Hi, Plug-ins that comes with the core install are listed below. Many of the core plug-ins in BASE 2 are supporting core functionality such as imports and exports whereas some other are analysis plug-ins.
There is one external (that is, non-core) plug-in available at http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress for normalization of Affymetrix experiments. Cheers, Jari The list of all 22 available core plug-ins in BASE 2.1 with a short description. I'll add them to http://base.thep.lu.se * Base1PluginExecuter - This plug-in simulates the plug-in runner from Base 1.2 to enable old plug-ins to be executed. * Bioassay set file exporter - Supported formats: + Tab Delimited, Multiple Sample Files (TDMS Format) for use in MeV (available from http://www.tm4.org). + BASE 1.2.17 BASEFile format export will be delivered in 2.1.1 shortly. * Formula intensity calculator - Calculate intensities from raw data creating an initial root bioassay set. The intensities are calculated using Formula objects registered for the experiment's raw data type. Thus, the functionality of this plugin can be extended by adding more formula objects to the database. * Help texts exporter - Exports a client applications help texts to a XML-file. The help tests can later be imported by the corresponding import plug-in. * Help texts importer - Import of help texts from a XML-file to BASE. * JEP extra value calculator - Calculates extra values for a bioassay set using expressions entered by the user. * JEP filter plugin - Filtering of one bioassay set, creating a new bioassay set with fewer spots in it. The filter is based on expressions entered by the user. The functionality of this plugin is very flexible. * JEP intensity transformer - Transforms the intensities of a bioassayset using expressions entered by the user. * Normalization: Lowess - This is an efficient java implementation by Johan Enell of the LOWESS algorithm. It provides intensity-based normalization. The window size is the only smoothness parameter available in this implementation. The higher it is, the smoother the function will be. Tweaking the other two parameters allows you to gain performance at the price of a small precision loss. The default values are usually good. For more info on LOWESS: Cleveland WS, Devlin SJ: Locally weighted regression: an approach to regression analysis by local fitting. J Am Stat Assoc 1988, 83:596-610. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15. * Normalization: Median ratio - This normalizer scales the intensities in such a way that their geometric mean (sqrt(i1 * i2)) is kept constant but the median of their ratios (i1/i2) is shifted to 1. The normalizer lets you exclude a percentage of the highest and lowest intensities as well as all spots with at least one intensity below a fixed value. * Plate importer - Import of plates from a simple flat file. * Plate mapping exporter - Export of plate mappings, which maps the coordinates of one or more source plates to coordinates on one or more destination plates. * Plate mapping importer - Import of plate mappings, which maps the coordinates of one or more source plates to coordinates on one or more destination plates. * Plugin configuration importer - Export of plug-in configurations to an XML-file. The plugin configurations can later be imported by the corresponding import plug-in. * Plugin configuration exporter - Import of configuration for a BASE plugin from an XML-file. * Print map importer - Import of array design from a print map file. * Raw data importer - Import of raw data from a simple text file. * Reporter importer - Import of reporters from a simple flat file. * Reporter map importer - Import features to an ArrayDesign from a simple flat file. * Simple export - Export all lists (in the GUI) as tab-separated text files or as XML. * Spot images creator - Converts a full-size scanned image into smaller preview jpg images for each individual spot. * ZIP file unpacker - Plug-in to unpacks a zip file on the BASE file system. Useful for upload of many files at once. Supports zip and jar files. Paddy Tighe wrote: > Hi, > Am currently running base 1.2.17, looking at installing Base 2.0 – what > plugins are part of the core install - I can’t seem to find this listed > on the Base site? > > Regards > > Paddy > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses, which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > > ------------------------------------------------------------------------ > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Jari Hakkinen, PhD Complex Systems Division mailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
