Sequences to Systems: Creating the CompGen Engine at Illinois
10 May 2016 - 10 May 2016

The growth of sequencing data now far outstrips today’s computer technologies with genomic data quadrupling every year while compute power at best doubling. Many bioinformatics algorithms rely on direct comparisons of nucleotide sequences and optimization combined with statistical techniques that do not scale to massive datasets. To realize the biological and healthcare innovations and breakthroughs promised by advances in genome sequencing, new and disruptive algorithms and computational models must be invented. To this end, working with a multi-disciplinary team of computer engineers/scientists, biologists, clinicians and statisticians, we have designed the CompGen engine - a software framework supported by custom FPGA based accelerators to significantly speed up the variant calling workflows, while maintaining its accuracy.

While accelerating variant calling is often an essential first step, it is indeed the subsequent analysis of the determined variants jointly with clinical and other data that is necessary to derive patient-specific actionable intelligence. Described as predictive hypotheses, such information can then be used by clinicians and biologists for accurate diagnoses or discovery testing in the labs, thereby reducing costs and time to scientific and clinical breakthroughs. Some examples our work include: unsupervised learning to infer drug mechanisms in breast cancer, game theoretic approach to predicting lung adenocarcinoma, probabilistic graphical models to study diabetic populations in Singapore and prediction of brain trauma.

This talk will outline the features and performance of our NSF funded and industry supported project aimed at building the CompGen Engine as well as subsequent analysis, in collaboration with Mayo Clinic and with NUH in Singapore to derive actionable intelligence from sequenced and clinical data.

Ravishankar K. Iyer Coordinated Science Laboratory & Institute for Genomic Biology
Department of Electrical and Computer Engineering
University of Illinois at Urbana-Champaign

Ravishankar 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 and is affiliate faculty of the National Center for Supercomputing Applications (NCSA) and the Carl R. Woese Institute for Genomic Biology at Illinois. 

Iyer has led several large successful projects funded by the National Aeronautics and Space Administration (NASA), Defense Advanced Research Projects Agency (DARPA), National Science Foundation (NSF), and industry. He currently co-leads the CompGen Initiative at Illinois. Funded by NSF and partnering with industry leaders, hospitals, and research laboratories, CompGen aims to build a 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 Institute of Electrical and Electronics Engineers (IEEE), and the Association for Computing Machinery (ACM). He has received several awards, including the American Institute of Aeronautics and Astronautics (AIAA) 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.

No of Participants: 13