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

Henrik Bengtsson hb at maths.lth.se
Tue Dec 6 00:54:45 CET 2005

David Ruau wrote:
> 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:
> http://base.thep.lu.se/
> 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...

To add to this, I have written a BASE plugin dispatcher for R called 
aroma.Base that does all the file parsing, logging, exception handling, 
parameter validation, HTML report generation via RSP etc using handlers 
onParameters(), onRun() [you have to supply this one] and onError() 
methods; you don't have to know much about BASE to write a plugin for it R.
No root access is needed to install the plugin.  The plugin is for for 
BASE v1.2 (stable). For details, see http://www.braju.com/R/ and follow 
links for PDF poster.



> David
> 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
>>I saw longhorn which is still in development based on
>>SMD (which is tied to Solaris/Oracle)
>>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:
>>also 2003/9 latest entry with no db software
>>download link.
>>Thank you very much for your answers.
>>Ido Tamir
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
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