SODA: an Open-Source Library for Visualizing Biological Sequence Annotation

Author

Jack W. Roddy, The University Of MontanaFollow
Travis J. Wheeler, The University Of MontanaFollow

Year of Award

2021

Document Type

Thesis

Degree Type

Master of Science (MS)

Degree Name

Computer Science

Department or School/College

Computer Science

Committee Chair

Travis Wheeler

Commitee Members

Douglas Brinkerhoff, Cory Palmer

Keywords

Bioinformatics, biological annotation, visualization, software library

Publisher

University of Montana

Subject Categories

Bioinformatics | Graphics and Human Computer Interfaces | Software Engineering

Abstract

Genome annotation is the process of identifying and labeling known genetic sequences or features within a genome. Across the various subfields within modern molecular biology, there is a common need for the visualization of such annotations. Genomic data is often visualized on web browser platforms, providing users with easy access to visualization tools without the need for installing any software or, in many cases, underlying datasets. While there exists a broad range of web-based visualization tools, there is, to my knowledge, no lightweight, modern library tailored towards the visualization of genomic data. Instead, developers charged with the task of producing a novel visualization must either adopt a complex system or fall back on general purpose visualization frameworks. Here, I present SODA, a web-based genomic annotation visualization library implemented in TypeScript as an abstraction over D3. SODA is designed to be lightweight and flexible, empowering developers with the tools to easily create customized and nuanced genomic visualizations.

Recommended Citation

Roddy, Jack W. and Wheeler, Travis J., "SODA: an Open-Source Library for Visualizing Biological Sequence Annotation" (2021). Graduate Student Theses, Dissertations, & Professional Papers. 11677.
https://scholarworks.umt.edu/etd/11677