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Bringing the data for precision medicine
July 2017
by Mel J. Yeates  |  Email the author


BOSTON—The tranSMART Foundation and IBM have announced their collaboration and the general availability of the tranSMART platform version 16.2 on IBM’s Power8 servers. The translational research platform is running on IBM Power8 servers at the tranSMART Foundation’s Center of Excellence at the University of Michigan.
In addition, tranSMART announced in May the completion of its merger with i2b2, to become the i2b2 tranSMART Foundation. The mission of the i2b2 tranSMART Foundation is to enable effective collaboration for precision medicine through the sharing, integration, standardization and analysis of heterogeneous data from healthcare and research through engagement and mobilization of a life sciences-focused open-source, open-data community.
Dr. Keith Elliston, executive director of the i2b2 tranSMART Foundation, said, “We believe that by coming together into one single organization, we can link clinical research and translational research through our open-source platforms and our active community of scientists and technologists to enable and accelerate innovation in precision medicine. We believe that the most viable business model for developing the big data infrastructure needed for precision medicine is the open-source model, and the i2b2 tranSMART Foundation is leading this effort.”
In order to help meet the computing and storage demands of i2b2 tranSMART, IBM has helped to optimize the platform for i2b2 tranSMART by leveraging the performance, scalability and speed offered by IBM Power8, IBM Elastic Storage Server and IBM Spectrum Scale.
“IBM is a powerhouse in the technology industry and this endeavor will further enable us to bridge the scientific and technology communities to further life-science research,” Elliston said. “IBM Power8 is an ideal platform for handling our users’ big data requirements. tranSMART users are leveraging large scientific datasets in their research and need to be able to easily load, integrate and analyze the data to help generate and potentially validate hypotheses and discover cohorts in translational and clinical research.”
“We have seen cases where some scientists have been left waiting for hours to get the genotypic and clinical data from tranSMART’s database on legacy infrastructure,” said Sumit Gupta, vice president for high-performance computing and AI in IBM’s Cognitive Systems. “By utilizing IBM’s Power systems and high-performance storage solutions, we are able to provide the same data in minutes rather than hours.”
According to Dr. Rudy Potenzone, vice president of Marketing at the i2b2 tranSMART Foundation, “Interestingly, there were a few customers who purchased Power8 servers and were interested in running our tranSMART Platform for their scientists who are doing translational medicine research. One in particular was a group at LSU. Through IBM, they connected with a tranSMART Partner, Rancho BioSciences in San Diego, who worked with IBM to get the platform running and the scientists able to start using tranSMART on the Power8.”
“After an introduction from Rancho CEO Julie Bryant to IBM, we started discussions on a potential collaboration,” Potenzone continues. “This is the first collaboration between the i2b2 tranSMART Foundation and IBM. But there was also some interaction around our platform and IBM Watson with another i2b2 tranSMART Partner, Imperial College of London Prof. Yike Guo.”
“The collaboration has been going smoothly. It does sometimes take a few iterations when working with a very large organization like IBM. But we have made steady progress, and we are delighted to see our latest version running on our Power8 environment which is housed at another partner, the University of Michigan,” he says.
The Foundation is using Power8 servers at the University for research and development and to host its web-based training for the tranSMART platform. These servers also serve as a public showcase of what can be done with the Foundation’s open-source, open-data and open-science approach to translational research on this powerful hardware environment. IBM and i2b2 tranSMART Foundation are working together to introduce the new version of the tranSMART Platform at various local events, in cooperation with partner Rancho BioSciences (a tranSMART Foundation Member). Early customers of the new version are already using the platform in their translational research programs.
“At our symposium during BioIT World, the IBM team presented their optimization efforts to maximize performance of the i2b2 tranSMART Platform on the Power8. The IBM team showed improvements in data loading by a factor of two and analysis results up to 10 times faster on the Power8,” notes Potenzone. “This sort of speed improvements allows scientists and clinicians who are doing research to explore their hypothesis quicker and to examine larger amounts of data.”
“The Power8 provides a state-of-the-art parallel system to optimize the types of analyses that every tranSMART user depends upon for their research,” Potenzone explains. “Coupled with the IBM ESS, this is an ideal platform for the research community that allows scientists and clinicians to directly use the tool and test their hypothesis in an efficient manner.”
“The ability to look at more data and perform more complex analyses will provide medical research teams a tool that helps to look across more studies in the course of a project. They will be able to access the growing amounts of genomic information, variants and genome-wide studies,” Potenzone continues. “The expectations from translational medicine and broader access to deeper genomic information coupled with the application of machine learning will finally be in reach.”
Potenzone says they are working to release the latest version of the platform, v16.2, on the IBM Power8. He notes that Power8 will be included “in all future releases going forward,” and that Power8 servers are being integrated into their research programs.
Code: E071709



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