Biomedical Researchers Gain Faster Insights; Cut Research Costs in Half, Saving $5 Million
Scripps Research Institute, The
Researchers at The Scripps Research Institute processed test results manually, inhibiting the pace of work and limiting the time to think creatively about their work. To boost productivity, they adopted a custom high-performance computing (HPC) solution based on Windows® HPC Server 2008. Now, test results are processed 600 percent faster; researchers analyze their work more thoroughly and identify more productive research directions..
Business Needs
Some of the world’s most important advances in immunology, molecular and cellular biology, chemistry, the neurosciences, and autoimmune and cardiovascular diseases have all come from one place: The Scripps Research Institute, one of the largest private research institutions in North America.
Among the hundreds of projects being carried out at any time at the institute is one overseen by Dr. Vadim Cherezov: a project to study the structure and function of protein receptors transmitting signals inside human cells. These proteins help researchers to understand the effects of pharmaceuticals on humans—and to create new pharmaceuticals to advance human health.
Because the receptors are highly dynamic molecules, the research is both complex and time-consuming; it can take years to crystallize a membrane receptor and to obtain useful structural models.
Cherezov and his colleagues refused to wait that long to help advance human health. They also wanted to eliminate the human error inevitably associated with manual processing of test results.
High-performance computing (HPC) offered a way to take advantage of the massive compute power of distributed computers organized into a single cluster. The institute already had such a cluster running on an alternative operating system. But it wasn’t what the researchers were looking for. A generic cluster would require the lab to maintain a separate computing infrastructure; users would need separate passwords; and users could well have problems if they tried to open their 2007 Microsoft® Office files on an alternative system. Also, the institute found that there were few easy-to-use applications that allowed processed data to be submitted to the Microsoft SQL Server® data management software that it used. And it proved cumbersome for the institute to move data between a generic cluster and its workstations running the Windows Vista® operating system.
Finally, the HPC solution would need to enable developers to quickly develop custom HPC applications, so that researchers could take advantage of the power of HPC to further their research.
Solution
"When we have more time to explore more receptors, we can be more creative in how we pursue our research."
–Dr. Vadim Cherezov, The Scripps Research Institute
The Scripps Research lab found the solution that it was looking for in an HPC solution based on Windows® HPC Server 2008 running on Dell dual-core x64-based computers. The solution also uses custom applications created with Microsoft Visual Studio® Team System 2008 Development Edition and the Microsoft .NET Framework version 3.5; a database running on Microsoft SQL Server 2008; Windows Vista; and other Microsoft technologies.
The lab’s imaging system takes information from the receptors’ prescreening experiments and stores that information in Microsoft Office Excel® spreadsheets, creating a pair of spreadsheets that record different aspects of the results for each experiment. The spreadsheets are then stored on a file server. The spreadsheets are forwarded to the HPC cluster for processing. The results are sent to the SQL Server–based database, which researchers can query to view and analyze results from their Windows Vista–based computers.
Researchers can also view and analyze results from their homes or while they’re traveling. Terminal Services, a feature in Windows Server 2008, enables researchers to access and view test results over the Internet through a browser-based version of the solution.
Josh Kunken, System Developer at The Scripps Research Institute, deployed the cluster by himself in a couple of hours, using a highly automated process based on the built-in HPC management tools in Windows HPC Server. User access to each compute node was also automated, taking advantage of the Active Directory® service that the lab already had in place.
A server-side application processes the spreadsheet data on an hourly basis. A client-side application queries the database and presents the results through streamlined tables, drop-down lists, and intuitive graphs. To create the applications, Kunken used the Visual Studio Team System 2008 development system, including the Visual C#® development tool, and the .NET Framework.
Benefits
By adopting a custom solution based on Windows HPC Server 2008 and related technologies, the institute has enabled researchers to gain greater insights into their work more quickly, while application development and solution deployment and management are fast, easy, and cost-effective.
The institute has dramatically slashed the time and cost of processing the results of its crystallization prescreening experiments. Single experiments that formerly took more than an hour to complete are now completed in minutes. A series of 96 experiments that previously took three days to complete are now finished overnight—600 percent faster. As a result, crystals that once took years to develop are now developed in a few months.
The greatest benefit of that faster speed is greater insight into the research, according to Cherezov. “When we have more time to explore more receptors, we can be more creative in how we pursue our research,” he says.
An additional benefit of the faster processing of test results is lower cost. It can cost up to U.S.$10 million to identify a molecular structure that advances the institute’s research.
“We hope that the HPC solution will help to cut our research costs by at least 50 percent by reducing the number of protein constructs we have to create,” says Cherezov.
These benefits come both from the greater computing power made possible by Windows HPC Server and from the ease with which institute researchers can take advantage of it. “This is high-performance computing that doesn’t require any specialized tools or training,” says Kunken. “If you know Windows, you know Windows HPC Server.”
Kunken created the custom HPC applications in a week, aided by the integration of Windows HPC Server with the Visual Studio Team System 2008 development environment, with which he was already familiar.
Kunken says that the HPC-based solution is as cost-effective to deploy and manage as it is to develop applications for.
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