Geranium

geranium

Genomic data visualization retrieval for authoring with multimodality

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

1. Navigate to the server directory:

   cd server
   

2. Create and activate a Python virtual environment:

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

3. Install the required dependencies:

   python3 -m pip install -r requirements.txt
   

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

4. Start the server:

   flask --app app.py run
   

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

Client Installation

1. Open a new terminal and navigate to the client directory:

   cd client
   

2. Install the necessary dependencies:

   npm install
   

3. 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.

Contributing

Contributions are welcome! If you'd like to contribute, please open an issue or submit a pull request.