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README.md

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-emoji: 🧬
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-sdk_version: "3.50.2"
-app_file: app.py
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 # 🧬 GeneForgeLang: Symbolic-to-Sequence & Cross-Modality Biomolecular Design Toolkit
 
-**GeneForgeLang** is a symbolic, generative language that allows scientists to design and interpret DNA, RNA, and protein sequences with unified syntax and AI support.
+**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 toolkit enables:
-- Generation of realistic proteins from symbolic design
-- Translation of symbolic phrases across DNA ↔ RNA ↔ Protein
-- Structured, human-readable and AI-trainable syntax
-- Semantic equivalence across molecular layers
+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
 
+---
 
-## 🚀 Features
+## 🚀 Key Features
 
 | Module                      | Description |
 |----------------------------|-------------|
-| 🧠 Phrase → Protein         | Generate realistic protein sequences from symbolic phrases |
-| 🔁 Transcode Across Molecules | Translate GeneForgeLang phrases between DNA, RNA, and Protein |
-| 📚 Universal Grammar        | One structure to rule them all: motifs, domains, PTMs, splicing |
-| 🧬 Compact Notation         | Prefixes, accents, and structural markers for efficiency |
-| 🧠 AI-Ready Output          | Compatible with transformer-based models like ProtGPT2 |
+| 🧠 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
 
-### DNA → RNA
-
-~d:Prom-Exon1-Intr1-Exon2 ↓ :r:Cap5'-Ex1-Ex2-UTR3'
-
-shell
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-
-### RNA → Protein
-
-:r:Ex1-Ex2 ↓ ^p:Dom(Kin)-Mot(NLS)
+```text
+~d:Prom[TATA]-Exon1-Intr1-Exon2
+↓
+:r:Cap5'-Ex1-Ex2-UTR3'
+↓
+^p:Dom(Kin)-Mot(NLS)*AcK@147
+```
 
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+---
 
+## ▶️ How to Use Locally
 
-## ▶️ How to Use
+1. Clone this repo:
+```bash
+git clone https://github.com/Fundacion-de-Neurociencias/GeneForgeLang.git
+cd GeneForgeLang
+```
 
-1. Clone this repo
 2. Install dependencies:
 ```bash
 pip install -r requirements.txt
-Launch the interface:
+```
 
-bash
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+3. Launch the interface:
+```bash
 python app.py
-Navigate to:
-
-cpp
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-http://127.0.0.1:7860
-📁 Files
-
-File	Description
-app.py	Full Gradio app (all tabs)
-semillas.json	Seed dictionary
-transcoder.py	Script for DNA/RNA/protein conversion
-requirements.txt	Python dependencies
-README.md	This file
-🧠 Developed by
-Fundación de Neurociencias
-MIT License
-
-Join us in shaping symbolic bio-AI.
+```
+
+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!