Utility supercomputing leader and stem cell researcher team up to index gene expression

NEW YORK, Oct. 2 — Cycle Computing today announced that its inaugural Big Science Challenge winner, Victor Ruotti, of the Morgridge Institute for Research, has successfully completed his breakthrough utility supercomputing run. A computational biologist, Ruotti applied his $10,000 of CycleCloud computation time and $9,500 of credit from Amazon Web Services (AWS) to begin constructing a knowledgebase indexing system for stem cells and their derivatives. BigData met BigCompute as Cycle's software ran one million compute hours against 78 terabytes of data for Ruotti on AWS – over a compute century of run-time in just one week, for the cost of four servers, or 100 times cheaper than buying the cluster.

Ruotti works at the Morgridge Institute for Research as part of the regenerative biology team, in the laboratory of stem cell researcher James Thomson, who in 1998 was the first to successfully isolate human embryonic stem cells. Using the power of utility supercomputing, Ruotti is furthering the research on stem cells and their derivatives by creating an indexing system of the cells, which will allow researchers to quickly classify the cells based on their expression pattern and identify genes and regions of the genome that are critical for establishing and maintaining cell states that have potential for clinical applications.

"By using Cycle's utility supercomputing software, and infrastructure from Amazon Web Services, we were able to run 115 years of computation in just one week," said Ruotti. "We now have the components needed to build an index to help identify cells in a laboratory setting, based upon the genes that have been expressed. The goal is to use these results to build a database to speed development of potential therapies using stem cells. The emergence of utility supercomputing as an available and affordable research tool could completely transform the class of problem we can solve, enabling larger breakthroughs than were possible before."

Ruotti's run included a total of 1,003,404 core-hours against 11,955 pairs of samples processed. The compute price was $0.0175 per core-hour and $19,555 total for the run. Buying 400 servers to get the equivalent cluster would have cost 100 times the cost of this run, not including the cost of 78 TB of storage. Ruotti's run harnessed the power of 5,000 cores on average, 8,000 cores at peak, and used 78TB of storage in the AWS cloud.

The Big Science Challenge winner was selected based on the project's long-term benefit to humanity and its originality, creativity and suitability to run on CycleCloud clusters launched within AWS. The finalists were judged by Jason Stowe, CEO, Cycle Computing, and a panel of industry luminaries, including Kevin Davies, editor-in-chief of Bio-IT World, Matt Wood, technology evangelist for AWS and Peter S. Shenkin, vice president at Schrödinger.

AWS provided an additional $9,500 in credits for the winner of the Big Science Challenge, and Matt Wood, product manager for big data and high performance computing, AWS, participated as a judge. He said, "AWS provides the resources to allow scientists to deliver on the vision of their research, by removing the constraints of traditional IT with a low cost, productive, utility environment. We congratulate Victor Ruotti on this great accomplishment."

"Cycle launched the Big Science Challenge to give researchers like Victor the opportunity to take advantage of utility supercomputing technology to do science that could benefit humanity," said Stowe. "This million hour run exemplifies the classes of breakthroughs possible with utility supercomputing, made possible by the cloud and Cycle's software. We are very excited about Victor's inventive work to move forward the state of the art in IPS experimentation, and applaud his efforts to make stem cells more accessible for disease treatment."

Cycle Computing is also pleased to announce the next Cycle BigScience Challenge, and will be opening for applications in the coming weeks. For more information, please see the Cycle Computing blog at http://blog.cyclecomputing.com.

About Cycle Computing:

Cycle Computing is the leader in Utility Supercomputing software. As a bootstrapped, profitable software company, Cycle delivers proven, secure and flexible high performance computing (HPC) and data solutions since 2005. Cycle helps clients maximize existing infrastructure and speed computations on servers, VMs, and on-demand in the cloud. Cycle's products help clients maximize internal infrastructure and increase power as research demands, like the 10000-core cluster for Genentech and the 30000+ core cluster for a Top 5 Pharma that were covered in Wired, TheRegister, BusinessWeek, Bio-IT World, and Forbes. Starting with three initial Fortune 100 clients, Cycle has grown to deploy proven implementations at Fortune 500s, SMBs and government and academic institutions including JP Morgan Chase, Purdue University, Pfizer and Lockheed Martin.

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Source: Cycle Computing