= Tab2MageImporter = == Short description == Imports into BASE 2, raw data files and experimental metadata from a zipped archive containing a tab2mage formatted description of the experiment and a set of raw data files. == Long description == The Tab2MageImporter plugin batch loads raw data files and inserts all experimental descriptors in BASE2 by parsing a tab2mage file and raw data files from a zipped archive. The tab2mage specifications is provided by the Microarray Informatics Team at the EBI, at the EBI, Cambridge and are available from http://tab2mage.sourceforge.net/. The Tab2MageImporter plugin is started from the Experiment Item View Page. This means that the user needs to create an experiment first and then execute the plugin from this page by clicking on the Import tab. The displayed wizards asked for the zip file containing the meta- data i.e. tab2mage file and the raw data files. Furthermore, the user’s email server name could be specified to received notices of success or failure of the uploading or can be omitted to receive no message. Please read the next section to ensure the BASE environment has been properly set up before trying to run Tab2MageImporter plugin. == Prerequisites == Base 2.2 and above [[BR]] AnnotationTypeCvImporter Plugin – Required for loading annotation types. The plugin must have a proper configuration defined to import an annotation type file created by the Tab2MageImporter plugin when parsing the tab2mage file.[[BR]] Reporter Importer Plugin - for loading reporter corresponding to the raw data file[[BR]] Reporter Map Importer Plugin – for adding features to array design [[BR]] Raw Data Importer Plugin – loads raw data. This must have a configuration that could import the raw data files. [[BR]] The definition for the plug-in is available by default. The configuration should be done by administrator and shared to everyone or a suitable group that all the target users belong. [[BR]] Please ensure that you have used all the plugins above appropriately, before running Tab2Mage importer. Further information on AnnotationTypeCvImporter Plugin is available on Base2plugin website and for other plugins, please read base2 documentation. === Optional === [http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.AffyArrayDesignImproter AffyArrayDesignImproter Plugin ]. – for batch uploading affymetrix array designs. Useful to upload all array designs used in an experiment in one go before running the Tab2Mage Importer.[[BR]] If you want to use messaging, mail.jar and activation. jar for messaging is required- these jar files should be downloaded and copied to your base installation class path /web-inf/lib folder. [[BR]] == Documentation == The [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt README.txt] contains information on how to install and use the plug-in. ==== FAQs ==== ==== Sample Tab2Mage Spreadsheets ==== [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/tab2mage-%20affymetrix.txt Affymetrix], [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/ta2mage-%20agilent.txt Agilent] and [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/tab2mage-%20genepix.txt Genepix] == Maintenance plan == Bugs will be fixed. == License == [http://www.gnu.org/copyleft/gpl.html GNU General Public License version 2]. == Author == Dominic Oyeniran – European Bioinformatics Institute, Cambridge, UK [[br]] http://www.ebi.ac.uk [[BR]] [http://www.ebi.ac.uk/~oyeniran Project Page] [[BR]] email: oyeniran@ebi.ac.uk Philippe Rocca-Serra – European Bioinformatics Institute, Cambridge, UK, Net-Project technical coordinator. [[br]] email: rocca@ebi.ac.uk == Credits == We would like to thank: Misha Bayer , Sajoscha Sauer and Charles Girardot at EMBL, Germany whose batchimporter and Base1Loader code respectively, were used and adapted for this tab2mage importer implementation and last but not least the base 2 team at Lund, keep up the good work guys. [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/credit.txt Credit.txt]. == Download == plugin jar file: [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/Tab2MageImporter.jar?format=raw Tab2MageImporter.jar][[BR]]