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

[Beg-sysbiol] lemone update
by Eric Bonnet 21 Nov '07

21 Nov '07

Hi there, I updated the bingo class again, with some fresh code from Steven: - bingo parameters are read directly from the jar file, - some bingo param. are then overridden by values specified in the lemone property file (species, annotation file name, etc..) - output is now one (big) file for each module set, written in the bingo_results directory (created in the current directory). Be sure to link to the latest bingo jar file which is in: /group/biocomp/projects/segal/java/lib/BiNGO_11-2007/BiNGO.jar Bingo parameters example: #BiNGO parameters BiNGO=true signif_def=0.05 annotation_file_def=A_thaliana_default ontology_file_def=GO_Biological_Process annotation_default=true ontology_default=true -- Eric

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[Beg-sysbiol] This is (one of the things) that I hope we can start doing as well in the near future ...
by Yves Van de Peer 21 Nov '07

21 Nov '07

http://www.biomedcentral.com/1752-0509/1/49 -- 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] I guess we have little chance with ours, no? Yves
by Yves Van de Peer 21 Nov '07

21 Nov '07

-------- Original Message -------- Subject: [Fwd: FW: ESF-UB Conference on Systems Biology - Spain, April 2008] Date: Thu, 15 Nov 2007 09:34:34 +0100 From: Christine Tire <chtir(a)psb.ugent.be> To: beg(a)psb.ugent.be FYI ------------------------------------------------------------------------ *From:* Corinne Wininger - Le Moal [mailto:clemoal@esf.org] *Sent:* woensdag 14 november 2007 16:37 *To:* clemoal-list *Cc:* Corinne Wininger - Le Moal *Subject:* ESF-UB Conference on Systems Biology - Spain, April 2008 FIRST CALL FOR APPLICATIONS Dear Sir or Madam, Please find below information on an ESF Research Conference which may be of particular interest to you: *ESF-UB Conference* Systems Biology Hotel Eden Roc, Sant Feliu de Guixols, Spain *12-17 April 2008* Chaired by: Luis Serrano, Centre for Genomic Regulation, Barcelona, ES, Roel van Driel, University of Amsterdam, NL & Rudolf Aebersold, Swiss Federal Inst. of Technology, CH The ESF-UB Conference on Systems Biology attempts to give a comprehensive overview of the recent developments in the different aspects that are included in systems biology. Thus we will cover network analysis, network modeling, -omics approaches in Systems Biology, relationship between Systems Biology and disease and briefly touch the future avenue of Synthetic Biology. The conference will be organized around senior speakers presenting the advances in their fields and junior talks selected from abstracts. Special emphasis will be given to poster sessions and open discussions to favor communication between senior and junior scientists. Scientific programme (including detailed list of invited speakers) and application form are accessible on-line through www.esf.org/conferences/08234 <http://www.esf.org/conferences/08234>. Closing date for applications as well as for abstract submission: *6 January 2008*. Some grants available for young researchers to cover the conference fee and possibly part of the travel costs. Grant requests should be made by ticking appropriate field(s) in the paragraph "Grant application" of the application form <http://www2.esf.org/asp/esfrcaf.asp?confcode=234&meetno=1> (Ctrl + Click to follow the link). Many thanks for passing on the attached flyer to your colleagues who may be interested in this event. Kind regards, Corinne Wininger Communications Officer - ESF Conferences European Science Foundation - Communications Unit 1 quai Lezay-Marnésia, BP 90015 67080 Strasbourg Cedex, France Phone: +33 (0)388 76 21 50 Fax: +33 (0)388 76 71 80 clemoal(a)esf.org <mailto:clemoal@esf.org> www.esf.org/conferences <http://www.esf.org/conferences> -- ================================================================== Christine Tire Tel:+32 (0)9 331 38 03 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM chtir(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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[Beg-sysbiol] Re: anyone up for lunch? (Chess cafe, somewhere else, but I have to be back at 1:30)
by Steven Maere 21 Nov '07

21 Nov '07

I'm joining. I'm currently working at home because I have to watch Saartje for a few hours, until Marijke gets back. I'll be in by 11.00. S Yves Van de Peer wrote: > -- ================================================================== 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] bingo class update
by Eric Bonnet 20 Nov '07

20 Nov '07

Hey there, I made a few changes to the bingo class in LeMone, to take into account the multiple module sets that are now generated by the program. All you need is to have in your current directory the bingo_gui.properties file and a BiNGO directory containing the GO and annotation files (or a link to those files). The class will then generate a bingo_results directory containing the .bgo files for each module of each module set. See the javadoc or the class for details. Changes are in the svn repository. -- Eric

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[Beg-sysbiol] paper
by Eric Bonnet 19 Nov '07

19 Nov '07

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures http://www.nature.com/nature/journal/v450/n7167/abs/nature06340.html

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[Beg-sysbiol] The road to modularity. [Nat Rev Genet. 2007] - PubMed Result
by Yves Van de Peer 18 Nov '07

18 Nov '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] Modeling protein network evolution under genome du...[BMC Syst Biol. 2007] - PubMed Result
by Yves Van de Peer 18 Nov '07

18 Nov '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] Fwd: DREAM2 prediction evaluations and program
by Tom Michoel 16 Nov '07

16 Nov '07

To see our prediction results, go to the site mentioned below and choose challenge "5_1: UNSIGNED_GenomeScale", we are Team 41. Tom Begin forwarded message: > From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> > Date: Fri 16 Nov 2007 06:39:31 GMT+01:00 > To: DREAM2 Call For Participation <DREAM2_Call_For_Participation% > IBMUS(a)us.ibm.com>, DREAM2 Authors of Accepted Posters > <DREAM2_Authors_of_Accepted_Posters%IBMUS(a)us.ibm.com>, DREAM2 > Authors of Accepted Submissions > <DREAM2_Authors_of_Accepted_Submissions%IBMUS(a)us.ibm.com>, DREAM2 > Invited Speakers <DREAM2_Invited_Speakers%IBMUS(a)us.ibm.com>, DREAM2 > Program Committee <DREAM2_Program_Committee%IBMUS(a)us.ibm.com>, > DREAM Steering Committee <DREAM_Steering_Committee% > IBMUS(a)us.ibm.com>, CompBioSeminars%IBMUS(a)us.ibm.com > Cc: califano(a)c2b2.columbia.edu, jpaul(a)nyas.org > Subject: DREAM2 prediction evaluations and program > > > SINCERE APOLOGIES IF YOU RECEIVE THIS ANNOUNCEMENT MORE THAN ONCE > > > DREAM2: DIALOGUE ON REVERSE ENGINEERING > ASSESSMENT AND METHODS 2 > December 3 - 4, 2007, NY Academy of Sciences, New York > > > > Dear colleagues > > As you may know, an important component of DREAM2 is its experiment > at blind prediction of known biological networks from different > data types. > We had 5 challenges (some with several sub-challenges) for which 36 > teams submitted 110 predictions. We have evaluated all the network > prediction > submitted to the DREAM2 conference, and we have produced the scores > for all the participants. The results of the hard efforts at > producing predictions > of all participating teams can be found at our web site: > > http://wiki.c2b2.columbia.edu/dream/results/ > > This site is accessible to the world, and because of that the team > names have been anonymized. > > I think there is a lot to learn from these results. For example, it > is clear that there are some challenges for which there is a lot of > work ahead > (e.g., the protein-protein interaction network, the Five Gene > Network Challenge, chip version), and others that appear to > be more amenable to "reverse engineer". At the conference we will > present several analyses from these aggregate data. > > We are also attaching the conference program. If you are planning > to attend the conference, please register, as registration is > limited and there > are only a few places left. > > > Information on the DREAM Project: > http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM_Project > > Information on the DREAM2 Conference: > http://wiki.c2b2.columbia.edu/dream/index.php/ > DREAM2:_The_2nd_DREAM_Conference > > Information on lodging > http://wiki.c2b2.columbia.edu/dream/index.php/ > DREAM2:_The_2nd_DREAM_Conference#Information_on_Lodging > > > Sincerely, > > DREAM2 Conference Organizers: > Gustavo Stolovitzky (chair), IBM Research > Andrea Califano, Columbia University > > > Gustavo A. Stolovitzky, Ph.D. > Adj. Assoc Prof of Biomed Informatics, Columbia Univ > Mngr, Func Genomics & Sys Biology, IBM Research > P.O.Box 218 Office : (914) 945-1292 > Yorktown Heights, NY 10598 Fax : (914) 945-4217 > http://www.research.ibm.com/people/g/gustavo > http://domino.research.ibm.com/comm/research_projects.nsf/pages/ > fungen.index.html > > -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] meeting on monday
by Tom Michoel 15 Nov '07

15 Nov '07

Hi all, On Monday, Ying would give a short (and very informal!) presentation about her Master's thesis work. Then the rest of us can also give a brief description of what we are working on. Cheers, Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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