> > 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.
I speak only as a beginner user, but BASE does indeed allow you to apply normalisations and filters, and it keeps a permanent record of them. This should be great for multi-site or multi-group collaboration. We looked at Longhorn (mainly through the Stanford web interface to public data) and concluded that it couldn't do this at all. I recently wrote a bolt-on bulk uploader for 1.2.17. Actually it's two uploaders, one for samples, extracts, labeled extracts and the other creates the hybs and uploads images and raw data. They are Perl CGI scripts that do 'robot clicks' on your BASE site to do all the creation and uploading (raw and image files need to be uploaded by baseftpd first). It even does the JPEG spot image extraction. The GUI looks and feels like BASE - except that you have to enter your username/password again (to authorise the robot). If anyone is interested I can send the scripts - I'll need to add a bit more documentation though, and note that it has only been tested on two-colour genepix data. hope that helps, cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
