Seminars & Events

Argonne Leadership Computing Facility
"Scalable Solutions for DNA Sequence Analysis"

DATE: March 11, 2010 to March 11, 2010
TIME: 10:30 AM - 11:30 AM
SPEAKER: MIchael Schatz, PhD Candidate, University of Maryland
LOCATION: Building 240 / Conference Room 4301, Argonne National Labortory

Description:
We are at the dawn of a new era in computational biology. DNA sequencing projects that required years of effort and hundreds of millions of dollars of equipment just a few years ago, can now be performed quickly and cheaply by individual labs. This dramatic shift is expanding the scale and scope of sequencing to previously unimaginable limits, and will ultimately lead to new discoveries of our basic biology, the diversity of life, and personalized medicine. However, these ambitious goals can only be realized if we can develop new computational methods that can effectively analyze the overwhelming volumes of data generated.
In my presentation, I’ll describe my research developing efficient methods for analyzing large biological datasets, including by using the parallel computing framework MapReduce developed by Google. My programs CloudBurst, Crossbow, and Contrail demonstrate how this technology can be applied to the critical tasks of large-scale alignment and genome assembly, enabling genotyping and de novo assembly of whole human genomes from billions of short reads in an afternoon. Coupled with inexpensive cloud computing, these programs can quickly, cheaply, and accurately analyze tremendous biological datasets and have the potential to make otherwise infeasible studies practical.

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