Hi! I have to cluster the whole Arabidopsis proteome (~30.000 proteins), tested under 940 and 85 different conditions. I tried to do the 85*30000 set with Genesis (to find among the Network Programs) and after 20 minutes or so it runs out of memory. Has anyone a script with which I can do the clustering (well, I only know Perl and a bit of R)? Who from our group works on this? Thanks! Esther.
Mh, I wrote this mail 1.5 hours ago. By now I've found the C Clustering Library as solution (http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html#...). + the Perl module to access it. Any remarks? Esther-Kristin Lather wrote:
Hi!
I have to cluster the whole Arabidopsis proteome (~30.000 proteins), tested under 940 and 85 different conditions. I tried to do the 85*30000 set with Genesis (to find among the Network Programs) and after 20 minutes or so it runs out of memory. Has anyone a script with which I can do the clustering (well, I only know Perl and a bit of R)? Who from our group works on this?
Thanks! Esther.
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VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM eslat@psb.ugent.be http://www.psb.ugent.be ==================================================================
Esther-Kristin Lather wrote:
Hi!
I have to cluster the whole Arabidopsis proteome (~30.000 proteins), tested under 940 and 85 different conditions. I tried to do the 85*30000 set with Genesis (to find among the Network Programs) and after 20 minutes or so it runs out of memory. Has anyone a script with which I can do the clustering (well, I only know Perl and a bit of R)? Who from our group works on this?
Thanks! Esther.
_______________________________________________ Binari Intellectuals Need And Require Insanity https://maillist.psb.ugent.be/mailman/listinfo/binari
Several people work on it. I'd say your best shot is to ask either Thomas Abeel or Anagha (but both use primarily Java). Can't you run the Genesis-program in 64-bit mode on werewulf (or any other high-memory machine)? Michiel -- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.ugent.be http://www.psb.ugent.be ==================================================================
participants (2)
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Esther-Kristin Lather -
Michiel Van Bel