The advance of next-generation sequencing (NGS) technology has dramatically reduced the cost of genome sequencing, which is a key technology to enable precision medicine. However, processing and analyzing the huge amount of data collected from NGS sequencers introduces significant computation challenges, and has become the bottleneck in many research and clinical applications. This has become a major workload for the Center for Domain-Specific Computing (CDSC) for acceleration in the past three years. In this talk, I shall present our ongoing study on characterizing and accelerating the best practice pipeline for genomic sequencing and analysis recommended by the Broad Institute. Our study includes the use of SSD and hardware accelerators on individual workstations, local computing clusters, and public clouds, such as Amazon AWS and Google Compute Engine.

Jason Cong received his B.S. degree in computer science from Peking University in 1985, his M.S. and Ph. D. degrees in computer science from the University of Illinois at Urbana-Champaign in 1987 and 1990, respectively. Currently, he is a Distinguished Chancellor’s Professor at the UCLA Computer Science Department, the director of Center for Customizable Domain-Specific Computing (CDSC). He served as the department chair from 2005 to 2008. Dr. Cong’s research interests include electronic design automation, energy-efficient computing, customized computing for big-data applications, and highly scalable algorithms. He has over 400 publications in these areas, including 10 best paper awards, and the 2011 ACM/IEEE A. Richard Newton Technical Impact Award in Electric Design Automation. He was elected to IEEE Fellow in 2000 and ACM Fellow in 2008. He received the IEEE Circuits and System (CAS) Society Technical Achievement Award in 2010 and the IEEE Computer Society Technical Achievement Award in 2016. He was elected to the National Academy of Engineering in 2017.

Dr. Cong has graduated 35 PhD students. One of them is now an IEEE Fellow, six of them got the highly competitive NSF Career Award, one of them received the ACM SIGDA Outstanding Dissertation Award and another received the EDAA Outstanding PhD Dissertation Award. Nine of them are now faculty members in major research universities, including Cornell, Fudan Univ., Georgia Tech., Peking Univ., Purdue, SUNY Binghamton, UCLA, UIUC, and UT Austin. Dr. Cong has successfully co-founded three companies with his students and postdocs, including Aplus Design Technologies for FPGA physical synthesis and architecture evaluation (acquired by Magma in 2003, now part of Synopsys), AutoESL Design Technologies for high-level synthesis (acquired by Xilinx in 2011), and Falcon Computing Solutions, a startup dedicated to enabling FPGA-based customized computing in data centers. He is also a distinguished visiting professor at Peking University.