[Pipet Devel] Open DX as a loci skeleton?

Harry Mangalam mangalam at home.com
Tue Feb 15 12:21:34 EST 2000

thanks Brad!

I had heard about a biojava group, but I wasn't aware that they existed as
a formal entity yet.  And now I'm a subscriber...
And I'm just now reading thru the PNAS paper that you mentioned.

See what I mean about this list providing the most-useful URLs? :) 


Brad Chapman wrote:
> >  I'm helping to write
> > gene expression database analysis tools that will help people see
> what
> > their data means in a larger context.  Even in tiny genomes like
> bacteria,
> > you have 4.6MB of DNA, ~4300 ORFs, very complex interrelationships
> on a
> > gene regulation level, more on a biochemical pathway level.  How do
> you
> > hope to have people conceptualize those relations?
> If you're doing gene expression stuff, have you checked out the code
> available from biojava (http://www.biojava.org with API docs at
> http://www.sanger.ac.uk/Users/td2/biojava-docs/)? I know that they
> have some Suppor Vector Machine (SVM) code, which seems to be the most
> current "popular" method to cluster expression data. The paper in PNAS
> that I read on this also has a SVM implementation
> (http://www.cse.ucsc.edu/research/compbio/genex/genex.html), so they
> might be interesting to compare.
> > but we (NCGR) need something that works right
> > now and even tho DX was born years ago (like unix), it's been
> > well-thought-out and debugged (like unix) and may, with only a little
> > meddling at an external interface, support a tremendous amount of the
> > functionality that we need.  And I personally would rather design
> nifty
> > analytical tools than infrastructure.
>     Makes sense, especially when you're on a limited time frame. I'll
> be interested to hear how it works out.
> Brad
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Harry J Mangalam -- (949) 856 2847 -- mangalam at home.com

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