August 2008 - BBClist - maillist.psb.ugent.be

Lecture series on computational modeling of plants, next week in Ghent, 1-5 september, 10:00 - 12:30 daily (9:00 on Tuesday)
by Roeland Merks 27 Aug '08

27 Aug '08

Next week, from September 1st to September 5th, the VIB Department for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium, will host a one-week summer school on mathematical and computational modeling for plant systems biology: http://www.psb.ugent.be/plantmodels. The course features a series of general lectures by international experts on computational modeling of plants. The week will start with phenomena occurring at the subcellular and cellular scale, including photosynthesis, cell cycle regulation and the organization of the cytoskeleton. Then it will gradually “scale up” to the tissue, organ, and whole plant levels. It will conclude with pattern formation in tissues, the mechanics of growth, and whole plant development and evolution. The morning lectures are accessible to a general audience of plant biologists and are open to everyone without registration. Unfortunately, afternoon computer lab sessions will be accessible only to registered attendants and registration has closed. Lectures will start at 10:00 in the Jozef Schell seminar room on all days except for Tuesday, when the lectures will start at 9:00. The full program is included below. For more information and abstracts, please visit http://www.psb.ugent.be/plantmodels. Best wishes, Roeland Merks Gerrit Beemster Dirk Inzé Xavier Draye ---- Monday, 1st September 2008 Genetic and metabolic networks 10:00-11:00 Xin-Guang Zhu (Shanghai, China). Dynamic models of photosynthetic metabolism 11:15-12:15 Joe Pomerening (Bloomington, IN, USA). Coupled positive and negative feedback loops drive transitions in embryonic and somatic cell cycles Tuesday, 2nd September 2008 Single cell shape and mechanics 9:00-10:00 François Nédélec (Heidelberg, Germany). Models of microtubule organization in fission yeast 10:15-11:15 Bela Mulder (Amsterdam/Wageningen, Netherlands). Modelling cellulose biosynthesis and plant cell wall architecture 11:15-12:15 Verônica Grieneisen (Utrecht, Netherlands). Auxin gradients in root development Wednesday, 3rd September 2008 Multicellular pattern formation 10:00-11:00 Hans Meinhardt (Tübingen, Germany). Models of biological pattern formation applied to plant development 11:15-12:15 Richard Smith (Bern, Switzerland). Simulation models of auxin transport-based patterning in plants. Thursday, 4th September 2008 Plant growth mechanics 10:00-11:00 Alain Goriely (University of Arizona, Tucson, AZ, USA). Continuum models of plant growth and remodeling 11:15-12:15 Roeland Merks (VIB Department of Plant Systems Biology, Ghent, Belgium). Cell-centered modeling of plant tissues Friday, 5th September 2008 Whole plant development and evolution. 10:00-11:00 Xavier Draye (Louvain-la-Neuve, Belgium). Model integration: building multidisciplinary, soil, plant and atmosphere models 11:15-12:15 Przemyslaw Prusinkiewicz (Calgary, Canada). Cells to ecosystems: multiscale modeling of plant development and form

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Vacancy Researcher Bioinformatics for Metabolomics
by Ham, Roeland van 26 Aug '08

26 Aug '08

Researcher Bioinformatics for Metabolomics Wageningen Universiteit & Research Centre, Plant Research International Wageningen (The Netherlands), 36 hours per week Reference number: 08.Biosc.04-A Background: Metabolomics is a rapidly evolving functional genomics technology that aims to provide a comprehensive, qualitative and quantitative characterization of the biochemical composition of a biological sample. With the increasing sophistication and throughput of current high-resolution mass spectrometry platforms used in metabolomics, the resulting datasets are becoming ever larger and more complex. This not only calls for powerful software tools with which data can be processed and managed prior to their statistical analysis and biological interpretation, but also calls for the use of dedicated workflow management with which robust, extensible and reusable computational pipelines can be built, maintained and exchanged between researchers. Within the context of the BioAssist programme, the Netherlands Bioinformatics Centre (NBIC) in collaboration with the Netherlands Metabolomics Centre (NMC) aims to develop a Metabolomics support platform based on an advanced ICT infrastructure, a metabolomics data warehouse and webservices and workflow management technology. This will be achieved by a network of scientists and scientific programmers collaborating in the BioAssist <http://www.nbic.nl/support/bioassist/> programme of NBIC. Job description: A position for a researcher is available in the Bioinformatics group at Plant Research International (PRI) to participate as scientific programmer in the development of the BioAssist metabolomics support platform. Within PRI this development is central to various projects related to bioinformatics for metabolomics and the candidate is expected to take a proactive and coordinating role in this area. Specific tasks will include the implementation and further development of the data warehouse Metware <http://metware.wiki.sourceforge.net/> and development of standards and webservices for existing metabolomics software tools and their implementation in the workflow management system Taverna. Profile: We are looking for a communicative team player with: * A recent PhD in chemoinformatics, chemometrics, bioinformatic or related area * Advanced programming and database development skills (fluent in Java, SQL, and preferably in C++, Perl, or Python) * Knowledge of BioMoby, tomcat, SQL, JSF, bioMART and semantic web (e.g. RDF, OWL) * Basic knowledge of mass spectrometry and metabolomics technology is essential * The drive, ambition and skills to acquire a leading role in the development of a metabolomics data analysis platform within PRI and to initiate new projects in this field Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a broad range of comparative and functional genomics related topics; a state-of-the art computational infrastructure; close collaboration with one of the worlds leading labs in plant metabolomics. The position is available for one year, with a possible extension of two years, full time. Maximum gross salary will be € 4372,- (scale 11) per month, depending on qualifications and experience. Information: dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl or Dr. Robert Hall, +31-317-480441, robert.hall(a)wur.nl. Application: Send your letter with CV, list of publications and the names of two references before September 19, 2008 to Mrs. Lydia Bikker, Plant Research International, Department Personnel & Organisation, P.O. Box 16, 6700 AA Wageningen, The Netherlands. E-mail: vacaturemeldingen.psg(a)wur.nl When applying for this job always mention the vacancy number 08.Biosc.04-A

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Call for participation: The Benelux Bioinformatics Conference 2008
by Andra Waagmeester 25 Aug '08

25 Aug '08

This year the annual Benelux Bioinformatics Conference will be organised by BiGCaT-Bioinformatics of Maastricht University. Registration and abstract submission is now open see: http://www.nbic.nl/bbc2008. Key dates: Deadline for abstract submission October 1st, 2008 Notification of selection of oral and poster presentations October 15th, 2008 Deadline for early registration October 21st, 2008 Deadline for late registration December 1st, 2008 Benelux Bioinformatics Conference December 15 and 16, 2008 For additional information go the website or contact Andra Waagmeester (andra.waagmeester(a)bigcat.unimaas.nl) or Susan Coort (susan.coort(a)bigcat.unimaas.nl) (telephone: +31 (0)43 388 2913

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MLSB08: final call for poster and early registration deadline extended
by Pierre Geurts 14 Aug '08

14 Aug '08

[apologies for multiple postings] UPDATES: - Early registration deadline has been extended to August 16 http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08/registration.html - The list of accepted papers is now available here http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08/program.html ********************** Final Call for Posters ************************ 2nd International Workshop on Machine Learning in Systems Biology 13-14 September 2008, Brussels, Belgium ******************************************************************** http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08 MOTIVATION Molecular biology and also all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the "-omics" suffix in theirname. These include in particular genomics, transcriptomics, proteomics and metabolomics devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. The availability of these new, highly effective tools for biological exploration is dramatically changing the way one performs research in at least two respects. First of all, the amount of available experimental data is not at all a limiting factor any more; on the contrary, there is a plethora of it. The challenge has shifted towards identifying the relevant pieces of information given the question, and how to make sense out of it (a "data mining" issue). Secondly, rather than to focus on components in isolation, we can now try to understand how biological systems behave as the result of the integration and interaction between the individual components that one can now monitor simultaneously (so called "systems biology"). Taking advantage of this wealth of "genomic" information has become a conditio sine qua non for whoever ambitions to remain competitive in molecular biology and more generally in biomedical sciences. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms. OBJECTIVE The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to complex biological and medical questions by bringing together method developers and experimentalists. We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. A non-exhaustive list of topics suitable for this workshop: Methods Machine Learning Algorithms Bayesian Methods Data integration/fusion Feature/subspace selection Clustering Biclustering/association rules Kernel Methods Probabilistic Inference Structured output prediction Systems identification Graph inference, completion, smoothing Semi-supervised learning Applications Sequence Annotation Gene Expression and post-transcriptional regulation Inference of gene regulation networks Gene Prediction and whole genome association studies Metabolic pathway modeling Signaling networks Systems biology approaches to biomarker identification Rational drug design methods Metabolic Reconstruction Protein Structure Prediction Protein Function Prediction Protein-protein interaction networks SUBMISSION OF POSTER PRESENTATIONS We invite you to apply for poster presentations on topics of relevance to the workshop. Each poster presentation should be described in a 1 page summary and be submitted by August 20, 2008 via the Easychair submission system: http://www.easychair.org/conferences/?conf=mlsb08 Formatting instructions are given on the workshop website http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08/submission.html PROGRAM The lists of invited speakers and accepted papers are available here http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08 IMPORTANT DATES - 20 August: deadline for submissions of poster presentations - 25 August: notification of acceptance to authors - 13-14 September: workshop LOCATION The workshop will take in place Brussels at the Palais des Académies of Académie royale des Sciences, des Lettres et des Beaux-Arts de Belgique. CONTACT For further information, please contact mlsb08(a)gmail.com or see the conference website: http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08 MLSB08 CHAIRS Louis Wehenkel and Pierre Geurts, GIGA-Research, University of Liège, Belgium Florence d’Alché-Buc, IBISC CNRS FRE 2873, University of Evry-Val d’Essonne, France Yves Moreau, ESAT, Katholieke Universiteit Leuven, Belgium SCIENTIFIC PROGRAMME COMMITTEE Florence d’Alché-Buc (University of Evry, France) Christophe Ambroise (University of Evry, France) Pierre Geurts (University of Liège, Belgium) Mark Girolami (University of Glasgow, UK) Samuel Kaski (University of Helsinki, Finland) Kathleen Marchal (Katholieke Universiteit Leuven, Belgium) Elena Marchiori (Vrije Universiteit Amsterdam, The Netherlands) Yves Moreau (Katholieke Universiteit Leuven, Belgium) Gunnar Rätsch (FML, Max Planck Society, Tübingen) Juho Rousu (University of Helsinki, Finland) Céline Rouveirol (University of Paris XIII, France) Yvan Saeys (University of Gent, Belgium) Rodolphe Sepulchre (University of Liège, Belgium) Koji Tsuda (Max Planck Institute, Tuebingen) Jacques Van Helden (Université Libre de Bruxelles, Belgium) Kristel Van Steen (University of Liège, Belgium) Jean-Philippe Vert (Ecole des Mines, France) Louis Wehenkel (University of Liège, Belgium) David Wild (University of Warwick, UK) Jean-Daniel Zucker (University of Paris XIII, France)

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Postdoc Position Computational Systems Biology
by Hans van Beek 12 Aug '08

12 Aug '08

*Postdoc Position Computational Systems Biology* *'Systems Bioinformatics: Computational Modelling Methods'* * * *Position: * Postdoc at the Centre for Integrative Bioinformatics (IBIVU; http://www.ibivu.nl) VU University Amsterdam (Vrije Universiteit). The term of the position is about 45 months. The IBIVU is a recently founded broad-based Research and Education Centre that is carried by the Faculty of Sciences (FEW) and the Faculty of Earth and Life Sciences (FALW) with strong endorsement from the University Board. The IBIVU is going through a phase of expansion both in staffing and research projects as a result of university and grant-based funding. More information is available at the website (http://www.ibivu.nl) *Title:* Systems Bioinformatics: Computational Modelling Methods** *Goal:* To develop and implement computer methods for computational modelling of biological systems. This encompasses methods for computational model assembly, maintenance, modification, execution and analysis. ** *Outline of Project:* The project focusses on developing and implementing computational methods generically useful for computational modelling of biological systems. This encompasses workflows for computational model assembly, modification, maintenance, execution, simulation, optimisation, etc. Multiscale modelling methods, parameter sensitivity spectrum analysis, ensemble simulation, model-based data analysis techniques, visualisation of results, data assimilation methods etc. may be part of the project. This project is funded by The Netherlands Consortium for Systems Biology (NCSB). In the NCSB five bioinformatics centres collaborate in the Systems Bioinformatics project. This bioinformatics project in turn entails collaboration with several experimental projects in the consortium. In addition the Systems Bioinformatics group is part of the BioAssist programme of the Netherlands BioInformatics Centre. The VU group coordinates the Systems Bioinformatics group. The postdoc shall play an active role in coordination of the Systems Bioinformatics project with the partners. ** *Requirements:* The candidate for the postdoc position is expected to have a PhD degree or equivalent in bioinformatics, computational biology, systems biology, or a related field, with a strong background in software development and biological systems modelling and in addition should possess good communication skills. Contact: /For more information and applications please contact:/ Dr Hans van Beek VU University Medical Centre & Centre for Integrative Bioinformatics VU e-mail: hans.van.beek(a)falw.vu.nl phone +31 (0)20 5987738 (temporary until September) fax. +31 (0)20 5987229

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Vacancy: postdoctoral researcher Federated Proteomics Pipelines
by Morris Swertz 11 Aug '08

11 Aug '08

Dear colleagues, We are currently searching for an enthusiastic Bioinformatics/Computer science POSTDOC (1.0 FTE) to work and publish on "federated" proteomics analysis pipelines. http://www.academictransfer.org/00347-723 <http://www.academictransfer.nl/vacaturebank/zoeken/index.cfm?fuseaction=det…> Job description: New technological developments in proteomics research have lead to an explosive expansion of generated data. You will be responsible for the development of a flexible software platform that enables proteomics researcher groups to share data and processing pipelines (or components thereof) in a consortium of Dutch universities (BioASSIST program). Use of model-driven tools (MOLGENIS for data, TAVERNA for workflows), extensible data standards, web services, adaptable GUIs, and GRID technologies will result in a dynamic and scalable solution. We seek: An independent researcher with extensive track-record in distributed, computation- and/or data-intensive software applications. You are experienced in analytical workflows, statistical tools R and Matlab, web services, database modelling, (web) user interfacing, and eclipse/java/subversion/cvs. The ideal candidate also has a background in model-driven development, parallelization, proteomics, biology, medicine or statistics. We offer: The University of Groningen offers a salary dependent on qualifications and work experience up to a maximum of € 4284 (scale 11) gross per month for a full-time position. The appointment is for one year, with the perspective of prolongation for another two years. You will be member of a multidisciplinary project team of software engineers, bioinformaticians and chemists, have strong interaction with senior scientists, postdocs and PhD students and you will have access to state-of-the-art software engineering technologies, facilities and equipment. How to apply: You can apply for this job before 03-09-2008 by sending your application to: University of Groningen Personnel and Organization Office P.O. Box 72 9700 AB Groningen The Netherlands E-mail address: vmp(a)rug.nl <mailto:vmp@rug.nl?subject=Application%20Postdoc%20%28programmer%29%20position%20in%20Federated%20Proteomics%20Pipelines> When applying for this job always mention the vacancy number AT208208. More information. http://www.academictransfer.org/00347-723 <http://www.academictransfer.nl/vacaturebank/zoeken/index.cfm?fuseaction=det…> http://www.rug.nl/gbic <http://www.rug.nl/gbic> Kind regards, Morris Swertz

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Vacancy @ Netherlands proteomics Centre
by Breukelen, dr. ir. B. van (Bas) 06 Aug '08

06 Aug '08

Dear Collegues, We are currently searching for enthusiastic Bioinformaticians and/or Computer scientists, to work on and build a proteomics data analysis pipeline. Your aim will be to facilitate the storage and integrated analysis of proteomics data. For this we are developing a pipeline, partially based upon existing tools, that addresses every aspect of MS data analysis. As a basis we build our tools upon the PRIDE (EBI) proteomics data repository. We encourage you to visit our website(s) http://www.netherlandsproteomicscentre.nl/ and http://www.pharm.uu.nl/bioms/ to find an overview of our current research topics. Additionally you can write or call me to receive more background information on the current (bioinformatics) projects (see signature). What we seek. A creative (bio)informaticians [1.0 fte] or Computer scientist with at least a BsC in (bio)informatics and an interest in proteomics research. Good experience in programming (JAVA, Perl, PHP), parallel computing or GRID computing. Additionally we are seeking for a PhD student willing to work part time at the EBI (Hinxton UK), on a collaborative project where we are going to extend the PRIDE repository to encompass quantitative proteomics results followed by an in depth analysis of these (combined) datasets. What we offer An interesting vivid work environment. You will be able to collaborate with excellent proteomics researchers that use very modern technology and the latest Mass Spectometers and enthusiastic bioinformaticians The job offer concerns a fulltime position for 3 years. The salary will be dependent on relevant experience (scale 9/10 CAO Netherlands Universiteit). Kind regards, Bas ________________________________________________________________________ _____ Wentbuilding Z315, Sorbonnelaan 16, 3584 CA, Utrecht +31 (0)30 253 9761 (T), +31 (0)6 24996046 (M) b.vanbreukelen (skype) and b.vanbreukelen(a)uu.nl <mailto:b.vanbreukelen@uu.nl> <http://www.pharm.uu.nl/bioms/>

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[Fwd: PhD Position]
by jeroen raes 06 Aug '08

06 Aug '08

fyi: glycobioinformatics positions at the DKFZ here in Heidelberg. cheers, jeroen -- Jeroen Raes, PhD EMBL - Computational Biology Unit (Bork group) Meyerhofstrasse 1, D-69117 Heidelberg, Germany Tel: +49 6221 387372 jeroen.raes<>embl.de http://www.embl.de/~raes/ http://www-db.embl.de/jss/EmblGroupsHD/g_27.html -------- Original Message -------- Subject: PhD Position Date: Wed, 06 Aug 2008 10:42:05 +0200 From: Sean Powell <spowell<>embl.de> To: jeroen raes <raes<>embl.de> Hi, The glycobioinformatics position is part of an EU financed project that is looking for non-German applicants that have not lived in Germany for the past 12 months. The glycobiology PhD position is open to anyone, however non-German applicants are very welcome. If, you know of anyone that could be interested, please do not hesitate to forward this mail to them. Cheers, Sean

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