PhD student Chanaka Mannapperuma (photo: Lena Maria)
[2020-06-04] Chanaka Mannapperuma, PhD student in Nathaniel Street’s group at the Department of Plant Physiology and co-supervised by John Waterworth from the Department of Informatics, 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. He improved the design of the tools based on user experiences and general principals of the field of Human-computer interaction. Chanaka Mannapperuma will defend his PhD thesis at Umeå University on Thursday, 11th of June.
The topic of your PhD thesis is unusual for UPSC. What aroused your interest in this topic?
When I started at UPSC, there were not so many analysis tools available for Biologists to do their analysis easily. I have 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. I thought that this type of work is useful for UPSC and Stefan Jansson, Nathaniel Street, Andreas Sjödin and Simon Birve made me more interested and motivated to continue this work at the beginning.
How was it for you to do this type of work at UPSC?
I had a great companionship and pleasurable friendly working atmosphere at UPSC during my work. Most of my colleagues are plant biologists and they wanted to have a database system to store, filter and analyse their data. Thanks to my supervisor and his team, we managed to establish a web resource specialised for Biologists to make their research easier. I want to express my gratitude towards my colleagues and fellows at UPSC who offered constant support, availability and productive suggestions which were a determining factor for the success of my thesis.
Did it help that John Waterworth from the Department of Informatics, who is an expert in Human-computer interaction (HCI), was your second supervisor?
Yes, it was a great experience to work with John – already since I was a student in Human-computer interaction. He is an expert in this field as he has many years of experience as a psychologist. Being a psychologist, John has a good understanding and exceptional knowledge of human perception and cognitive behaviour. He was a great help to accomplish this work and thanks to John for this. Many more people from the Department of Informatics also contributed to this work. Anna Croon Fors, Karin Danielsson, Mikael Wiberg and Patrik Bjornfot are among others.
What is meant with Human-computer interaction?
The aim is 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. This 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.
Your thesis contains different aspects: programming, design and I guess a lot of communication with users. Which aspect did you like most?
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. 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.
Was it difficult to get usable feedback from the users of your tools?
We used online surveys as our initial usability methods. However, we realised that although we have 1000 users that are using the PlantGenIE platform, very few of them were willing to answer the survey questions. But thanks to the technology, we had alternative usability methods such as web analytics to gain implicit user feedback. So, we could easily capture the user feedback.
I guess many biologists are very grateful for your work. Do you plan to continue working in this direction?
It 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. In addition to that, I have an excellent supervisor with a nice team. I am planning to continue working at UPSC and improving the resource for a while.
Chanaka Mannapperuma started to work at UPSC in 2010 as programmer with the task to develop an online tool to do a simple BLAST (Basic Local Alignment Search Tool) search for gene analyses as part of the PopGenIE website. This tool allows to compare a gene or protein sequences with a library of sequences and to identify similarities between the sequence of interest and library sequences. After four years working as programmer, he started his PhD and developed the primary tool further into an extended web resource with different functionalities for gene and genome analyses. The web resource can be found here: https://plantgenie.org/
Screenshot from the PlantGenIE sites About the public defence:
The public defence will take place on Thursday, 11th of June at Umeå University. Faculty opponent will be Marek Mutwil from The School of Biological Sciences, Nanyang Technological University, Singapore. Chanaka Mannapperuma's supervisors are Nathaniel Street from the Department of Plant Physiology (UPSC) and John Waterworth from the Department of Informatics. The dissertation will be live broadcasted via Zoom.
Title of the thesis: Human-computer interaction principles for developing web-based genomics resources
Link to the thesis:
http://umu.diva-portal.org/smash/record.jsf?pid=diva2%3A1426665&dswid=9080
Link to the Zoom live broadcast:
https://umu.zoom.us/j/62366789113?pwd=Mjc2N3RVWlhaOXlYODJsRjREVy9KUT09
Meeting ID: 623 6678 9113
Password: 878277
For more information, please contact:
Chanaka Mannapperuma
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email: