Open Access News

News from the open access movement


Tuesday, May 22, 2007

Sean Eddy on open access and open source

Kevin Davies, Eddy Celebrates Open Access in Franklin Speech, BioIT World, May 22, 2007.  Excerpt:

Sean Eddy accepted the 2007 Benjamin Franklin Award....

Open access to software, journal articles, and data is an issue of profound importance to researchers across the community. The first journals, created in the mid 1600s, were founded with a tacit quid pro quo: disseminate your research, allow others to reproduce your work, and gain a measure of fame in the process....

Four centuries later, the issue hasn’t changed so much. In 2001, Celera published its assembly of the human genome in Science, but refused to freely distribute the sequence without restrictions. Eddy said he uses Celera’s DVD as a coffee coaster, because the terms barred him from redistributing the sequence data.

In the aftermath of the controversy, the National Academy of Sciences convened the Cech Report, reaffirming the quid pro quo of science publication. “If you’re not disclosing anything, why should you get credit?” said Eddy. “All members of the scientific community … are playing on the same playing field. [If] Celera publishes a paper, their genome sequence should be available. [If] I publish a paper, my software should not be made available to academics only, but to [everyone].”

Eddy devoted most of his talk to the topic of data dissemination and open access. “We want not just humans to be able to read the literature, but computers to be able to read the literature.” Said Eddy: “The bioinformatics community is the canary in the coalmine for this kind of issue, we’re affected by this issue. We’re the ones trying to integrate large datasets. If the dataset is there but not integratable, we know about it first…. The literature affects us very much.” ...

“For me, open access is secondary. The goal is to create systems that work… open access is necessary but not sufficient.” Eddy made a strong case that it is worth academics taking time away from their top priority – writing papers – to “create tools and make sure that they get used by the community.” There are several keys to doing that successfully, including choosing the right problem, preparing a simple manual, making it freely and readily available, and ensuring that it is integrated into the community’s system.

Eddy is best known for a program called HMMER, for running profile hidden Markov models on sequence families. The software is easily downloadable, and runs on anything, said Eddy. There is one page of instructions for installation, another page for getting started....

Curiously, Eddy noted that the International Society for Computational Biology has a policy against open source software. Some members, he said, think they should be able to make money from industry for writing software. “Some people with a similar mindset as me have infiltrated the board of directors,” and will work to change the system....