Version 203 (modified by 9 years ago) ( diff ) | ,
---|
BASE
The latest stable BASE can be downloaded from the BASE main site. BASE comes pre-installed with a set of core plug-ins, information about these is available elsewhere (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 |
Example code 1.7 | Examples | 3.4 | Lund team | A package with several "Hello world" examples and other extensions and plug-ins |
External files support 1.1 | Extension | 3.3 | Lund team | Adds support for external file access over FTP, FTPS and SFTP |
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 |
HDFS 1.0 | Extension | 3.0 | Lund team | An extension that adds support for accessing files on a HDFS file system |
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. |
LabEnv 1.3 | Extension | 3.4 | 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 |
MeLuDi 1.2.2 | Extension | 3.4.0 | Lund team | An extension allowing storage of data for melanoma-lung cancer projects |
MEV Launcher 1.11 | Extension + Export | 3.3 | Lund team | Integrates BASE with TIGR Multi Experiment Viewer (MEV) |
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. |
Print package 1.2 | Extension | 3.4 | Lund team | An extension that add better support for printing from BASE. |
Reggie 3.2.2 | Extension | 3.4 | Lund team | An extension that adds a specialized interface for registering biosources, samples and extracts. |
Skin collection 1.1 | Skins | 3.4 | Lund team | An extension that provides a few alternate skins for BASE |
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 |
YubiKey authentication 1.2 | Authentication | 3.3 | Lund team | A package for authenticating users with YubiKey one-time-password sticks |
- 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 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 |
AffyArrayDesignBatchImporter | Import | 2.2 | None | Imports batches of Affymetrix array design. |
Affymetrix plug-in for BASE | Normalization | 2.0 | Lund team | Affymetrix normalization with RMAExpress or Plier (download latest MD5). |
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. |
AnnotationTypeCvImporter | Import | 2.0 | None | Import annotation type and controlled vocabularies from a simple flat file. |
BatchDataImporter | Import | 2.2 | Micha Bayer | Imports batches of data files into BASE, creating a single RawbioAssay for each file. |
Example extensions 1.2 * | Examples | 2.13 | Lund team | A package with several "Hello world" examples and other extensions |
Example plug-ins 2.6 * | Examples | 2.6 | Lund team | A package with some example plug-ins |
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 |
GCRMA | Normalization | 2.0 | Patrick Ahles | Normalization of Affymetrix data |
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. |
MAGE-TAB exporter | Export | 2.16.1 | Paweł Sztromwasser | From BASE experiment the plugin exports the experimental metadata in the MAGE-TAB format. |
MEV Launcher 1.7 * | Extension + Export | 2.16 | Lund team | Integrates BASE with TIGR Multi Experiment Viewer (MEV) |
Normalization package * | Normalization | 2.7 | Lund team | A package with different kinds of normalization plug-ins. |
Reggie 1.6 * | Extension | 2.17.1 | Lund team | An extension that adds a specialized interface for registering biosources, samples and extracts. |
Tab2MageExporter | Export | 2.14.1 | None | Exports an experiment meta-data in the tab2mage specification. |
Tab2MageImporter | Import | 2.2 | None | Imports raw data files and an experiment meta-data in the tab2mage specification. |
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
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 | |
BaseFile | Other | 1.0 (MD5) | 1.2.17+ 2.8 | Lund team | Java utility package for reading the BASEFile format. Required for many se.lu.onk-series plug-ins. Not tested with BASE 1.2.17+ but expected to work. |
CGH Data Dumper | Export | 1.2.17+ 2.8 | Lund team | Dumps bioassay sets in several formats, useful for non-CGH data as well. Not tested with BASE 1.2.17+ but expected to work | |
Median/mean centering | Transformation | 2.2 (MD5) | 1.2.17+ 2.8, 3.2 | Lund team | The center plug-in allows the user to center the expression levels either per gene or per array. Not tested with BASE 1.2.17+ but expected to work. |
Merge BioAssay | Transformation | 2.1 (MD5) | 1.2.17+ 2.8 | Lund team | Merge bioassays by grouping them according to annotation types or syntactical differences in the name. Not tested with BASE 1.2.17+ but expected to work. |
popLowess | Normalization | 1.2.17+ | Lund team | ||
ReplicateError | Filter | 1.3 (MD5) | 1.2.17+ 2.8 | Lund team | Implementation of 'Analysis of replicates' Yang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062 http://genomebiology.com/2002/3/11/research/0062 Not tested with BASE 1.2.17+ but expected to work. |
Smooth | Transformation | 1.2.17+ 2.7 | Lund team | Smooth can be used to reduce experimental noise over a chromosome profile | |
Virtual Array | Transformation | 1.2 (MD5) | 1.2.17+ 2.10, 3.2 | Lund team | Create a virtual array design for bioassays. Not tested with BASE 1.2.17+ but expected to work. |
WeNNI | Transformation | 0.6 | 1.2.17+ 2.6 | Lund team | A missing value imputation algorithm, Johansson et al. BMC Bioinformatics 2006, 7:306 http://www.biomedcentral.com/1471-2105/7/306 |
One class Z-test | Analysis | 1.2.17+ | Lund team |
Attachments (1)
- BASE-plugindevkit-1.2.17.tar.gz (38.5 KB ) - added by 19 years ago.
Download all attachments as: .zip