sponsored byACMIEEE The International Conference for High Performance 
Computing, Networking, Storage and Analysis
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SCHEDULE: NOV 15-20, 2015

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IGen: The Illinois Genomics Execution Environment

SESSION: Regular & ACM Student Research Competition Poster Reception

EVENT TYPE: Posters, Receptions, ACM Student Research Competition

EVENT TAG(S): HPC Beginner Friendly, ACM Student Research Competition Poster

TIME: 5:15PM - 7:00PM

SESSION CHAIR(S): Michela Becchi, Manish Parashar, Dorian C. Arnold

AUTHOR(S):Subho Sankar Banerjee

ROOM:Level 4 - Lobby


There has been a great optimism for the usage of DNA sequence data in clinical practice, notably for diagnostics and developing personalized treatments tailored to an individual's genome. This poster, presents a study of software tools used in identifying and characterizing mutations in a genome. We present IGen, a runtime framework which executes this workflow as a data-flow graph over a partitioned global address space. Preliminary results on the Blue Waters supercomputer show that IGen is able to accelerate single node performance (alignment - 1.2x, variant calling - 9x), as well as distribute the computation across several machines with near-linear scaling. Theoretical models for performance of the entire workflow suggest that IGen will have a ~3x improvement in runtime on a single node with near linear scaling across multiple nodes.

Chair/Author Details:

Michela Becchi, Manish Parashar, Dorian C. Arnold (Chair) - University of Missouri|Rutgers University|University of New Mexico|

Subho Sankar Banerjee - University of Illinois at Urbana-Champaign

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