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

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

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 1.6	Add array platform	2.16	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 released

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.

Name	BASE version	Maintainer	Comment
FTP Server 1.1	2.16	Lund team	An extension that adds an FTP server to BASE, making it possible to upload/download files to/from BASE using regular FTP client software
MEV Launcher 1.7 / 1.8-alfa	2.16, 3.0-alfa	Lund team	Integrates BASE with ​TIGR Multi Experiment Viewer (MEV)
Reggie 1.5	2.17.1	Lund team	An extension that adds a specialized interface for registering biosources and samples.

• 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.
  • Extensions that have no maintainer are indicated with 'None'. Unmaintained extensions are included in the table until they are reported to be broken. If you want to volunteer to maintain an extension then make yourself known through the ​BASE developer mailing list.
  • 'Lund team' refers to the BASE core team at Lund University.

Example code

Name	Type	BASE version	Maintainer	Comment
Example code for BASE	Plug-in+extensions	3.0-alfa	Lund team	A package with several "Hello world" examples and other extensions and plug-ins
Example plug-ins for BASE2	Plug-in	2.6	Lund team	A package with example plug-ins intended for developers
Web services examples for BASE 2	Web services	2.6	Lund team	A package with a Java client application that uses web services to get information from a BASE 2 server
Example extensions for the BASE web client	Extensions	2.13	Lund team	A package with several "Hello world" examples of extensions to the web client

• Type is categorization of the package.
• 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.
  • Example code that have no maintainer is indicated with 'None'. Unmaintained example code is included in the table until it is reported to be broken. If you want to volunteer to maintain an example code package then make yourself known through the ​BASE developer mailing list.
  • 'Lund team' refers to the BASE core team at Lund University.

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. Maintenance is restricted to BASE 2 functionality. Do not expect these plug-ins to be developed further.

Name	Type	Version	BASE version	Comment
BaseFile	Other	​1.0 (​MD5)	1.2.17+ 2.8	Lund team	Java utility package for reading the BASEFile format. Required for many se.lu.onk-series plug-ins. Not tested with BASE 1.2.17+ but expected to work.
CGH Data Dumper	Export		1.2.17+ 2.8	Lund team	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	Lund team	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	Lund team	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+	Lund team
ReplicateError	Filter	​1.3 (​MD5)	1.2.17+ 2.8	Lund team	Implementation of 'Analysis of replicates' Yang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062 ​http://genomebiology.com/2002/3/11/research/0062 Not tested with BASE 1.2.17+ but expected to work.
Smooth	Transformation		1.2.17+ 2.7	Lund team	Smooth can be used to reduce experimental noise over a chromosome profile
Virtual Array	Transformation	​1.1 (​MD5)	1.2.17+ 2.10	Lund team	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	Lund team	A missing value imputation algorithm, Johansson et al. BMC Bioinformatics 2006, 7:306 ​http://www.biomedcentral.com/1471-2105/7/306
One class Z-test	Analysis		1.2.17+	Lund team

• 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.
    
• Version is the latest released version of the plug-in.
• 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.