“Ruotti’s Run” links stem cells, supercomputing software

In a bold effort to harness the power of supercomputing software for new research with stem cells, Victor Ruotti of the Morgridge Institute for Research has completed a breakthrough project involving more than a “century” of computing time in just one week.

Working in the Thomson lab as part of the Morgridge Institute’s regenerative biology team, Ruotti started the collaborative project with members of the core computational technology team and the University of Wisconsin–Madison’s Center for High Throughput Computing. The effort to develop an indexing system for stems cells and their derivatives quickly gained momentum when Cycle Computing named Ruotti the winner of its Big Science Challenge. The award involved $10,000 of CycleCloud computation time and a $9,500 credit from Amazon Web Services.

Using the power of utility supercomputing, Ruotti developed a system that will allow researchers to quickly classify stem 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 exceed the cost of this run by 100 times, not including the cost of 78 terabytes of cloud storage. Ruotti’s run harnessed the power of 5,000 cores on average, 8,000 cores at peak, and used 78 terabytes of storage in the Amazon Web Services cloud.

Cycle Computing Announces BigScience Challenge Winner
Wisconsin Stem Cell Group Wins Cycle Computing $10,000 Challenge