Database for Microarray Data - request for user stories
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@james-w-macdonald-5106
Last seen 9 hours ago
United States
Have you looked at BASE? http://base.thep.lu.se/ Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Ido M. Tamir" <tamir at="" imp.univie.ac.at=""> 12/04/05 3:26 PM >>> 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
Microarray Annotation GUI Cancer probe Microarray Annotation GUI Cancer probe • 565 views
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