[Bioperl-l] Re: Bioperl-l digest, Vol 1 #251 - 10 msgs

[Adam Witney]

Hi Finny,

We have been working on microarrays for the last year or so, and we have
designed a database (running in Sybase) to store all our experimental info
and we now use Perl to interact with the database and to perform various
statistical analyses in order to generate reports from the data.

I think Perl is very good for manipulating the data, however the biggest
problem right now is coming up with the analysis strategy rather than in
which language to code it. When analysis approaches become accepted as
standard then it would be easier to write more systematic programs.

There seem to be various database systems that can be downloaded from
various sites... take a look at

http://www.ebi.ac.uk/microarray/
www.microarrays.org
http://genome-www4.stanford.edu/cgi-bin/SMD/login.pl

I would be happy to talk about this more off list if you would like

adam


 
> Date: Thu, 8 Mar 2001 04:58:59 -0500 (EST)
> From: Finny Kuruvilla <kuruvill@fas.harvard.edu>
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] microarray analysis in perl
> 
> I'm a biologist/programmer who has been doing microarray work the past
> couple years. (For the type of work, look on Pubmed for Current
> Biology 2000; 10(24): 1574-1581, Proc Natl Acad Sci USA. 1999;
> 96(26):14866-70 if anyone is interested.)  In the course of analyzing
> data we've generated, I've written code in languages like Visual Basic
> and Matlab.  But my efforts have been non-systematic thus far.
> 
> 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."
> 
> Coming from more of a Matlab/Lisp background myself (no Perl expert),
> I'm hoping for some insights from some of you.  First, do you think
> that Perl is the right language for this?  If not, what do think would
> work best?  What open-source efforts do you know that are going on
> right now in this?
> 
> To me the time seems ripe to tackle these issues, but I would really
> appreciate any advice (truly -- anything at all) that those of you
> more experienced could offer.
> 
> Thanks.
> 
> Finny 
> 
> *****************************************************************
> Finny Kuruvilla
> MD-PhD Program, Harvard Medical School
> Schreiber Group, Department of Chemistry and Chemical Biology
> Harvard University -- Cambridge, Massachusetts
> kuruvill@fas.harvard.edu
> 
> 
> --__