Version 78 (modified by 14 years ago) (diff)  ,

Plugin and extensions download
This page provides easy access to BASE 1 and 2 plugins for users who prefer not to use the subversion repository for downloading the plugins
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
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 The Plier algorithm in this plugin is superseded by the APT plugin.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. This extensions is currently available as a beta. Works with BASE 2.8 and later.
 MEV Launcher
 Integrates BASE with TIGR MultiExperiment Viewer (MEV). Works with BASE 2.7 and later.
 Example extensions?
 A package with several "Hello world" examples of extensions to the web client. Works with BASE 2.7 and later.
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.
External BASE 2 plugin developer sites
The MicroArray Datawarehouse Resource@LCB develops BASE plugins, please visit their development site at http://madr.lcb.uu.se/.
BASE 1.2 plugins
Plugins created for BASE 1.2 can be made to work in BASE 2 using the Base1PluginExecuter plugin.
Name  Version  BASE version  Comment 
Filter  
ReplicateError  1.3 (MD5)  1.2.17+, 2.8  Not tested with BASE 1.2.17+ but expected to work. 
Transformation  
Median/mean centering  2.1 (MD5)  1.2.17+, 2.8  Not tested with BASE 1.2.17+ but expected to work. 
Merge BioAssay  2.1 (MD5)  1.2.17+, 2.8  Not tested with BASE 1.2.17+ but expected to work. 
WeNNI  0.6  1.2.17+  Missing value imputation 
Other  
BaseFile  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. 
 Quality Control (QC)
 Export

CGH Data Dumper: Dumps bioassay sets in several formats, useful for nonCGH data as well. Works with BASE 1.2.17+
 Transformation

Smooth: Works with BASE 1.2.17+
 Normalization

popLowess: Works with BASE 1.2.17+
 Analysis

One class Ztest: Works with BASE 1.2.17+
Attachments (1)
 BASEplugindevkit1.2.17.tar.gz (38.5 KB)  added by 17 years ago.
Download all attachments as: .zip