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

Bioinformatics positions for postdoc in toxicogenomics and a databasemanager/scientific programmer in Maastricht
by Evelo Chris (BIGCAT) 21 Jul '08

21 Jul '08

Please see the attachments, Best, Dr. Chris Evelo Dr.Ir. Chris T.A. Evelo PhD Department of Bioinformatics - BiGCaT <http://www.bigcat.nl/> Maastricht University (UNS50, Box 18) P.O. Box 616; NL-6200 MD Maastricht; The Netherlands tel: +31 (0)43 3881231/81417; fax: +31 (0)43 3884149 e-mail: Chris.Evelo(a)bigcat.unimaas.nl visit: Universiteitssingel 40, room 5.580

1 0

Vacancy: Scientific programmer and database manager NTC
by Gaj Stan (BIGCAT) 19 Jul '08

19 Jul '08

Please check out the attached job description and feel free to distribute this further. -- Stan ========== Scientific programmer and database manager for the Netherlands Toxicogenomics Center M/F 1,0 fte Project description. Your aim will be to facilitate the storage and integrated analysis of transcriptomics, proteomics, metabonomics, and microRNA related data. The basis of all storage and analysis systems will be the NuGO blackbox project. You will configure and manage an Arraytrack database on an Oracle based storage server and a computation server that will run large scale R/Bioconductor tasks plus a number of bioinformatics clients. You will participate in the data storage and data publication (to e.g. Arrayexpress) and analysis. Your first task will be to allow data storage and secure sharing within the consortium from which you will move on to facilitation and participation in data analysis. To do this you will install, configure and tune existing bioinformatics tools and develop workflows for often encountered tasks (using e.g. Genepattern or Taverna). Understanding genomics data involves computational mapping of large scale experimental results on formalized descriptions of scientific knowledge. To allow such descriptions the bioinformatics department BiGCaT collaborates with other groups on wikipathways.org. You will participate in the Wikipathways project in order to create and improve pathways relevant to toxicogenomics. This project is part of a major research program from the Netherlands Toxicogenomics Centre. It will be done in collaboration with many partners in Maastricht (BiGCaT) and other universities and research institutes in the Netherlands. What we seek. A creative (bio)informatician [1.0 fte] with at least a BsC in (bio)informatics and an interest in modern biological research. Experience in Linux system management and database management (preferably Oracle based) is essential. What we offer An interesting vivid work environment. You will be able to collaborate with excellent toxicogenomics researchers that use very modern technology to evaluate the risks of chemicals and with skilled and enthusiastic bioinformaticians that work on groundbreaking new tools like the NuGO blackbox project, wikipathways.org and the analysis tool PathVisio. The job offer concerns a fulltime position for 5 years. The salary will be dependent on relevant experience. The gross monthly salary will amount to max. 3352,- euros conform salary scale 9 of the CAO Netherlands Universities. Information and applications. You will be appointed at Maastricht University, Maastricht, The Netherlands For inquiries: Dr. J.H.M. van Delft (043-3881092, j.vandelft(a)grat.unimaas.nl) Department of Health Risk Analysis and Toxicology, Maastricht University, PO Box 616, 6200 MD Maastricht

1 0

MLSB08 call for posters and registration
by Pierre Geurts 18 Jul '08

18 Jul '08

[apologies for multiple postings] Dear Colleagues, Please find below the call for posters for MLSB08. The deadline for poster submission is August 20. The list of invited speakers is now complete: Yoav Freund, Computer Science and Engineering, UCSD Lukas Käll, Department of Genome Sciences, University of Washington Pamela A. Silver, Department of Systems Biology, Harvard Medical School Lodewyk Wessels, Bioinformatics and Statistics group, Netherlands Cancer Institute, Amsterdam The full workshop program will be available soon. http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08/program.html Registration and accomodation booking is now open on the workshop website. http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08/registration.html The early-registration deadline is August 11. Because of the high hotel occupancy in Brussels, we strongly advise early hotel reservation. Accommodation via the workshop website can only be guaranteed up to August 14, 2008. Best regards, Louis Wehenkel, Florence d'Alché-Buc, Yves Moreau, Pierre Geurts ********************** 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 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)

1 0

Vacancy Bioinformatics/elab ResearchAssistant (Wageningen, the Netherlands)
by Ham, Roeland van 15 Jul '08

15 Jul '08

Please feel free to further distribute this ad roeland Bioinformatics/elab ResearchAssistant (V/M) Wageningen University & Research Centre, Plant Research International Wageningen (The Netherlands), 36 hours per week Reference number: 08.Biosc.06 Background: The cluster Applied Bioinformatics (Business Unit Bioscience, Plant Research International) participates in the Bioinformatics and Biostatistics program of the Centre for BioSystems Genomics 2012 (CBSG2012), one of the five genomics expertise centres of the Netherlands. The bioinformatics program contributes to the aims of CBSG2012 in unravelling and improving plant (tomato, potato, Brassica) germplasm for breeding and application. Research attention focuses on genome data (HTP sequencing, assembly and annotation, marker discovery and functional genomics). Within the program, stronger interaction with the wet-lab researchers is being accomplished. Job description: The bioinformatics/e-lab assistant will contribute to the further integration of bioinformatics in the wet-lab activities of CBSG2012 by hands-on analysis, tool implementation and adjustment as well as small tool development in close collaboration with CBSG2012 researchers. Activities will be in line with developments in the Netherlands Bioinformatics Consortium (NBIC). Profile: The position requires a HBO researcher with proven expertise in and interest for applied bioinformatics, preferably holding a Bachelor degree in Bioinformatics. Enthusiastic collaborator, good in communication with wet-lab biologists and a project-oriented attitude directed towards service provision. · Knowledge of and demonstrable experience in a LINUX environment · Good programming and databasing skills (SQL, Perl, Python, Java) and knowledgeable of applied statistics (R package) · Appropriate knowledge of molecular biology and related 'omics' fields · Keen eye for new technological developments, both in silico (Taverna workflow management) and at the bench (HTP sequencing) · Knowledge of plant genetics would be an asset Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a range of comparative and functional genomics related topics; a state-of-the art computational infrastructure; close collaboration with laboratory experts in genomics and sequencing. The position is available for one year, full time, with a possible extension. Maximum gross salary will be EUR 3048,- (scale 8) per month, depending on qualifications and experience. Information: For more information about this position, please contact dr. Roeland van Ham, Cluster leader Applied Bioinformatics, Plant Research International, +31-317-481053, roeland.vanham(a)wur.nl <mailto:roeland.vanham@wur.nl> , or Dr. Ir. J.P. Nap, Cluster leader CBSG Bioinformatics, +31-317-480984, janpeter.nap(a)wur.nl. Application: Send your letter with CV and the names of two references before July 25, 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 <mailto:lydia.bikker@wur.nl> . When applying for this job please always mention the vacancy number.

1 0

Vacancy researcher Researcher Plant Genome Analysis (Wageningen, the Netherlands)
by Ham, Roeland van 15 Jul '08

15 Jul '08

Please feel free to further distribute this ad roeland Researcher Plant Genome Analysis Wageningen Universiteit & Research Centre, Plant Research International Wageningen (The Netherlands), 36 hours per week Reference number: 08.Biosc.05 Background: Wageningen University and Research Centre (WUR) is involved in the international efforts to sequence the genomes of the Solanceous crops tomato and potato. The potato genome is being sequenced by the Potato Genome Sequencing Consortium (PGSC), which is an initiative of the Netherlands Genomics Initiative (NGI) and the WUR and is currently composed of research teams from sixteen different countries. All activities of the consortium are coordinated from Wageningen, where the potato genome database is being maintained. To support our genomics efforts, the WUR has recently extended its sequencing capacity with the acquisition of a next generation sequencing platform. The platform is used in the potato genome project and in the near future, we expect to also employ it for the sequencing of other plant genomes. Our activities in plant genome sequencing are supported by a strong team of bioinformaticians involved in (comparative) genome analysis and responsible for the development and application of genome assembly and annotation strategies. Job description: A position for a researcher is available in the Bioinformatics group at Plant Research International (PRI) to work on the structural and functional annotation and analysis of plant genomes, in particular that of potato, and to develop a strong and innovative research program in plant genome annotation and comparative analysis. The candidate will further participate in a team involved in the development of a bioinformatics platform for next generation sequencing technologies, which will be based on an advanced ICT infrastructure (Grid computing) and webservice and workflow management technology. This development is linked to the BioAssist <http://www.nbic.nl/support/bioassist/> initiative of the Netherlands Bioinformatics Centre (NBIC). Profile: We are looking for a communicative team player with: * A recent PhD in bioinformatics or related area and a strong publication record * Strong background in (plant) genome annotation and comparative genomics * Advanced programming and database development skills (Java, SQL, C++, Perl, or Python) * Knowledge of DAS, webservices, preferably BioMoby, and workflow management systems, preferably Taverna * The drive, ambition and skills to acquire a leading role in the area of plant genome annotation and comparative analysis and to initiate new projects in this field Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a range of comparative and functional genomics related topics; a state-of-the art computational infrastructure; close collaboration with laboratory experts in genomics and sequencing. The position is available for one year, full time, with a possible extension. Maximum gross salary will be EUR 4372,- (scale 11) per month, depending on qualifications and experience. Information: dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl <mailto:roeland.vanham@wur.nl> . Application: Send your letter with CV, list of publications and the names of two references before August 1, 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 <mailto:lydia.bikker@wur.nl> . When applying for this job always mention the vacancy number 08.Biosc.05

1 0

Vacancy researcher Bioinformatics for Metabolomics (Wageningen, the Netherlands)
by Ham, Roeland van 15 Jul '08

15 Jul '08

Please feel free to further distribute this ad roeland Researcher Bioinformatics for Metabolomics Wageningen Universiteit & Research Centre, Plant Research International Wageningen (The Netherlands), 36 hours per week Reference number: 08.Biosc.04 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 EUR 4372,- (scale 11) per month, depending on qualifications and experience. Information: dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl <mailto:roeland.vanham@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 August 1, 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

1 0

ELIXIR wants to hear from you ! (Re: bioinformatics users survey)
by BEN 14 Jul '08

14 Jul '08

[ you might receive this message more than once because you are in different mailing lists ] Dear all, We forward you this message from ELIXIR. Note that it concerns as well researchers active in the field of bioinformatics as those who occasionally use bioinformatics as a tool. The idea is that the survey should be filled in by ONE person per laboratory or research unit, preferably the manager or the person most involved in bioinformatics. Regards, Guy Bottu --------------------------------------------------------------------------- ELIXIR (http://www.elixir-europe.org) solicits your participation in the “Bioinformatics User Survey” and invites you to complete the online questionnaire on behalf of your group. This survey addresses the needs and priorities for long term support of infrastructures for biological information (i.e. general and specialized biomolecular databases) from end-users’ point of view. To enter the survey, please click on the link below: http://www.surveymonkey.com/s.aspx?sm=Uk_2bB7xwtqRe_2fCzqzZCqhmA_3d_3d Once you have started to complete the survey, you may stop at any time and return (from the same computer – i.e. IP address) to the questionnaire later if needed. The survey results will be distributed to all respondents that have provided an email address within the questionnaire. (Note: email addresses will be not disclosed to any third party.) Please share this information with colleagues who may be interested. We will be happy to answer any questions you may have about this survey, please contact Sandrine Palcy (sandrine.palcy(a)u-bordeaux2.fr) Thank you in advance for your participation! ELIXIR User Survey Coordinators http://www.elixir-europe.org/ ---------------------------------------------------------------------------- BEN - Belgian EMBnet Node at the Brussels Free Universities Computing Centre Marc Colet - Guy Bottu - David Coornaert Tel. +32/2/6505146 | Address BEN ULB CP 257 Fax +32/2/6505124 | Boulevard du Triomphe email ben(a)vub.ac.be | B-1050 Bruxelles ----------------------------------------------------------------------------

1 0