August 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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BeNeLux Bioinformatics Conference 2012: register now!
by Femke Francissen 31 Aug '12

31 Aug '12

BeNeLux Bioinformatics Conference 2012: register now! The 7th edition of the BeNeLux conference (BBC12) will be organised by the Centre for Molecular and Biomolecular Informatics (CMBI) and the Netherlands Bioinformatics Centre (NBIC). This year's key theme will be "Bioinformatics at the interface". Both registration and abstract submission for the BBC12 are now open. Dates: 10 & 11 December 2012 Venue: UMC St Radboud, Nijmegen, the Netherlands Website: http://www.nbic.nl/bbc2012 Click here<http://www.nbic.nl/about-nbic/events/bbc2012/registration/> to register! We look forward to welcoming you in Nijmegen. CMBI & NBIC Barbara van Kampen (CMBI) Femke Francissen (NBIC)

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final program invited lectures symposium Radboud University Nijmegen 6 september
by elenam＠cs.ru.nl 29 Aug '12

29 Aug '12

Dear Colleague, Please find below the final program of the invited lectures of the one-day symposium on the integrative analysis of brain diseases to be held at the Radboud University Nijmegen, The Netherlands (see http://macbrain2012.cs.ru.nl/program) A pdf version of the program with abstracts of talks can be downloaded at http://macbrain2012.cs.ru.nl/files/program-with-abstracts.pdf Registration at http://macbrain2012.cs.ru.nl/registration Could you please distribute this information to your colleagues? Thanks in advance. Kind regards, Elena Marchiori --------------- Program Thursday 6 September 2012 Opening: Elena Marchiori and Inge Huitinga 9:00 9:30 Registration, coffee and opening Session 1: Brain Banks Chair: James Ironside 9:30 10:20 Jean-Paul Vonsattel Director of the New York Brain Bank at Columbia University The NYBB at Columbia University and donor data 10:20 11:10 Maree Webster Director SMRI Brain Collection and Research Laboratory The Stanley Medical Research Institute (SMRI) Brain Collection and Database 11:10 11:30 Coffee break Session 2: Data Mining and Machine Learning Chair: Pedro Larranaga 11:30 12:20 Sophia Ananiadou Director of the National Centre for Text Mining (NaCTeM) Extracting Events of Biological Relevance from Text 12:20 13:10 Yves Moreau KU Leuven ESAT-SCD & SymBioSys Center for Computational Systems Biology Candidate Gene Prioritization by Genomic Data Fusion 13:10 14:00 Lunch break Session 3: Clinical and Pathological Studies Chair: Peter Lucas 14:00 14:50 Amanda Kiliaan Department of Anatomy/Cognitive Neurosciences, Radboud University Nijmegen On Diet and the Brain: from mice to men 14:50 15:40 Harro Seelaar Erasmus MC Genetic background of frontotemporal dementia and its relation with the neuropathology 15:40 16:00 Coffee break 16:00 16:40 Tineke van Veen Dept. of Psychiatry, Leiden University Medical Centre, The Netherlands Cross-linking pathological and clinical observations in depression and anxiety: building a genetic bridge 16:40 17:10 Inge Huitinga and Elena Marchiori Netherlands Brain Bank & Radboud University Machine Learning in Action: Mining the Netherlands Brain Bank 17:10 18:00 Closure and Drinks

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vacancies at Galapagos
by Véronique Deiteren 21 Aug '12

21 Aug '12

Dear Sir, Dear Madam, Please find below 3 vacancies in BioInformatics/BioIT for Galapagos for our Mechelen (Belgium) and Leiden (Netherlands) sites. More information can be found in attachment [Description: blocks.png] Senior Scientist Bioinformatics, MEC-115 As member of the Discovery Informatics team you will give day to day support to the research teams using dedicated BioIT/research software and perform daily bioinformatics tasks supporting the different research projects of Galapagos. Where needed you will adapt or develop new BioIT/BioInformatics applications. You will maintain the different sequence annotation pipelines and further develop new bioinformatics annotation pipelines where needed. You will configure dedicated research software in order to optimally support the research teams. You will continuously guard data consistency and data integrity over the different applications and databases. You will closely collaborate with the multidisciplinary disease biology and drug discovery teams. This position offers an exciting opportunity to develop and provide information-based services to the science and business at Galapagos. [Description: blocks.png] Scientist Bioinformatics, MEC-115b As member of the Discovery Informatics team you will give day to day support to the research teams using dedicated BioIT/research software and perform daily bioinformatics tasks supporting the different research projects of Galapagos. Where needed you will adapt or develop new BioIT/BioInformatics applications. You will maintain the different sequence annotation pipelines and further develop new bioinformatics annotation pipelines where needed. You will configure dedicated research software in order to optimally support the research teams. You will continuously guard data consistency and data integrity over the different applications and databases. You will closely collaborate with the multidisciplinary disease biology and drug discovery teams and this position offers an exciting opportunity to develop and provide information-based services to the science and business at Galapagos. [Description: blocks.png] Bioinformatician, LEI-032 This position offers a unique experience to work in an exciting and dynamic environment of a well-known international biotech company. You will give day to day support to the research teams by performing bioinformatics tasks such as data collection and analysis and by configuring dedicated research software for data management and analysis. You will continuously guard data consistency and data integrity over the different applications and databases. Where needed, you will adapt or develop new BioIT/bioInformatics applications supporting the research teams. Best regards Veronique Deiteren HR Manager Galapagos NV Generaal De wittelaan L11 A3 2800 Mechelen Belgium Tel 015 342 900 Fax 015 342 910 -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.

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6 september: one-day symposium on machine learning, brain banks and health
by E.Marchiori＠cs.ru.nl 20 Aug '12

20 Aug '12

Dear Colleague, You are cordially invited to participate to the one-day symposium on the integrative analysis of brain diseases: program and abstracts are available at http://macbrain2012.cs.ru.nl/program Registration fee is 50, 25 for master and PhD students. It includes coffee breaks, lunch and drinks. Please register at http://macbrain2012.cs.ru.nl/registration. The registration can be also paid in cash on the same day. Kind regards, Elena Marchiori

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ECCB12: Workshop Bioinformatics Training for Life Scientists: Showcases and Challenges from tutors perspectives
by Celia van Gelder 15 Aug '12

15 Aug '12

Dear colleagues, We invite you to register to the*Workshop Bioinformatics Training for Life Scientists: Showcases and Challenges from tutorsÂ perspectives* taking place on 9 September, 2012, Basel Switzerland (as a Satellite event of the European Conference on Computational Biology ECCB'12). The exciting programme can be found at: http://www.eccb12.org/WS4 *Target Audience* - Experienced and beginner trainers - Researchers involved in training *Advantages in attending* Get inspiration for your own training Be acquainted with training methods that are effectively used by expert trainers Have the opportunity to connect to the network of trainers & organizers (BTN) Be recognized by and become part of the training community This workshop represents a platform where those involved in bioinformatics training to life scientists can meet, confront and share experiences, as well as discuss future directions and collaboration in joint efforts. By the way, send your questions and remarks to celia.van.gelder(a)nbic.nl <mailto:celia.van.gelder@nbic.nl> now, and we will have the pleasure to address them during the Panel discussion of the workshop. Register now at: http://www.eccb12.org/WS4 and forward this information to any one potentially interested. Looking forward to meeting you in Basel on 9 Sept! *The organisers * Patricia Palagi (SIB Swiss Institute of Bioinformatics) Vicky Schneider (European Bioinformatics Institute, EBI) Allegra Via (Dept of Physics, Sapienza University of Rome) Celia van Gelder (Netherlands Bioinformatics Centre, NBIC) -- ECCB'12 - European Conference on Computational Biology 2012 9-12 September 2012, Basel Switzerland http://eccb12.org ---- Stay informed: http://www.eccb12.org/info.html http://twitter.com/eccb12 http://www.facebook.com/eccb12

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NGS workshop Ghent, Belgium
by Michiel Van Bel 13 Aug '12

13 Aug '12

Dear, The Bioinformatics and Systems Biology division of the Department of Plant Systems Biology (VIB -- Ghent University, Belgium) is organizing a scientific event from the 25th of November 2012 until the 5th of December 2012 about *Generation and Analysis of Next Generation Sequence (NGS) data*. This two-week workshop is sponsored by the *European Science Foundation (ESF)*, and will discuss recent advances and future perspectives in next generation sequence analysis, together with the necessary applications on the data of user submitted projects. The workshop is open to participants from across Europe, and is *fully reimbursed* (see http://bioinformatics.psb.ugent.be/ngs_workshop/workshop/registration) through the ESF. Applicants will need to fill in a one page motivation letter which will allow us to identify individuals with suitable bioinformatics experience. The deadline to submit an application is August 15. Please visit http://bioinformatics.psb.ugent.be/ngs_workshop/ for more information. kind regards, The organizing commitee PS: Can this information also be spread to interested European colleagues not subscribed to the BBC-list?NGS workshop -- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel(a)psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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(Associate) Scientist Bioinformatics @ DSM
by Roubos, Hans 10 Aug '12

10 Aug '12

Vacancy: (Associate) Scientist Bioinformatics @ DSM The Challenge As a member of the DBC Genetics Bioinformatics group, you will take part in multi-disciplinary project teams working on rational strain engineering, bioprocess development and novel bio-based products for food, feed, pharma and industrial biotechnology. Another important responsibility will be your participation in the organization, design and development of in-house data repositories and custom software. Specific duties may include database design, setting up analytical workflows, developing requirements for user interfaces, and participation in software testing. This will require effective communication and collaboration with end users, other bioinformatics experts and protein engineers. Depending on your experience, processing NGS, transcriptomics, proteomics and metabolomics data, or metabolic engineering and strain design, will be part of your activities. The Ideal We are looking for candidates with a minimum of 3 years bioinformatics experience, including thesis work, post-doctoral and/or professional experience. Expertise in NGS data analysis, integration of data from different "omics" assay types, and/or systems biology is preferred. The successful applicant will have a combined expertise on bioinformatics, computers and biology. Preferably, you are familiar with micro-organisms, HT screening and/or biotech processes. Hands-on experience with the organization and/or programming of software pipelines will be an advantage. You are a multidisciplinary team player, who takes initiative. Personal skills like problem analysis, judgment, creativity, leadership and adaptability characterize your identity. You are a good communicator. Further details: http://www.dsm.com/taleo-portal-component/en_US/cworld/index.do;jsessionid=… Hans Roubos, PhD Senior Scientist Bioinformatics DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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