September 2012 - BBClist - maillist.psb.ugent.be

NBIC PhD course on Managing Life Science Information: registration is open!
by Celia van Gelder 01 May '13

01 May '13

*NBIC PhD Course on Managing Life Science Information (2nd edition) *Course coordinators: Marco Roos, Scott Marshall _Date:_ 17-21 October 2011 (one week of tutorials) and a final workshop on Friday 28 October 2011 to discuss project results _Location:_ Science Park, Amsterdam _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/managing-life-science-information/ Did you ever suspect that the data that you need is somewhere but neither discoverable nor accessible? Have you ever produced valuable data that nobody can use anymore, including yourself? Have you ever wondered how to create a federation of distributed data sources? If you do not want your data to end up in a data graveyard, and for many other information management issues, we have organised a course for you. In this course we will teach you methods to make data shareable and self-describing. You will learn how: 1. the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration 2. to expose your local data (including relational databases) for use in other systems. 3. Web Services can be used to analyse data from anywhere. 4. text mining can be applied to link resources such as biobanks. 5. human knowledge can be made computable and associated with data. 6. to make your data publishable artifacts for which you can get scientific credit. 7. to use tools such as MolGenis <http://www.molgenis.org/>, Taverna <http://www.taverna.org.uk/>, SPARQL <http://www.w3.org/TR/sparql11-query/>, D2RQ <http://www4.wiwiss.fu-berlin.de/bizer/d2rq/>, SWObjects <http://tinyurl.com/swobjects-swat4ls>, NCBO's BioPortal <http://bioportal.bioontology.org/>, Anni <http://www.biosemantics.org/index.php?page=anni-2-0>, LarKC <http://larkc.org/>(Large Knowledge Collider). 8. to collaboratively solve an information management problem _Program_ (tentative) Monday: Introduction by leading Semantic Web expert Prof. Dr. Frank van Harmelen; Hands-on with RDF and SPARQL (Scott Marshall) Tuesday: XML, RDF, Minimal information models, and exposing data from local databases (Scott Marshall); hands-on with MolGenis (Erik Roos) Wednesday: Data integration with Web Services (Katy Wolstencroft); hands-on with Taverna (Katherine Wolstencroft) Thursday: Knowledge management and nano-publication (Andrew Gibson); hands-on federated queries with SWObjects (Scott Marshall) Friday: Text mining for linking biobanks and hands-on with Anni (Marco Roos, Kristina Hettne); Hands-on with LarKC (Spyros Kotoulas); DRINKS!!! -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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Bioinformatics Postdoc
by Lodewyk Wessels 02 Dec '12

02 Dec '12

POST DOCTORAL BIOINFORMATICIAN IDENTIFICATION AND VALIDATION OF NEW TARGETS FOR COLORECTAL CANCER OVERALL OBJECTIVES The aim of this project is to redefine colorectal cancer (CRC) at the molecular level, by identifying and validating new activated pathways and specific drug targets for defined CRC patient populations. The project will employ the complementary expertise and tools at Astra Zeneca, two academic laboratories (those of Lodewyk Wessels and Rene Bernards at the Netherlands Cancer Institute, Amsterdam) and a leading diagnostics company with an established presence in oncology (Agendia BV, Amsterdam). PROJECT OUTLINE AND STRATEGY We will first use computational approaches to perform a ‘pathway’ or ‘module’ level integration of molecular profiling (gene expression and next generation sequencing data) and extensive clinical annotation data from a collection of 400 CRC tumours to identify and prioritise pathways that are deregulated in each CRC sub-disease. Next, we will define for each pathway, targets that are amenable to drug discovery efforts, and that can be validated in cell culture models. To enable target validation, we will develop approaches to identify, based on molecular profiling data, CRC cell lines in the AZ collection that represent each molecular sub-disease. Once these are in place, target validation experiments will be conducted, using established RNAi methodology. Targets whose functions are shown to be essential for cell viability in the appropriate cell line models will then be recommended for new drug discovery projects. These results will be fed back to refine the target section procedure based on the tumor data. EMPLOYER INFORMATION The Netherlands Cancer Institute is a dedicated cancer center conducting research in all major areas of cancer, with a strong emphasis on translational research. The Bioinformatics and Statistics group (Wessels lab.) provides leadership on the collection and analysis of data for the research programs of the institute, by developing novel compuational approaches and performing state of the art analyses of a wide array of data types, including laboratory and animal experiments, clinical trials, and epidemiologic studies. REQUIREMENTS The ideal candidate is a highly motivated postdoc with a strong background in bioinformatics or computational biology. The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners: Bernards lab, Astra Zeneca and Agendia. The ideal candidate has a background in the analysis of high throughput molecular data, computational diagnostics, bioinformatics, computer science, statistics or physics with strong analytical and algorithmic skills. EMPLOYMENT CONDITIONS The temporary employment will be for a period of three years. The gross monthly salary for a Postdoc will range from €3140,- to €3.495,- and depends on previous experience. We can help you find housing. The NKI-AVL has been listed in the top 25 of ‘Best Employers’ in 2009 offering a specialized cancer research institute and hospital with good working conditions and an excellent atmosphere. INTERESTED? Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr George Orphanides, Director of Discovery Medicine, tel. +44 1625 232312 or e-mail George.Orphanides(a)astrazeneca.com. When applying please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. http://bioinformatics.nki.nl CLOSING DATE 1 May 2011

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Autumn School "Biomolecular Structure and Function - Computational Approaches"
by Barbara van Kampen 08 Nov '12

08 Nov '12

The Netherlands Society on Biomolecular Modelling (NSBM) and NBIC would like to inform you about the Autumn School "Biomolecular Structure and Function - Computational Approaches" which will be held in Essen, Germany (November 26 - 30, 2012) and in Nijmegen, the Netherlands (December 3 - 7, 2012). Overview of the programme: The autumn school will have two parts, both with a mixture of short lectures, presentations, hands-on exercises, and project work. In week 1 (26 - 30 November, 2012) one will focus on methods based on physical models of biomolecular systems. Topics of this week include molecular dynamics simulation, biomolecular electrostatics, protein-protein docking and matching, and machine learning for functional analysis. In week 2 (3 - 7 December, 2012/)/ one will deal with methods that make empirical knowledge available for modelling proteins. Topics of this week include homology modeling, ligand docking, computational solutions for structural analysis with X-ray, NMR, SAXS, or Cryo-EM. Further details are available at the websites: swift.cmbi.ru.nl/autumnschoolbioinformatics/ www.uni-due.de/autumnschoolbioinformatics/ Enclosed you will find the flyer. with kind regards, Barbara van Kampen -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl

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NSBM Fall Meeting November 26 2012
by Barbara van Kampen 11 Oct '12

11 Oct '12

The NSBM cordially invites you to visit its fall meeting November 26 2012. During the meeting, the floor will be given to PhD students and postdocs who study protein structure and/or structural bioinformatics or related topics (see a list below). The main topic for this year’s meeting will be: */“Dissecting and designing interactions”/* As guest speaker, *Dr. Carlos Camacho*of Pittsburgh University, USA, will give a lecture on an "Interactive and efficient discovery tool of small molecule protein-protein interaction antagonists". ** * * *Abstract Format* Abstracts should be limited to a maximum of 10 lines, with 12-pt font and single-spaced text, giving a short description of the research done. Please include a title in bold. The name(s) and affiliation(s) of the author(s) should follow the title. The opportunity will be given to present a poster, though this is not mandatory. If you wish to present a poster, please indicate so. *Abstract Submission* All abstracts, should be submitted electronically in MSWord via e-mail attachment to science.secr.nmr(a)uu.nl <mailto:science.secr.nmr@uu.nl>with as subject line /“NSBMmeeting 2012”/. The deadline for receipt of all abstracts is November 5^th 2012. Selected candidates will be notified no later than November 13^th 2012. Presentations will be 20 min, including a 5 min discussion. Starting PhD students are particularly encouraged to present their research. For questions regarding the abstract or meeting please contact Gerry Nicolaes, +31-(0)43 3881688, g.nicolaes(a)maastrichtuniversity.nl <mailto:g.nicolaes@maastrichtuniversity.nl> *Registration* Registration can be made free of charge via e-mail to science.secr.nmr(a)uu.nl <mailto:science.secr.nmr@uu.nl>with as subject line /“NSBMmeeting 2012”/. A lunch and coffee/tea breaks will be provided for. Should a lack of funding be a hurdle for visiting the NSBM Spring Meeting, please contact prof. Gert Vriend at vriend(a)cmbi.ru.nl <mailto:vriend@cmbi.ru.nl>so that an arrangement can be made.** ** *Topics for presentations may include, but are not limited to:* ** • Computational Biology and Bioinformatics • Computer-aided drug design • Drug design and drug discovery • Grid computing • Homology modelling • Molecular and supramolecular dynamics • Molecular modeling and simulation • Mutational analysis • Protein crystallography • Protein NMR • Protein structure analysis • Protein structure prediction • Protein-protein interactions • Protein-small molecules interaction • Protein software design • Proteomics • Structural bioinformatics • Structure-function analysis • Text mining & information extraction • Virtual screening Conference Chairs: *Prof. Dr. Alexandre Bonvin*, professor of Computational Structural Biology and *Dr. Gerry Nicolaes*, Cardiovascular Research Institute Maastricht -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl

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BeNeLux Bioinformatics Conference 2012 (BBC12): call for abstracts
by Femke Francissen 27 Sep '12

27 Sep '12

BeNeLux Bioinformatics Conference 2012 (BBC12): call for abstracts The 7th edition of the BBC12 will be organized in Nijmegen, the Netherlands on 10-11 December 2012. Key theme: "Bioinformatics at the interface". Confirmed keynote speakers: - Franca Fraternali, Molecular Structure group at King's College, London - Christine Orengo, University College London Call for abstracts: Abstracts can report research results in any area of bioinformatics, computational biology or related disciplines. Abstracts submission: http://www.nbic.nl/about-nbic/events/bbc2012/abstract-submission/ Submission deadline: 22 October 2012. Conference website: http://www.nbic.nl/bbc2012 Click here<http://www.nbic.nl/about-nbic/events/bbc2012/registration/> to register! Organizers: Barbara van Kampen<mailto:b.vankampen@cmbi.ru.nl> (Centre for Molecular and Biomolecular Informatics) Femke Francissen<mailto:femke.francissen@nbic.nl> (Netherlands Bioinformatics Centre)

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[Gtpb] Fwd: ANNOUNCEMENT: HPND12 - "Hunting for Promoters" Bioinformatics Training Course
by Pedro Fernandes 20 Sep '12

20 Sep '12

ANNOUNCEMENT HPND12 - Hunting for Promoters with NGS data with Alexander Kel, Martin Enge and Chritian Zinser Course description: This course is set-up to review the basic principles of gene regulation, first of all, by prediction of promoters and distant enhancers and silencers and by analysis of structure of the gene regulatory regions and identification of binding sites for transcription factors. The most intriguing parts of genomes, still hiding from clear understanding, are the gene regulatory regions -- promoters and enhancers. Analysis and prediction of the regulatory sites in the genome, which is now a hot topic as a result of the growth of the number of newly sequenced genomes, and the result of high throughput sequencing methodologies becoming commonplace. Also, the introduction of high throughput-sequencing based techniques for genome-wide epigenetic analysis such as ChIP-seq has revolutionized our ways for studying the gene regulatory mechanisms. of First of all, effective and robust methods for annotation of new genomes are urgently needed now.But also, recognition and analysis of these areas in the new and existing genomes becomes one of the most important parts of understanding the mechanisms of genome functioning. In this course, the attendees will learn several techniques of finding promoters and enhancers and the principles on which these methods are based. Through "hands on" exercises, several analytical tools will be displayed and the results citicized in the light of assessing their reliability and the possibilities that they open of assigning gene function based on automatic prediction. Also, the course will include an overview of the state of the art in lab techniques for studying gene regulation as well as a detailed account of data analysis for the more commonly used techniques such as ChIP-seq. Objectives The course will consist of lectures that lay out the conceptual framework as needed and and "hands on" exercises will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degree of independence. Participants will know how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how its quality can be assessed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomics and transcriptomics studies. Target Audience: The course is directed to researchers in biology, bioinformatics, biochemistry and medicine. Background knowledge in elementary bioinformatics is not absolutely necessary, but can be very useful. Please note that the PathProt brainstorming event takes place on the week just before this course. You will need to register in PathProt separately, though. Please use its specific PathProt website Course Pre-requisites: Basic biochemistry. Elementary computing skills Futher details, including application instructions available at http://gtpb.igc.gulbenkian.pt/bicourses/HPND12 thank you for your interest Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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NBIC advanced NGS course: RNA-seq data analysis course on October 15-17th
by Patrick Koks 05 Sep '12

05 Sep '12

RNA-seq data analysis course On October 15-17th, NBIC, LUMC and AMC will organise the 2nd edition of the NBIC advanced NGS course: RNA-seq data analysis. The course is open for application. Course description The course is focussed on data pre-processing, quality control, and statistical methods for detection of differential gene expression. This is an expert course for people with experience in NGS and a follow-up course on the NBIC/LUMC NGS data analysis course (September 2012 in Rotterdam.) The course will consist of seminars and hands-on Galaxy and R practicals and will focus on data pre-processing, quality control, and statistical methods for detection of differential gene expression. * RNA-seq experimental approaches * Alignment and de novo assembly * Statistics for differential gene expression * eQTL analysis and allele specific expression * Software for RNA-seq data analysis Participants of the RNA-seq course should preferably have participated in the NGS data analysis course or have demonstrated hands-on experience with NGS data analysis. Dates: October 15-17th, 2012 Venue: AMC, Amsterdam, The Netherlands Coordinator: Peter-Bram 't Hoen (LUMC) For more information and registration see our website: www.nbic.nl/?id=NGSRNAseq www.nbic.nl/?id=rnaseqappform2012 Or send e-mail to Patrick Koks (education(a)nbic.nl) The NBIC BioWise Life Sciences (BioWise-LS; www.nbic.nl/education) programme currently offers five bioinformatics courses focussing on application and data-analysis of Next-generation sequencing (NGS). All NBIC NGS courses are co-developed and co-organised by experts in the field and in close collaboration with leading research groups throughout the Netherlands. All NBIC courses are taught in English and are open to PhD students and researchers worldwide. Patrick Koks, NBIC BioWise - Education phone: #31-(0)24-3615210 e-mail: Patrick.koks(a)nbic.nl web: www.nbic.nl, www.ebiomics.org Postal Address: CMBI 260 Radboud University / UMC / NCMLS PO Box 9101, 6500 HB Nijmegen, The Netherlands __________ Information from ESET NOD32 Antivirus, version of virus signature database 7448 (20120905) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com

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