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Published: 2020-06-11

Helping biologists to understand their complex data

NEWS Chanaka Mannapperuma has developed bioinformatics tools that help biologists to analyse their complex genomics data. His aim was to create intuitive, easy to use tools that do not require specialized bioinformatics knowledge. Chanaka Mannapperuma will defend his PhD thesis at Umeå University on Thursday 11th of June.

Text: Anne Honsel och Ingrid Söderbergh

When Chanaka Mannapperuma started working at Umeå Plant Science centre, UPSC, in 2010 as a programmer there were not so many analysis tools available for biologists to do their analysis easily. Chanaka has a computer science and interaction design education background, so this was a good opportunity to apply previous knowledge to make a database system and tools for plant biologists. Since most biologists are not familiar with programming, they needed tools to analyse their data without learning to program themselves. The idea of a doctoral project arouse.

In his thesis, Chanaka Mannapperuma has improved the design of the tools based on user experiences and general principals in the field of human-computer interaction, HCI. The aim was to study how users interact with computer interfaces and how to use design principles, and visualization techniques to improve user interaction and make usable systems.

HCI is a multidisciplinary field combining design, computer science, psychology, anthropology, sociology, ergonomics and others.

“The interdisciplinary approach will help us to understand how we perceive different signals, process and interpret them using our cognitive abilities and evaluate the outcome. These are some of the main questions in HCI, and the entire design process helps us to make user-friendly tools”, says Chanaka Mannapperuma.

The design process starts with the prototype or the production tool of the previous version. To be specific, starting with the prototype, then apply design principles and visualisation techniques to reshape the tool and use heuristic evaluation methods to make usable tools with the help of user feedback. Users expect an interactively engaging and appealing experience in addition to the usable tool. Mere iteration of the design process will make better user-friendly and usable tools.

“Design, programming and user interaction are well connected. I am enjoying all three aspects and the entire design process, especially making useful tools for biologists that they can explore to gain biological insights”, says Chanaka Mannapperuma.

Do you plan to continue working in this direction?

“My doctoral work was a pleasant experience, and I am enjoying work in this direction. I can also see the need for designing user centred tools that will help biologist to do their analysis much more easy. I am planning to continue working at UPSC and improving the resource for a while”.

Read the whole thesis

Press photos

About the public defence:

On Thursday, 11th of June, Chanaka Mannapperuma, Department of Plant Physiology at Umeå University, will defend his thesis entitled: Human-computer interaction principles for developing web-based genomics resources. The dissertation will be live broadcasted via Zoom.
The dissertation takes place in Stora hörsalen, KBC, KB3B1, at 9-13.
Faculty opponent is Marek Mutwil from The School of Biological Sciences, Nanyang Technological University, Singapore.
Supervisors are Nathaniel Street,the Department of Plant Physiology (UPSC), and John Waterworth, the Department of Informatics.