= BASE = The latest stable BASE can be downloaded from the [http://base.thep.lu.se/ BASE main site]. BASE 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/coreplugins.html list of BASE core plug-ins]). == BASE 3 compatible plug-ins and extensions == These packages are not expected to work with BASE 2. || '''Name''' || '''Type''' || '''BASE version''' || '''Maintainer''' || '''Comment''' || || [wiki:net.sf.basedb.examplecode Example code 1.8] || Examples || 3.10 || Lund team || A package with several "Hello world" examples and other extensions and plug-ins || || [wiki:net.sf.basedb.xfiles External files support 1.7] || Extension || 3.18 || Lund team || Adds support for external file access over FTP, FTPS and SFTP || || [wiki:net.sf.basedb.ftp FTP Server 1.4] || Extension || 3.3 || 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.hdfs HDFS 1.0] || Extension || 3.0 || Lund team || An extension that adds support for accessing files on a HDFS file system || || [wiki:net.sf.basedb.illumina Illumina plug-ins package 1.7] || Add array platform || 3.0 || Lund team || A package of plug-ins for Illumina Sentrix and Illumina SNP arrays. || || [wiki:net.sf.basedb.labenv LabEnv 1.7] || Extension || 3.15 || Lund team || An extension allowing storage of regular measurements of lab environment data through !ThermoWorks Thermo Recoder TR-702W sensors placed in the labs, and inspection of the stored values || || [wiki:net.sf.basedb.meludi MeLuDI 1.4.3] || Extension || 3.7 || Lund team || An extension allowing storage of data for melanoma-lung cancer projects || || [wiki:net.sf.basedb.mev MEV Launcher 1.11] || Extension + Export || 3.3 || Lund team || Integrates BASE with [http://www.tm4.org/mev.html TIGR Multi Experiment Viewer] (MEV) || || [wiki:net.sf.basedb.normalizers Normalization package 1.0 and 1.1-beta2] || Normalization || 3.0 and 3.2.4 || Lund team || A package with different kinds of normalization plug-ins. || || [wiki:net.sf.basedb.opengrid Job scheduler extension 1.14] || API || 3.19.8 || Lund team || A package that provides an API and services for other extensions that want to submit and monitor jobs on an Open Grid Scheduler or Slurm cluster. || || [wiki:net.sf.basedb.otp OTP login 1.3] || Authentication || 3.15 || Lund team || A package for authenticating users with one-time passcodes (Google authenticator compatible) || || [wiki:net.sf.basedb.print Print package 1.5] || Extension || 3.18.1 || Lund team || An extension that add better support for printing from BASE. || || [wiki:net.sf.basedb.reggie Reggie 5.4] || Extension || 3.20 || Lund team || An extension that adds a specialized interface for registering biosources, samples and extracts. || || [wiki:net.sf.basedb.relax Relax 1.10] || Extension || 3.20 || Lund team || An extension for batch importing of data created by the "Release export" plug-in in the Reggie package. || || [wiki:net.sf.basedb.skincollection Skin collection 1.2] || Skins || 3.18.1 || Lund team || An extension that provides a few alternate skins for BASE || || [wiki:net.sf.basedb.thumbnails Thumbnails 1.2] || Extension || 3.17 || Lund team || A package for generating and displaying thumbnails of images and other files. Supported file formats: JPG, PNG, SVG, TIF, PDF and NDPI. || || [wiki:net.sf.basedb.varsearch Variant Search 1.16] || Extension || 3.20 || Lund team || An extensions for indexing and searching variants in VCF files. Works with the variant calling files created by Reggie which are also available on the Relax server. || || [wiki:net.sf.basedb.examples.webservices Web service examples 3.1] || Examples || 3.1-3.3 || Lund team || '''Discontinued, last supported version is BASE 3.3'''. A package with a Java client application that uses web services to get information from a BASE server || || [wiki:net.sf.basedb.yubikey YubiKey authentication 1.6] || Authentication || 3.15 || Lund team || A package for authenticating users with !YubiKey one-time-password sticks || || [wiki:net.sf.basedb.webauthn WebAuthn authentication 1.0] || Authentication || 3.19.3 || Lund team || A package for authenticating users with WebAuthn Security Keys || - ''BASE version'' refers to the earliest BASE version usable with the latest release of the plug-in. There may be other releases for earlier BASE versions. - ''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. - ''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. == BASE 2 compatible plug-ins and extensions == Most of these packages are not expected to work on BASE 3. || '''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:net.sf.basedb.examplecode Example extensions 1.2] * || Examples || 2.13 || Lund team || A package with several "Hello world" examples and other extensions || || [wiki:net.sf.basedb.examples.plugins Example plug-ins 2.6] * || Examples || 2.6 || Lund team || A package with some example plug-ins || || [wiki:net.sf.basedb.ftp FTP Server 1.1] * || Extension || 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: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:no.uib.cbu.base.magetabexport MAGE-TAB exporter] || Export || 2.16.1 || Paweł Sztromwasser || From BASE experiment the plugin exports the experimental metadata in the MAGE-TAB format. || || [wiki:net.sf.basedb.mev MEV Launcher 1.7] * || Extension + Export || 2.16 || Lund team || Integrates BASE with [http://www.tm4.org/mev.html TIGR Multi Experiment Viewer] (MEV) || || [wiki:net.sf.basedb.normalizers Normalization package] * || Normalization || 2.7 || Lund team || A package with different kinds of normalization plug-ins. || || [wiki:net.sf.basedb.reggie Reggie 1.6] * || Extension || 2.17.1 || Lund team || An extension that adds a specialized interface for registering biosources, samples and extracts. || || [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. || || [wiki:net.sf.basedb.examples.webservices Web service examples 2.6] * || Examples || 2.6 || Lund team || A package with a Java client application that uses web services to get information from a BASE server || '''*''' This package also exists in a BASE 3 compatible version. == 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''' == BASE 1.2 plug-ins == Plug-ins created for BASE 1.2 can be made to work in BASE 2 and 3 using the Base1PluginExecuter plug-in. Maintenance is restricted to BASE 2/3 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-2.2.tgz?format=raw 2.2] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.Center/Center-2.2.tgz.MD5?format=raw MD5]) || 1.2.17+ [[br]] 2.8, 3.2 || 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-1.2.tgz?format=raw 1.2] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.VirtualArray/VirtualArray-1.2.tgz.MD5?format=raw MD5]) || 1.2.17+ [[br]] 2.10, 3.2 || 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 || ||