Appendix A. Core plug-ins shipped with BASE

Table of Contents

A.1. Core analysis plug-ins
A.2. Core export plug-ins
A.3. Core import plug-ins
A.3.1. Core batch import plug-ins
A.4. Core intensity plug-ins
A.5. Uncategorized core plug-ins

Here is a categorized list of all plug-ins installed with a pristine BASE installation. Some plug-ins must be configured before use. The requirements are listed below and configuration samples are given for for plug-ins that supports/requires configurations. Use the right-click menu of the mouse to download these XML files for further import into BASE (see Section 22.2.2, “Importing and exporting plug-in configurations”).

Contributed plug-ins are available at http://baseplugins.thep.lu.se . These plug-ins are either developed outside the core team or require external non-Java compilers and tools. These packages are excluded from the BASE package to make the installation process somewhat simpler.

A.1. Core analysis plug-ins

BASE 1 plug-in executor

Simulates the plug-in runner from Base 1.2. Must be configured before use. The recommended approach is to use the plug-in configuration file from the BASE 1.2 installation. See Section 22.1.3, “BASE version 1 plug-ins” for more information.

External program executor

Export data from BASE and execute an external program for analysis. Afterwards, data can be imported back to BASE. A configuration is needed to run this plug-in. The plug-in is very flexible and can handle several export/import data formats (which can be extended by adding special export/import plug-ins). Here is a list of the built-in exporter/importer implementations.

  • BASEFile exporter for the ExternalProgramExecutor: Exporter implementation that export data in BASE file format.

  • BASEfile importer for the ExternalProgramExecutor: Importer implementation that can import data in BASEfile format.

  • BFS exporter for the ExternalProgramExecutor: Exporter implementation that export data in BFS file format.

  • BFS importer for the ExternalProgramExecutor: Importer implementation that can import data in BFS file format.

  • File-only importer for the ExternalProgramExecutor: Importer implementation that simply upload all created files to BASE.

[Note] Note

This plug-in can in theory handle everything (and more) that the BASE 1 plug-in executor can, except that it doesn't do any translation of field names used in BASE 1.

Formula extra value calculator

Calculates extra values for a bioassay set using a user-defined formula. No configuration is needed.

Formula filter

Filters a bioassay set using a user-defined formula. No configuration is needed.

Formula intensity transformer

Creates a new bioassay set with transformed intensity values using a user-defined formula. No configuration is needed.

Manual derived bioassay creator, Manual transformation

Allows a user to manually register an external analysis procedure that has happened outside of BASE and to register the parameters used and the generated output files. On plug-in create a derived bioassay set and the other a transformation/bioassay set. Both plug-ins need a configuration to register possible parameters and output files.

Normalisation: Lowess

Normalisation using LOWESS algorithm. No configuration is needed.

Normalisation: Median ratio

Normalisation based on median ratio. No configuration is needed.

A.2. Core export plug-ins

Unless otherwise noted, none of the export plug-ins need a configuration.

BASEfile exporter

Exports bioassay set data to serial or matrix BASEfile format.

BFS exporter

Exports bioassay set data to BFS format.

GAL exporter

Exports the features of an array design to a GAL file.

Help texts exporter

Exports help texts to an XML file.

Packed file exporter

Exports files and directories as an archive-file. A configuration is needed to specify compression format. Support for the following formats are included in BASE:

  • BZipped TAR archive: Collects the selected files/directories into a TAR file and compress it with BZIP2.

  • GZipped TAR archive: Collects the selected files/directories into a TAR file and compress it with GZIP.

  • TAR archive: Collects the selected files/directories into an uncompressed TAR file.

  • ZIP archive: Collects the selected files/directories into a ZIP file.

See Section 26.6.4, “File packer plug-ins” for information about implementing support for other file formats.

Plate mapping exporter

Exports plate mappings.

Plugin configuration exporter

Exports plug-in configurations to an XML file.

Table exporter

Exports data from table listings in the web-interface to a TAB-separated text file or XML file.

A.3. Core import plug-ins

There are many import plug-ins in BASE. Their use are in most cases seamless and the user does not need to be aware of detailed plug-in usage. However, there is a set of batch import plug-ins that are targeted for importing multiple items into BASE. These batch importers require some user knowledge for proper and efficient use of them. The batch plug-ins are listed in the Section A.3.1, “Core batch import plug-ins” sub-section below together with pointers to further reading on how to use the plug-ins.

Affymetrix CDF probeset importer

This plug-in is used to import probesets (reporters in BASE language) from an Affymetrix CDF file. It can be used in import mode from the reporter list view and from the array design view and in verification mode from the array design view. The plug-in can only set the name and ID of the reporters, since the CDF file doesn't contains any annotation information. Probesets already in BASE will not be affected by the import. No configuration is needed.

Annotation importer

Imports annotation to any annotatable item in BASE. Configurations are supported but not required.

GTF reporter importer

Imports reporter information from GTF (Gene transfer format) files. Configurations are supported but not required. BASE has pre-installed configurations that uses the gene_id or transcript_id as reporter id.

GTF reporter map importer

Imports array design features from GTF (Gene transfer format) files. A configuration is needed. BASE has pre-installed configurations that uses the gene_id or transcript_id as reporter id.

Help texts importer

Imports help texts from an XML file into BASE. No configuration is needed.

Illumina raw data importer

This plug-in is used to import raw data from Illumina BeadStudion data files. No configuration is needed.

Plate importer

Imports plates from a simple flat file. A configuration is needed. BASE has pre-installed configurations for 96- and 384-well plates.

Plate mapping importer

Imports plate mappings exported by the Plate mapping exporter. No configuration is needed.

Plugin configuration importer

Imports plug-in configurations from an XML file. No configuration is needed.

Print map importer

Imports array design features from TAM or MwBR files. This plug-in require that the array design is connected with plates. No configuration is needed.

Raw data importer

Imports raw data from a text file. A configuration is needed. BASE has pre-installed configurations for GenePix and Cufflinks data files.

Reporter importer

Import reporter (probeset) information from a file. A configuration is not needed, but is recommended. BASE has pre-installed configurations for several different file types.

Since BASE 2.0, available configurations:

Reporter map importer

Imports array design features from text files. This plug-in can be used without connection to plates. A configuration is needed. BASE has pre-installed configurations for some file formats.

A.3.1. Core batch import plug-ins

The batch import plug-ins all work similarly and their usage is described in Section 19.2, “Batch import of data”. All batch importers have support for configurations but can also be used without.

Array batch importer

Imports and updates array batches in a batch.

Array design importer

Imports and updates array designs in a batch.

Array slide importer

Imports and updates array slides in a batch.

Bioplate importer

Imports and updates bioplates in a batch. Note that this import can't be used to put biomaterial on the bioplates.

Biosource importer

Imports and updates biosources in a batch.

Derived bioassay importer

Imports and updates derived bioassays in a batch.

Extract importer

Imports and updates extracts in a batch.

Physical bioassay importer

Imports and updates physical bioassays in a batch.

Raw bioassay importer

Imports and updates raw bioassays in a batch.

Sample importer

Imports and updates samples in a batch.

A.4. Core intensity plug-ins

Formula intensity calculator

Calculate intensities from raw data using a user-defined formula. No configuration is needed, but formulas must be defined using ViewFormulas.

A.5. Uncategorized core plug-ins

Spot images creator

Converts a full-size image into JPEG images for each spot. No configuration is needed.

TAR file unpacker

Unpacks a tar file on the BASE file system. It also supports TAR files compressed with GZIP or BZIP algorithms. This plug-in can be used to automatically unpack files during upload. No configuration is needed.

ZIP file unpacker

Unpacks ZIP and JAR files on the BASE's file system. This plug-in can be used to automatically unpack files during upload. No configuration is needed.

BZip2 file unpacker

Unpacks BZip2 compressed files to the BASE file system. This plug-in can be used to automatically unpack files during upload. No configuration is needed.

GZip file unpacker

Unpacks GZip compressed files to the BASE file system. This plug-in can be used to automatically unpack files during upload. No configuration is needed.