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понеделник, 9 май 2016 г.

Two Intel-powered supercomputers help revise Charles Darwin’s work two centuries later

Supercomputers Help Refine Darwin’s “Tree of Life”


How many species of life exist on Earth? UC Berkeley researchers are using supercomputers to study DNA of thousands of species to help put them in their place in the tree of life that Darwin began in 1837, according to this brief by Slashdot Media Contributing Editor Wylie Wong
UC-Berkeley researchers recently deployed supercomputers to draw up a new “tree of life,” which outlines the evolution of life on Earth and now includes more than 1,000 new types of bacteria and single-celled microorganisms called Archaea.
Charles Darwin had diagrammed the first tree of life in 1837 in attempt to show how plants, animals and bacteria are related to one another. In the newly revised tree of life, UC Berkeley professor Jill Banfield and former UC Berkeley postdoctoral researcher Laura Hug studied the DNA of more than 3,000 species: 2,072 known species and 1,011 newly discovered organisms whose genomes were recently sequenced, according to a recent New York Times article.
The new microscopic organisms come from a variety of environments, including hot springs, salt flats, terrestrial and wetland sediments, meadow soil and even the inside of a dolphin’s mouth, a UC-Berkeley press release said.
“The tree of life is one of the most important organizing principles in biology,” Banfield said in the release. “The new depiction will be of use not only to biologists who study microbial ecology, but also biochemists searching for novel genes and researchers studying evolution and earth history.”
They used the Intel Xeon-based Gordon and Comet supercomputers from the San Diego Supercomputer Center (SDSC) to compare the DNA information between species and build the new tree of life.
More specifically, they used the CIPRES Science Gateway, a web-based portal that allows researchers to use SDSC’s supercomputers to explore evolutionary relationships between species.
“The CIPRES Science Gateway was critical to our work,” said Hug, who is now on the biology faculty at the University of Waterloo in Canada. “I spent over a month attempting to conduct these jobs on other servers with no success – the jobs always failed prior to finishing.”
Using SDSC’s Gordon and Comet, they successfully ran two jobs over a period of five days, using a total of 48 cores. Their study was recently published in the journal Nature Microbiology.
Posted on April 29, 2016 by Wylie, Slashdot Media Contributing Editor
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