Hi Pierre, I can't give you much direct help, but both as a tip and a test: have you tried looking for helpful examples on myExperiment.org? If you have any trouble with myExperiment, let the developers know. It will make myExperiment better.
Furthermore, I would probably look for local widgets, such as for regexp operations. I'm not sure if table widgets exist (could be a nice addition). I am curious how you would use UCSC data. The last time I looked (which is a while ago) there were no Web Services for UCSC genome data. These would be very valuable to me and many others I think. Good luck! Marco. Pierre LINDENBAUM wrote: > Hi all, > I'm trying to use taverna, but I'm a little bit lost in the workbench about > how to find the right tool. For example, one common task I'd like to perform > would be: > > + open a tab delimited file > + 'grep' for the SNPs ( lines containing the regex rs[0-9]+ ) > + 'cut' the 'Xth' column containing the SNPs > + find the positions of those SNP on a given build of the human genome ( > using the mysql anonymous server of the UCSC) > + find the distinct Genes overlaping those SNP ( again, using the mysql > anonymous server of the UCSC) > + output the result to a file > > Can anyone help ? I would be interested in how you find the right nodes and > how you fill the information. > > Thanks in advance > > Pierre > > > > > > > > > > > . > > > > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > taverna-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/taverna-users > Documentation: http://www.mygrid.org.uk/usermanual1.7/ > FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq > Biological Services: > http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices > -- Marco Roos Faculty of Science University of Amsterdam Kruislaan 403, room F1.02 1098 SJ Amsterdam tel. +31 (0) 20 525 7522 http://home.medewerker.uva.nl/m.roos1 (includes links to social networks) Note the change of e-mail address to [email protected] ------------------------------------------------------------------------------ _______________________________________________ taverna-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/taverna-users Documentation: http://www.mygrid.org.uk/usermanual1.7/ FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq Biological Services: http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices
