BASE

The latest stable BASE can be downloaded from the ​BASE main site. BASE comes pre-installed with a set of core plug-ins, information about these is available elsewhere (​list of BASE core plug-ins).

BASE 3 compatible plug-ins and extensions

These packages are not expected to work with BASE 2.

Name	Type	BASE version	Maintainer	Comment
Example code 1.8	Examples	3.10	Lund team	A package with several "Hello world" examples and other extensions and plug-ins
External files support 1.5	Extension	3.15	Lund team	Adds support for external file access over FTP, FTPS and SFTP
FTP Server 1.4	Extension	3.3	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
HDFS 1.0	Extension	3.0	Lund team	An extension that adds support for accessing files on a HDFS file system
Illumina plug-ins package 1.7	Add array platform	3.0	Lund team	A package of plug-ins for Illumina Sentrix and Illumina SNP arrays.
LabEnv 1.7	Extension	3.15	Lund team	An extension allowing storage of regular measurements of lab environment data through ThermoWorks Thermo Recoder TR-702W sensors placed in the labs, and inspection of the stored values
MeLuDI 1.4.3	Extension	3.7	Lund team	An extension allowing storage of data for melanoma-lung cancer projects
MEV Launcher 1.11	Extension + Export	3.3	Lund team	Integrates BASE with ​TIGR Multi Experiment Viewer (MEV)
Normalization package 1.0 and 1.1-beta2	Normalization	3.0 and 3.2.4	Lund team	A package with different kinds of normalization plug-ins.
Open Grid Scheduler service 1.3	API	3.15	Lund team	A package that provides an API and services for other extensions that want to submit and monitor jobs on an Open Grid Scheduler cluster.
OTP login 1.3	Authentication	3.15	Lund team	A package for authenticating users with one-time passcodes (Google authenticator compatible)
Print package 1.5	Extension	3.18.1	Lund team	An extension that add better support for printing from BASE.
Reggie 4.36	Extension	3.19	Lund team	An extension that adds a specialized interface for registering biosources, samples and extracts.
Relax 1.6	Extension	3.15	Lund team	An extension for batch importing of data created by the "Release export" plug-in in the Reggie package.
Skin collection 1.2	Skins	3.18.1	Lund team	An extension that provides a few alternate skins for BASE
Thumbnails 1.2	Extension	3.17	Lund team	A package for generating and displaying thumbnails of images and other files. Supported file formats: JPG, PNG, SVG, TIF, PDF and NDPI.
Variant Search 1.5	Extension	3.18	Lund team	An extensions for indexing and searching variants in VCF files. Works with the variant calling files created by Reggie which are also available on the Relax server.
Web service examples 3.1	Examples	3.1-3.3	Lund team	Discontinued, last supported version is BASE 3.3. A package with a Java client application that uses web services to get information from a BASE server
YubiKey authentication 1.6	Authentication	3.15	Lund team	A package for authenticating users with YubiKey one-time-password sticks

• BASE version refers to the earliest BASE version usable with the latest release of the plug-in. There may be other releases for earlier BASE versions.
• 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.
• 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.

BASE 2 compatible plug-ins and extensions

Most of these packages are not expected to work on BASE 3.

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.
Example extensions 1.2 *	Examples	2.13	Lund team	A package with several "Hello world" examples and other extensions
Example plug-ins 2.6 *	Examples	2.6	Lund team	A package with some example plug-ins
FTP Server 1.1 *	Extension	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
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.
MAGE-TAB exporter	Export	2.16.1	Paweł Sztromwasser	From BASE experiment the plugin exports the experimental metadata in the MAGE-TAB format.
MEV Launcher 1.7 *	Extension + Export	2.16	Lund team	Integrates BASE with ​TIGR Multi Experiment Viewer (MEV)
Normalization package *	Normalization	2.7	Lund team	A package with different kinds of normalization plug-ins.
Reggie 1.6 *	Extension	2.17.1	Lund team	An extension that adds a specialized interface for registering biosources, samples and extracts.
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.
Web service examples 2.6 *	Examples	2.6	Lund team	A package with a Java client application that uses web services to get information from a BASE server

* This package also exists in a BASE 3 compatible version.

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

BASE 1.2 plug-ins

Plug-ins created for BASE 1.2 can be made to work in BASE 2 and 3 using the Base1PluginExecuter plug-in. Maintenance is restricted to BASE 2/3 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	​2.2 (​MD5)	1.2.17+ 2.8, 3.2	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	​1.2 (​MD5)	1.2.17+ 2.10, 3.2	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