Open-source software describes program code that is made publicly available for anyone to copy, change or even sell. The best-known open-source programs, such as Linux and Apache, are the product of a collaborative process of software development that takes advantage of the contributions of thousands of programmers all over the world. It's not only a cheap way to produce software; with so many eyes looking at the code, the theory is, bugs are found and fixed more quickly than with proprietary software.

Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM and Sun Microsystems. But it has always had its strongest fans in the academic world, where open-source software is seen as a natural extension of the idea that the fruits of academic research should be shared with everyone.

But now some academic programmers on the cutting edge have found that the licensing office is proving a more formidable obstacle to progress than the limits of their imagination and skill.

Pete Beckman, formerly a senior computer scientist at the federal laboratory in Los Alamos, N.M., is a pioneer in creating clusters of servers that rival the power of mainframe supercomputers. He had to fight with lab lawyers for months before receiving permission to open-source his department's work on the clusters.

Part of the lab's reticence was concern about letting computer technology fall into the hands of America's enemies, according to Beckman. "But the lab's other motive for keeping technology private is the misguided belief they can license it and make money on the lab system," he says. "They have whole departments dedicated to extracting intellectual property from the labbies."

Before Beckman led the fight at Los Alamos to establish a protocol for making lab software public, "the only way to get your code released [open source] was to declare it worthless," he says. Beckman won his fight back in 1999, but the old standard still applies at other federal labs.

"Some federal labs can release code, others can't," Beckman says. "There are whole departments that create valuable new technology, and they can't get it out to the world because [the lab] is trying to make money off it." Software for modeling global climate change, the behavior of viral epidemics and traffic patterns are among the programs researchers can't get released, he says.

In a white paper Beckman authored on the problem, he wrote, "Seeking to control computer-science research by putting intellectual property concerns before the goal of good science has destroyed countless projects."

Just how many is hard to say. Most researchers are reluctant to criticize their administrators. It is rare that universities flat out refuse a request to release software, but the hassle of getting permission can discourage those who might otherwise release their work. "It's tricky to find examples," says Rebecca Eisenberg, a law professor at the University of Michigan who specializes in intellectual property policy. "Because most technology fails, it's hard to say something would have succeeded" if only it had been put in the public domain.

Nevertheless, Eisenberg is convinced that university interest in licensing intellectual property for profit is often at odds with the advancement of science. "You can make a clear case that research is being slowed by intellectual property claims," she says.

"Universities aren't distinguishing between times when it's important to have a patent in place to get something disseminated and times when it's not," Eisenberg says. "They're just looking to see if they can make money. It retards innovation and taxes development."

It took Chris Johnson, a computer-science professor at the University of Utah, several years of negotiation with his technology transfer office to get permission to make public a program his team had worked on for years.

Called SCIRun (pronounced "ski run"), the program is a software platform for modeling and solving all sorts of complicated scientific problems. One of its most promising applications is as a tool for designing new medical devices. Because it is a foundation upon which other programs can be built, Johnson felt that making it an open-source-code project was fundamental to its value.

"The hope is people will take this and put in their own applications and share those back with the community," Johnson says. But to do that, they have to be able to see and use the code without having to pay for it or get permission. "A lot of smart people out there can show you new and better ways for you, if they can see under the hood," Johnson says.

But when he tried to explain to the university administration that the best way to maximize the value of SCIRun was to give it away, he ran into a roadblock. "We wanted to open-source it," Johnson says. "But they said that would undermine its commercial value."

The negotiations began, a clash of differing cultures and interests. "No one really knew what we were doing at the beginning," Johnson says. "We didn't really understand intellectual property law, and they didn't really understand open source. The university just didn't want to let commercial value go. We're academics who wanted to push the envelope."

After two years of haggling, they reached a compromise. In March, the software was released under a license that allows academics free access to the code but reserves the right to royalties if the code makes its way into a commercial software product.

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