geranium

Geranium

Genomics Visualization Retrieval for Authoring with Multimodality

Citation

Preprint: Nguyen, Huyen N., Sehi L’Yi, Thomas C. Smits, Shanghua Gao, Marinka Zitnik, and Nils Gehlenborg. “Multimodal Retrieval of Genomics Data Visualizations.” OSF Preprints, 2025.

@article{nguyen2025multimodal,
  title={Multimodal Retrieval of Genomics Data Visualizations},
  author={Nguyen, Huyen N and L’Yi, Sehi and Smits, Thomas C and Gao, Shanghua and Zitnik, Marinka and Gehlenborg, Nils},
  year={2025},
  publisher={OSF Preprints},
  url={https://osf.io/zatw9_v1},
  doi={10.31219/osf.io/zatw9_v1},
}

Overview

Geranium is a multimodal retrieval system that helps researchers efficiently find genomics visualization examples using image, text, or specification-based queries. Search results function as adaptable templates/scaffolds that researchers can modify with their own data and design preferences.

Features

Flexible query approaches: Choose your preferred search method - example images, natural language queries, or partial Gosling specification queries for precise visualization retrieval
Adaptable visualization scaffolds: Search results function as modifiable templates, not just static examples
Integrated live editor: Edit and customize retrieved visualizations directly within the application
Triplet output: Each resulting visualization is returned as a triplet of image, text, and its corresponding Gosling specification
Diverse Collection: The collection spans single-view to multi-view visualizations for specialized genomic applications like epigenomics and structural variation analysis

Installation

The application consists of two components: a server and a client that need to be run separately.

Server Installation

Navigate to the server directory:
```
 cd server
```

Create and activate a Python virtual environment:

 python3 -m venv .venv
 source .venv/bin/activate

Install the required dependencies:

 python3 -m pip install -r requirements.txt

Alternatively, if using uv package manager: uv pip install -r requirements.txt

Start the server:
```
 flask --app app.py run
```

The server will start on http://localhost:5000 by default.

Client Installation

Open a new terminal and navigate to the client directory:
```
 cd client
```
Install the necessary dependencies:
```
 npm install
```
Start the client application:
```
 npm run dev
```

Once started, the client will be available at http://localhost:5173/.

Usage

After both the server and client are running, open your browser and navigate to http://localhost:5173/ to start using Geranium.

Make sure the server is running before accessing the client.
The client will attempt to interact with the backend hosted by Flask on its default port.

Troubleshooting

If the client does not run properly, you may need to update your Node.js and/or Vite versions.

Current Node.js version used: v22.8.0

Check your Node.js version

node -v

If you are using an older version, consider updating Node.js.

Reinstall dependencies

Sometimes deleting the node_modules folder and reinstalling dependencies can resolve issues:

rm -rf node_modules
npm install

Update Vite

To update Vite to the latest version, run:

npm update vite

Contributing

Contributions are welcome! If you’d like to contribute, please open a new issue or submit a pull request. Please read CONTRIBUTING.md to find more guidelines.

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