Version 103 (modified by 15 years ago) ( diff ) | ,
---|
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.
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). |
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 working with 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.
- 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 releaed
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.
- 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 2.14 or later 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+ |
Attachments (1)
- BASE-plugindevkit-1.2.17.tar.gz (38.5 KB ) - added by 19 years ago.
Download all attachments as: .zip