[Bioperl-l] microarray databases and Perl

[Eric Snyder]

In message <Pine.OSF.4.10.10103080447080.6546-100000@is06.fas.harvard.edu>, Fin
ny Kuruvilla wrote:
>We've been thinking about writing a more elegant solution to tackle
>these kinds of issues and I was thinking about using MySQL/Perl to do
>so.  I saw on your list of projects that although microarray analysis
>was listed, that no one was working on it at the moment.  In fact, the
>site reads, "This is a rapidly moving field and it may be a while
>before standards emerge. Perl may not be best for analysis of array
>data."

About six months ago, I looked at a system called ArrayDB which sounds similar to what you are working on.  It is an open-source mySQL-based database being developed at NHGRI.  I am no mySQL expert so I was not able to get it running but it did appear to have some interesting features.  ArrayDB is written in Perl and includes a number of Perl modules for doing various things.  When I looked at it originally, it was admittedly very "pre-release".  I check the web site today and they now have a beta version available for testing.  It might be more stable at this point.  

Maybe someone with a little more familiarity with mySQL could try to get it running and report back to the mailing list.  In fact, if the authors are not already involved, maybe their should be encouraged to do so.

Here is the site:

http://genome.nhgri.nih.gov/arraydb/ 


Enjoy,


Eric E. Snyder
Associate Professor
Pennington Biomedical Research Center
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