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Software Development Community of Applied Biosystems looks to new bioinformatics tools

Applied Biosystems : 08 February, 2008  (New Product)
Applied Biosystems’ Software Development Community has established relationships resulting in two formal agreements intended to help scientists address next-generation sequencing bioinformatics challenges.
Geospiza and GenomeQuest will develop bioinformatics tools that are expected to advance data analysis and management for life scientists utilising data generated by the SOLiD System, the life science industry’s highest throughput system for next-generation sequencing.

Geospiza, a leading provider of fully integrated data management infrastructure solutions for genetic analysis, has signed an agreement expanding its relationship with Applied Biosystems to include next-generation sequencing instrumentation.

Applied Biosystems also formed an agreement with GenomeQuest, which provides an integrated sequence information platform allowing researchers to search and analyse genomic sequence data as a hosted service or as a hardware appliance.

The SOLiD System is capable of generating sequence data that exceeds 4 gigabases (GB), which is more than the approximately 3 billion bases of the human genome. The solutions offered by Geospiza and GenomeQuest are expected to help address managing this vast amount of genomic data by providing complementary services, including the IT infrastructure to manage the data, as well as the ability to process the data and align it to a reference sequence.

Applied Biosystems expects that its relationships with Geospiza and GenomeQuest will help drive innovation and speed the development of new tools that will enable researchers to find answers faster and more cost-effectively, thereby helping scientists to realise the full potential of next-generation genomic analysis.

Applied Biosystems has shared file formats, sample data sets and analysis pipeline information with Geospiza and GenomeQuest so that they may configure their products, services and capabilities to address customer challenges associated with generating, analysing and managing research data in key applications for the SOLiD System.

As part of Geospiza’s participation in Applied Biosystems’ Software Development Community, Geospiza developed a software system designed to automate sequencing workflows for capillary electrophoresis (CE) instrumentation.

Applied Biosystems’ agreement with Geospiza is expected to extend Geospiza’s Finch Suite software and its knowledge of 3130 Series Genetic Analyzers and 3730 Series DNA Analyzers 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, which will enable them to integrate and visualize the two data sets from both technologies. The integrated solution is expected to enable researchers to utilize both the SOLiD System for discovery applications and CE systems for validation, connecting the research continuum.

The development is expected to benefit many organizations, including the University of Washington, which is a user of the FinchLab software and an early adopter of the SOLiD System. Scientists in the university’s High Throughput Sequencing Solutions Laboratory recognise the challenges associated with the vast amount of data being generated from next-generation sequencing systems.

“As a Geospiza FinchLab customer and a laboratory that has acquired a SOLiD System sequencer, any collaborative effort between Geospiza and Applied Biosystems to help laboratory directors meet the coming next-generation sequencer data management and analytics challenges would be a welcome relationship for the research community,” said D. Michael Dorschner, the director of the University of Washington’s High Throughput Sequencing Solutions Laboratory.

Geospiza plans to deepen the integration between its FinchLab Next Gen Edition software product and the SOLiD System to provide a comprehensive solution that includes data management systems to define experiments, and the ability to track data through production, and process genetic analysis platforms in a scaleable high capacity storage system.

“By expanding our long-standing relationship with Applied Biosystems, we are answering the call for bioinformatics solutions to help accelerate research on next-generation genomics analysis platforms,” said Rob Arnold, president, Geospiza. “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. Our platform is specifically designed to scale with the lab as their needs grow.”

GenomeQuest has 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.

GenomeQuest’s solution is also expected to enable SOLiD System customers to seek assistance with data alignment and analysis, including SNP (single nucleotide polymorphism) detection. In addition to increasing productivity, GenomeQuest’s solution enables scalability 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,” said 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.”

Through its Software Development Community, Applied Biosystems is the first manufacturer of next-generation instrument systems to make software development tools broadly available to the bioinformatics community. The community supports life scientists and independent software vendors in the development and potential commercialisation of bioinformatics applications for next-generation genomic analysis platforms.
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