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July 14, 2014

Supercomputing Adds Depth to Animal Conservation Efforts

Tiffany Trader

A collaboration between the U.S. Geological Survey (USGS) and the San Diego Zoo Institute for Conservation Research holds new promise for wildlife conservation efforts. The new approach developed by the researchers combines 3D supercomputing and advanced range estimator technologies to track terrestrial, avian, and aquatic wildlife.


A paper detailing the project, called Movement-based Estimation and Visualization of Space Use in 3D for Wildlife Ecology and Conservation, was recently published in the PLoS-ONE online science journal. The three species that were selected were pandas (terrestrial tracking), California condors (air tracking), and dugongs, a close relative of the manatee (ocean-based tracking). The project is generating crucial data for conservation efforts.

The team worked with researchers from the San Diego Supercomputing Center (SDSC) to turn their tracking data into detailed visualizations. In order to create the 3D models the team first had to optimize the codes to make the best use of available supercomputing time.

“We were able to speed up their software by several orders of magnitude,” said Robert Sinkovits, SDSC’s Director of the Scientific Applications Group. “In this case, calculations that had formerly taken four days to complete were finished in less than half an hour.”

The project used two of SDSC’s most powerful computing systems, Gordon and Trestles. A key part of the project is making sure it can scale as it grows. This means minimizing data movement and replication, says Amit Chourasia, senior visualization scientist at SDSC. Chourasia explains that the next step is to fuse additional data about topography and climate in order to better understand the habitats of these animals.

The 3D approach to animal tracking is what sets this research effort apart. While, traditionally ecologists have used 2D tracking systems, the team’s 3D approach adds a vertical component, which is especially important for animals that fly, travel on steep terrain or dive into the water.

“Biologists and ecologists are only beginning to recognize the value of incorporating the vertical aspect into analyses, which more realistically represents the space used by an animal,” states Jeff Tracy, an ecologist at the USGS and lead author of the PLoS-ONE study.

“Disregarding the vertical component may seriously limit understanding of animal habitat use and niche separation,” according to the study’s authors.

While 3D increases realism, it is much more computationally demanding, and these computing challenges have limited increased adoption of the technique. By optimizing the software, the improved tracking method could be a huge boon to conservation efforts, like those that have helped repopulate the California Condor. The population of this endangered animal now stands at approximately 400 birds – up from only 22 in the mid- 1980s. Despite the increase, the effort has been hampered by a lack of understanding about movement and habitat use.

The 3D tracking system will be used as a “predictive management tool to inform conservation efforts to restore condor populations, particularly with regard to emerging threats such as climate change and wind energy impacts,” states team member  James Sheppard, a senior researcher within the Applied Animal Ecology Division of the San Diego Zoo’s Institute for Conservation Research.

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