- BBClist - maillist.psb.ugent.be

2 Positions (1 Post Doc, 1 Research Assistant) in Cambridge, UK
by Rekin's Janky 23 Sep '09

23 Sep '09

2 Bioinformatician Positions (1 Post Doc, 1 Research Assistant) at University of Cambridge, Department of Haematology Transcriptional Networks in Blood Stem Cells and Leukaemia The molecular control of blood stem cell development and differentiation is underpinned by regulatory networks that define the gene regulatory state of blood stem/progenitor cells, and in response to external stimuli control cell fate decisions. Work in the Gottgens group employs both experimental and bioinformatic approaches to identify and characterise blood stem cell regulatory networks. We are now looking for enthusiastic bioinformaticians to join our multidisciplinary team. The postholders will apply and further develop bioinformatic tools to analyse ChIP‐Seq and gene expression datasets as well as perform comparative genomic analysis of gene regulatory elements. The Gottgens group is based in the Cambridge Institute for Medical Research, the flagship Institute of the Medical School of Cambridge University with excellent infrastructure and a vibrant research environment. The group enjoys productive collaborations with research groups both within Cambridge and beyond. The group has been highly productive with over 40 papers in the last 4 years as well as a paper in Developmental Cell and a paper in Nature currently in press. Please contact Bertie Gottgens at bg200(a)cam.ac.uk for more information. For more details on the group, please see: http://www.cimr.cam.ac.uk/investigators/gottgens/index.html http://hscl.cimr.cam.ac.uk/index.html

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Call for participation: CompMod 2009, Nov 3, 2009, Eindhoven, the Netherlands
by Ion Petre 22 Sep '09

22 Sep '09

Second International Workshop on Computational Models for Cell Processes Eindhoven, the Netherlands, November 3, 2009 http://combio.abo.fi/compmod09/ In conjunction with Formal Methods 2009 ---------------------------------------------------------------------------- --- === Date: November 3, 2009 === === Webpage: http://combio.abo.fi/compmod09/ === === Related event: Tutorial on Computational Systems Biology, Nov 2, 2009 === === http://combio.abo.fi/tcsb09/ === ---------------------------------------------------------------------------- --- THE MEETING ----------- 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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position for scientific programmer
by AHC van Kampen 21 Sep '09

21 Sep '09

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Fwd: EXTENDED DEADLINE SEPT 28th: EMBNET-RIBio Oct25-29 2009 Internatl. Conference
by Jacques van Helden 18 Sep '09

18 Sep '09

From: Julio Collado Vides <collado(a)ccg.unam.mx> Date: 18 September 2009 00:14:36 GMT+02:00 To: collado(a)ccg.unam.mx Cc: BJ Morrison <bj(a)sdsc.edu> Subject: EXTENDED DEADLINE SEPT 28th: EMBNET-RIBio Oct25-29 2009 Internatl. Conference Dear colleagues: We would like to remind you of the SEPTEMBER 28th EXTENDED DEADLINE TO SUBMIT AN ABSTRACT FOR THE International EMBnet-RIBio Conference 2009, jointly organized by the European Molecular Biology network (EMBnet) and the Red Iberoamericana de Bioinformática (RIBio) at the Paradisus Riviera Cancun Resort, located at the Mayan Riviera, Quintana Roo, Mexico, from the 26th to the 29th of October, 2009. Visit the conference site: http://www.embnet.org/en/EMBnet-RIBio2009 Monday October 26th we will give official birth to the Iberoamerican Society for Bioinformatics, you are welcome to be a funding member ¡¡ We are pleased to announce RESOURCES FOR PARTIAL FUNDING for students, posdocs and researchers from Iberoamerica to attend the meeting PROVIDED THEY SUBMIT AN ABSTRACT to the conference. There is also funding for ISCB affliiated students to attend the meeting with similar requirements. Don't miss the deadline of this exciting conference in a wonderful setting in the Mexican Caribbean! The Organizing Committee ------------------------------------------------------------------ ------------------------------------------------------------------ More detailed information: This will be the first time the EMBnet's Annual General Meeting will take place outside of Europe, bringing together bioinformaticians from all over the world, together with the Iberoamerican Annual General Meeting, and representatives of other major Bioinformatics societies in the World. We will give official birth to the Iberoamerican Bioinformatics Society. Tri Institutional Professor Chris Sander (http://www.mskcc.org/mskcc/html/11655.cfm ), an authority in bioinformatics and founder of the field will give a keynote lecture at the conference. The conference is open to submissions. The main topics will be: High Throughput Technologies, the Interface of Bioinformatics and Systems Biology and Open Software for Bioinformatics, but we are accepting submissions in all areas of bioinformatics (such as genomics, proteomics, trancriptomics, metagenomics, data and text-mining, ontologies, education and e-learning tools available in Bioinformatics, among others) --See the Abstract guidelines--. Additionally, selected papers will be reviewed and published on the "EMBnet.news 15.4" (EMBnet.news is a quarterly publication with a peer reviewed research section indexed by PubMed (starting from 15.4), devoted to research, projects, events, news and announcements related with the bioinformatics, biomedical and in general to the "bio-" and "omics-" communities & industry all-over the world). All information dealing with submitting abstracts, registration and hotel booking can be found in the site of the conference at: http://www.embnet.org/EMBnet-RIBio2009 Don't miss the deadline of this exciting conference in a wonderful setting in the Mexican Caribbean! On behalf of The Organizing Committee -- Julio Collado-Vides, Ph.D. Head of the Program on Computational Genomics Center for Genomic Sciences, UNAM Av. Universidad s/n. Cuernavaca, Col. Chamilpa, Morelos 62210; Mexico phone: (52) 777-313-2063; 55-5622-7693 Fax: (52) 55 5622-7694 http://www.ccg.unam.mx/Computational_Genomics/

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IUAP BioMaGNet Annual meeting 2009
by Klaas Vandepoele 15 Sep '09

15 Sep '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, abstracts can be submitted for the poster session. Invited speakers: -Mark Veugelers, Integration Manager VIB -Stein Aerts, Laboratory of Computational Biology -Florence d'Alché-Buc, Université d'Evry-Val d'Essonne 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 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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CFP NIDISC'2010
by talbi 15 Sep '09

15 Sep '09

********************************************************************** The 13th International Workshop on Nature Inspired Distributed Computing (NIDISC'10) http://www.lifl.fr/~talbi/nidisc10 held in conjunction with The 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS'2010) 19-23 April 2010 Atlanta, USA http://www.ipdps.org ********************************************************************** Workshop Theme : ============= Techniques based on metaheuristics and nature-inspired paradigms can provide efficient solutions to a wide variety of problems. Moreover, parallel and distributed metaheuristics can be used to provide more powerful problem solving environments in a variety of fields, ranging, for example, from finance to bio- and health-informatics. This workshop seeks to provide an opportunity for researchers to explore the connection between metaheuristics and the development of solutions to problems that arise in operations research, parallel computing, telecommunications, bioinformativs, and many others. Topics of interest include, but are not limited to: * Nature-inspired methods (e.g. ant colonies, GAs, cellular automata, DNA and molecular computing, local search, etc) for problem solving environments. * Parallel and distributed metaheuristics techniques (algorithms, technologies and tools). * Applications combining traditional parallel and distributed computing and optimization techniques as well as theoretical issues (convergence, complexity, etc). * Other algorithms and applications relating the above mentioned research areas. Prospective authors of high quality research contributions are invited to submit an electronic copy of their manuscript not exceeding 8 two-column pages including figures and references in the traditional IEEE format used in IPDPS. Please, use Postscript or PDF when possible. In your email, please indicate paper title, author(s), and the corresponding author. A selected group of papers from the workshop will be invited to submit extended versions of their papers to a special issue of an international scholarly journal. Further announcements will be made during the workshop. General Chair : ============ - Albert Y. Zomaya The University of Sydney -Australia- (zomaya(a)it.usyd.edu.au) Program Co-chairs : ============== - Enrique Alba, University of Málaga –Spain– ( eat(a)lcc.uma.es ) - Franciszek Seredynski, Polish Academy of Sciences – Poland ( sered(a)ipipan.waw.pl ) - El-ghazali Talbi, University of Lille, INRIA –France– ( talbi(a)lifl.fr ) Program Committee (to be completed) : ===================================== M. Affenzeller, Univ. of Hagenberg, Austria A. Al-Dubai, Edinburgh Napier University, United Kingdom A. Al-Jumaily, University of Technology Sydney, Australia L. Bononi, University of Bologna, Italy A. Boukerche, University of Ottawa, Canada P. Bouvry, University of Luxembourg, Luxembourg J. Branke, University of Karlsruhe, Germany E. Cantú-Paz, Lawrence Livermore National Laboratory, USA C. Coello, CINVESTAV-IPN, Mexico B. Di Martino, Univ. of Naples, Italia T. El-Ghazawi, George Washington University, USA P. Herrero, UPM, Spain A. Lewis, Griffith University, Australia M. Middendorf, University of Leipzig, Germany N. Melab, University of Lille, France M. D. Moore, Texas A & M - Corpus Christi, USA S. Mostaghim, Univ. of Karlsruhe, Germany A. J.Nebro, Univ. of Málaga, Spain C. Ribeiro, Univ. of Fluminense, Brazil H. Sarbazi-azad, Sharif University of Technology, Iran G. Spezzano, University of Calabria, Italy Z. Tari, RMIT University, Australia M. Tomassini, University of Lausanne, Switzerland F. Xhafa, Universitat Politècnica de Catalunya, Spain Papers should be submitted to: ============================== - E. Alba, University of Málaga –Spain– ( eat(a)lcc.uma.es ) - F. Seredynski, Polish Academy of Sciences – Poland ( sered(a)ipipan.waw.pl ) - E-G. Talbi, University of Lille, INRIA –France– ( talbi(a)lifl.fr ) Important Dates: ================ - Submission Deadline - December 4, 2009 - Notification of Acceptance - January 8, 2010 - Final Copy Due - February 1, 2010 http://www.lifl.fr/~talbi/nidisc10 -- 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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Master en Bioinformatique et Modélisation à l'Université Libre de Bruxelles
by Jacques van Helden 11 Sep '09

11 Sep '09

Un Master en bioinformatique et Modélisation à Bruxelles (ULB) et un Master International Bruxelles-Paris (ULB-UPMC). Depuis une décennie, les méthodes à haut débit (séquençage, transcriptome, protéome) ont suscité une augmentation exponentielle des données biologiques, dont le décryptage constitue un défi majeur pour les sciences biomédicales du 21ème siècle. L'analyse des génomes et des réseaux moléculaires fournit des outils conceptuels nouveaux pour élucider les processus biologiques et leur évolution. Les domaines d’application sont nombreux: diagnostique de maladies génétiques, analyses de données d'expression des gènes impliqués dans des maladies telles que le cancer, conception rationnelle de médicaments, pharmacocinétique, pharmacodynamique, pour n'en citer que quelques-unes. Le secteur de la recherche académique et les entreprises biotechnologiques et pharmaceutiques innovantes cherchent à recruter de jeunes scientifiques capables de développer de nouvelles approches et de les appliquer à l'analyse de ce type de données. Pour répondre à ce défi, l'Université Libre de Bruxelles (ULB) organise un Master en Bioinformatique et Modélisation en deux ans (MA- BINF 120 ETCS). Site Web: http://www.bioinfomaster.ulb.ac.be/ Les cours incluent une formation méthodologique théorique et pratique (bases de données, analyse de séquences, programmation), ainsi qu'une large couverture de 3 domaines d'application: 1) Génomique, protéomique et évolution 2) Biophysique et bioinformatique structurale 3) Biologie des systèmes (modélisation dynamique) Les cours combineront une introduction aux concepts théoriques et des applications concrètes. Un travail de fin d'études sera réalisé dans l'un des nombreux laboratoires ULB spécialisés en bioinformatique et modélisation (http://babylone.ulb.ac.be/CINBIOS/) Le Master est accessibles aux étudiants porteurs d'un diplôme de Bachelor universitaire (BA+3, "Licence" française) de mathématiques, informatique, physique, chimie, biologie, bioingénieur ou ingénieur. Les étudiants porteurs d'un diplôme de Master dans l'une de ces disciplines peuvent, sur examen du dossier académique, bénéficier de dispenses leur permettant de suivre la formation en un an. Ce programme s'intègre également dans le diplôme de Master International organisé conjointement par l'Université Libre de Bruxelles (ULB) et l'Université Pierre et Marie Curie (UPMC, Paris VI). Information détaillée: http://www.bioinfomaster.ulb.ac.be/ Contact: Marianne Rooman <mrooman(a)ulb.ac.be>, Albert Goldbeter <agoldbet(a)ulb.ac.be > ===================== Jacques van Helden <Jacques.van.Helden(a)ulb.ac.be> http://www.bigre.ulb.ac.be/Users/jvanheld/ Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) Université Libre de Bruxelles, CP263 Boulevard du Triomphe, Campus Plaine. B-1050 Bruxelles, Belgium

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Postdoc positions in Comparative Genomics
by Marc van Driel 10 Sep '09

10 Sep '09

Postdoc positions in Comparative Genomics The CMBI at the Nijmegen Center for Molecular Life Sciences has two open positions for talented and motivated scientists to do bioinformatics research into: 1) Unraveling patterns behind mental retardation: We have compiled a catalogue of more than 400 genes, mutations in which give rise to mental retardation. Several of these genes have already been demonstrated to act together in molecular pathways. However, the global biological coherence behind mental retardation genes is unknown. The challenge is to address this, e.g. via analyzing protein-protein interactions, via expression in specific tissues, via shared phenotypes in human and model organisms and via their shared evolutionary origin. You will query various types of genomics data, including proprietary gene-expression and functional data in Drosophila, to uncover shared pathways. Your work will shed light onto genetic design principles that underlie human brain function and will identify new candidate genes for mental retardation. 2) Evolutionary deconstruction of the Ciliome: The cilium is a eukaryotic organelle whose malfunction has been shown to be responsible for a wide array of genetic diseases. Already the evolutionary analysis of known ciliary proteins and other genomics data has successfully predicted new ciliary proteins. You will map the origin and evolution of the ciliome among the eukaryotes to find new candidate ciliary proteins, to detect sub-modules within the cilium and in general to link the evolution of the cilium to its functions. The projects combine the expertise of the Huynen group in the analysis of genomics data to predict protein function with the expertise in studying genetic disease of the groups of Annette Schenck and Ronald Roepman (Human Genetics, Nijmegen Center for Molecular Life Sciences). This collaboration ensures direct experimental testing of interesting newly predicted candidate proteins and pathways. The positions are initially for two years with ample possibilities for extension. Requirements: You have PhD in Bioinformatics or in Natural Sciences with a published affinity for large-scale Bioinformatics analyses coupled to in depth study of biological systems. Salary: starting at 40.458 - 46.695 Euro, depending on experience. For more information please contact Martijn Huynen (huynen(a)cmbi.ru.nl <mailto:huynen@cmbi.ru.nl> , www.cmbi.ru.nl) To apply, please e-mail a letter describing research interests and past research activities, a CV, and the names of three referees before October 15th , 2009.

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Vacature Docent Bioinformatica HAN Nijmegen
by Paffen I 07 Sep '09

07 Sep '09

De Hogeschool van Arnhem en Nijmegen (HAN) zoekt ten behoeve van de Faculteit Techniek (FT) voor de campus in Nijmegen zo spoedig mogelijk een Docent Bio-informatica 0,8-1,0 fte Wat zijn uw werkzaamheden? U verzorgt onderwijs in de Nederlandse en Engelse taal voor alle studiejaren. U ontwikkelt nieuw competentiegericht onderwijs en past bestaand onderwijs aan. Ook begeleidt u leerprocessen (onder andere in de rol van tutor en expert) en stages en afstudeeropdrachten, zowel nationaal als internationaal. U voert scholings- en onderzoeksactiviteiten uit voor externe relaties. Wat zijn uw kwaliteiten? U hebt: - een academisch denk- en werkniveau op het gebied van bio-informatica - kennis van en ervaring met moleculaire biologie - bij voorkeur deskundigheid in programmeren en/of chemie - affiniteit met onderwijs U bent: - communicatief en sociaal vaardig - enthousiast en flexibel - resultaatgericht - collegiaal Wat bieden wij u? Een interessante en afwisselende functie in een dynamische, informele werkomgeving. Aanstelling vindt plaats voor de duur van een jaar met uitzicht op een vast dienstverband. Afhankelijk van uw ervaring bedraagt het bruto maandsalaris maximaal € 4.203,83 (cao-hbo schaal 11) bij een fulltime aanstelling. Het salaris is exclusief 8% vakantietoeslag en 8,3% eindejaarsuitkering. Daarnaast biedt de HAN goede voorzieningen op het vlak van pensioen, ziektekosten, scholingsfaciliteiten, mobiliteit en betaald ouderschapsverlof. Wilt u meer informatie? Meer over de HAN vindt u op www.han.nl. Voor meer informatie over deze functie kunt u contact opnemen met de heer C.W. van Verseveld, Directeur, T (024) 353 19 05. Hebt u belangstelling? Herkent u zich in bovenstaand profiel en voldoet u aan de eisen? Reageert u dan voor 18 september 2009 door uw sollicitatiebrief met CV te sturen naar: Hogeschool van Arnhem en Nijmegen, Service Unit P&O, t.a.v. mevrouw H. Beekman, Secretaresse, Postbus 5375, 6802 EJ Arnhem. U kunt ook solliciteren via e-mail: Hilletje.Beekman(a)han.nl Wilt u daarbij vacaturenummer 09-116 vermelden? Waar gaat u werken? De Faculteit Techniek verzorgt de technische opleidingen van de HAN. Studenten volgen competentiegericht onderwijs in moderne werkvormen en in diverse trajecten, zoals in voltijd, deeltijd en duaal. Ze worden opgeleid tot gekwalificeerde bachelors/ingenieurs in het specifieke beroepenveld. Medewerkers van de Faculteit Techniek (FT) kunnen naast het leveren van een bijdrage aan het reguliere onderwijs, ook activiteiten verrichten voor post-hbo-, internationale en masteropleidingen, voor toegepaste onderzoeksopdrachten van én voor bedrijven en instellingen. Acquisitie naar aanleiding van deze advertentie wordt niet op prijs gesteld.

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Invitation: workshop on "Data Mining & Bioinformatics for Proteomics" - september 18, 2009 - Antwerpen
by Kris Laukens 04 Sep '09

04 Sep '09

Dear all, we cordially invite you for an interdisciplinary workshop on "Data Mining & Bioinformatics for Proteomics" on september 18, 2009 in Antwerp. With the ever growing speed of proteome data accumulation, computational techniques become an increasingly important aspect in proteome analysis. This interdisciplinary meeting aims to bring together proteome researchers, bioinformaticians and computational scientists to discuss ongoing work and the challenges of handling and interpretation of all types of proteome data. The meeting offers an opportunity to discuss all levels of data interpretation, from raw data processing to biological systems modeling. You can download the full program here [pdf]: http://www.flandersproteomics.be/files/u1/Workshop-DM-BIOI-proteomics-2nd.p… All information (program, registration details, location) is available on the KVCV Proteomics website: http://www.flandersproteomics.be If you like to attend the workshop, we kindly ask you to register online, not later than Sunday september 13, 2009. The registration fee covers lunch and coffee, and equals 20€ (or 10€ for KVCV members). For people who are active in the field of computational proteomics / proteome bioinformatics, we intend to have a short brainstorm on better joining forces (projects, collaborations, ...). We invite all interested groups to be represented by one or more group members at a short submeeting during the lunch break (starting 12:45). Feel free to distribute this information among interested colleagues. We are looking forward to see you there! Kris Laukens -- Kris Laukens - Postdoc Intelligent Systems Laboratory (ISLab) Dept. of Mathematics and Computer Science University of Antwerp - Campus Middelheim Middelheimlaan 1, G.219, B-2020 Antwerpen, Belgium tel.: +32 3 265 33 10 fax: +32 3 265 32 04 http://www.islab.ua.ac.be http://www.bioframe.net

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