July 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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[Gtpb] ARANGS12 - Bioinformatics Training Course anouncement
by Pedro Fernandes 31 Jul '12

31 Jul '12

ANNOUNCEMENT Here is a useful NGS analysis course suitable for a wide variety of researchers. The requirements are minimal. Participants will understand usage of NGS data analysis tools and will know how to chain them into very handy analytical pipelines. Plenty of worked examples and exercises in 4 days. NOTE: The application deadline is quite short, our excuses. We are using an unforeseen window of availabilities. It does matter to apply quickly, as the course dates are in early September. BIOINFORMARICS HANDS-ON TRAINING COURSE ARANGS12 - Automated and reproducible analysis of NGS data with Rutger Vos (Naturalis, Leiden, NL) and Darin London (Duke University, USA) IMPORTANT DATES for ARANGS12 Deadline for applications: August 27th 2012 Notification of acceptance dates: EARLY: August 15th 2012 (on special request, see Application) NORMAL: September 3rd 2012 Course date: September 11th - September 14th 2012 Course Description Next generation sequencing (NGS) technologies for DNA have resulted in a yet a bigger deluge of data. Researchers are learning that analysing such data sets is becoming the bottleneck in their work. In many cases, several steps in these analyses are fairly generic (e.g. quality control filtering, alignment to reference sequences, typing) so that off-the-shelf pipelines can be applied. In other cases, novel research approaches require development of new analysis pipelines. Either way, all analysis steps should be repeatable and any changes made to the data (e.g. renaming, annotation, alignment) should be recorded so that the provenance of the results is clear and inferences are reproducible. In this brief workshop we will establish several best practices of reproducibility and provenance recording in the (comparative) analysis of data obtained by NGS. In doing so we will encounter the commonly used technologies that enable these best practices by working through use cases that illustrate the underlying principles. Target audience This course is aimed at researchers who've recently embarked on NGS projects and now, faced with large amounts of data, would like to learn how to automate generic analysis steps and develop new ones in a reproducible (and shareable) way. The course will be illustrated with examples from specific single-celled and multicellular taxa but the concepts are applicable to any species not explicitly referred to in the course. The ideal attendee is a scientist who is not afraid to get his/her hands dirty to acquire the computer-literacy skills for dealing with the informatics side of data analysis. Futher details, including application instructions available at http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS12 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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PhD Position: Engineering Executable Models of Biological Networks
by Anton Feenstra 31 Jul '12

31 Jul '12

Dear colleagues, Please find attached a vacancy for a a PhD position in our group on /Engineering Executable Models of Biological Networks/. Deadline for application: September 1st. Sincerely, Anton Feenstra _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam | |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 | | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | |_____________|_______________________________________________________|

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BIOCOMP BG 2012 Call for Abstracts! Only 1 month left to submit your abstract.
by Michiel Van Bel 27 Jul '12

27 Jul '12

*Only 1 month left to submit your abstract to BIOCOMP BG 2012!* * * *International Conference on Bioinformatics and Computational Biology - BIOCOMP BG 2012 *(http://biocomp.bio.uni-plovdiv.bg/). *Topics* * * Topics of interest include, but are not limited to: High-performance bio-computing High-throughput sequencing data analysis (NGS) Bio-ontologies Molecular evolution Comparative genomics Molecular modeling and simulation Computational genetics Computational proteomics Data mining and visualization Software tools and applications Gene expression analysis Gene networks Structural biology Genome analysis Databases Systems biology *Publications* * * All accepted abstracts will be published in the conference abstract book. Best 20 abstracts will be peer-reviewed and published as full text manuscripts in a Special Issue of Springer and Elsevier journals: *Interdisciplinary Sciences: Computational Life Sciences (ISSN: 1867-1462).* ***Journal of Computational Science (ISSN: 1877-7503) * * Venue* The venue of the conference is 4-star All-inclusive Sunny Day Black Sea resort, Bulgaria *Registration and abstract submission* All the actions related to the *BIOCOMP 2012 * (abstract submission, registration etc) may be completed via the Conference website at http://biocomp.bio.uni-plovdiv.bg/ * * *Accommodation* * * IMPORTANT: Accommodation is included in the conference registration fee. *Important dates* * * Abstract Submission Deadline - 20 August 2012 (submitted abstracts will be notified for acceptance after 48h of submission) Early Registration Fee Payment Deadline - 20 August 2012 Arriving, Poster set up, Registration -- 19 September 2012 Plenary and Poster Sessions -- 20-21 September 2012 You may find details of the Conference visiting the Conference website at http://biocomp.bio.uni-plovdiv.bg/ Looking forward to see you in Bulgaria! Dr. Vesselin Baev Research Assistant Professor University of Plovdiv Dept. Plant Phys. and Molecular Biology Bioinformatics SMART Group Tzar Assen 24,Plovdiv 4000, BULGARIA Office:+359 32 261 (560); Mobile:+359 89 43 80 945 vebaev(a)gmail.com <mailto:vebaev@gmail.com>; baev(a)uni-plovdiv.bg <mailto:baev@uni-plovdiv.bg>; CV: http://plantgene.eu/ -- ================================================================== 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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Job Opening: Bioinformatician at OpenAnalytics (Belgium)
by tobias.verbeke＠openanalytics.eu 24 Jul '12

24 Jul '12

OpenAnalytics is an international company providing data analysis services and products across geographies and industrial sectors. We are currently looking to expand our team of bioinformaticians with a candidate who fits the following profile: Bioinformatician: MSc / PhD in Computational Biology, Bioinformatics or Computer Science A detailed description can be found at http://www.openanalytics.eu/jobs Kind regards, Tobias Verbeke -- Tobias Verbeke Manager OpenAnalytics BVBA Kortestraat 30A 2220 Heist-op-den-Berg Belgium E tobias.verbeke at openanalytics.eu M +32 499 36 33 15 http://www.openanalytics.eu

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NGS workshop Ghent
by Michiel Van Bel 23 Jul '12

23 Jul '12

Dear, The Bioinformatics and Systems Biology division of the Department of Plant Systems Biology (VIB -- Ghent University) 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? -- ================================================================== 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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Position Available: Bioinformatics & Integrative Genomics Specialist, VIB & KU Leuven
by Stein Aerts 19 Jul '12

19 Jul '12

Bioinformatics & Integrative Genomics Specialist - Manager Bioinformatics Consulting Core The VIB Center for the Biology of Disease at the University of Leuven is a vibrant and international research centre where key issues relevant to major human health challenges are tackled. Within this Center, we are seeking a highly motivated and experienced Bioinformatics & Integrative Genomics Specialist. You will collaborate with the 14 research groups within the Center and provide essential input on computational biology aspects of their research projects. In this job you will be confronted with exciting research questions in cancer and neurodegeneration; and with a broad spectrum of computational challenges and omics data sets. You will be embedded in the Laboratory of Computational Biology at the University of Leuven (Stein Aerts Lab: http://med.kuleuven.be/bioinformatics) and you will be part of an active bioinformatics community in Leuven, allowing daily interactions with colleague bioinformaticians. Your main activity will be to provide support for large-scale data analysis, and to setup and manage a Bioinformatics consulting core within the Center through which: you will collaborate with wet-lab scientists on a variety of research problems. You will deal with the data analysis part of the research project. The focus of the service will be mainly on genome bioinformatics: microarrays, RNA-Seq, ChIP-Seq, exome/genome re-sequencing, gene regulation, network biology, pathway analysis, gene prioritization, data integration, text-mining, etc. you will gradually manage a team of 1-3 Bioinformatics experts you will interact with the core facility of the VIB-BITS (http://www.bits.vib.be/) with the Genomics Core facility at the University Hospital (allowing close interaction with the next-generation sequencing instruments Illumina HiSEQ2000, Illumina MiSEQ, Roche 454, PacBio), and with other consulting units and research groups, for example for advanced biostatistics or proteomics data analysis. you will make hardware (e.g., local linux servers, high performance computing, cloud), software (e.g., a local Galaxy instance), and analysis pipelines (e.g., scripts, workflows) available to scientists; train and guide scientists to analyze their own datasets; and organize training courses and seminars. you will take your own initiatives to continuously optimize the bioinformatics flux through the Center, through the VIB and through the Group of Biomedical Sciences, for example to organize a weekly "data clinic" where small user problems can be solved. Qualifications: Master's degree in Life sciences or computational field PhD degree is strongly preferred At least five years bioinformatics experience Proven track record of high-impact publications in the field of computational biology, analysis of high-throughput data sets, data integration Solid experience with Linux, programming (e.g. Java), and database management (sql and no-sql). Solid experience with bioinformatics programming and statistics for bioinformatics, including scripting (e.g., Python), R (incl. Bioconductor), Galaxy, UCSC Genome Browser, Ensembl API, etc. Thorough understanding of molecular and developmental biology, and of disease biology (preferably cancer and/or neurological disorders). Experience with the analysis of next-generation sequence data is a plus: whole exome re-sequencing, whole-genome re-sequencing, SNP/indel calling, CNV, Structural variation; RNA-Seq, ChIP-Seq Experience with pathway analysis and cis-regulatory sequence analysis is a plus. Knowledge of machine learning and data mining is a plus. Links: The Center for the Biology of Disease The Laboratory of Computational Biology Center for Human Genetics University of Leuven Highly motivated candidates can apply by sending a motivation letter, names and contact information for three references, publication list, and CV to stein.aerts(a)med.kuleuven.be.

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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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