Researchers developing 'BIGDATA' toolbox to help genome researchers

Oct. 3, 2012 — Today's life scientists are producing genomes galore. But there's a problem: The latest DNA sequencing instruments are burying researchers in trillions of bytes of data and overwhelming existing tools in biological computing. It doesn't help that there's a variety of sequencing instruments feeding a diverse set of applications.

Iowa State University's Srinivas Aluru is leading a research team that's developing a set of solutions using high performance computing. The researchers want to develop core techniques, parallel algorithms and software libraries to help researchers adapt parallel computing techniques to high-throughput DNA sequencing, the next generation of sequencing technologies.

Those technologies are now ubiquitous, "enabling single investigators with limited budgets to carry out what could only be accomplished by an international network of major sequencing centers just a decade ago," said Aluru, the Ross Martin Mehl and Marylyne Munas Mehl Professor of Computer Engineering at Iowa State.

"Seven years ago we were able to sequence DNA one fragment at a time," he said. "Now researchers can read up to 6 billion DNA sequences in one experiment.

"How do we address these big data issues?"

A three-year, $2 million grant from the BIGDATA program of the National Science Foundation and the National Institutes of Health will support the search for a solution by Aluru and researchers from Iowa State, Stanford University, Virginia Tech and the University of Michigan. In addition to Aluru, the project's leaders at Iowa State are Patrick Schnable, Iowa State's Baker Professor of Agronomy and director of the centers for Plant Genomics and Carbon Capturing Crops, and Jaroslaw Zola, a former research assistant professor in electrical and computer engineering who recently moved to Rutgers University.

The majority of the grant -- $1.3 million -- will support research at Iowa State. And Aluru is quick to say that none of the grant will support hardware development.

Researchers will start by identifying a large set of building blocks frequently used in genomic studies. They'll develop the parallel algorithms and high performance implementations needed to do the necessary data analysis. And they'll wrap all of those technologies in software libraries researchers can access for help. On top of all that, they'll design a domain specific language that automatically generates computing codes for researchers.

Aluru said that should be much more effective than asking high performance computing specialists to develop parallel approaches to each and every application.

"The goal is to empower the broader community to benefit from clever parallel algorithms, highly tuned implementations and specialized high performance computing hardware, without requiring expertise in any of these," says a summary of the research project.

Aluru said the resulting software libraries will be fully open-sourced. Researchers will be free to use the libraries while developing, editing and modifying them as needed.

"We're hoping this approach can be the most cost-effective and fastest way to gain adoption in the research community," Aluru said. "We want to get everybody up to speed using high performance computing."

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Researchers identify ways to exploit 'cloud browsers' for large-scale, anonymous computing

Nov. 28, 2012 — Researchers from North Carolina State University and the University of Oregon have found a way to exploit cloud-based Web browsers, using them to perform large-scale computing tasks anonymously. The finding has potential ramifications for the security of "cloud browser" services.

At issue are cloud browsers, which create a Web interface in the cloud so that computing is done there rather than on a user's machine. This is particularly useful for mobile devices, such as smartphones, which have limited computing power.The cloud-computing paradigm pools the computational power and storage of multiple computers, allowing shared resources for multiple users.

"Think of a cloud browser as being just like the browser on your desktop computer, but working entirely in the cloud and providing only the resulting image to your screen," says Dr. William Enck, an assistant professor of computer science at NC State and co-author of a paper describing the research.

Because these cloud browsers are designed to perform complex functions, the researchers wanted to see if they could be used to perform a series of large-scale computations that had nothing to do with browsing. Specifically, the researchers wanted to determine if they could perform those functions using the "MapReduce" technique developed by Google, which facilitates coordinated computation involving parallel efforts by multiple machines.

The research team knew that coordinating any new series of computations would entail passing large packets of data between different nodes, or cloud browsers. To address this challenge, researchers stored data packets on bit.ly and other URL-shortening sites, and then passed the resulting "links" between various nodes.

Using this technique, the researchers were able to perform standard computation functions using data packets that were 1, 10 and 100 megabytes in size. "It could have been much larger," Enck says, "but we did not want to be an undue burden on any of the free services we were using."

"We've shown that this can be done," Enck adds. "And one of the broader ramifications of this is that it could be done anonymously. For instance, a third party could easily abuse these systems, taking the free computational power and using it to crack passwords."

However, Enck says cloud browsers can protect themselves to some extent by requiring users to create accounts -- and then putting limits on how those accounts are used. This would make it easier to detect potential problems.

The paper, "Abusing Cloud-Based Browsers for Fun and Profit," will be presented Dec. 6 at the 2012 Annual Computer Security Applications Conference in Orlando, Fla. The paper was co-authored by Vasant Tendulkar and Ashwin Shashidharan, graduate students at NC State, and Joe Pletcher, Ryan Snyder and Dr. Kevin Butler, of the University of Oregon. The research was supported by the National Science Foundation and the U.S. Army Research Office.

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