New Field of 'Computational Ecology' Uses Electronic Circuit Theory to

Model Wildlife Habitat

    WALTHAM, Mass., April 17 /PRNewswire/ -- Researchers at the University
 of California, Santa Barbara (UCSB) are harnessing supercomputers and
 electronic circuit theory to help save wildlife from ever-shrinking
 habitats in an emerging scientific field called "computational ecology."
 The project is run by the University's National Center for Ecological
 Analysis and Synthesis (NCEAS).
     NCEAS scientists are applying electronic circuit theory to model
 wildlife migration and gene flow across fragmented landscapes. The research
 could be instrumental in smart conservation planning, helping organizations
 decide which lands to preserve or restore - and where to best invest their
 tight conservation budgets - in order to preserve habitat and connectivity
 for wildlife populations.
     Due to the massive volume of landscape data and the novel application
 of algorithms from circuit theory, NCEAS is working to speed up their code
 using state of the art sparse linear solvers, graph computations,
 vectorization and parallelization of their code with Interactive
 Supercomputing Inc.'s (ISC) Star-P(TM). The result has been a dramatic
 reduction in computing time from days to minutes on their 8-core server.
     "It turns out that circuit theory shares a surprising number of
 properties with ecological theory describing animal movements and
 connectivity," said Brad McRae, the NCEAS project leader. "We can now
 represent landscapes as conductive surfaces - with features like forests
 and highways having different resistance to movement - and analyze
 connectivity across them using powerful circuit algorithms. Unlike standard
 conservation planning tools, these algorithms simultaneously incorporate
 all possible pathways when predicting how corridors, barriers, and other
 features affect movement and gene flow over large areas."
     Corridors are areas that connect important habitats in human-altered
 landscapes. They provide natural avenues along which animals can travel,
 plants can propagate, genetic interchange can occur, species can move in
 response to environmental changes and natural disasters, and threatened
 populations can be replenished from other areas. A good example is "Y2Y,"
 or the Yellowstone to Yukon corridor, where U.S. and Canadian conservation
 organizations are trying to identify which habitats to conserve to protect
 species from harmful decline or extinction.
     In applying their software to these problems, NCEAS scientists have
 modeled mountain lion movements in Southern California to identify
 important connective habitats and corridors. In Central America they
 modeled how habitat connectivity affects gene flow among threatened
 populations of mahogany throughout the species' range. They are also
 analyzing connectivity among populations of wolverines, kit foxes and
 jaguars. For each species, researchers analyze geographic datasets
 representing habitat suitability over vast areas - in some cases spanning
 entire continents.
     The challenge was choosing between how large or how finely-scaled the
 maps should be, explained McRae. "Even a relatively small region like the
 three- county area of Southern California can contain millions of raster
 cells, but our computing resources limited how finely we could grid those
 locations. While a mountain lion might perceive its habitat at a scale of
 about 100 meters, we originally had to increase the cell sizes to around a
 kilometer to keep our data requirements manageable," he said. "And even at
 these lower resolutions, running the models on a single-processor computer
 without optimized code took three days to complete."
     A key step of the NCEAS simulations is a computation on a large graph
 (or network) that represents the connectivity of the landscape. UCSB
 Computer Scientist Viral Shah worked with the NCEAS researchers to
 integrate their code with GAPDT, a Star-P toolbox for graph computation
 developed by Shah and John Gilbert of UCSB's Combinatorial Scientific
 Computing Laboratory together with ISC Vice President of Advanced Research
 Steve Reinhardt. Said Shah, "The graph toolbox allows researchers who are
 not experts in the field of combinatorial scientific computing to leverage
 its methods in their own research."
     "The combination of vectorization with Star-P's graph toolbox and
 efficient sparse linear solvers has allowed scientists to take full
 advantage of their 8-processor server (with 32 gigabytes of memory) to run
 their models," says Reinhardt. "The result: scientists can now model larger
 maps with much finer grids, while cutting computing time from three days to
 about 15 minutes for typical problems."
     Star-P is an interactive parallel computing platform that lets
 scientists use their preferred desktop tools - MATLAB(R), Python, R and
 others - to model landscape connectivity, but run the models interactively
 while gaining the benefits of scalable HPC solutions. It eliminates the
 need to re-program the models in C, FORTRAN or MPI languages to run on the
 parallel computer, dramatically improving the researchers' productivity.
     "Habitat reduction and fragmentation are accelerating the decline of
 many native wildlife species," said Ilya Mirman, vice president of
 marketing at ISC. "NCEAS' novel approach of applying circuit theory to
 solve this problem blends well with Star-P's novel way of making parallel
 computing available to anyone."
     About the National Center for Ecological Analysis and Synthesis
     The National Center for Ecological Analysis and Synthesis (NCEAS)
 provides the intellectual atmosphere, facilities, equipment, and staff
 support to promote the analysis and synthesis of ecological information.
 Since 1995, NCEAS has hosted 3,500 individuals and supported 400 projects
 that have yielded more than 1,000 scientific articles. The projects have
 produced a wide array of outcomes, from specific results to general
 knowledge about ecology and its application to conservation and the
 management of resources. The Center has engaged hundreds of graduate
 students and grade school children, and has developed information access
 tools that are becoming the standard for the discipline.
     About Interactive Supercomputing
     Interactive Supercomputing (ISC) launched in 2004 to commercialize
 Star-P, an interactive parallel computing platform. With automatic
 parallelization and interactive execution of existing desktop simulation
 applications, Star-P merges two previously distinct environments - desktop
 computers and high performance servers - into one. Based in Waltham, Mass.,
 the privately held company markets Star-P for a range of biomedical,
 financial, and government laboratory research applications. Additional
 information is available at www.interactivesupercomputing.com.
     Star-P is a trademark of Interactive Supercomputing Inc. All other
 trademarks mentioned herein are the property of their respective owners.
     Contacts:
     Ilya Mirman                              Michelle Dillon
     Interactive Supercomputing               Beaupre & Co. Public Relations
     781-419-5088                             603-559-5835
                                              mdillon@beaupre.com
 
 

SOURCE Interactive Supercomputing

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