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Presentation: Visualizing Phylogenetic Landscapes: A Case for Agile Research Computing Cyberinfrastructures
Visualizing Phylogenetic Landscapes: A Case for Agile Research Computing Cyberinfrastructures
March 7, 2013
1 - 3 p.m.
401 and 402 Walter Library
Research Associate, Department of Scientific Computing
Director of High Performance Computing
Florida State University
In this talk I will discuss the merits and the challenges of visualizing phylogenetic landscapes and relate this work to the development of FSU’s multidisciplinary Research Computing Center. Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. The steps required to get a phylogenetic landscape from raw DNA exemplify the challenges that a growing number of research disciplines face today. These challenges often have more to do with the alignment of data storage, network, computing, and visualization resources than with their capacity or performance. Research computing at FSU puts a premium on core-infrastructure components, so that a wide variety of systems can be easily deployed to support application workflow requirements.
About the Speaker:
James (Jim) Wilgenbusch is a Research Associate in the Department of Scientific Computing and the founding director of Florida State University’s Research Computing Center. In addition to his management responsibilities, Jim maintains research activities in the study and implementation of models and search algorithms used in phylogenetic inference. Prior to coming to FSU in 2001, he worked at the Smithsonian Institution's Laboratory of Molecular Systematics (now the Laboratories of Analytical Biology) and the Division of Amphibians and Reptiles. While at the Smithsonian Institution Jim employed molecular techniques to obtain DNA sequences for several groups of lizards in order to learn about their evolutionary history and worked on the support and development of widely used programs for phylogenetic inference. Jim did his Ph.D. training at George Mason University in Fairfax, VA. After completing his undergraduate degree in Biology, Jim was an Associate Director of George Mason University's (GMU) Center for Experiential Education in Fairfax, Virginia and managed the opening of Bull Run Marina under a joint management agreement between GMU and the Northern Virginia Regional Park Authority. When not working behind a computer, Jim is either spending time with his family, running, or figuring out ways to combine both activities.