Changes between Version 1 and Version 2 of uk.ac.ebi.Tab2MageImporter


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Timestamp:
Aug 14, 2007, 6:35:01 PM (14 years ago)
Author:
basepluginswiki
Comment:

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  • uk.ac.ebi.Tab2MageImporter

    v1 v2  
    1 = !Tab2MageImporter =
     1= Tab2MageImporter =
    22
    33== Short description ==
     
    77== Long description ==
    88
    9 This !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 (link) informatics team at the EBI, Cambridge. The imported experiment can later be exported by the corresponding tab2mage export plugin. (link).
     9The 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 (link) informatics team at the EBI, Cambridge. The imported experiment can later be exported by the corresponding tab2mage export plugin. (link).
    1010
    1111The 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.
     12
     13
     14== Prerequisites ==
     15
     16Base 2.2.1 and above [[BR]]
     17
     18AnnotationTypeCvImporter Plugin – For loading annotation types.  This must have a configuration that could import an annotation types (.txt) file.[[BR]]
     19
     20Reporter Importer - for loading reporter corresponding to the raw data file[[BR]]
     21
     22Reporter map importer – for adding features to array design [[BR]]
     23
     24Raw Data Importer Plugin – loads raw data. This must have a configuration that could import the raw data files. [[BR]]
     25
     26The 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]]
     27
     28Please 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.
     29
     30=== optional ===
     31
     32AffyArrayDesignImproter Plugin – for batch uploading affymetrix array designs.  Useful to upload all array design in one go.[[BR]]
     33
     34if  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 folde. [[BR]]
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    1336
     
    1942== Maintenance plan ==
    2043
    21 Bugs will be fixed. Volunteers welcome to help extend the plug-in.
    22 
     44Bugs will be fixed.
    2345
    2446== License ==
     
    2951== Author ==
    3052
    31 Micha Bayer - Plant Bioinformatics Group, Scottish Crop Research Institute [[br]]
    32 http://www.scri.ac.uk [[BR]]
    33 http://www.scri.sari.ac.uk/MichaBayer.htm [[BR]]
    34 micha dot bayer at scri dot ac dot uk
     53Dominic Oyeniran – European Bioinformatics Institute, Cambridge, UK  [[br]]
     54http://www.ebi.ac.uk [[BR]]
     55http://www.ebi.ac.uk/~oyeniran [[BR]]
     56oyeniran@ebi.ac.uk
     57
     58Philippe Rocca- Serra – European Bioinformatics Institute, Cambridge, UK for his co -design and expert input. [[br]]
     59
     60== Credits ==
     61
     62Einstein once said “If I have seen farther than others, it is because I stand on the shoulders of giants”.
     63
     64Hence appreciation to to the ff:
     65
     66Misha Bayer  <sbrn@scri.ac.uk>, Sajoscha Sauer <sauer@embl.de> and
     67Charles Girardot <charles.girardot@embl.de> at EMBL, Germany whose code were  used  and adapted for this tab2mage importer implementation and last but not least the base 2 team at Lund.
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    3669