[biosqueak] The extent of BioSqueak?

Richard A. O'Keefe ok at cs.otago.ac.nz
Thu May 9 03:30:59 UTC 2002


Aaron J Reichow <reic0024 at d.umn.edu> wrote about BioSqueaking:
	One of my beefs with the latest 'bioinformatics' craze is that it seems
	that biology and bioinformatics = genetics, leaving out all the other
	subfields of biology.  I use Squeak to analyze and visualize ecological
	data, and that is within the realm of bioinformatics.

I wouldn't mind hearing about that.  It sounds an interesting application
of Squeak, and I know of someone who might be interested in using it.

	Consequently, all the Bio* libraries only deal with this rapidly
	growing, but exclusive part of biology.
	
I think that part of the reason is that studying genes and proteins leads
to huge databases full of very long sequences; algorithms for processing
these things form a coherent subdiscipline of computer science.  (Which I
am beating my brains out trying to get my head around.  Oodles of books that
tell you how to run program Foo, papers scattered all over the library that
are original sources, very very few books that clearly explain how the
darned things *work*.)

Ecological modelling and analysis is also a well-studied area.  It is
about biology, and it's informatics, but it has different problems and
methods.

	What do we, those who are/will be working on biosqueak, want the
	extent of BioSqueak to be?

Squeak's Squeak.  I can't imagine anything interesting being turned away.
I can't imagine it working in the next release but one either, but that's
another story.

	Or do we want to have class libraries that assist with genomics
	(with similar capabilities as the other packages available) as
	well as other fields of biology like phylogeny, ecology, or
	others?
	
Phylogeny is commonly included in bioinformatics,
* because many biologists are interested in genes and proteins primarily
  as a way of getting characters to base phylogenies on, and
* because having a phylogeny can help "focus" some alignment algorithms
  so that people who are interested in the genes want phylogenies so they
  can get the genes faster.
No two ways about it, phylogeny belongs in.




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