Genome visualisation and user studies in biologist-computer interaction

Jakubowska, Joanna (2009) Genome visualisation and user studies in biologist-computer interaction. PhD thesis, University of Glasgow.

Abstract

We surveyed a number of genome visualisation tools used in biomedical research. We recognised that none of the tools shows all the relevant data geneticists who look for candidate disease genes would like to see. The biological researchers we collaborate with would like to view integrated data from a variety of sources and be able to see both data overviews and details. In response to this need, we developed a new visualisation tool, VisGenome, which allows the users to add their own data or data downloaded from other sources, such as Ensembl. VisGenome visualises single and comparative representations of the rat, the mouse, and the human chromosomes, and can easily be used for other genomes. In the context of VisGenome development we made the following research contributions. We developed a new algorithm (CartoonPlus) which allows the users to see different kinds of data in cartoon scaling depending on a selected basis. Also, two user studies were conducted: an initial quantitative user study and a mixed paradigm user study. The first study showed that neither Ensembl nor VisGenome fulfil all user requirements and can be regarded as user-friendly, as the users make a significant number of mistakes during data navigation. To help users navigate their data easily, we improved existing visualisation techniques in VisGenome and added a new technique CartoonPlus. To verify if this solution was useful, we conducted a second user study. We saw that the users became more familiar with the tool, and found new ways to use the application on its own and in connection with other tools. They frequently used CartoonPlus, which allowed them to see small regions of their data in a way that was not possible before.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Keywords: Human-Computer Interaction, Usability, Genome Visualisation
• Subjects: Q Science > Q Science (General)
• Colleges/Schools: College of Science and Engineering > School of Computing Science
• Supervisor's Name: Hunt, Dr Ela and Chalmers, Dr Matthew
• Date of Award: 2009
• Depositing User: Dr Joanna Jakubowska
• Unique ID: glathesis:2009-482
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 20 Nov 2008
• Last Modified: 10 Dec 2012 13:19
• URI: https://theses.gla.ac.uk/id/eprint/482