BactoGENIE

A Large-Scale Comparative Genome Visualization for Big Displays

The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics—which aim to enable analysis tasks across collections of genomes—suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets.

In this project, completed collaboratively with researchers in industry, we developed a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We called the final application BactoGeNIE, or Bacterial Gene Neighborhood Investigation Environment.

We evaluated BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process.

BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.

I was the primary developer and researcher on this project, in collaboration for bacterial genomics researchers in industry. Thanks for Jason Leigh (Hawaii) and Khairi Reda (IUPUI) for brainstorming and design ideas.

Publications

BactoGeNIE: A Large-Scale Comparative Genome Visualization for Big Displays.

Jillian Aurisano, Khairi Reda, Andrew Johnson, G. Elisabeta Marai and Jason Leigh. BMC Bioinformatics Journal, August 2015

Visualizing Large, Heterogenous Data in Hybrid Reality Display Environments.

Khairi Reda, Alessandro Febretti, Aaron Knoll, Jillian Aurisano, Jason Leigh, Andrew Johnson, Mike E. Papka and Mark Hereld. IEEE Computer Graphics and Applications, July 2013

Bacterial Gene Neighborhood Investigation Environment: A Large-Scale Genome Visualization for Big Displays

Jillian Aurisano, Khairi Reda, Andrew Johnson, Jason Leigh.Poster presented at the Large Data Analysis and Visualization conference at IEEE VisWeek in Paris, France on November 9th 2014

BEST POSTER AWARD

Bacterial Gene Neighborhood Investigation Environment: A Large-Scale Genome Visualization for Big Displays

Jillian Aurisano, Khairi Reda, Andrew Johnson, Jason Leigh.Poster presented at the Biological Data Visualization conference in Boston, MA on July 11th 2014

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