Once again I find myself recommending a link from Snowdeal and a link to The Scientist, specifically this article on software maintenance (free registration).
Some really choice quotes here (and as an aside, some confusion over the noun for "one who practices bioinformatics" - they try "bioinformatician" and the surely-misspelt "bioinformatist"):
"Meanwhile, new grad students and postdocs don't want to work on a project that already has a solution, even if that solution has nobody fixing bugs and providing service. The discipline cherishes innovation and creativity, not sound technical support."
"The very concept of creating a proprietary program whose source code is kept secret and which is sold for profits is anathema to the entire academic biocomputing community."
"In academia there is no reward structure for maintaining and supporting a piece of software," Myers says. "It would not be good for the postdoc's career and I would not advise them to do so. There's just no academic incentive for it."
"Bioinformaticians are the first ones to the chopping block when a drug company needs to cut somewhere," says Joe Landman, who founded his own consulting firm, Scaled Informatics.
Washington University's Eddy recommends a more dramatic change to the structure of the world bioinformatics system. "I think it's time to start thinking about extending the length of postdocs in our field so that they have time to identify a problem, create a solution and then get all the bugs out," he says.
Comments
No easy solution
Currently the only solutions seem to be spinning off the software into a company or securing a grant to develop upgrades. In Europe at least I think it could be part of a big center like EBI could play. Not only developing and maintaining databases but also software that is used by the community at large. I guess the other possibility is open source development. If the code is useful and visible than I think people would pick it up to develop it and maintain it.
survival of fittest?
I think your point about open source repositories is a good one. I download a lot of free stuff, particularly for structural biology, some of which is years old and with virtually no documentation. It's useful to me, but I think if something is seen to be useful, it will survive and be maintained. There's a lot of really good GPL'd stuff around (e.g. Gromacs) and around 350 sourceforge projects under the 'bioinformatics' heading, so good software does have a home to go to. I like the Eddy group's work, but I have to disagree with him that we need longer postdocs purely for software development! What we need is a career structure for postdocs.
for what it's worth...
I never told Jaffe I believed that we needed longer postdocs.
I told him I think we need a better career path for software
dev people in bioinformatics. So I'm in agreement with you.
- Sean Eddy