USU Biologist Collaborates with Intel on Scientific Simulation
For a tense 30 seconds Utah State University biologist Aaron Duffy wondered if he’d be able to make his stage entrance for an interview in Portland, Ore., with Intel Corporation chief technology officer Justin Rattner. The doctoral student had been invited to appear with Rattner during the Nov. 14 opening address of SuperComputing 2009, a premier international conference for high performance computing professionals that draws more than 10,000 attendees each year.
“I could hear the stage crew technician counting down and asking, ‘Aaron, where are you?’” says Duffy, a doctoral student in Professor Paul Wolf’s Plant Evolutionary and Population Genetics Lab.
In the nick of time, Duffy appeared on stage with Rattner not as himself, but as a virtual avatar on a huge screen waving from a futuristic lab overlooking hills teeming with plant life. Duffy, seated at his computer on USU’s Logan campus, was demonstrating the power of harnessing a 3D Web application to simulate a real-world scientific research environment.
“My Web browser crashed just as I was preparing for my entrance but I was able to log back on in time,” says Duffy, who proceeded to present a successful demonstration of his creation “Fernland,” a simulated population of more than 100,000 ferns in an environment with customizable terrain, soil, weather, seasons and physics.
His mishap was apropos, as the title of Rattner’s address was “The Road to High Performance Isn’t Always Paved.” (The 60-minute talk is available online; Duffy’s appearance occurs about 13 minutes into the address.)
In his talk, Rattner stressed the need for a “killer app” or powerful application platform with adequately robust computing power that will allow users to aggressively drive research and development and advance simulation technology. He suggested that 3D Web tools, as Duffy’s example demonstrated, might fill the bill.
Duffy, who began his studies at USU in 2006, stumbled onto “OpenSimulator,” an open source server platform for hosting virtual worlds, last fall. He was searching for a software tool to simulate how environmental changes and unique aspects of the fern life cycle affect the evolution of fern populations. While working in “OpenSim,” as the application is also known, Duffy sought help from other users and learned of “ScienceSim,” an Intel-sponsored community of researchers and technology strategists working to advance experimentation in virtual worlds.
“Intel saved the day and helped me scale my simulation to a useful size,” he says. “ScienceSim provides the perfect collaborative environment for divergent areas of science. Intel’s programmers were eager to find real-world scientific applications like mine to push open simulation technology in ways it had never been pushed before.”
With Fernland, Duffy simulates the entire life cycle of ferns, which includes three distinct stages: spore, gametophyte and sporophyte.
“We can view how these plants respond to such factors as weather, altitude and overcrowding at each stage of life and track their genetic makeup,” he says. “Over time, we can observe patterns of genetic diversity that emerge.”
In the process, Duffy collects data on each plant and can graphically illustrate genetic distribution at varied altitudes, in varied soils and in varied temperature ranges.
“I could hear the stage crew technician counting down and asking, ‘Aaron, where are you?’” says Duffy, a doctoral student in Professor Paul Wolf’s Plant Evolutionary and Population Genetics Lab.
In the nick of time, Duffy appeared on stage with Rattner not as himself, but as a virtual avatar on a huge screen waving from a futuristic lab overlooking hills teeming with plant life. Duffy, seated at his computer on USU’s Logan campus, was demonstrating the power of harnessing a 3D Web application to simulate a real-world scientific research environment.
“My Web browser crashed just as I was preparing for my entrance but I was able to log back on in time,” says Duffy, who proceeded to present a successful demonstration of his creation “Fernland,” a simulated population of more than 100,000 ferns in an environment with customizable terrain, soil, weather, seasons and physics.
His mishap was apropos, as the title of Rattner’s address was “The Road to High Performance Isn’t Always Paved.” (The 60-minute talk is available online; Duffy’s appearance occurs about 13 minutes into the address.)
In his talk, Rattner stressed the need for a “killer app” or powerful application platform with adequately robust computing power that will allow users to aggressively drive research and development and advance simulation technology. He suggested that 3D Web tools, as Duffy’s example demonstrated, might fill the bill.
Duffy, who began his studies at USU in 2006, stumbled onto “OpenSimulator,” an open source server platform for hosting virtual worlds, last fall. He was searching for a software tool to simulate how environmental changes and unique aspects of the fern life cycle affect the evolution of fern populations. While working in “OpenSim,” as the application is also known, Duffy sought help from other users and learned of “ScienceSim,” an Intel-sponsored community of researchers and technology strategists working to advance experimentation in virtual worlds.
“Intel saved the day and helped me scale my simulation to a useful size,” he says. “ScienceSim provides the perfect collaborative environment for divergent areas of science. Intel’s programmers were eager to find real-world scientific applications like mine to push open simulation technology in ways it had never been pushed before.”
With Fernland, Duffy simulates the entire life cycle of ferns, which includes three distinct stages: spore, gametophyte and sporophyte.
“We can view how these plants respond to such factors as weather, altitude and overcrowding at each stage of life and track their genetic makeup,” he says. “Over time, we can observe patterns of genetic diversity that emerge.”
In the process, Duffy collects data on each plant and can graphically illustrate genetic distribution at varied altitudes, in varied soils and in varied temperature ranges.
“We wouldn’t be able to do this in the field,” he says. “The amount of data collection required would be staggering if not impossible. The simulation offers quick snapshots of a very lengthy biological process.”
Duffy sees simulation as a valuable teaching tool.
“This highly visual environment makes it easy to see the connection between mathematical models of genetics and the patterns we see in real-world populations,” he says. “Plus, we can help students understand the whole data collection and research process before they ever set foot in the field or laboratory. Virtual world technology opens up great opportunities for education and outreach.”
Related Links
ScienceSim
Wolf Lab
USU Department of Biology
USU College of Science
Contact: Aaron Duffy
Writer: Mary-Ann Muffoletto, 435-797-3517
Duffy sees simulation as a valuable teaching tool.
“This highly visual environment makes it easy to see the connection between mathematical models of genetics and the patterns we see in real-world populations,” he says. “Plus, we can help students understand the whole data collection and research process before they ever set foot in the field or laboratory. Virtual world technology opens up great opportunities for education and outreach.”
Related Links
ScienceSim
Wolf Lab
USU Department of Biology
USU College of Science
Contact: Aaron Duffy
Writer: Mary-Ann Muffoletto, 435-797-3517
Posing in his 'Fernland' simulation as an avatar, USU doctoral student Aaron Duffy participated in a live interview with Intel CTO Justin Rattner during the opening address of the recent SuperComputing ’09 conference in Portland, Ore.
A biologist in Paul Wolf's Plant Evolutionary and Population Genetics Lab, Duffy is using virtual world simulation to study the evolution of fern populations.
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