Changes between Version 121 and Version 122 of PluginDownload


Ignore:
Timestamp:
Nov 2, 2011, 2:05:46 PM (6 years ago)
Author:
nicklas
Comment:

Re-organized the page (fewer lists). Fixes links.

Legend:

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  • PluginDownload

    v121 v122  
    11= Plug-in and extensions download =
    22
    3 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.
     3The latest stable BASE can be downloaded from the [http://base.thep.lu.se/ BASE main 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.
    44
    5 = BASE 2 =
     5= BASE =
    66
    7 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]).
     7BASE 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]).
    88
    9 == Plug-ins ==
     9== BASE 3 compatible plug-ins and extensions ==
    1010
    11 Plug-ins available for download are listed in the table below.
     11These packages are not expected to work with BASE 2.
    1212
    13 || ''Name'' || ''Type'' || ''BASE version'' || ''Maintainer'' || ''Comment'' ||
     13|| '''Name''' || '''Type''' || '''BASE version''' || '''Maintainer''' || '''Comment''' ||
     14|| [wiki:net.sf.basedb.examplecode Example code 1.3] || Examples || 3.0 || Lund team || A package with several "Hello world" examples and other extensions and plug-ins ||
     15|| [wiki:net.sf.basedb.ftp FTP Server 1.2] || Extension || 3.0 || 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 ||
     16|| [wiki:net.sf.basedb.mev MEV Launcher 1.8] || Extension + Export || 3.0 || Lund team || Integrates BASE with [http://www.tm4.org/mev.html TIGR Multi Experiment Viewer] (MEV) ||
     17|| [wiki:net.sf.basedb.examples.webservices Web service examples 3.0] || Examples || 3.0 || Lund team || A package with a Java client application that uses web services to get information from a BASE server ||
     18
     19 - ''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.
     20 - ''Type'' is categorization of plug-ins.
     21  - 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.
     22 - ''Maintainer'' shows the current maintainer of a plug-in.
     23  - 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].
     24  - 'Lund team' refers to the BASE core team at Lund University.
     25
     26== BASE 2 compatible plug-ins and extensions ==
     27
     28Most of these packages are not expected to work on BASE 3.
     29
     30|| '''Name''' || '''Type''' || '''BASE version''' || '''Maintainer''' || '''Comment''' ||
    1431|| [wiki:uk.ac.ebi.AffyArrayDesignBatchImporter AffyArrayDesignBatchImporter] || Import || 2.2 || None || Imports batches of Affymetrix array design. ||
    1532|| [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]). ||
     
    1734|| [wiki:uk.ac.ebi.AnnotationTypeCvImporter AnnotationTypeCvImporter] || Import || 2.0 || None || Import annotation type and controlled vocabularies from a simple flat file. ||
    1835|| [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. ||
     36|| [wiki:net.sf.basedb.examplecode Example extensions 1.2] * || Examples || 2.13 || Lund team || A package with several "Hello world" examples and other extensions ||
     37|| [wiki:net.sf.basedb.examples.plugins Example plug-ins 2.6] * || Examples || 2.6 || Lund team || A package with some example plug-ins ||
     38|| [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 ||
    1939|| [wiki:nl.unimaas.bigcat.GCRMA GCRMA] || Normalization || 2.0 || Patrick Ahles || Normalization of Affymetrix data ||
    2040|| [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. ||
     41|| [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) ||
    2142|| [wiki:net.sf.basedb.normalizers Normalization package] || Normalization || 2.7 || Lund team || A package with different kinds of normalization plug-ins. ||
     43|| [wiki:net.sf.basedb.reggie Reggie 1.5] || Extension || 2.17.1 || Lund team || An extension that adds a specialized interface for registering biosources and samples. ||
    2244|| [wiki:uk.ac.ebi.Tab2MageExporter Tab2MageExporter] || Export || 2.14.1 || None || Exports an experiment meta-data in the tab2mage specification. ||
    2345|| [wiki:uk.ac.ebi.Tab2MageImporter Tab2MageImporter] || Import || 2.2 || None || Imports raw data files and an experiment meta-data in the tab2mage specification. ||
     46|| [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 ||
    2447
    25  - ''Type'' is categorization of plug-ins.
    26   - 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]]
    27  - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]]
    28  - ''Maintainer'' shows the current maintainer of a plug-in.
    29   - 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].
    30   - 'Lund team' refers to the BASE core team at Lund University.
     48'''*''' This package also exists in a BASE 3 compatible version.
    3149
    32 === Plug-ins announced but not yet released ===
     50== Plug-ins announced but not yet released ==
    3351
    3452[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'''
    3553
    3654
    37 == Web client extensions ==
     55== BASE 1.2 plug-ins ==
    3856
    39 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.
    40 || ''Name'' || ''BASE version'' || ''Maintainer'' || ''Comment'' ||
    41 || [wiki:net.sf.basedb.ftp FTP Server 1.1 / 1.2-beta] || 2.16, 3.0-beta || 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 ||
    42 || [wiki:net.sf.basedb.mev MEV Launcher 1.7 / 1.8-alfa] || 2.16, 3.0-alfa || Lund team || Integrates BASE with [http://www.tm4.org/mev.html TIGR Multi Experiment Viewer] (MEV) ||
    43 || [wiki:net.sf.basedb.reggie Reggie 1.5] || 2.17.1 || Lund team || An extension that adds a specialized interface for registering biosources and samples. ||
     57Plug-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.
    4458
    45  - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]]
    46  - ''Maintainer'' shows the current maintainer of a plug-in.
    47   - 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].
    48   - 'Lund team' refers to the BASE core team at Lund University.
    49 
    50 
    51 
    52 == Example code ==
    53 
    54 || ''Name'' || ''Type'' || ''BASE version'' || ''Maintainer'' || ''Comment'' ||
    55 || [wiki:net.sf.basedb.examplecode Example code for BASE] || Plug-in+extensions || 3.0-alfa || Lund team || A package with several "Hello world" examples and other extensions and plug-ins ||
    56 || [wiki:net.sf.basedb.examples.webservices Web services examples for BASE] || Web services || 2.6, 3.0-beta || Lund team || A package with a Java client application that uses web services to get information from a BASE server ||
    57 || [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 ||
    58 || [wiki:net.sf.basedb.examplecode 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 ||
    59 
    60  - ''Type'' is categorization of the package.
    61  - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]]
    62  - ''Maintainer'' shows the current maintainer of a plug-in.
    63   - 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].
    64   - 'Lund team' refers to the BASE core team at Lund University.
    65 
    66 = BASE 1.2 plug-ins =
    67 
    68 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.
    69 
    70 || ''Name'' || ''Type'' || ''Version'' || ''BASE version'' || ''Comment'' ||
     59|| '''Name''' || '''Type''' || '''Version''' || '''BASE version''' || '''Comment''' ||
    7160|| [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. ||
    7261|| [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 ||
     
    8069|| [wiki:se.lu.onk.ZTest One class Z-test] || Analysis || || 1.2.17+ || Lund team || ||
    8170
    82  - ''Type'' is categorization of plug-ins.
    83   - 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]]
    84  - ''Version'' is the latest released version of the plug-in.
    85  - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]]
    86  - ''Maintainer'' shows the current maintainer of a plug-in.
    87   - 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].
    88   - 'Lund team' refers to the BASE core team at Lund University.