- beg-sysbiol@psb.ugent.be - maillist.psb.ugent.be

[Beg-sysbiol] A Predicted Interactome for Arabidopsis. [Plant Physiol. 2007] - PubMed Result
by Yves Van de Peer 12 Aug '07

12 Aug '07

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

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[Beg-sysbiol] MOVE: A Multi-level Ontology-based Visualization a...[In Silico Biol. 2007] - PubMed Result
by Yves Van de Peer 12 Aug '07

12 Aug '07

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

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[Beg-sysbiol] Innovation and robustness in complex regulatory ge...[Proc Natl Acad Sci U S A. 2007] - PubMed Result
by Yves Van de Peer 12 Aug '07

12 Aug '07

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

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[Beg-sysbiol] enigma on cell cycle data (with figure)
by Steven Maere 08 Aug '07

08 Aug '07

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[Beg-sysbiol] enigma on cell cycle data
by Steven Maere 08 Aug '07

08 Aug '07

Dear all, The first run of ENIGMA on the cell cycle data has been completed. Out of 500+ experiments, approx 300 qualified as perturbational and could be used directly by ENIGMA. 120 of those featured less than 10 differentially expressed genes. These were discarded, the other 180 were kept. You can view the results in the folder stmae/enigma_cell_cycle on the psb drive (P:). For interpretation of the result files, see the ENIGMA website (http://bioinformatics.psb.ugent.be/ENIGMA/main.htm) for interpretation of the figures, see the legend of the sample figure below. Bear in mind that this is the first run, there are some things that I plan to check/improve, such as (i) discard experiments with pleiotropic effects, these tend to give rise to unnaturally large modules that may mask smaller modules (see e.g. first module figures) (ii) try to include more data that was not yet included in the compendium and/or did not qualify directly for use by ENIGMA (iii) reconsider the preprocessing protocol, include more informative experiment labels, update Arabidopsis GO data and include Arabidopsis TF motif data if possible. I'm gone on holidays until thursday August 16th, I'm interested in any suggestions/comments you might have by then. Best, 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] Increased glycolytic flux as an outcome of whole-g...[Mol Syst Biol. 2007] - PubMed Result
by Yves Van de Peer 05 Aug '07

05 Aug '07

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

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[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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