Chinese Crunch Human Genome With Videogame Chips.

Wired News (01/06/12) Eric Smalley

BGI, a Chinese supercomputer lab, recently switched to servers that use graphics processing units (GPUs) built by NVIDIA, which enabled it to cut its genome analysis time by more than an order of magnitude. The feat that enabled BGI and NVIDIA to accomplish this was porting key genome analysis tools to NVIDIA’s GPU architecture, a nontrivial accomplishment that the open source community and others have been working toward, says the Jackson Laboratory’s Gregg TeHennepe. With GPUs, BGI gets faster results for its existing algorithms or it can use more sensitive algorithms to achieve better results, says bioinformatics consultant Martin Gollery. In addition, GPUs can be used to analyze genomes that could allow researchers studying biology and drug development to better treat patients. “The researcher now no longer has to own a sequencer or a cluster, and does not have to have employees to manage both of these technologies,” Gollery says. GPU-enabled cloud services will be useful once the data is in the cloud, and cloud service providers are increasingly adding GPU capabilities. Another advantage of GPU-enabled cloud services is that research organizations can test GPU versions of algorithms without having to have a GPU system in-house, Gollery notes.

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