May 2006 - beg-sysbiol@psb.ugent.be - maillist.psb.ugent.be

[Beg-sysbiol] paper Harbison
by Steven Maere 31 May '06

31 May '06

excellent chip-data to cross-validate the content of our modules and the relevance of our regulation programs with... S -- ================================================================== Steven Maere Dept. of Plant Systems Biology, Biocomputing research group Ghent University / VIB tel: +32 9 33 13 692 Technologie Park 927 fax: +32 9 33 13 809 B-9052 Gent BELGIUM email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://www.psb.ugent.be/cbd/ ==================================================================

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[Beg-sysbiol] maybe this has been sent around before ... sorry for that then ...
by Yves Van de Peer 22 May '06

22 May '06

http://bioinformatics.oxfordjournals.org/cgi/content/short/22/9/1122?rss=1

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[Beg-sysbiol] FYI: Cell cycle modeling meeting
by Roeland Merks 16 May '06

16 May '06

Hi all, There will be a meeting on cell cycle modeling in Lille this Friday, in conjunction with a cancer & modeling meeting. I will be going there. See attachment and http://www.iri.cnrs.fr/data/eve/vicanne.html for more information. Cheers, Roeland -- Roeland Merks Department of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Ghent, Belgium http://www.psb.ugent.be Tel. +32-(0)9-33 13825 email: post(a)roelandmerks.nl http://www.roelandmerks.nl weblog: http://biolog.volkskrantblog.nl

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[Beg-sysbiol] [Fwd: EMS Summerschool "Mathematics in Molecular Cell Biology"]
by Roeland Merks 16 May '06

16 May '06

-------- Original Message -------- Subject: EMS Summerschool "Mathematics in Molecular Cell Biology" Date: Wed, 10 May 2006 13:48:26 +0200 From: Martin Burger <martin.burger(a)jku.at> To: bernd(a)agnld.uni-potsdam.de, boushabak(a)hotmail.com, a.herz(a)itb.biologie.hu-berlin.de, a.salvador(a)mail.telepac.pt, A.V.Panfilov(a)bio.uu.nl, a.van.ooyen(a)nih.knaw.nl, abakumov(a)iacp.dvo.ru, abrodzik(a)mitre.org, adheiden(a)uni-wh.de, adormehl(a)telkomsa.net, aksaha(a)upng.ac.pg, alarcon(a)maths.ox.ac.uk, Albert.Sorribas(a)cmb.udl.es, alberto.d'onofrio(a)ieo.it, alcapone4u2(a)yahoo.com, ales.fajmut(a)uni-mb.si, Alexandru-Floares(a)xnet.ro, alexf(a)iasi.mednet.ro, alexis.zrimec(a)bion.si, alexis(a)bytefocus.com, alina_butu(a)yahoo.com, alyona_e(a)hotmail.com, anderson(a)maths.dundee.ac.uk, andreas.bohn(a)physik.tu-darmstadt.de, andrej.vilfan(a)ijs.si, andresvs85(a)yahoo.com, angelica.todireanu(a)mcgill.ca, anjan(a)yahoo.com, Anna.Marciniak(a)iwr.uni-heidelberg.de, anu.kettunen(a)danisco.com, ardsg(a)uottawa.ca, arindin(a)study.haifa.ac.il, arino(a)math.mcmaster.ca, armen(a)math.botik.ru, arnab.math(a)gmail.com, arnab.math(a)gmail.com, arnabtmc2001in(a)rediffmail.com, arndt(a)physics.ucsd.edu, arnold(a)grbb.polymtl.ca, arunpeter(a)yahoo.com, asad.rahman(a)uni-koeln.de, asantemoses(a)hotmail.com, aviswana(a)euclides.uniandes.edu.co, avoss(a)math.tu-dresden.de, axhun(a)osc.kiku.dk, ayeh_sh(a)yahoo.com, aziz.alaoui(a)univ-lehavre.fr, baake(a)zi.biologie.uni-muenchen.de, babinec(a)fmph.uniba.sk, baer(a)mpipks-dresden.mpg.de, bahrom(a)vega.tashkent.su, bahrom(a)vega.tashkent.su, bahrom(a)vega.tashkent.su, bamirheidari(a)yahoo.co.uk, bangermann(a)niaid.nih.gov, barhell(a)imse.med.tu-muenchen.de, barryi(a)ks.uiuc.edu, bas(a)bio.vu.nl, bcallen56(a)yahoo.com, bekkal(a)bondy.ird.fr, benny(a)quellenvielfalt.de, berec(a)entu.cas.cz, bernd(a)bio.vu.nl, beyer(a)zappa.cs.uni-dortmund.de, bhattacharyya_samit(a)rediffmail.com, bibhashin(a)yahoo.com, bioinfovv(a)gmail.com, 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isallam(a)magma.ca, issim(a)microbio.bas.bg, ivanvvn6(a)cs.com, ivona_zerajic(a)physik.tu-darmstadt.de, J.Bakker(a)biol.rug.nl, j.crawford(a)tay.ac.uk, j.l.elson(a)ncl.ac.uk, j.w.dietrich(a)medizinische-kybernetik.de, J.Weimar(a)tu-bs.de, jaapk(a)science.uva.nl, jacekwan(a)ibib.waw.pl, jack.beusmans(a)astrazeneca.com, james-christense(a)uiowa.edu, Jan.Praetorius(a)web.de, janaki(a)rri.res.in, bqft90(a)yahoo.com, janr(a)icm.edu.pl, janusz.byczkowski(a)usa.net, jaseltapia(a)hotmail.com, javorszky(a)eunet.at, jayaseelan_74(a)yahoo.com, jdimos(a)molbio.princeton.edu, jean-michel.peyrin(a)cep.u-psud.fr, jert(a)universia.net.co, Jertf(a)universiia.net.co, jeti(a)fdm.uni-freiburg.de, jfaro(a)igc.gulbenkian.pt, jitheshpv(a)yahoo.com, jkarpale(a)cc.hut.fi, jldeneub(a)ulb.ac.be, jliu(a)scri.sari.ac.uk, jm(a)scms.rgu.ac.uk, jmscholey(a)ucdavis.edu, jmt_biomaths(a)yahoo.co.uk, johan.elf(a)icm.uu.se, john.allen(a)nuth.northy.nhs.uk, Johnny(a)ruc.dk, joni(a)ime.unicamp.br, jono.burns(a)utoronto.ca, josem.muinyo(a)cmb.udl.es, jotla(a)jyu.fi, jourjine(a)mpipks-dresden.mpg.de, jtk(a)cmp.uea.ac.uk, juhe(a)fdm.uni-freiburg.de, jungck(a)beloit.edu, k.farnsworth(a)qub.ac.uk, kaiser(a)mpipks-dresden.mpg.de, kalita(a)softlab.ii.uj.edu.pl, kalyan(a)u.washington.edu, kamp(a)theo-physik.uni-kiel.de, Karsten.Weicker(a)informatik.uni-stuttgart.de, kerstin(a)techfak.uni-bielefeld.de, kgordon(a)maths.dundee.ac.uk, kinder(a)bafg.de, kjaffe(a)usb.ve, kl280(a)cam.ac.uk, klaud6(a)wp.pl, klipp(a)molgen.mpg.de, Koch(a)indiana.edu, koolsuman(a)del3.unimi.it, kprank(a)techfak.uni-bielefeld.de, kre(a)mpi-magdeburg.mpg.de, Kreft(a)uni-bonn.de, krivan(a)entu.cas.cz, kschulte(a)ks.uiuc.edu, kuerten(a)ap.univie.ac.at, lamgebreel(a)hotmail.ccom, lars.meinhold(a)iwr.uni-heidelberg.de, lars.moehler(a)vst.uni-magdeburg.de, lburkhar(a)uos.de, lebiedz(a)iwr.uni-heidelberg.de, lee(a)wisdom.weizmann.ac.il, leigh(a)uchicago.edu, leipoldt(a)rulsfb.leidenuniv.nl, lemaire(a)crm.umontreal.ca, Lia.Hemerik(a)mat.dpw.wag-ur.nl, liberati(a)elet.polimi.it, lieberme(a)molgen.mpg.de, liebscher(a)gsf.de, linz(a)physik.uni-augsburg.de, lovefemmy4ever(a)yahoo.co.uk, luca.formaggia(a)mate.polimi.it, luisalima(a)horsewonder.com, M.Kirilova(a)imech.imbm.bas.bg, m.orguil(a)biologie.hu-berlin.de, M.R.Owen(a)lboro.ac.uk, m.steel(a)math.canterbury.ac.nz, m.t.figge(a)phys.rug.nl, mackey(a)cnd.mcgill.ca, madadi_sridevi(a)yahoo.com, magd45(a)yahoo.com, magd45(a)yahoo.com, Magnus.L.Andersson(a)astrazeneca.com, maheshmahendrakar(a)yahoo.com, mail(a)mkaiser.de, maithreye(a)yahoo.com, malchow(a)uos.de, maleonel(a)rc.unesp.br, marcus.hauser(a)physik.uni-magdeburg.de, marjet.elemans(a)mtc.ki.se, Mark.Huiskes(a)ztw.wk.wau.nl, mark.smits(a)algemeen.beng.wau.nl, marko.marhl(a)uni-mb.si, Mark_Smith(a)hc-sc.gc.ca, marten.astrom(a)fiiskeriverket.se, martin.moehle(a)uni-tuebingen.de, martina(a)mpipks-dresden.mpg.de, martinetz(a)informatik.mu-luebeck.de, marx(a)mpasmb.desy.de, matidick(a)yahoo.com, matthew.johnston(a)trinity.ox.ac.uk, mbuiatt(a)tin.it, mcolvin(a)ucmerced.edu, merle.fuchs(a)technologiecontor.de, meyer-hermann(a)physik.tu-dresden.de, MHilt(a)lusi.uni-sb.de, mhoffman(a)pmail.hki-jena.de, michael(a)hearne.co.uk, mick(a)blood.ru, middendorf(a)informatik.uni-leipzig.de, mikko.karttunen(a)hut.fi, milen(a)mail.bol.bg, mirjam.kretzschmar(a)rivm.nl, mitten(a)life.uiuc.edu, mjhernan(a)strix.ciens.ucv.ve, mkkolev(a)yahoo.com, morale(a)mat.unimi.it, moreira(a)zhr.tu-dresden.de, mostafa.bachar(a)uni-graz.at, msafan2001(a)yahoo.com, msantos(a)lncc.br, msingh(a)swin.edu.au, msm(a)gwu.edu, mtbio(a)ecostat.nl, mtyran(a)us.edu.pl, mulder(a)amolf.nl, muller_v(a)ludens.elte.hu, muntaser_safan(a)yahoo.com, muntaser_safan(a)yahoo.com, murlich(a)usa.net, musante(a)entelos.com, muthukumar2k3(a)gmail.com, mvano(a)ceh.ac.uk, mwalton(a)gmx.net, N.A.Hill(a)Leeds.ac.uk, n.a.ww.v.riel(a)tue.nl, n.monk(a)shef.ac.uk, naikdhiraj(a)hotmail.com, neenunair84(a)yahoo.com, nestr(a)thsun1.jinr.ru, nickw(a)isengard.demon.co.uk, nieves(a)fmmeteo.usc.es, nikolabu(a)lycos.com, nmorais(a)gcsi.ist.utl.pt, o.richter(a)tu-bs.de, olaf.wolkenhauer(a)umist.ac.uk, oleg(a)nature.berkeley.edu, Oliver.Jensen(a)nottingham.ac.uk, olsson(a)pan.zoo.uni-jena.de, oriana_ponta(a)yahoo.it, ortmanns(a)ThPhys.Uni-Heidelberg.De, oscar(a)gauss.mat.eup.uva.es, p-comtois(a)crhsc.umontreal.ca, p.hogeweg(a)bio.uu.nl, p.vanazzi(a)bluewin.ch, pablo.gomez.mourelo(a)upm.es, paul.torgerson(a)access.unizh.ch, peitz(a)rhrk.uni-kl.de, penteriani(a)ebd.csic.es, peter.hinow(a)vanderbilt.edu, peter.ruoff(a)tn.his.no, peter.saunders(a)kcl.ac.uk, peter.teunis(a)rivm.nl, prasad(a)ces.iisc.ernet.in, prasant_k_s(a)yahoo.com, praveenbiomed(a)yahoo.co.uk, preziosi(a)polito.it, primoz.peterlin(a)mf.uni-lj.si, priya_vellingiri(a)yahoo.co.in, pugliese(a)science.unitn.it, quiron(a)unisantos.com.br, r.c.jansen(a)plant.wag-ur.nl, RR.J.DeBoer(a)bio.uu.nl, r.kempter(a)biologie.hu-berlin.de, rafacosta(a)deb.uminho.pt, rainer(a)bioc.unizh.ch, rasidiarmin(a)yahoo.com, ray(a)helix.nih.gov, rburri(a)gmail.com, rdiez(a)maths.ac.uk, redewasu(a)hotmail.com, reinker(a)math.ubc.ca, rejniak(a)maths.dundee.ac.uk, rguthke(a)pmail.hki-jena.de, Rich.Strauss(a)ttu.edu, richard.zinck(a)gmx.de, richard(a)cbiol.leeds.ac.uk, rlanzara(a)bio-balance.com, rlr(a)servidor.unam.mx, robertsm(a)agresearch.cri.nz, rocchini(a)unisi.it, roel(a)science.uva.nl, rosutem-miftakhov(a)uiowa.edu, rrgrygie(a)cyf-kr.edu.pl, rudnev(a)inm.ras.ru, rueffler(a)rulsfb.leidenuniv.nl, rusvls(a)rus.sas.com, s.maheswaran(a)eastman.ucl.ac.uk, s.rabouille(a)nioo.knaw.nl, s.thutupalli(a)utoronto.ca, s.tornow(a)gsf.de, s.zietz(a)usip.edu, sabine(a)mathematik.uni-bielefeld.de, samit_math(a)rediffmail.com, sanita(a)uaic.ro, sarah(a)scharp.org, sarkar(a)mail.utexas.edu, sarote.s(a)ku.ac.th, sato(a)sys.eng.shizuoka.ac.jp, sauter(a)isr.uni-stuttgart.de, savana9mk(a)yahoo.com, sblower(a)biomath.medsch.ucla.edu, sc21(a)hotmail.com, schlosser(a)ciit.orgg, schneitz(a)wzw.tum.de, schoeberl(a)mpi-magdeburg.mpg.de, schreibe(a)ipk-gatersleben.de, schueler(a)holz.uni-hamburg.de, schwehm(a)informatik.uni-tuebingen.de, schweitzer(a)gmd.de, seckart(a)mpi-magdeburg.mpg.de, sekimura(a)isc.chubu.ac.jp, semovsky(a)lin.irk.ru, shankssita(a)lycos.com, shieazsf(a)ludens.elte.hu, shu-fang.hsu(a)stat.unibe.ch, shw1129(a)263.net, siamak(a)neda.net, siarry(a)univ-paris12.fr, sigal_p(a)hotmail.com, simon.carpenter(a)bbsrc.ac.uk, singhkapil(a)hotmail.com, sinha(a)gene.ccmbindia.org, skhadar(a)gmail.com, sloot(a)science.uva.nl, sloot(a)science.uva.nl, smahdi(a)uwichill.edu.bb, smith(a)stats.ox.ac.uk, srotas(a)yahoo.com, ssd(a)prodigilab.com, ssgtlizt(a)yahoo.com, stareca(a)hotmail.comm, stephane.bersier(a)chiphy.unige.ch, stephen.coombes(a)nottingham.ac.uk, steve.mcdougall(a)pet.hw.ac.uk, stig.omholt(a)ihf.nlh.no, stroeve(a)nlr.nl, sumpter(a)maths.ox.ac.uk, Suzanne.Touzeau(a)jouy.inra.fr, svanadze(a)gol.ge, Sven.Mesecke(a)gmx.net, swanson(a)amath.washington.edu, t.bretschneider(a)uni-bonn.de, tanya.soboleva(a)aggresearch.co.nz, thalassa.pca(a)ed.ac.uk, thecloonfleming(a)eircom.net, theoretical_biologist(a)yahoo.com, thepolytechnicsibadan(a)yahoo.com, thillen(a)math.ualberta.ca, Thimo.Rohlf(a)mis.mpg.de, thomas.beielstein(a)udo.edu, thomas.bley(a)mailbox.tu-dresden.de, thomas.mair(a)physik.uni-magdeburg.de, Thomas.Wennekers(a)plymouth.ac.uk, thomp(a)rice.edu, timothy.newman(a)asu.edu, titz(a)wisc.edu CC: Vincenzo Capasso <Vincenzo.Capasso(a)unimi.it>, Yasmin Dolak-Struss <yasmin.dolak-struss(a)univie.ac.at> Dear all, I would like to bring to your attention asummer school we are organizing in Linz this fall. I attach the announcement and would like to ask you to forward the information to possibly interested candidates. We still have few funds in particular to support PhD students and young postdocs from EU member and associated states. Regards Martin Burger Vincenzo Capasso _______________________________________________ EMS Summer School at RICAM, Linz, Austria, September 06 An EMS Summer School on "Mathematics in Molecular Cell Biology" will take place at the Johann Radon Institute for Computational and Applied Mathematics (RICAM), in Linz, Austria, September 9-23, 2006. The topic of the school include cell motility, ion channels, and molecular dynamics. Key lectures (4 x 90 minutes each) will be given by Willi Jaeger (University Heidelberg) "Multiscale Models of Cells" Alex Mogilner (University of California Davis) "Quantitative Approaches to Cell Motility and Division" Wolfgang Nonner (University of Miami) "Modeling and Simulation of Ion Channels" Hans Othmer (University of Minnesota) "Analysis of Complex Reaction Networks" Christoph Schuette (Free University Berlin, MATHEON) "Metastability in Biological Systems" See also the webpage http://www.ricam.oeaw.ac.at/emsschool/ for further information In case of interest please register until May 31, 2006 at: emsschool(a)ricam.oeaw.ac.at or Johann Radon Institute for Computational and Applied Mathematics Altenbergerstr. 69, A 4040 Linz Austria, Europe EMS Financial support: The school is sponsored by the European Commission (contract MSCF-CT-2005-029473). Participants from EU countries (and associated countries such as Israel, Norway and Switzerland) who have received their MSc. or Diploma degree (or equivalent) within the past ten years are eligible for reimbursement of travel and living expenses. Europeans currently living outside the EU are eligible for financial support without any time constraints with regard to when they received their respective degrees. Financial support can also be provided for few participants outside the EU. Please indicate the need for financial support in your registration. For applications on financial support please include a CV and a research summary. -- Martin Burger Institut fuer Industriemathematik, Johannes Kepler Universitaet and RICAM (OEAW) Altenbergerstr. 69 A 4040 Linz Austria e-mail: martin.burger(a)jku.at www.indmath.uni-linz.ac.at/people/burger -- Roeland Merks Department of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Ghent, Belgium http://www.psb.ugent.be Tel. +32-(0)9-33 13825 email: post(a)roelandmerks.nl http://www.roelandmerks.nl weblog: http://biolog.volkskrantblog.nl

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[Beg-sysbiol] subversion
by Eric Bonnet 16 May '06

16 May '06

Hi there, I've created a version management system for the project, using the tool subversion. Feel free to play and get used to work with it, I will probably re-create an official entry later, once everybody is used to this system. The repository is in /nas/biocomp/project/segal/java/svnroot but you should *never* edit this directory directly. Use the different subversion commands to get and update new code. See also the manual done by Francis & others on the biocomp wiki website. https://bioinformatics.psb.ugent.be/knowledge/wiki-bioinformatics/Version_C… first create a directory to store the project files eg src. then "checkout" the project with the command: svn checkout file:////nas/biocomp/projects/segal/java/svnroot/modnet src this will copy all the "modnet" project files under src. the main code is in src/trunk cd src/trunk if you edit Split.java, make modifs and that you are happy with the results, you can "commit" the results: this will update the repository: svn commit Split.java -m "Revision test erbon" after -m is a comment. Do not commit .class files or other text files, only source code files. If you want to get the latest version of a file: svn update Split.java If you want to see all the logs for a file: svn log Split.java get a previous version: svn update -r <version number> Split.java you can get the version number by looking at the log for a given file.

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[Beg-sysbiol] PhD Steven
by Steven Maere 10 May '06

10 May '06

Dear all, I've put my PhD thesis on the web at http://www.psb.ugent.be/cbd/papers/phd_stmae/PhD. And yes, it's a quite large pdf file again (I kinda like large files). Please don't distribute this address just yet. If you have any questions, you can ask them during my defense ;-) S -- ================================================================== Steven Maere Dept. of Plant Systems Biology, Biocomputing research group Ghent University / VIB tel: +32 9 33 13 692 Technologie Park 927 fax: +32 9 33 13 809 B-9052 Gent BELGIUM email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://www.psb.ugent.be/cbd/ ==================================================================

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[Beg-sysbiol] introducing Anagha
by Tom Michoel 05 May '06

05 May '06

Hi, We'd like to have a meeting to introduce our new beg-sysbiol member Anagha, and talk about some topics she could be working on. The Boss proposes next Tuesday at 4:30pm. Fine for everyone? Cheers, Tom

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[Beg-sysbiol] next meeting?
by Tom Michoel 04 May '06

04 May '06

Hi there, I have implemented the alternative regulation program learning proposed on our last meeting, as well as a probabilistic assignment of regulators to internal nodes. Initial results look quite interesting. Should we have another meeting to keep you up to date? Tomorrow afternoon or next week monday or tuesday would suit me fine. If you want to have a look at some figures: /nas/biocomp/projects/segal/java/tomic/testresults/test13/modules13.pdf The numbers on each internal node are the score gained by the split and the log probability of the regulator assignment. A yellow regulator means it belongs to the module itself (no cyclicity tests for the moment). Cheers, Tom

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