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ABI Opens File Formats for Sequencers, PCR Instruments In Bid to Build External Software Development Community

In a move that should be welcome news to many life science researchers, Applied Biosystems has released the file formats for its line of genetic analyzers and PCR instruments as the first step in a broad overhaul of its bioinformatics strategy.
The company released the file formats to kick off its Software Community Program, an initiative intended to provide customers and third-party software partners with free software, formats, file converters, and other tools that will help them manage data from ABI instruments.
The program signals a sharp turnaround for ABI, which has historically kept the file formats for its sequencers and other instruments strictly proprietary.
A number of factors, however — including the downturn in the commercial bioinformatics market, a parallel trend toward open source tools, increasing competitive pressure in the instrumentation market, and a complete management overhaul at ABI — have caused the company to rethink that philosophy, according to John Oakley, chief architect at Applied Biosystems.
“We have a new management team, it’s a new business environment we’re in, and the time is now right to revisit policies in that area,” Oakley told BioInform. “We may be a little late coming to the game, but it’s something that we now understand. The basic tenet is that the customer owns their own data, and we’re just going to make it easier for them to be able to work with it.” 
The program is initially focused on the company’s line of genetic analyzers and PCR instruments (see sidebar for details), but Oakley said that the new open philosophy will eventually extend across ABI’s entire product line. “The policy is openness,” he said. “The philosophy is across the board on all products — provided we don’t give away the crown jewels.”
Oakley acknowledged that a number of details have yet to be ironed out regarding other product lines, such as mass spectrometers, but he stressed that the company’s aim is to eventually build a community of software developers around all of its product areas.
“I think it’s important that we actually put a stake in the ground,” he said. The launch of the Software Community Program is “a statement of intent,” he said, “and although it’s not a specific statement of intent, it should be an indicator to our partners that we’re going to work together with them on a new way of doing business, to some degree.”
Geospiza is the first formal software partner under the program. The company has expanded a co-development and marketing agreement that it signed with ABI early last year to integrate its Finch data-management suite with ABI’s LS*LIMS platform [BioInform 02-14-05]. Under the expanded collaboration, Geospiza will integrate Finch with ABI’s GeneMapper and SeqScape software tools.
Oakley said that ABI is in discussions with other potential ISV partners, but noted that the company is still “gathering the requirements to see what would make it attractive for other people to be involved in this.”
While Oakley didn’t have data on the number of software or file format downloads related to the program since its launch on August 28, he noted that the company is fielding more calls than it had anticipated, but is so far seeing many more inquiries than downloads. “There’s a sort of reticence to get feet wet at this point in time,” he said.
Eliminating the Guesswork
For those who have overcome their doubts, ABI’s new policy is “phenomenal news for software developers,” Kevin Banks, vice president of business development at Geospiza, told BioInform.
In addition to the resources available through the Software Community Program, Banks said that Geospiza developers will now be able to work more closely with the developers of ABI’s genetic analysis tools, which will ensure tighter integration between Finch and ABI software.
While the file formats for ABI’s genetic analyzers have technically been publicly available for some time — having been reverse-engineered by the bioinformatics community years ago — Banks said that the new open policy at ABI will provide external software developers with greater insight into what the company is developing, “rather than guessing at what they’re doing.”
Banks said that bioinformatics software developers can now spend their time “developing applications that people can use, rather than figuring out proprietary formats.”
Sign of the Times
ABI appears to be taking a page from the Affymetrix playbook. The microarray giant launched the Affymetrix Developer Network — a mechanism for releasing file formats and other tools for third-party developers — several years ago, and last fall kicked off the GeneChip-Compatible Applications Program, a more formal version of the ADN under which Affy ensures that certain software packages are compatible with its GeneChips for particular applications [BioInform 09-15-05].
Affy’s own migration towards an open philosophy has been an unqualified success among bioinformatics developers — the company currently lists products from 25 commercial partners in its GeneChip-Compatible catalog and claims to have thousands of people on the ADN mailing list — and ABI is clearly trying to replicate that same spirit among its own customers and partners.  
“The trend is toward openness,” Oakley said. “One of the limitations of a non-open approach is that the ability to use the products you produce is limited by the things that you think of in-house or with your contracted partners. By providing open access to the information, there’s no limit to what our customers might think they want to do with the data itself.”
Geospiza’s Banks noted that the ABI and Affy programs are a sign of a “broad shift as the industry is maturing” into an “ecosystem where they can all play together rather than each one trying to do it all.” Instrument vendors are moving away from software development, he said, to focus on what they do best. “It’s extremely difficult to be successful at both,” he said.
ABI began inching toward more of an open position more than a year ago, when it released its PANTHER (Protein Annotation Through Evolutionary Relationships) classification system into the public domain [BioInform 01-10-05]. A few months later, ABI sister company Celera Genomics released the Celera Discovery System genomics database, which was marketed by ABI, into the public domain as well [BioInform 05-02-05].
But while those moves were a response to the downturn in the commercial market for bioinformatics tools and services, the new Software Community Program is viewed as an opportunity for growth at ABI.
“The whole purpose of this is to drive revenue, and the more people we can get thinking about what our instruments do, and what our products do, the more this will happen,” Oakley said.

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