vibedna 1.0.0

Binary ↔ DNA Encoding and Computation System - Convert data to DNA sequences and back

VibeDNA

Where Digital Meets Biological

VibeDNA is a comprehensive binary-to-DNA and DNA-to-binary encoding system that enables computation and file management using DNA sequences as the storage and processing medium.

Features

• Multi-Scheme Encoding: Support for 4 encoding schemes optimized for different use cases

  • Quaternary: Standard 2-bit per nucleotide (highest density)
  • Balanced GC: Maintains 40-60% GC content for synthesis compatibility
  • Run-Length Limited (RLL): Prevents homopolymer runs for sequencing accuracy
  • Redundant Triplet: 3x redundancy for maximum error tolerance

• Error Correction: Reed-Solomon error correction adapted for GF(4) arithmetic

  • Corrects up to 8 nucleotide errors per block
  • Automatic error detection and correction
  • Configurable redundancy levels

• DNA Computation: Perform computations directly on DNA-encoded data

  • Logic gates: AND, OR, XOR, NOT, NAND, NOR, XNOR
  • Arithmetic: Addition, subtraction, multiplication, division
  • Comparison and bitwise shift operations

• DNA File System: Virtual file system with DNA sequence storage

  • Full CRUD operations
  • Hierarchical directory structure
  • Search and indexing capabilities

• CLI & REST API: Multiple interfaces for integration

  • Feature-rich command-line interface
  • RESTful API with OpenAPI documentation

Installation

From PyPI (Recommended)

# Install from PyPI
pip install vibedna

# Verify installation
vibedna --version

From Source

# Clone the repository
git clone https://github.com/ttracx/VibeDNA.git
cd VibeDNA

# Install with pip
pip install .

# Or install in development mode
pip install -e .

# Or install with development dependencies
pip install -e ".[dev]"

Requirements

• Python 3.10 or higher
• pip 21.0 or higher (for PEP 517 support)

Quick Start

Command Line

# Encode a file to DNA
vibedna encode document.pdf -o document.dna

# Decode back to original
vibedna decode document.dna -o recovered.pdf

# Quick text encoding (no headers)
vibedna quick "Hello, DNA World!"

# Perform DNA computation
vibedna compute gate XOR ATCG GCTA

# Store file in DNA file system
vibedna fs cp ./report.docx /documents/report.docx

Python SDK

from vibedna import DNAEncoder, DNADecoder, DNAFileSystem

# Encode data
encoder = DNAEncoder()
dna_sequence = encoder.encode(b"Hello World", filename="hello.txt")
print(f"Encoded: {dna_sequence[:50]}...")

# Decode back
decoder = DNADecoder()
result = decoder.decode(dna_sequence)
print(f"Decoded: {result.data}")
print(f"Filename: {result.filename}")

# File system operations
fs = DNAFileSystem()
fs.create_file("/hello.txt", b"Hello DNA!")
data = fs.read_file("/hello.txt")
print(f"Read from DNA FS: {data}")

REST API

# Start the API server
uvicorn vibedna.api.rest_server:app --host 0.0.0.0 --port 8000

# Encode data
curl -X POST "http://localhost:8000/encode" \
  -H "Content-Type: application/json" \
  -d '{"data": "SGVsbG8gV29ybGQh", "filename": "hello.txt"}'

# Quick encode text
curl -X POST "http://localhost:8000/quick/encode" \
  -H "Content-Type: application/json" \
  -d '{"text": "Hello World"}'

Encoding Specification

Primary Mapping (Quaternary)

Binary	DNA
00	A (Adenine)
01	T (Thymine)
10	C (Cytosine)
11	G (Guanine)

DNA Sequence Structure

┌─────────────────────────────────────────────────────────────────┐
│                        DNA FILE FORMAT                          │
├─────────────────────────────────────────────────────────────────┤
│ HEADER (256 nucleotides)                                        │
│ ├── Magic: ATCGATCG (8 nt)                                      │
│ ├── Version: 4 nt                                               │
│ ├── Scheme: 4 nt                                                │
│ ├── File Size: 32 nt                                            │
│ ├── Filename: 128 nt                                            │
│ ├── MIME Type: 32 nt                                            │
│ ├── Checksum: 32 nt                                             │
│ └── Reserved: 16 nt                                             │
├─────────────────────────────────────────────────────────────────┤
│ DATA BLOCKS (Variable)                                          │
│ ├── Block Header: 16 nt per block                               │
│ └── Block Data: 1024 nt per block                               │
├─────────────────────────────────────────────────────────────────┤
│ ERROR CORRECTION                                                │
│ └── Reed-Solomon Parity: 64 nt per block                        │
├─────────────────────────────────────────────────────────────────┤
│ FOOTER (32 nucleotides)                                         │
│ ├── End Marker: GCTAGCTA (8 nt)                                 │
│ ├── Block Count: 8 nt                                           │
│ └── Checksum: 16 nt                                             │
└─────────────────────────────────────────────────────────────────┘

Project Structure

vibedna/
├── core/               # Encoding/decoding engines
├── storage/            # DNA file system
├── error_correction/   # Reed-Solomon, Hamming codes
├── compute/            # DNA logic gates and arithmetic
├── cli/                # Command-line interface
├── api/                # REST API
├── utils/              # Utilities and constants
└── tests/              # Test suite

API Documentation

Full API documentation is available at /docs when running the API server.

Key endpoints:

• POST /encode - Encode data to DNA
• POST /decode - Decode DNA to data
• POST /compute - Perform DNA computations
• GET /fs/list - List files in DNA storage
• POST /fs/store - Store file in DNA storage

Docker

# Build the image
docker build -t vibedna .

# Run the API server
docker run -p 8000:8000 vibedna

Testing

# Run all tests
pytest

# Run with coverage
pytest --cov=vibedna

# Run specific test file
pytest tests/unit/test_encoder.py

Encoding Scheme Comparison

Scheme	Bits/nt	GC Balanced	Homopolymer Safe	Error Tolerance
Quaternary	2.0	No	No	None
Balanced GC	2.0	Yes	No	None
RLL	~1.8	No	Yes	None
Triplet	0.33	No	No	High

Performance

• Encoding: ~200 KB/s (quaternary scheme)
• Decoding: ~250 KB/s
• Error correction: Up to 8 errors per 1024 nucleotides

Contributing

This is proprietary software. Please contact NeuralQuantum.ai for licensing information.

License

Proprietary - All Rights Reserved

Support

For support and inquiries:

• Website: https://vibecaas.com
• Email: [e-mail]

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