- BBClist - maillist.psb.ugent.be

volunteers asked to take over the maintenance of the list !
by BEN 05 Jan '10

05 Jan '10

Dear readers of the BBClist, I guess I do not have to tell you about the usefulness of the BBC mailing list, from which you receive each week a few messages. This list (first Belgian, later Benelux) has since its begin been managed by the now defunct Belgian EMBnet Node. I have untill now continued to do the management on a voluntary basis but it is not reasonable that I should keep doing this forever. Therefore we are searching a volunteer to take over the list, preferably a person or a group with a stable position in the field of bioinformatics and involved in collaborations within one or more countries of the Benelux. You can choose between two options : Either you install the list on a MailMan or MajorDomo server of you own OR The list stays on the MailMan server of the BBPF, which can without problem continue to host our list for several years to come, and you only take the responsability to do the administrative management. As manager you must do 3 things : 1. The list is currently configured in such a way that mails coming from adresses in the list are stored for moderation and mails coming from other adresses are automatically discarded. If there are mails in the queue the server sends overnight a warning to the manager. So, the first moment of the day that I check my mail I attend the moderation of the list. I have only once seen a spam, but I have several times seen the same mail send twice (and then I forward only one copy). You could of course decide to change the way you want to handle the list. 2. You must each year obtain from the organizers of the BBC the adresses of the participants and add them to the list. 3. Although the readers of the list can manage themselves their (un)subscription there are occasionally punctual interventions (add/change/remove addresses) to do for the sake of persons who have forgotten their password or otherwise need assistance, but this happens no more than about a dozen times a year. So, you see, it is really not much work. If you are interested, answer by returning mail (do not forget to present yourself and tell which of the two options you go for). Happy 2010 ! Guy Bottu ---------------------------------------------------------------------------- BEN - Belgian EMBnet Node at the Brussels Free Universities Computing Centre | Address BEN ULB CP 257 Fax +32/2/6505124 | Boulevard du Triomphe email ben(a)vub.ac.be | B-1050 Bruxelles ----------------------------------------------------------------------------

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Workshop on Advances in Bio Text Mining : Preliminary Call for Abstracts
by Sofie Van Landeghem 22 Dec '09

22 Dec '09

------- Apologies for multiple postings ------- =================== Preliminary Call for Abstracts =================== Workshop BioTM-2010 Advances in Bio Text Mining May 10-11, 2010, Ghent, Belgium http://www.clips.ua.ac.be/BioTM2010/index.html ==================== Abstracts are invited for the two-day workshop to be held in Ghent on the 10th and 11th of July 2010. Text mining has become indispensible in many biological and biomedical sciences. Having to keep up with an increasing number of publications, text mining techniques enable retrieval and analysis of large amounts of documents in a fully automated fashion. They allow for extraction of facts described in the literature that have not yet been recorded in databases, thus providing a necessary tool to obtain a complete overview of all available knowledge. Recently, the application of text mining and natural language processing techniques to the biological and medical sciences has recieved increasing interest. In addition to many new workshops and conferences arising in this domain, recently also a number of community-wide tasks were conducted to benchmark text mining techniques on specific challenges (e.g. BioCreative, BioNLP Shared Task, ...). By discussing the latest developments and potentially new applications in text mining amongst scientists in both academia and industry, this workshop aims to provide a broad view on text mining tools in biology and biomedicine. We are reaching out to a broad public, including researchers with an interest in text mining but with little or no experience in this domain. To this end, the workshop will start with an extensive tutorial on text mining in the bio-sciences, providing sufficient background knowledge for novices. Next, a number of keynote talks will be given by leading scientists, presenting the latest advances in the field. Furthermore, participants are highly encouraged to submit an abstract describing their own work. They will be given the opportunity to present this work in 5min flash presentations, as well as to present a poster during the coffee and lunch breaks. Finally, we plan on having a round-table discussion about the broader applicability of text-mining tools in the biological sciences, trying to bridge the gap between theoretical algorithms and experimental work. SCOPE Submissions should present work related to any aspect of biomedical text mining and bioinformatics. Additionally, we strongly encourage submissions that describe shortcomings of current existing techniques, tools, or resources, in order to detect problematic issues and work towards their improvement. SUBMISSIONS Participants are encouraged to submit a poster to the workshop in order to present their work to the audience. Posters will be first introduced in a five minute bullet talk and then they will be presented in a poster session. Submitted posters will be reviewed by the organising committee. Submission is blind. An abstract of the poster of maximum 500 words should be submitted to the following e-mail address in pdf format: biotm2010 at gmail dot com . IMPORTANT DATES 1 April 2010 Submission deadline 15 April 2010 Notification of acceptance 10-11 May 2010 Workshop in Ghent ORGANISATION / PROGRAM COMMITTEE Yvan Saeys Sofie Van Landeghem Bioinformatics and Evolutionary Genomics group VIB Department of Plant Systems Biology Ghent University Belgium Walter Daelemans Roser Morante Vincent Van Asch CLiPS - Text Mining Group Faculty of Arts University of Antwerp Belgium -- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be

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proteases and protease inhibitors
by Lambeir Anne-Marie 18 Dec '09

18 Dec '09

On Friday, February 5th, 2010 Prof W. Bode (Max Planck Institute , Martinsried, Germany) will present the FEBS lecture entitled : "Proteases and Protease Inhibitors: a Crystallographer's perspective" during the 202nd meeting of the Belgian Society of Biochemistry and Molecular Biology. This meeting which is devoted to the subject "proteases and protease inhibitors" will take place near Antwerp on the Campus Drie Eiken (Wilrijk) and is organized by Prof. Anne-Marie Lambeir. The meeting is now open for registration via the BMB website: http://www.icp.ucl.ac.be/bsbmb/202nd/202nd.html <http://www.icp.ucl.ac.be/bsbmb/202nd/202nd.html> Please note that the deadline for abstracts is 23 December. Prof. Anne-Marie Lambeir Laboratory of Medical Biochemistry University of Antwerp - Campus Drie Eiken Universiteitsplein 1 blg S room S.515 B-2610 Wilrijk, Belgium ph +32-3-2652549 email anne-marie.lambeir(a)ua.ac.be

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CFP Statistical Methods for Post-Genomic Data workshop
by Yvan Saeys 17 Dec '09

17 Dec '09

CFP Statistical Methods for Post-Genomic Data workshop ------------------------------------------------------ SMPGD10, 14-15/1/10, Marseille, Luminy The 2010 edition of Statistical Methods for Post-Genomic Data workshop, SMPGD10, http://iml.univ-mrs.fr/sta/SMPGD2010/welcome.html will be held the 14th and 15th of January in Luminy, Marseille. This edition will welcome three invited speakers, three invited sessions and one contributed session. Among others, the following topics will be discussed: Epigenetics (ChIP) Networks Analysis Comparative Genomics Feature Selection and Statistical Learning Contribution session: This session will include few presentations. All statistical aspects of genomic and post-genomic data analysis are welcome. Submission may yet be posted on the workshop website. Final decisions will be published soon. The complete program and further practical information will be available on the workshop website. -- ================================================================== 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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The BBC mailing list
by BEN 17 Dec '09

17 Dec '09

Dear friends, Some of you will have received a wellcome message for the BBC mailing list. This is because each year we add the E-mail addresses of the attendants of the Benelux Bioinformatics Conference. The BBC list is hosted on the Mailman server of the Belgian Biodiversity Facility (http://www.biodiversity.be) and is moderated by the former staff of the Belgian EMBnet Node (http://www.be.embnet.org) You can send a mail to this this list (BBClist(a)biodiversity.be) if you want to announce a public lecture or a job opening, if you have a question or if you want to start a discussion about bioinformatics in the Benelux. Note that only members of the list are allowed to post and that, because of the moderation, the messages are delivered with some delay (usually te next day in the morning). You can unsubscribe or customize the way you receive messages at http://mailman.biodiversity.be/mailman/listinfo/bbclist (do use the password mentioned in the wellcome message). On the same site you can consult archived messages and interested friends of yours can subscribe. In case of problems you can send an Email to the moderator at ben(a)vub.ac.be. Enjoy biocomputing, Guy Bottu, ---------------------------------------------------------------------------- Belgian EMBnet Node at the Brussels Free Universities Computing Centre | Address BEN ULB CP 257 Fax +32/2/6505124 | Boulevard du Triomphe email ben(a)vub.ac.be | B-1050 Bruxelles ----------------------------------------------------------------------------

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Fwd: EMBO Practical Course on Computational Molecular Evolution
by Wouter Van Gool 09 Dec '09

09 Dec '09

Computational Molecular Evolution 3-12 May 2010 Iraklio (Heraklion), Crete http://cwp.embo.org/pc10-25/ Deadline for applications: 31 January 2010 Course summary This EMBO Practical Course aims to provide researchers with the theoretical knowledge and practical skills required to carry out molecular evolutionary analysis on their own data and on data drawn from sequence databases. The course will combine basic assumptions and ideas fundamental to the field with discussion of cutting-edge methodologies, and is therefore relevant to researchers with a range of different experience levels. This course is essentially the same as that which ran successfully as a Wellcome Trust Advanced Course at the European Bioinformatics Institute, Hinxton, UK, in Spring 2009. Programme * interpretation of molecular phylogenetic trees and sequence alignments * genomics resources and sequence alignments * phylogeny reconstruction models * hypothesis testing in phylogenetics * coalescent model and inference from population data Course organisers * Nick Goldman (European Bioinformatics Institute, Hinxton, UK) * Ziheng Yang (University College London) * Aidan Budd (European Molecular Biology Laboratory, Heidelberg) * Alexandros Stamatakis (Technical University of Munich) * Giorgos Kotoulas (Institute of Marine Biology and Genetics, Hellenic Center for Marine Research, Heraklion) Guest instructors * Michail Averof (Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion) * Martin Embley (University of Newcastle) * Olivier Gascuel (LIRMM, Montpellier) * Javier Herrero (European Bioinformatics Institute, Hinxton, UK) * John Huelsenbeck (University of California, Berkeley) * Carolin Kosiol (Veterinary Medical University, Vienna) * Aoife McLysaght (Trinity College Dublin) * Rasmus Nielsen (University of California, Berkeley) * Bill Pearson (University of Virginia) * Antonis Rokas (Vanderbilt University) * Mikkel Schierup (Aahrus University, Denmark) * Jeff Thorne (North Carolina State University) * Ken Wolfe (Trinity College Dublin) For full details, see http://cwp.embo.org/pc10-25/ or http://tinyurl.com/cme2010 ----------------------------------------------------------------------- Nick Goldman tel: +44-(0)1223-492530 EMBL - European Bioinformatics Institute fax: +44-(0)1223-494468 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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Fwd: Inserm workshop: Interactomics, spring 2010
by Jacques van Helden 07 Dec '09

07 Dec '09

Begin forwarded message: Chers collègues, Vous trouverez ci-dessous l'annonce de notre atelier INSERM. N'hesitez pas à la diffuser autour de vous! Merci encore pour votre participation à l'atelier. Cordialement, Christine Brun - Jérôme Reboul - Nicolas Thierry-Mieg ------------------------------------------------------ Atelier de Formation Inserm 203 Interactomique: à l'intersection de la biologie et la bioinfomatique / Interactomics: at the crossroads of biology and bioinformatics Registration dealine: January 29, 2010 Info and registration forms: http://www.rh.inserm.fr/INSERM/IntraRH/RHPublication.nsf/mDisplayMotsClefsW… Phase I • Critical assessment March 30- April 1, 2010 • Saint-Raphaël • France Aims: Proteins rarely act alone: they often interact with other macromolecules in order to accomplish their functions. Protein-protein interactions are therefore critical to most biological processes. Systematic approaches for identifying them have been developped over the years, such as yeast two-hybrid or affinity purification-mass spectrometry. These methods have enabled the mapping of complex interaction networks in various model organisms, which are profoundly modifying our understanding of cellular mechanisms by providing us with an integrated view of biological processes. However, due to their complexity, such networks can be intimidating and difficult to take advantage of by hypothesis-driven experimental biologists. The main difficulties are typically methodological and technical (for example knowledge and application of bioinformatics tools), but also and more fundamentally they stem from the changes in reasoning required by the systems biology approach. Protein-protein interaction networks being a very rich but neglected source of information, the workshop will present the main strengths and challenges in producing and using this data. Indeed, a better understanding of the processes, questions and solutions proposed by labs that produce and analyze interactomics data should facilitate its general use. Audience: Researchers, physicians, post-docs, technicians, engineers and students interested in the interactome approach and the analysis of existing protein-protein interaction data, in order to benefit to their own research projects. The topics addressed will include 1) identifying protein-protein interactions: high-throughput methods, validation of results, quality assessment; 2) protein-protein interaction databases: contents, standards, direct submissions; 3) topological and functional analysis of protein-protein interaction networks: methods and tools; 4) application to biological questions: candidate genes, signaling, host-pathogen interactions, development, evolution. Confirmed speakers: Javier De Las Rivas (Salamanca, Spain), Etienne Formstecher (Paris, France), Anne-Claude Gavin (Heidelberg, Germany), Kristin Gunsalus (New York, USA), Henning Hermjakob (Hinxton, UK), Carl Herrmann (Marseille, France), Vincent Lotteau (Lyon, France), Fabio Piano (New York, USA), Evelyne Goillot (Lyon, France), Jolanta Polanowska (Marseille, France), Sylvie Ricard-Blum (Lyon, France), Benno Schwikowski (Paris, France), Jacques van Helden (Bruxelles, Belgium), Marc Vidal (Boston, USA). Phase II • Technical workshop May 2010 • Marseille Program: Participants will learn to use existing tools for extracting functional information from publicly available molecular interaction data. The course is aimed at two subgroups of participants, depending on their computer skills. The goal is to enable the participants to study their own results in the light of previously known biomolecular interactions. 15 participants will be selected among the phase I participants. Organizers: Christine Brun (TAGC, Marseille), Jérôme Reboul (CRCM, Marseille), Nicolas Thierry-Mieg (TIMC-IMAG, Grenoble)

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CfP: Special issue of Trans Comp Sys Biol on "Computational models for cell processes"
by Ion Petre 04 Dec '09

04 Dec '09

Call for papers: Transactions on Computational Systems Biology, special issue on Computational models for cell processes. Submission deadline: March 31, 2010 http://combio.abo.fi/special_issue_10.php Guest editors: - Ralph Johan Back (Åbo Akademi University, Finland) - Ion Petre (Åbo Akademi University, Finland) - Corrado Priami (Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Italy) - Erik de Vink (Eindhoven University of Technology, the Netherlands) LNBI Transactions on Computational Systems Biology calls for paper submissions for a special issue on Computational Models for Cell Processes. Original papers and surveys are sought in all areas that relate to the relevance and potential of formal methods and computational modeling and simulation in systems biology. Of special interest are contributions that present biological processes requiring special tools and techniques that have not been investigated so far in the context of formal methods, as well as extensions of already existing formalisms introduced to improve their applicability in the life sciences. Topics of interest include, but are not limited to: Formal models for cellular pathways Qualitative biological modeling Quantitative formal methods Theoretical comparison of formalisms for biological processes Biologically-inspired extensions to formal methods and concurrency theory Differential, discrete and/or stochastic modeling languages Reconstruction of biological networks based on empirical data Decomposition and modularization of large biological networks Applications of formal methods and computational modeling Membrane systems as a modeling platform The list of topics is suggestive rather than exhaustive. We are open to a wide range of approaches from theoretical methodological papers to case studies. Papers should be submitted to ipetre(a)abo.fi in the LNCS format (see link below). Manuscripts submitted to this special issue should have at most 25 pages, including figures, tables, and the list of references. For queries about this special issue, please feel free to contact the special issue guest editors, Ralph-Johan Back (backrj(a)abo.fi) Ion Petre (ipetre(a)abo.fi) Corrado Priami (priami(a)cosbi.eu) and Erik de Vink(evink(a)win.tue.nl). Important dates: - Paper submissions: March 31, 2010 - Acceptance notification: June 30, 2010 - Final papers: August 31, 2010 Submission guidelines: - http://www.springer.com/computer/lncs - http://www.springer.com/computer/lncs?SGWID=0-164-7-72376-0

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PhD Fellowships in Computational Biology and Scientific Computing
by Leonor Palmeira 03 Dec '09

03 Dec '09

>> from Hannes Luz @ Max Planck, Berlin: Dear colleague, the International Max Planck Research School for Computational Biology and Scientific Computing, a joint graduate program of the Freie Universitaet Berlin and the Max Planck Institute for Molecular Genetics, Berlin, invites applications for a PhD program. The PhD program is open for international students holding a Master (or equivalent) degree in bioinformatics, computer science, physics, mathematics, or biology. The closing date for applications is February 21, 2010. We would be grateful if you could communicate the announcement to interested students. A poster can be downloaded from http://www.imprs-cbsc.mpg.de/download/poster2010.pdf For further details and the application procedure, please visit http://www.imprs-cbsc.mpg.de Thanks for your efforts, the IMPRS-CBSC team ----------------------------------------------------------------------- International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC) Contact: Hannes Luz Max Planck Institute for Molecular Genetics | Tel: +49 30 8413-1154 Computational Molecular Biology | Fax: +49 30 8413-1152 Ihnestrasse 73 | Email:luz@molgen.mpg.de D-14195 Berlin, Germany | www.imprs-cbsc.mpg.de -----------------------------------------------------------------------

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EMBL Practical Bioinformatics Course Protein Sequence Analysis
by Wouter Van Gool 30 Nov '09

30 Nov '09

Hi All, I'd like to draw your attention to some nice bioinformatics course about protein sequence analysis organized at the EMBL, this next January. You can find more information and register online at: http://www.embl.de/training/courses_conferences/course/2010/EMP10-01/ Or read below for a short course summary. Best Regards, Wouter Van Gool EMPA2010 - Protein Sequence Analysis Practical Bioinformatics Course EMBL-Heidelberg Tuesday 19th - Friday 22nd January 2010 This 3.5 day practical bioinformatics course, aimed at wet-lab biologists with only limited experience, will focus on protein sequence analysis, and analysis/prediction of protein modular architecture. www.embl.de/courses/empa2010 The deadline for applications is Friday 4 December 2009, and there is an application fee of 250 euros (which also covers meals and accommodation). The course is aimed at wet-lab biologists who are looking to exploit bioinformatic tools in their work - setting the scene by introducing the biological concepts behind protein architecture modules and providing extensive hands-on application of the relevant bioinformatics tools with appropriate example proteins. The power - but also the limitations, which remain substantial - of the currently available software will be examined. People should feel free to get in touch with Aidan (budd(a)embl.de) if they've any questions about the course.

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