ABI opens up its code

Applied Biosystems has decided to provide life scientists and independent software vendors open access to its genetic analysis data file format and a data file converter.

Jeffrey Bouley
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FOSTER CITY, Calif.—To encourage innovation in life science research software applications, Applied Biosystems (ABI), an Applera Corp. business, has decid­ed to provide life scientists and independent soft­ware vendors (ISVs) open access to its genetic anal­ysis data file format and a data file converter and launch a new software development community.
The idea of creating such a community, ABI says, is to facilitate the development of next-generation bioinformatics applications that can advance productivity and data sharing on ABI's genetic analyzers and real-time PCR sequence detection systems.
"The basic idea behind it is the realization that we've really got to get out of the way of the custom­ers and let them choose how they want to handle their data and analyses," says John Oakley, chief architect for ABI. "In the past, we've decided how the instruments would be used based on software we would pro­vide.
"But we realized that more companies—in life sciences and other industries—were releasing formats for their data and compa­nies were coming up with ideas that wouldn't have been thought of otherwise or would have been shunted to a back burner because they didn't seem important enough."
In the end, he says, the goal is to help improve cycle times by giv­ing researchers more flexibility to make decisions about the discov­ery work that they are doing.
"Applied Biosystems under­stands that in order for the life sciences community to ultimately achieve its goal of targeted medi­cine, an environment of collabora­tion and innovation is required," says Dr. Dennis A. Gilbert, CSO for ABI. "Our mission is to cre­ate a more collaborative environ­ment that provides an open and widely accessible pool of resourc­es."
ABI has already initiated a number of new collabo­rations with leading ISVs directly and through organizations such as the BioIT Alliance, a cross-indus­try working group spearheaded by Microsoft Corp. that brings together pharmaceutical, biotech, hardware and software companies to explore new ways to share com­plex biomedical data and speed the pace of discovery in the life sci­ences.
Geospiza, a developer of IT solu­tions to automate genetic testing, analysis and data production, is one of the first companies to join the ABI software development community, having developed a tool that improves data analysis workflow and provides better sharing of research and dis­covery project data across work­groups. The new solution uses the Geospiza Finch Suite, a software platform that facilities clinical and preclinical genetic testing based on DNA sequence analysis.
"Historically, Applied Bio has been more of a closed shop," notes Dr. Kevin Banks, VP of business development at Geospiza. "By cre­ating this software development community, the company is really allowing software companies to do what they do best and create a larger ecosystem of providers to serve the needs of drug discovery researchers. "
ABI isn't the first com­pany to recognize the value of opening up some of its code to developers, Banks admits, noting that Affymetrix was one of the first to do so. But ABI is coming to the table early enough to make a difference in the community and stay ahead of the curve, he says.
"In IT terms, it would be anal­ogous to how Apple tried to do everything itself, but Microsoft took a partner approach," he explains. "Applied Bio is taking the latter approach and really empow­ering the software community to fully support drug discovery."

Jeffrey Bouley

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