More on Grid stuff

Doug Smith dsmith at ucsd.edu
Mon Jul 3 12:34:57 EST 2000


I am interested in how well ACEDB can adapt to handling and display of
the large data sets associated with DNA microarray analyses, Mummi.
New display approaches and software are being developed by many groups,
including an effort at SDSC here at UCSD.  So I see two important
aspects here:
1. storage and retrieval of data
2. display in various forms, either via code within ACEDB or via
   external called programs ala Blixem and Dotter.

Two favorite data sets for development purposes here at UCSD/SDSC are
the following:

1. rather early Pat Brown group data:
paper:  DeRisi,  J.L., Iyer, V.R. and Brown, P.O.,
  "Exploring the metabolic and genetic control of gene expression on
  a genomic scale", Science 278, 680-686, 1997.
complete data available at:
  http://cmgm.stanford.edu/pbrown/explore/

2. subsequent Brown and Botstein effort including clustering and
dendrogram displays:
paper:  Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D.,
  "Cluster analysis and display of genome-wide expression patterns",
  Proc. Natl. Acad. Sci. USA 95,14863-14868, 1998.
complete data available at:
  http://rana.Stanford.EDU/clustering/

There are now of course many other data sets as well.

Perhaps the ACEDB tree display would be useful in a similar dendrogram
display approach?

-Doug








> I would like to add something  to Ed's notes in the newsletter
>regarding the microarray-display issue: would it be possible to somehow
>extend the grid display (already quite flexible, in layout at least) to
>display much larger datasets, without requiring a massive effort to
>write such an array display from scratch. At least it does deserved a
>chance.
>
>   I will be discussing this with a couple of those that are actually
>working with expression data and see their view on this. Perhaps I can
>extract some more intelligent (than mine) info on what kind of setup
>would be must useful for expression analysis.
>
>
>                      Mummi
>
>
>Sent via Deja.com http://www.deja.com/
>Before you buy.


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Douglas W. Smith
Professor of Biology                     UCSD Phone: 858-534-2620
Department of Biology, 0116              UCSD FAX:   858-534-7108
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La Jolla, CA  92093-0116                 email:   dsmith at ucsd.edu
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