Visualizing the genome
Visualizing the genome
We develop Integrated Genome Browser, a tool designed to present genomic data sets in a highly interactive, flexible format. Originally developed at Affymetrix for visualization of data from genome tiling arrays and SNP genotyping chips, we updated IGB to display new types of data from high-throughput sequencing experiments, especially RNA-Seq and ChIP-Seq experiments.
IGB implements visualization techniques inspired by advances in information visualization and visual analytics, notably animated zooming. We have also developed techniques designed specifically for visualization of genomic data, such as edge matching, moveable, adjustable tracks, the zoom stripe pointer, rich link-outs to external databases, and more.
Essential to IGB function is the idea that zooming and panning through a genome should be easy and fast, creating the impression of effortless flight through the genomic landscape. Regardless of zoom level or position, we should see cues that tell us where to go next. Just as importantly, as we zoom and pan, we need stable landmarks that help us stay oriented. All of these principles are well-known in information visualization; we aim to adapt them to genomics visualization and build flexible, fast, and free tools scientists love to use.
Visualization for genomics
New high-throughput sequencing and well-established DNA microarray technologies produce massive amounts of data, more than most researchers’ current computer or software systems can easily handle.
We are interested in developing tools to help biologists manage, share, visualize and explore their own data sets together with data and annotations harvested from the public domain.
We are interested in creating new visualization techniques that will help biologists make the most of large-scale data sets from ‘omics experiments, especially high-throughput sequencing and tiling array data sets.
More generally, we would like to discover what kinds of interactions and tools work best for biologists, bioinformaticians, students, and clinicians. We want to know: What data visualization and interaction techniques stimulate insight and discovery? What kinds of views will expose previously undiscovered and significant patterns in the data and suggest new directions for research?
Software for genomics
The pattern of RNA-Seq alignments (in blue) exposes a tandem duplication in the A. thaliana genome.