= Plug-in and extensions download = 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://base2.thep.lu.se/base1.2/ BASE 1.2.x download area] 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 = BASE 2 comes pre-installed with a set of core plug-ins, information about these is available elsewhere ([http://base.thep.lu.se/chrome/site/latest/html/appendix/appendix.coreplugins.html 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'' || || [wiki:uk.ac.ebi.AffyArrayDesignBatchImporter AffyArrayDesignBatchImporter] || Import || 2.2 || None || Imports batches of Affymetrix array design. || || [wiki:se.lu.thep.affymetrix Affymetrix plug-in for BASE] || Normalization || 2.0 || Lund team || 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]). || || [wiki:net.sf.basedb.agilent 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. || || [wiki:uk.ac.ebi.AnnotationTypeCvImporter AnnotationTypeCvImporter] || Import || 2.0 || None || Import annotation type and controlled vocabularies from a simple flat file. || || [wiki:uk.ac.scri.batchimporter BatchDataImporter] || Import || 2.2 || Micha Bayer || Imports batches of data files into BASE, creating a single !RawbioAssay for each file. || || [wiki:nl.unimaas.bigcat.GCRMA GCRMA] || Normalization || 2.0 || Patrick Ahles || Normalization of Affymetrix data || || [wiki:net.sf.basedb.illumina Illumina plug-ins package 1.6] || Add array platform || 2.16 || Lund team || A package of plug-ins for Illumina Sentrix and Illumina SNP arrays. || || [wiki:net.sf.basedb.normalizers Normalization package] || Normalization || 2.7 || Lund team || A package with different kinds of normalization plug-ins. || || [wiki:uk.ac.ebi.Tab2MageExporter Tab2MageExporter] || Export || 2.14.1 || None || Exports an experiment meta-data in the tab2mage specification. || || [wiki:uk.ac.ebi.Tab2MageImporter 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. [[br]] - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]] - ''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 [http://base.thep.lu.se/wiki/MailingLists BASE developer mailing list]. - 'Lund team' refers to the BASE core team at Lund University. === Plug-ins announced but not yet released === [wiki:se.lu.onk.BAFsegmentation 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'' || || [wiki:net.sf.basedb.ftp FTP Server 1.1] || 2.16 || 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 || || [wiki:net.sf.basedb.mev MEV Launcher 1.7] || 2.16 || Lund team || Integrates BASE with [http://www.tm4.org/mev.html TIGR Multi Experiment Viewer] (MEV) || || [wiki:net.sf.basedb.reggie Reggie 1.0] || 2.16 || Lund team || An extension that adds a specialized interface for registering biosources and samples. || - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]] - ''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 [http://base.thep.lu.se/wiki/MailingLists BASE developer mailing list]. - 'Lund team' refers to the BASE core team at Lund University. == Example code == || ''Name'' || ''Type'' || ''BASE version'' || ''Maintainer'' || ''Comment'' || || [wiki:net.sf.basedb.examples.plugins Example plug-ins for BASE2] || Plug-in || 2.6 || Lund team || A package with example plug-ins intended for developers || || [wiki:net.sf.basedb.examples.webservices 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 || || [wiki:net.sf.basedb.examples.extensions 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. [[br]] - ''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 [http://base.thep.lu.se/wiki/MailingLists 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'' || || [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+ [[br]] 2.8 || Lund team || 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+ [[br]] 2.8 || Lund team || 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+ [[br]] 2.8 || Lund team || 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+ [[br]] 2.8 || Lund team || 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+ || Lund team || || || [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+ [[br]] 2.8 || Lund team || Implementation of 'Analysis of replicates' Yang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062 [[br]] http://genomebiology.com/2002/3/11/research/0062 Not tested with BASE 1.2.17+ but expected to work. || || [wiki:se.lu.onk.Smooth Smooth] || Transformation || || 1.2.17+ [[br]] 2.7 || Lund team || 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+ [[br]] 2.10 || Lund team || 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+ [[br]] 2.6 || Lund team || A missing value imputation algorithm, Johansson et al. BMC Bioinformatics 2006, 7:306 [[br]] http://www.biomedcentral.com/1471-2105/7/306 || || [wiki:se.lu.onk.ZTest 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. [[br]] - ''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. [[br]] - ''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 [http://base.thep.lu.se/wiki/MailingLists BASE developer mailing list]. - 'Lund team' refers to the BASE core team at Lund University.