README.md

---
title: GeneForgeLang
emoji: 🧬
colorFrom: indigo
colorTo: blue
sdk: gradio
sdk_version: "3.50.2"
app_file: app.py
pinned: true
---

# 🧬 GeneForgeLang: Symbolic-to-Sequence & Cross-Modality Biomolecular Design Toolkit

**GeneForgeLang** is a symbolic and generative language for cross-modality biomolecular design.  
It enables unified AI-powered workflows to **design, interpret and translate DNA, RNA, and protein sequences** using a compact, human-readable grammar.

This project provides:
- **A symbolic language** spanning all biological layers (genomic, transcriptomic, proteomic)
- **Realistic sequence generation** via AI models like ProtGPT2
- **Scientific interpretation** of symbolic phrases in natural language
- **Cross-modality transcoders** (e.g., DNA → RNA → Protein and vice versa)
- **An interactive Gradio-based UI** for easy use and integration

---

## 🚀 Key Features

| Module                      | Description |
|----------------------------|-------------|
| 🧠 Phrase → Sequence        | Generate DNA, RNA, or protein from symbolic design |
| 🔁 Transcode Phrases        | Translate GeneForgeLang phrases across modalities |
| 📖 Phrase → Description     | Generate scientific English descriptions of symbolic inputs |
| 🔄 Sequence → Phrase        | Infer functional phrases from real sequences |
| 🧬 Mutate Sequence (WIP)    | Generate variants for symbolic seeds (under development) |
| 📦 Export to FASTA (WIP)    | Save generated sequences to .fasta (to be implemented) |
| 📊 Analyze Sequence (WIP)   | Visualize amino acid composition or base content |

---

## 🧪 Example Input Phrases

```text
~d:Prom[TATA]-Exon1-Intr1-Exon2
↓
:r:Cap5'-Ex1-Ex2-UTR3'
↓
^p:Dom(Kin)-Mot(NLS)*AcK@147
```

---

## ▶️ How to Use Locally

1. Clone this repo:
```bash
git clone https://github.com/Fundacion-de-Neurociencias/GeneForgeLang.git
cd GeneForgeLang
```

2. Install dependencies:
```bash
pip install -r requirements.txt
```

3. Launch the interface:
```bash
python app.py
```

4. Navigate to:  
[http://127.0.0.1:7860](http://127.0.0.1:7860)

---

## 📁 File Structure

| File                          | Description |
|------------------------------|-------------|
| `app.py`                     | Full Gradio app (4 tabs) |
| `semillas.json`              | Phrase-to-seed dictionary |
| `generate_from_phrase.py`    | Symbolic-to-sequence generator |
| `describe_phrase.py`         | Phrase interpreter to scientific English |
| `translate_to_geneforgelang.py` | Sequence-to-symbolic phrase translation |
| `transcoder.py`              | Modality switcher (DNA ↔ RNA ↔ Protein) |
| `requirements.txt`           | Python dependencies |
| `README.md`                  | This file |

---

## 🧠 Developed by

**Fundación de Neurociencias**  
Licensed under the MIT License

> Join us in shaping the future of symbolic bio-AI. Contributions welcome!