Changes between Version 104 and Version 105 of PluginDownload


Ignore:
Timestamp:
Mar 10, 2010, 2:14:31 PM (12 years ago)
Author:
Jari Häkkinen
Comment:

Restructured all downloads to be in tables.

Legend:

Unmodified
Added
Removed
Modified
  • PluginDownload

    v104 v105  
    55= BASE 2 =
    66
    7 BASE 2 come 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 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]).
    88
    99== Plug-ins ==
     
    3030  - 'Lund team' refers to the BASE core team at Lund University.
    3131
    32 === Plug-ins announced but not yet releaed ===
     32=== Plug-ins announced but not yet released ===
    3333
    3434[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'''
     
    3838
    3939An 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] || 2.10 || 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]' || 2.14 || Lund team || Integrates BASE with [http://www.tm4.org/mev.html TIGR MultiExperiment Viewer] (MEV) ||
    4043
    41    ''[wiki:net.sf.basedb.ftp FTP Server]''::
    42      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.
     44 - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]]
     45 - ''Maintainer'' shows the current maintainer of a plug-in.
     46  - 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].
     47  - 'Lund team' refers to the BASE core team at Lund University.
    4348
    44    ''[wiki:net.sf.basedb.mev MEV Launcher]''::
    45      Integrates BASE with [http://www.tm4.org/mev.html TIGR MultiExperiment Viewer] (MEV). Works with BASE 2.7 and later, but BASE 2.14 or later is recommended.
     49
    4650
    4751== Example code ==
    4852
    49   ''Plug-ins''::
    50   [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'''
     53|| ''Name'' || ''Type'' || ''BASE version'' || ''Maintainer'' || ''Comment'' ||
     54|| [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 ||
     55|| [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 ||
     56|| [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 ||
    5157
    52   ''Web services''::
    53   [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'''
    54 
    55   ''Extensions''::
    56   [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, but BASE 2.13 is recommended.
    57 
     58 - ''Type'' is categorization of the package.
     59 - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]]
     60 - ''Maintainer'' shows the current maintainer of a plug-in.
     61  - 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].
     62  - 'Lund team' refers to the BASE core team at Lund University.
    5863
    5964= BASE 1.2 plug-ins =
    6065
    61 Plug-ins created for BASE 1.2 can be made to work in BASE 2 using the Base1PluginExecuter plug-in.
     66Plug-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.
    6267
    6368|| ''Name'' || ''Type'' || ''Version'' || ''BASE version'' || ''Comment'' ||
    64 || [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 or later || 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. ||
    65 || [wiki:se.lu.onk.CGHDataDumper CGH Data Dumper] || Export || || 1.2.17+ [[br]] 2.8 or later || 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 ||
    66 || [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 or later || 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. ||
    67 || [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 or later || 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. ||
    68 || [wiki:se.lu.onk.popLowess popLowess] || Normalization || || 1.2.17+ || ||
    69 || [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 or later || 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. ||
    70 || [wiki:se.lu.onk.Smooth Smooth] || Transformation || || 1.2.17+ [[br]] 2.7 or later || Smooth can be used to reduce experimental noise over a chromosome profile ||
    71 || [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 or later || Create a virtual array design for bioassays. [[br]] Not tested with BASE 1.2.17+ but expected to work. ||
    72 || [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 or later || A missing value imputation algorithm, Johansson et al. BMC Bioinformatics 2006, 7:306 [[br]] http://www.biomedcentral.com/1471-2105/7/306 ||
    73 || [wiki:se.lu.onk.ZTest One class Z-test] || Analysis || || 1.2.17+ || ||
     69|| [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. ||
     70|| [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 ||
     71|| [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. ||
     72|| [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. ||
     73|| [wiki:se.lu.onk.popLowess popLowess] || Normalization || || 1.2.17+ || Lund team || ||
     74|| [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. ||
     75|| [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 ||
     76|| [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. ||
     77|| [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 ||
     78|| [wiki:se.lu.onk.ZTest One class Z-test] || Analysis || || 1.2.17+ || Lund team || ||
     79
     80 - ''Type'' is categorization of plug-ins.
     81  - 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]]
     82 - ''Version'' is the latest released version of the plug-in.
     83 - ''BASE version'' refers to the earliest BASE version usable with the current release of the plug-in. [[br]]
     84 - ''Maintainer'' shows the current maintainer of a plug-in.
     85  - 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].
     86  - 'Lund team' refers to the BASE core team at Lund University.