Microsoft Makes HPC Moves at Supercomputing 2010

Microsoft made a series of high-performance computing moves at the Supercomputing 2010 show, including exposing a critical medical research tool, NCBI BLAST, to the Windows Azure cloud platform.

Microsoft made a series of high-performance computing (HPC) announcements at the Supercomputing 2010 conference, including implementing an innovative medical search tool available on the Microsoft Windows Azure cloud platform.

At Supercomputing 2010, which ran Nov. 13-19, Microsoft announced the release of the National Center for Biotechnology Information Basic Local Alignment Search Tool, also known as NCBI BLAST, on Windows Azure. The new application enables a broader community of scientists to combine desktop resources with the power of cloud computing for biological research. At the conference, Microsoft showcased the enormous scale of the application on Windows Azure, demonstrating its use for 100 billion comparisons of protein sequences in a database managed by the NCBI.

Built on Windows Azure, NCBI BLAST on Windows Azure enables researchers to take advantage of the scalability of the Windows Azure platform to perform analysis of vast proteomics and genomic data in the cloud. BLAST is a suite of programs that is designed to search all available sequence databases for similarities between a protein or DNA query and known sequences. BLAST allows quick matching of near and distant sequence relationships, providing scores that allow the user to distinguish real matches from background hits with a high degree of statistical accuracy.

BLAST on Windows Azure extends the power of the BLAST suite of programs by allowing researchers to rent processing time on the Windows Azure cloud platform, Microsoft said. The availability of these programs over the cloud allows laboratories, or even individuals, to have large-scale computational resources at their disposal at a very low cost per run, the company said. For researchers who don't have access to large computer resources, this greatly increases the options to analyze their data. They can now undertake more complex analyses or try different approaches that were simply not feasible before.

"NCBI BLAST on Windows Azure gives all research organizations the same computing resources that traditionally only the largest labs have been able to afford," said Bob Muglia, president of the Server and Tools Business at Microsoft, in a statement. "It shows how Windows Azure provides the genuine platform-as-a-service capabilities that technical computing applications need to extract insights from massive data, in order to help solve some of the world's biggest challenges across science, business and government."

Researchers in bioinformatics, energy, drug research and many other fields use BLAST to sift through large databases, to help identify new animal species, improve drug effectiveness and produce biofuels, as well as for other purposes. NCBI BLAST on Windows Azure provides a user-friendly Web interface and access to Windows Azure cloud computing for very large BLAST computations, as well as smaller-scale operations. The application will allow scientists to use and collaborate with their private data collections, as well as data hosted on Windows Azure, including NCBI public protein data collections and the results of Microsoft's large protein comparison.

The NCBI BLAST on Windows Azure software is available from Microsoft at no cost, and Windows Azure resources are available at no charge to many researchers through Microsoft's Global Cloud Research Engagement Initiative. More information is available at

In an interview with eWEEK, Kyril Faenov, general manager of HPC, who is leading the Technical Computing Group at Microsoft, said, "We expect a large number of bioinformatics researchers to take advantage of this."

Faenov said researchers at Seattle Children's Hospital were able to solve a six-year problem in one week using NCBI BLAST on Windows Azure. According to a Microsoft Research article, at Seattle Children's Hospital, researchers interested in protein interactions wanted to know more about the interrelationships of known protein sequences. Due to the sheer number of known proteins-nearly 10 million-this would have been a very difficult problem for even the most state-of-the art computer to solve. When the researchers first approached the Microsoft Extreme Computing Group (XCG) to see if NCBI BLAST on Windows Azure could help solve this problem, initial estimates indicated that it would take a single computer more than six years to find the results. But by leveraging the power of the cloud, they could cut the computing time substantially.

BLAST on Windows Azure enabled the researchers to split millions of protein sequences into groups and distribute them to data centers in multiple countries (spanning two continents) for analysis. By using the cloud, the researchers obtained results in about one week. This has been the largest research project to date run on Windows Azure, Microsoft said.