[Pipet Devel] Open DX as a loci skeleton?

[Brad Chapman]

>  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