Emil Lundberg wrote: > Hi all, > > Our site will likely wish to store Illumina array data in BASE 2 in the > near future. Sifting through the mailing list archive, this seems indeed > possible (based on the post below, from july '06). > > My question is has anyone implemented this already (Reha Y.?) and is > willing to share the specifications and/or will this find its way into > BASE 2 proper some day?
If somebody is willing to implement it. Right now we have to focus on other things. We can put it into the standard BASE distribution if someone: * comes up with a <raw-data-type> definition for the Illumina Chip * provides one or more plugin configurations for importing the data files For an example of the existing plugin configurations see: http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html /Nicklas > > > regards, > > /Emil > > ________________________________ > Emil Lundberg / Sysadm > Linnaeus Centre for Bioinformatics > Uppsala University > > >> Reha Yildirimman wrote: >> > Hello, >> > >> > using Base2 we are trying to implement the Illumina Chip design. >> In order >> > to use the raw data files describing coordinates and intensities >> of probes >> > there is a need to define a new raw data type besides the given ones >> > (affymetrix,agilent,spotfinder,...). >> > >> > Is this already implemented, is there a way around the "data >> type" problem >> > or am I looking at the wrong spot in base2 ? >> >> Yes, you can add raw data types to Base2. You have to find and modify >> the file 'raw-data-types.xml'. It should be located in the >> <basedir>/www/WEB-INF/classes directory. >> >> Add a tag <raw-data-type> for the Illumina Chip for example: >> >> <raw-data-type >> id="illumina" >> channels="2" >> name="Illumina" >> table="RawDataIllumina" >> > >> >> Then add as many <property> tags as you need. The last step is to run >> the <basedir>/bin/updatedb.sh script to create the new table. >> >> /Nicklas > > > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > 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] ------------------------------------------------------------------------- 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]
