Compgen Initiative: New Interfaces Between Computing and Genomics

Gene Robinson and Ravishankar K. Iyer
R K Shyamasundar
Wednesday, 5 Dec 2012, 14:30 to 15:30
AG-66 (Lecture Theatre)
Given the rate of innovation in gene sequencing technologies, through which the cost of sequencing a genome has fallen exponentially for decades, the amount of genomic data is quickly becoming difficult to manage and index. Although the genomes of two members of a species or the genomes of two closely-related species share significant structure, much of the science necessary to identify and understand the implications of this structure has yet to be done, in part because of the relative unavailability, until quite recently, of large data sets. As a result, many algorithmic approaches rely on simpler comparisons of genetic sequences or genomes and optimization techniques that may not scale to the massive data sets that are already becoming common. Indeed, current algorithms and the underlying hardware and software architectures are increasingly becoming the limiting factors. The large volume of genomic data now available provides an opportunity to identify the structural relationships that will support algorithmic innovations and configurable hardware extensions to enable scalable comparisons with a broad range of existing data.  This opportunity could lead to major advances in scientific understanding through a combination of improved statistical models, algorithmic advances, efficient parallel computation, and genomic data management.   This talk will outline some of the opportunities for collaboration being investigated by an inter-disciplinary group of researchers centered at the Institute of Genomic Biology working in close collaboration with computer engineers and scientists in the departments of Electrical and Computer Engineering and Computer Science at Illinois. 

Professor Gene Robinson is the Swanlund Chair Professor and the Director of the Institute for Genomic Biology  with appointments in the department of Entomology and the Beckman Institute at the University of Illinois at Urbana Champaign.

Professor Ravishankar K. Iyer is the George and Ann Fisher Distinguished Professor of Engineering with appointments is the Department of Electrical ad Computer Engineering, Computers Science and the Coordinated Science Laboratory at the University of Illinois at Urbana Champaign.