Hi, here is answers from a BASE2 perspective.
David Waring wrote: > I am looking for a database solution for the microarray facility at > Fred Hutchinson Cancer Center. We are a core facility with dozens of > users from labs around the Center and outside. I am looking carefully > at BASE, TM4, Longhorn, and maxdLoad2. I have a few questions about > BASE that would help me make this decision. Any feedback would be > very much appreciated. > > Is BASE support for PostgreSQL as strong as support for MySQL? In BASE2, we use Hibernate on top of the database layer. The simple answer is then that the database support depends on how well Hibernate support the different database flavours. We develop BASE 2 with MySQL as the database backend but do tests with PostgreSQL (and some others). There is one known issue with BASE2/PostgreSQL/Hibernate that awaits resolution from the Hibernate team. > Can I get a detailed version of the schema? All I can find is a > general schema overview with tables listed but no fields. The html > version of the schema description http:// > opensource.microarray.omrf.org/wiki/bin/view/BASE/DatabaseSchema is > apparently cut off or just was never finished. This page may be out of date. For BASE 1.2.x refer to http://base.thep.lu.se/documentation.phtml For BASE2 there is a lot of developer information, but no complete schema. Implementation details are given for most details of BASE2. See http://lev.thep.lu.se/trac/base/wiki/DeveloperInformation for more information. > Are there tools for batch upload of data? Particularly, I am looking > at the situation where our users have designed an experiment, and > hybridizations, we (the core lab) will perform the hybridization, > scan the array, run a spot analysis (GenPix) upload the data > (hopefully not using a web based interface one image at a time). We > will then perform standard normalizations / filters and need to get > all this into the database so that our users can analyze the data > later. I this a situation that BASE would be strong at? For BASE 1.2.x there is a mass data import feature. For BASE2 the core supports batch upload of data but there is no UI for it yet. > When will BASE 2.0 be ready for production? The milestone for production ready BASE 2.0 is in the end of August, see http://lev.thep.lu.se/trac/base/roadmap > How many labs are currently using BASE? Our estimate is that more than 100 labs use BASE 1.2.x, and there is already a handful users of BASE2. > If you have any ideas about how the various alternatives stack up > please let me know. Be as technical as needed, I am an experienced > programmer and with lots of database experience. I would go for BASE2, but then again, I am somewhat biased. > Is there support for HUGE datasets like Tiling arrays? In these cases > we would not necessarily want to hold all of the results as > individual records but rather would want to hold the .cel files in > some structure so that our users could get to them for analysis using > other tools. BASE 2.0 is supporting Affymetrix soon, so in principle Tiling arrays are possible. The "raw" data for Affy will be the .cel files, i.e. these will be used in subsequent analysis. > Thanks > > David Thank you for you interest in BASE. Jari _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
