Newswise — (New York, NY – November 18, 2019) Mount Sinai Health System, one of New York’s largest integrated health systems, announced today that it has been awarded a grant from the U.S. Department of Health and Human Services valued at $2 million to build a second “big omics data engine” (BODE 2) that will enable Mount Sinai researchers to explore more complex scientific questions more quickly.
“Supercomputers have become essential in biomedical scientific discovery, and Mount Sinai has been a leader on this front, making investments in computational and data science that are advancing our understanding of and ability to treat complex diseases,” said Dennis S. Charney, MD, Anne and Joel Ehrenkranz Dean, Icahn School of Medicine at Mount Sinai, and President for Academic Affairs, Mount Sinai Health System. “With BODE 2, we are renewing our commitment to push the boundaries of scientific research, tackle questions that we did not previously have the computational power to take on, and achieve breakthroughs that transform clinical care worldwide.”
BODE 2 will launch at the end of this year and will replace BODE, a previous supercomputer that was used by 61 basic and translational researchers at Mount Sinai representing more than $100 million in NIH funding, along with their collaborators at 75 external institutions. BODE enabled scientific findings that appeared in more than 167 publications, including Nature and Science, with a total of 2,427 citations in three years.
“BODE has proven to be a vital tool for groundbreaking research across a broad range of fields, but as Mount Sinai’s faculty continues to grow, there is concurrent growth in research initiatives, necessitating investment in a new supercomputer that has sufficient computational throughput and storage space to support this activity,” said Patricia Kovatch, Senior Associate Dean for Scientific Computing and Data Science at the Icahn School of Medicine at Mount Sinai, member of the Icahn Institute for Data Science and Genomic Technology, and Associate Professor of Genetics and Genomic Sciences, and Pharmacological Sciences.
The new BODE 2 supercomputer is a Lenovo ThinkSystem SR360 that consists of 3,840 Intel Cascade Lake cores, with 15 terabytes of memory, 14 petabytes of raw storage, and 11 petabytes of usable storage. It will produce approximately 28 million core compute hours per year at a frequency of 2.6 GHz and it will have a peak speed of 220 teraflops per second—approximately double that of BODE. Researchers will have broad, user-friendly, integrated access to more diverse data sources with robust, secure, bidirectional information flow between research and point-of-care programs. BODE 2 will also enable innovative application of translational bioinformatics research and data-driven medicine.
“Based on our experiences with BODE, BODE 2 is designed to provide our researchers and clinicians, and their external partners in Mount Sinai-led national research projects, with the necessary infrastructure to achieve faster results for greater scientific throughput, increased fidelity in their simulations and analysis, and seamless migration of research applications to the software environment for enhanced scientific productivity,” Ms. Kovatch said. “Computing capability of this size and speed is not available widely, and Mount Sinai’s investment in building this infrastructure will translate into more robust genetics and population analysis, gene expression, machine learning, and structural and chemical biology investigations, and result in new insights and advances in a wide range of diseases including Alzheimer’s, autism, influenza, prostate cancer, schizophrenia, and substance use disorders.”
Research projects that will be facilitated by BODE 2 include:
Understanding the Mechanism of SPl1-Dependent Alzheimer Disease Risk: BODE 2 will provide both the necessary storage for whole-genome-sequencing data sets from more than 10,000 study subjects and the processing power (approximately 12 million compute hours) to analyze the data using machine learning techniques. The analyses will be used to enhance current treatments or explore new therapies.
The Trans-Omics for Precision Medicine (TOPMed) Program: BODE 2 will provide the 1.75 petabytes of storage necessary for the whole-genome-sequencing data, other omics, and molecular, behavioral, imaging, environmental, and clinical data for this unprecedented exploration of the biological causes underlying heart, blood, lung, and sleep disorders. It will also provide the hundreds of terabytes required for intermediate results storage, and the approximately 7 million compute hours necessary for the highest-powered analysis of the TOPMed data. These processes can be greatly accelerated on BODE 2 versus running them on standalone machines.
“This new supercomputer will enable us to mine deep databases of genomic and clinical information using machine-learning approaches to propel the personalized medicine of today into better medicine tomorrow,” said Eimear Kenny, PhD, Associate Professor of Medicine (General Internal Medicine), and Genetics and Genomic Sciences, at the Icahn School of Medicine at Mount Sinai, Director of the Center for Genomic Health, and a Principal Investigator of the TOPMed Program. “The technology will help fuel innovative research programs to further our understanding of disease progression and management.”
About the Mount Sinai Health System
The Mount Sinai Health System is New York City's largest integrated delivery system, encompassing eight hospitals, a leading medical school, and a vast network of ambulatory practices throughout the greater New York region. Mount Sinai's vision is to produce the safest care, the highest quality, the highest satisfaction, the best access and the best value of any health system in the nation. The Health System includes approximately 7,480 primary and specialty care physicians; 11 joint-venture ambulatory surgery centers; more than 410 ambulatory practices throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and 31 affiliated community health centers. The Icahn School of Medicine is one of three medical schools that have earned distinction by multiple indicators: ranked in the top 20 by U.S. News & World Report's "Best Medical Schools", aligned with a U.S. News & World Report's "Honor Roll" Hospital, No. 12 in the nation for National Institutes of Health funding, and among the top 10 most innovative research institutions as ranked by the journal Nature in its Nature Innovation Index. This reflects a special level of excellence in education, clinical practice, and research. The Mount Sinai Hospital is ranked No. 14 on U.S. News & World Report's "Honor Roll" of top U.S. hospitals; it is one of the nation's top 20 hospitals in Cardiology/Heart Surgery, Diabetes/Endocrinology, Gastroenterology/GI Surgery, Geriatrics, Gynecology, Nephrology, Neurology/Neurosurgery, and Orthopedics in the 2019-2020 "Best Hospitals" issue. Mount Sinai's Kravis Children's Hospital also is ranked nationally in five out of ten pediatric specialties by U.S. News & World Report. The New York Eye and Ear Infirmary of Mount Sinai is ranked 12th nationally for Ophthalmology, Mount Sinai St. Lukes and Mount Sinai West are ranked 23rd nationally for Nephrology and 25th for Diabetes/Endocrinology, and Mount Sinai South Nassau is ranked 35th nationally for Urology. Mount Sinai Beth Israel, Mount Sinai St. Luke's, Mount Sinai West, and Mount Sinai South Nassau are ranked regionally.