PSC Joins Pitt and Carnegie Mellon to Launch New Effort to Improve Multi-scale Modeling of Biological Systems
NIH Awards $9.3 Million to Establish Biomedical Technology Research Center
By filling in the missing pieces between modeling efforts at disparate scales of structural biology, cell modeling and large-scale image analysis, this new collaborative initiative seeks to identify the molecular and cellular mechanisms that control neurotransmission and signaling events, which in turn could lead to the development of novel treatments for nervous system disorders.
“With these tools, our goal is to better understand and appreciate the impact of defective proteins and interactions at the cellular level, and their effects on the central nervous system behavior,” said Ivet Bahar, Ph.D., professor and John K. Vries Chair of the Department of Computational and Systems Biology at the Pitt School of Medicine. “We hope to bridge the gaps between molecular-, cellular- and tissue-level information to build integrated models of cell signaling and regulation.”
Bahar is the principal investigator for the award, titled “High Performance Computing for Multi-scale Modeling of Biological Systems,” from the NIH’s National Institute of General Medical Sciences. Robert F. Murphy, Ph.D., director of the Lane Center for Computational Biology in Carnegie Mellon’s School of Computer Science, will lead CMU’s participation. The Pittsburgh Supercomputing Center’s long-established National Resource for Biomedical Supercomputing (NRBSC), headed by Markus Dittrich, Ph.D., was seminal to and is the third major partner in the new BTRC. The collaboration also includes the Salk Institute for Biological Studies in La Jolla, Calif.
“We have imagined this new center as a Pittsburgh center, joining the two universities, the University of Pittsburgh and Carnegie Mellon, with PSC strengths in training and biomedical supercomputing,” said Dr. Murphy, the Ray and Stephanie Lane Professor of Computational Biology and professor of biological sciences, biomedical engineering and machine learning. “We now have an opportunity to combine that work with work in the Lane Center on image-derived modeling of cellular organization and machine learning for structural biology to go beyond what we’ve done before.”
Dr. Dittrich said the collaboration opens many opportunities for his National Resource for Biomedical Supercomputing (NRBSC). “As core members in the new BTRC we continue our work in cellular modeling, structural biology, and large-scale volumetric image analysis and welcome the synergy of working with the outstanding computational biology programs at the University of Pittsburgh and Carnegie Mellon,” he said.
As part of the NIH grant, a supplementary award of $1.1 million provides two years of additional support for the Anton supercomputer, which the NRBSC has made available to U.S. biomedical scientists since 2010. The special-purpose computing system from D.E. Shaw Research has achieved exceptional results in the simulation of proteins and other biomolecules.
Dr. Bahar’s team will tailor computational models for five biomedical research projects including neurotransmitter signaling, immune cell regulation and neuronal circuit reconstruction that are under way at Pitt, Caltech, Allen Brain Institute (Seattle), and UT Southwestern Medical Center.
“Until now, experimental scientists have been collecting data that are not testable by computational methods, while the computational scientists have been building models and making predictions that can’t be verified experimentally,” Dr. Bahar noted. “We aim to bridge this communication gap, too, so that we can solve relevant problems computationally while generating new hypotheses that can be tested in the lab.”
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About the University of Pittsburgh School of Medicine
As one of the nation’s leading academic centers for biomedical research, the University of Pittsburgh School of Medicine integrates advanced technology with basic science across a broad range of disciplines in a continuous quest to harness the power of new knowledge and improve the human condition. Driven mainly by the School of Medicine and its affiliates, Pitt has ranked among the top 10 recipients of funding from the National Institutes of Health since 1997.
Likewise, the School of Medicine is equally committed to advancing the quality and strength of its medical and graduate education programs, for which it is recognized as an innovative leader, and to training highly skilled, compassionate clinicians and creative scientists well-equipped to engage in world-class research. The School of Medicine is the academic partner of UPMC, which has collaborated with the University to raise the standard of medical excellence in Pittsburgh and to position health care as a driving force behind the region’s economy. For more information about the School of Medicine, see www.medschool.pitt.edu.
About Carnegie Mellon University
Carnegie Mellon (www.cmu.edu) is a private, internationally ranked research university with programs in areas ranging from science, technology and business, to public policy, the humanities and the arts. More than 11,000 students in the university’s seven schools and colleges benefit from a small student-to-faculty ratio and an education characterized by its focus on creating and implementing solutions for real problems, interdisciplinary collaboration and innovation. A global university, Carnegie Mellon’s main campus in the United States is in Pittsburgh, Pa. It has campuses in California’s Silicon Valley and Qatar, and programs in Africa, Asia, Australia, Europe and Mexico. The university is in the midst of “Inspire Innovation: The Campaign for Carnegie Mellon University,” which aims to build its endowment, support faculty, students and innovative research, and enhance the physical campus with equipment and facility improvements.
About the Pittsburgh Supercomputing Center
The Pittsburgh Supercomputing Center (https://wp-dev.psc.edu) is a joint effort of Carnegie Mellon University and the University of Pittsburgh together with Westinghouse Electric Company. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry, and is a partner in the National Science Foundation XSEDE program. The National Resource for Biomedical Supercomputing (NRBSC) was established in 1987. As part of PSC, the NRBSC focuses on computational biomedical research at the interface of supercomputing and the life sciences.
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Anita Srikameswaran / Pitt Schools of the Health Sciences / 412-578-9193 / SrikamAV@upmc.edu
Byron Spice / Carnegie Mellon University / 412-268-9068 / bspice@cs.cmu.edu
Cheryl Begandy / Pittsburgh Supercomputing Center / begandy@psc.edu / 412.268.4960
Shandra Williams / Pittsburgh Supercomputing Center / shandraw@psc.edu / 412.268.4960
