Version 94 (modified by 13 years ago) (diff)  ,

Plugin 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 development site and the latest BASE 1.2 plugin development kit may be needed for some of the BASE 1 plugins.
BASE 2
BASE 2 come preinstalled with a set of core plugins, information about these is available elsewhere (list of BASE 2 core plugins).
Plugins
Plugins created for BASE 2 do not work with BASE 1.x.
 Additional array platform support

Illumina plugins package: A package of plugins for working with Illumina Sentrix and Illumina SNP arrays. Works with BASE 2.9 and later
 Analysis
 Category empty
 Filter
 Category empty
 Import/Export?

AffyArrayDesignBatchImporter: Imports batches of affymetrix array design into base 2. Works with BASE 2.2 and later
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 metadata in the tab2mage specification from base 2. Works with BASE 2.2 and later
Tab2MageImporter: Imports raw data files and an experiment metadata in the tab2mage specification into base 2. Works with BASE 2.2 and later  Normalization

Affymetrix plugin for BASE: Affymetrix normalization with RMAExpress or Plier
(download latest MD5). The Plier algorithm in this plugin is superseded by the APT plugin. Works with BASE 2.0 and later
APT: Affymetrix Power Tools execution plugin. Currently aptprobesetsummarize and aptprobesetgeneotype from APT is acccessible through this plugin. Works with BASE 2.4 and later
Normalization package: A package with different kinds of normalization plugins. Works with BASE 2.7 and later  Quality Control (QC)
 Category empty
 Transformation
 WeNNI: Missing value imputation. Not released yet
 Uncategorized

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 2.12 is recommended.
Example code
 Plugins
 Example plugins for BASE2: A package with example plugins 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 plugins
Plugins created for BASE 1.2 can be made to work in BASE 2 using the Base1PluginExecuter plugin.
Name  Type  Version  BASE version  Comment 
BaseFile  Other  1.0 (MD5)  1.2.17+, 2.8  Java utility package for reading the BASEFile format. Required for many se.lu.onkseries plugins. Not tested with BASE 1.2.17+ but expected to work. 
CGH Data Dumper  Export  1.2.17+, 2.8  Dumps bioassay sets in several formats, useful for nonCGH 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  The center plugin 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  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  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  Smooth can be used to reduce experimental noise over a chromosome profile  
Virtual Array  Transformation  1.1 (MD5)  1.2.17+, 2.10  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  A missing value imputation algorithm, Johansson et al. BMC Bioinformatics 2006, 7:306 http://www.biomedcentral.com/14712105/7/306 
One class Ztest  Analysis  1.2.17+ 
Attachments (1)
 BASEplugindevkit1.2.17.tar.gz (38.5 KB)  added by 17 years ago.
Download all attachments as: .zip