You ought to be in pictures

IBM grant allows University of Pittsburgh researchers to use high-powered in silico modeling techniques

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PITTSBURGH—Using high-powered computing technology providedto them through an award from Armonk, N.Y.-based IBM, the University ofPittsburgh's McGowan Institute for Regenerative Medicine is borrowing similartechniques as used for special effects in films to study chronic hepatitis,liver cancer and other diseases through in silico models—with IBM noting that Pitt researchers "have begun buildingastonishingly realistic models of organs and diseases, and seeingmolecular-level effects of drugs on them."
By using computational techniques to simulate inflamed livercells morphing into cancer—instead of creating imaginary characters to fillmovie battle scenes, for example—the researchers are seeing not only how tumorsdevelop, but how drugs or other interventions could affect disease progression.
According to IBM and Pitt, the level of in silico modeling being put to work through thiscorporate-academic pairing so closely mimics reality that it can produce imagesvery similar to what pathologists see with tissues under the microscope. Sofar, the Pitt research team has already simulated liver tissue to study how achronic hepatitis infection can lead to liver cancer, simulated lung tissues tostudy viral infection and chronic obstructive pulmonary disease, and simulatedskin to study how patients with spinal cord injuries develop pressure ulcers.
The project uses an IBM supercomputer—the IBM Power575—which is put to work on such computationally-intensive workloads such asweather and climate modeling, physics, fluid dynamics and biological research.The project is part of a Shared University Research (SUR) award to Pitt fromIBM, under which IBM will provide its hardware, software and services, and itties into IBM's "A Smarter Planet" initiatives.
Although Dr. Yoram Vodovotz, director of the Center forInflammation and Regenerative Modeling at the McGowan Institute and a professorof surgery at Pitt's School of Medicine, is putting the IBM technology to workon a variety of disease modeling tasks, one of his core goals is to study therole of immune system-regulated inflammatory pathways in a variety ofconditions. Inflammation, he notes, seems to lie at the root of many diseasesaffecting both industrialized and developing societies. The computer technologyfrom IBM, both on the hardware and software sides, will simulate the multitudeof molecular interactions that occur both in normal tissues and those affectedby disease or illness.
"I think the world has come to a general consensus thatinflammation plays large roles in many disease state that we are concernedwith, from wound healing to trauma, neurodegenerative diseases to cancer, andmore," Vodovotz says. "But while that may sound like we've found a simpleconnection between many diverse conditions, it's complicated, becauseinflammation is the ultimate 'no free lunch' paradigm. There is no simple wayto handle one aspect of inflammation with a compensatory response that mightcause additional problems elsewhere in the body."
Much of the work has been in a diagnostic andpathology-oriented vein, but Vodovotz and his team actually have three broadgoals moving forward: personalized diagnostics, the creation of virtualclinical trials, and rational drug and device design.
Computer modeling isn't new for the Pitt researchers, butthe power of their equipment both for processing, analysis and storage has beenfar more limited than they would like over the years. Vodovotz says that the insilico modeling power he can bring to bearwith the IBM technology can help him and his fellow Pitt researchers understandbasic biological processes better, screen drugs computationally to determinetheir impact on the human body, focus in on the best intervention for a givendisease, shorten the treatment evaluation process—and through all that, greatlycut the time and expense of getting drugs developed and onto the market.
"With these techniques, we could reduce the number ofparticipants needed for human trials by creating some of them in silico, understand individual variation by exploring it ina digital world, and better visualize how the body responds when a drug ordevice enters it," Vodovotz explains. "We want to use this technology to applymore engineering-style principles instead of just brute-force testing our waythrough things or using reductionist thought patterns as to how a drug orprocess might work. Instead, we want to run as much as possible in simulation."
This is not IBM's largest SUR Award, but it is in excess of$500,000, which makes it one the largest that IBM has awarded this year, notesHolli Haswell of the External Relations department of IBM Global Healthcare andLife Sciences. The SUR Award program is designed to, among other things,increase access to and successful use of IBM technologies for research and incurriculum, and it strives to connect researchers at universities with IBMResearch, IBM Life Sciences, IBM Global Services and IBM's development andproduct labs.
Speaking to the power of the SUR Awards to help advanceresearch in biological, pharmaceutical and many other intensive researchefforts, IBM Global University Programs Director Jim Spohrer remarks that hehas passed by California's Moffett Federal Airfield numerous times in dailytravel in Silicon Valley, and made note of the huge wind tunnel structures onthe site.
"They are still used for research, but not very often anymore," hesays, "because these are the kind of things we can do on computers now so muchmore efficiently and cost effectively."
Spohrer says that out of the more than 5,000 universityrelationships IBM has formed worldwide, this one with Pitt stands out for it'swide-ranging potential, which is why this award is one of IBM's larger ones."Each year, we're going to see more and more of what we do now in wet labsbeing done in silico," he says. "It'sgoing to allow us to model the world more accurately and advance science morerapidly."

Smarter is cooler
ARMONK, N.Y—The IBM Power 575 supercomputing node being putto use at the University of Pittsburgh for disease modeling and other purposesoffers "a highly scalable system with extreme parallel processing performanceand dense, modular packaging" for high-performance computing applications likeweather and climate modeling, computational chemistry, physics, computer-aidedengineering, computational fluid dynamics and petroleum exploration. With asmany as 448 POWER6 processor cores per frame, each one running at 4.7 GHz andsupported by up to 3.5 terabytes of memory per frame, the 32-core Power 575supercomputing node is designed for speed and tuned for performance, notes IBMGlobal University Programs Director Jim Spohrer.

But just as IBM's "A Smarter Planet" initiative is trying tomake better use of resources and research by connecting industry with academiaand academics with other academics across the planet, so too is it looking tomake supercomputer a much "greener" process.
"One of the things I don't think gets enough press is thatnot only are we deploying these tremendously more powerful computing systems,"Spohrer says, "but we're bringing down the problems of overheating and ofenergy usage, which is good for the environment and also bringing down theinfrastructure cost of research."
IBM touts that with the computing nodes injected with achilled coolant to enable peak performance, "this system is a supersonic racecar on the IT highway."
Reportedly, this Power 575 system uses a first-of-its-kindsystem in which water-chilled copper plates are located above eachmicroprocessor, continually removing heat from the electronics. IBM says thatthe Power 575 can reduce the number of air-conditioning units required in atypical customer configuration of clusters by more than 80 percent, and IBMscientists estimate that water can be up to 4,000-times more effective incooling computer systems than air.

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