PhD Dissertation

Data Visualization Tools for Large Biological Data Sets

ABSTRACT

Researchers have access to an ever-growing volume of data available at multiple levels of biological analysis. Many visual analytic tools have been developed to display a variety of biological data types but many of these tools are challenging to use and only examine one biological level of analysis at a time. The development and testing of hypotheses is difficult when the information is hard to integrate and laborious to interpret. The application of data visualization principles and user experience design best practices could improve systems biology research workflows by providing visual analytic tools with what is known in the information visualization community as a “transparent” user interface.

This thesis consists of four chapters that explore two central questions: 1) What is the best way to represent biological information at different levels of analysis? and 2) How do we enable researchers to explore and interact with their data as naturally and intuitively as possible? The first chapter describes, ePlant, a tool for visualizing multiple levels of data that was developed using an agile process that included several rounds of user testing. The second chapter presents Gene Slider, a tool for visualizing the conservation and entropy of orthologous DNA and protein sequences using a data visualization paradigm that takes better advantage of preattentive visual processing than current methods. The third chapter describes Topo-phylogeny, a tool for visualizing phylogenetic relationships using a topographic map visualization paradigm that requires less cognitive processing to interpret than iii traditional tree diagrams. The final chapter demonstrates the importance of user testing when developing a “rapid serial visual presentation” interface for identifying genes of interest using electronic fluorescent pictographs.

Together these chapters illustrate the complexities and benefits of applying data visualization principles and user experience design best practices to building data visualization tools for the analysis of large biological data sets. Given that hypothesis generation is fundamentally a creative process, any tools or techniques that can help researchers consider their data at a deeper level should be valuable to the scientific community.

Conference Presentations

IEEE VIS 2019 Application Spotlight: "Does AI mean data visualization is dead? A discussion with IBMers working at the intersection of AI and data visualization about the opportunities and challenges of building next generation business intelligence products." Vancouver Convention Centre, October 23, 2019. Jamie Waese, Anne Stevens, Afrooz Samaei, Stephen O'Connell, Frank van Ham.
http://ieeevis.org/year/2019/info/application-spotlights

Designing & Building Data Visualization Tools for Large Biological Data Sets. SORA-TABA Workshop & DLSPH Biostatistics Research Day. Hospital for Sick Children (SickKids), Peter Gilgan Centre for Research and Learning Auditorium, May 5, 2017
http://sorataba.org/sorataba-workshop-2017/
Download Slides Here

ePlant: An agile approach to visualizing multiple levels of biological data. Jamie Waese, Asher Pasha, Nicholas Provart, International Conference of Arabidopsis Researchers at Paris, July 9, 2015.

Gene Slider: A new visualization tool for the AIP. Jamie Waese, Asher Pasha, Nicholas Provart. Arabidopsis Information Portal Developer Workshop at the Texas Advanced Computing Center, University of Texas at Austin, November 5, 2014.

ePlant: A user friendly data visualization tool for integrating and exploring multiple levels of biological data. Jamie Waese, Asher Pasha, Nicholas Provart, International Conference of Arabidopsis Researchers at Vancouver, June 29, 2014.

Data Sets, Webservices and Visualization Apps from the Bio-Analytic Resource for use in the AIP and other Cyberinfrastructure Assets. Nicholas Provart, Jamie Waese, Zhenming Yu, Asher Pasha, Rohan V. Patel, Sylva Donaldson, Adrian Platts, Mathieu Blanchette and Stephen I. Wright. International Arabidopsis Informatics Consortium session at the XXII Plant and Animal Genome conference in San Diego, January 13, 2014.

Building Data Visualization Tools For Large Biological Datasets, Toronto Bioinformatics Users Group (TorBUG), March 27, 2013

Medium Articles

What TV Taught Me About Design Presentations

Seven principles of storytelling to elevate your next presentation. Published in the Shopify UX Medium Channel on February 3, 2022. Based on a 30-minute talk I gave to the #Writers-of-Shopify interest group.
Read it here.

Data Visualization and AI

Stephen O’Connell, Afrooz Samaei, Anne Stevens and Jamie Waese. Does Artificial Intelligence Mean Data Visualization is Dead? Nightingale - The Journal of the Data Visualization Society, Medium.com. January 10, 2020.
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Refereed Posters

ePlant: A user friendly data visualization tool for integrating and exploring multiple levels of biological data. Jamie Waese, Asher Pasha, Nicholas Provart, International Conference of Arabidopsis Researchers 2014.

Gene Slider: A Sequence Logo Interactive data visualization tool for Education and Research, Jamie Waese, Asher Pasha, Nicholas Provart, BioVis 2013.