[Pipet Devel] updated model

tim jabbo at yahoo.com
Mon Dec 21 16:02:43 EST 1998

(I'm back in touch with the world -- sorry for the absence)

tools needed:

-- device driver for Linux, FreeBSD, etc for ABI sequencers (not sure
about this)
-- "fuzzy" CLIPS-style inference engine for "expert" per-base
-- a tutorial

that's what my father said when I asked him what people want in a
replacement for GCG-Wisc.  (he has worked on the molecular genetics of
childhood cancer for 20 years) In fact, the second item -- assistance in
recognizing which type of NA a base is even when it looks like the peaks
in the chromatogram could go either way -- is what he stated was missing
in most commercial packages today.  Basically, his conclusion was that
many people dislike GCG and would switch if a better alternative was
available (esp. one which could be extended/customized).

Me personally, I'm still trying to understand all of this
comparison-matrix stuff for searching.  But it is very challenging (i.e.
cool) and hopefully will be a good excuse for having written a simple
parser-tokenizer for raw base-by-base sequences.  Speaking of
challenging, I have become a bit stumped with GTK.

I still don't entirely understand how GTK is designed -- if the GTK
gurus on this project were willing to offer some assistance, I might
progress beyond simple "Sign your timecard today!" boxes that I run from
cron twice a month. ;-)  Part of this is that I'm a crappy C programmer
and haven't applied myself to the tutorial, but when I follow along with
the tutorial, I feel like I'm just going through the motions, rather
than figuring out what's being designed.

I also realized that (and this is probably irrelevant to TULIP, but
still) I need someone academic and respected to goon for me if I am
going to hold a real job yet stay involved in protein folding / nucleic
acid folding for real.  If anyone on this list knows such a person at
UVM, Middlebury, Dartmouth, or UNH, please let me know; this is really
important to me personally.

My mailbox is full of TULIP messages -- I will now go read them.

ps.  What does that stand for?

    "We all enter this world in the same way:
      naked; screaming; soaked in blood. 
     But if you live your life right, that kind of thing
      doesn't have to stop there."          --Dana Gould

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