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Applied Biosystems’ Software Initiative for Next-Gen

By Kevin Davies

Oct. 10, 2007 | Applied Biosystems (AB) has launched an initiative to help life scientists and independent software vendors develop software applications for its SOLiD next-generation DNA sequencing platform. AB says it is expanding its software development community to include sample data sets, data file formats, and data conversion tools for the newly released SOLiD.

The SOLiD system enables “myriad applications in genotyping, sequencing, epigenomics, and gene expression,” says Michael Hadjisavas, AB’s director of commercial development. “One potential expectation of the software initiative in this area is to enable the development and availability of analysis software that will enable researchers to visualize and interpret data for these various applications.”

AB says it is the first next-generation sequencing manufacturer to make these tools available to the bioinformatics community, and wants to help tackle the significant challenges associated with analyzing and managing the vast amounts of sequence data. Last summer, dozens of researchers from academic and commercial institutions gathered at AB’s headquarters in Foster City, CA, to share best practices on various next-generation sequencing software development initiatives.

“The promise that next-generation [sequencing] technologies will generate better data, faster, and at a lower cost will only be realized when there are sufficient software applications that allow researchers to analyze this data,” said Michael Wittig, a bioinformatician at the Institute for Clinical Molecular Biology in Kiel.

A key issue, according to Darren Platt, head of informatics at the Joint Genome Institute (JGI), is not just the “the quality of the data each platform generates, but ... how willing each vendor is to collaborate with the research community to provide the necessary tools and resources for developing the required software applications.” AB’s willingness to share information about the SOLiD system “will enable us to rapidly develop the software applications our laboratories need to accelerate next-generation research projects,” says Platt.

Another goal of the software initiative, says Hadjisavas, is “to enable the development and availability of analysis software that is independent of application and viewed as foundational to all types of analysis. Examples of such foundational analyses include software for alignment, assembly, annotation, quantitation, management, and visualization.”

Hadjisavas expects the initiative “will alleviate the potential bottlenecks that researchers will encounter that are related to analysis, visualization, management, and interpretation of data. He says AB is “proactively engaging” in discussions with customers and vendors to develop software requirements that will stimulate the development and availability of software tools for this “compelling technology.”

AB is looking to aid a bioinformatics community to further application development in a variety of research areas, including whole genome sequencing, chromatin immunoprecipitation (ChIP), microbial sequencing, gene expression, microRNA discovery, digital karyotyping, and epigenetics.

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