- BBClist - maillist.psb.ugent.be

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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Tenure Track Position - Personal Genomic Data Analysis
by Yves Moreau 01 Sep '09

01 Sep '09

Dear Colleagues, We have a full-time tenure-track position opening up at the University of Leuven for a candidate with an interest in bioinformatics and computational biology for next-generation sequencing, personal genomes, etc. Deadline for application is September 30. Through our collaboration with the University Hospitals and the Genomics Core, we offer a great environment for this kind of research. Best regards, Yves Moreau ================================== Tenure Track Position - Personal Genomic Data Analysis The Science, Engineering and Technology Group of K.U.Leuven invites applications for a full-time academic position in genomic data analysis at the Department of Electrical Engineering-ESAT. See http://www.kuleuven.be/personeel/jobsite/vacatures/ engineering.html for more information DUTIES Research The tenure track positions are intended to foster high quality research in strategically selected domains. The successful candidate will be expected to develop a research programme that delivers excellent, international level research results and to support and enhance national and international research collaboration in genomic data analysis for personalized medicine. This research will concentrate on integrative data mining methodologies that leverage complex genomic data towards emerging strategies for personalized medicine. Specifically, array and next- generation sequencing technologies deliver unprecedented amounts of data that need to be translated into both fundamental and practical insights towards human health and disease, including congenital disease, complex disorders, and cancer. In particular, the research will focus on how genetic variation causes or modulates disease in different individuals, and how such knowledge can be translated into improved diagnosis, understanding of the disease pathways, or better drug treatments. While a specific therapeutic area could be targeted, the analysis strategies should be broadly applicable and part of the work will be dedicated towards setting up an infrastructure that can deploy such strategies in a broad range of collaborations across the university. Research will be conducted within the framework of the research centre BioSCENTer and the centre of excellence SymBioSys, and in close collaboration with several of the genomic facilities of the university. Teaching The successful candidate will take on teaching responsibilities in the Master of Bioinformatics and/or in other faculties. He or she is expected to meet the reigning K.U.Leuven standards regarding academic program level and orientation and to adhere to the K.U.Leuven’s concept of education. Commitment to quality of education as a whole is a matter of course. QUALIFICATIONS Candidates should hold a PhD or doctoral degree in Engineering, Computer Science or related fields. They are expected to be excellent researchers who show independence and originality. They are dedicated to high-quality teaching and will contribute to the quality of both research and teaching at the Faculty and the Department. The candidate's research ability of the candidate should be evidenced by publications in international peer-reviewed journals. International research experience is most important. In their application, candidates should include a description of objectives they wish to realise/methods they plan to use during the five-year period of the position. At K.U.Leuven the main language of instruction is Dutch. Successful applicants, who are not proficient in Dutch, will be provided language training in order to be able to also instruct in the Dutch language within three years time. Near-native proficiency in the English language is expected of all applicants. The full-time position will be offered for a period of five years starting on March 15, 2010 at the level of assistant professor (docent). A positive evaluation at the end of the five-year appointment will result in a tenured appointment as associate professor (hoofddocent). The K.U.Leuven pursues a policy of equal opportunity and diversity. Contact person: Prof. Yves Moreau, yves.moreau(a)esat.kuleuven.be If you experience any technical difficulties while completing your online application, please contact Katoe Buyle, katoe.buyle(a)pers.kuleuven.be tel.: +32 (0)16 328 324. DEADLINE September 30, 2007 Yves Moreau, K.U.Leuven ESAT-SCD & SymBioSys tel: +32 16 32 17 09 www.kuleuven.be/symbiosys fax: +32 16 32 19 70 www.kuleuven.be/bioinformatics If it is important, call my mobile +32 478 32 40 11 --- do not rely on email. *** ECCB10 *** www.eccb10.org *** ECCB10 *** *** Join us @ ECCB10, Belgium, Sept. 26-29, 2010 *** European Conference on Computational Biology

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Group coordinator position for Proteomics Identifications Database (PRIDE)
by Henning Hermjakob 10 Aug '09

10 Aug '09

http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2009/w_09_063_ebi/ind… -- Best regards, Henning

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Bioinformatics Postdoc, Amsterdam, NL
by Lodewyk Wessels 05 Aug '09

05 Aug '09

BIOINFORMATICS POSTDOC Topic: Pathway-based tumour characterisation by alignment against cell panels along multiple molecular dimensions. Research: Astra Zeneca Oncology has constructed large cell panels to serve as in vitro models for drug response. These cell panels have been extensively characterized by mutation analysis, mRNA expression, aCGH, response to a wide variety of drugs, micro-RNA expression and phosphoprotein characterization. In parallel, the same measurements are being performed on a collection of colorectal samples. In this project two aims are pursued. First, a comparative analysis will be performed between the cell line data and the tumor data to determine the multi-dimensional molecular states spanned by the cell lines and whether these states faithfully recapitulate the space spanned by a representative and clinically relevant selection of tumor samples. Guided by this mapping and by following a pathway-based approach, integrative modeling will be applied on the cell line panel data to construct models predictive of resistance. Job description: The successful candidate will be responsible for the bioinformatics analysis of the cell line and tissue data. More specifically, these tasks include 1) constructing a comprehensive gene list of the PI3K and ERK network; 2) Molecular characterisation of the colorectal cell panel and tumour samples through integrative analysis of the various data sources within the space spanned by the identified network genes and 3) Pathway-based alignment of cell panel to tumours to determine the extent to which the cell panel recapitulates the heterogeneity in the tissue set. Location: The position is embedded within the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) at the Netherlands Cancer Institute, Amsterdam and the Oncology Informatics group, Discovery Medicine, Astra Zeneca, Alderley Park, UK lead by Dr Tim French. We plan to have regular meetings, and the postdoc will also spend time at both locations. Requirements: Candidates should fulfill the following criteria. - MSc or PhD in one of the following areas: bioinformatics, engineering, computer science, statistics, physics, biotechnology, or biology. - Knowledge of fundamental aspects of cancer biology, especially signalling pathways. - Knowledge of fundamental aspects of computer science (algorithms and data structures, programming languages). - Knowledge or experience of informatics. - Knowledge of statistics, artificial intelligence or bioinformatics is highly desirable. Conditions of Employment: The successful candidate will be employed by the Netherlands Cancer Institute. The employment conditions follow general employment rules as laid down in the 'CAO' for hospitals. The salary will be determined depending on education and experience. Contact and Applications: Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr Tim French Discovery Medicine, Cancer Bioscience, tel. +44 1625-519922 or e-mail: Tim.French(a)AstraZeneca.com. Applicants should send a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. Website: http://bioinformatics.nki.nl Closing date: 30 January 2009 L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/ L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/

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progress report
by fred opperdoes 18 Jul '09

18 Jul '09

Dear All, We got almost at 350 signatures in 4 days for our petition "Keep BEN Alive" http://bit.ly/fJ5Ep . Not bad at all:-). We got also strong support from users of many EMBNet Nodes in the other European countries . Don't stop now!. Maybe we will get 400 signatures this WE? Thank you all! Fred R. Opperdoes, Secretary Belgian Society of Biochemistry and Molecular Biology Avenue Hippocrate 74-75, B-1200 Brussels, Belgium Tel: ++32-2-764.74.39 Fax: ++32-2-762.68.53 E-mail: info(a)biochemistry.be PGP key: 0x037DDD42 Web site: http://www.biochemistry.be Blog: http://www.biochemistry.be/bmb_blog/ Twitter: http://twitter.com/biochem_be Facebook: http://www.facebook.com/profile.php?id=100000004937038&ref=nf

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GMOD Community Meeting, 6-7 August, 2009, Oxford UK
by Dave Clements 18 Jul '09

18 Jul '09

There will be a GMOD Community Meeting, 6-7 August, 2009 at the University of Oxford, in Oxford, UK. GMOD (http://gmod.org) is a collection of interoperable, open-source software components for managing, visualizing, annotating, and sharing biological data. GMOD is also a community of users and developers addressing common challenges with their biological data. The popularity of next generation sequencing and other high-throughput methods has made this GMOD meeting particularly timely. GMOD meetings are an excellent opportunity to learn best practices from other researchers, to meet GMOD users and developers, and to learn and affect what is coming in the project. As with previous meetings, there will be a mixture of project talks, component-focused talks, and user talks. Registration for the meeting is now open and space is available on a first come, first served basis. Attendance is limited to the first 55 people to register. The meeting cost is £50. See http://gmod.org/wiki/August_2009_GMOD_Meeting to register for more. Please join us in Oxford this August. Cheers, Dave Clements GMOD Help Desk -- Register now for the August GMOD Meeting: http://gmod.org/wiki/August_2009_GMOD_Meeting

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