November 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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NBIC PhD Course Pattern Recognition 21-25 January 2013, Amsterdam
by Celia van Gelder 05 Dec '12

05 Dec '12

With apologies for double posting , the mail from Oct 19 contained the wrong hyperlink to the course page! * * *NBIC PhD Course Pattern Recognition (3rd edition)* Date: 21-25 January 2013 Location: Amsterdam Course Coordinator: Perry Moerland (AMC)<http://www.nbic.nl/education/nbic-phd-school/course-schedule/optimisation-t…> Website:http://www.nbic.nl/education/nbic-phd-school/course-schedule/pattern-recognition/ Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ On Jan 21-25, 2013 the NBIC PhD School organises the third edition of the PhD Course 'Pattern Recognition' in Amsterdam. The course aims at PhD students with a background in bioinformatics, computer science or a related field. The course introduces basic techniques from the fields of pattern recognition and machine learning to solve bioinformatics problems. After having followed this course, a student should have an overview of basic pattern recognition techniques and be able to recognize what method is most applicable to classification problems (s)he encounters in bioinformatics applications. This course is part of the Education Programme of the NBIC PhD School. The PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on the NBIC website (www.nbic.nl <http://www.nbic.nl> -> Education -> NBIC PhD School). For more information about the course you can contact Celia van Gelder (NBIC Education) at education(a)nbic.nl -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail:C.vanGelder@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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NBIC advanced NGS course: "de novo assembly from NGS data"
by Patrick Koks 30 Nov '12

30 Nov '12

De novo assembly from NGS data This advanced NGS course is part of the NBIC PhD-school On January 8-9th, NBIC, WUR and LUMC will organise the PhD advanced NGS course: "De novo assembly from NGS data". Course Coordinators: Gabino Sanchez-Perez (WUR), Jan van Haarst (WUR), Johan den Dunnen (LUMC), Leon Mei (NBIC) Venue: Wageningen UR, The Netherlands De novo assembly from (short read) NGS data is challenging and may require tailored approaches for different complex genomes like those of polyploid plants. After a quick introduction into NGS techniques and platforms, this course will cover topics like: Sequencing strategies using short– or long-read sequences, paired-end and mate-pairs and having a (remotely related) reference genome or not. Elementary steps like Quality assurance and read filtering are essential and much of your results depend on the wise choice of the right algorithm and assembler with your specific type of data, data coverage and genome. Closing the gaps and finishing strategies, functional annotation and comparative genomics will conclude this course. This hands-on course is targeted at PhD's and researchers with experience in genomics or NGS data analysis. For more information, check: http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsdenovo/ The course programme and additional information for travelling and staying will be published here soon. For registration and information about course fees, you can also directly go to: http://www.nbic.nl/education/nbic-phd-school/enrolment/ Here, you can also go to the pre-registration page where you can express your interest in our other courses that are planned but not scheduled yet. This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organize high level education and training for PhD-students in bioinformatics and life sciences. All NBIC 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. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website (www.nbic.nl<http://www.nbic.nl> -> Education -> NBIC PhD School). For more information, you can send e-mail to Patrick Koks (education(a)NBIC.NL<mailto:education@NBIC.NL>) Regards, The NBIC BioWise team Patrick Koks, NBIC BioWise – Education Tuesday – Wednesday - Thursday phone: #31-(0)24-3615210 e-mail: Patrick.koks(a)nbic.nl<mailto:Patrick.koks@nbic.nl> web: www.nbic.nl<http://www.nbic.nl/>, www.ebiomics.org<http://www.ebiomics.org/> Postal Address: CMBI 260 Radboud University / UMC / NCMLS PO Box 9101, 6500 HB Nijmegen, The Netherlands

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BBC12 - Extended registration deadline: November 28!
by Femke Francissen 26 Nov '12

26 Nov '12

*BeNeLux Bioinformatics Conference (BBC12) - extended registration deadline - November 28!* Two more days to register for the BBC12! Register now via: http://www.nbic.nl/about-nbic/events/bbc2012/registration/ The 7th edition of the BBC12 will be organized in Nijmegen, the Netherlands on 10-11 December 2012. Key theme: "Bioinformatics at the interface". Conference website: http://www.nbic.nl/bbc2012 Contact: Barbara van Kampen (b.vankampen(a)cmbi.ru.nl<mailto:b.vankampen@cmbi.ru.nl>), Centre for Molecular and Biomolecular Informatics, UMC St Radboud Nijmegen Femke Francissen (femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>), Netherlands Bioinformatics Centre

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Invitation of Plant Genomics Minisymposium
by Yao-Cheng Lin 22 Nov '12

22 Nov '12

Reminder: It's an open seminar. No need for registration. sorry for cross-posting Dear Colleagues: We would like to invite you to the "Plant Genomics Minisymposium" organized by Prof. Yves Van de Peer (PSB, VIB-UGent). This minisymposium is in conjunction with the ESF sponsored workshop "Generation and Analysis of Next Generation (NGS) Data". You can find the up-to-date progresses and the future perspective in the field of plant genomics during this minisymposium. Plant Genomics Minisymposium Date: 27th of November (Tuesday), 2012 Location: Jozef Schell seminar room, VIB FVMS building, Technologiepark 927 Zwijnaarde Program: 9:00 – 9:45 Sequencing complex plant genomes : the impact of New Sequencing Technologies. Prof. Patrick Wincker (Genoscope, France) 9:45 – 10:30 The past, present, and future of RNA sequencing and expression quantification. Prof. Manfred Grabherr (Uppsala University, Sweden) 10:30 - 11:00 Coffee break 11:00 – 11:45 Journey through the past: 200 million years of plant evolution Prof. Yves Van de Peer (Ghent University, Belgium) Contact: More information of this minisymposium please contact Dr. Yao-Cheng Lin (yalin(a)psb.vib-ugent.be)

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Fwd: Vacant position bioinformatics SESVanderHave
by Olivier Delgrange 20 Nov '12

20 Nov '12

-------- Message original -------- Sujet: vacant position bioinformatics SESVanderHave Date : Mon, 19 Nov 2012 11:14:28 +0000 De : Willems, Glenda <Glenda.Willems(a)sesvanderhave.com> Pour : olivier.delgrange(a)umons.ac.be <olivier.delgrange(a)umons.ac.be> Cher Dr. Delgrange, Je suis employée en tant que bioinformaticienne à la société SESVanderHave, située à Tirlemont. Nous produisons des semences de betteraves qui sont vendues mondialement. Nous sommes actuellement à la recherche d'un(e) bioinformaticien(ne) pour renforces notre équipe a Tirlemont. L'annonce de ce poste est attachée à cet email. Est-ce que vous pourriez faire circuler cette offre au sein de votre département, et/ou laboratoire, ou encore la transférer à des personnes qui pourraient être intéressés par ce job ? S'il est possible de publier cette annonce sur internet, sur le site des offres d'emplois pour les anciens étudiants par exemple, n'hésitez pas à le faire, ou à transférer cette email aux personnes compétentes. Merci d'avance de votre aide. Sincères salutations, Glenda Willems *Glenda**Willems* Bioinformatician Description: spacer *SESVANDERHAVE N.V./S.A.** *Phone: +32 16808392 www.sesvanderhave.com Description: S:\Workdata\SESV\SESVanderHave Email Template (83002-SESV)\ontwerp\Signature\Signature HTML - before install\img\logo.gif Description: environmentalwarning Please consider the environment before printing this e-mail

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NGS data manager (in dutch)
by Tim De Meyer 16 Nov '12

16 Nov '12

Gelieve te verspreiden via de bbc list, hartelijk dank, Tim De Meyer Vacature: Data manager next-generation sequencing data (ATP) Functie-inhoud High-throughput toepassingen, zoals next-generation sequencing, worden steeds belangrijker in het hedendaags biologisch en medisch wetenschappelijk onderzoek. Het labo voor Bioinformatica en Computationele Biologie "BIOBIX", (Vakgroep Mathematische Modellering, Statistiek en Bioinformatica aan de faculteit Bio-ingenieurswetenschappen UGent), werkt nauw samen met het sequencing team van NXTGNT. BIOBIX zorgt in deze samenwerking voor de preprocessing en statistische verwerking van de bekomen data. We zoeken op korte termijn een enthousiaste medewerker om ons team van "genome hackers" te versterken, initieel voor een periode van 4 jaar (onmiddellijk te beginnen). De belangrijkste taak is het dagelijkse management van grote hoeveelheden next-generation sequencing data , i.e. data transfer, veilige opslag en preprocessing. Daarnaast word je nauw betrokken in een onderzoeksproject "PLASTOSCINE" dat leerprocessen in de hersenen op moleculair niveau in kaart brengt. Functieprofiel Je hebt een diploma niveau graduaat of industrieel ingenieur in de bioinformatica (brede zin), of equivalent door ervaring. Grondige kennis van PERL en SQL en het kunnen werken in een linux-omgeving (command line) zijn absolute vereisten. Ervaring met website-ontwikkeling, server beheer (soft- en hardware) en statistische data-analyse (bij voorkeur in R) zijn een plus. De kandidaat werkt graag in teamverband en bezit tevens voldoende verantwoordelijkheidszin en flexibiliteit om zelfstandig en accuraat problemen op te lossen. Goede kennis van Nederlands en Engels zijn noodzakelijk. Hoe solliciteren? Stuur je CV, motivatie en 2 referenties naar Tim.DeMeyer(a)UGent.be voor 15 december 2012. ----------------------------------------------- Prof. Tim De Meyer, PhD MRP Nucleotides 2 Networks BIOBIX Lab. for Bioinformatics and Computational Genomics BW10 - Dept. of Mathematical Modelling, Statistics and Bioinformatics Faculty of Bioscience Engineering Coupure Links 653, 9000 Ghent Ghent University - Belgium www.biobix.be / www.nucleotides2networks.be / www.researcherid.com/rid/D-3892-2011 Tel.: +3292649922 (office)

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BBC12 - programme online & register now!
by Femke Francissen 16 Nov '12

16 Nov '12

*BeNeLux Bioinformatics Conference (BBC12) - programme online* The 7th edition of the BBC12 will be organized in Nijmegen, the Netherlands on 10-11 December 2012. Key theme: "Bioinformatics at the interface". You can now find the final programme on the conference website! Registration is still possible until November 26th, but the number of hotel rooms is limited, so if you would like to book a hotel room, please register a.s.a.p.! Specials for Students @ BBC12 The RSG Netherlands invites PhD-students and junior researchers for a social event on "BBC Eve", Sunday December 9th, starting from 5:30 pm in Nijmegen. The event will provide a great opportunity to explore the oldest city of the Netherlands, and to meet other (PhD-)students who will visit the BBC the next two days. You can register for the social event by sending an e-mail to rsg-netherlands(a)iscbsc.org<mailto:rsg-netherlands@iscbsc.org>. Participation of MSc and BSc students to the BBC is sponsored by the NBIC Education Programme BioWise and by CMBI (Radboud UMC Nijmegen). Students can participate by paying a reduced conference fee of 15 Euro per conference day. MSc and BSc students who want to visit the conference are requested to register themselves by sending an email to Barbara van Kampen (b.vankampen(a)cmbi.ru.nl<mailto:b.vankampen@cmbi.ru.nl>). Conference website: http://www.nbic.nl/bbc2012 Registration via: http://www.nbic.nl/about-nbic/events/bbc2012/registration/ Contact: Barbara van Kampen (b.vankampen(a)cmbi.ru.nl<mailto:b.vankampen@cmbi.ru.nl>), Centre for Molecular and Biomolecular Informatics, UMC St Radboud Nijmegen Femke Francissen (femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>), Netherlands Bioinformatics Centre

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opened position: Postdoc - Bioinformatics, University of Liège
by marc.hanikenne＠ulg.ac.be 14 Nov '12

14 Nov '12

Dear all, Please find here below and in attached pdf a Bioinformatics job offer. Could you please forward this announcement to your contacts? Many thanks, With best regards, Marc Marc Hanikenne, PhD FRS-FNRS Research Associate Functional Genomics and Plant Molecular Imaging Center for Protein Engineering (CIP) Plant Biology Institute, B22 Dpt of Life Sciences University of Liège Blv du rectorat, 27 B4000 Liège Belgium Tel. +32-4-3663844 Fax. +32-4-3662960 skype: marc_hanikenne >>>>>>>>>>>>>>>>>>>> Postdoctoral position - Bioinformatician A bioinformatic postdoctoral position is available at the Unit of Functional Genomics and Plant Molecular Imaging (Dr. Marc Hanikenne) of the Centre For Protein Engineering (CIP, University of Liège, Belgium). The position is opened to non-belgian residents for an initial period of one year, with the possibility of an extension up to 2 years after positive evaluation. The start date is April 1st 2013, but is opened for discussion. Context In the course of evolution, plants adapted to widely differing metal availabilities in soils. The Brassicaceae Arabidopsis halleri is a so-called metal hyperaccumulator plant. A. halleri tolerates heavy pollution of soils by zinc and cadmium and accumulates high zinc concentrations in leaf biomass. Metal hyperaccumulators constitute fascinating models to study adaptations to hostile environments, the mechanisms of speciation and the evolution of naturally-selected complex traits. Job description The Postdoc will be involved in the analysis of NGS data (RNA-Seq, epigenome sequencing) aiming to determine the contribution of DNA methylation in gene regulation and adaptation in A. halleri. The Postdoc will also be in charge of setting-up and running the computational tools necessary for data analyses. Profile We are seeking a candidate with a degree in Biology and/or Bioinformatics with doctoral or postdoctoral experience in the analysis of NGS data. Experience with the UNIX command shell is required. Programming skills (perl, python and/or R) are a plus. The candidate should be fluent in English, have good ability to work in an interdisciplinary environment and have a demonstrable publication track record. Contact Please submit a cover letter, a full C.V., and the contact details (with name, email, address, phone number) of at least 2 reference persons to marc.hanikenne(a)ulg.ac.be. http://www.cip.ulg.ac.be/

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