Magazine article University Business

High-Performance Computing: How the Investment in Heavy-Duty Computer Processing Power Is Paying off in Research Output

Magazine article University Business

High-Performance Computing: How the Investment in Heavy-Duty Computer Processing Power Is Paying off in Research Output

Article excerpt

Imagine thinking thousands of thoughts at the same time. What if each thought was one piece of a really big problem--a problem now solvable in hours or days rather than years because of this simultaneous thought process? That's what high-performance computing (HPC) does.

HPC is a lot of computer processing power linked together, thinking through and solving different pieces of big problems in parallel. HPC makes it possible to answer big questions in a fraction of the time it would take when using individual desktop PCs. With HPC resources, some problems can be solved that could never be solved before.

With this problem-solving capability, scientists start to ask questions they would never have thought to ask. And universities are increasingly the hubs of the HPC systems that ask these questions, solve these problems, and change the world.

High-performance computing does, however, come at a high cost. "The typical investment varies from under $100,000 per year (within an individual research group) to tens of millions per year," says Henry J. Neeman, director of the OU Supercomputer Center for Education & Research (OSCER) at Oklahoma University.

While the majority of colleges and universities don't make this investment, nearly one-quarter do. When colleges and universities with high, medium, and low research intensity were surveyed by the Educause Center for Applied Research, 23 percent of respondents reported providing central IT (centralized HPC) services for research computing. That's according to the November 2012 report "Research Computing: The Enabling Role of Information Technology."

Here's what researchers at three institutions are doing to make use of their investments in HPC.

HPC and Cancer Research

In the University of Pittsburgh Department of Biomedical Informatics, Xinghua Lu and his colleague Songjian Lu study signaling pathways in tumors, which lead to improved cancer treatments. Their research relies on use of the Pittsburgh Supercomputing Center's Sherlock, which is a modified YarcData uRiKa graph analytics appliance from Cray. A National Science Foundation Strategic Technologies for Cyberinfrastructure award funded the Sherlock project at a cost of approximately $1 million, shares Nicholas A. Nystrom, director of strategic applications for the Pittsburgh Supercomputing Center.

Signaling pathways, according to the NCI Dictionary of Cancer Terms, are groups of molecules in a cell that work together to control one or more cell functions. As Lu and Lu note, these pathways consist primarily of signaling proteins that transmit cellular signals, which regulate cell activity such as cell death and cell proliferation.

"Cancers are mainly caused by the mutations in the proteins affecting certain signaling pathways," says Songjian Lu, a post-doctoral associate who works in Xinghua Lu's lab.

They identify chains of signals that cause cancer, using existing technologies to compare tumor cells with normal cells and detect the mutated genes in tumors. Then, using knowledge mining, data mining, and graph models, they ultimately connect the genetic mutations in the tumors to the mutated proteins that cause cancer.

The calculations these researchers run to discover the mutated proteins are huge. As biological systems are complex, they explain, many computational problems stemming from the biological problems are so difficult that even supercomputers cannot solve them exactly. This does not, however, prevent them from using HPC to pinpoint the mutated proteins that cause the genetic mutations in cancer.

In the end, this research is very important because new and existing drugs that treat cancer often target cellular signaling pathways. "better understanding of perturbed [changed] signaling pathways will help design new drugs to target these pathways," says Xinghua Lu.

And for institutional administrators, highlighting research projects is an opportunity to share a good story with potential donors and students. …

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