Hi Micha, Thank you for the comprehensive reply. Actually, I had e-mailed Philippe before, but I guess I hadn't fully understood all the functionality of the importer he is developing. I'll see what I can do with the current plugins, and wait for the new importer to become available.
Best regards, Paulo On Tuesday 22 July 2008 09:25, Micha Bayer wrote: > Hi Paulo, > > There are currently two plugins on the BASE plugins website that do this > sort of thing. > > The batch importer plugin > (http://baseplugins.thep.lu.se/wiki/uk.ac.scri.batchimporter) lets you > load a batch of raw data files into BASE and these get associated with > an experiment that you have previously created. > > The Tab2Mage importer > (http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageImporter) includes > the code from the batch importer (i.e. it uploads raw data for you) but > in addition it also imports metadata about the experiment and all > associated entities (samples, extracts, hybridizations etc) in a MIAME > compliant format from a spreadsheet (the latter needs to be in tab2mage > format, see http://tab2mage.sourceforge.net/). > > Both of these plugins are community contributions, rather than core BASE > plugins, and as such they suffer from the same problems that a lot of > academic software suffers from -- lack of continuity due to staff > turnover, fixed term projects with no ongoing support etc. The current > state of affairs with these plugins is that they are out of date and not > actively maintained and may well not work with the current version of > BASE. > > The main reason for this is that efforts regarding import plugins are > now focused on a new importer plugin which will likely replace the two > previous ones once it is out. Philippe Rocca-Serra from the EBI is > developing a MAGE-Tab format importer in conjunction with an Italian > group and I think an early version will probably be available by the end > of the summer at the latest (and will likely be announced on this list). > > Sorry, this is probably less than helpful at this stage. Do try the > current plugins by all means if you don't want to wait for the new one, > but as I said, they may incompatible with newer versions of BASE. > > Cheers > > Micha > > ================================== > Dr Micha M Bayer > Bioinformatics Specialist > Genetics Programme > The Scottish Crop Research Institute > Invergowrie > Dundee > DD2 5DA > Scotland, UK > Telephone +44(0)1382 562731 ext. 2309 > Fax +44(0)1382 562426 > http://www.scri.ac.uk/staff/michabayer > ================================== > > > -----Original Message----- > > From: [EMAIL PROTECTED] [mailto:basedb-users- > > [EMAIL PROTECTED] On Behalf Of Paulo Almeida > > Sent: 21 July 2008 13:43 > > To: General BASE discussion > > Subject: [base] Setting up an automatic import system > > > > Hi, > > > > I am trying to set up a Base installation where I can automatically > > upload the > > microarray data from an Affymetrix facility. I was reading through the > > documentation but I got a bit overwhelmed. Can someone point me to the > > right > > plugins, or what I need to read in order to accomplish that? > > > > Thanks, > > Paulo Almeida > > ----------------------------------------------------------------------- > > > -- > > This SF.Net email is sponsored by the Moblin Your Move Developer's > > challenge > > Build the coolest Linux based applications with Moblin SDK & win great > > prizes > > Grand prize is a trip for two to an Open Source event anywhere in the > > world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > _______________________________________________ > > The BASE general discussion mailing list > > basedb-users@lists.sourceforge.net > > unsubscribe: send a mail with subject "unsubscribe" to > > [EMAIL PROTECTED] > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > SCRI, Invergowrie, Dundee, DD2 5DA. > The Scottish Crop Research Institute is a charitable company limited by > guarantee. 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