2 ms·
As a former bioinformatician (if that’s a word), I’m not sure there’s much value in this. There’s high dispersion in the performance requirements of bioinformat
by smabie 7y ago
As a former bioinformatician (if that’s a word), I’m not sure there’s much value in this. There’s high dispersion in the performance requirements of bioinformatics tools. The processes that need to be fast (alignment, BLAST, whatever, tree creation, etc) are already super fucking optimized (though, unfortunately, still slow). The things that don’t need to be fast can use whatever you want (I used Haskell and Racket for my own tools at the time). Python is.. not the greatest. The major value add is the multitude of scientific libraries. If you’re gonna throw that all away, why not just use something better? Things like Julia, OCaml, Haskell, etc. I personally think Julia is pretty dope and is what I would use today for bioinformatics research. Or maybe if I was feeling a little subversive, K/Q or J. Q’s time-series database KDB+ could probably be used for sequences. And maybe even for great effect. And the performance would be off the charts!
It seems like the purpose of this is Python without the performance penalty, which doesn’t make much sense to me. I’ve found Haskell absolutely perfect for bioinformatics as most operations you are doing are functional data transformations. Moreover, it’s pretty damn fast if you need it to be.
I’ve been out of the field a long time though (Roche-454 was still the main workhorse at the time). But let me tell you, bioinformatics is/was a fucking shit-show. The tools and ecosystem are/were like Linux in the mid 90s: fucking terrible. And another language is just gonna make it worse.