Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization

Overview

Journal IEEE Trans Vis Comput Graph

Specialty Medical Informatics

Date 2021 Oct 1

PMID 34596551

Citations 20

Authors

Sehi LYi

Qianwen Wang

Fritz Lekschas

Nils Gehlenborg

Affiliations

Soon will be listed here.

Abstract

The combination of diverse data types and analysis tasks in genomics has resulted in the development of a wide range of visualization techniques and tools. However, most existing tools are tailored to a specific problem or data type and offer limited customization, making it challenging to optimize visualizations for new analysis tasks or datasets. To address this challenge, we designed Gosling-a grammar for interactive and scalable genomics data visualization. Gosling balances expressiveness for comprehensive multi-scale genomics data visualizations with accessibility for domain scientists. Our accompanying JavaScript toolkit called Gosling.js provides scalable and interactive rendering. Gosling.js is built on top of an existing platform for web-based genomics data visualization to further simplify the visualization of common genomics data formats. We demonstrate the expressiveness of the grammar through a variety of real-world examples. Furthermore, we show how Gosling supports the design of novel genomics visualizations. An online editor and examples of Gosling.js, its source code, and documentation are available at https://gosling.js.org.

Citing Articles

AltGosling: automatic generation of text descriptions for accessible genomics data visualization.

Smits T, LYi S, Mar A, Gehlenborg N Bioinformatics. 2024; 40(12).

PMID: 39540740 PMC: 11630506. DOI: 10.1093/bioinformatics/btae670.

Understanding Visualization Authoring Techniques for Genomics Data in the Context of Personas and Tasks.

van den Brandt A, LYi S, Nguyen H, Vilanova A, Gehlenborg N IEEE Trans Vis Comput Graph. 2024; 31(1):1180-1190.

PMID: 39288066 PMC: 11875953. DOI: 10.1109/TVCG.2024.3456298.

Learnable and Expressive Visualization Authoring Through Blended Interfaces.

LYi S, van den Brandt A, Adams E, Nguyen H, Gehlenborg N IEEE Trans Vis Comput Graph. 2024; 31(1):459-469.

PMID: 39255109 PMC: 11875996. DOI: 10.1109/TVCG.2024.3456598.

KNowNEt:Guided Health Information Seeking from LLMs via Knowledge Graph Integration.

Yan Y, Hou Y, Xiao Y, Zhang R, Wang Q IEEE Trans Vis Comput Graph. 2024; 31(1):547-557.

PMID: 39255106 PMC: 11875928. DOI: 10.1109/TVCG.2024.3456364.

Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit.

Lavikka K, Oikkonen J, Li Y, Muranen T, Micoli G, Marchi G Gigascience. 2024; 13.

PMID: 39101783 PMC: 11299109. DOI: 10.1093/gigascience/giae040.

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