Dennis Jen

As a data visualization engineer at Bluefin Labs, I build tools for visualizing our massive amounts of TV, ad, and social media data. This was a big departure in domain from my work at the Broad Instiute of MIT and Harvard, where I built tools for visualizing genomic features on genomes and tools for understanding comparative genomics. Working with users to devise innovative and thoughtful visualizations to bring insight to their investigations is a passion of mine I discovered while getting my M.S. at the University of North Carolina at Chapel Hill. During my tenure there, I published a first author paper at IEEE Conference on Visualization. In this work, I collaborated with neuroscientists to help them understand where calcium was located on small neuronal structures.

After graduating, I worked at the Pacific Northwest National Laboratory, where I took on several interesting projects, ranging from visualizing relationships between a massive number of documents to helping analysts understand fish moving across a local dam and was awarded a key contributor award for my part. At this time, tabletop displays weren't as prevalent as they are now, and I was fortunate enough to work with a small team investigating user interaction with such a device coupled with a large projector display.

I came to Boston to work at the Martinos Center for Biomedical imaging to work on neuro-imaging projects. I worked mainly with diffusion tensor imaging, an extension of magnetic resonance imaging (MRI), to develop algorithms for understanding the flow of blood in the brain. I was even able to participate in a few of the studies and run various analyses on data collected from my brain.

Projects:

MEDEA: Comparative Genomic Visualization with Adobe Flash

MEDEA is a suite of comparative genome visualization tools that my team and I worked on at the Broad Institute.

The suite of tools consists of the Circular Genome Viewer, Stack Map, ChromoMap, Dot Plot, and Viral Viewer. Each was built in ActionScript and employs different visual representations to reveal similarities and differences between genomes at various levels of zoom and detail.

By using a RESTful service to save the state in the URL, we enabled the user to bookmark and share the current views with collaborators. We played to the strengths of each visualization by allowing users to easily open views of the same genomic region in different tools.

I presented this work in a talk at Pecha Kucha, as well as at posters at retreats and conferences, including IEEE Visualization 2009.

[MEDEA]

ImageSurfer

While at graduate school at The University of North Carolina at Chapel Hill, I took a scientific visualization class. The final project eventually morphed into a full fledged research project where I worked with neuroscientists eager to understand the correlation between two chemicals.

I built a tool for reconstructing the neuronal structures into a surface and then color the surface based on presence of a chemical of interest. Using a six-degree-of-freedom device (or a simple mouse if you didn't happen to have one), the user was able to slice a the structures at arbitrary angles to understand the distribution of the chemical within the structures and perform further analysis.

This project became ImageSurfer and resulted in a first author publication in IEEE Visualization 2004 and a subsequent publication in the Journal of Neuroscience, in addition to posters at the Society for Neuroscience meetings.

1369 Coffee House

1369 Coffee House has been around since 1993, and their original web site was probably built around then too. Gevi Marotz of Design Like You Mean It designed a new site, and with great honor and respect for a Cambridge, MA institution, I implemented it.

Because the owner wanted the site to be easily maintained, to post content to the main page, and change images on other pages easily, I built the web site on a Wordpress platform for simple content management. The programming was done in JavaScript and PHP.

The owner and staff of 1369 Coffee House were very pleased, and the new web site was showcased on Smashing Magazine.

[1369 Coffee House]

Argo

Argo is the Broad Institute's genome annoation and visualization tool that I helped further develop. The tool, built in Java and Swing, was able to provide whole genome gene density overviews and enable biologists to zero in on areas of interest at a gene level or nucleotide level.

The most challenging project I contributed to was in Argo's comparative visualizations. We were charged with building an interactive tool with a variety of levels of detail for comparing multiple genomes. By using a variety of visual encodings, including color, texture, and shape, we were able to highlight areas of genome insertion, deletion, and mutation.

[Argo]

POI-Stats

The goal of the POI-Stats (Path-of-Interest Statistics) algorithm is to calculate the highest probability path between two user-defined seed regions from magnetic resonance diffusion tensor data (to discover pathways in brains). The best path is determined by minimizing the energy of the entire path through randomization of the position of the control points of a spline curve drawn through the data and of the position of the endpoints.

While at the Martinos Center for Biomedical Imaging, I ported this algorithm from its matlab implemention to a C++ version that I integrated into the Insight Toolkit (ITK) and 3D Slicer.