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New supercomputer will chase novel genes

June 16, 2011
Technical University of Denmark (DTU)
A new supercomputer having Northern Europe's largest 'shared memory' can quickly and efficiently process the enormous quantities of genetic information, which is key to advances in green biotechnology, using DNA from tens of thousands of microorganisms to create new cell factories.

With 4000 times as much memory as an ordinary PC, the new supercomputer enables DTU researchers to rapidly identify new genes and proteins that can be used in future sustainable biotechnology industrial processes. The computer, which is an Altix UV 1000 model supplied by SGI, has been named Anakyklosis which is the Greek word for recycling. The name reflects its importance to a biologically sustainable future.

"Systems Biology involves research that combines and integrates extremely large data sets, including genetic information. The new supercomputer has a huge so-called 'shared memory', which enables us to handle these data more quickly and flexibly. The computer's capacity will considerably expand our ability to answer the basic biological questions we face, such as how to get a cell to produce something it was not originally made for," explains Søren Brunak, director at the Center for Biological Sequence Analysis at DTU Systems Biology, where Anakyklosis already has been linked up to other supercomputers.

"The need for larger and faster computers has become very urgent due to the development of the metagenomics research area. This deals with mapping the entire genome content of bacterial communities, such as those found in the deep oceans, in wastewater or in our own gut. The resulting amount of data is several thousand times larger than the entire human genome, "says senior researcher Nikolaj Blom from the new Novo Nordisk Foundation Center for Biosustainability at DTU, which has funded the computer. Metagenomics systems biology will be one of the center's six main research areas, and the supercomputer will be part of the center's search for new enzymes for the biotech industry and the construction of biological cell factories. The goal of the center's research is to produce tomorrow's chemicals in living cells from inexpensive and sustainable raw materials and thereby reduce world dependence on oil.

"It's mainly the memory of our computers, which currently limits how much data we can process at a time, and thus how quickly we make progress with our analysis," says Thomas Sicheritz-Pontén, who will direct the research in metagenomics at the Novo Nordisk Foundation Center for Biosustainability. "Anakyklosis can hold the equivalent of 2500 human genomes in its working memory at once, so it opens up new opportunities for systems biology research."

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Materials provided by Technical University of Denmark (DTU). Note: Content may be edited for style and length.

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Technical University of Denmark (DTU). "New supercomputer will chase novel genes." ScienceDaily. ScienceDaily, 16 June 2011. <>.
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