Hi Jim We never actually got this far in the discussion on Monday, but I have since spoken to Dominic Oyeniran from the EBI who has developed a first version of the Tab2MAGE exporter module and he says that he will now work on the Tab2MAGE importer next (he is on this list too BTW).
We have agreed that we will combine my batch importer and his Tab2MAGE importer so that users will be able to enter all the MIAME required data about their experiment (including scan details) into a spreadsheet and then upload this and all the raw data from their experiment into BASE in one single transaction. The timeline question is - as always - near impossible to answer but it is the next item on our agenda. We're probably looking at several weeks worth of work anyway. 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.sari.ac.uk/MichaBayer.htm ============================= > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Collett, James R > Sent: 28 March 2007 07:39 > To: basedb-users@lists.sourceforge.net > Subject: [base] Batch Data Importer plugin dev future? > > Micha and other BatchMasters, > > What was the consensus of the BASE dev team on the future of the > BatchDataImporter plugin? Any time line on what it may become and when? > > Thanks, > > Jim Collett > > James R. Collett, Ph.D. > Systems Biology Fellow > Battelle Memorial Institute > Biological Sciences Division > Pacific Northwest National Laboratory > PO Box 999 > MS P7-58 > Richland, WA 99354 > > voice: (509) 376-2954 > fax: (509) 372-6544 > [EMAIL PROTECTED] > > > --------------------------------------------- > > Hi James, > > glad to hear the plugin is getting put to good use. > > We are due to have a telecom with the BASE dev team on the 26th and we are > then going to decide about the future of this plugin, among other things. > It is well possible that we will turn it into something a lot more fancy > and there has even been talk of merging it with the Tab2MAGE plugin that > EBI are working on so that we can have an all-singing, all-dancing import > of everything people want to attach to an experiment (including the data, > obviously). > > I'll certainly add your request to the list but things won't happen in a > hurry for now -- we need to have this strategy meeting for now. > > 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.sari.ac.uk/MichaBayer.htm > <http://www.scri.sari.ac.uk/MichaBayer.htm> > ============================= > > > > -----Original Message----- > > From: [EMAIL PROTECTED] [mailto:basedb-users > <mailto:basedb-users> - > > [EMAIL PROTECTED] On Behalf Of Collett, James R > > Sent: 16 March 2007 08:25 > > To: basedb-users@lists.sourceforge.net > > Subject: [base] Batch importer wish list: batch-associating an > > existingsingle scan item with every new raw biaossay during a job run > > > > Micha et al, > > > > I'm a big fan of the Batch importer plugin; it's worked great for me > so > > far. > > > > We are developing antibody ELISA microarrays for cancer biomarker > > screening. Our slides are divided into 16 wells, with identically > printed > > blocks of 25-30 antibodies in quadruplicate in each well. In each > well we > > perform a single hybridization, but our methods are identical > throughout. > > We then batch-scan 20 slides at a time, using the same settings for > every > > scan in a run. > > > > > > Would you be interested in adding a list box and code to the plugin > > interface that would allow the user to select an existing scan that > would > > be automatically associated with all of the new raw bioassays when > running > > the plugin? In this way, every raw bioassay in a batch could inherit > > annotations from the same scan and its parent hybridization. > Currently, > > one has to open every newly-imported raw bioassay in the batch and > then > > manually associate each one with a scan. > > > > Any help you could provide in adding this functionality would be > greatly > > appreciated. > > > > Thanks, > > > > Jim Collett > > > > > > James R. Collett, Ph.D. > > Systems Biology Fellow > > Battelle Memorial Institute > > Biological Sciences Division > > Pacific Northwest National Laboratory > > PO Box 999 > > MS P7-58 > > Richland, WA 99354 > > > > voice: (509) 376-2954 > > fax: (509) 372-6544 > > [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). > > > > > > > James R. Collett, Ph.D. > Systems Biology Fellow > Battelle Memorial Institute > Biological Sciences Division > Pacific Northwest National Laboratory > PO Box 999 > MS P7-58 > Richland, WA 99354 > > voice: (509) 376-2954 > fax: (509) 372-6544 > [EMAIL PROTECTED] ------------------------------------------------------------------------- Take Surveys. Earn Cash. 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