Phylogenetic trees are used by researchers across multiple fields of study to display historical relationships between organisms or genes. Trees are used to examine the speciation process in evolutionary biology, to classify families of viruses in epidemiology, to demonstrate co-speciation in host and pathogen studies, and to explore genetic changes occurring during the disease process in cancer, among other applications. Due to their complexity and the amount of data they present in visual form, phylogenetic trees have generally been difficult to render for publication and challenging to directly interact with in digital form. To address these limitations, we developed PhyloPen, an experimental novel multi-touch and pen application that renders a phylogenetic tree and allows users to interactively navigate within the tree, examining nodes, branches, and auxiliary information, and annotate the tree for note-taking and collaboration. We present a discussion of the interactions implemented in PhyloPen and the results of a formative study that examines how the application was received after use by practicing biologists — faculty members and graduate students in the discipline. These results are to be later used for a fully supported implementation of the software where the community will be welcomed to participate in its development.
Affiliation: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida, USA
Software engineer by day, aspiring PhD student by night. I graduated from the University of Central Florida with a B.S. in Computer Science in 2011 and an M.S. in Computer Science in 2012. I work at ASRI, a R&D company, as a senior software engineer. I am a PhD student at UCF, with Dr. Hassan Foroosh as my current advisor. My PhD research is currently compressive sensing in the field of computer vision, but I also have experience in software integration, accelerated processing, and sensor data visualization, as well as computer graphics and traditional, pen-and-touch, and 3D (a la Kinect) user interface design and implementation.