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.”

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