February 2011 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] Smokey
by kenes 24 Feb '11

24 Feb '11

I'll be burdening smokey periodically really heavy this afternoon for long times (CPU, not really memory). If anyone should need smokey, let me know and I'll give smokey a breather. Kevin

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[Beg-sysbiol] Cluster jobs
by Cedric Simillion 18 Feb '11

18 Feb '11

Dear all, At the moment I'm occupying 64 cores (on 8 machines with 8 cores) on the cluster. There are still some 64-bit nodes available, but if anyone needs a large-ish number of nodes urgently, let me know and I'll kill a few of my jobs. With apologies for my computational greed, Cedric -- ================================================================== Cedric Simillion, PhD Tel:+32 (0)9 331 38 23 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM http://bioinformatics.psb.ugent.be ==================================================================

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[Beg-sysbiol] urgent ...
by Yves Van de Peer 18 Feb '11

18 Feb '11

Dear all, Does someone has high quality (high resolution) jpg or tiff figures of networks? We need to provide some nice figures for a University leaflet on the MRP (speerpunt). Thanks, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and Systems Biology Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ Check out! http://www.plantgenomeevolution.com/

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[Beg-sysbiol] Plant systems biology: network matters. [Plant Cell Environ. 2011] - PubMed result
by Yves Van de Peer 13 Feb '11

13 Feb '11

http://www.ncbi.nlm.nih.gov/pubmed/21309807?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and Systems Biology Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ Check out! http://www.plantgenomeevolution.com/

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[Beg-sysbiol] Fwd: Release of the AllegroMCODE plugin
by stefanie.debodt＠gmail.com 10 Feb '11

10 Feb '11

---------- Forwarded message ---------- From: Jun Yoon <junsungy...(a)gmail.com> Date: Feb 9, 9:28 am Subject: Release of the AllegroMCODE plugin To: cytoscape-announce Hi everyone, We are pleased to announce the first relase of the AllegroMCODE plugin. The AllegroMCODE plugin is a Cytoscape plugin that find clusters, or highly interconnected groups of nodes in a large complex network such as a protein interaction network and a social network. This plugin generates the same clustering results with the well-known MCODE plugin, but it can process several hundred times faster than the MCODE plugin for large complex networks by exploiting our high performance GPU computing architecture. You can also enjoy the processing speedup without any special graphics hardware since it interfaces with our free GPU computing server. Your analysis task of large complex network will be faster than ever by using the AllegroMCODE plugin. For example, it takes 0.52 seconds to find clusters from a large PPI netwrok which has 31,215 nodes and 317,706 edges by using the AllegroMCODE plugin with our free GPU computing server. Compatibility: Cytoscape 2.6, 2.7, and 2.8 Availability: through the Cytoscape plugin manager under the "Analysis" category. You can get more information from our website:http:// www.allegroviva.com/allegromcode Sincerely, Jun Yoon CEO & Co-Founder AllegroViva Corporation

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