Synteny Explorer

An Interactive Visualization Application for Teaching Genome Evolution

Chris Bryan, Gregory Guterman, Kwan-Liu Ma, Harris Lewin, Denis Larkin, Jaebum Kim, Jian Ma, Marta Farré

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Rapid advances in biology demand new tools for more active research dissemination and engaged teaching. This paper presents Synteny Explorer, an interactive visualization application designed to let college students explore genome evolution of mammalian species. The tool visualizes synteny blocks: segments of homologous DNA shared between various extant species that can be traced back or reconstructed in extinct, ancestral species. We take a karyogram-based approach to create an interactive synteny visualization, leading to a more appealing and engaging design for undergraduate-level genome evolution education. For validation, we conduct three user studies: two focused studies on color and animation design choices and a larger study that performs overall system usability testing while comparing our karyogram-based designs with two more common genome mapping representations in an educational context. While existing views communicate the same information, study participants found the interactive, karyogram-based views much easier and likable to use. We additionally discuss feedback from biology and genomics faculty, who judge Synteny Explorer's fitness for use in classrooms.

Original languageEnglish (US)
Article number7539391
Pages (from-to)711-720
Number of pages10
JournalIEEE Transactions on Visualization and Computer Graphics
Volume23
Issue number1
DOIs
StatePublished - Jan 1 2017

Fingerprint

Teaching
Visualization
Genes
Animation
DNA
Education
Students
Color
Feedback
Testing
Genomics

Keywords

  • Bioinformatic visualization
  • chromosome
  • education
  • genome evolution
  • learning
  • user study

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Computer Vision and Pattern Recognition
  • Computer Graphics and Computer-Aided Design

Cite this

Synteny Explorer : An Interactive Visualization Application for Teaching Genome Evolution. / Bryan, Chris; Guterman, Gregory; Ma, Kwan-Liu; Lewin, Harris; Larkin, Denis; Kim, Jaebum; Ma, Jian; Farré, Marta.

In: IEEE Transactions on Visualization and Computer Graphics, Vol. 23, No. 1, 7539391, 01.01.2017, p. 711-720.

Research output: Contribution to journalArticle

Bryan, Chris ; Guterman, Gregory ; Ma, Kwan-Liu ; Lewin, Harris ; Larkin, Denis ; Kim, Jaebum ; Ma, Jian ; Farré, Marta. / Synteny Explorer : An Interactive Visualization Application for Teaching Genome Evolution. In: IEEE Transactions on Visualization and Computer Graphics. 2017 ; Vol. 23, No. 1. pp. 711-720.
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