November 6, 2012
9am PT/ 12 pm ET
Built on SGI UV with 16 TB of shared memory, the Pittsburgh Supercomputing Center's (PSC) Blacklight has become an invaluable tool for assembly and analysis of next-generation sequencing data, including projects in behavioral genomics and metagenomics. â€œNext generation" sequencing tools have taken genomics well beyond the Human Genome Project to studies of nearly every kind of organism. These short-read sequencing technologies can generate in a week what would take a year to generate using prior technology. Consequently, genomics has shifted into data-intensive overdrive. While it's an unprecedented breakthrough for the life sciences, it's also an unprecedented challenge for data processing and analysis.
Blacklight's large shared memory makes it possible to contain entire base-pair datasets in random-access memory (RAM) — dramatically improving workflow and throughput time, as compared to non-shared memory clusters, for genomics assembly and analysis.
Using Blacklight, researchers from Oklahoma State completed the largest metagenome assembly to date, assembling sequencing data from soil with the goal to find enzymes that can efficiently break down non-livestock feed plants, such as switchgrass, wheat straw, and others that have the potential to yield biofuel more efficiently than feed-stock plants like corn. With the assembly requiring nearly 4 Terabytes of RAM, the Oklahoma State team would not have been able to tackle this huge computational challenge on any other system.
- Nick Nystrom, Director, Strategic Applications, Pittsburgh Supercomputing Center
- Phil Blood, Senior Scientific Specialist, Pittsburgh Supercomputing Center
- Brian Couger, Researcher, Oklahoma State University
- Jill Matzke, Director Server Products, SGI
For background info, see: