The human genome is incredibly information dense, consisting of approximately 25,000 protein-coding genes contained within 24 unique chromosomes. An aspect of the genome that is critically important is maintaining spatial context which assists in understanding gene interactions and relationships. Existing methods of genome visualization that utilize spatial awareness are inefficient and prone to limitations in gene information and spatial context. The solution proposed in this thesis was the development and evaluation of alternative methods of genome visualization and exploration using virtual reality and desktop. To determine the optimal location of gene information within virtual reality and the influence of virtual reality, three interaction methods were implemented that interact with the ideograms. Multi-focus was applied to the ideogram interaction design to assist in visualizing multiple locations within the genome without sacrificing gene information detail or spatial awareness of the user. Two interaction methods were developed in virtual reality to determine if gene information is better suited embedded within the chromosome ideogram or separate from the ideogram. The final interaction method was implemented as a desktop application to evaluate if virtual reality provided an advantage. Results from the user study conducted determined that the use of virtual reality gave users a higher degree of confidence when navigating the chromosome ideograms and was preferred over desktop. In addition, depending on the type of task, the placement of gene information within the visualization had a notable impact on the ability of a user to work the task. / Master of Science / From the viewpoint of a dataset, the human genome is incredibly information dense. It consists of approximately 25,000 protein-coding genes contained within 24 unique chromosomes. An aspect of the genome that is critically important is maintaining spatial context which assists in understanding gene interactions and relationships. Existing methods of genome visualization that utilize spatial awareness are inefficient and prone to limitations in gene information and spatial context. In this work, an alternative method of genome visualization and interaction utilizing virtual reality and desktop was proposed. To determine the optimal location of gene information within virtual reality and the influence of virtual reality, three genome interaction methods were implemented that operate through interactions with chromosome ideograms. Two interaction methods were developed in virtual reality to determine if gene information is better suited embedded within the chromosome ideogram or separate from the ideogram. The final interaction method was implemented as a desktop application to evaluate if virtual reality provided an advantage. Results from the user study conducted determined that the inclusion of virtual reality gave users a higher degree of confidence when navigating the chromosome ideograms and was preferred over desktop. In addition, depending on the type of task, the placement of gene information within the visualization had a notable impact on the ability of a user to work the task.
| Identifer | oai:union.ndltd.org:VTETD/oai:vtechworks.lib.vt.edu:10919/115855 |
| Date | 25 July 2023 |
| Creators | Reiske, Gunnar William |
| Contributors | Computer Science and Applications, Yang, Yalong, Gracanin, Denis, Polys, Nicholas F. |
| Publisher | Virginia Tech |
| Source Sets | Virginia Tech Theses and Dissertation |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Format | ETD, application/pdf, application/pdf |
| Rights | Creative Commons Attribution-ShareAlike 4.0 International, http://creativecommons.org/licenses/by-sa/4.0/ |
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