Upload README.md

README.md

@@ -1,106 +1,94 @@
-Gracias por compartir el `README.md` actual. Está bastante bien estructurado, pero podemos mejorarlo para que refleje **todos los módulos reales incluidos** y su utilidad práctica, y además reforzar el interés del proyecto de cara a visitantes y posibles contribuidores.
-
-A continuación te presento una versión revisada y ampliada, lista para reemplazar el contenido actual:
-
----
-
-```markdown
----
-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!
-
-```
-
----
+---
+title: GeneForgeLang
+emoji: 🧬
+colorFrom: indigo
+colorTo: blue
+sdk: gradio
+sdk_version: "3.50.2"
+app_file: app.py
+pinned: true
+---
+
+
+markdown
+Copiar
+Editar
+emoji: 🧬
+colorFrom: indigo
+colorTo: blue
+sdk_version: "3.50.2"
+app_file: app.py
+pinned: true
+
+# 🧬 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.
+
+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
+
+
+## 🚀 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 |
+
+
+## 🧪 Example Input Phrases
+
+### DNA → RNA
+
+~d:Prom-Exon1-Intr1-Exon2 ↓ :r:Cap5'-Ex1-Ex2-UTR3'
+
+shell
+Copiar
+Editar
+
+### RNA → Protein
+
+:r:Ex1-Ex2 ↓ ^p:Dom(Kin)-Mot(NLS)
+
+yaml
+Copiar
+Editar
+
+
+## ▶️ How to Use
+
+1. Clone this repo
+2. Install dependencies:
+```bash
+pip install -r requirements.txt
+Launch the interface:
+
+bash
+Copiar
+Editar
+python app.py
+Navigate to:
+
+cpp
+Copiar
+Editar
+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.