April 2008 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] ENFIN-DREAM conference Madrid
by Tom Michoel 30 Apr '08

30 Apr '08

Hi all, Just a few points to remember from the ENFIN-DREAM conference (<http://www.enfin.org/page.php?page=enfin_dream>) I attended this week: - ENFIN seems like a very succesful network: partners really share data and collaborate on various projects. If there's a successor to this project, we should try to be part of it. Let's get ourself known to these people, perhaps by inviting some for a seminar? - There will be a DREAM3 conference in Boston end of october/early november 2008. New challenges will also feature model based inference (predicting behavior of unseen data) which is good news for us. The conference will be organized back-to-back with a recomb sysbiol satellite meeting and another meeting organized by Manolis Kellis. - A few talks mentioned "method integration" as we have discussed here as well (to integrate results from enigma and lemone), so this is certainly a topic of interest right now. They used a simple approach of converting all predictions of different methods as p-values which can be combined in weighted sums by the method of <http://www.pnas.org/cgi/content/abstract/102/48/17296>. - Jaak Vilo talked about a method to predict new genes participating in known pathways by overlaying them with expression data (an extension of their tool KEGGanim <http://biit.cs.ut.ee/kegganim/>). They used a completely trivial method (pairwise Pearson correlations with genes in the pathway). I have the feeling it's very easy to improve by modeling the condition dependent expression of genes in a pathway using our tools and then compute the probability for new genes to belong to that pathway. This might be a good project for a new phd student, e.g. focused on combining our arabidopsis expression data with the pathways in reactome. Leuven is also interested in these kind of things. - For Sofie: do you know the BioCreative text mining competitions? <http://www.pdg.cnb.uam.es/BioLINK/BioCreative.eval.html> <http://biocreative.sourcefourge.net> Might be good to participate in the next one to promote genefetch. If you want to know more about specific talks, take a look at the program and ask me. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] [Fwd: ENFIN / Second Advanced Course on Systems Modeling - Paris-Cachan July 8-10]
by Tom Michoel 30 Apr '08

30 Apr '08

A free course in Paris, recommended. Tom -------- Original Message -------- Subject: ENFIN / Second Advanced Course on Systems Modeling - Paris-Cachan July 8-10 Date: Tue, 29 Apr 2008 16:26:40 +0100 From: Pascal Kahlem <pkahlem(a)ebi.ac.uk> To: Ana Rojas Mendoza <arojas(a)cnio.es>, crosales(a)cnio.es, Martin Krallinger <mkrallinger(a)cnio.es>, Ildefonso Cases <icases(a)cnio.es>, ranea(a)uma.es, dicamill(a)dei.unipd.it, tom.michoel(a)psb.ugent.be, Kathleen Marchal <kathleen.marchal(a)biw.kuleuven.be>, medina(a)uma.es, Mario Lauria <lauria(a)tigem.it>, Hui Zhao <hui.zhao(a)biw.kuleuven.be>, Francesco Iorio <iorio(a)tigem.it>, Belcastro Vincenzo <belcastro(a)tigem.it>, Tim Van den Bulcke <tim.vandenbulcke(a)esat.kuleuven.be>, Layka Abbasi <laykaabbasi(a)gmail.com>, Hedi Peterson <peterson(a)quretec.com>, Robert Rentzsch <rentzsch(a)biochem.ucl.ac.uk>, manickam.muthuraman(a)med.ovgu.de, Alberto de la Fuente <alf(a)crs4.it>, alessio_cardin(a)hotmail.it, dixonp(a)maths.ox.ac.uk, skalko(a)clinic.ub.es, vedrana tabor <v.tabor(a)googlemail.com> Dear colleagues, This is the announcement of the Second Advanced Course on Systems Modeling - Paris-Cachan, organized in July 8-10 by the European Networks of Excellence ENFIN and hosted at the Ecole Normale Supérieure in Paris-Cachan. The program of the course is now available at: http://www.enfin.org/page.php?page=ENS_course This Advanced Course will host a maximum of 20 students, having already a background in bioinformatics. >>>> All costs will be covered by the European network ENFIN, except travel costs. <<<<< Applicants should register online before June 15, 2008, after-what the final list of students will be established. Please spread this announcement around. Kind regards, Pascal ________________________________________________________________________ _ Dr. Pascal KAHLEM Project Manager European Network of Excellence ENFIN on Systems Biology - www.enfin.org EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Line +44(0)1223492588 / Mob +49(0)15209854747 / Fax +44(0)1223494468 Email: pkahlem(a)ebi.ac.uk Skype: pascalkahlem ________________________________________________________________________ _ -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] @home
by Eric Bonnet 24 Apr '08

24 Apr '08

hi there, I'm a little bit sick so I'll keep my microbes for me, see you guys on monday! Eric

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[Beg-sysbiol] late again tomorrow
by Tom Michoel 17 Apr '08

17 Apr '08

Another appointment at the hospital at 10:15, now to see the pictures they took last week of my shoulder. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] not recovered as well as I thought -> working at home today
by Steven Maere 16 Apr '08

16 Apr '08

-- ================================================================== 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] Re: for gardeners
by Steven Maere 14 Apr '08

14 Apr '08

Ping, I can give a good home to all your plants if you don't find any other volunteers. My internet just started working again, I'm ill and at home, but I'll probably be back tomorrow. Steven Eric Bonnet wrote: > For the (lucky) people who owns a garden or even a terrasse we have a > couple of plants that we would give for free: > > - An apple-tree (1m) the decorative one, actually not producing apples > but a lot of flowers in spring. > - An hortensia (Hydrangea macrophylla), 80 cm > - 2 small Buxus (in pots, at the moment) 60 cm > - 1 snowball tree ~1m http://en.wikipedia.org/wiki/Viburnum_opulus > > Please ping me if you're interested by any of those.. > > Eric -- ================================================================== 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] [Fwd: Noam Kaplan]
by Steven Maere 13 Apr '08

13 Apr '08

Dear all, Next week, Noam Kaplan from the Weizmann Institute (PhD student of Eran Segal) is coming to the VIB Science Club on Genetics (on Thursday in Leuven). Anybody interested in joining for dinner on Wednesday evening (in Gent or Leuven, Marnik ?). 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] might be late tomorrow
by Tom Michoel 10 Apr '08

10 Apr '08

I have an appointment at 9am to get a scan of my shoulder, no idea how long this will take. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] Can you please also suggest some names (to me): preferably European hotshots please ... Thanks, Yves
by Yves Van de Peer 09 Apr '08

09 Apr '08

-------- Original Message -------- Subject: vervanging reviewer Peer Bork Date: Wed, 9 Apr 2008 09:19:38 +0200 From: Lieve Ongena <Lieve.Ongena(a)vib.be> To: Yves Van de Peer <yves.vandepeer(a)psb.ugent.be> Hallo Yves, Voor onze recente PI call zijn we dringend op zoek nr een aantal namen voor potentiële internationale reviewers ter vervanging van Peer Bork, die blijkbaar een conflict of interest heeft met 2 dossiers. Martijn Huynen hebben we al voor een aantal andere dossiers. De topics waar we nog iemand voor zoeken zijn : Systems biology of gene regulation Understanding growth-controlling systems : mechanisms of rhythmic growth Kan jij me nog een paar namen doorgeven aub /Lieve / -- 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://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] We should discuss about who can help with this ... or should we hire someone else already?
by Yves Van de Peer 08 Apr '08

08 Apr '08

Shall we discuss this somewhere next week? Thanks Yves -------- Original Message -------- Subject: mais project Date: Mon, 07 Apr 2008 18:12:37 +0200 From: Tom Beeckman <tobee(a)psb.ugent.be> To: Yves Van de Peer <yves.vandepeer(a)psb.ugent.be> CC: Leen Jansen <lejan(a)psb.ugent.be> Beste Yves, Zoals je je wellicht nog herinnert is er binnen het maisproject (dat eigenlijk pas per 1 april gestart is) door Leen Jansen van mijn groep reeds een microarray experiment uitgevoerd. Leen heeft een shortlist van +/- 500 potentieel interessante genen kunnen opstellen en hiervan gaan we binnenkort de sequenties krijgen. Hier is het punt in het project waar jouw groep erbij komt (althans voor dit microarray experiment, de rest volgt pas veel later). Heb jij binnen je groep reeds iemand "pinpointen" om mee aan dit project te werken en Leen te helpen bij het analyseren van de mais-sequenties en die we hiervoor kunnen contacteren? Met vriendelijke groeten, Tom -- ROOT DEVELOPMENT GROUP Tom Beeckman Tel:+32 (0)9 331 39 30 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM tobee(a)psb.ugent.be http://www.psb.ugent.be ================================================================== -- 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://bioinformatics.psb.ugent.be/

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