We request funds to purchase 120 parallel computer nodes and 10 high-memory, many-core nodes to support computationally- and data-intensive NIH-funded biomedical research at Vanderbilt University. The proposed system will facilitate a wide range of compute-intensive applications and specific data-intensive applications that require high-memory and/or tightly coupled supercomputer performance, at a small fraction of the cost. This system will be built aside our successful 6000-processor parallel computer known as the Advanced Computing Center for Research and Education (ACCRE) at Vanderbilt, which supports high- performance computing for research ranging from elementary particle investigations using the Large Hadron Collider, to model system genetics and human behavioral studies. Despite our successes with the existing cluster, state-of-the-art biomedical computing has been in high demand and recently these data sets have outgrown the capability of our current system. These projects include macromolecular structure prediction, next-generation sequencing, vaccine design, and multi-dimensional imaging. ACCRE users have access to the instrument and training through our established infrastructure. ACCRE is a grass-roots organization that was initially created by faculty from throughout the institution and later awarded the strong institutional support it enjoys today. It was initially established through a Major Research instrumentation Grant from NIH in 2004 along with Departments of Defense and Energy grants to the School of Engineering and Department of Physics. ACCRE was upgraded through NIH Shared Instrumentation Grants awarded in 2009 and 2012. ACCRE is managed by three co-directors, one each from the College of Arts and Science, School of Engineering, and School of Medicine. Policy and procedures are set by the co-directors upon recommendations of the Faculty Advisory Board, which consists of ten active PI users. The proposed parallel computer will be used directly by forty NIH-funded research groups and its impact will reach many more investigators through outreach efforts of centralized facilities such as our Center for Structural Biology, Biostatistics Collaboration Center, Vanderbilt Vaccine Center, VANTAGE, Vanderbilt Institute for Imaging Science, and Mass Spectrometry Research Center. In this manner, the requested equipment will support more than 100 NIH grants. The ten major users of the requested system have primary appointments in nine different departments within the Vanderbilt University School of Medicine, College of Arts and Science, and School of Engineering. Research programs with unmet demand for high memory and high-core nodes are concentrated in genetics. Together, the 130 requested nodes will replace 200 six-year- old nodes, making it possible to carry out data and computationally intensive biomedical investigations that would otherwise not be feasible.
High-performance computing has become an indispensible tool in biomedical research, and is currently used for analyzing the extremely large data sets produced by biological and medical imaging, genomics, proteomics, and increasingly detailed simulations of biological processes. These computations can often guide research down a more efficient pathway that saves resources and effort. The cost-effective super- computer architecture that we are requesting will support key research projects at Vanderbilt in Personalized Medicine, Immunology, Structural Biology, Imaging, and Psychology.
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