# VibeDNA Documentation

![VibeDNA Logo](images/VibeDNA.png)

## Binary-to-DNA Computing & Storage Platform

Welcome to the VibeDNA documentation. VibeDNA is a revolutionary platform that bridges the digital and biological worlds by converting traditional computer data into DNA sequences and enabling computation directly on DNA-encoded data.

---

## Quick Navigation

| Document | Description |
|----------|-------------|
| [Executive Briefing](EXECUTIVE_BRIEFING.md) | Comprehensive overview for leadership and stakeholders |
| [Quick Start Guide](guides/QUICKSTART.md) | Get up and running in minutes |
| [API Reference](api/README.md) | Complete API documentation |
| [Architecture](architecture/README.md) | System design and components |
| [Agent System](agents/README.md) | Multi-agent orchestration documentation |

---

## Guides

### Getting Started
- [Quick Start Guide](guides/QUICKSTART.md) - Installation and first steps
- [Deployment Guide](guides/DEPLOYMENT.md) - Production deployment options

### Core Concepts
- [Encoding Schemes](guides/ENCODING_SCHEMES.md) - Understanding DNA encoding methods
- [DNA Computing](guides/DNA_COMPUTING.md) - Logic and arithmetic on DNA
- [Error Correction](guides/ERROR_CORRECTION.md) - Reed-Solomon implementation

---

## What is VibeDNA?

```
┌─────────────────────────────────────────────────────────────────────────┐
│                        VIBEDNA AT A GLANCE                              │
├─────────────────────────────────────────────────────────────────────────┤
│                                                                         │
│   ENCODE              STORE               COMPUTE            DECODE     │
│   ══════              ═════               ═══════            ══════     │
│                                                                         │
│   Binary    ───►    DNA         ───►    DNA        ───►    Binary      │
│   Data              Sequence            Operations          Data        │
│                                                                         │
│   01001000  ───►    TACA...     ───►    AND/OR/XOR  ───►   01001000    │
│                                                                         │
│   ┌──────────────────────────────────────────────────────────────────┐ │
│   │  • 215 PB storage density per gram of DNA                        │ │
│   │  • 1000+ year data durability                                    │ │
│   │  • Zero energy for passive storage                               │ │
│   │  • Native DNA computation without decode/encode cycles           │ │
│   └──────────────────────────────────────────────────────────────────┘ │
│                                                                         │
└─────────────────────────────────────────────────────────────────────────┘
```

---

## Key Features

### 🧬 Multiple Encoding Schemes
- **Quaternary**: Maximum density (2 bits/nucleotide)
- **Balanced GC**: Optimized for DNA synthesis
- **Run-Length Limited**: Prevents sequencing errors
- **Redundant Triplet**: Maximum error tolerance

### 📁 DNA File System
- Full CRUD operations on DNA-encoded files
- Hierarchical directory structure
- Metadata preservation
- Content-addressable storage

### ⚡ DNA Computing
- Logic gates (AND, OR, XOR, NOT, NAND, NOR, XNOR)
- Arithmetic operations (add, subtract, multiply, divide)
- Direct computation without decoding

### 🤖 AI Agent Orchestration
- 15+ specialized agents across 3 tiers
- Intelligent workflow management
- Self-healing error recovery
- MCP server communication

### 🛡️ Error Correction
- Reed-Solomon codes in GF(4)
- Configurable redundancy levels
- Automatic error detection and correction

---

## Installation

### Quick Install (pip)
```bash
pip install vibedna
```

### From Source
```bash
git clone https://github.com/neuralquantum/vibedna.git
cd vibedna
pip install -e .
```

### Docker
```bash
docker pull neuralquantum/vibedna
docker run -p 8000:8000 neuralquantum/vibedna
```

---

## Quick Example

```python
from vibedna import Encoder, Decoder

# Encode binary data to DNA
encoder = Encoder(scheme="quaternary")
dna_sequence = encoder.encode(b"Hello, DNA!")
print(f"DNA: {dna_sequence}")
# Output: DNA: TACATGTCTGCATGCATGCGTACA...

# Decode DNA back to binary
decoder = Decoder()
original_data = decoder.decode(dna_sequence)
print(f"Original: {original_data.decode()}")
# Output: Original: Hello, DNA!
```

---

## Architecture Overview

```
┌─────────────────────────────────────────────────────────────────────────┐
│                        VIBEDNA ARCHITECTURE                             │
├─────────────────────────────────────────────────────────────────────────┤
│                                                                         │
│                         ┌─────────────────┐                             │
│                         │   API Gateway   │                             │
│                         │  REST / CLI     │                             │
│                         └────────┬────────┘                             │
│                                  │                                      │
│   ╔══════════════════════════════════════════════════════════════════╗ │
│   ║                   ORCHESTRATION TIER                             ║ │
│   ║  ┌────────────┐  ┌────────────┐  ┌────────────┐                 ║ │
│   ║  │  Master    │  │  Workflow  │  │  Resource  │                 ║ │
│   ║  │Orchestrator│  │Orchestrator│  │Orchestrator│                 ║ │
│   ║  └────────────┘  └────────────┘  └────────────┘                 ║ │
│   ╚══════════════════════════════════════════════════════════════════╝ │
│                                  │                                      │
│   ╔══════════════════════════════════════════════════════════════════╗ │
│   ║                    SPECIALIST TIER                               ║ │
│   ║  ┌────────┐ ┌────────┐ ┌────────┐ ┌────────┐ ┌────────┐        ║ │
│   ║  │Encoder │ │Decoder │ │Compute │ │  File  │ │  More  │        ║ │
│   ║  │ Agent  │ │ Agent  │ │ Agent  │ │ Agent  │ │ Agents │        ║ │
│   ║  └────────┘ └────────┘ └────────┘ └────────┘ └────────┘        ║ │
│   ╚══════════════════════════════════════════════════════════════════╝ │
│                                  │                                      │
│   ╔══════════════════════════════════════════════════════════════════╗ │
│   ║                      SUPPORT TIER                                ║ │
│   ║  ┌────────┐ ┌────────┐ ┌────────┐ ┌────────┐ ┌────────┐        ║ │
│   ║  │ Index  │ │Metrics │ │Logging │ │  Docs  │ │Security│        ║ │
│   ║  └────────┘ └────────┘ └────────┘ └────────┘ └────────┘        ║ │
│   ╚══════════════════════════════════════════════════════════════════╝ │
│                                  │                                      │
│                    ┌─────────────────────────┐                          │
│                    │      MCP Servers        │                          │
│                    │  core│fs│compute│...    │                          │
│                    └─────────────────────────┘                          │
│                                                                         │
└─────────────────────────────────────────────────────────────────────────┘
```

---

## Documentation Structure

```
docs/
├── README.md                    # This file
├── EXECUTIVE_BRIEFING.md        # Executive overview
├── images/                      # Logos and diagrams
│   ├── VibeDNA.png
│   └── VibeDNA-Icon.png
├── api/                         # API documentation
│   └── README.md
├── architecture/                # Architecture docs
│   └── README.md
├── agents/                      # Agent system docs
│   └── README.md
└── guides/                      # How-to guides
    ├── QUICKSTART.md
    ├── DEPLOYMENT.md
    ├── ENCODING_SCHEMES.md
    ├── DNA_COMPUTING.md
    └── ERROR_CORRECTION.md
```

---

## Support & Resources

- **GitHub**: [github.com/neuralquantum/vibedna](https://github.com/neuralquantum/vibedna)
- **Documentation**: [docs.vibedna.io](https://docs.vibedna.io)
- **API Reference**: [api.vibedna.io](https://api.vibedna.io)
- **Community**: [community.vibecaas.com](https://community.vibecaas.com)

---

## License

VibeDNA is proprietary software developed by NeuralQuantum.ai LLC.

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© 2026 VibeDNA powered by VibeCaaS.com a division of NeuralQuantum.ai LLC. All rights reserved.
