- BBClist - maillist.psb.ugent.be

META'2010 call for papers
by talbi 13 Jan '10

13 Jan '10

********************************************************************** META'2010 International Conference on Metaheuristics and Nature Inspired Computing 28-30 Oct 2010 Djerba Island, Tunisia http://www.lifl.fr/META10 ********************************************************************** The 2nd International Conference on Metaheuristics and Nature Inspired Computing, META’10, will held in Djerba Island, Tunisia from 28 to 30 Oct 2010. The Conference will be an exchange space thanks to the sessions of the research works presentations and also will integrate tutorials and a vocational training of metaheuristics and nature inspired computing. The scope of the META’2010 conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, … * Evolutionary algorithms, swarm optimization, scatter search, … * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, … * Parallel algorithms and hybrid methods with metaheuristics, machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, … * Application to: logistics and transportation, telecommunications, scheduling, data mining, engineering design, bioinformatics, … * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, … * Application to multi-objective optimization * Application in dynamic optimization, problems with uncertainty, … Submission papers: _________________ - Submission of papers should be in shape of an abstract of two pages sent before the 15st May 2010 via the website. - Selected papers will be published in international journals (ISI journals): COR, ITOR, JMMA, ... - Predefined styles are available on the website http://www.lifl.fr/META10 that we invite you to visit regularly and which evolves when the organization progresses. - Invited sessions and tutorials: Deadline 15th May 2010. contact talbi(a)lifl.fr E-G. Talbi ( Conference Chair) K. Mellouli (Co-chair) PC Members (to be completed) - B. Aghezzaf (MO) - M. Aider (DZ) - A. M. Alimi (TN) - E. Alba (ES) - R. Battiti (IT) - M. Batouche (SA) - F. Ben Abdelaziz (TN) - J. Blazewicz (PL) - C. Blum (ES) - P. Bouvry (LX) - E. Burke (UK) - A. Caminada (FR) - H. Chabchoub (TN) - T. Crainic (CA) - K. F. Doerner (AT) - M. Dorigo (BE) - H-B. Duan (CN) - P. Festa (IT) - S. Fidanova (BU) - J. Figueira (PO) - M. Gendreau (CA) - M. Gourgand (FR) - M. Gravel (CA) - S. Hanafi (FR) - J-K. Hao (FR) - M. Haouari (TN) - P. Isasi (ES) - M. Krajecki (FR) - M. Laguna (US) - A. Lokketangen (NW) - T. Loukil (TN) - S. Martins (BR) - R. Middendorf (D) - N. Monmarché (FR) - I. H. Osman (LE) - M. Pirlot (BE) - G. Raidl (AT) - M. Resende (US) - C. Ribeiro (BR) - M. Schoenauer (FR) - M. Sevaux (FR) - P. Siarry (FR) - K. Sorensen (BE) - T. Stutzle (BE) - J. Teghem (BE) - M. Toulouse (CA) - K-C. Tan (SG) - X-S. Yang (GB) - A. Zomaya (AU) Organizing Committee (to be completed): * Laetitia Jourdan (chair) * Clarisse Dhaenens (INRIA) * Arnaud Liefooghe (INRIA) * Marie-Eléonore Marmion (INRIA) * H. Masri (ISG, Tunisia) * A. Klabi (ISG, Tunisia) ------------------New book -------------------- "Metaheuristics: from design to implementation" E-G. Talbi Wiley 2009 (624pp), http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470278587.html ISBN: 978-0-470-27858-1 ----------------------------------------------- Prof. El-Ghazali TALBI University of Lille - INRIA - CNRS http: www.lifl.fr/~talbi

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Call for Abstracts ISNB 2010
by AHC van Kampen 12 Jan '10

12 Jan '10

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OPENING FOR POSTDOC IN BIOINFORMATICS ON GENOMICS / EPIGENOMICS (Brussels)
by François Fuks 12 Jan '10

12 Jan '10

Dear Colleague, I would greatly appreciate if you could distribute the announcement below for a post-doctoral position in the Laboratory of Cancer Epigenetics, ULB, Brussels. Best wishes, and thanks in advance. François Fuks ___________________________________________ François Fuks, PhD Laboratory of Cancer Epigenetics University of Brussels (U.L.B.) Faculty of Medicine, C.P. 614, Bât. GE, 5th floor 808 route de Lennik tel.: 32-2-555 62 45 1070 Brussels fax: 32-2-555 62 57 Belgium email: ffuks(a)ulb.ac.be lab website: http://www.ulb.ac.be/medecine/fukslab Job description: A postdoctoral position is available for a successful candidate to join a dynamic team located in Brussels (Belgium). Our group is interested to study genomics and epigenomics in cancer. The candidate will tackle integrative analysis of higth-throughput transcriptomics, genomics and epigenomics data sets generated using cutting edge genome-wide technologies. Both clinical and fundamental aspects of cancerogenesis will be addressed. The position is funded for 2 years, with possible extension. Screening of applications begins immediately and continues until an outstanding candidate is selected. Profile : Applicants should demonstrated proficiency in programming, and statistics and/or machine learning. Experience with sequence data, genome-wide data sets and demonstrated interest in oncogenomics will be assets. How to apply?: Informal enquiries, CV and names of two referees should be send to: Dr. François Fuks (ffuks(a)ulb.ac.be) Faculty of Medicine, Free University of Brussels, 808 route de Lennik, Brussels, Belgium. Tel.: 32-2-555 62 45. Fax: 32-2-555 62 57. Lab website: http://www.ulb.ac.be/medecine/fukslab Selected publications: - Brenner et al. EMBO J. 2005 24:336-46. - Viré et al. Nature 2006 439:871-4. - Brenner & Fuks Dev. Cell 2007 12:843-4 - Villa et al. Cancer Cell 2007 11:513-25 - Feldman et al. Nature SMB. 2008 15:1176-83 - Denis et al. Mol Cell Biol. 2009 29:4982-93.

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Symposium 'Comparing Building Blocks' at VU, Amsterdam
by Anton Feenstra 11 Jan '10

11 Jan '10

Dear bioinformaticians, On the occasion of Walter Pirovano defending his thesis "Comparing building blocks of life - Sequence alignment and evaluation of predicted structural and functional features" at the VU University ('Vrije Universiteit'), Amsterdam, the IBIVU Centre for Integrative Bioinformatics will organise a symposium: * Date and Venue Date: Friday 15 January, 2010 Time: 9.00-12.00 Location: VU University De Boelelaan 1083A - 1081HV Amsterdam W&N building room C121 * Programme 09.00 Coffee & Tea 09.15 Opening & Introduction 09.30 - Des Higgins University College Dublin Fast scalable clustering of huge numbers of sequences (for making guide trees) 10.00 - Willy Taylor William Taylor, NIMR, London What to do with poor alignments and bad secondary structure predictions? 10.30 Coffee Break 10.45 - Jack Leunissen Wageningen University Perspective of orthology 11.15 - Roland Siezen CMBI, Nijmegen Prediction and comparison of extracellular proteins of bacteria 11.45 Closing remarks 13.45 Thesis defense (viva) Walter Pirovano See also the online announcement on http://www.ibi.vu.nl/symposium/comparing_building_blocks_of_life.php and attached poster. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam | |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 | | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | |_____________|_______________________________________________________|

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Bioinformatician Position
by Erik van Beers 05 Jan '10

05 Jan '10

Dear BBC member, please feel free to circulate this ad amongst potential candidates. Beste regards, Erik Erik H. van Beers, PhD Head Research and Development Skyline Diagnostics BV Erasmus University Medical Center Dr Molewaterplein 50, room Ee1924 3015 GE Rotterdam the Netherlands T +31 10 7043431 F +31 10 7043076 www.skyline-diagnostics.nl <http://www.skyline-diagnostics.nl/>

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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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