to HTML:

   pygmentize -f html -O full,style=colorful -o DNA_Fountain_Project_1.html DNA_Fountain_Project_1.py

2. Convert HTML to PDF:

   pandoc DNA_Fountain_Project_1.html -o DNA_Fountain_Project_1.pdf

Picture representation of project

License

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

Feel free to contribute to this project by opening issues and submitting pull requests, or send me a message at [email protected]