Version 104 (modified by Jari Häkkinen, 14 years ago) ( diff )

Adding Agilent plug-in

Plug-in and extensions download

The latest stable BASE can be downloaded from the BASE 2 development site. The latest BASE 1 release is available from BASE 1.2.x download area and the latest BASE 1.2 plug-in development kit may be needed for some of the BASE 1 plug-ins.


BASE 2 come pre-installed with a set of core plug-ins, information about these is available elsewhere (list of BASE 2 core plug-ins).


Plug-ins available for download are listed in the table below.

Name Type BASE version Maintainer Comment
AffyArrayDesignBatchImporter Import 2.2 None Imports batches of Affymetrix array design.
Affymetrix plug-in for BASE Normalization 2.0 Lund team Affymetrix normalization with RMAExpress or Plier (download latest MD5).
Agilent plug-ins package Add array platform 2.14 Lund team Adds support for Agilent 1-channel data and a background correction plug-in to BASE.
AnnotationTypeCvImporter Import 2.0 None Import annotation type and controlled vocabularies from a simple flat file.
BatchDataImporter Import 2.2 Micha Bayer Imports batches of data files into BASE, creating a single RawbioAssay for each file.
GCRMA Normalization 2.0 Patrick Ahles Normalization of Affymetrix data
Illumina plug-ins package Add array platform 2.12 Lund team A package of plug-ins for Illumina Sentrix and Illumina SNP arrays.
Normalization package Normalization 2.7 Lund team A package with different kinds of normalization plug-ins.
Tab2MageExporter Export 2.14.1 None Exports an experiment meta-data in the tab2mage specification.
Tab2MageImporter Import 2.2 None Imports raw data files and an experiment meta-data in the tab2mage specification.
  • Type is categorization of plug-ins.
    • Plug-ins of 'Add array platform' type will extend a BASE installation to support further array platforms. A base set of plug-ins are provided such as import of raw data and normalization.
  • BASE version refers to the earliest BASE version usable with the current release of the plug-in.
  • Maintainer shows the current maintainer of a plug-in.
    • Plug-ins that have no maintainer are indicated with 'None'. Unmaintained plug-ins are included in the table until they are reported to be broken. If you want to volunteer to maintain a plug-in then make yourself known through the BASE developer mailing list.
    • 'Lund team' refers to the BASE core team at Lund University.

Plug-ins announced but not yet releaed

BAFsegmentation: Segments B allele frequencies from SNP arrays to identify regions of allelic imbalance. Maintainer is Johan Staaf, Lund University. Not released yet

Web client extensions

An extension mechanism was introduced in the BASE 2.7 web client. Extensions are mainly used for adding functionality the GUI, such as extra menus and buttons.

FTP Server
An extension that adds an FTP server to BASE, making it possible to upload/download files to/from BASE using regular FTP client software. Works with BASE 2.10 and later.
MEV Launcher
Integrates BASE with TIGR MultiExperiment Viewer (MEV). Works with BASE 2.7 and later, but BASE 2.14 or later is recommended.

Example code

Example plug-ins for BASE2: A package with example plug-ins intended for the developer. Works with BASE 2.6 and later
Web services
Web services examples for BASE 2: A package with a Java client application that uses web services to get information from a BASE 2 server. Works with BASE 2.6 and later
Example extensions for the BASE web client: A package with several "Hello world" examples of extensions to the web client. Works with BASE 2.7 and later, but BASE 2.13 is recommended.

BASE 1.2 plug-ins

Plug-ins created for BASE 1.2 can be made to work in BASE 2 using the Base1PluginExecuter plug-in.

Name Type Version BASE version Comment
BaseFile Other 1.0 (MD5) 1.2.17+
2.8 or later
Java utility package for reading the BASEFile format. Required for many plug-ins.
Not tested with BASE 1.2.17+ but expected to work.
CGH Data Dumper Export 1.2.17+
2.8 or later
Dumps bioassay sets in several formats, useful for non-CGH data as well.
Not tested with BASE 1.2.17+ but expected to work
Median/mean centering Transformation 2.1 (MD5) 1.2.17+
2.8 or later
The center plug-in allows the user to center the expression levels either per gene or per array.
Not tested with BASE 1.2.17+ but expected to work.
Merge BioAssay Transformation 2.1 (MD5) 1.2.17+
2.8 or later
Merge bioassays by grouping them according to annotation types or syntactical differences in the name.
Not tested with BASE 1.2.17+ but expected to work.
popLowess Normalization 1.2.17+
ReplicateError Filter 1.3 (MD5) 1.2.17+
2.8 or later
Implementation of 'Analysis of replicates' Yang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062 Not tested with BASE 1.2.17+ but expected to work.
Smooth Transformation 1.2.17+
2.7 or later
Smooth can be used to reduce experimental noise over a chromosome profile
Virtual Array Transformation 1.1 (MD5) 1.2.17+
2.10 or later
Create a virtual array design for bioassays.
Not tested with BASE 1.2.17+ but expected to work.
WeNNI Transformation 0.6 1.2.17+
2.6 or later
A missing value imputation algorithm, Johansson et al. BMC Bioinformatics 2006, 7:306
One class Z-test Analysis 1.2.17+

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