Biomedical Institute Speeds Researcher Productivity 600 Percent for ...

By Deborah Jackson,2014-12-03 16:42
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Biomedical Institute Speeds Researcher Productivity 600 Percent for ...

     Biomedical Institute Speeds Researcher

    Productivity 600 Percent for Faster Insights

     Overview ―This is high-performance computing that doesn’t

    Country or Region: United States require any specialized tools or training. If you know Industry: HealthcareLife sciences

    Windows, you know Windows HPC Server.‖

    Customer Profile Josh Kunken, System Developer, The Scripps Research Institute The Scripps Research Institute, based in La Jolla, California, and Jupiter, Florida, is a

    leading center for basic biomedical science, contributing to the betterment of Structural biology researchers at The Scripps Research Institute, a health and the human condition. It has leading biomedical research center, used to process test results 3,000 employees.

     manually, inhibiting the pace of their work and limiting the time Business Situation they could spend thinking creatively about their research. To boost Crystallography prescreening tests were

    being processed manually, resulting in productivity, they adopted a custom high-performance computing slow, error-prone results that inhibited the (HPC) solution based on Windows? HPC Server 2008. Now, test speed of research and the productivity of

    researchers. results are processed 600 percent faster, giving researchers the time they need to analyze their work more thoroughly and to Solution

    The structural biology lab adopted a high-identify more productive research directions. The HPC applications performance computing solution based on for the solution were created quickly and easily using Microsoft? Windows? HPC Server 2008 and related

    Microsoft? technologies. development tools, and the entire solution life cycle is managed centrally and effectively by a single system developer. Benefits ; Speeds research 600 percent, yielding

    greater insights

    ; Enables rapid application development

    ; Boosts IT productivity

    Situation Cherezov and his Some of the world’s most important To prescreen dozens of modified receptor colleagues refused to advances in immunology, molecular and constructs and thousands of environmental cellular biology, chemistry, the neurosciences, conditions, the scientists at Scripps Research wait to help advance and autoimmune and cardiovascular hit upon the idea of an experiment combining human health. diseases have all come from one place: The the power of microscopes and lasers. This Scripps Research Institute, one of the largest presented another problem: processing test private research institutions in North America. results had traditionally taken far longer than running the experiments that produced those Among the hundreds of projects being carried results. For example, testing and processing out at any time at the institute is one a single lab plate with 96 experiments could overseen by Dr. Vadim Cherezov: a project to take a weekand researchers need to

    study the structure and function of protein conduct tens of thousands of experiments to receptors transmitting signals inside the cells advance each stage of their research. of the human body. These receptors are

    responsible for a variety of physiological Cherezov and his colleagues refused to wait activities, such as the increased heart rate that long to help advance human health. They and blood pressure that the body experiences also wanted to eliminate the human error when the receptors come into contact with inevitably associated with manual processing, adrenaline. That makes these proteins an which could delay the processing of results ideal object of study when the goal is to even more.

    understand the effects of pharmaceuticals on

    humansand to create new pharmaceuticals Fortunately, they didn’t have to. High-

    to advance the cause of human health. performance computing (HPC) offered a way

     to take advantage of the massive compute Although they may be highly important power of distributed computers organized objects of study from a biomedical standpoint, into a single cluster. The institute already had receptors aren’t easy objects of study. such a cluster running on the Linux operating

     system. But it wasn’t what the molecular-

    To understand how these receptor molecules modeling researchers were looking for. function, researchers seek to determine

    atomic-resolution, three-dimensional They identified several challenges in adopting structures of the molecules. To achieve this, a generic cluster. First, the lab would have to they assemble individual molecules into maintain a separate computing infrastructure crystals and ―interrogate‖ them with powerful to support it, driving up the time and money x-ray beams generated by synchrotron spent on IT management. Second, users sources. would need a separate password authentica-

     tion and administration system in addition to Because the membrane receptors are highly the single sign-on passwords they use for dynamic molecules, the research is both com-their existing environment, which is based on plex and time-consuming; it can take years to the Windows Server? 2008 and Windows

    crystallize a membrane receptor and to Vista? operating systems. Finally, they also obtain useful structural models. For this class anticipated problems if users tried to open of receptors, a breakthrough came when the 2007 Microsoft? Office filessuch as Office

    receptors were genetically engineered and Excel? spreadsheets and Office Word additionally stabilized by inserting them into a documentson an alternative system.

    lipidic mesophase matrix.

    ? Team System 2008 Development Finally, the HPC solution that the lab chose Studio

    Edition and the Microsoft .NET Framework for its crystallography work would need to do

    version 3.5; a database running on Microsoft more than promote IT productivity and facili-

    SQL Server? 2008 database management tate easy use by researchers. It also would

    software; Windows Vista; and other Microsoft have to enable the rapid development of

    technologies. custom HPC applications, so that researchers

     could take advantage of the power of HPC to

    The lab’s imaging system takes information further their research.

    from the receptors’ prescreening experiments

    Solution and stores that information in Office Excel The Scripps Research lab found the solution spreadsheets, creating a pair of spread-that it was looking for in an HPC solution sheets that record different aspects of the based on Windows? HPC Server 2008 results for each experiment. (See Figure 1.) running on Dell dual-core x64based The spreadsheets are then stored on a file computers. The solution also uses custom server (step 1). The spreadsheets are no applications created with Microsoft Visual longer processed manually, but rather are

    forwarded to the HPC cluster for processing experiments, movies recorded by the imaging ―When we have more (step 2). The results are sent to the SQL system that show changes to samples over time to explore more Serverbased database (step 3), which time, and single frames that show the results researchers can query to view and analyze of bombarding the samples with laser light. receptors, we can be results from their Windows Vistabased more creative in how we computers (step 4). To create the applications, Kunken used the

     Microsoft Visual Studio Team System 2008 pursue our research.‖ Researchers can also view and analyze development system, including the Visual Dr. Vadim Cherezov, The Scripps Research ? development tool, and the .NET results from their homes or while they’re C#Institute Framework, especially its Windows traveling. Terminal Services, a feature in

    Communication Foundation and Windows Windows Server 2008, enables researchers to access and view test results over the Presentation Foundation components. Internet through a browser-based version of Windows Communication Foundation the solution. provides the infrastructure for the rapid

     transmission of processed spreadsheet data

    to SQL Server, while Windows Presentation Deploying the HPC Cluster

    Foundation provides the components that Josh Kunken, System Developer at The

    Kunken used to create the highly responsive Scripps Research Institute, deployed the

    and visual user interface. cluster by himself in a couple of hours, using

     the built-in HPC management tools in

    Benefits Windows HPC Server. After imaging the head

    By adopting a custom solution based on node, he used the management tools to

    Windows HPC Server 2008 and related reflect the same image over the network to

    technologies, the institute has enabled the various compute nodes, eliminating the

    researchers to gain greater insights into their need for him to touch each computer, or even

    work more quickly, while application develop-to configure each node separately.

    ment and solution deployment and manage-

    ment are fast, easy, and cost-effective. User access to each compute node was also

     automated as a result of the authorizations

    Speeds Research 600 Percent, Yielding that Kunken created for the head node. To

    Greater Insight create user authorization to the cluster, he

    ? The institute has dramatically slashed the took advantage of the Active Directory

    service that the lab already had in place, so time and cost of processing the results of its he did not have to maintain separate crystallization prescreening experiments. accounts and user directories for the HPC Single experiments that formerly took more solution and for other lab infrastructure. than an hour to complete are now completed

     in minutes. A series of 96 experiments that Creating the Applications previously took three days to complete are Before researchers could take advantage of now finished overnight600 percent faster.

    the HPC cluster, the institute had to create As a result, crystals that once took years to two applications for it. A server-side appli-develop are now developed in a few months. cation processes the spreadsheet data on an

    hourly basis. A client-side application queries The greatest benefit of that faster speed is the database and presents the results greater insight into the research, according to through streamlined tables, drop-down lists, Cherezov. ―When we have more time to and intuitive graphs. Researchers can explore more receptors, we can be more request the processed results of specific creative in how we pursue our research,‖ he

    says. ―We can spend more time analyzing our and third-party components such as com-―We hope that the HPC results because, with Windows HPC Server pilers and debugging toolkits. solution will help to cut 2008, we spend less time processing them.

    ? And more time for analysis means we can ―Visual Studio features like IntelliSenseour research costs by at make life a lot easier because I don’t have to gain greater insight more quickly. We can least 50 percent.‖ go to the MSDN? Library to look up how a identify positive avenues of research and method or class is referenced or called,‖ says achieve greater success in our work.‖ Dr. Vadim Cherezov, The Scripps Research Kunken. ―And one of the beauties of Visual Institute Studio 2008 and .NET Framework com-An additional benefit of the faster processing ponents such as Windows Presentation of test results is lower cost. The structure-Foundation is the ability to design highly solving process isn’t just time-consuming—it’s expensive. It can cost up to U.S.$10 million to visual user interfaces that look like the end

    identify a molecular structure that advances product you’re trying to create. That makes it

    the institute’s research. easier to focus on the business logic of the


     ―We hope that the HPC solution will help to And even creating that business logic was cut our research costs by at least 50 percent simplified, according to Kunken, thanks by reducing the number of protein constructs to .NET Framework components such as we have to create, providing the ability to Windows Communication Foundation, which solve twice as many receptor structures in provides the ―plumbing‖ or low-level the same period of time,‖ says Cherezov.

    infrastructure for connectivity among

    application elements. These benefits come both from the greater

     computing power made possible by Windows

    ―The .NET Framework gives you power that HPC Server and from the ease with which

    you wouldn’t have otherwise,‖ says Kunken. institute researchers can take advantage of it. ―Everything communicates and works with ―This is high-performance computing that

    everything else, and you can create your doesn’t require any specialized tools or train-

    application quickly in a modular way.‖ ing,‖ says Kunken. ―If you know Windows, you

     know Windows HPC Server.‖

    Boosts IT Productivity

    Kunken says that the HPC-based solution is Enables Rapid Application Development

    as cost-effective to deploy and manage as it With sole responsibility for the technology is to develop applications for. It boosts the infrastructure in the crystallography lab, productivity of the system developer by Kunken didn’t have much time to devote to

    dramatically simplifying overall deployment, creating applications for the HPC computing administration, and management over the environment. Fortunately, he didn’t need

    entire system lifetime, while helping to much time. Kunken created functional appli-ensure interoperability with existing system cations in a week, aided by the integration of infrastructure. Windows HPC Server with the Visual Studio

     Team System 2008 development environ-

    ―I deployed the compute nodes from the ment, with which he was already familiar. head node without having to touch each

    machine,‖ says Kunken. ―I deployed my Visual Studio Team System provides a com-

    applications just as easily. The HPC Manager prehensive, parallel-processing development in Windows HPC Server monitors the health system, with support for standard interfaces of every node for me, including the job status

    For More Information on each node. I can see what’s happening on Microsoft Server Product Portfolio For more information about Microsoft each processor on each node in real time. For more information about the Microsoft

    products and services, call the Microsoft And the HPC Manager snaps into the server product portfolio, go to:

    Sales Information Center at (800) 426-Microsoft Management Console I already use 9400. In Canada, call the Microsoft with other Microsoft technologies.‖

    Canada Information Centre at (877) 568-

    2495. Customers who are deaf or hard-of-

    hearing can reach Microsoft text telephone

    (TTY/TDD) services at (800) 892-5234 in

    the United States or (905) 568-9641 in

    Canada. Outside the 50 United States and

    Canada, please contact your local

    Microsoft subsidiary. To access information

    using the World Wide Web, go to:

For more information about The Scripps

    Research Institute, call (858) 784-7179 or

    visit the Web site at:

     Software and Services ; Technologies

    ; Microsoft Server Product Portfolio ? Active Directory

    ? Windows HPC Server 2008 ? Microsoft .NET Framework 3.5

    ? Windows Server 2008 ? Terminal Services

    ? Microsoft SQL Server 2008 ; Windows Vista

    ; Microsoft Office

    ? Microsoft Office Excel 2007 Hardware

    ; Visual Studio ; PowerEdge SC 1435 computers

    ? Microsoft Visual Studio Team System

    2008 Development Edition

    This case study is for informational purposes only. MICROSOFT MAKES NO WARRANTIES, EXPRESS OR IMPLIED, IN THIS SUMMARY. Document published September 2008

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