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GenIE-Sys: Genome Integrative Explorer System
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
Umeå University, Faculty of Social Sciences, Department of Informatics.ORCID iD: 0000-0001-9419-0682
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: 0000-0001-6031-005x
(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 [en]
Bioinformatics, Databases, Genomics, Visualization
National Category
Bioinformatics and Systems Biology Genetics
Identifiers
URN: urn:nbn:se:umu:diva-170112DOI: 10.1101/808881OAI: oai:DiVA.org:umu-170112DiVA, id: diva2:1426559
Available from: 2020-04-27 Created: 2020-04-27 Last updated: 2020-05-05
In thesis
1. Human-computer interaction principles for developing web-based genomics resources
Open this publication in new window or tab >>Human-computer interaction principles for developing web-based genomics resources
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Mänskliga-datorinteraktion principer för utveckling av webb-baserade resurser för genomik
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:nbn:se:umu:diva-170109 (URN)978-91-7855-284-9 (ISBN)978-91-7855-285-6 (ISBN)
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

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Mannapperuma, ChanakaWaterworth, JohnStreet, Nathaniel

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