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!

Data Vortex Users Contemplate the Future of Supercomputing

October 19, 2017

Last month (Sept. 11-12), HPC networking company Data Vortex held its inaugural users group at Pacific Northwest National Laboratory (PNNL) bringing together about 30 participants from industry, government and academia t Read more…

By Tiffany Trader

AI Self-Training Goes Forward at Google DeepMind

October 19, 2017

DeepMind, Google’s AI research organization, announced today in a blog that AlphaGo Zero, the latest evolution of AlphaGo (the first computer program to defeat a Go world champion) trained itself within three days to play Go at a superhuman level (i.e., better than any human) – and to beat the old version of AlphaGo – without leveraging human expertise, data or training. Read more…

By Doug Black

Researchers Scale COSMO Climate Code to 4888 GPUs on Piz Daint

October 17, 2017

Effective global climate simulation, sorely needed to anticipate and cope with global warming, has long been computationally challenging. Two of the major obstacles are the needed resolution and prolonged time to compute Read more…

By John Russell

HPE Extreme Performance Solutions

Transforming Genomic Analytics with HPC-Accelerated Insights

Advancements in the field of genomics are revolutionizing our understanding of human biology, rapidly accelerating the discovery and treatment of genetic diseases, and dramatically improving human health. Read more…

Student Cluster Competition Coverage New Home

October 16, 2017

Hello computer sports fans! This is the first of many (many!) articles covering the world-wide phenomenon of Student Cluster Competitions. Finally, the Student Cluster Competition coverage has come to its natural home: H Read more…

By Dan Olds

Data Vortex Users Contemplate the Future of Supercomputing

October 19, 2017

Last month (Sept. 11-12), HPC networking company Data Vortex held its inaugural users group at Pacific Northwest National Laboratory (PNNL) bringing together ab Read more…

By Tiffany Trader

AI Self-Training Goes Forward at Google DeepMind

October 19, 2017

DeepMind, Google’s AI research organization, announced today in a blog that AlphaGo Zero, the latest evolution of AlphaGo (the first computer program to defeat a Go world champion) trained itself within three days to play Go at a superhuman level (i.e., better than any human) – and to beat the old version of AlphaGo – without leveraging human expertise, data or training. Read more…

By Doug Black

Student Cluster Competition Coverage New Home

October 16, 2017

Hello computer sports fans! This is the first of many (many!) articles covering the world-wide phenomenon of Student Cluster Competitions. Finally, the Student Read more…

By Dan Olds

Intel Delivers 17-Qubit Quantum Chip to European Research Partner

October 10, 2017

On Tuesday, Intel delivered a 17-qubit superconducting test chip to research partner QuTech, the quantum research institute of Delft University of Technology (TU Delft) in the Netherlands. The announcement marks a major milestone in the 10-year, $50-million collaborative relationship with TU Delft and TNO, the Dutch Organization for Applied Research, to accelerate advancements in quantum computing. Read more…

By Tiffany Trader

Fujitsu Tapped to Build 37-Petaflops ABCI System for AIST

October 10, 2017

Fujitsu announced today it will build the long-planned AI Bridging Cloud Infrastructure (ABCI) which is set to become the fastest supercomputer system in Japan Read more…

By John Russell

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Intel Debuts Programmable Acceleration Card

October 5, 2017

With a view toward supporting complex, data-intensive applications, such as AI inference, video streaming analytics, database acceleration and genomics, Intel i Read more…

By Doug Black

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

NERSC Scales Scientific Deep Learning to 15 Petaflops

August 28, 2017

A collaborative effort between Intel, NERSC and Stanford has delivered the first 15-petaflops deep learning software running on HPC platforms and is, according Read more…

By Rob Farber

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

Oracle Layoffs Reportedly Hit SPARC and Solaris Hard

September 7, 2017

Oracle’s latest layoffs have many wondering if this is the end of the line for the SPARC processor and Solaris OS development. As reported by multiple sources Read more…

By John Russell

US Coalesces Plans for First Exascale Supercomputer: Aurora in 2021

September 27, 2017

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, in Arlington, Va., yesterday (Sept. 26), it was revealed that the "Aurora" supercompute Read more…

By Tiffany Trader

Google Releases Deeplearn.js to Further Democratize Machine Learning

August 17, 2017

Spreading the use of machine learning tools is one of the goals of Google’s PAIR (People + AI Research) initiative, which was introduced in early July. Last w Read more…

By John Russell

GlobalFoundries Puts Wind in AMD’s Sails with 12nm FinFET

September 24, 2017

From its annual tech conference last week (Sept. 20), where GlobalFoundries welcomed more than 600 semiconductor professionals (reaching the Santa Clara venue Read more…

By Tiffany Trader

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in Read more…

By Tiffany Trader

Leading Solution Providers

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Amazon Debuts New AMD-based GPU Instances for Graphics Acceleration

September 12, 2017

Last week Amazon Web Services (AWS) streaming service, AppStream 2.0, introduced a new GPU instance called Graphics Design intended to accelerate graphics. The Read more…

By John Russell

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Cray Moves to Acquire the Seagate ClusterStor Line

July 28, 2017

This week Cray announced that it is picking up Seagate's ClusterStor HPC storage array business for an undisclosed sum. "In short we're effectively transitioning the bulk of the ClusterStor product line to Cray," said CEO Peter Ungaro. Read more…

By Tiffany Trader

Intel Launches Software Tools to Ease FPGA Programming

September 5, 2017

Field Programmable Gate Arrays (FPGAs) have a reputation for being difficult to program, requiring expertise in specialty languages, like Verilog or VHDL. Easin Read more…

By Tiffany Trader

IBM Advances Web-based Quantum Programming

September 5, 2017

IBM Research is pairing its Jupyter-based Data Science Experience notebook environment with its cloud-based quantum computer, IBM Q, in hopes of encouraging a new class of entrepreneurial user to solve intractable problems that even exceed the capabilities of the best AI systems. Read more…

By Alex Woodie

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

  • arrow
  • Click Here for More Headlines
  • arrow
Share This