| Version 9 (modified by , 17 years ago) ( diff ) |
|---|
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.
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 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.
Download
plugin jar file: Tab2MageImporter.jar
