- BBClist - maillist.psb.ugent.be

Fwd: Recrutement bioinfo, suite... avec description du poste !
by Jacques van Helden 30 Oct '09

30 Oct '09

Dear colleagues Jean-Louis Ruelle asked me to forward this announcement for a job opening at GSK. Best regards Jacques van Helden ============================================ Begin forwarded message: From: jean-louis.ruelle(a)gskbio.com Date: 30 October 2009 09:37:43 CET To: Jacques van Helden <jacques.van.helden(a)ulb.ac.be> Subject: Fw: Recrutement bioinfo, suite... avec description du poste ! Job Purpose =========== The Bioinformatics group within the R&D of GSK Biologicals is currently seeking a highly motivated scientist-bioinformatician to be involved in cutting-edge research comprising data analysis and interpretation of microarray data, as well as investigating systems biology approaches relevant to the field of vaccines. The ideal candidate will have an interdisciplinary background in biology and bioinformatics/computational biology, particularly in the analysis and interpretation of microarray and/or proteomics data, working knowledge of statistical and machine learning data analysis methods, the reconstruction of signaling networks, computational network inference from experimental expression data, and the integration of public data sources/biological ontology to enable systems biology research. Responsibilities ================ The job involves: - Performing data analysis of µarray experiments, and collaborating with molecular and cellular biology and immunology for their biological interpretation - Using available methods, or developing new ones, to make sense of gene expression data in terms of signaling pathways, expression regulatory networks and modules, transcription factors activation. - Technology watch to stay up-to-date in this rapidly moving field - Sharing expertise and know-how - Driving contacts with external colleagues and academic research. - Reporting on progress and results to the research project teams. Profile ======= - A PhD in Life Sciences or Computer Sciences or equivalent; familiarity with immunology would be a plus. - Expertise in data analysis and statistics, especially machine learning methods, more generally computational biology. - Expertise in using genome wide approaches to study transcriptional regulation and signaling pathways; experience in computational network inference and modeling would be a plus. - Familiarity with processing of gene expression microarray data (QC, normalization, etc ), preferably with R+Bioconductor - You are willing to learn everyday, you are open, creative, you can work autonomously. - You have excellent communication and organizational skills. - You are fluent in English (oral and written). Contact and information: ======================= Please apply via the GSK Biologicals website : http://www.gsk-bio.com/english/html/online/apply.html and quote the following requisition number : 27260 Jean-Louis Ruelle <jean-louis.ruelle(a)gskbio.com> R&D GSKBiologicals Rix B62-J406 +32 2 656 8451

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PathVisio 2.0 pathway tool released
by Martijn van Iersel 20 Oct '09

20 Oct '09

The BiGCaT Bioinformatics group at Maastricht University is happy to announce the release of PathVisio 2.0. [1] What is PathVisio? PathVisio is a tool for creating and analysing biological pathway diagrams. Stay organized by using PathVisio as a notebook to collect the various bits of information related to a biological research subject. Create images suitable for presentation or publication. Draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl or Entrez gene, and add comments and literature references from pubmed. PathVisio is fully compatible with WikiPathways [2], a wiki where researchers can contribute pathway knowledge. What is new? New in PathVisio 2.0 is the ability to import experimental datasets and visualize them on top of pathways. Explore large datasets in a way that is more interesting and understandable than just a huge spreadsheet. Import microarray, proteomics or metabolomics data. Microarray reporters will be automatically converted to gene or protein identifiers. You can customize the visualization, using gradients, boolean color rules, or colored icons. Perform over-representation analysis to find the pathway that was most affected by experimental conditions. We prepared a Visual Tour [3] to get an overview of new and old features. For Developers: PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods and new pathway formats. PathVisio is fully open source, and we're always looking for Java developers who are interested in contributing, either to new plugins or to the core of the program. Contact us on our mailinglist [4]. [1] http://www.pathvisio.org/ [2] http://www.wikipathways.org/ [3] http://www.pathvisio.org/wiki/VisualTour [4] http://www.pathvisio.org/wiki/MailingLists

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Benelux Bioinformatics Conference 2009: deadline extended
by Pierre Geurts 15 Oct '09

15 Oct '09

[apologies for multiple postings] Deadline for abstract submission has been extended to ** MONDAY, OCTOBER 26 ** **************** Second Call for Abstracts ************************* Fifth Benelux Bioinformatics Conference December 14-15, 2009, Liège, Belgium ********************************************************************** http://www.montefiore.ulg.ac.be/services/stochastic/bbc09 SCOPE The Benelux Bioinformatics Conference is a two-day international conference on bioinformatics. It is the primary community event for bioinformatics researchers in the Netherlands, Belgium, and Luxemburg with excellent networking opportunities. The conference is aimed at both academic and industry researchers. This year's edition, BBC 2009, will take place in Liège, Belgium on December 14-15, 2009. Check out the conference web site at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/. CALL FOR ABSTRACTS The BBC 2009 program will feature four invited talks together with oral presentations and poster sessions. Participants are cordially invited to submit an abstract (max. 500 words) for their conference contribution. Submissions can be done using the form at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/ submission.php. VENUE The conference will take place at the Academic Room of the University of Liège, place du 20-Août, 7, 4000 Liège, Belgium. The venue is located in the heart of Liège, near Christmas markets and other tourist interests. Liège is a thousand-year-old city with a historical centre and numerous monuments, churches, and museums. Liège is located one hundred kilometers east of Brussels. KEY DATES * Deadline for abstract submission October 26, 2009 * Notification of selection of oral contributions November 16, 2009 * Deadline for early registration November 23, 2009 * Conference December 14-15, 2009 LOCAL ORGANIZING COMMITEE Louis Wehenkel, Pierre Geurts, Kristel Van Steen, Eric Bullinger Department of EE and CS and GIGA-R, University of Liège, Belgium

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vacancy: bioinformatics scientist sequence applications
by Antoine Janssen 12 Oct '09

12 Oct '09

Keygene n.v., internationally operating biotechnology company located in Wageningen is looking for a BIOINFORMATICS SCIENTIST sequence applications Vacancy number 09004 Position As a scientist you will be responsible for the analysis and method development for next generation sequencing applications. You will take the scientific lead for sequence analysis in the field of plant breeding application, with the use of novel methods for assembly, mapping and variation detection. You will be responsible for quality control and method implementation. You will work in a team of 5 professional Bioinformaticians and in close collaboration with researchers from other research domains. The team operates under the supervision of a team leader. Candidate Required: * A PhD degree in bioinformatics or comparable experience * Broad experience with sequence assembly, mapping and various analyses for marker discovery and genotyping * Good knowledge and preferably hands on experience with the available tools and methods in the field * Ambition to work in a pioneering research field * Keen on leveraging research results in a project centered environment * Leading personality Preferential: * Experience with the analyses of Roche GS (FLX) and Illumina GA (II) data * Experience with the use of cluster and grid infrastructure KeyGene offer KeyGene offers you a dynamic job with a competitive salary and benefits in a challenging, highly innovative and ambitious research company with an internationally recognized position in plant genetic research. You will be able to further build on the already existing modern facilities (Bioinformatics high performance computing power and high tech lab equipment such as robots and various next generation sequencing platforms). Furthermore, you will have full access to supporting services (IP and legal support, financing). More information Additional information can be obtained from Antoine Janssen, Keygene N.V., telephone +31 317 466866, email Antoine.Janssen(a)keygene.com<mailto:Antoine.Janssen@keygene.com>. If you are interested in this position you can send your letter of application and resume to: Keygene N.V. Attn. Ms A. Philipsen, HR manager, P.O. Box 216, 6700 AE Wageningen, The Netherlands or by email: Angelique.Philipsen(a)keygene.com<mailto:Angelique.Philipsen@keygene.com>. Please mention the vacancy number 09004 in your application. For more information on Keygene n.v., please visit www.keygene.com<http://www.keygene.com/>

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Reminder IUAP BioMaGNet Annual meeting 2009 :: Registration deadline October 16th 2009
by Klaas Vandepoele 07 Oct '09

07 Oct '09

Dear colleagues, The Bioinformatics and Evolutionary Genomics division of the Department of Plant Systems Biology (VIB -- Ghent University) is organizing *BioMaGNet's Annual Meeting* on *October 22nd 2009*. We invite all scientists working on bioinformatics, modelling or related disciplines to participate in this one-day symposium which will focus on research topics covered by the different national and international partners of the Interuniversity Attraction Pole BioMaGNet. Apart from the keynote talks and contributed BioMaGNet presentations (cfr. Program), abstracts can be submitted for the poster session. _Invited speakers: _ -Mark Veugelers, Integration Manager VIB 'Surfing the wave of emerging technologies in life sciences' -Stein Aerts, Laboratory of Computational Biology 'Mapping gene regulatory networks in Drosophila' -Florence d'Alché-Buc, Université d'Evry-Val d'Essonne 'Network inference : coupling graph and parameter estimation' The meeting will take place at the "Fiers-Schell-Van Montagu" FSVM research building at the Technologiepark 927 in Ghent, Belgium. For more information about registration, abstract submission and updates of the program, please visit http://bioinformatics.psb.ugent.be/biomagnet_2009 The registration deadline is *October 16th 2009*. We are looking forward to see you at the conference! The organization committee -- 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/ ---------------------------------------------------------

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post-doc position KULeuven - CGH arrays analysis
by Enrico Carlon 07 Oct '09

07 Oct '09

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CfPart: Tutorial on Comp. SysBio, Workshop on Computational Models for Cell Processes
by Ion Petre 06 Oct '09

06 Oct '09

Call for participation for two events connecting computer science and biology, in conjunction with Formal Methods 2009: 1. Tutorial on Computational Systems Biology Eindhoven, the Netherlands, November 2, 2009 http://combio.abo.fi/tcsb09/ Registration deadline: October 16, 2009 2. Second International Workshop on Computational Models for Cell Processes Eindhoven, the Netherlands, November 3, 2009 http://combio.abo.fi/compmod09/ Registration deadline: October 19, 2009 1. Tutorial on Computational Systems Biology (November 2, 2009, full day event) -------------------------------------------- - Lecturers: Ion Petre and Ralph-Johan Back, Abo Akademi University, Finland - Content: This one-day tutorial provides an introduction to computational systems biology, starting with a crash course on molecular biology for computer scientist and continuing with discrete, continuous and stochastic modeling techniques, as well as formal methods-based approaches. A demonstration is included on Copasi (Complex Pathway Simulator), a useful tool for modeling and simulating sysbio projects. The well-known heat shock response, that the lecturers and their research groups have been working on already for some years, will serve as a running example connecting the various topics. - Registration deadline: October 16, 2009 2. Workshop on Computational Models for Cell Processes (November 3, 2009) ------------------------------------------------------ FOCUS ----- Computational systems biology is an exciting new application area for applied mathematics and computer science. This workshop of the 16th International Symposium on Formal Methods fosters an excellent platform gathering researchers in formal methods and related fields that are interested in the wealth of opportunities and challenges in systems biology. INVITED SPEAKERS ---------------- - Jasmin Fisher (Microsoft Research Cambridge) - Hidde de Jong (INRIA Grenoble - Rhone-Alpes) - Grzegorz Rozenberg (University of Leiden) ACCEPTED PAPERS --------------- - Bogdan Aman and Gabriel Ciobanu. Mobile Membranes with Timers - Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo Schettini and Paolo Milazzo. On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems - Jiri Barnat, Lubos Brim, Ivana Cerna, Sven Drazan, Jana Fabriková and David Safranek. BioDiVinE: A Framework for Parallel Analysis of Biological Models - Daniela Besozzi, Paolo Cazzaniga, Matteo Dugo, Dario Pescini and Giancarlo Mauri. A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis - Luca Bortolussi and Alberto Policriti. Hybrid Semantics of Stochastic Programs with Dynamic Reconfiguration. - Mario Coppo, Ferruccio Damiani, Elena Grassi, Mike Guether and Angelo Troina. Modelling an Ammonium Transporter with SCLS - Laurence Loewe, Stuart Moodie and Jane Hillston. Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA - Heike Siebert. Dynamical and Structural Modularity of Discrete Regulatory Networks REGISTRATION AND IMPORTANT DATES --------------------------------- - Registration: http://www.win.tue.nl/fm2009/ - Registration deadline: October 19, 2009 - Late registration: after October 19, including on-site registration - Workshop: November 2, 2009 PROGRAMME COMMITTEE ------------------- - Ralph Back, Abo Akademi, Finland - Lubos Brim, Masaryk University, Czech Republic - Muffy Calder, University of Glasgow, UK - Eugen Czeizler, Abo Akademi, Finland - Vincent Danos, University of Edinburgh, UK - Russ Harmer, University of Paris 7, France - Monika Heiner, Brandenburg University of Technology Cottbus, Germany - Jane Hillston, University of Edinburgh, UK - Ina Koch, Max Planck Institute for Molecular Genetics, Germany - Vincenzo Manca, University of Verona, Italy - Giancarlo Mauri, University of Milan-Bicocca, Italy - Satoru Miyano, University of Tokyo, Japan - Andrei Paun, Louisiana Tech University, US - Ion Petre, Abo Akademi, Finland - Jaco van de Pol, University of Twente, the Netherlands - Alberto Policriti, University of Udine, Italy - Erik de Vink, Eindhoven University of Technology, the Netherlands ORGANIZERS ---------- - Ion Petre, ipetre 'AT' abo.fi - Erik de Vink, evink 'AT' win.tue.nl - Ralph-Johan Back, backrj 'AT' abo.fi VENUE: Technische Universiteit Eindhoven, the Netherlands

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Invitation_"Schrödinger_seminar"
by Prevost Martine 30 Sep '09

30 Sep '09

INVITATION "Schrödinger seminar" The Application of Recent Advances in Biomolecular Modeling to Drug Discovery Problems *** Dear Colleague, We are pleased to invite you to attend a Schrödinger seminar to take place on Wednesday October 21st, 2009 at the Université Libre de Bruxelles, http://www.ulb.ac.be/ Language: English Organizers: The seminar is jointly organized by Dr. Martine Prevost, Structure and Function of Membrane Biology Laboratory at the Université Libre de Bruxelles (http://sfmb.ulb.ac.be/index_uk.html) , and Schrödinger Inc. (http://www.schrodinger.com/) Schedule The seminar is divided up into two sessions: - A morning session with presentation of case studies highlighting the use of key techniques such as loop refinement, protein flexibility in ligand docking via «Induced Fit Docking », detection of multiple binding modes in ligand-based design, QM/MM methods and the exposure of the XP scoring function to identify key protein/ligand interactions for lead optimization. - The afternoon session will provide an opportunity for introductory demo on the use of Schrödinger software and for direct interaction with Schrödinger Application Scientist. Registration Participation is free of charge, but we kindly ask you to register by contacting me (katia.dekimeche(a)schrodinger.de) at your earliest convenience as seats are limited. Who Should Attend? The Seminar is suitable for attendees with varying backgrounds, from those with little experience of the use of computational techniques wanting to learn more about their potential impact on drug discovery, through to practicing computational chemists wanting to learn more about the use of recent advances in the Schrödinger suite and take advantage of the introductory training and direct contact with Schrödinger scientists. Agenda 9:00 Welcome & Coffee 9:30 General presentation of the Schrödinger suite with a focus on the application of key computational techniques to real world problems · Modeling and Simulation o The use of active site characterization tools to exploit regions of the binding site and optimize ligand interactions o The use of improved loop refinement to build missing information · Structure Based Design o Use of Docking methods with a focus on the Induced Fit Docking procedure to explore protein flexibility involved in the P38 DFG in/out loop movements o The use of fragment docking and exposure of the Glide XP scoring function to elucidate key interactions in 1kv2 structure · Ligand Based Design o Use of ligand based pharmacophores methods with a focus on multiple binding mode detection techniques to identify the two binding modes in P38 DFG in/out in the absence of protein data 12:30 Lunch 13:30 Demo · Short introduction on QM and QM/MM methods · How to get started with Maestro o Importing, exporting o Concept of the Project (Project Table) o Tools bar and Short-cut o Protein and Ligand Preparation o Recap of Interface for Morning Applications o Job submission, job monitoring o Analysis tools o Help and Documentation Videos Webinars · How to automate Schrödinger workflows using KNIME or Python 15:30 Questions/Answers 16:30 END Thank you and we look forward to welcome you there! Kind Regards, Katia Dekimeche Senior Account Manager, Academia and Government Schrödinger T: +33 1 46 55 85 17 M: +33 6 74 50 63 55 F: +33 1 70 24 86 78 katia.dekimeche(a)schrodinger.de http://www.schrodinger.com <http://www.schrodinger.com/> __________________________________________________________ Siège de la société /Registered Office: Schrödinger GmbH, Dynamostr 13, D-68165 Mannheim Directeur Général/Managing Director: Dr. Jörg Weiser Numéro dimmatriculation/Commercial Register: HRB 9583 , Tribunal d'instance: Mannheim -------------------------------------------- Martine Prévost Structure et Fonction des Membranes Biologiques CP 206/2 Université Libre de Bruxelles Bld du Triomphe B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 5382 E-mail: mprevost(a)ulb.ac.be --------------------------------------------

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Last CFP AICCSA'2010
by talbi 30 Sep '09

30 Sep '09

========================================================================== The Eight ACS/IEEE International Conference on Computer Systems and Applications AICCSA 2010 May 16-19, Hammamet, Tunisia http://www.lifl.fr/AICCSA2010 =========================================================================== The eight ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-2010) will be held in Hammamet, Tunisia May 2010. This is an ideal time to be in Tunisia. AICCSA is the premier Computer Science and Engineering Conference in the Middle East and North Africa. Authors are invited to submit papers describing new advances in computer systems and their applications. We welcome papers that are theoretical, conceptual, descriptive in nature, or a survey of the state of the art. Topics of interest include, but are not limited to: Algorithms and Bioinformatics Computer Architecture and Real time Systems Database and Data Mining DSP/Image Processing/Pattern Recognition/Multimedia· Modeling and Simulation Networking and Telecommunications Parallel and Distributed Systems Security and Information Assurance Soft Computing (AI, Neural Networks, Fuzzy Systems, Evolutionary algorithms, etc.) Software engineering -------------------------------------------------------------------------- Important Due Dates: Paper and Poster Submissions: October 13, 2009 (Firm)-11:59 pm (EST) Workshop, Tutorial and Panel Submissions: October 13, 2009 (Firm)-11:59 pm (EST) Notification of acceptance: December 19, 2009 Camera ready copy due: February 5, 2010 Author Registration: February 5, 2010 -------------------------------------------------------------------------- Proceedings Papers selected for presentation will appear in the Conference Proceedings, which will be published by the IEEE Computer Society and be available at IEEE XploreTM. Extended versions of selected papers will be considered for possible publication in scholarly international journals. Submission Guidelines To submit a paper, visit http://www2.lifl.fr/AICCSA2010/index.php?n=Main.AuthorsInstructions Regular Papers Papers must be submitted electronically by October 13, 2009. Each paper will be evaluated by at least three reviewers, and will be accepted based on its originality, significance and clarity. Submissions should not exceed 8 two-column, 8.5x11 inch pages (including figures, tables, and references) in 10 point fonts. Please include 5-10 keywords, complete postal and e-mail address, and fax and phone numbers of the corresponding author. If you have difficulties with electronic submission, please contact Technical Program Co-Chairs. Papers must not be published or under consideration to be published elsewhere. Short Papers Submitted papers that are deemed of good quality but could not be accepted as regular papers will be accepted as short papers. Workshops, Tutorials and Panels Submissions Proposals for workshops, tutorials and panels should be submitted directly to the appropriate chair. Posters and Doctoral Symposium Research still in early stages and doctoral research proposals may be submitted as extended abstracts that must not exceed 750 words. Accepted abstracts will be included in a special poster session dedicated to doctoral research proposals and related research. Extended abstracts should be submitted directly to the Posters Chair. -- Prof. El-Ghazali TALBI University of Lille - INRIA - CNRS http: www.lifl.fr/~talbi ------------------New book -------------------- "Metaheuristics: from design to implementation" E-G. Talbi Wiley 2009 (624pp) ISBN: 978-0-470-27858-1 -----------------------------------------------

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Benelux Bioinformatics Conference 2009: first call for abstracts
by Pierre Geurts 25 Sep '09

25 Sep '09

******************** First Call for Abstracts ************************* Fifth Benelux Bioinformatics Conference December 14-15, 2009, Liège, Belgium *********************************************************************** http://www.montefiore.ulg.ac.be/services/stochastic/bbc09 SCOPE The Benelux Bioinformatics Conference is a two-day international conference on bioinformatics. It is the primary community event for bioinformatics researchers in the Netherlands, Belgium, and Luxemburg with excellent networking opportunities. The conference is aimed at both academic and industry researchers. This year's edition, BBC 2009, will take place in Liège, Belgium on December 14-15, 2009. Check out the conference web site at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/. CALL FOR ABSTRACTS The BBC 2009 program will feature four invited talks together with oral presentations and poster sessions. Participants are cordially invited to submit an abstract (max. 500 words) for their conference contribution. Submissions can be done using the form at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/ submission.php. VENUE The conference will take place at the Academic Room of the University of Liège, place du 20-Août, 9, 4000 Liège, Belgium. The venue is located in the heart of Liège, near Christmas markets and other tourist interests. Liège is a thousand-year-old city with a historical centre and numerous monuments, churches, and museums. Liège is located one hundred kilometers east of Brussels. KEY DATES * Deadline for abstract submission October 19, 2009 * Notification of selection of oral contributions November 9, 2009 * Deadline for early registration November 20, 2009 * Conference December 14-15, 2009 LOCAL ORGANIZING COMMITEE Louis Wehenkel, Pierre Geurts, Kristel Van Steen, Eric Bullinger Department of EE and CS and GIGA-R, University of Liège, Belgium

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