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Human-computer interaction principles for developing web-based genomics resources
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0003-1589-9138
2020 (English)Doctoral thesis, comprehensive summary (Other academic)Alternative title
Mänskliga-datorinteraktion principer för utveckling av webb-baserade resurser för genomik (Swedish)
Abstract [en]

Genomics projects, including genome sequencing, transcriptomics, genome-wide association mapping and epigenetics assays, producevast quantities of data. Extracting the required information from such complex datasets is a significant challenge and even where software tools do exist, these are often not intuitive or designed fornon-specialist users. This dissertation details how I have applied design principles from the field of Human-Computer Interaction (HCI) to the development of intuitive bioinformatics web-based resources for exploring genomics data. In the first part of the thesis I detail the development of a specialised genomics resource that enables non specialists who lack bioinformatics skills to access, explore and extract new knowledge from a variety of genomics data types. These tools were developed in collaboration with wet lab biologists and bioinformaticians who represent typical end-users. The tools developed have been integrated within the PlantGenIE (Plant Genome IntegrativeExplorer) web resource, which has been established as a platform for exploring genomics data for Populus, conifer, Eucalyptus and Arabidopsisgenomics data. Even though the ability to collect, store and manage data is increasing faster due to new technologies and science, our ability to understand it remains constant. To help address this, in the second part of this dissertation I focus on the usability enhancement of tools based on the HCI and User Experience (UX) practices. To achieve this, I utilised visualisation techniques and design principles in the design process for the improvement of the PlantGenIEUser Interface (UI), and applied usability methods to evaluate the UX of PlantGenIE tools. These results were then used to inform adaptations and fine-tuning of those. I show that utilisation of these research methods and practices with the development life cycle represents a framework for designing usable bioinformatics tools. Wider-scale use of these methods by future designers and developers will enable the creation of more usable bioinformatics resources.

Place, publisher, year, edition, pages
Umeå: Umeå Universitet , 2020. , p. 62
National Category
Bioinformatics and Systems Biology Genetics Human Computer Interaction
Identifiers
URN: urn:nbn:se:umu:diva-170109ISBN: 978-91-7855-284-9 (print)ISBN: 978-91-7855-285-6 (electronic)OAI: oai:DiVA.org:umu-170109DiVA, id: diva2:1426665
Public defence
2020-06-11, Stora hörsalen (KB3B1), KBC-huset, Umeå, 09:00 (English)
Opponent
Supervisors
Available from: 2020-05-20 Created: 2020-04-27 Last updated: 2020-05-25Bibliographically approved
List of papers
1. Designing Usable Bioinformatics Tools for Specialized Users
Open this publication in new window or tab >>Designing Usable Bioinformatics Tools for Specialized Users
2019 (English)In: Information Technology and Systems: Proceedings of ICITS 2019 / [ed] Rocha Á., Ferrás C., Paredes M., Cham: Springer, 2019, p. 649-670Chapter in book (Refereed)
Abstract [en]

Visualization - the process of interpreting data into visual forms - is increasingly important in science as data grows rapidly in volume and complexity. A common challenge faced by many biologists is how to benefit from this data deluge without being overwhelmed by it. Here, our main interest is in the visualization of genomes, sequence alignments, phylogenies and systems biology data. Bringing together new technologies, including design theory, and applying them into the above three areas in biology will improve the usability and user interaction.

The main goal of this paper is to apply design principles to make bioinformatics resources, evaluate them using different usability methods, and provide recommended steps to design usable tools.

Place, publisher, year, edition, pages
Cham: Springer, 2019
Series
Advances in Intelligent Systems and Computing, ISSN 2194-5357, E-ISSN 94-5365 ; 918
Keywords
User Experience Designing, Participatory Design, Bioinformatics
National Category
Media and Communications Human Computer Interaction
Research subject
media and communication studies; human-computer interaction
Identifiers
urn:nbn:se:umu:diva-153032 (URN)10.1007/978-3-030-11890-7_62 (DOI)978-3-030-11889-1 (ISBN)978-3-030-11890-7 (ISBN)
Conference
ICITS'19 - The 2019 International Conference on Information Technology & Systems
Available from: 2018-11-02 Created: 2018-11-02 Last updated: 2020-05-05Bibliographically approved
2. GenIE-Sys: Genome Integrative Explorer System
Open this publication in new window or tab >>GenIE-Sys: Genome Integrative Explorer System
(English)Manuscript (preprint) (Other academic)
Abstract [en]

There are an ever-increasing number of genomes being sequenced, many of which have associated RNA sequencing and other genomics data. The availability of user-friendly web-accessible mining tools ensures that these data repositories provide maximum benefit to the community. However, there are relatively few options available for setting up such standalone frameworks. We developed the Genome Integrative Explorer System (GenIE-Sys) to set up web resources to enable search, visualization and exploration of genomics data typically generated by a genome project.

GenIE-Sys is implemented in PHP, JavaScript and Python and is freely available under the GNU GPL 3 public license. All source code is freely available at the GenIE-Sys website (https://geniesys.org) or GitHub (http://github.com/plantgenie/geniesys.git). Documentation is available at http://geniesys.readthedocs.io.

Keywords
Bioinformatics, Databases, Genomics, Visualization
National Category
Bioinformatics and Systems Biology Genetics
Identifiers
urn:nbn:se:umu:diva-170112 (URN)10.1101/808881 (DOI)
Available from: 2020-04-27 Created: 2020-04-27 Last updated: 2020-05-05
3. The Eucalyptus Genome Integrative Explorer: an online resource for systems genetics in forest tree species
Open this publication in new window or tab >>The Eucalyptus Genome Integrative Explorer: an online resource for systems genetics in forest tree species
Show others...
2020 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313XArticle in journal (Other academic) Accepted
Place, publisher, year, edition, pages
John Wiley & Sons, 2020
National Category
Other Computer and Information Science Other Biological Topics
Identifiers
urn:nbn:se:umu:diva-170113 (URN)
Available from: 2020-04-27 Created: 2020-04-27 Last updated: 2020-05-25
4. Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
Open this publication in new window or tab >>Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
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2019 (English)In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, article id 813Article, review/survey (Refereed) Published
Abstract [en]

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
Keywords
database, content management system, forest tree, bioinformatics, web services
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-161586 (URN)10.3389/fpls.2019.00813 (DOI)000473047200001 ()
Available from: 2019-07-22 Created: 2019-07-22 Last updated: 2020-05-05Bibliographically approved
5. PlantGenIE-PLAZA: integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline
Open this publication in new window or tab >>PlantGenIE-PLAZA: integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline
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2020 (English)In: Article in journal (Other academic) In press
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-170114 (URN)
Available from: 2020-04-27 Created: 2020-04-27 Last updated: 2020-05-25

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