March 2010 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] Revealing strengths and weaknesses of methods for ... [Proc Natl Acad Sci U S A. 2010] - PubMed result
by Yves Van de Peer 29 Mar '10

29 Mar '10

http://www.ncbi.nlm.nih.gov/pubmed/20308593?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and Systems Biology 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] (no subject)
by Eric Bonnet 26 Mar '10

26 Mar '10

hi there, I have a flexware (SBO project) meeting this morning, will be in the lab this afternoon. cu later, e.

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[Beg-sysbiol] FW: Next SAM Meeting and Bioinf challenge
by Klaas Vandepoele 25 Mar '10

25 Mar '10

Dear, who from sysbiol can join us in the week of April 19th to help? Preferably someone who has access to the Lemone/Enigma plant modules. thanks, Stefanie Dirk Klaas *Bioinformatics challenge: Background info:* We all face the situation, that we have a gene sequence in our hand and don´t know the function. Usually we have limited time (max a few hours) to find data and to decide on whether the gene is of interest for us or not. We also have a limited understanding how good or bad we are in comparison to others, since a pure *quantitative* comparison of softwares and hardwares would only lead to limited results. In order to compare our capabilities in a more* qualitative* way we agreed to do a joint test case by cross comparing our capabilities to find functions for a give gene (sequence). * The principle is a follows:* Each of the 4 entities (Dirk, Lothar, Xing Wang, Jürgen) will provide one gene sequence (out of yield area, where the respective entity is a specialist) to all other entities with request to come up with suggestions about the function(s) - time to deliver : one day (24hours). The entities are challenged to find out everything they can about that particular gene and a potential gene product. The respective gene providing entity will compare the findings -- what findings were similar, different, new, and why and will report to the others. The results corresponding to the provided gene belong to the entity that provided the gene sequence. * Detailed workflow:* Each entity provides - a s_equence file_ (nucleotides/protein)*/ in a wild type form, with start and stop codon/* / *- the organism of origin */ - the _contact emai_l to Jürgen Logemann prior to the start time. At 9:00 hrs german time Jürgen Logemann will distribute the 4 sequence files to all contact emails with a cc to the SAM members. Each entity will work on the 3 sequences with */approx. 2 FTEs./* 24 hrs later, at 9:00 hrs german time the feedback of each entity has to be in the e-mail of Jürgen Logemann. The feedback should be in a digestable form, so that a person, being not an expert understands the message (sequence, function, structure etc.) Jürgen Logemann will distribute the feedback to all entities, the respective gene providing entity will check and compare/rank the content related to its gene At the next SAM meeting all entities discuss the results by phone. * Open points:* - Metalife might join as a 5th entity (Jürgen L to check) - We will need a short contract being signed before starting day, describing who owns what (Jürgen L and all) *options: everybody owns his own results - everybody owns all results on his sequences* - What happens to the ownership of results, if one entity provides a gene sequence, where the other entity is also working on ? (all) - The final day for the challenge and for the results discussion needs to be agreed - week of April 19th ? (all) *- What about negative controls? What about also adding three random nucleotide sequences ( containing ORF´s obviously) (all)* *- Do we need to define what description / annotation level we want to reach (all)* *Juergen Logemann* Vice President Technology Management Phone: +49 621 60-27204, Mobile: +49 172 7470513, Fax: +49 621 60-28685, E-Mail: juergen.logemann(a)basf.com Postal Address: BASF Plant Science Company GmbH, BPS_TECM - LI439, 67117 Limburgerhof, Germany *BASF - The Chemical Company* BASF Plant Science Company GmbH Legal Headquarter 67056 Ludwigshafen, Germany Registration Office: Amtsgericht Ludwigshafen Eintragungsnummer HRB 4516Lu Executive Management: Peter Eckes, Jürgen Schweden, Marc Ehrhardt -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on out and change the world (around us)

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[Beg-sysbiol] working@home this morning
by Steven Maere 24 Mar '10

24 Mar '10

================================================================== Steven Maere, PhD Group leader, Evolutionary Systems Biology group Dept. of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3805 fax: +32 9 331 3809 email: stmae(a)psb.vib-ugent.be http://www.psb.ugent.be/esb/ ==================================================================

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Re: [Beg-sysbiol] marcotte paper
by Yves Van De Peer 24 Mar '10

24 Mar '10

Thanks. Steven, appreciate it! Yves ----- Original Message ----- From: beg-sysbiol-bounces(a)psb.vib-ugent.be <beg-sysbiol-bounces(a)psb.vib-ugent.be> To: beg-sysbiol(a)psb.vib-ugent.be <beg-sysbiol(a)psb.vib-ugent.be> Sent: Tue Mar 23 23:30:17 2010 Subject: Re: [Beg-sysbiol] marcotte paper I'll gladly squeeze out a few lines, love this paper... S On Mar 23, 2010, at 8:10 PM, Yves Van de Peer wrote: > > Could someone write a few lines about this, so I can recommend it for > Faculty of 1000 (they are on my back for a next review, but I'm so > terribly busy ...). Thanks in advance, > > Yves > > -- > Yves Van de Peer, PhD. > > Professor in Bioinformatics and Genome Biology > Associate Department Director, VIB Department of Plant Systems Biology > Group Leader Bioinformatics and Systems Biology > 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.vib-ugent.be > > http://bioinformatics.psb.ugent.be/ > > _______________________________________________ > Beg-sysbiol mailing list > Beg-sysbiol(a)psb.ugent.be > https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol ================================================================== Steven Maere, PhD Group leader, Evolutionary Systems Biology group Dept. of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3805 fax: +32 9 331 3809 email: stmae(a)psb.vib-ugent.be http://www.psb.ugent.be/esb/ ================================================================== _______________________________________________ Beg-sysbiol mailing list Beg-sysbiol(a)psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol

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[Beg-sysbiol] marcotte paper
by Steven Maere 23 Mar '10

23 Mar '10

This is probably what Marcotte presented at the RECOMB satellite conf in Boston last year, right ? ================================================================== Steven Maere, PhD Group leader, Evolutionary Systems Biology group Dept. of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3805 fax: +32 9 331 3809 email: stmae(a)psb.vib-ugent.be http://www.psb.ugent.be/esb/ ==================================================================

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[Beg-sysbiol] (no subject)
by Yves Van de Peer 23 Mar '10

23 Mar '10

'Phenologs reveal functionally coherent, evolutionarily conserved gene networks—many predating the plant-animal divergence' This is really cool. Vanessa, there must be conserved networks between worms, flies, humans as well ... Let's try to find them ;-) Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and Systems Biology 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] [Fwd: Systems Biology and New Sequencing Technologies (SBNST 2010), 16-18 June 2010, Barcelona]
by Tom Michoel 23 Mar '10

23 Mar '10

-------- Original Message -------- Subject: Systems Biology and New Sequencing Technologies (SBNST 2010), 16-18 June 2010, Barcelona Date: Tue, 23 Mar 2010 15:29:12 +0100 From: Blanka Wysocka <blanka.wysocka(a)crg.es> To: Blanka Wysocka <blanka.wysocka(a)crg.es> Dear friend/colleague, I would like to draw your attention to the conference on "Systems Biology and New Sequencing Technologies" (SBNST 2010), 16-18 June 2010, Barcelona (Spain). It is organized by Gustavo Stolovitzky (IBM Research, USA), Raul Rabadan (Columbia University, USA), Pascal Kahlem (European Bioinformatics Institute, UK), Roderic Guigó (CRG, Barcelona, Spain) and Luis Serrano (CRG, Barcelona, Spain). We will focus on the parallel advances in two relatively disconnected areas of science that are boosting our understanding of biological systems. On the one hand, systems biology, with its integration of high-throughput biological data and its emphasis on quantitative modeling and simulation, is providing a global perspective of biology that goes beyond classical reductionist approaches. On the other hand, new sequencing technologies are developing at an enormous speed, and provide whole genome data that revealed previously unexplored genomic features such as functional intergenic regions, copy number variations and other genomic differences between members of the same species. In this meeting, we will gather an inter-disciplinary group of scientists with roots in these two disciplines with the aim to create a forum to discuss new ideas and explore what lies in overlap between these two growing fields. You can find more information on the web page of the Symposium (www.enfin.org/sbnst) and in the poster enclosed. Participants should register here: www.regonline.com/sbnst2010 Please, feel free to forward this message to any person who might be interested in this meeting. Best regards, /Gustavo Stolovitzky (IBM Research, USA) / /Raul Rabadan (Columbia University, USA)/ /Pascal Kahlem (European Bioinformatics Institute, UK)/ /Roderic Guigó (CRG, Barcelona, Spain) / /Luis Serrano (CRG, Barcelona, Spain)/ */Blanka Wysocka/** */Systems Biology/// */ /* */CRG -/**/ /**/Centre de Regulació Genòmica/** *Dr. Aiguader 88 08003 Barcelona Ph: +34933160145 Fax: +34933969983 blanka.wysocka(a)crg.es <mailto:blanka.wysocka@crg.es> www.crg.es/systems_biology <http://www.crg.es/systems_biology> www.crg.es <http://www.crg.es/> -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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Re: [Beg-sysbiol] Fwd: VIB Quiz 2010
by Yves Van De Peer 10 Mar '10

10 Mar '10

Me too! ----- Original Message ----- From: beg-sysbiol-bounces(a)psb.vib-ugent.be <beg-sysbiol-bounces(a)psb.vib-ugent.be> To: beg-sysbiol(a)psb.vib-ugent.be <beg-sysbiol(a)psb.vib-ugent.be> Sent: Wed Mar 10 14:58:45 2010 Subject: Re: [Beg-sysbiol] Fwd: VIB Quiz 2010 yes, why not... although I am very bad at this, but it should be fun! Steven Maere wrote: > Anybody interested to form a sysbiol team ? > > Begin forwarded message: > >> *From: *VIB Quiz <vibquiz(a)psb.vib-ugent.be >> <mailto:vibquiz@psb.vib-ugent.be>> >> *Date: *March 10, 2010 1:37:54 PM GMT+01:00 >> *To: *all(a)psb.ugent.be <mailto:all@psb.ugent.be>, >> chantal.bogaert(a)dmbr.vib-ugent.be >> <mailto:chantal.bogaert@dmbr.vib-ugent.be> >> *Subject: **VIB Quiz 2010* >> *Reply-To: *vibquiz(a)psb.vib-ugent.be <mailto:vibquiz@psb.vib-ugent.be> >> >> Dear All, >> >> >> >> After the great success of last year, we organize this year another >> VIB quiz. The quiz takes place on Wednesday evening May 12 in the >> Melac, Dorpsstraat 14 in Zwijnaarde (Walking distance from the FSVM >> building) Please register your team (Max 5 people) by mailing to >> vibquiz(a)psb.vib-ugent.be <mailto:vibquiz@psb.vib-ugent.be> with your >> team name and team members. A registration fee of 1 euro per person >> can be paid to Chantal Bogaert (DMBR), Robin Vanden Bossche (E015 >> Lab Alain) or Hendrik Labeeuw (V113 IT Support) >> >> Places are limited, so register asap. >> >> >> >> Kind regards, >> >> >> >> The Quiz Team >> > > ================================================================== > Steven Maere, PhD > > Group leader, Evolutionary Systems Biology group > Dept. of Plant Systems Biology > VIB / Ghent University > Technologiepark 927 > B-9052 Gent BELGIUM > tel: +32 9 331 3805 > fax: +32 9 331 3809 > email: stmae(a)psb.vib-ugent.be <mailto:stmae@psb.vib-ugent.be> > http://www.psb.ugent.be/esb/ > ================================================================== > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Beg-sysbiol mailing list > Beg-sysbiol(a)psb.ugent.be > https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol > -- ===================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 38 10 Fax:+32 (0)9 3313809 Bioinformatics and Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM vamei(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ====================================================================== _______________________________________________ Beg-sysbiol mailing list Beg-sysbiol(a)psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol

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[Beg-sysbiol] Fwd: VIB Quiz 2010
by Steven Maere 10 Mar '10

10 Mar '10

Anybody interested to form a sysbiol team ? Begin forwarded message: > From: VIB Quiz <vibquiz(a)psb.vib-ugent.be> > Date: March 10, 2010 1:37:54 PM GMT+01:00 > To: all(a)psb.ugent.be, chantal.bogaert(a)dmbr.vib-ugent.be > Subject: VIB Quiz 2010 > Reply-To: vibquiz(a)psb.vib-ugent.be > > Dear All, > > After the great success of last year, we organize this year another VIB quiz. The quiz takes place on Wednesday evening May 12 in the Melac, Dorpsstraat 14 in Zwijnaarde (Walking distance from the FSVM building) Please register your team (Max 5 people) by mailing to vibquiz(a)psb.vib-ugent.be with your team name and team members. A registration fee of 1 euro per person can be paid to Chantal Bogaert (DMBR), Robin Vanden Bossche (E015 Lab Alain) or Hendrik Labeeuw (V113 IT Support) > Places are limited, so register asap. > > Kind regards, > > The Quiz Team ================================================================== Steven Maere, PhD Group leader, Evolutionary Systems Biology group Dept. of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3805 fax: +32 9 331 3809 email: stmae(a)psb.vib-ugent.be http://www.psb.ugent.be/esb/ ==================================================================

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