July 2007 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] DREAM2 data
by Tom Michoel 30 Jul '07

30 Jul '07

Data sets for the different DREAM2 challenges can be found under: /group/biocomp/projects/segal/DREAM2 Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] Learning gene regulatory networks in Arabidopsis thaliana
by Tom Michoel 30 Jul '07

30 Jul '07

Abstract of a poster at ISMB. It's about expanding a known network of a few genes to a network of a few tens of genes. Different from what we are doing, but it could be an interesting approach for some of the wet-lab people who have such small-scale networks. And it's probably quite feasible to do with standard Bayesian networks software. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] interesting?!
by Yves Van de Peer 20 Jul '07

20 Jul '07

-------- Original Message -------- Subject: [BBC] First announcement: 5th Annual Cytoscape Public Symposium and Developers Retreat Date: Wed, 18 Jul 2007 13:35:42 +0200 From: piet molenaar <piet.amc(a)gmail.com> To: BBClist(a)biodiversity.be *_5th Annual Cytoscape Public Symposium and Developers Retreat _* Amsterdam - Netherlands *November 8, 2007: Public Symposium:* */Integrative Bioinformatics: At the cutting edge of network analysis and biological data integration/* *Leroy Hood* –Institute of Systems Biology *Ewan Birney* – European Bioinformatics Institute *Peter Sorger* – Harvard University *Trey Ideker* – University of California, San Diego *Chris Sander* – Memorial-Sloan-Kettering Cancer Center *Benno Schwikowski* – Institute Pasteur *Andrew Hopkins*—Pfizer Global Research & Development* * *November 6,7 and 9, 2007: Developers retreat * *Department of Human Genetics, **Academic** **Medical** **Center* *University of Amsterdam**, **Netherlands* We are pleased to announce the forthcoming 2007 Cytoscape Symposium and Retreat to be held at the Academic Medical Center, University of Amsterdam , Netherlands on 6-9 Nov 2007. More information, updates and registration will be available at: http://www.cytoscape.org/retreat2007 This years meeting is particularly exciting since it is the first time it will be held in Europe, specifically in the vibrant historic city of Amsterdam. 'Floating' on a web of canals, with its unique combination of old-world charm and cosmopolitan culture, Amsterdam is one of the most popular European cities for international visitors. To reach Cytoscape's large European user base a Public Symposium will be held on November 8th for which there is a formidable list of confirmed speakers. Apart from the Symposium the retreat consists of hands-on demo's, user-training sessions and informal, technically focused developer meetings: * *Tues 6th Nov:* Cytoscape Developer's Discussions * *Wed 7th Nov:* *Application showcase, hands-on sessions, tutorials * * *Thur 8th Nov:* */Public Symposium/* * *Fri 9th Nov:* Development of Cytoscape Roadmap for 2007, 2008 The Symposium on the 8th is of general interest to both biologists and informaticians. Current and future users of Cytoscape are invited to visit the Application showcase on the 7th also. The developers days are targeted at the core developers of Cytoscape and plugins. We hope that you can join us! The Organizing Committee, 5^th Cytoscape Retreat 2007 Annette Adler - Agilent Technologies Piet Molenaar - Human Genetics Department AMC Guy Warner - Unilever /Contact/: cytoretreat(a)cytoscape.org <mailto:cytoretreat@cytoscape.org>/ / /The retreat is supported by/: Unilever (www.unilever.com <http://www.unilever.com/>) Netherlands Bioinformatics Center (NBIC) ( www.nbic.nl <http://www.nbic.nl/>) Agilent ( www.agilent.com <http://www.agilent.com/>) /About Cytoscape:/ Cytoscape (www.cytoscape.org <http://www.cytoscape.org/>) is an open source bioinformatics software platform for */visualizing/* molecular interaction networks and */integrating /*these interactions with gene expression profiles and other state data. The software architecture enables adaptation of Cytoscape functionality to the specific needs of biologists and bioinformaticians. It is jointly developed by the groups of Benno Schwikowski (Pasteur Institute, Paris), Trey Ideker (University of California San Diego), Chris Sander (Memorial Sloan-Kettering Cancer Center), Lee Hood (Institute of Systems Biology, Seattle), Annette Adler (Agilent Technologies, Santa Clara, CA) and Bruce Conklin (Gladstone/UCSF, GenMAPP). PS: Excuse us for cross-posting; we're trying to avoid this as much as possible. However, to reach a large audience we decided to include several relevant maillists also thereby increasing the risk that users get this mail several times. -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent 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.ugent.be http://www.psb.ugent.be/bioinformatics/ _______________________________________________ BBClist mailing list BBClist(a)biodiversity.be http://mailman.biodiversity.be/mailman/listinfo/bbclist

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[Beg-sysbiol] working@home in the morning
by Steven Maere 13 Jul '07

13 Jul '07

Hi Yves, I'm working at home this morning since I'm expecting the delivery of a new dishwasher and Marijke has to go to a job interview. Sorry for the short notice... See you at noon, Steven -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-sysbiol] Identifying regulatory targets of cell cycle trans...[BMC Bioinformatics. 2007] - PubMed Result
by Yves Van de Peer 08 Jul '07

08 Jul '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=Abstract&db=PubM…

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[Beg-sysbiol] BioMed Central | Abstract | 1752-0509-1-29 | Metabolic network visualization eliminating node redundance and preserving metabolic pathways
by Yves Van de Peer 08 Jul '07

08 Jul '07

http://www.biomedcentral.com/1752-0509/1/29

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[Beg-sysbiol] Poster ISMB
by Tom Michoel 07 Jul '07

07 Jul '07

Attached is my poster draft for ISMB, comments are welcome. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] Arabidopsis reloaded
by Eric Bonnet 06 Jul '07

06 Jul '07

Hi there, I've launched a second run on the Arabidopsis dataset, using the *stochastic* LeMoNe. The program is running on smokey, in the directory /group/biocomp/projects/segal/java/ath_cc/run1 You can check the file ath_run1.log from time to time to see if something is still going on... I've also moved the data from the first run into /group/biocomp/projects/segal/java/ath_cc/run0 I'll send a mail to the other users of the machine to inform them about this run. -- Eric

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[Beg-sysbiol] Segal & the noncoding RNAs
by Eric Bonnet 05 Jul '07

05 Jul '07

Nice paper, though not exactly a systems biology approach, about the crucial role of several noncoding RNAs controlling the expression of clustered HOX genes. http://www.cell.com/content/article/abstract?uid=PIIS0092867407006599

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[Beg-sysbiol] FYI
by Steven Maere 02 Jul '07

02 Jul '07

The paper that I submitted last week to Genome Biology... Also check out http://bioinformatics.psb.ugent.be/ENIGMA/main.htm. S -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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