One of my pet issues in bioinformatics is that of methodology versus discovery. In other words – is your new, cute and clever piece of software any use if biologists are not using it to discover interesting things?
It’s a complex problem. On the one hand without software development, we don’t have the new tools with which to make discoveries. On the other if the focus is entirely on software development, programmers are free to publish endless short papers without practical application and biologists fail to see the
point of bioinformatics and so become ever more ignorant of and disenfranchised from the process of computational biology.
Ultimately I suppose, there can be a forum for both aspects. I think we are seeing this in the way that journals are developing. Bioinformatics, for instance, seems to be very much a forum for methods and algorithms these days, whereas journals such as Genome Research seem more focused on the application of tools to biological discovery.
Still, I worry that your “average” biologist, turning to a hard-core bioinformatics journal is likely to ask “what use is all this?”