On Oct 22, 2010, at 12:39 PM, Richard Ree wrote:
Both technology and users' needs evolve rapidly - so the "gaps" will never be closed, at least in the time frame required by grants, etc. Also, in phylogenetics a lot of developers are themselves users, so quick and dirty solutions to scratch individual itches is inevitable. It's a good thing, IMO.
I agree entirely with the "solutions to scratch individual itches is inevitable and a Good Thing(tm)".
What I don't agree with is if this is portrayed as being mutually exclusive with reusable and more sustainable software. Projects like Bioconductor, the Bio* libraries, and other similar ones demonstrate that it clearly does not need to be mutually exclusive if we don't want it to be. Every piece of code in BioPerl is there because it first scratched someone's itch. The rate of innovation in Bioconductor is pretty rapid.
The barrier, if there is perceived to be one, is social, not technical or scientific. If we as a community of practice don't care about sustainable software, it won't happen, and we'll continue to lose software. If we want to think that the software we produce is an integral part of our science, we lose part of our science every time a piece of software is no longer maintained. And if we want to think that writing a new piece of software is part of our scientific progress, then every time someone writes code for something that code has already been written for, our rate of scientific progress is slowed down unnecessarily.
Again, just my own $0.02.
-hilmar