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Design and evaluation of a visualization application for the analysis of transcriptome data

Tijsma, L. (2006) Design and evaluation of a visualization application for the analysis of transcriptome data. Master's Thesis / Essay, Computing Science.

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Abstract

Data from DNA micro-arrays provide biologists with huge amounts of information on gene activity. Following statistical analysis of the raw gene expression values, genes can be grouped in clusters exhibiting the same expression patterns. Relating the cluster information to known biological processes by hand is tedious and error-prone. To assist biologists in analyzing these data, the computer application FIVA (Functional Information Viewer and Analyzer) was developed. The application combines cluster information with information on known biological processes and generates colormaps showing the obtained functional profile. FIVA was developed from a biological point of view and was in need of a redesign. To guide us in creating a new design and implementation of FIVA, we used known concepts from the field of information visualization like the visualization mantra about interaction, eight guidelines on multiple views and color gradient interpretation information. The visualization in the new version of FIVA uses two different view types. One view displays an overview of all information, the other view shows the details a user has selected. To test whether the new implementation of FIVA satisfies real-life users, it was subjected to a usability study with ten specialized biologists as participants. We used a think-aloud protocol with coaching to study the interaction of the participants with FIVA when solving a set of real-world biological problems. After completing the tasks, participants were subjected to an interview. All participants stated that. they. 'iere satisfied and were planning to use the application in the future. The main, usability problems include the lack of an adequate filtering option, inconsistent buttonlocations, ihecolors that are used in the visualization and navigating through the overview diagram. The analysis of these usability problems showed that some problems could be traced back to violation of two multiple view guidelines and providing too little support for a part of the visualization mantra. The solutions to usability problems that could quickly be solved were implemented after the usability study.

Item Type: Thesis (Master's Thesis / Essay)
Degree programme: Computing Science
Thesis type: Master's Thesis / Essay
Language: English
Date Deposited: 15 Feb 2018 07:30
Last Modified: 15 Feb 2018 07:30
URI: http://fse.studenttheses.ub.rug.nl/id/eprint/8928

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