VibeDNA - Where Digital Meets Biological
Author: NeuralQuantum.ai LLC
Description: VibeDNA - Binary-DNA Interconversion System. Where Digital Meets Biological. Transform your data into DNA sequences with lossless encoding, error correction, and computation capabilities.
Keywords: DNA encoding, binary to DNA, data storage, DNA computing, VibeDNA, digital DNA

### Live Encoding Demo

Input Text Hello, DNA World!
DNA Sequence
Click "Convert to DNA" to see the result
Encoding Scheme: Quaternary (2-bit)
Compression: -
Capabilities

## Powerful Features for DNA Computing

A comprehensive toolkit for binary-to-DNA conversion, storage, and computation

### Multi-Scheme Encoding

Four optimized encoding schemes for different use cases: Quaternary for density, Balanced GC for synthesis, RLL for sequencing, and Triplet for error tolerance.

Quaternary Balanced GC RLL Triplet

### Reed-Solomon Error Correction

Robust error correction adapted for GF(4) arithmetic. Automatically detects and corrects up to 8 nucleotide errors per block, ensuring data integrity.

Reed-Solomon Hamming CRC32

### DNA Computation Engine

Perform computations directly on DNA-encoded data with logic gates (AND, OR, XOR, NOT) and arithmetic operations (add, subtract, multiply, divide).

Logic Gates Arithmetic Expressions

### DNAFS Virtual File System

Store and manage files as DNA sequences with full CRUD operations, hierarchical directories, metadata handling, and powerful search capabilities.

CRUD Search Metadata

### CLI & REST API

Feature-rich command-line interface with rich output formatting, plus a RESTful API with OpenAPI documentation for seamless integration.

CLI REST WebSocket

### Container Format

Versioned file format with headers, data blocks, ECC parity, and footers. Deterministic encoding ensures reproducible results every time.

Versioned Deterministic Checksums
Process

## How VibeDNA Works

A simple yet powerful encoding pipeline

01

### Binary Input

Any file or data is converted to a binary stream of 0s and 1s

`01001000 01100101 01101100 01101100 01101111`
02

### Codec Encoding

Bits are mapped to nucleotides using the selected encoding scheme

`00` → A `01` → T `10` → C `11` → G
03

### Container Wrapping

Data is packaged with headers, checksums, and error correction codes

Header Data Blocks ECC Footer
04

### DNA Sequence

Final output: a complete, verifiable DNA sequence ready for use

ATCGATCGTAGCTAGC
Encoding Schemes

## Choose Your Codec

Four encoding schemes optimized for different requirements

Q

### Quaternary

Highest Density

Standard 2-bit per nucleotide encoding. Maximum information density for general-purpose use.

Bits/Nucleotide 2.0
GC Balanced No
Homopolymer Safe No
`00→A 01→T 10→C 11→G`
B

### Balanced GC

Synthesis Ready

Rotating mapping maintains 40-60% GC content. Ideal for compatibility with synthesis requirements.

Bits/Nucleotide 2.0
GC Balanced Yes
Homopolymer Safe No
`Rotating schedule every N bases`
R

### Run-Length Limited

Sequencing Optimized

Prevents homopolymer runs for improved sequencing accuracy. Uses deterministic escaping scheme.

Bits/Nucleotide ~1.8
GC Balanced No
Homopolymer Safe Yes
`Max run length configurable`
T

### Redundant Triplet

Error Tolerant

3x redundancy for maximum error tolerance. Decode by majority voting for robust recovery.

Bits/Nucleotide 0.33
GC Balanced No
Error Tolerance High
`0→ATC 1→GAC`
System Design

## Modular Architecture

A layered design for flexibility and extensibility

Interfaces
CLI
REST API
WebSocket
Python SDK
Core Layer
Encoder
Decoder
Codec Registry
Bit Stream
Storage Layer
DNAFS
Index Catalog
Metadata
Compute Layer
Logic Gates
Arithmetic
Expressions
Error Correction
Reed-Solomon
Hamming
Checksums
Mutation Detector
Integration

## Simple Integration

Multiple interfaces for every use case

bash

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

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

    # Quick text encoding (no container headers)
    vibedna quick "Hello, DNA World!"
    # Output: TACGTACGTACGATCG...

    # Perform DNA computation
    vibedna compute gate XOR ATCGATCG GCTAGCTA
    # Output: GGGCGGGC

    # DNA File System operations
    vibedna fs cp ./report.docx /documents/report.docx
    vibedna fs ls /documents/
    vibedna fs export /documents/report.docx ./output/

python

    from vibedna import DNAEncoder, DNADecoder, DNAFileSystem
    from vibedna.core.encoder import EncodingConfig, EncodingScheme

    # Initialize encoder with configuration
    config = EncodingConfig(scheme=EncodingScheme.QUATERNARY)
    encoder = DNAEncoder(config)

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

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

    # DNA File System usage
    fs = DNAFileSystem()
    fs.create_file("/docs/report.txt", b"Report content")
    data = fs.read_file("/docs/report.txt")

    # DNA Computation
    from vibedna.compute import DNALogicGates
    gates = DNALogicGates()
    result = gates.xor("ATCG", "GCTA")
    print(f"XOR Result: {result}")

bash

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

    # Encode data (base64 input)
    curl -X POST "http://localhost:8000/encode" \
      -H "Content-Type: application/json" \
      -d '{
        "data": "SGVsbG8gV29ybGQh",
        "filename": "hello.txt",
        "scheme": "quaternary"
      }'

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

    # Decode DNA sequence
    curl -X POST "http://localhost:8000/decode" \
      -H "Content-Type: application/json" \
      -d '{"sequence": "ATCGATCG..."}'

    # Perform DNA computation
    curl -X POST "http://localhost:8000/compute" \
      -H "Content-Type: application/json" \
      -d '{
        "operation": "XOR",
        "sequence_a": "ATCGATCG",
        "sequence_b": "GCTAGCTA"
      }'

bash

    # Pull the VibeDNA image
    docker pull vibedna/vibedna:latest

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

    # Run CLI commands via Docker
    docker run vibedna/vibedna vibedna encode /data/file.pdf

    # Build from source
    docker build -t vibedna .

    # Run with volume mount for file access
    docker run -v $(pwd)/data:/data \
      -p 8000:8000 \
      vibedna/vibedna

    # Docker Compose for full stack
    docker-compose up -d

Specification

## VibeDNA File Format

A robust container format with built-in integrity verification

Header 256 nt
Magic8 nt
Ver4 nt
Scheme4 nt
File Size32 nt
Filename128 nt
MIME32 nt
Checksum32 nt
Reserved16 nt
Data Blocks Variable
Block Header16 nt
Block Data1024 nt
RS Parity64 nt
× N blocks

#### Magic Sequence

`ATCGATCG`

Identifies valid VibeDNA files

#### End Marker

`GCTAGCTA`

Marks the end of data stream

#### Checksum

`SHA-256`

Ensures complete data integrity

## Ready to Transform Your Data?

Get started with VibeDNA today and explore the intersection of digital and biological computing.

View on GitHub
Download v1.0
`pip install vibedna`