IBM Partnership “Brokers” Disease Research Breakthrough

By Nicole Hemsoth

July 14, 2011

IBM has partnered with high performance cloud computing company, CloudBroker, to aid researchers at ETH Zurich, a leading science and technology university in Switzerland, in their quest to find new antibiotics to fight virulent, antibiotic-resistant pathogens.

The race against time to make key discoveries against drug-resistant strains of disease-causing microorganisms has gathered steam since the recent report from the World Health Organization (WHO) that found a dramatic rise in the number of antimicrobial-resistant pathogens.  

The WHO reports there are burgeoning but significant problems with treating once-curable pathogen-borne illnesses like which is leading to tuberculosis and malaria, but new research like that being performed with aid from IBM’s SmartCloud Enterprise, the open source Rosetta software, and the HPC cloud application queuing and data management service from CloudBroker could change that in coming years.  

Researchers harnessing the Rosetta software via IBM hardware and cloud services and CloudBroker’s backend HPC cloud-enabling platform “were able to identify nearly 250 potential virulence factors, or molecules that are secreted by bacteria, fungi or protozoa and then multiply within humans, and create nearly 2.3 million three-dimensional models with nearly 30,000 background data packets to study the function of these harmful, disease causing pathogens.”

ETH Zurich scientists were granted access to nearly 250,000 computing hours on a total of 1,000 parallel CPUs to produce data on the structure of the exact proteins found in bacteria like that which causes strep throat.

Rosetta, which is able to predict and model protein structures, folding processes and interactions, was delivered on the cloud via the technology partnership between IBM and CloudBroker, allowing the team to perform their complete analysis in two weeks versus the several months they would have had to allot if this was run on the hardware available to them on site.

Stefan Ruckstuhl, IT Architect Cloud Computing for IBM Switzerland said that “it was important to understand how the HPC software Rosetta could be used most efficiently in an existing cloud environment. Therefore, a clear understanding of the infrastructure design and variable interfaces was needed.” He said that when they evaluated the needs against what they were able to do with CloudBroker’s automation, management and maintenance platform they  “found a high degree of end-to-end automation it would not have been possible to build and control a compute grid based on 1000 virtual CPUs out of the cloud otherwise.”

ClouBroker’s CEO, Dr. Wibke Sudhot pointed to the ETH Zurich research as an ideal use case to highlight the value of what they provide. She said, “ Setting up and operating such high performance computing resources in the cloud is quite complex, so what the researchers really need is access to their applications in the cloud—as a service. This is exactly what we provide.”

CloudBroker is a Swiss startup that got its start in 2008 directly out of ETH Zurich via support from a university start-up aid program. They provide “high performance computing as a service” by developing software solutions to allow applications to perform well in a cloud computing environment. They target one of the most complex problems for researchers and enterprise users who want to tap into clouds—handling the porting and running of applications (which includes everything from provider selection to migrating, installing, configuring, and maintaining the software running off-site). In addition to removing the challenges of porting applications more generally, they also handle licensing, security and accounting.

The company’s primary offering is their CloudBroker Platform, which they describe as an “application store for high performance computing in the cloud.” At its most basic, this platform allows users to select a number of scientific and technical applications from their store and execute them almost immediately on any number of cloud computing resources. They also aid in software development and consulting services for those with particularly complex needs.

 They tout ease of use as the primary benefit, something that appeals to many researchers who want to shed the complications of compute complexity to focus on their scientific endeavors, including Dr. Lars Malmstrom, who heads the research effort at ETH Zurich. He said that one of the primary benefits of this IBM and CloudBroker partnership was that “cloud computing allow us to reserve computing capacity whenever researchers need it and is available quickly.” He went on to state that another advantage is that “research teams do not need to set it up or maintain it and thus can concentrate better on their research.”

As Roland Reifler, ISV Solutions Manager for IBM Switzerland said that “CloudBroker belongs to a growing number of solution vendors whose business model is based on cloud infrastructure and they are becoming more important for IBM. This project with its challenging requirements and unique use case was a great opportunity for us to showcase and prove the capabilities of IBM’s cloud services. Cloudbroker software platform facilitates access to HPC in the cloud for a market that we think holds a huge potential.”

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!

AI in the News: Rao in at Intel, Ng out at Baidu, Nvidia on at Tencent Cloud

March 26, 2017

Just as AI has become the leitmotif of the advanced scale computing market, infusing much of the conversation about HPC in commercial and industrial spheres, it also is impacting high-level management changes in the industry. Read more…

By Doug Black

Scalable Informatics Ceases Operations

March 23, 2017

On the same day we reported on the uncertain future for HPC compiler company PathScale, we are sad to learn that another HPC vendor, Scalable Informatics, is closing its doors. Read more…

By Tiffany Trader

‘Strategies in Biomedical Data Science’ Advances IT-Research Synergies

March 23, 2017

“Strategies in Biomedical Data Science: Driving Force for Innovation” by Jay A. Etchings is both an introductory text and a field guide for anyone working with biomedical data. Read more…

By Tiffany Trader

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its assets. Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HFT Firms Turn to Co-Location to Gain Competitive Advantage

High-frequency trading (HFT) is a high-speed, high-stakes world where every millisecond matters. Finding ways to execute trades faster than the competition translates directly to greater revenue for firms, brokerages, and exchanges. Read more…

Google Launches New Machine Learning Journal

March 22, 2017

On Monday, Google announced plans to launch a new peer review journal and “ecosystem” Read more…

By John Russell

Swiss Researchers Peer Inside Chips with Improved X-Ray Imaging

March 22, 2017

Peering inside semiconductor chips using x-ray imaging isn’t new, but the technique hasn’t been especially good or easy to accomplish. Read more…

By John Russell

LANL Simulation Shows Massive Black Holes Break ‘Speed Limit’

March 21, 2017

A new computer simulation based on codes developed at Los Alamos National Laboratory (LANL) is shedding light on how supermassive black holes could have formed in the early universe contrary to most prior models which impose a limit on how fast these massive ‘objects’ can form. Read more…

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Read more…

By John Russell

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its assets. Read more…

By Tiffany Trader

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Read more…

By John Russell

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the campaign. Read more…

By John Russell

CPU-based Visualization Positions for Exascale Supercomputing

March 16, 2017

In this contributed perspective piece, Intel’s Jim Jeffers makes the case that CPU-based visualization is now widely adopted and as such is no longer a contrarian view, but is rather an exascale requirement. Read more…

By Jim Jeffers, Principal Engineer and Engineering Leader, Intel

US Supercomputing Leaders Tackle the China Question

March 15, 2017

Joint DOE-NSA report responds to the increased global pressures impacting the competitiveness of U.S. supercomputing. Read more…

By Tiffany Trader

New Japanese Supercomputing Project Targets Exascale

March 14, 2017

Another Japanese supercomputing project was revealed this week, this one from emerging supercomputer maker, ExaScaler Inc., and Keio University. The partners are working on an original supercomputer design with exascale aspirations. Read more…

By Tiffany Trader

Nvidia Debuts HGX-1 for Cloud; Announces Fujitsu AI Deal

March 9, 2017

On Monday Nvidia announced a major deal with Fujitsu to help build an AI supercomputer for RIKEN using 24 DGX-1 servers. Read more…

By John Russell

HPC4Mfg Advances State-of-the-Art for American Manufacturing

March 9, 2017

Last Friday (March 3, 2017), the High Performance Computing for Manufacturing (HPC4Mfg) program held an industry engagement day workshop in San Diego, bringing together members of the US manufacturing community, national laboratories and universities to discuss the role of high-performance computing as an innovation engine for American manufacturing. Read more…

By Tiffany Trader

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

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

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

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

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

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

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

Leading Solution Providers

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

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

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the campaign. Read more…

By John Russell

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

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

US Supercomputing Leaders Tackle the China Question

March 15, 2017

Joint DOE-NSA report responds to the increased global pressures impacting the competitiveness of U.S. supercomputing. Read more…

By Tiffany Trader

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Read more…

By John Russell

Intel and Trump Announce $7B for Fab 42 Targeting 7nm

February 8, 2017

In what may be an attempt by President Trump to reset his turbulent relationship with the high tech industry, he and Intel CEO Brian Krzanich today announced plans to invest more than $7 billion to complete Fab 42. Read more…

By John Russell

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