Massive computing contest won with RNA-Seq data analysis

Cloud ComputingThe winner of the Big Science Challenge, a contest convened last year by Cycle Computing to provide $10,000 in cloud computing resources for groundbreaking biomedical research, has successfully completed the first phase of its project while logging more than 115 compute years on the Amazon Cloud.

Victor Ruotti and colleagues from the Morgridge Institute for Research at the University of Wisconsin claimed top prize in the challenge.  The intense computing for Ruotti’s experiment – a pariwise comparison of RNA-Seq signatures for 124 stem cell lines — was performed over a week using very high memory instances – each core had 8 Gigabytes (GB) memory. About 1.6 million jobs were scheduled using Condor, although Stowe says other schedulers such as GridEngine could also be used. Spot availability varied over time – up to a maximum of 8,000 cores concurrently, with an average of 5,000 cores running.

The result was 7-8 Terabytes (TB) BAM files.

“The goal of the Big Science Challenge was to help people think bigger than they normally would, to do things that would be impossible on a local cluster,” said Cycle Computing CEO Jason Stowe

(read more at Bio-IT World…)