By Kevin Davies
March 13, 2012 | Victor Ruotti, a computational biologist at the Morgridge Institute for Research, University of Wisconsin-Madison, has won the 2012 CycleCloud BigScience Challenge. Ruotti will be awarded $10,000 of computation time on the Amazon cloud—or the equivalent of eight hours on a 30,000-core cluster.
Cycle Computing founder and CEO Jason Stowe announced the contest a few months ago, seeking to encourage and reward exciting and impactful research projects from non-profit organizations “to further humanity and state-of-the-art research using utility supercomputing.” In addition to Stowe, the contest judges included Matt Wood (technology evangelist, Amazon Web Services), Peter Shenkin (VP, Schrödinger) and Kevin Davies (editor, Bio-IT World).
The submission from Ruotti—who works in the laboratory of famed stem cell researcher James Thomson at UW—detailed the construction of a knowledgebase for human embryonic stem cells (hES) using the power of utility supercomputing. To harness the therapeutic potential of hES cells and their derivatives, researchers must first acquire a genetic fingerprint or profile of the various cell types, which requires hours of computational time.
“When I first approached James Thomson, he said, ‘Oh really, you can do that?!’ We’re really excited to work with Cycle Computing and starting this big run… The entire lab is extremely excited about this approach we’re taking,” Ruotti told Bio-IT World.
His group is trying to find the means to identify various cell types that are created during the process of stem cell differentiation in various experiments. By building a stem cell encyclopedia of sorts, “We hope to aid every single experiment done in the lab, because we’ll be able to find the identity of the cells in every experiment.” Ruotti says the resource will allow his colleagues to identify a range of cell types with high probability, allowing biologists to verify the results.
“By having this index in place, we could have a really fast turnaround,” Ruotti continued, enabling the larger group to translate basic research findings into the clinic. “We want to have the ability to recognize components of diseases, to cure diseases as well as to identity key components of a particular pathway for treatment.”
“The high throughput computing power of CycleCloud will enable the classification of currently uncharacterized cell types, including hES cells and [induced pluripotent stem] cells from our laboratory,” said Ruotti. His group will characterize and compare next-gen sequencing transcription profiles for multiple cell types to create a cellular index and understand the steps to derive those cell types in the laboratory.
“Victor’s project truly stood out to all the judges as his aspirations to help stem cell research could truly have a significant impact on future treatments in a short timeframe,” said Stowe. “We wanted researchers to ask questions they didn’t think they could before and push the boundaries of what’s available to not only the life science industry, but all seeking computing power formerly reserved for larger enterprises.”
Ruotti said his team has already outgrown its own compute resources. “We can’t survive with our 40-core cluster,” he said. His group is currently accessing a larger cluster at the Center for High Throughput Computing at UW-Madison, where they are working with the creator of Condor, Professor Miron Livny.
Ruotti narrowly beat out an entry from Alan Aspuru-Guzik, from the Harvard Clean Energy Project. Aspuru-Guzik received an honorable mention for his work to improve organic photovoltaics for solar cells, which could provide abundant cheap alternative energy in the third world, among other applications. Aspuru-Guzik and two other finalists receive a $1,500 credit from Cycle Computing and AWS.
Finalists were selected based on their proposal’s long-term benefit to humanity, originality, creativity and suitability to run on CycleCloud clusters in AWS. In addition to the $10,000 grand prize, in the form of a credit from Cycle Computing and four hours of CycleCloud engineering support, Ruotti also wins an additional $2,500 credit from AWS.