September 2011 - 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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Integrative Bioinformatics 2011: 2nd call for abstracts
by Jack Leunissen 16 Jul '12

16 Jul '12

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We invite you to register for the conference, and to send in an abstract for a presentation at the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the IB2011 Special Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract is January 15th; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011. The best poster will receive an award sponsored by IMBio e.v. The conference website is open for registration and abstract submission, and can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. We hope to meet you in March in Wageningen. On behalf of the organizing committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V. == Disclaimer: We have tried our best to remove duplicate e-mail addresses from our mailing list to reduce the amount of clutter in your mailbox. It may nevertheless still happen that you receive this mail via different channels. We apologize if you receive this mail more than once.

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Bioinformatics PhD student job opening at Radboud University Nijmegen Medical Centre
by Sacha van Hijum 23 Dec '11

23 Dec '11

Dear all, there is a job-opening for a bioinformatics PhD student at the Radboud University Nijmegen Medical Centre. Closing date: 2nd of October 2011. For those interested, please see below for details. Best regards, Sacha van Hijum Job profile The PhD student will work in a multidisciplinary team with other scientists and medical doctors to discuss, plan and perform bioinformatics research in a highly stimulating environment. Work-place will be the Laboratory of Pediatric Infectious Diseases (Prof. dr. P. Hermans) and the Bacterial Genomics group (Dr. S. van Hijum). • Independently generate and analyze data • Present results at (inter)national scientific meetings and in international peer-reviewed journals Requirements • Msc degree in (molecular) life sciences, specializing in bioinformatics • Background in statistics and understanding of bioinformatics algorithms. Knowledge of Perl/Python and R is a plus • Preferably experience in microbiology, molecular biology and biochemistry • Fluent in English (speaking, reading and writing) • An independent and well-structured working style • Teamplayer and a strong motivation to succeed in scientific and translational research Organization unit Laboratory of Pediatric Infectious Diseases The Laboratory of Pediatric Infectious Diseases at Radboud University Nijmegen Medical Centre is an academic research lab in which scientists and medical doctors work closely together to conduct translational research on the pathogenesis, immunology, and epidemiology of pediatric respiratory tract infections. Our studies aim to increase the molecular and clinical understanding of the interactions occurring between host and pathogen during infection. This knowledge is used to design improved and novel diagnostic, therapeutic, and preventive strategies. The Laboratory of Pediatric Infectious Diseases participates in the Nijmegen Institute for Infection, Inflammation, and Immunity (N4i) and the Nijmegen Center for Molecular Life Science (NCMLS), with focus on basic science and its translation into pioneering treatments for disease. The innovations are advanced through technology platforms such as genomics, proteomics, and molecular imaging. The Laboratory of Pediatric Infectious Diseases works in close collaboration with the… Bacterial Genomics group Focus of the Bacterial Genomics group (Radboud University Nijmegen Medical Centre) is on the bioinformatics analysis of ~omics data of (consortia of) bacteria in the context of industrial fermentations, health and safety. The research involves (meta)genome sequencing and assembly, annotation, comparative genomics, RNA-seq, transcriptomics and multivariate analysis of ~omics datasets, all in relation to exploration and exploitation of the enormous microbial diversity that is found in Nature. The Bacterial Genomics group is part of the CMBI (Centre for Molecular and Biomolecular Informatics). The CMBI pursues a rigorous research program with topics ranging from computational small-molecule chemistry to bioinformatics. The CMBI is among the largest bioinformatics departments in the Netherlands producing dozens of high impact peer-reviewed publications each year. It consists of 4 research groups (Prof. Vriend, Prof. Huynen, Prof. de Vlieg and Dr. van Hijum) with strong connections with the NBiC, centre of excellence and the largest bioinformatics cluster in the Netherlands. Information Prof. dr. P.W.M. Hermans, head of the laboratory, (024) 3666406, P.Hermans(a)cukz.umcn.nl Dr. A.L. Zomer, bioinformatician, (024) 3651545, A.Zomer(a)cukz.umcn.nl Dr. S.A.F.T. van Hijum, group leader Bacterial Genomics (024) 3619389, svhijum(a)cmbi.ru.nl More information and online application via this link: http://www.umcn.nl/OverUMCstRadboud/werkenbij/Pages/Vacature.aspx?VacatureN… -- Dr. Sacha van Hijum Group leader CMBI Bacterial Genomics Group leader Bioinformatics NIZO food research B.V. Bioinformatics coordinator Top Institute Food and Nutrition T: +31(0)318 659 570 F: +31(0)318 650 400 M: +31(0)624782895 E: sacha.vanhijum(a)nizo.nl or svhijum(a)cmbi.ru.nl P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands

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CAMDA'11 Announcement
by Yves Moreau 12 Oct '11

12 Oct '11

On behalf of Simon Lin, chair of CAMDA'11 > > ------------------- > CAMDA'11 - ISMB Satellite Meeting, Vienna, 15-16 July 2011 -- > > www.camda.info > > Programme announcement & Call for Posters > > Dear colleague! > > We enthusiastically invite you to attend this year's conference on > > Critical Assessment of Massive Data Analysis (CAMDA) . > > which will be held 15-16 July 2011 in Vienna, Austria (www.camda.info) > > > The early registration discount for CAMDA/ISMB ends 3 June – book now if you want to join us! This year's exciting line up of keynote speakers includes Terry Speed (WEHI), John Storey (Princeton) and Stefano Volinia (Ferrera). See the full two-day programme for details on papers and events... > > CAMDA still accepts poster submissions (abstracts will be published in the conference proceedings). > > > CAMDA was founded in 2000 to provide a forum for the critical assessment of different techniques used in large-scale data analysis in the life-sciences, such as for high-dimensional gene expression profiling. It aims to establish state-of-the-art analysis methods, as well as identify progress and highlight promising directions for future efforts. To this end, CAMDA adopted the approach of a scientific community-wide contest, with everybody analysing the same data sets. Researchers worldwide are invited to take the CAMDA challenge, which has become a prominent fixture (cf. Nature Methods 5, 569). Accepted contributions are presented through talks and posters, and the results and methods of the different analyses are discussed and compared at the conference. > > As a special focus this year, we consider the integrated analysis of a particularly rich structured data set that includes gene and miRNA expression, DNA SNPs, copy number variation, and methylation for about 500 matched samples. With the fast ongoing development of novel genome-wide experimental techniques (such as next generation sequencing), an assessment of how we can gain better insight from an integration of heterogeneous large-scale data is particularly topical. > > CAMDA was founded by Simon Lin and Kimberly Johnson at Duke University (Nature 411, 885. Nature 424, 610). In 2006 CAMDA became a roving conference, with recent venues including Valencia and Chicago. This year, we will host CAMDA in Austria. For the first time, the conference is run as an official Satellite meeting of ISMB/ECCB, providing further opportunities for interaction with colleagues at the conference. > > We can still accept suitable posters for presentations of recent topical work in the dedicated poster session. Poster abstracts are published in the conference proceedings. > > Please also distribute this announcement to other colleagues who might be interested. > > We look forward to seeing you in Vienna! > > > David Kreil (Boku) > Joaquin Dopazo (CIPF) > Simon Lin (Northwestern) > (chairs) > > > Submission of poster abstracts: open (accepted in order of submission) > Early registration closes: 3 Jun 2011 > CAMDA 2011 Conference: 15-16 Jul 2011 > ISMB/ECCB 2011 Conference: 17-19 Jul 2011

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NBIC PhD course Protein Structures: production, prowess, power, promises, and problems
by Celia van Gelder 27 Sep '11

27 Sep '11

*NBIC PhD course Protein Structures: production, prowess, power, promises, and problems * _Date:_ 31 Oct- 4 Nov 2011 _Course coordinator_: Gert Vriend _Location:_ Center for Molecular and Biomolecular Informatics (CMBI), UMC Radboud, Nijmegen, the Netherlands _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/ _ _ _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ *Target audience//* The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. *Course Description //* In the right hands, protein structures are a 'power'ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the 'production' of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro's and cons so a certain 'prowess' is needed to follow all 'promises' and start attacking bio-medical 'problems' using protein structures. The course will be split in three parts. Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. Part 3) Applying all that was learned in real-life example studies. *Course topics * Day 1: Homology modelling Day 2: Protein structure determination and validation Day 3: Electrostatics and molecular dynamics Day 4: Protein structure comparison Day 5: Own project executed with help from CMBI staff. Examples of questions you will be able to answer after follwing the course: 1) Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? 2) This enzyme converts mannose. Can I make is specificity broader? 3) This enzyme doesn't function in my in vitro assay. Should I add some ions? 4) I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? 5) This receptor binds a ligand, but if I look at the structure, that ligand doesn't fit at all. Can I predict motions that take place upon ligand binding? More information about the course programme can be found on:/ /http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/./ / *NBIC PhD School//* This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on http://www.nbic.nl => Education => NBIC PhD School. *More information//* For more information about the course you can contact Celia van Gelder (NBIC Education) at celia.van.gelder(a)nbic.nl. ** -- 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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Seminar invitation of Complete Genomics
by Joachim Jacob 09 Sep '11

09 Sep '11

*** SEMINAR INVITATION *** Complete Genomics, a whole human genome re-sequencing service provider, and BITS, the VIB Bioinformatics Training and Services Facility, are pleased to invite you to a complimentary event including presentations from leading researchers. Discover how large-scale, accurate and affordable whole human genome sequencing helps researchers advance their understanding of the impact of genetic changes on cancer and other diseases. *** When *** Monday, October 3, 2011 10:00 a.m. -- 5:15 p.m. *** Where *** University of Leuven, Gasthuisberg Campus Pentalfa Auditorium Teaching and Research Building, Herestraat 4, 3000 Leuven, Belgium *** Flyer *** Download on http://dl.dropbox.com/u/18352887/VIB-Agenda.pdf *** Registration*** - Lunch and refreshments will be served. - Space being limited, please register today for this complimentary event: http://info.completegenomicsinc.com/VIB-October-2011.html *** About *** Complete Genomics is the complete human genome sequencing company that has developed and commercialized an innovative DNA sequencing platform. The Complete Genomics Analysis Platform (CGA^(TM) Platform) combines Complete Genomics' proprietary human genome sequencing technology with its advanced informatics and data management software. Complete Genomics offersthis solution as an innovative, end-to-end, outsourced service, CGA Service, which provides customers with data that is immediately ready-to-use for genome-based research. ================================================================= Please feel free to pass along this email to other colleagues who may be interested in learning about accurate and affordable whole human genome sequencing provided as a turnkey service.

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