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 The current state of affairs with these plugins is that they are out of date and not actively maintained and may well not work with the current version of BASE.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. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ------------------------------------------------------------------------- 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]
