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Convey Computer, Bluebee to Co-distribute Products, Collaborate on Bioinformatics Tool Development

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NEW YORK (GenomeWeb) – Convey Computer and Bluebee have signed a distribution agreement that lets both companies sell their respective software products to clients in the next-generation sequencing market.

Under the terms of the partnership, which started about a year ago, Convey can resell Bluebee's Genome Analytics suite, a software solution that encapsulates open-source algorithms — the Burrows-Wheeler Aligner, Smith-Waterman, and a deBruijn graph constructor — optimized for hybrid-core computing infrastructure.

By the same token, Bluebee can incorporate components from Convey's existing bioinformatics suite into the Genome Analytics software suite and sell Convey's combined software and hardware product to clients in the whole-genome analysis market, Convey's CEO Bruce Toal told BioInform this week. Along with its field-programmable gate array-based hardware architecture, Convey has over the years sold what it says are faster implementations of algorithms for sequence assembly, mapping, and alignment, most of which are incarnations of the same algorithms available in Bluebee's solution. Convey's suite includes GraphConstructor, used for de novo short read assembly; Smith-Waterman for local sequence alignment; BWA, which is used for reference mapping; and PacBioToCA, a correction pipeline that facilitates the assembly of genomes sequenced with Pacific Biosciences' single-molecule real-time sequencing technology.

However, Bluebee's solution will have additional algorithms not currently available in either platform, the partners said. Bluebee is extending the Genome Analytics solution to include BWA-MEM, a member of the BWA family of algorithms that is designed specifically for mapping sequence reads of 70 basepairs or longer, according to the developer website. The Bluebee suite will also include a new variant calling module that's currently being developed, tested, and should be on the market by the end of the year, according to Bluebee CEO Hans Cobben.

This works out well for Convey, according to CEO Toal. He said that his company had planned to add BWA-MEM to its bioinformatics portfolio this year or early next year but had not been able to do so because of competing business priorities and limited resources. At present, Convey's staff is wrapped up in a number of other projects, he said, one of which is a partnership with Dell focused on resizing jpeg images rapidly for social media purposes for an unnamed client. Bluebee had already done some work on optimizing open source algorithms for sequencing analysis and it made sense to try to "leverage [their] excitement and talent and expertise," he said. They also provide Convey with an opportunity to expand its business footprint in the European market.

Privately held Bluebee launched in 2011 as a spinout from Delft University of Technology in the Netherlands and Imperial College London. Initially, the company developed and sold software products for the financial and seismic industries. However, seeing an opportunity to bring its computational expertise to bear in a new domain, the company set its sights on the genomics market about a year ago and now channels its resources almost exclusively towards developing and improving the performance of the open source bioinformatics algorithms that make up its solution, Cobben said.

Pricing for the Bluebee Genome Analytics suite depends on the way a customer chooses to access and use the software. Bluebee offers three options in that regard. In the first instance, customers can purchase components of the software and have their in-house bioinformatics experts implement the solution on their local infrastructure. Alternatively, the company can provide the components as part of a pipeline that customers can tweak and tune to suit their needs. A third option, which is still being developed, will provide a version of the suite that can run on cloud infrastructure. The exact dollar amounts for each option are not disclosed, but Cobben said that under the first two options customers are charged for licenses while the cloud-based option, when it is available, will be run under a pay-per-use scheme.

Bluebee chose to partner with Convey, Cobben said, because the computer vendor was already established and active in the sequencing and biotechnology markets, and working with the firm would put the global life science research market — and possibly the clinical genomics market — within Bluebee's reach. Convey's customers include the German Cancer Research Center (DKFZ), the Broad Institute, and Jackson Laboratory. Furthermore, Convey has a good grasp of how best to use heterogeneous computing infrastructure effectively, he added. Engineers from the two firms have been working closely over the past year on "designing the architecture of [their] solutions" and optimizing them to run on Convey hardware. "We are basically complementing the offering at this point" and at the same time freeing Convey to "focus on their core business," he told BioInform.

Finally, offering a product that couples local hardware with software makes Bluebee a more competitive player in the marketplace, according to Cobben. That's especially true for clients who prefer to run their analysis within the confines of local firewalls as opposed to the more public cloud infrastructure. The company is also banking on the fact that it uses better performing versions of well known and generally accepted open source algorithms in its offering to set it apart from commercial vendors whose systems rely on proprietary algorithms that may not have been vetted by the scientific community and whose results cannot be properly verified, he added.

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