= Plug-in and extensions download = This page provides easy access to BASE 1 and 2 plug-ins for users who prefer not to use the subversion repository for downloading the plug-ins The latest stable BASE can be downloaded from the [http://base.thep.lu.se/ BASE 2 development site]. The latest BASE 1 release is available from [http://base1.thep.lu.se BASE 1.2.x development site] and the latest [http://baseplugins.thep.lu.se/attachment/wiki/PluginDownload/BASE-plugindevkit-1.2.17.tar.gz?format=raw BASE 1.2 plug-in development kit] may be needed for some of the BASE 1 plug-ins. = BASE 2 = == Plug-ins == Plug-ins created for BASE 2 do not work with BASE 1.x. ''Additional array platform support'':: [wiki:net.sf.basedb.illumina Illumina plug-ins package]: A package of plug-ins for working with Illumina Sentrix and Illumina SNP arrays. Works with BASE '''2.9 and later'''[[br]] ''Analysis'':: Category empty ''Filter'':: Category empty ''Import/Export'':: [wiki:uk.ac.ebi.AffyArrayDesignBatchImporter AffyArrayDesignBatchImporter]: Imports batches of affymetrix array design into base 2. Works with BASE '''2.2 and later''' [[BR]] [wiki:uk.ac.ebi.AnnotationTypeCvImporter AnnotationTypeCvImporter]: Import annotation type annd controlled vocabularies from a simple flat file into base 2. Works with BASE '''2.0 and later'''[[BR]] [wiki:uk.ac.scri.batchimporter BatchDataImporter]: Imports batches of data files into BASE, creating a single !RawbioAssay for each file. Works with BASE '''2.2 and later''' [[br]] [wiki:uk.ac.ebi.Tab2MageExporter Tab2MageExporter]: Exports an experiment meta-data in the tab2mage specification from base 2. Works with BASE '''2.2 and later''' [[BR]] [wiki:uk.ac.ebi.Tab2MageImporter Tab2MageImporter]: Imports raw data files and an experiment meta-data in the tab2mage specification into base 2. Works with BASE '''2.2 and later''' ''Normalization'':: [wiki:se.lu.thep.affymetrix Affymetrix plug-in for BASE]: Affymetrix normalization with RMAExpress or Plier ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.thep.affymetrix/base_affymetrix_plugin-0.7.tar.gz?format=raw download latest] [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.thep.affymetrix/base_affymetrix_plugin-0.7.tar.gz.MD5?format=raw MD5]). The Plier algorithm in this plug-in is superseded by the [http://madr.lcb.uu.se/wiki/APT APT] plug-in. Works with BASE '''2.0 and later''' [[br]] [http://madr.lcb.uu.se/wiki/APT APT]: Affymetrix Power Tools execution plug-in. Currently apt-probeset-summarize and apt-probeset-geneotype from APT is acccessible through this plug-in. Works with BASE '''2.4 and later'''[[BR]] [wiki:net.sf.basedb.normalizers Normalization package]: A package with different kinds of normalization plug-ins. Works with '''BASE 2.7 and later''' ''Quality Control (QC)'':: Category empty ''Transformation'':: [wiki:se.lu.thep.WeNNI WeNNI]: Missing value imputation. '''Not released yet''' ''Un-categorized'':: [wiki:se.lu.onk.BAFsegmentation BAFsegmentation]: Segments B allele frequencies from SNP arrays to identify regions of allelic imbalance. '''Not released yet''' [[br]] [wiki:nl.unimaas.bigcat.GCRMA GCRMA]: Works with BASE '''2.0 and later'''[[BR]] == 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. ''[wiki:net.sf.basedb.ftp 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. ''[wiki:net.sf.basedb.mev MEV Launcher]'':: Integrates BASE with [http://www.tm4.org/mev.html TIGR MultiExperiment Viewer] (MEV). Works with BASE 2.7 and later, but BASE 2.11 is recommended. ''[wiki:net.sf.basedb.examples.extensions Example extensions]'':: A package with several "Hello world" examples of extensions to the web client. Works with BASE 2.7 and later. == Example code == ''Plug-ins'':: [wiki:net.sf.basedb.examples.plugins Example plug-ins for BASE2]: A package with example plug-ins intended for the developer. Works with BASE '''2.6 and later'''[[br]] ''Web services'':: [wiki:net.sf.basedb.examples.webservices 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'''[[br]] ''Extensions'':: [wiki:net.sf.basedb.examples.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 plug-in developer sites == The !MicroArray Datawarehouse Resource@LCB develops BASE plug-ins, please visit their development site at http://madr.lcb.uu.se/. = 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'' || || [wiki:se.lu.onk.BaseFile BaseFile] || Other || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw 1.0] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.8 || Java utility package for reading the BASEFile format. Required for many se.lu.onk-series plug-ins. [[br]] Not tested with BASE 1.2.17+ but expected to work. || || [wiki:se.lu.onk.CGHDataDumper CGH Data Dumper] || Export || || 1.2.17+, 2.8 || Dumps bioassay sets in several formats, useful for non-CGH data as well. [[br]] Not tested with BASE 1.2.17+ but expected to work || || [wiki:se.lu.onk.Center Median/mean centering] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.Center/Center-2.1.tgz?format=raw 2.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.Center/Center-2.1.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.8 || The center plug-in allows the user to center the expression levels either per gene or per array. [[br]] Not tested with BASE 1.2.17+ but expected to work. || || [wiki:se.lu.onk.MergeBioAssay Merge BioAssay] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.MergeBioAssay/MergeBioAssay-2.1.tgz?format=raw 2.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.MergeBioAssay/MergeBioAssay-2.1.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.8 || Merge bioassays by grouping them according to annotation types or syntactical differences in the name. [[br]] Not tested with BASE 1.2.17+ but expected to work. || || [wiki:se.lu.onk.popLowess popLowess] || Normalization || || 1.2.17+ || || || [wiki:se.lu.onk.ReplicateError ReplicateError] || Filter || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.ReplicateError/ReplicateError-1.3.tgz?format=raw 1.3] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.ReplicateError/ReplicateError-1.3.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.8 || Implementation of 'Analysis of replicates' Yang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062. Epub 2002 Oct 24. [[br]] Not tested with BASE 1.2.17+ but expected to work. || || [wiki:se.lu.onk.Smooth Smooth] || Transformation || || 1.2.17+, 2.7 || Smooth can be used to reduce experimental noise over a chromosome profile || || [wiki:se.lu.onk.VirtualArray Virtual Array] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.VirtualArray/VirtualArray-1.1.tgz?format=raw 1.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.VirtualArray/VirtualArray-1.1.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.10 || Create a virtual array design for bioassays. [[br]] Not tested with BASE 1.2.17+ but expected to work. || || [wiki:se.lu.thep.WeNNI WeNNI] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/WeNNI/wenni-0.6.tar.gz?format=raw 0.6] || 1.2.17+, 2.6 || Implementation of a published missing value imputation algorithm [[br]] http://www.biomedcentral.com/1471-2105/7/306 || || [wiki:se.lu.onk.ZTest One class Z-test] || Analysis || || 1.2.17+ || ||