Issue No. 01 - Jan. (2017 vol. 23)
Chris Bryan , University of California, Davis
Gregory Guterman , University of California, Davis
Kwan-Liu Ma , University of California, Davis
Harris Lewin , University of California, Davis
Denis Larkin , Royal Veterinary College, University of London
Jaebum Kim , Konkuk University, Seoul
Jian Ma , Carnegie Mellon University
Marta Farre , Royal Veterinary College, University of London
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.
Genomics, Bioinformatics, Biological cells, Visualization, Animals, Vegetation, Education
C. Bryan et al., "Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution," in IEEE Transactions on Visualization & Computer Graphics, vol. 23, no. 1, pp. 711-720, 2017.