There was also a bit of a stir at the Open Data and Software BoF which centers around the ISCB’s statement about guidelines for open source software (you should provide feedback if you feel strongly about this and are an ISCB member: policy<-at->iscb.org).
The discussion was prompted in part because Mike Eisen and Sean Eddy both turned down their complementary ISCB memberships stemming from recent publications in PLoS CompBio (oh the benefits of publishing in PLoS CompBio) because of their disagreement with the policy. The Board took notice enough to organize a BoF at the conference. Unfortunately it was during lunch so you had to either choose between food and session or wolf down food very fast and run over to the room.
Some usual suspects were there that had a variety of opinions on open source – I don’t have the complete list written down though. There was an open-mic session after a panel of ISCB directors presented their opinions. It seemed like most of the audience members were in support of revising the statement to be more supportive of open-source although not everyone wanted to make it a requirement that source code be available commiserate with publication. To me there are a lot of messy ends here rather than having a discussion about the principals it ended up being about individuals personal stories that supported or discouraged a requirement of open source. Some people see it as too much of a burden to release their software (it is written either poorly or too hard-coded for their internal compilation system).
Others argued in not so many words that sell their software and don’t want to be told how they can operate – the argument is couched under statements like “papers should be well-enough written to describe an algorithm so that it can be reproduced”. Great so now in order to move forward in a field we have to re-implement everything that came before?
There were also some arguments against open-source made like: “we made our source available for our project and we have 50 users and never have received a bug fix”. So the lack of contribution to one project by users justifies not encouraging it for all other projects? A poorly managed open-source project will not succeed any more than a poorly managed in-house closed source project. It takes work to communicate with users and solicit input and will also depend on the computational saavyness of the users in the first place.
Some people lobbied for open source software because they can’t afford to buy commercial software and they need things like R, bioconductor, BLAST, etc. In the same way that the government pays twice for research: grants pay for research which is published in journals and then grant overhead pays for journal subscriptions for others to read about the work. Similarly I fail to see why granting agencies would want to fund software developers in many parallel labs to reimplement the same thing or to pay a subscription for software that was developed under government grants.
The cost argument shouldn’t be overlooked, but I don’t think it is as convincing as the ability to build on other people’s work. For me it is because we want to build larger systems from the basic components and only when we have access to the individual pieces that we can tweak and manipulate can we construct larger systems from them.
Anyways, by the end I felt like I was at a purely ideological debate rather than a potentially interesting discussion. There was mostly rhetoric and essentially no one was really budging on hearing other points of view. I appreciated hearing the concerns of non-open-source proponents to at least see what the concerns were about actually releasing code, but I can’t really support their point of view since it seems to be really in fear of not being able to sell their expensive software or be bothered with the hassle of people using their software in ways they didn’t expect.
One thing that was clear that needs to be resolved outside this debate is that journals that support open-access don’t enforce software which supports a paper be made available and open-source. This lack of policy from journals was an argument against endorsing open-source from ISCB. Similarly there were different interpretations for the National Academies report on open-data sharing (I am failing to find the link right now). There are different reasons that people might not want to make the source code available (but is often available on request). Why don’t they want to release it? I think Carole made the point in her keynote somewhere; it must to come down to embarrassment of poorly written code, code which doesn’t actually do what they say it does, or some sort of expectation to be able to sell the software. At any rate it seems like there is big need for journals, editors, and reviewers to make some decisions about whether or not it is critical for the source code to be available as part of a publication that uses the software.
Sadly we never got to the discussion of open-data sharing which I think is just as pertinent. perhaps there will be more deliberate effort by people to give feedback to ISCB board members about the policy (email the committee: policy<-at->iscb.org)