[Biosqueak] The germ of an idea

Blaine Wishart wishart at pacbell.net
Thu Aug 30 20:42:22 UTC 2001


I'm not sure I fully understand people's interests here & I'm not sure
I'm knowledgeable enough to form my questions well.
--Concerning speed: I'd expect the direction here needs to be more
architectural than language specific. C on the fastest machines
available next few years is not close the speed need for many problems. 
--Where does the modeling take place? If Bioinformatics is just a code
word for sequencing & genomics, the modeling may all be done &
reflecting it with good visualization may be a great step. But
proteomics, cell simulation, inter-cell communication, etc. may be at a
different stage & have different requirements. [I notice that BioJava is
moving toward a richer model than many of us might have predicted.] Does
intensive string processing suggest the right abstractions for all
Bioinformatics?
--What is the role of 'glue'? Is it always part of the picture, or does
the need for it represent a weak architecture?
--Are 'number crunching', 'glue', and 'visualization' and adequate parts
list? Are repositories like Bimolecular Interaction Network Database
(BIND) part of the mix? What are the implications of the FDA's move to
electronic submission for clinical trials? The supply chain work might
not excite the Squeak community, but I wonder about the ability of
Squeak to make clinical trials understandable to lay people & suspect
this may be properly part of Bioinformatics. 

I'd hate to see the Squeak community limit its view of Bioinformatics to
providing visualizations of the current work inspired by the genome 
project, valuable as that work might be. Smalltalk's strong simulation
and modeling history and Squeak's particular potential for learning and
education suggest a broader direction and this may be where John G. is
headed.

Whether or not biologist in 2011 and 2021 will work as they do now may
be worth thinking about. 

-b

"Randal L. Schwartz" wrote:

  >>>>> "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 {snip}
  jhgillespie> {snip}  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.

  {snip} 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.{snip}

"Randal L. Schwartz" wrote:
> 
> >>>>> "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!




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