This is the WIP project of our group project VarViz3D. Current working version is https://github.com/omadik/gvv

The first completed release, done in our group, is on @sukhanovaxenia at https://github.com/sukhanovaxenia/VarViz3D

🧬 Gene Browser

An interactive web application for exploring genetic variant data.
Gene Browser lets you search for a gene, view gene information, visualize data in 2D and 3D, and browse RSIDs with short explanations and PubMed evidence counts.

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🚀 Features

• Gene Info Tab – Displays a gene’s summary, coordinates, and metadata.
• 2D View – Visualizes:
  • Mean allele frequency distributions
  • ClinVar variant positions
  • Gene structure diagrams
• 3D View – Interactive protein structure viewer.
• RSID Browser – Searchable list of RSIDs with:
  • Allele frequency
  • HGVS notation
  • PubMed reference counts
  • One-click functional explanations

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📦 Tech Stack

• Backend: FastAPI, Python
• Frontend: HTML, CSS, Vanilla JavaScript
• 3D Visualization: NGL Viewer / 3Dmol.js
• 2D Visualization: Plotly.js, Chart.js

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🛠️ Installation & Usage

1. Clone the repository

git clone https://github.com/<username>/<repository>.git
cd <repository>

2. Create & activate a virtual environment

python -m venv venv
source venv/bin/activate   # macOS/Linux
venv\Scripts\activate      # Windows

3. Install dependencies

pip install -r requirements.txt

4. Run the backend server

uvicorn app.main:app --reload --port 8000

This will start the FastAPI backend at:

http://127.0.0.1:8000

5. Open the frontend

Open frontend/index.html in your browser.

project_root/
├── app/                # FastAPI backend
│   ├── main.py          # Entry point for backend
│   ├── routes/          # API endpoints
│   ├── plots2d_api.py   # 2D visualization routes
│   └── ...
├── frontend/           # Static HTML/JS frontend
│   └── index.html
├── 3d/                 # 3D viewer scripts
├── requirements.txt
└── README.md

💡 Example Workflow

Enter a gene name (e.g., BRCA1) in the search field. Click Load Variants to retrieve gene data. Explore:

Gene Info – Coordinates, summary, metadata.

2D View – Charts and gene structure visualization.

3D View – Protein structure in interactive mode.

Browse RSIDs in the right-hand column and click one to see its functional explanation.