Tab2MageImporter

Short description

Imports raw data files and an experiment meta-data in tab2mage specification into BASE.

Long description

The Tab2MageImporter imports raw data files and an experiment meta-data in the tab2mage specification into base 2. The tab2mage specification is provided by the microarray informatics team at the EBI, Cambridge. The imported experiment can later be exported by the corresponding tab2mage export plugin. (link).

The entry point for this plugin in base is the detail view page of an experiment. Hence, the user needs to create an experiment first and 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.

Prerequisites

Base 2.2.1 and above

AnnotationTypeCvImporter Plugin – For loading annotation types. This must have a configuration that could import an annotation types (.txt) file.

Reporter Importer - for loading reporter corresponding to the raw data file

Reporter map importer – for adding features to array design

Raw Data Importer Plugin – loads raw data. This must have a configuration that could import the raw data files.

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.

Please ensure that you have used all the plugins above appropriately, before running Tab2Mage importer. Further information on AnnotationTypeCvImporter is available on Base2plugin website and for other plugins, please read base2 documentation.

Optional

AffyArrayDesignImproter Plugin – for batch uploading affymetrix array designs. Useful to upload all array design in one go.

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.

Documentation

The ​README.txt contains information on how to install and use the plug-in.

FAQs

Sample Tab2Mage Spreadsheets

​Affymetrix, ​Agilent and ​Genepix

Maintenance plan

Bugs will be fixed.

License

​GNU General Public License version 2.

Author

Dominic Oyeniran – European Bioinformatics Institute, Cambridge, UK
​http://www.ebi.ac.uk
​Project Page
oyeniran@…

Philippe Rocca- Serra – European Bioinformatics Institute, Cambridge, UK co -designer and domain expert.
rocca@…

Credits

Appreciation to to the ff:

Misha Bayer <sbrn@…>, Sajoscha Sauer <sauer@…> and Charles Girardot <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.

​Credit.txt.

Download

plugin jar file: ​Tab2MageImporter.jar