README.md

metadata

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

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🚀 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

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🧪 Example Input Phrases

~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

1. Clone this repo:

git clone https://github.com/Fundacion-de-Neurociencias/GeneForgeLang.git
cd GeneForgeLang

2. Install dependencies:

pip install -r requirements.txt

3. Launch the interface:

python app.py

4. Navigate to:
   http://127.0.0.1:7860

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📁 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

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🧠 Developed by

Fundación de Neurociencias
Licensed under the MIT License

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