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. Cheers Henrik > 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 >>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 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >