[Biosqueak] The germ of an idea

Randal L. Schwartz merlyn at stonehenge.com
Wed Aug 29 03:46:04 UTC 2001


>>>>> "jhgillespie" == jhgillespie  <jhgillespie at 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. :)

-- 
Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095
<merlyn at stonehenge.com> <URL:http://www.stonehenge.com/merlyn/>
Perl/Unix/security consulting, Technical writing, Comedy, etc. etc.
See PerlTraining.Stonehenge.com for onsite and open-enrollment Perl training!




More information about the Squeak-dev mailing list