Integrating Biological Science: Equivalent of Manned Mission to Mars

Loraine Lawson
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Data Integration Remains a Major IT Headache

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The Department of Energy is undertaking what project leaders call the "computational equivalent of a manned mission to Mars." The reason for this more than $60 million effort: integration of biological data silos containing everything known about plants and microbes.


That's a whopper of an integration project that requires a team of computer scientists at several institutions, building seven data centers and leveraging cloud computing as well as high-performance computing resources across the Department of Energy's system of labs. The integrated Systems Biology Knowledgebase's (Kbase) goal is to support various DOE missions, such as cleaning up environmental pollution, producing biofuels and containing carbon in the ecosystem, according to @brookhaven Today. Brookhaven computer scientists and biologists are among those participating in the multi-institution project.


"There are many different silos of information that have been painstakingly collected; and there are a number of existing tools that bring some strands of data into relation," Michael Schatz, a quantitative biologist, is quoted as saying in HPC Wire. "But there is no overarching tool that can be used across silos."


The project started in 2008. The research and development for Kbase's design and implementation was completed last year. The current timetable calls the hardware platform to be completed in the next 12 months, with the first version of Kbase operational within 18 months.


Kbase will also include social networking features to foster collaboration among scientists, according to the @brookhaven Today article.


What's promising about this is it will serve as a model for other scientific databases and perhaps even applications like health care, according to Internet Evolution. Plus, it's being built with open access, meaning the data and methods will be available for anyone to use - so, potentially, private companies and other government agencies could take advantage of Kbase.


It's also being built using open source code and principles of open development, meaning anyone can contribute to the development of Kbase resources by following guidelines defined by the community. Reports HPC Wire:

While Kbase is an ongoing project, the model for its integration and collaboration developments will extend to other disciplines, allowing greater, more open access to scientific data across the world. ... the need for such integration is clear-but it is a slow climb to full data integration, sharing and use for biology researchers.

Well, in that regard, it's not unique. But regardless, it's an exciting integration project that could not only deliver on ROI, but on some of civilization's most deadly challenges.

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