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Seven Bridges Taps BioTeam's SlipStream to Run Cloud-based Informatics Platform Locally


BOSTON (GenomeWeb) – Seven Bridges Genomics will soon begin testing a local version of its cloud-based bioinformatics platform that will run SlipStream, an appliance that is developed and sold by bioinformatics consultancy BioTeam.

Seven Bridges previewed the product at the Bio-IT World Conference held this week in Boston. Kate Blair, the company's director of product management, told BioInform during the meeting that the company will launch an early access program this summer to test the features of the newly minted appliance and that it plans to begin shipping the first systems this fall. The company is still mulling pricing for the product and considering multiple business models including whether to charge customers a subscription fee or a to have them pay a one-time purchase price. It is also determining what the standard specifications for the combined appliance will be, she said.

Seven Bridges is launching the appliance to offer an alternative system to customers who can't use its existing cloud-based offering for their projects either for regulatory reasons, as a result of international restrictions, or because of the high costs associated with transferring data to and from the cloud. It also will enable the firm to cater to clients who don't have ready and consistent access to high-speed internet connections.

The cloud version of the company's platform provides access to storage space and over 200 open-source and internally built sequence data analysis tools and applications that help researchers in academic and industry manage and run all aspects of their NGS workflow including sample and metadata management, secondary analysis, and data annotation and visualization.

For their analyses needs, customers can use the available tools to build custom pipelines for RNA-Seq, whole-genome, and whole-exome analysis, as well as de novo transcriptome assembly. Seven Bridges developers have also designed tools for generating standardized quality control reports as well as visualization applications that let users interactively analyze and interpret their results. Customers also have access to reference datasets for human, mouse, and other organisms and they can request additional reference genomes if needed.

Other features of the platform include a resource management layer that offers efficient dynamic scaling, job scheduling, and provisions storage as needed, and a python-based software development toolkit developed around Docker — an open-source resource for deploying applications as containers that can run on various hardware — that customers can use to wrap their in-house pipelines to make them interoperable with the company's infrastructure. Also, Seven Bridges uses database infrastructure from MongoDB to store pipeline schemas and handle versioning.

Customers can link their sequencers directly to the company's platform and upload data from sequencing runs directly to the platform, and they can use the company's application programming interfaces to link existing software, such as laboratory information management systems, to Seven Bridges' cloud. The company operates a tiered licensing structure for its cloud-based offering, under which customers are charged annually for access to the Seven Bridges platform and services including commercial and bioinformatics support.

The local version of the infrastructure has the same user interface as its cloud counterpart, but customers will be able to tailor their appliances to only include the applications and workflows that that they want to run, Blair told BioInform. These clients will be able to connect their appliances to the cloud and update their systems as the company releases new versions of software, patches, and fixes; they'll be able to download new pipelines and workflows from the cloud and run them locally, and they'll also have the option to move their analyses to the cloud if their projects require more compute power than the appliance provides, she said. Users will also have the option to combine multiple SlipStream appliances to create larger compute clusters.

Seven Bridges chose to work with BioTeam because of the consultancy's "decade of experience in IT infrastructure and hardware for research" and in using that expertise to deliver bioinformatics solutions, according to Seven Bridges CTO Igor Bogicevic.

BioTeam unveiled SlipStream last summer and simultaneously launched an early access program for the first incarnation of the product called SlipStream Appliance: Galaxy Edition, which, as the name implies, couples the SlipStream server with the open-source Galaxy analysis infrastructure. For the EAP, which is still running, Stan Gloss, BioTeam's CEO, told BioInform that the company shipped six units to unnamed clients for testing. In the last year, it has made several improvements to the tool based on feedback from these clients including optimizing the solution to run on a newer iteration of hardware from Intel, which has resulted in a 40 percent improvement in performance over earlier versions of the tool, Gloss said. The company also has a better grasp on what customers needs are and has tailored the appliance to meet those requirements, he added.

BioTeam plans to release SlipStream: Galaxy edition more broadly this summer. It had intended to launch the product last November but delayed the release to incorporate improvements based on EAP feedback. The company will continue to pursue partnerships with other industry and academic partners that are similar to the ones it already has with Galaxy and Seven Bridges, Gloss said.