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NSF Awards Grant to U of Maryland for Cloud-Based Next-Gen Sequence Analysis

NEW YORK (GenomeWeb News) – The National Science Foundation said today that it has awarded a research team at the University of Maryland a grant to develop software for next-generation sequence analysis that will run on the "cloud" — high-performance compute clusters that can be accessed over the Internet.

The grant, awarded to Mihai Pop and Steven Salzberg at the university's Center for Bioinformatics and Computational Biology, is one of 14 grants totaling more than $5 million that the NSF announced today as part of its Cluster Exploratory Program, or CluE. Under the program, funded researchers will use software and services running on an IBM/Google cloud to explore new ideas for data-intensive scientific computing.

According to an NSF database, Pop and Salzberg have been awarded $379,919 to date for the two-year project.

The grant "will be used to find out if remote clusters of computers are a better option for DNA sequence analysis than local clusters of computers," Pop said in a statement.

"The first question is how to best split up the process of DNA sequence analysis to fit these computer clusters," Pop said. "The second is whether or not the benefits of cloud computing outweigh the costs of data transfer and storage."

According the grant abstract, Pop and Salzberg will focus on developing algorithms for sequence alignment and sequence assembly, and will adapt string matching and graph algorithms to the "Map-Reduce paradigm" — a software framework that Google developed for distributed computing.