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SDSC's 'big data' expertise aiding genomics research
Date:3/20/2012

alth (NIH) Roadmap for Bioinformatics and Computational Biology.

Conceived as a collaborative computational environment to improve access to health data and software, iDASH provides biomedical and behavior scientists with access to a sophisticated, secure privacy-preserving infrastructure to contribute, integrate, and analyze their data, as well as potentially reuse data from others (given permissions set up by data contributors) and leverage other research results.

"The iDASH center addresses fundamental challenges to research progress by providing a secure, privacy-preserving computational environment in which researchers can analyze molecular, clinical, and behavioral data," said Ohno-Machado.

SDSC also has multiple collaborations with the Scripps Translational Science Institute (STSI), which has a dedicated 1gigabit-per-second (Gb/s) network connection to the center, along with 140 terabytes of online project storage. STSI has purchased time on SDSC's Triton Resource to conduct research on a number of projects.

One such collaboration is called the Human Tumor Study, or HuTS, which is using SDSC's Triton Resource to search for genome variants between blood and tumor tissue. Software used in this project includes the Genome Analysis Toolkit (GATK), the SOAPdenovo assembler, and various aligners such as ATAC, BLAT, and BWA.

Another collaboration involving SDSC, STSI, and others is called W115. In this project, Pfeiffer is using the Velvet and ABySS assemblers and the ATAC and BFAST aligners on the Triton Resource to study the full genome sequence of a 115 year-old woman to determine how many mutations occur in a long, healthy lifetime.

Further collaborations between SDSC and other genomic institutions including STSI are expected, said Norman, noting that Gordon and its data storage facilities have the bandwidth needed for such research. "The end goal here is to develop a rapid learning system for guiding indiv
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Contact: Jan Zverina
jzverina@sdsc.edu
858-534-5111
University of California - San Diego
Source:Eurekalert

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