CycleCloud BigScience Challenge Boosts Stem Cell Research

By Tiffany Trader

March 13, 2012

Cycle Computing has proclaimed the winner of the 2011 CycleCloud BigScience Challenge. Victor Ruotti, a computational biologist at the Morgridge Institute for Research, will receive $10,000 in credit from Cycle Computing and four hours of CycleCloud engineering support, plus an additional $2,500 in credit from Amazon Web Services. The award will be used for cutting-edge stem cell research.

The Challenge, which was revealed in detail at the SC11 conference, was open to non-profit researchers who could harness the power of utility supercomputing to answer big science questions that have the potential to offer real benefits to humanity. The results are being announced after a careful evaluation of the five finalists. HPC in the Cloud spoke with Cycle Computing CEO Jason Stowe and the winning finalist, Victor Ruotti, to learn more.

Located on the campus of the University of Wisconsin-Madison, the Morgridge Institute for Research is a private, not-for-profit interdisciplinary biomedical research organization that seeks to accelerate the movement of science from the laboratory to the clinic. Ruotti works in the Thomson Laboratory, run by stem cell pioneer James A. Thomson. Thomson was part of a team that first transformed adult cells into stem cells called iPS cells in 2007. This was a huge breakthrough and has had a significant impact on science and medicine in the years since.

Ruotti’s research group is working on developing a knowledge base indexing system for human embryonic stem cells and their derivatives. The science is based on a fascinating regenerative process called dedifferentiation, which allows the researchers to take an adult cell and turn it into a human embryonic cell, and then further transform that into different cell types.

“You start with a cell and treat it with a certain differentiation factor and these cells which are human embryonic stem cells turn into a particular cell. This is a very complicated process because sometimes we don’t know what cell type they are turning into,” says Ruotti.

He explains this requires RNA sequencing to find more information based on genetic markers and morphology using 3-dimensional pictures. But still it’s difficult to tell what cells they are turning into. After performing over 1,000 different RNA sequences, Ruotti came up with the idea of creating a sort of dictionary to assist in the identification of cell types. This knowledge base indexing system will provide a percent probability that a certain cell is neural, or cardiac, or smooth muscle, or any other cell. The work they are doing now is laying the foundation for their ultimate goal, which is enabling advances in real-world regenerative biology.

Stowe chimes in: “The thing that got us excited about Victor’s work is the huge potential of the knowledge base that he’s putting together. It says if I start out with an undifferentiated cell and want it to end up in a particular direction, here are the probabilities for that to happen. But the primary blocker here in terms of doing the analysis is raw compute horse power. Taking advantage of a really large numbers of compute hours, a quarter million computer hours should really benefit his research.”

When Ruotti initially went to lab founder James Thomson with a detailed explanation of the knowledge base proposal, he was met with raised eyebrows: “You can do that?” Thomson asked?

“We can if we get this number of compute nodes,” replied Ruotti.

“Oh, great! Then do that,” Ruotti recalls Thomson telling him.

The basis of their research is identifying the differentiated cells, but to do this, the team must first perform a series of very computationally-intensive analyses. The science was hinging on the computational power. This is exactly the kind of project Cycle CEO Jason Stowe had in mind when he formulated the BigScience Challenge.

“There are a huge number of potential clinical applications for helping people build treatments based on differentiated cells. It’s a great fit, answering the big questions that couldn’t be answered without utility supercomputing,” says Stowe.

In addition to the grand prize winner, the contest judges selected a final runner-up, Alan Aspuru-Guzik, from the Harvard Clean Energy Project, for his material science analysis aimed at creating more efficient photo-voltaic cells.

All finalists were awarded both an initial $500 credit from Cycle Computing and an additional $1,000 credit from Amazon Web Services (AWS). Aspuru-Guzik, as the runner-up, will also receive access to some of the idle capacity that Cycle generates as part of executing and building its software.

The top projects were selected based on their creativity, benefit to society and on the appropriateness of a running their workloads on Cycle clusters in the AWS cloud. In addition to the top two choices, there were three other finalists in the pool: Jesus Izaguirre from the University of Notre Dame (diabetes research); Soumya Ray from Harvard Medical School (Parkinson’s research); and Martin Steinegger from TU Munich ROSTLAB (mapping genomic diversity). Tasked with having to sort through all these worthy candidates were judges Jason Stowe, CEO, Cycle Computing; Kevin Davies, editor-in-chief, Bio-IT World; Matt Wood, technology evangelist for Amazon Web Services; and Peter S. Shenkin, vice president, Schrödinger.

The next step, according to Stowe, will be to connect Ruotti with Cycle engineers to give them a better idea of the specific workloads and the technical requirements. Then it will be up to Ruotti and his team from an execution standpoint. The other finalists will also be given the chance to advance their research with the awards they received, and HPC in the Cloud will be sure to report on future findings.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Nvidia Debuts Turing Architecture, Focusing on Real-Time Ray Tracing

August 16, 2018

From the SIGGRAPH professional graphics conference in Vancouver this week, Nvidia CEO Jensen Huang unveiled Turing, the company's next-gen GPU platform that introduces new RT Cores to accelerate ray tracing and new Tenso Read more…

By Tiffany Trader

HPC Coding: The Power of L(o)osing Control

August 16, 2018

Exascale roadmaps, exascale projects and exascale lobbyists ask, on-again-off-again, for a fundamental rewrite of major code building blocks. Otherwise, so they claim, codes will not scale up. Naturally, some exascale pr Read more…

By Tobias Weinzierl

STAQ(ing) the Quantum Computing Deck

August 16, 2018

Quantum computers – at least for now – remain noisy. That’s another way of saying unreliable and in diverse ways that often depend on the specific quantum technology used. One idea is to mitigate noisiness and perh Read more…

By John Russell

HPE Extreme Performance Solutions

Introducing the First Integrated System Management Software for HPC Clusters from HPE

How do you manage your complex, growing cluster environments? Answer that big challenge with the new HPC cluster management solution: HPE Performance Cluster Manager. Read more…

IBM Accelerated Insights

Super Problem Solving

You might think that tackling the world’s toughest problems is a job only for superheroes, but at special places such as the Oak Ridge National Laboratory, supercomputers are the real heroes. Read more…

NREL ‘Eagle’ Supercomputer to Advance Energy Tech R&D

August 14, 2018

The U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) has contracted with Hewlett Packard Enterprise (HPE) for a new 8-petaflops (peak) supercomputer that will be used to advance early-stage R&a Read more…

By Tiffany Trader

STAQ(ing) the Quantum Computing Deck

August 16, 2018

Quantum computers – at least for now – remain noisy. That’s another way of saying unreliable and in diverse ways that often depend on the specific quantum Read more…

By John Russell

NREL ‘Eagle’ Supercomputer to Advance Energy Tech R&D

August 14, 2018

The U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) has contracted with Hewlett Packard Enterprise (HPE) for a new 8-petaflops (peak Read more…

By Tiffany Trader

CERN Project Sees Orders-of-Magnitude Speedup with AI Approach

August 14, 2018

An award-winning effort at CERN has demonstrated potential to significantly change how the physics based modeling and simulation communities view machine learni Read more…

By Rob Farber

Intel Announces Cooper Lake, Advances AI Strategy

August 9, 2018

Intel's chief datacenter exec Navin Shenoy kicked off the company's Data-Centric Innovation Summit Wednesday, the day-long program devoted to Intel's datacenter Read more…

By Tiffany Trader

SLATE Update: Making Math Libraries Exascale-ready

August 9, 2018

Practically-speaking, achieving exascale computing requires enabling HPC software to effectively use accelerators – mostly GPUs at present – and that remain Read more…

By John Russell

Summertime in Washington: Some Unexpected Advanced Computing News

August 8, 2018

Summertime in Washington DC is known for its heat and humidity. That is why most people get away to either the mountains or the seashore and things slow down. H Read more…

By Alex R. Larzelere

NSF Invests $15 Million in Quantum STAQ

August 7, 2018

Quantum computing development is in full ascent as global backers aim to transcend the limitations of classical computing by leveraging the magical-seeming prop Read more…

By Tiffany Trader

By the Numbers: Cray Would Like Exascale to Be the Icing on the Cake

August 1, 2018

On its earnings call held for investors yesterday, Cray gave an accounting for its latest quarterly financials, offered future guidance and provided an update o Read more…

By Tiffany Trader

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This