Hi all, Following this with interest as we are putting together some Java tools to do on-the-fly analysis for web display on data stored in BASE2, through an API we have built on top of the BASE2 API. Perhaps we should have invested the time in plugin development instead, but that's another debate/story.
Just one quick comment below. McMurry, Andrew J. writes: > Thank you Nick, Tony: > To be clear, there are three distinct use cases: > (1) UI for complete LIMS management system > (2) API for reading existing microarray results and loading them into a DB > (3) Querying that database using webservices such as those supported by > BioMoby > > I am primarily interested in #2 -- you are probably not suprised to find > that harvard medical school has troves of unpublished array results (affy > cel files, etc) scattered across many desktops just waiting to be uploaded > to locally controlled repository (not GEO, unpublished results). Hence, the > Base2 API could be attractive if I dont have to rewrite the array file > parsers for CEL/MINIML/etc. I'm hoping that user intervention wouldn't > really be required, and that I could write an adapater for Base2 that would > simply INSPECT a folder of say, CGH results, and load it into a local Base2 > instance on a scheduled basis. (our investigators are always over stretched > for time and will likely not take the time to submit each sample > individually). > As someone who loads data from several labs and institutes around the world, I really doubt you can just point your software at a bunch of directories full of raw data files and expect to have all the data loaded in a meaningful way. It does unfortunately take some curation. Perhaps with Affy data you have less to worry about (ready-annotated probesets, only one channel, no dye swaps etc), but maybe you don't just have Affy? I doubt the experimental factor annotations will just fall into place without some curation. > As for #3, these locally controlled instances would (later) indeed need to > be queried and aggregated. We already have a query-aggregator technology > (SPIN) which we are extending for this purpose. That said, the serialized > XML query payload could be made very close to BIOMoby, if appropriate. We > are open source advocates so any upgrades/extensions would be of course > donated back to this community freely. > > thoughts? > --andy cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
