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U Pittsburgh Receives IBM HPC Node for Biology Modeling Work


Using in silico modeling, researchers are able to create images of liver inflammation and cancer that are similar to what might be seen under the microscope.

The University of Pittsburgh in Pennsylvania has received an infusion of high performance computing technology from IBM for its intensive studies in biology. The university's McGowan Institute for Regenerative Medicine, which brings together scientists studying tissue engineering, cell therapies, and artificial organs and "biodevices," received an IBM research award for its "in silico" work, which uses computer simulations to explore biological pathways and test therapeutic interventions.

This type of modeling is similar to those used to generate animated movie characters. But in this case, it's used to build representational models of organs and diseases and see at a molecular level the effects of drugs on them. Pitt scientists are applying computational techniques to simulate, for example, inflamed liver cells morphing into cancer. That allows them to see not only how tumors develop, but how drugs or other interventions could affect disease progression.

IBM has donated an IBM Power 575 water-cooled supercomputer, also known as the Hydro-Cluster, along with software to the research center to enable scientists to do high performance computing for their work, which involves collaboration between both the engineering and biosciences departments. The computer currently features a single high-performance computing node running 32 POWER6 processor cores at 4.7 GHz, expandable up to 448 cores. Through the use of cold plates, chilled coolant is pumped over the processors to lower overheating and reduce energy usage.

IBM stocked the hardware with WebSphere middleware, DB2 database software, Rational development software, and Cognos software for collaboration and data. The company also did installation of the node. The gift, which is a Shared University Research (SUR) Award, allows researchers at the university to gain access to IBM's researchers. They've already met with IBM's cloud team, and additional collaboration with IBM Research is planned, according to a spokesman.


Yoram Vodovotz, director of the Center for Inflammation and Regenerative Modeling at the University of Pittsburgh.

Researchers at the institute said they intend to use the IBM technology to expand their capabilities in biological modeling. Yoram Vodovotz, professor of surgery at Pitt's School of Medicine, a director at the institute, and principal investigator for the IBM SUR grant work, said that in silico modeling can so closely mimic reality that it can produce images that look much the same as the tissues that pathologists see under the microscope. "But to make the next set of quantum leaps, we require a computational foundation and related resources, which we call the Platform for Innovative Translational Modeling-Assisted Projects, or PITMAP," Vodovotz said.

The computer technology, both hardware and software, will simulate the multitude of molecular interactions that occur both in normal tissues and those affected by disease or illness.

"We aim to cover three bases: virtual clinical trials, personalized diagnostics, and rational drug or device design," Vodovotz added. "With these techniques, we could reduce the number of participants needed for human trials by creating some of them in silico; understand individual variation by exploring it in a digital world; and better visualize how the body responds when a drug or device enters it."

About the Author

Dian Schaffhauser is a writer who covers technology and business for a number of publications. Contact her at dian@dischaffhauser.com.

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