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!

Battle Brews over Trump Intentions for Funding Science

February 27, 2017

The battle over science funding – how much and for what kinds of science – Read more…

By John Russell

Google Gets First Dibs on New Skylake Chips

February 27, 2017

As part of an ongoing effort to differentiate its public cloud services, Google made good this week on its intention to bring custom Xeon Skylake chips from Intel Corp. Read more…

By George Leopold

Thomas Sterling on CREST and Academia’s Role in HPC Research

February 27, 2017

The US advances in high performance computing over many decades have been a product of the combined engagement of research centers in industry, government labs, and academia. Read more…

By Thomas Sterling, Indiana University

Advancing Modular Supercomputing with DEEP and DEEP-ER Architectures

February 24, 2017

Knowing that the jump to exascale will require novel architectural approaches capable of delivering dramatic efficiency and performance gains, researchers around the world are hard at work on next-generation HPC systems. Read more…

By Sean Thielen

HPE Extreme Performance Solutions

Manufacturers Reaping the Benefits of Remote Visualization

Today’s manufacturers are operating in an ever-changing atmosphere, and finding new ways to boost productivity has never been more vital.

This is why manufacturers are ramping up their investments in high performance computing (HPC), a trend which has helped give rise to the “connected factory” and Industrial Internet of Things (IIoT) concepts that are proliferating throughout the industry today. Read more…

Weekly Twitter Roundup (Feb. 23, 2017)

February 23, 2017

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

HPE Server Shows Low Latency on STAC-N1 Test

February 22, 2017

The performance of trade and match servers can be a critical differentiator for financial trading houses. Read more…

By John Russell

HPC Financial Update (Feb. 2017)

February 22, 2017

In this recurring feature, we’ll provide you with financial highlights from companies in the HPC industry. Check back in regularly for an updated list with the most pertinent fiscal information. Read more…

By Thomas Ayres

Rethinking HPC Platforms for ‘Second Gen’ Applications

February 22, 2017

Just what constitutes HPC and how best to support it is a keen topic currently. Read more…

By John Russell

Thomas Sterling on CREST and Academia’s Role in HPC Research

February 27, 2017

The US advances in high performance computing over many decades have been a product of the combined engagement of research centers in industry, government labs, and academia. Read more…

By Thomas Sterling, Indiana University

Advancing Modular Supercomputing with DEEP and DEEP-ER Architectures

February 24, 2017

Knowing that the jump to exascale will require novel architectural approaches capable of delivering dramatic efficiency and performance gains, researchers around the world are hard at work on next-generation HPC systems. Read more…

By Sean Thielen

HPC Technique Propels Deep Learning at Scale

February 21, 2017

Researchers from Baidu’s Silicon Valley AI Lab (SVAIL) have adapted a well-known HPC communication technique to boost the speed and scale of their neural network training and now they are sharing their implementation with the larger deep learning community. Read more…

By Tiffany Trader

IDC: Will the Real Exascale Race Please Stand Up?

February 21, 2017

So the exascale race is on. And lots of organizations are in the pack. Government announcements from the US, China, India, Japan, and the EU indicate that they are working hard to make it happen – some sooner, some later. Read more…

By Bob Sorensen, IDC

TSUBAME3.0 Points to Future HPE Pascal-NVLink-OPA Server

February 17, 2017

Since our initial coverage of the TSUBAME3.0 supercomputer yesterday, more details have come to light on this innovative project. Of particular interest is a new board design for NVLink-equipped Pascal P100 GPUs that will create another entrant to the space currently occupied by Nvidia's DGX-1 system, IBM's "Minsky" platform and the Supermicro SuperServer (1028GQ-TXR). Read more…

By Tiffany Trader

Tokyo Tech’s TSUBAME3.0 Will Be First HPE-SGI Super

February 16, 2017

In a press event Friday afternoon local time in Japan, Tokyo Institute of Technology (Tokyo Tech) announced its plans for the TSUBAME3.0 supercomputer, which will be Japan’s “fastest AI supercomputer,” Read more…

By Tiffany Trader

Drug Developers Use Google Cloud HPC in the Fight Against ALS

February 16, 2017

Within the haystack of a lethal disease such as ALS (amyotrophic lateral sclerosis / Lou Gehrig’s Disease) there exists, somewhere, the needle that will pierce this therapy-resistant affliction. Read more…

By Doug Black

Azure Edges AWS in Linpack Benchmark Study

February 15, 2017

The “when will clouds be ready for HPC” question has ebbed and flowed for years. Read more…

By John Russell

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

US, China Vie for Supercomputing Supremacy

November 14, 2016

The 48th edition of the TOP500 list is fresh off the presses and while there is no new number one system, as previously teased by China, there are a number of notable entrants from the US and around the world and significant trends to report on. Read more…

By Tiffany Trader

Lighting up Aurora: Behind the Scenes at the Creation of the DOE’s Upcoming 200 Petaflops Supercomputer

December 1, 2016

In April 2015, U.S. Department of Energy Undersecretary Franklin Orr announced that Intel would be the prime contractor for Aurora: Read more…

By Jan Rowell

D-Wave SC16 Update: What’s Bo Ewald Saying These Days

November 18, 2016

Tucked in a back section of the SC16 exhibit hall, quantum computing pioneer D-Wave has been talking up its new 2000-qubit processor announced in September. Forget for a moment the criticism sometimes aimed at D-Wave. This small Canadian company has sold several machines including, for example, ones to Lockheed and NASA, and has worked with Google on mapping machine learning problems to quantum computing. In July Los Alamos National Laboratory took possession of a 1000-quibit D-Wave 2X system that LANL ordered a year ago around the time of SC15. Read more…

By John Russell

IBM Wants to be “Red Hat” of Deep Learning

January 26, 2017

IBM today announced the addition of TensorFlow and Chainer deep learning frameworks to its PowerAI suite of deep learning tools, which already includes popular offerings such as Caffe, Theano, and Torch. Read more…

By John Russell

Enlisting Deep Learning in the War on Cancer

December 7, 2016

Sometime in Q2 2017 the first ‘results’ of the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) will become publicly available according to Rick Stevens. He leads one of three JDACS4C pilot projects pressing deep learning (DL) into service in the War on Cancer. Read more…

By John Russell

Tokyo Tech’s TSUBAME3.0 Will Be First HPE-SGI Super

February 16, 2017

In a press event Friday afternoon local time in Japan, Tokyo Institute of Technology (Tokyo Tech) announced its plans for the TSUBAME3.0 supercomputer, which will be Japan’s “fastest AI supercomputer,” Read more…

By Tiffany Trader

HPC Startup Advances Auto-Parallelization’s Promise

January 23, 2017

The shift from single core to multicore hardware has made finding parallelism in codes more important than ever, but that hasn’t made the task of parallel programming any easier. Read more…

By Tiffany Trader

Leading Solution Providers

CPU Benchmarking: Haswell Versus POWER8

June 2, 2015

With OpenPOWER activity ramping up and IBM’s prominent role in the upcoming DOE machines Summit and Sierra, it’s a good time to look at how the IBM POWER CPU stacks up against the x86 Xeon Haswell CPU from Intel. Read more…

By Tiffany Trader

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

Nvidia Sees Bright Future for AI Supercomputing

November 23, 2016

Graphics chipmaker Nvidia made a strong showing at SC16 in Salt Lake City last week. Read more…

By Tiffany Trader

TSUBAME3.0 Points to Future HPE Pascal-NVLink-OPA Server

February 17, 2017

Since our initial coverage of the TSUBAME3.0 supercomputer yesterday, more details have come to light on this innovative project. Of particular interest is a new board design for NVLink-equipped Pascal P100 GPUs that will create another entrant to the space currently occupied by Nvidia's DGX-1 system, IBM's "Minsky" platform and the Supermicro SuperServer (1028GQ-TXR). Read more…

By Tiffany Trader

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. Read more…

By Tiffany Trader

Dell Knights Landing Machine Sets New STAC Records

November 2, 2016

The Securities Technology Analysis Center, commonly known as STAC, has released a new report characterizing the performance of the Knight Landing-based Dell PowerEdge C6320p server on the STAC-A2 benchmarking suite, widely used by the financial services industry to test and evaluate computing platforms. The Dell machine has set new records for both the baseline Greeks benchmark and the large Greeks benchmark. Read more…

By Tiffany Trader

Is Liquid Cooling Ready to Go Mainstream?

February 13, 2017

Lost in the frenzy of SC16 was a substantial rise in the number of vendors showing server oriented liquid cooling technologies. Three decades ago liquid cooling was pretty much the exclusive realm of the Cray-2 and IBM mainframe class products. That’s changing. We are now seeing an emergence of x86 class server products with exotic plumbing technology ranging from Direct-to-Chip to servers and storage completely immersed in a dielectric fluid. Read more…

By Steve Campbell

What Knights Landing Is Not

June 18, 2016

As we get ready to launch the newest member of the Intel Xeon Phi family, code named Knights Landing, it is natural that there be some questions and potentially some confusion. Read more…

By James Reinders, Intel

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