wiki:PluginDownload

Version 254 (modified by nicklas, 3 weeks ago) (diff)

Released Reggie 4.13

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 1.3 Extension 3.11 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 1.5 Extension 3.8 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 1.1 API 3.11 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.
Print package 1.3 Extension 3.5 Lund team An extension that add better support for printing from BASE.
Reggie 4.13 Extension 3.11 Lund team An extension that adds a specialized interface for registering biosources, samples and extracts.
Relax 1.0 Extension 3.11 Lund team An extension for batch importing of data created by the "Release importer" plug-in in the Reggie package.
Skin collection 1.1 Skins 3.4 Lund team An extension that provides a few alternate skins for BASE
Thumbnails 1.0 Extension 3.5 Lund team A package for generating and displaying thumbnails of images and other files. Supported file formats: JPG, PNG and PDF.
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 1.4 Authentication 3.9 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

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