[BioC] Database for Microarray Data - request for user stories

David Ruau druau at ukaachen.de
Mon Dec 5 10:42:56 CET 2005

We use BASE to store data here, it's a great system which include a 
LIMS and a retrieval system of the data. It can rely on MySQL or 
postgreSQL as you want. You can store Affy or 2 color arrays.
check out:
It's rather easy to install and there is a mailing list, not as active 
as the R one but...
There is plugin, API etc...

On Dec 4, 2005, at 21:26, Ido M. Tamir wrote:

> Hi all,
> I hope you don't consider this question completely off topic.
> (I didn't find a thread on this in the archive)
> How are your experiences with some of the publicly available
> database systems for microarray data (including commercial ones)?
> I don't want to roll my own unless I have to.
> Did you create your own and why?
> ----
> My requirements are:
> LIMS ( probe, spotting, annotation )
> microarray data storage
> accessibility by GUI and API esp. for analysis with
> bioconductor (so the question is not off topic ;-))
> It does not necessarily need a GUI for bioconductor.
> Spitting out gal, gpr and target files is enough.
> And for the nimblegen data I would use SQL.
> If source code is available it would be a plus
> java is also a plus (for bug fixing, enhancements)
> Analysis facilities are not that important.
> Important is efficient and reliable retireval of
> huge data sets (in house two color and
> nimblegen datasets, maybe affymetrix one color).
> Ability to easily migrate from our current
> database would also be important.
> ----
> MARS seems very interesting but provides no source
> http://genome.tugraz.at/Software/MARS/MARS.html
> I saw longhorn which is still in development based on
> SMD (which is tied to Solaris/Oracle)
> http://www.longhornarraydatabase.org/
> GEOSS/GeneX2/GeneXl ite
> which already confuses me, but some people
> say choice is good.
> 2003-09-20 seems to be the latest news
> on genex 2 so the project is dead.
> Another dead project seems to be the
> yale microarray database:
> http://info.med.yale.edu/microarray/status.htm
> also 2003/9 latest entry with no db software
> download link.
> Thank you very much for your answers.
> Ido Tamir
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