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Old 04-22-2011, 03:19 PM   #14
Senior Member
Location: Oakland, California

Join Date: Feb 2008
Posts: 236

Michael: I think you're preaching to the choir - but really, there's a huge difference between documentation for developers and documentation for users. Conflating the two - or trying to discuss them both at once - isn't going to result in a productive set of action items.

Personally, I've spent far more time maintaining, cleaning and documenting my code than my committee or my advisor really would like. It slows down development and only shows benefits in the long term. As long as code is being developed by people who expect to work on a project for less than a year or so, you're going to have a hard time convincing them of the benefits of good coding practice. And, I think it's relatively obvious, post-docs and grad students rarely have that kind of long term vision unless the project is actively managed by their PI or an institute staff member. (I'd like to think my own code is an exception to the rule, just because I really believe strongly in good coding practices.)

At any rate, I really like Nils' suggestion of an open source repository for bioinformatics software. I currently use SourceForge (as a few others do), but there's no sense of developer community specific to bioinformatics in that environment. Nor is there a "bioinformatics app-store" specific for that community - thus, it would also be able to help with organizing projects and directing people to contribute to existing software, as well as providing forums much more tailored to bioinformatics needs. Even better, if it could be used to do automatic nightly builds of the software, it would force developers to use unit tests to keep from breaking the head of their trees - nightly builds are a good indication of the stability of software.

Edit: Just to be clear, nightly builds + nightly unit tests would be a great indication of the stability, as long as the visitors to the site get some stats on the number of unit tests passed, etc. I realize that nightly builds on their own would only fail when compilation errors are present, which, on it's own would be good start.
The more you know, the more you know you don't know. —Aristotle

Last edited by apfejes; 04-22-2011 at 04:20 PM. Reason: clarity
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