Question: Database for Microarray Data - request for user stories
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gravatar for Ido M. Tamir
14.0 years ago by
Ido M. Tamir320
Ido M. Tamir320 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
microarray annotation gui probe • 589 views
ADD COMMENTlink modified 14.0 years ago by jon butchar50 • written 14.0 years ago by Ido M. Tamir320
Answer: Database for Microarray Data - request for user stories
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gravatar for jon butchar
14.0 years ago by
jon butchar50
jon butchar50 wrote:
On Sun, 04 Dec 2005 21:26:17 +0100 "Ido M. Tamir" <tamir at="" imp.univie.ac.at=""> 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? > > <snip specific="" examples=""> Our setup is almost certainly simpler than what you're after but I created our own here using FreeBSD, PostgreSQL, PHP and Apache. Why? When something goes wrong (and things have, wow...), I know exactly where to look and what to change in order to fix it. Also it's completely, completely customizable from the ground up. Finally, cost was a small issue at the time; we hadn't yet put in the grant application but still needed to move forward. If you've got some good computer folks there (e.g., not just a bumbling biologist like me), they'll easily be able to whip up a first-rate, solid setup wrapped around your specific needs. Maybe you could even work it as a project for undergrad students in a database programming class? hth, jon b
ADD COMMENTlink written 14.0 years ago by jon butchar50
Answer: Database for Microarray Data - request for user stories
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gravatar for David Ruau
14.0 years ago by
David Ruau110
David Ruau110 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... 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 >
ADD COMMENTlink written 14.0 years ago by David Ruau110
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 > >
ADD REPLYlink written 14.0 years ago by Henrik Bengtsson2.4k
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