January 2013 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] next-gen ontology
by Bram Slabbinck 30 Jan '13

30 Jan '13

fyi http://www.nature.com/nmeth/journal/v10/n2/full/nmeth.2353.html An approach to cluster and organize systems biology data yields NeXO, a data-driven ontology. Where biology was small before, it now is frequently large. Data points have become data sets. Research studies now commonly examine not just one gene or protein but all of them. It has become a truism to say that this situation produces formidable challenges when it comes to analysis of the resulting vast data sets. The Gene Ontology (GO) has proven to be a widely used resource for analyzing systems biology data. Built manually from the literature by expert curators, GO attempts to synthesize available biological knowledge into an organized hierarchy of biological terms, linking genes to function. Large-scale data sets are frequently analyzed in light of GO to assess whether they capture meaningful patterns of gene function. In a recently published study, Trey Ideker and Janusz Dutkowski at the University of California, San Diego, and their colleagues, effectively turn this way of thinking on its head. They explore, in other words, whether 'omics' data sets themselves have meaningful ontological structure, akin to that of GO, and whether methods can be found to reveal it. The result is a parallel ontology to GO, which they call the network-extracted ontology, or NeXO. -- ========================================================== Bram Slabbinck, PhD Bioinformatics & Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================== Services and consulting in bioinformatics http://www.arctix.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] Fwd: [statseq] [Call for contributed talks] Gene network inference meeting, Paris, 28-29 March
by Klaas Vandepoele 25 Jan '13

25 Jan '13

fyi -------- Original Message -------- From: Thomas Schiex <Thomas.Schiex(a)toulouse.inra.fr> Sent: Fri Jan 25 15:01:52 CET 2013 To: statseq(a)listes.inra.fr Subject: [statseq] [Call for contributed talks] Gene network inference meeting, Paris, 28-29 March Dear colleagues, We would like to invite you to submit a proposal for a contributed talk to be presented in the forthcoming 'Gene Network Inference' meeting organized by the STATSEQ COST action (www.statseq.eu) in Paris, March 28-29. The meeting is presented in more details on: http://carlit.toulouse.inra.fr/wikiz/index.php/Gene_Network_Inference_Meeti… If you want to propose a talk, just send a one page PDF abstract (using a Times font in 11pt) to GNISG13-bia-org(a)toulouse.inra.fr before: the 15th of February if you want an early feedback on acceptation or before the 20th of March if you are ready to come to the meeting on short notice. Note that room being quite limited, priority will be given to early submissions. Best regards B. Mangin & T. Schiex INRA, Toulouse, France -- Klaas Vandepoele Sent from my Android phone.

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[Beg-sysbiol] cake
by Vanessa Vermeirssen 23 Jan '13

23 Jan '13

Hi all, because of my birthday last week, I will serve some self-baked (artisanal almost, because our mixer broke down ;-) ) apple cake this afternoon around 3 pm in the lounge room. Come and taste it! Vanessa -- ===================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 35 36 Fax:+32 (0)9 331 38 09 Bioinformatics and Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM room V311 vamei(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ======================================================================

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[Beg-sysbiol] MotifLab: a tools and data integration workbench
by Bram Slabbinck 23 Jan '13

23 Jan '13

FYI MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis Background Traditional methods for computational motif discovery often suffer from poor performance. In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. In recent years, genome-wide studies have generated a lot of data that has the potential to improve our ability to identify functional motifs and binding sites, such as information about chromatin accessibility and epigenetic states in different cell types. However, it is not always trivial to make use of this data in combination with existing motif discovery tools, especially for researchers who are not skilled in bioinformatics programming. Results Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab supports comprehensive motif discovery and analysis by allowing users to integrate several popular motif discovery tools as well as different kinds of additional information, including phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, transcription factor interactions and gene expression. MotifLab offers several data-processing operations that can be used to create, manipulate and analyse data objects, and complete analysis workflows can be constructed and automatically executed within MotifLab, including graphical presentation of the results. Conclusions We have developed MotifLab as a flexible workbench for motif analysis in a genomic context. The flexibility and effectiveness of this workbench has been demonstrated on selected test cases, in particular two previously published benchmark data sets for single motifs and modules, and a realistic example of genes responding to treatment with forskolin. MotifLab is freely available at http://www.motiflab.org. http://www.biomedcentral.com/1471-2105/14/9/abstract -- ========================================================== Bram Slabbinck, PhD Bioinformatics & Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================== Services and consulting in bioinformatics http://www.arctix.be ========================================================== Please consider the environment before printing this email

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