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 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

Plug-ins available for download are listed in the table below. The maintainer of the plug-ins are indicated and plug-ins that have no assigned maintainer is indicated with 'None known'. Unmaintained plug-ins are included in this table until they are reported to be broken.

Name	Type	BASE version	Maintainer	Comment
Illumina plug-ins package	Additional array platform support	2.9 and later	Lund team	A package of plug-ins for working with Illumina Sentrix and Illumina SNP arrays.
AffyArrayDesignBatchImporter	Import	2.2 and later	None known	Imports batches of affymetrix array design into BASE

Import/Export

AnnotationTypeCvImporter: Import annotation type annd controlled vocabularies from a simple flat file into base 2. Works with BASE 2.0 and later
BatchDataImporter: Imports batches of data files into BASE, creating a single RawbioAssay for each file. Works with BASE 2.2 and later
Tab2MageExporter: Exports an experiment meta-data in the tab2mage specification from base 2. Works with BASE 2.14.1 and later
Tab2MageImporter: Imports raw data files and an experiment meta-data in the tab2mage specification into base 2. Works with BASE 2.2 and later

Normalization

Affymetrix plug-in for BASE: Affymetrix normalization with RMAExpress or Plier (​download latest ​MD5). The Plier algorithm in this plug-in is superseded by the ​APT plug-in. Works with BASE 2.0 and later
​APT: Affymetrix Power Tools execution plug-in. Currently apt-probeset-summarize and apt-probeset-geneotype from APT is acccessible through this plug-in. Works with BASE 2.4 and later
Normalization package: A package with different kinds of normalization plug-ins. Works with BASE 2.7 and later

Quality Control (QC)

Category empty

Transformation

WeNNI: Missing value imputation. Not released yet

Un-categorized

BAFsegmentation: Segments B allele frequencies from SNP arrays to identify regions of allelic imbalance. Not released yet
GCRMA: Works with BASE 2.0 and later

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 2.13 is recommended.

Example code

Plug-ins

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

Extensions

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 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 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 ​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 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 ​http://www.biomedcentral.com/1471-2105/7/306
One class Z-test	Analysis		1.2.17+