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

[Beg-sysbiol] Trends in Plant Science: Plant systems biology comes of age
by Tom Michoel 25 Mar '08

25 Mar '08

http://dx.doi.org/10.1016/j.tplants.2008.02.003 -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0

[Beg-sysbiol] mailing list
by Stefanie De Bodt 25 Mar '08

25 Mar '08

Hallo Kenny, Kan ik toegevoegd worden aan de sysbiol mailing list? Thanks! Stefanie -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://bioinformatics.psb.ugent.be ==================================================================

1 0

[Beg-sysbiol] Aviv's suggestion to further improve LeMoNe
by Nathalie Pochet 25 Mar '08

25 Mar '08

Hi LeMoNe-people, As you know, I talked with Aviv about the Arabidopsis project I'm working on. I also explained the (latest) version of the LeMoNe algorithm that I'm using - running Gibbs sampling several times to find different gene and experiment clustering results, creating tight clusters from these results, and then learn regulatory programs for these tight clusters. Aviv really liked this approach a lot, especially since it intends to tackle the weak points of the Geronemo approach such as creating robust clusters (allowing genes to be filtered out) and improving computational efficiency. She suggested that this LeMoNe approach might further be improved by running the full original LeNoNe version (iterative optimization of both learning the regulatory programs for each module and gene reassignment to the regulatory program that best explains the particular gene's expression behaviour) on the tight clusters, so not just learning the regulatory programs on the tight clusters, but also allowing genes to be reassigned to their best regulatory program, and then to optimize both iteratively. This adaptation will likely decrease LeMoNe's computational efficiency but might lead to better results. I tought this suggestion might be of interest to all LeMoNe people? See you tomorrow! Kind regards, Nathalie

1 0

[Beg-sysbiol] Fwd: Think twice before drinking another beer ...
by Greg Amoutzias 19 Mar '08

19 Mar '08

I don't know what to think about this article... belgians won't like it for sure!!! > > > http://www.nytimes.com/2008/03/18/science/18beer.html?_r=1&oref=slogin

3 2

[Beg-sysbiol] Learning and Inference in Computational Systems Biology
by Yvan Saeys 17 Mar '08

17 Mar '08

http://www.dcs.gla.ac.uk/masamb/licsb/index.htm Is anyone planning to attend this workshop ? -- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys@ugent.be http://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ==================================================================

1 0

[Beg-sysbiol] Arabidopsis microarray data
by Stefanie De Bodt 16 Mar '08

16 Mar '08

Dear, We would like to update our local compendium of publicly available microarray data for Arabidopsis. As this takes some effort and it results in a huge amount of data, we would like to centralize the data and provide the necessary annotation (replicates, treatment vs control, type of experiment, etc.) so that anyone working with Arabidopsis microarray data can consult up-to-date information. To organize this, we propose to have a meeting to discuss which experiments to include and the procedure to download and annotate data in an efficient and standardized manner. This meeting would take place on Tuesday, 18th of March or Thursday, 20th of March (afternoon). Please let me know if you are willing to participate and if one of these dates is ok for you. Thanks a lot in advance! Stefanie & Steven M.

2 2

[Beg-sysbiol] [Fwd: Seminar Konstantin Doubrovinski 13/03]
by Roeland Merks 11 Mar '08

11 Mar '08

Hi Systems Biologists, This Thursday Konstantin Doubrovinksi will give a seminar on modeling cytoskeletal pattern formation. Hopefully he will come to Ghent and do his postdoc here on modeling protein translocation, much along the lines of this paper: Stochastic model for Soj relocation dynamics in Bacillus subtilis, www.pnas.org/cgi/reprint/102/28/9808.pdf?ck=nck (see attachment). I think Konstantin's work can be very interesting for you, so apart from encouraging you to go to his lecture, I would like to ask you if you be interested in discussing with him on Thursday afternoon. If so, please contact Nathalie and she will put you in the program. Cheers, Roeland -------- Originele bericht -------- Onderwerp: Seminar Konstantin Doubrovinski 13/03 Datum: Fri, 7 Mar 2008 17:17:05 +0100 Van: Nathalie Vanden Hautte <nahau(a)psb.UGent.be> Aan: <research(a)psb.ugent.be> *REMINDER* Dear all, Please find enclosed the announcement of our next talk. If you would like to meet Konstantin Doubrovinski, please let me know ASAP. Best regards, Nathalie ========================================= Nathalie Vanden Hautte Administrative Assistant VIB Department of Plant Systems Biology, UGent Technologiepark 927 9052 Gent Belgium Tel: +32 (9) 33 13 800 Fax: +32 (9) 33 13 809 Http://www.psb.ugent.be -- ================================================================== Roeland Merks Group Leader "Plant Systems Modeling" Tel:32 (0)9 3313823 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 ==================================================================

1 0

[Beg-sysbiol] Integrating scientific cultures
by Yves Van de Peer 09 Mar '08

09 Mar '08

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17… -- 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/

1 0

[Beg-sysbiol] [Fwd: REGISTER TODAY! 6th International Conference on Pathways, Networks, and Systems]
by Eric Bonnet 05 Mar '08

05 Mar '08

1 0

[Beg-sysbiol] [Fwd: DREAM News: e-briefing, BCL6 gold standard]
by Tom Michoel 04 Mar '08

04 Mar '08

-------- Original Message -------- Subject: DREAM News: e-briefing, BCL6 gold standard Date: Mon, 3 Mar 2008 17:23:22 -0500 From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> To: DREAM2 Call For Participation <DREAM2_Call_For_Participation%IBMUS(a)us.ibm.com> PLEASE LET ME KNOW IF YOU WANT TO BE REMOVED FROM THIS MAILING LIST. SINCERE APOLOGIES IF YOU RECEIVE THIS ANNOUNCEMENT MORE THAN ONCE. *DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS** * * DREAM NEWS* *DREAM2 e-Briefing * If you are interested in exploring the contents of the recent DREAM2 conference, including invited speakers talks (with audio) and slides, please visit the New York Academy of Sciences e-briefing site: <http://www.nyas.org/dream2007> _http://www.nyas.org/dream2007_ This write-up really captures the interesting discussions and salient items in the past DREAM2 conference. *BCL6 gold-standards* Of all the challenges for the past DREAM2 conference, only the gold standard for the BCL6 targets are not yet public. (The reason is that the data owners have not yet published their corresponding paper.) However, you can make predictions against that gold standard and find out your performance using the following web site. _http://wiki.c2b2.columbia.edu/dream/data/upload/roc/_ Note that you have to registrer in order to get access to this web-tool. Also, only 5 predictions are allowed per team, so that the gold standard is not reverse engineered by successive predictions of the whole data set. *Web tool to test predictions of DREAM2 challenges 2, 3, 4 and 5* Alberto de la Fuente (from the CRS4 Bioinformatics lab) has kindly provided a nice web-tool to test predictions for challenges 2, 3, 4 and 5. Please go to _http://www.bioinformatica.crs4.org/dream-eval/_ to use Alberto's group prediction tool. *DREAM discussion forum* Please use the DREAM discussion forum http://wiki.c2b2.columbia.edu/dream/discuss/ to share your ideas on Reverse Engineering. Also, if you want to help curate the DREAM project web site, send me your coordintes so that we give you access. Gustavo Stolovitzky IBM Research DREAM Organizer 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.inde… -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0