[Biosqueak] The germ of an idea

Helge Horch Helge.Horch at munich.netsurf.de
Wed Aug 29 12:09:33 UTC 2001


At 09:53 28.08.2001 -0700, John Tobler wrote:
>I will probably get rolling with implementing some of the simpler 
>bioinformatics routines, following models already available in Biopython, 
>Bioperl, and Bioruby.

Great initiative!

>I am also sure that bioinformatics processing will fully test Squeak's 
>mettle on text searching and pattern recognition.  Where do we find support for
>regular expressions and the like?

Well, we have Andrew Greenberg's REPlugin (on the Swiki), and Stefan 
Matthias Aust's Squeak port of Vassili Bykov's Regex class in pure 
Smalltalk (at <http://www.3plus4.de/squeak/>).

>I anticipate that trying to solve such real world problems as sequence 
>searching, sequence allignment, and protein structure prediction will 
>point out areas where we can improve Squeak's reach and performance.

That'll be a lot of work though, in a field as wide and fast-developing as 
bioinformatics.  While I see how all that will be fun and instructive to 
invent and improve, I personally lean more towards tapping the huge amount 
of software that's out there (BLAST, PHYLIP, CLUSTAL etc).  That, too, 
would require building object representations for sequences, alignments, 
features, enzymes and whatnot.  But I'd hesitate to play catch-up with the 
algorithms camp.  (OTOH, there are relatively new fields such as e.g. 
functional genomics/micro arrays, where an explorative environment could 
actually help finding new approaches.)

For my immediate needs, the well-maintained and constantly growing EMBOSS 
package (<http://www.sanger.ac.uk/Software/EMBOSS/>) implements a wide 
range of sequence analysis algorithms.  I have been thinking about using 
OSProcess and maybe Plugins to let EMBOSS do the ground work, parsing the 
results into Squeak.  To then do the fun stuff in Squeak: 2D/3D 
visualization, animation, flexible queries, mining.  (Pipe dreams for now.)

>This is just a "heads up" that Biosqueak is out there somewhere on the 
>vast horizon.

Thanks!  I'm interested, and hope to contribute some day.

Cheers,
Helge




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