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My personal impression isn't that bioinformatics needs a full language, but more tools in popular environments to lower the entry barrier for good software engi

My personal impression isn't that bioinformatics needs a full language, but more tools in popular environments to lower the entry barrier for good software engineering practices. Every bioinformatics codebase I've looked at has been a downright mess. Basically an ad hoc collection of scripts that transform data this way, maybe rendering some graphs or such, relying on 100 unstated assumptions. Nothing is maintainable, and often rely on messy approaches like loading your entire data set into memory (works fine for your 1-10GB data set, then not so much on a larger one) or what I would gently describe as mainframe compute in place of real software engineering.

downerending 7y ago
I'm reminded of this rant from Richard O'Keefe (of Prolog fame). It was a while ago, but little has changed. "I don't know what art these [bioinformatics] programs are state-of; possibly macrame. They certainly aren't even 1970's state of the programming art." "Is it reasonable to expect people with a biochemistry or mathematics background to write clean well-engineered code? No. For the importance of the topic, and the sums of money involved, is it reasonable to expect that they'll have their programs cleaned by someone else before release? I think it is. With the pervasive lack of quality I'm seeing, I don't trust _any_ of the results of these programs. I have to wonder how many published results obtained using these programs (and fed back into databases that are used to derive more results which are ...) are actually valid." http://catless.ncl.ac.uk/m/risks/21/98#subj8.1 http://catless.ncl.ac.uk/m/risks/21/98#subj8.1