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Is Bioinformatics--and Open-Source Software--in ABI s Future?

SAN FRANCISCO, Sept. 30 - What big prospect is primed to drive science in the next decade? If you're Michael Hunkapiller, the answer is bioinformatics.


Speaking at a recent panel discussion here, the Applied Biosystems president said there is a need among individual researchers to have access to information produced by 'big science'--that tangle of data produced by the huge academic and nonprofit labs ringing the planet.


This informatics link, Hunkapiller said, will turn the computer into a tool "viewed as a part of the research repertoire ... just as much as the DNA sequencer or mass spectrometer."


"In our view of the long-term," he said, "this is obviously a challenge we haven't yet met."


For ABI, this means building bioinformatics software that will allow its customers to navigate seamlessly between, say, results generated by tools in their own labs, big-science data available through public programs, and proprietary information available from Celera Genomics, Hunkapiller explained. He said this effort was informally dubbed ABI's internal "knowledge-business" program.


A 'knowledge business'


Today there exists "a lot of core reference information you didn't have [before] to start your experimental questioning and design," said Hunkapiller. "And so we're really now into the mode of trying to figure out how to meld" data that's come out of these big programs into the small-biology environment--namely, the individual investigator hunkered down in a hypothesis-driven research lab.


The goal, he said, is to have customers, working on their desktop, to "be able to in a facile way use the information coming out of these big [science] projects and do it on a daily basis rather than have them spend months and months cobbling together from disconnected sources the information they need."


How would ABI succeed at the business of bioinformatics where many high profile companies have stalled?


By not being a bioinformatics company, Hunkapiller stressed. ABI, he said, is in the business of supporting biological research, not bioinformatics. "I think bioinformatics failed because it is difficult to build a business just around bioinformatics," he said.


To be sure, Hunkapiller gave no details about how bioinformatics might look at ABI, but he pointed out that with computer scientists making up half of the company's R&D force, the software could be generated in-house.


I dare you


Lee Hood, president of the Institute for Systems Biology and a co-panelist at The Economist Innovation Awards and Summit here two weeks ago, agreed that integrating informatics with existing tools could be a boon to scientists, who would benefit from better-organized information. But he challenged ABI to go a step beyond merely beefing up its informatics: Make the software open source, he said.


"Even instrument companies should have open source in terms of software, including ABI," said Hood, who was instrumental in starting ABI. "Then users improve [the software] and ABI selects the best fixes."


Hunkapiller was mum when asked about the possibility of ABI going to open-source software.


Others weren't so quiet. Open sourcing "could have tremendous value for the community and Applied Biosystems," pointed out Steven Brenner, an assistant professor at the University of California, Berkeley, and an open-source advocate. Open sourcing "allows more people to integrate more systems."


Jeffrey Chang, a consultant with Dalke Scientific Software, agreed: "Their [bioinformatics] tools really aren't where they make money. Open-sourcing them could result in better quality and more widely usable tools, which would help out" ABI.


But a move toward open-sourcing would abound with challenges for ABI just as it presents challenges for most companies that decide to take the plunge.


Brenner, for example, stressed that while open sourcing "has potential in a generic sort of way," success depends on the operational and business models of specific companies.


Even considering a move to open sourcing can meet with resistance. "All of the instrument companies were brought up in closed-source shops, so they would have to change this fundamental attitude," explained Hood.


"For companies, it's a foreign idea to release their code for free," Chang chimed in. "It's counterintuitive for companies. I'm not sure what it will take to get traditional companies to see the value of it."


Silicon Graphics is one such firm that saw the value in open-source software. The Mountain View, Calif.-based company relies in part on the academic community to let it know what software should open sourced. Still, the company "only scratches the surface with what we might do with open-source bioinformatics," said Roger Cloud, Silicon Graphics' director of legal services. "There is not enough commerce of ideas between educational institutions and vendors of software" to fully explore the potential of open-source software.


If an academic institution does request open sourcing, it must be approved by SGI's open source review board.


Any company thinking about open sourcing should consider it carefully, said Cloud, who explained that in addition to licensing issues that may have to be hammered out, a company needs to monitor what happens with the software once it is open sourced in order to ensure the integrity of the informatics. "You don't just throw things over the fence," cautioned Cloud. "We try not to abandon the baby."

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