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When bioinformaticist Steve Brennerwas finishing his postdoc at StanfordUniversity and looking for a job, animportant issue was that hisemployment contract would allowhim to contribute to ‘open-source’software — software where thesource code is freely available, andderivative works can be made andredistributed. Unlike many of hiscolleagues, Brenner knew that mostuniversities prohibit the freedistribution of software, and indeed,at the University of California,Berkeley, he found this to be thecase. “I found that their rules were infact incompatible with open-sourcelicenses,” he says.

Brenner, now at Berkeley,decided to negotiate his contractbefore he accepted the position. Aseparate statement was ultimatelyadded, allowing him to contribute toopen-source software as long as allthe contributors to the softwareagreed, the funding agency agreed,and it didn’t violate any laws.Although he stresses that Berkeleywas very accommodating, he saysthat the process was time-consuming,confusing, and expensive, requiringhim to hire a lawyer. “The biggestissue was simply that they’d neverdone anything like this before, so noone really knew what the processwould be,” he says.

Open-source enthusiasts say thatopen-source software — whichpowers much of the Internet andoperating systems such as Linux —allows software to improve and

evolve faster than if the source codewere not freely available. But manyacademic bioinformaticists have beenunaware that their universitiesusually own the copyright to theirwork, including software, so theyaren’t legally free to distribute theirsoftware without permission fromtheir institution’s technology transferoffice. “Most people probablydistribute their software off theirwebsites and their universitieswouldn’t care, because most of thisstuff isn’t commercializable anyway,”says bioinformaticist Sean Eddy atWashington University in St. Louis,Missouri. But for potentiallycommercializable software, thetechnology transfer office would takenotice, he says.

If there is one certainty, it is thatevery university in the US has adifferent policy on copyright

Even academic technology transferoffices aren’t uniform on theircopyright policies, according toKaren Hersey, a lawyer with theMassachusetts Institute ofTechnology and past president of theAssociation of UniversityTechnology Managers. “If there’sone certainty, it is that everyuniversity in the US has a differentpolicy on copyright, who owns whatcopyrightable materials, and howthey should be distributed,” she

says. Assuming the funding agencyhas no specific requirements, thedecision ultimately depends on thewishes of the investigator and thetechnology transfer office, she says.

This contrasts with the moreuniform US university patent policydue to the 1980 Bayh–Dole Act,which allows universities to patentand commercialize discoveries madewith federal funds. “We’re definitelycaught in a vice here because wehave conflicting mandates,” saysEddy. On the one hand, theBayh–Dole Act encouragesdiscoveries to be commercialized, yetgranting agencies say that anythingresearchers develop must be madefreely available, he notes. Whetherthis explicitly applies to softwarehasn’t been clear, he says. Oneexception is the Howard HughesMedical Institute, which hasincluded software among theresearch tools that should be madefreely available, encouraging that thesource code be made available formodification for non-commercialpurposes and discouraging exclusivecommercial licenses.

Working with funding agencies isone way to keep software opensource, says bioinformaticist EwanBirney of the EuropeanBioinformatics Institute at Hinxton,near Cambridge, UK. For theEnsembl project, which he co-heads,“we deliberately said to theWellcome Trust that we’re going tomake this software open, and theysupported that,” he says.

In a similar vein, Jason Stewart,who heads the private consultingcompany openinformatics.com inTuscon, Arizona, has started apetition asking public fundingagencies such as the NationalInstitutes of Health and the National

Features

When software isn’t for sharing

Researchers in bioinformatics increasingly face a dilemma overwho owns any software they may develop during their research.Alka Agrawal looks at the problems facing open-source enthusiastsand what they can do to ensure that what they create can enterthe public domain.

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Science Foundation to require thatall funded software projects bereleased as open source. Stewart andhis colleagues have also argued in apaper being considered forpublication in Briefings inBioinformatics that since mostbioinformatics software is customizedfor particular applications, having thealgorithm available through thesource code is important for the peer-review process.

Brenner has proposed having astandard employment contract thatcould be used to allow researchers atany institution to produce open-source software. The effort is still innascent stages, he says, but there arepeople working on different versionsof the contract, such as versions forAmericans or Europeans at academicinstitutions, or people who work atcompanies who want to produceopen-source software in their sparetime.

And bioinformaticists point outthat there’s a simple solution: to havethe option of licensing softwareunder an open-source license or acommercial license. “In the casewhere you have a sole copyrightholder, and that’s true for all oursoftware, the copyright holder candistribute under any license they feellike,” says Eddy. But “you’ve got tobe pretty savvy to get yourself intothat situation,” says Birney.

But ultimately, bothbioinformaticists and lawyers seem toagree that it’s ultimately theinvestigator’s decision about howthey want to license their software.Brenner says that although hismodified contract could causeBerkeley to lose out oncommercialization opportunities, ‘theuniversity’s primary goal is not tomake money but to fosterknowledge, and I think that they sawthis as being something where thecost involved was worth thebenefits.’

Alka Agrawal is a freelance science writerbased in Stamford, Connecticut.