wiki:PluginDownload

Version 106 (modified by jari, 8 years ago) (diff)

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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 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 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 2.10 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 2.14 Lund team Integrates BASE with TIGR Multi Experiment Viewer (MEV)
  • 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 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.

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