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

[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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[Beg-sysbiol] code update
by Tom Michoel 29 Jun '07

29 Jun '07

I added my most recent LeMoNe code to the repository. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] [Fwd: meeting]
by Steven Maere 26 Jun '07

26 Jun '07

Would be good if we would be able to show something on Arabidopsis data... 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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[Beg-sysbiol] Dear All, could you (Postdocs) please have a look at this and give me some feedback within the next 2 weeks or so ...
by Yves Van de Peer 23 Jun '07

23 Jun '07

This could be good money (for some of you?) or new people ... Thanks in advance, Yves -------- Original Message -------- Subject: FP7--Things to do Date: Fri, 22 Jun 2007 14:46:36 +0300 From: Avi Levy <avi.levy(a)weizmann.ac.il> To: Avi Levy <avi.levy(a)weizmann.ac.il>, Naama Barkai <Barkai(a)wisemail.weizmann.ac.il>, Dani Zamir <zamir(a)agri.huji.ac.il>, Lothar Willmitzer <Willmitzer(a)mpimp-golm.mpg.de>, Thomas Altmann <Altmann(a)mpimp-golm.mpg.de>, FEUILLET Catherine <catherine.feuillet(a)clermont.inra.fr>, Boulos Chalhoub <chalhoub(a)evry.inra.fr>, "Mittelsten Scheid, Ortrun" <ortrun.mittelsten_scheid(a)gmi.oeaw.ac.at>, "ian bancroft (JIC)" <ian.bancroft(a)bbsrc.ac.uk>, Alan Schulman <alan.schulman(a)helsinki.fi>, Elisabetta Frascaroli <elisabetta.frascaroli(a)unibo.it>, Maarten Koornneef <koornnee(a)mpiz-koeln.mpg.de>, Michele Morgante <michele.morgante(a)uniud.it>, Wyatt Paul <wyatt.paul(a)biogemma.com>, Mark Aarts <mark.aarts(a)wur.nl>, Joost Keurentjes <Joost.keurentjes(a)wur.nl>, Anna Nadolska-Orczyk <a.orczyk(a)ihar.edu.pl>, Yves Van de Peer <yves.vandepeer(a)psb.ugent.be> Dear Heterosys participants, The participant list is close to complete. We need I think one or two more SMEs-- Suggestions are welcome. I attach a first document, describing in general terms the concept of the project. It is the fruit of discussions with Dani and Naama. I tried to write it as the best compromise I could between the wording of the call and reality. The general idea is to carry a comparative analysis of heterosis and ploidy responses in model species and crops and to try to link those responses to growth vigor phenotypes. Applications of large collaborative projects in FP7 are in two stages. The first stage has a deadline on Sept 11th. If it is approved we will be invited to submit a full proposal in Feb 2008. Funding (let's remain optimistic) should start by the end of 2008. Stage 1, is a ~20 pages application, it will be judged on 2 main criteria: Science and impact. What I need at this stage is explained in the attached document. As we did not meet yet as a group, the writing might take few drafts. With the summer vacations in the middle this means we should all do the effort to respond relatively quickly. Please send me the requested material within 10 days (July 2nd). All the best. Avi ============================================================= Avraham A. Levy Plant Sciences Department The Weizmann Institute of Sciences Rehovot, 76100 Israel Tel (W) 972 8 934 2734 Fax 972 8 934 4181 E-mail: avi.levy(a)weizmann.ac.il http://www.weizmann.ac.il/Plant_Sciences/levy/ ============================================================= -- 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/

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[Beg-sysbiol] Arabidopsis run results
by Eric Bonnet 23 Jun '07

23 Jun '07

/group/biocomp/projects/segal/java/ath_run0.tar The tar file contains: property file used to run the program log file results file (ath_run0.xml.gz) Results file is fairly big, so you need to allocate ~3 Gb to load it (java option: -Xmx3000m). Eric

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