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? :) Best hjm 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 > > _______________________________________________ > pipet-devel maillist - pipet-devel at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-devel -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 -- mangalam at home.com