Applied Bio SOLiD as a rock

Geospiza, GenomeQuest develop bioinformatics tools for company’s SOLiD platform

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FOSTER CITY, Calif.—Applied Biosystems took a step forward some five months ago in its Software Development Community concept with the addition of a community for its high-throughput next-gen sequencing SOLiD System—a move that has borne fruit as of early February with the announcement of two formal agreements regarding new bioinformatics tools, one with Geospiza and the other with GenomeQuest.

Geospiza, a provider of fully integrated data management infrastructure solutions for genetic analysis, has signed an agreement expanding its existing relationship with Applied Biosystems to include next-generation sequencing instrumentation.
GenomeQuest, for its part, inked an agreement with Applied Biosystems that provides an integrated sequence information platform allowing researchers to search and analyze genomic sequence data as a hosted service or as a hardware appliance.

"GenomeQuest and Geospiza represent the first two software vendors among the many we imagine that will be introducing new software through the community," says Roger Canales, senior manager of the SOLiD Software Development Community. "The Geospiza tools are mostly for core labs—though in a phase two portion they will release a tertiary downstream analysis tool on top of that—and the analysis tools that GenomeQuest is providing are a good one-stop-shopping option to enable analysis through the entire workflow. It's a good way to start off the community, but that being said, the next-gen sequencing software space is still in its infantile stage, so there is a lot of room for much more software development."

Specifically, Geospiza developed a software system to automate sequencing workflows for capillary electrophoresis (CE) instrumentation, and Applied Bio's agreement with them is expected to extend Geospiza's Finch Suite software to SOLiD System-specific IT infrastructure support, software and tools with its new FinchLab Next Gen Edition product. As life scientists expand their research capabilities by using the SOLiD System, Geospiza expects to support these customers by processing both CE and SOLiD data through a single data processing pipeline, enabling them to integrate and visualize the two data sets from both technologies. This should enable researchers to employ the SOLiD System for discovery applications and CE systems for validation, "connecting the research continuum," according to Applied Bio.

"Laboratory directors and end users should benefit equally from the more natural workflow as they switch between the software and the instrument for data generation, management and analysis," says Rob Arnold, president of Geospiza. "Our platform is specifically designed to scale with the lab as their needs grow."

GenomeQuest's offering is an integrated solution based on its database of reference sequences that is expected to transform raw sequence data from the SOLiD System into information that will reveal insights resulting from the sequencing run. This should enable SOLiD System customers to seek assistance with data alignment and analysis, including SNP detection. In addition to increasing productivity, GenomeQuest's solution is said to be scalable as customers accelerate their use of next-generation genomic analysis platforms.

"Our relationship with Applied Biosystems should ensure that SOLiD System customers will have a robust informatics platform that supports their needs, now and in the future," says Ron Ranauro, CEO of GenomeQuest. "The research community has clearly indicated that they need more than algorithms to adequately handle the immense volume of data generated by next-generation platforms."

Applied Biosystems established the Software Development Community in 2006 to encourage innovation in life science research software applications and to create a collaborative environment that provides a widely accessible pool of resources. This will enable customers and independent service providers to develop and bring to market innovative new applications that allow the research community to find more answers, faster and more cost-effectively. The company expanded the community in 2007 to directly address the industry-wide challenges associated with analyzing and managing the vast amounts of research data generated by ultra-high-throughput technology.


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