UW Genome Sciences
I am a graduate student in the UW Department of Genome Sciences in Seattle, WA. I work with Jay Shendure and Cole Trapnell on new technologies and computational methods for genomics. In addition to my main research, I have also worked on several substantial team software projects.
EPICViz: Expression Patterns in C. Elegans Visualization
This is a team software project done in collaboration with Timothy Durham, Melissa Chiasson, and Ning Li. The Waterston Lab in UW Genome Sciences has collected X,Y,Z position data from strains of C. Elegans embryos that each express a fluorescent reporter for expression of a single gene. This dataset is commonly referred to as the EPIC (expression patterns in C. Elegans) dataset. We compiled data from over 200 of these recordings into a single visualization that allows querying of cell position, gene expression, terminal tissue type, cell lineage, and several other factors.
DemoI worked extensively on the 3D visualization of cell positions, corresponding small multiple views, cell highlighting and popover information between views, PCA calculations and plotting, the tabbed heatmap and PCA view, the C. Elegans lineage tree and cartesian distortion, and the vast majority of the interface design and styling to integrate subplots and controls within the visualization. All programming is accomplished with Javascript, making heavy use of JQuery and D3.
This work is not yet published, but we are considering extending this project to upgrade functionality and performance of this initial tool and publish as a novel tool for exploration of the EPIC dataset.
Demo Draft Paper (PDF) GitHub