Table of Contents
A categorized list of all plug-ins installed with a pristine BASE installation. Some plug-ins must be configured before use, requirements are listed below and configuration samples are given for for plug-ins that supports/requires configurations. Use the right-click menu of the mouse to download these XML files for further import into BASE (see Section 22.4.2, “Importing and exporting plug-in configurations”).
Contributed plug-ins are available at http://baseplugins.thep.lu.se . These plug-ins are either developed outside the core team or require external non-Java compilers and tools. These packages are excluded from the BASE package to make the installation process somewhat simpler.
Simulates the plug-in runner from Base 1.2.
Since BASE 2.2, no configuration needed for the Base1PluginExecuter but may be required for the underlying BASE version 1.2 plug-ins.
Calculates extra values for a bioassay set.
Since BASE 2.1, no configuration needed.
Bioassay set filter. Expressions parsed with JEP.
Since BASE 2.0, no configuration needed.
Transforms the intensities of a bioassayset.
Since BASE 2.1, no configuration needed.
Allows a user to manually register an external analysis procedure that has happened outside of BASE and to register the parameters used and the generated output files.
Since BASE 2.12. Configuration is needed to register possible parameters and output files.
Normalisation using LOWESS algorithm.
Since BASE 2.0, no configuration needed.
Normalisation based on median ratio.
Since BASE 2.0, no configuration needed.
Exports bioassay set data to serial or matrix BASEfile format.
Since BASE 2.12, no configuration needed.
Exports the features of an array design to a GAL file.
Since BASE 2.7, no configuration needed.
Exports help texts to an XML file.
Since BASE 2.0, no configuration needed.
Exports files and directories as an archive-file.
Since BASE 2.4, no configuration needed.
Exports plate mappings.
Since BASE 2.0, no configuration needed.
Exports plug-in configurations to an XML file.
Since BASE 2.1, no configuration needed.
Exports table listings in the web-interface.
Since BASE 2.0, no configuration needed.
There are many import plug-ins in BASE. Their use are in most cases seamless and the user does not need to be aware of detailed plug-in usage. However, there is a set of batch import plug-ins that are targeted for importing multiple items into BASE. These batch importers require some user knowledge for proper and efficient use of them. The batch plug-ins are listed in the Section B.3.1, “Core batch import plug-ins” sub-section below together with pointers to further reading on how to use the plug-ins.
This plug-in is used to import probesets (reporters in BASE language) from an Affymetrix CDF file. It can be used in import mode from the reporter list view and from the array design view and in verification mode from the array design view. The plug-in can only set the name and ID of the reporters, since the CDF file doesn't contains any annotation information. Probesets already in BASE will not be affected by the import.
Since BASE 2.4, no configuration needed.
Imports annotation to any annotatable item in BASE.
Since BASE 2.4, no configuration needed.
Imports help texts from an XML file into BASE.
Since BASE 2.0, no configuration needed.
This plug-in is used to import raw data from Illumina data files.
Since BASE 2.4, no configuration needed.
Imports plates from a simple flat file.
Since BASE 2.0, available configurations: 384 wells-plate and 96 wells-plate
Imports plate mappings.
BASE 2.0, no configuration needed.
Imports plug-in configurations from an XML file.
Since BASE 2.1, no configuration needed.
Imports array designs from a print map.
Since BASE 2.0, no configuration needed.
Imports raw data from a text file.
Since BASE 2.0, available configurations: cy3/cy5 GenePix and cy5/cy3 GenePix
Import reporter (probeset) information from a file.
Since BASE 2.0, available configurations:
GenePix related 96 wells, 384 wells, and GenePix.
Affymetrix related, these samples import a small amount of information: HG-U133_Plus_2 and MG_U74Av2 and HG-U133A. The samples may work on other Affymetrix chips, the listed ones are tested and known to work.
Imports GenePix features from a gpr-file.
Since BASE 2.0, GenePix sample configuration available.
The batch import plug-ins all work similarly and their usage is described in Chapter 19, Import of data.
Imports and updates array batches in a batch.
Since BASE 2.8, no configuration required.
Imports and updates array designs in a batch.
Since BASE 2.8, no configuration required.
Imports and updates array slides in a batch.
Since BASE 2.8, no configuration required.
Imports and updates biosources in a batch.
Since BASE 2.8, no configuration required.
Imports and updates extracts in a batch.
Since BASE 2.8, no configuration required.
Imports and updates hybridizations in a batch.
Since BASE 2.8, no configuration required.
Imports and updates labeled extracts in a batch.
Since BASE 2.8, no configuration required.
Imports and updates raw bioassays in a batch.
Since BASE 2.8, no configuration required.
Imports and updates samples in a batch.
Since BASE 2.8, no configuration required.
Imports and updates scans in a batch.
Since BASE 2.8, no configuration required.
Calculate intensities from raw data.
Since BASE 2.0, no configuration needed.
Converts a full-size image into JPEG images for each spot.
Since BASE 2.0, no configuration needed.
Unpacks a tar file on the BASE file system. It also supports TAR files compressed with GZIP or BZIP algorithms.
Since BASE 2.1, no configuration needed.
Unpacks zip and jar file on the BASE's file system.
Since BASE 2.1, no configuration needed.