"jhgillespie" == jhgillespie jhgillespie@ucdavis.edu writes:
jhgillespie> I have been playing around with bioinformatics and jhgillespie> squeak. So far I have a class heirarchy for dna, jhgillespie> protein, and coding sequences with lots of useful jhgillespie> methods, mostly things like correction formulae, codon jhgillespie> usage, base frequencies, etc. In addition, I have a jhgillespie> class that parses the Genbank flat file format and can jhgillespie> produce sequences from a menu of the documented features. jhgillespie> I have used this a bit for my own research, but am now jhgillespie> planning to teach a computational genetics course to our jhgillespie> biology undergrads using Squeak...so the pressure is on jhgillespie> to turn all this into something useful and fun. Right jhgillespie> now I can drop sequence morphs onto a playfield and jhgillespie> produce things like dot matrix plots and phylogenetic jhgillespie> trees, but visually it ain't much. The speed issue jhgillespie> hasn't been a problem because I'm not trying to do jhgillespie> anything very ambitious. I ported this stuff from my jhgillespie> lisp code, where I used calls to C routines (like jhgillespie> clustal) to do hard calculations. Perhaps something jhgillespie> similar will solve the speed problem with squeak.
I recently presented a Perl-related keynote at a gene conference in Cambridge (UK). The audience was intently listening and interested, because as I was listening to them talk, it was all "perl perl perl" on the back end, "C C C" for number crunching, and "java java java" on the front end for fancy interfaces and visualization.
I think Squeak can (and should) take over the "java" portion of this arena. But I don't think Squeak is the right mix for the Perl portions (glue) or "C" portions (crunching). All three portions have their place, so don't offend a bioinformaticist by telling them that Squeak will do it all. But clearly creating the right Morphs would let the tech-heads create better interface building blocks so that the bio-scientist non-programmers could get the job done. Especially if it ran in the browser.
Just a thought.
p.s. bioinformatics is getting BIG funding, while dotcoms are shrinking. Good people are needed. Consider a career shift. :)