= 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. 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]] Reporter Importer Plugin - Required for loading Reporters [[BR]] Reporter Map Importer Plugin – Required for mapping features to Reporters when defining an Array Design [[BR]] Raw Data Importer Plugin – Required for loading raw data and import values associated to BASE rawBioassays. This is a critical requirement, for multi-channel experiments, before running the Tab2MageImporter. Users must make sure that a Raw Data Import plugin has been configured properly to deal with the raw data files. [[BR]] ''The definition for the above plug-ins is available by default in Base 2. The plugins should be configured by a Base 2 administrator and shared to everyone or a suitable group of target users. [[BR]]'' [http://lev.thep.lu.se/trac/baseplugins/wiki/uk.ac.ebi.AnnotationTypeCvImporter 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]] Please ensure that you have used all the plugins above appropriately, before running Tab2Mage importer. Click [http://lev.thep.lu.se/trac/baseplugins/wiki/uk.ac.ebi.AnnotationTypeCvImporter AnnotationTypeCvImporter] for further information on Annotation Type and Cv Importer plugin and for other plugins, please read base2 documentation. Also, do make sure that all non-Affymetrix Array Designs used in an Experiment have been properly created in BASE2. This means that Reporters have been loaded and Feature to Reporter Map have been attached to Array Designs. Those tasks can be only be achieved if the following plugins have been properly set up and configured. === Optional === [http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.AffyArrayDesignBatchImporter AffyArrayDesignBatchImporter 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. Volunteers welcome to help extend the plug-in. == 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: Charles Girardot and Sajoscha Sauer at EMBL, Germany whose tab2mage Base1Loader code, were used and adapted for this tab2mage importer implementation. Misha Bayer at the Plant Bioinformatics Group, Scottish Crop Research Institute whose batchimporter was also used and adapted to develop the tab2mage importer. Last but not least, the BASE 2 team at Lund, keep up the good work guys. == Download == plugin jar file: [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/Tab2MageImporter.jar?format=raw Tab2MageImporter.jar][[BR]]