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GENVO: GENE EVOLUTIONVISUALIZATION: A 3D reconciliation software for phylogenies
KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID.
2016 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
Genvo: visualisering av geners evolution : Ett reconcilieringsprogram för fylogenier i 3D (Swedish)
Abstract [en]

Gene evolution is important in several areas, not least the understanding of thehuman body. Since the time of Darwin, researchers have visualized evolution withrooted binary trees. Hence, genes evolve constrained to how species have evolvedand that relationship is interesting to understand and explore. To solve this, onemethod is to infer the gene tree into the species tree, a so called reconciliation, butvisualizing reconciled trees with classical binary trees often results in clutteredvisualizations that quickly become difficult to understand. Therefore, in this thesisI present a new visualization method, Genvo, for reconciled phylogenies, and definea simple tree layout algorithm. I also present a problem characterization for thedomain-specific tasks, performed when working with gene evolution visualizations.A prototype of Genvo is then studied in a small pair analytics study, where fivepairs of master students tested the developed a prototype of Genvo. The results areanalyzed compared to a workshop with three participants, all with prior knowledgein the field of gene evolution. The analysis indicates a faster understanding of thegene data in Genvo, most likely through the pre-attentive features.

Abstract [sv]

Att förstå geners evolution är relevant för flertalet områden, inte minst för attutforska den mänskliga kroppen. Ända sedan Darwin har forskare visualiseratevolution med hjälp av rotade binära träd. Dock utvecklas gener begränsat till hurdess arter utvecklats, och denna relation är av intresse att förstå och utforska. Attgöra en sammanslagning av ett gen-träd med sitt art-träd (reconciliation) är ett sättatt visualisera relationen, men lösningen blir ofta väldigt rörig och svårförståelig.Därför presenterar jag i detta examensarbete Genvo, ett reconciliation programsom använder en simpel träd-layout-algoritm för att visualisera geners evolution irelation till arters evolution i 3D. Jag presenterar även en gedigen problemkarakteriseringför de uppgifter forskarna utför när de jobbar med dagensvisualiseringsverktyg. En prototyp av Genvo testades sedan i en pairanalytics studie, med en testgrupp bestående av fem par. Studien är sedan jämfördmed en workshop där tre testpersoner, med tidigare erfarenhet, jobbade medsamma uppgifter. Analysen av studiernas resultat tyder på en snabbare förståelseav datan när användarna använde sig av Genvo.

Place, publisher, year, edition, pages
2016. , 34 p.
Keyword [en]
Visualization 3D Phylogenies binary tree reconciliation
National Category
Media and Communication Technology
Identifiers
URN: urn:nbn:se:kth:diva-189179OAI: oai:DiVA.org:kth-189179DiVA: diva2:943989
External cooperation
Lars Arvestad, NADA
Subject / course
Media Technology
Educational program
Master of Science in Engineering - Media Technology
Supervisors
Examiners
Available from: 2016-07-05 Created: 2016-06-28 Last updated: 2016-07-05Bibliographically approved

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CiteExportLink to record
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