March 2008 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] lemone :: bingo class update
by Eric Bonnet 31 Mar '08

31 Mar '08

hi there, for lemone users, I made some changes in the bingo class. Now you can either write a file containing the bingo stats for each module (by calling the GOwrite function) or annotate each module object by calling the GOmodule function. See the javadoc comments and/or ask me for further details.. Eric

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[Beg-sysbiol] BAD NEWS for PhD students: Electroshock helps learning better/faster
by Greg Amoutzias 28 Mar '08

28 Mar '08

From the article: "If the brain has to remember some detail in order to avoid a bad outcome, it will do it pretty quickly." http://news.bbc.co.uk/2/hi/health/7318673.stm --- Greg Amoutzias, Ph.D VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3758 Fax: +32 (0)9 331 3809 email: gramo(a)psb.ugent.be

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[Beg-sysbiol] $1000 DNA test can tell you whether you can metabolise coffee well.
by Greg Amoutzias 26 Mar '08

26 Mar '08

http://news.bbc.co.uk/2/hi/business/7303014.stm --- Greg Amoutzias, Ph.D VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3758 Fax: +32 (0)9 331 3809 email: gramo(a)psb.ugent.be

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[Beg-sysbiol] for those stressful days...
by Greg Amoutzias 25 Mar '08

25 Mar '08

http://www.flash-game.net/game/1174/pc-breaker.html --- Greg Amoutzias, Ph.D VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3758 Fax: +32 (0)9 331 3809 email: gramo(a)psb.ugent.be

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[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/>

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[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 ==================================================================

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[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

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[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

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[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/ ==================================================================

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[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.

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