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

[Beg-sysbiol] LeMoNe web/gui startup
by Tom Michoel 12 Sep '07

12 Sep '07

Thomas wrote a nice webstart application for LeMoNe: http://www.psb.ugent.be/~thpar/ws/ The idea is to help a new user choose parameter settings (though currently the "help" only contains the comments from the properties file, will be updated later), write a properties file and give the option to run LeMoNe without opening a command line. You can also run the Run class with option --gui to run the application locally, and all code is under svn (requires java 1.6 to compile). Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] ongoing conference
by Vanessa Vermeirssen 10 Sep '07

10 Sep '07

http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib07/prog.php -- ================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 38 23 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM vamei(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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[Beg-sysbiol] creating consensus modules from ensembles of clustering solutions
by Steven Maere 09 Sep '07

09 Sep '07

Hi all, I've been thinking a bit about the problem of having multiple clustering solutions and combining these into 'consensus modules'. I don't know how much and along which lines you have been working on this problem, Tom ? My first thought was to somehow cluster the weighted summary graphs that Tom and Anagha produce with their software. Weighted bipartite graph clustering algorithms might be ideally suited for this, and there are apparently some algorithms and implementations available. I've attached a few relevant articles. We could think about: - clustering the weighted bipartite regulator-gene graph produced by the more recent Lemone 'S' versions - clustering similarly constructed bipartite regulator-condition graphs, as Eric suggested, to see which conditions matter for which regulators Let's discuss further after Tom gets back from holidays. 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] Workshop on Biological Networks, ECCS'07, 1-5 October, Dresden
by Roeland Merks 07 Sep '07

07 Sep '07

Dear all, This might be an interesting opportunity for you guys. I think this will be a really nice conference; it is broad, but there are continuous biology sessions. No need to attend the sessions on traffic modeling or econophysics :-). I am speaking at another satellite conference (developmental biology) on 5 october. Cheers, Roeland ---------------------------------------------------- From: Fatihcan Atay <atay(a)member.ams.org> Date: Fri, 31 Aug 2007 23:57:08 +0200 Subject: Workshop on Biological Networks, ECCS'07, 1-5 October, Dresden Genetic and Biological Networks: Models, Dynamics, and Simulations A satellite workshop of the ECCS'07: European Conference on Complex Systems, 1-5 October 2007, Dresden, Germany Biological systems show emerging functional properties originating from their many interacting units and their inherent multi-level structure. In recent years, biologists, physicists, mathematicians, and computer scientists have been joining efforts in order to understand the different aspects of the collective phenomena exhibited by aggregates of cells and by regulatory networks. The aim of this meeting is to bring together experts in such fields to discuss and explore our understanding of complex biological networks and their applications in the life sciences. Specific topics include, but are not limited to, gene-regulatory, molecular, and metabolic networks, bioinformatics, population dynamics, neural systems, evolutionary dynamics, and mathematical biology. Interested researchers who wish to contribute a talk are invited to send a title and abstract to fatay(a)mis.mpg.de For further information please visit: http://personal-homepages.mis.mpg.de/fatay/eccs07 ---------------------------------------------------- -- ================================================================== Roeland Merks Group Leader "Plant Systems Modeling" Tel:32 (0)9 3313695 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM roeland.merks(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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[Beg-sysbiol] [Fwd: Fwd: urgent: visit of Gladis Casas and Maria del C.]
by Yves Van de Peer 05 Sep '07

05 Sep '07

Dear All, September 14th or 17th (not really sure ...) two Cuban students will arrive for a short stay (in the framework of VLIR, like Isis) in the lab. They work on networks (if I'm well informed, which is not always easy dealing with Cubans :-), and it would be nice if you could help them a little with their project, as Yvan did with Isis. Cuban students are pretty smart, but need sometimes a bit of guidance and I hope you can find some time to talk with them and exchange some ideas, and make them feel welcome. Many thanks in advance, See you in 3 weeks :-) Yves -------- Original Message -------- Subject: Fwd: urgent: visit of Gladis Casas and Maria del C. Date: Wed, 5 Sep 2007 17:14:41 +0200 From: Ann Nowé <ann.nowe(a)como.vub.ac.be> To: koen.vanhoof(a)uhasselt.be, Yves Van de Peer <yves.vandepeer(a)psb.ugent.be> References: <D245E0F5BAF259459C45224E06AADFA7011B1AC4(a)mail-02.uclv.edu.cu> Dag Yves en Koen, Hier het antwoord van Bello. Ze waren dus blijkbaar van plan om de 3 maanden in Gent te verblijven maar de eerste maand naar Hasselt te pendelen. Dit lijkt mij niet echt efficient. Van Yves begrijp ik dat in Gent alles reeds geregeld is. Misschien is het daarom beter om die studenten de eerste 2 maanden in Gent te laten, en dan is er tijd om de verhuis naar Hasselt te plannen. De reservatie van de kamer in Gent in korten tot 2 maanden is misschien nog mogelijk, in elk geval minder lastig dan die kamer nu te gaan annuleren. Dit is natuurlijk in de veronderstelling dat er nog geen kamer voorzien is in Hasselt, en Koen (of andere medewerkers) beschikbaar is half November. Wat denken jullie? Ann Begin forwarded message: > *From: *"Rafael Bello" <rbellop(a)uclv.edu.cu <mailto:rbellop@uclv.edu.cu>> > *Date: *Wed 5 Sep 2007 15:33:16 GMT+02:00 > *To: *Ann Nowé <ann.nowe(a)como.vub.ac.be <mailto:ann.nowe@como.vub.ac.be>> > *Subject: **RE: urgent: visit of Gladis Casas and Maria del C.* > > Dear Ann: > > > > You are right in the plan of Gladis and Maria. They told with me about > their plan recently. They had planned to live in Ghent all time and go > daily to Hasselt, but I recommend them that they live the firsts days > in Ghent but talk with Prof. Koen Vanhoof about the possibility of > living in Hasselt the first month. But, may be You can help them in > this aspect. > > > > Best regards, > > > > Rafael > > > > > ------------------------------------------------------------------------ > > *From:* Ann Nowé [mailto:ann.nowe@como.vub.ac.be] > *Sent:* miércoles, 05 de septiembre de 2007 4:53 > *To:* Rafael Bello > *Subject:* urgent: visit of Gladis Casas and Maria del C. > > > > Dear Rafael, > > > > This morning I have been contacted by Yves van der Peer, because there > is some confusion about the visit of Gladis Casas and Maria del C. > Yves is expecting them on the 14th of stepmber. Do you have a mail in > which he agrees with this plan. This plan was seems to be 1 month at > Univ of Hasselt, with Prof. Koen Vanhoff, and then 2 months at the > University of Ghent with Prof. Yves Van de Peer. > > Can you please provide me with the exact information > > Best wishes > > Ann > > > > > > -------------------------------------------- > > > > Prof. Ann Nowé > > > > Computational Modeling Lab > > > > Computer Science Department > > > > Vrije Universiteit Brussel > > > > Pleinlaan 2 > > > > B-1050 Brussels, Belgium > > > > email: ann.nowe(a)vub.ac.be <mailto:ann.nowe@vub.ac.be> > > > > > ------------------------------------------------------------------------ > Servicio de Correos del Grupo de Redes. UCLV > -Universidad 2008 del 11 al 15 de febrero del 2008. > Palacio de Convenciones. La Habana. Cuba. http: > //www.universidad2008.cu <http://www.universidad2008.cu> > - II Taller internacional -Vitualización en la Educación Superior-, > del 11 al 15 de febrero de 2008 > Palacio de Convenciones. La Habana, Cuba. http://virtual-es.uclv.edu.cu > ------------------------------------------------------------------------ -------------------------------------------- Prof. Ann Nowé Computational Modeling Lab Computer Science Department Vrije Universiteit Brussel Pleinlaan 2 B-1050 Brussels, Belgium email: ann.nowe(a)vub.ac.be <mailto:ann.nowe@vub.ac.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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[Beg-sysbiol] @home
by Eric Bonnet 03 Sep '07

03 Sep '07

Hi there, Just to say that I'll stay at home this morning (kid's adaptation to new creche). See you guys this afternoon. Eric

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[Beg-sysbiol] Genetdes: automatic design of transcriptional netw...[Bioinformatics. 2007] - PubMed Result
by Yves Van de Peer 02 Sep '07

02 Sep '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- 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] Tools for Visually Exploring Biological Networks. [Bioinformatics. 2007] - PubMed Result
by Yves Van de Peer 02 Sep '07

02 Sep '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- 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] Current progress in network research: toward refer...[Brief Bioinform. 2007] - PubMed Result
by Yves Van de Peer 02 Sep '07

02 Sep '07

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