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

[Beg-sysbiol] tornado
by Klaas Vandepoele 23 Jun '10

23 Jun '10

Dear all, I will use tornado for approx. 24h to do some high-memory calculations. best, Klaas -- 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/ --------------------------------------------------------- PLAZA, a resource for Plant Comparative Genomics http://bioinformatics.psb.ugent.be/plaza/ ---------------------------------------------------------

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[Beg-sysbiol] svdPPCS: ... method for conserved and divergent co-expression gene module identification (Paper)
by Bram Slabbinck 22 Jun '10

22 Jun '10

fyi http://www.biomedcentral.com/1471-2105/11/338 regards Bram -- ========================================================= ir. Bram Slabbinck, PhD Bioinformatics & Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 822 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be =========================================================

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[Beg-sysbiol] Deciphering the Arabidopsis Floral Transition Proc... [Plant Physiol. 2010] - PubMed result
by Yves Van de Peer 13 Jun '10

13 Jun '10

http://www.ncbi.nlm.nih.gov/pubmed/20530214?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] [Fwd: DREAM5 Systems Biology Prediction Challenges v2]
by Tom Michoel 10 Jun '10

10 Jun '10

-------- Original Message -------- Subject: DREAM5 Systems Biology Prediction Challenges v2 Date: Wed, 9 Jun 2010 22:12:41 -0400 From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> To: gustavo(a)us.ibm.com PLEASE LET ME KNOW IF YOU PREFER NOT TO RECEIVE ANNOUNCEMENTS FROM THE DREAM PROJECT SINCERE APOLOGIES IF YOU RECEIVE THIS ANNOUNCEMENT MORE THAN ONCE *Call for Systems Biology Predictions* *DREAM5: The 5^th DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS* Dear Colleague, We would like to you to participate in the following DREAM5 challenges (the first two challenges had been announced earlier) *RELEASED EARLIER: *1. *_Epitope-Antibody Recognition (EAR) Challenge_* <http://wiki.c2b2.columbia.edu/dream/index.php/D5c1>* *- Predict the binding specificity of peptide-antibody interactions. *RELEASED EARLIER:* 2. *_TF-DNA Motif Recognition Challenge_* <http://wiki.c2b2.columbia.edu/dream/index.php/D5c2>* - *Predict the specificity of a Transcription Factor binding to a 35-mer probe. *NEW: *3. *_Systems Genetics Challenge_* <http://wiki.c2b2.columbia.edu/dream/index.php/D5c3>* -* Predict disease phenotypes and infer gene networks from Systems Genetics data *NEW:* 4. *_Network Inference Challenge_* <http://wiki.c2b2.columbia.edu/dream/index.php/D5c4>* -*Infer simulated and in vivo gene regulatory networks from gene expression data We are releasing only one half of Challenge 3. The other half will be posted in our website shortly. To access the data sets, and descriptions of the DREAM5 challenges, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/Challenges_ . The best performers in these challenges will be invited to present in the joint RECOMB Systems Biology/Regulatory Genomics/DREAM5 conference. See _http://recombsat.c2b2.columbia.edu/_ for details on this conference. To learn more about the DREAM project, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM_Project_ *DREAM5 Challenge Submission Timeline* *Late May-Early June, 2010* Call for participation in the challenges. Challenges posted. *September 20, 2010* Predictions Submission Deadline. *Nov 16-20, 2010* RECOMB Systems Biology/Regulatory Genomics/DREAM5 conference. (The DREAM5 conference track is on November 16th.) Sincerely, DREAM5 Challenge Organizers: Gustavo Stolovitzky (chair), IBM Research Robert J Prill, IBM Research Julio Saez Rodriguez, Sys Bio Dept, Harvard University DREAM5 is part of a project we call the DREAM (Dialogue for Reverse Engineering Assessments and Methods) project. Its main objective is to catalyze the interaction between experiment and theory in the area of rigorous assessment of systems biology prediction methods. ===================================== Gustavo Stolovitzky, PhD. Manager, Functional Genomics and Systems Biology IBM Computational Biology Center P.O.Box 218, Yorktown Heights, NY 10598 Office: (914) 945- -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] Paper: Gene Set-Based Module Discovery Decodes cis-Regulatory Codes Governing Diverse Gene Expression across Human Multiple Tissues
by Bram Slabbinck 10 Jun '10

10 Jun '10

FYI (pdf) http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%… regards Bram -- ========================================================= ir. Bram Slabbinck, PhD Bioinformatics & Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 822 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be =========================================================

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[Beg-sysbiol] Ordered structure of the transcription network inherited from the yeast whole-genome duplication
by Tom Michoel 09 Jun '10

09 Jun '10

<http://www.biomedcentral.com/1752-0509/4/77/abstract> -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] greetings from Yokohama ;-)
by Eric Bonnet 09 Jun '10

09 Jun '10

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[Beg-sysbiol] Fwd: EXPANDER version 5.1 released
by Steven Maere 07 Jun '10

07 Jun '10

Some inspiration for lemone/enigma functionality increase. Thomas and Bram, is 'the organization' part of the sysbiol mailing list ? S Begin forwarded message: > From: EXPANDER Development Team <click(a)POST.TAU.AC.IL> > Date: June 7, 2010 11:00:47 AM GMT+02:00 > To: TAU-CS-EXPANDER-USERS(a)LISTSERV.TAU.AC.IL > Subject: EXPANDER version 5.1 released > Reply-To: EXPANDER Development Team <click(a)POST.TAU.AC.IL> > > Dear EXPANDER user, > > We are pleased to inform our large community of users that version 5.1 of > EXPANDER is now available. > > Version highlights include: > > * Analysis wizard: perform a pre-planned sequence of analysis steps > * KEGG pathway enrichment analysis > * Use differential expression analysis (t-test or SAM) to identify gene > groups > * Rule-based grouping: identify a set of genes with patterns similar to a > user-provided pattern > * View a clustering solution “projected" on another dataset > * Support for Aspergillus Fumigatus > > The version can be downloaded from: > http://acgt.cs.tau.ac.il/expander/registration.html. > Users of previous versions of EXPANDER do not have to re-register: From > the EXPANDER menu, select Help >> Open Download Page. > > > If you wish to be removed from the mailing list, please reply this message > with the word "Remove" in the title. > > As always, your comments, questions, problem reports and suggestions are > welcome. > > Sincerely yours, > The EXPANDER development team, > Ron Shamir's Computational Genomics Group > Tel-Aviv University > http://acgt.cs.tau.ac.il/expander/ ================================================================== 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] Network evolution
by Cedric Simillion 02 Jun '10

02 Jun '10

Hi Everyone, For those of you who don't know me yet: My name is Cedric. I've done my PhD with Yves, a long time ago. After having spent 4 years abroad, I've returned to PSB. My new project will (most likely) focus on the evolution of networks. Since it seems that some of you are also interested in this topic, it's probably a good idea to sit down together and discuss on how we can collaborate. Therefore, I suggest to have a meeting on Thursday, at 14h00 with everyone interested in network evolution. I'll give a brief presentation on the things I'm interested in. Maybe the rest of you can then give a brief summary of their project(s). Could you please confirm your attendance to this meeting? Also, let me know if you really would like to attend but can't make Thursday afternoon, so we can arrange another time. Hope to see you then, Cedric P.S. Does anyone know if we have to book a meeting room? -------------------------------------------------- The point, you see, is not the answers themselves, but the mental development we enjoy through striving for those answers. Arthur C. Clarke -- The Light of Other Days

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