Hi Gang,
    I need to understand the performance tradeoffs between modularized
implementations of a system versus optimized, monolithic implementations
that are tailored to specific application domains (as applied to Squeak).
    While modularity usually gains a certain amount of flexibility, the
price paid is a big hit in performance. Although I'm not sure about this,
is not the Linux kernel monolithic as opposed to various Mach-based
implementations of UNIX?
    Could the folks advocating a modular Squeak explain how the resulting
system will be useful in supporting high-performance applications?
Computations? Numerically intensive computations such as that described
below? I don't expect Moore's Law to continue to solve all of our
performance issues, but maybe I'm wrong.
Cheers, Roger.....

jhgillespie at ucdavis.edu wrote:
> 
> John
> 
> I have been playing around with bioinformatics and squeak.  So far I
> have a class heirarchy for dna, protein, and coding sequences with lots
> of useful methods, mostly things like correction formulae, codon usage,
> base frequencies, etc.  In addition, I have a class that parses the
> Genbank flat file format and can produce sequences from a menu of the
> documented features.  I have used this a bit for my own research, but am
> now planning to teach a computational genetics course to our biology
> undergrads using Squeak...so the pressure is on to turn all this into
> something useful and fun.  Right now I can drop sequence morphs onto a
> playfield and produce things like dot matrix plots and phylogenetic
> trees, but visually it ain't much.  The speed issue hasn't been a
> problem because I'm not trying to do anything very ambitious.  I ported
> this stuff from my lisp code, where I used calls to C routines (like
> clustal) to do hard calculations.  Perhaps something similar will solve
> the speed problem with squeak.
> 
> If any of this sounds useful, I could package it up in its current
> state.
> 
> John Gillespie
> jhgillespie at ucdavis.edu

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