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Computer Engineering Eminent Scholar Seminar: Computing for Genomics: From Architectures to Algorithms

April 25, 2014 @ 3:55 pm - 5:00 pm

Ravishankar K. Iyer
Coordinated Science Laboratory and
Department of Electrical and Computer Engineering
University of Illinois at Urbana Champaign
Urbana IL

Room 1034 ETB

ABSTRACT: Technological advances in sequencing, mapping, and analyzing genomes is proceeding at an extremely rapid pace, and the resulting explosion of genomics data is becoming difficult to manage. Sequencing human genomes would quickly add up to hundreds of petabytes of data, and the data created by analysis of gene interactions multiplies those further. To achieve the next generation of biological and consequent healthcare breakthroughs, new scalable algorithms and computational models must be researched. The growth of data makes algorithmic scalability a key challenge. Also, there are many quality concerns associated with this massive datasets and the underlying analytics. These concerns include quality differences between each of the NGS platforms that contribute source data, inherent problems associated with short-reads (2nd generation sequencing) and issues related to clinical interpretation. Technologies in use today do not meet the need. Addressing these needs requires deeper understanding of the data and integration of this knowledge into a domain-specific computational platform.
To address these challenges, we have assembled a team of computer engineers/scientists, biologists, bioinformaticians, statisticians, in partnership with industry, hospitals and research laboratories. With NSF support, this team is designing and implementing a computing platform to jointly address the issues of speed and quality control for a range of genomics applications. Our approach includes: defining new algorithmic techniques, constructing better accuracy metrics, extracting parallelism by defining mathematical primitives common to the underlying algorithms, designing new accelerators, and assessing the effect of architectural changes like die-stacked technologies. This talk will describe the underlying architecture and design of the CompGen machine together with early successes in achieving algorithmic efficiencies. Early performance and accuracy analysis from computing environments ranging from Illinois’ Blue Waters Supercomputer to individual VMs provide insight and support of our research.

BIO: Ravishankar K. Iyer
Professor Iyer is the George and Ann Fisher Distinguished Professor of Engineering at the University of Illinois at Urbana-Champaign. He holds joint appointments in the Department of Electrical and Computer Engineering, the Coordinated Science Laboratory (CSL) and the Department of Computer Science and serves as Chief Scientist of the Information Trust Institute. Iyer has led several large successful projects funded by NASA, DARPA and NSF and Industry. He currently is a co-leads the CompGen Center at Illinois. Funded by NSF and partnering with industry leaders, hospitals and research labs, CompGen aims to build new computational platform to address both accuracy and performance issues for a range of genomics applications. Professor Iyer is a Fellow of the American Association for the Advancement of Science, the IEEE, and the ACM. He has received several awards, including the AIAA (American Institute for Aeronautics and Astronautics) Information Systems Award, the IEEE Emanuel R. Piore Award and the 2011 Outstanding Contributions award by the Association of Computing Machinery – Special Interest Group on Security for his fundamental and far-reaching contributions in secure and dependable computing. Professor Iyer is also the recipient of the degree of Doctor Honaris Causa from Toulouse Sabatier University in France.
Host: Dr. Kumar


April 25, 2014
3:55 pm - 5:00 pm