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GenoSpace, TranSmart Sync Platforms to Expand Data Sharing and Analysis Capabilities

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This week, GenoSpace announced that its software system now supports the TranSmart knowledge management platform — an open source data sharing and analytics platform that's managed and run by the non-profit TranSmart Foundation.

GenoSpace CEO John Quackenbush said that the arrangement gives his firm's customers access to tools and high-quality data that they can use to address a range of basic, clinical, and translational research questions and support personalized medicine applications.

It's also a way, "for us to really be responsive to some of our clients and potential clients," especially pharmaceutical companies, who have begun using TranSmart to store and share data and want to combine it with analytical capabilities, he told BioInform.

Cambridge, Mass.-based GenoSpace, which launched its first product last June (BI 6/29/2012), offers cloud power and software to help researchers and clinicians analyze, share, and store both clinical and genomic information. GenoSpace for Research provides analysis, visualization, and collaboration tools; GenoSpace for Clinical Care facilitates clinically actionable interpretation of genomic data for precision medicine; and GenoSpace for Patient Communities enables patient-centric exploration as well as the return of data to clinical trials participants.

TranSmart combines a data warehouse with access to federated sources of open and commercial databases including some hosted by the National Center for Biotechnology Information and the European Bioinformatics Institute.

According to its developers, users can store and share phenotypic data such as clinical observations and adverse events; biomarker data from gene expression, genotyping, and other studies; unstructured text from sources such as journal articles and conference abstracts; reference data; and metadata. TranSMART also connects to both open source and commercial software such as Galaxy and GeneGo.

"Marrying TranSmart to our tools allows us to … really step up the quality and power of the analytical tools that people using TranSmart have access to today," Quackenbush said.

Also, "pharma plays a big part in the whole healthcare ecosystem, and a lot of the research data that [GenoSpace is] generating and handling are the kind of data pharma wants access to … I think this really represents an important move to help support their research needs and interests," he said.

Commenting on his group's newest ally, Brian Athey, co-CEO of the TranSmart Foundation and professor and chair of University of Michigan's computational medicine and bioinformatics department, said the partnership with GenoSpace provides TranSmart's users with "advanced genomics data-mining and -analysis tools" to help "accelerate their research."

It will also extend TranSmart's reach in the not-for-profit and academic research spaces, where GenoSpace already has inroads bagging customers such as the Multiple Myeloma Research Foundation, he told BioInform.

According to its website, the TranSmart Foundation aims to support and establish TranSmart as the go-to platform for sharing clinical and molecular biology data for translational biomedical research and to foster collaborations between academic, non-profit, and corporate research communities.

The TranSmart platform, Athey told BioInform, was developed internally by researchers at Johnson & Johnson "to break down silos of data and information amongst different research groups" in its research and development arm.

Following its successful internal use and in response to increasing interest in the platform from other pharmaceutical companies, J&J released TranSmart's code into the public domain under the GNU General Public License, allowing researchers to both use and modify the code, Athey said.

It's since been used by groups such as the European Translational Information and Knowledge Management Services, or eTRIKS — a nearly €24 million ($31.5 million) consortium funded by Europe's Innovative Medicines Initiative as well as pharmaceutical companies. It also caught the eyes of companies such as PerkinElmer and Thomson Reuters, with whom the TranSmart Foundation is currently holding partnership talks, Athey said.

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