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Biotelemetry Revolution -- Estimating animal space use in 3D to avoid costly environmental impacts

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Robert Sinkovits, Ph.D.
Interim Director for Scientific Computing Applications, SDSC
Expertise: High-performance computing, performance tuning and analysis, software parallelization, network analysis, structural biology

We describe an efficient implementation of a 3D movement-based kernel density estimator (MKDE) for determining animal space use from discrete GPS measurements. This new method provides more accurate results, particularly for species that make large excursions in the vertical dimension. The downside of this approach is that it is much more computationally expensive than simpler, lower-dimensional models. Through a combination of code restructuring, parallelization and performance optimization, we were able to reduce the time to solution by a factor of 1000x, thereby greatly improving the utility of the method. We will describe applications of the 3D MKDE to aquatic, avian and terrestrial species, with an emphasis on the California Condor.

About the Presenter
Robert Sinkovits, Ph.D. leads the scientific applications efforts at the San Diego Supercomputer Center. He has collaborated with researchers spanning a large number of fields including physics, chemistry, astronomy, structural biology, finance and the social sciences, always with an emphasis on making the most effective use of high end computing resources. Before returning to SDSC, he was the primary developer of the AUTO3DEM and IHRSR++ software packages used for solving the structures of icosahedral and helical macromolecular structures, respectively. He has approximately 50 journal publications, book chapters and conference proceedings. He is also an avid cyclist and mountain climber, having summited nearly 300 peaks.