October 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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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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Fwd: Bioinformatics position at ITB Milan
by Guy Bottu 25 Oct '12

25 Oct '12

-------- Original Message -------- Subject: Bioinformatics position at ITB Milan Date: Thu, 25 Oct 2012 10:20:12 +0200 From: Andreas Gisel <andreas.gisel(a)ba.itb.cnr.it> Reply-To: andreas.gisel(a)ba.itb.cnr.it To: emb-adm(a)embnet.org, Gianluca De Bellis <gianluca.debellis(a)itb.cnr.it> Dear EMBnetter Please, find attached the announcement for a bioinformatician position in ITB Milan. I would appreaciate if you could distribute this among your contacts. Best regards Andreas -- Italian EMBnet Node Institute for Biomedical Technologies - CNR Bioinformatics and Genomics Research Group Via Amendola 122/D 70126 Bari (Italy) Tel: +39 (0)80 5929662 Fax: +39 (0)80 5929690 e_mail:andreas.gisel@ba.itb.cnr.it http://www.ba.itb.cnr.it/ http://www.ba.itb.cnr.it/gisel/

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NBIC PhD Course Pattern Recognition 21-25 January 2013, Amsterdam
by Celia van Gelder 19 Oct '12

19 Oct '12

*NBIC PhD Course Pattern Recognition (3rd edition)* Date: 21-25 January 2013 Location: Amsterdam Course Coordinator: Perry Moerland (AMC) Website: http://www.nbic.nl/education/nbic-phd-school/course-schedule/pattern-recogn…. <http://www.nbic.nl/education/nbic-phd-school/course-schedule/optimisation-t…> 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(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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Last call for abstracts for BeNeLux Bioinformatics Conference (BBC12)
by Femke Francissen 17 Oct '12

17 Oct '12

*Last call for abstracts for BeNeLux Bioinformatics Conference (BBC12)* The 7th edition of the BBC12 will be organized in Nijmegen, the Netherlands on 10-11 December 2012. Key theme: "Bioinformatics at the interface". Abstracts can report research results in any area of bioinformatics, computational biology or related disciplines. Abstracts submission via: http://www.nbic.nl/about-nbic/events/bbc2012/abstract-submission/ *Submission deadline: Monday 22 October 2012* 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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status maillist
by Luc Van Wiemeersch 17 Oct '12

17 Oct '12

This maillist was unavailable due to maintenance, from 16 October till 17 October , 12h. Sorry for any incovenience --

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Job Announcement: bioinformatician/developer
by Lieven Sterck 17 Oct '12

17 Oct '12

Dear Colleagues, I also apologize for some of you who are in several mailing lists and may receive this message several time. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Open position in Informatics/Bioinformatics Crop Development Centre University of Saskatchewan College of Agriculture and Bioresources September 7, 2012 A 2-years Engineer position in Informatics/Bioinformatics: This position is funded by a research grant administered by the University of Saskatchewan under the direction of Dr. C Pozniak, Crop Development Centre, College of Agriculture and Bioresources. Background In support of the international effort (IWGSC - http://www.wheatgenome.org/) to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline (http://www.clermont.inra.fr/triannot) Its modular architecture allows for the annotation and masking of transposable elements, the structural and functional annotation of protein-coding genes with an evidence-based quality indexing, and for identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in 26 hours. It is accessible through a web interface for small scale analyses (< 100 sequences of 3Mb max) or through a server for large scale annotations (thousands of scaffolds). The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 additional genes based on new biological evidence, increasing the percentage of perfect gene prediction to 63%. TriAnnot was designed specifically for complex genomes like wheat, and systematically showed a higher fitness than other annotation pipelines. TriAnnot is easily adaptable to the annotation of other plant genomes, and should become a useful resource for the annotation of large and complex genomes in the future. However, there is a need for further improvements: - Build a virtual machine of the TriAnnot pipeline; - Improve the Gene modeling process - definitely make a choice between two combiners: Eugene and Augustus; - Incorporate new, well trained ab initio gene prediction programs; - Develop tools to display splicing variants; - Implement a module for the discovery of SNP markers; - Develop and incorporate three new panels: o mapping the gene models on selected genome models o mapping the gene models within a pre-calculated phylogeny tree o mapping the gene models within a known biological pathways; o evaluate the possibility to develop a "bogas-like" interface for wheat manual curation (see http://bioinformatics.psb.ugent.be/webtools/bogas/) Building a virtual machine is a high priority as the improved TriAnnot pipeline will be installed as a mirror site to improve the informatics infrastructure in Canada. In this respect, we would develop a collaboration with iPlant to install the TriAnnot virtual machine (TriAnnot-VM) within the iPlant cyber infrastructure located in the USA. Collaborations are already underway with the CNRS at Roscoff (C. Caron) and the IBCP at Lyon (C. Blanchet) to work on these aspects. The engineer hired for this position will be in contact with these different centers to build the virtual machine. The development of the "bogas-like" interface will be made in close collaboration with the VIB in Ghent, Belgium. Research Groups The candidate will work under the direction of Dr. C. Pozniak, University of Saskatchewan. The successful candidate will spend the first year as a Visiting Scientist in the group "Structure, Function and Evolution of the Wheat Genome" led by C. Feuillet and located at the UMR INRA-UBP GDEC in Clermont-Ferrand (France). She/he will improve further the TriAnnot pipeline (see above) and build the TriAnnot-VM in direct collaboration with P. Leroy, the research engineer in charge of the TriAnnot project in the group. She/he will interact with researchers and graduate students that are users of the pipeline. She/he will also interact with other groups involved in Genetics, Bioinformatics and with other international laboratories developing similar activities. In the second year of the project, the candidate will work at the Crop Development Centre, University of Saskatchewan, Canada in the research group led by Dr. Pozniak. She/he will install and test the TriAnnot-VM within the informatics infrastructure available at the University of Saskatchewan and use it to annotate the sequence of wheat chromosomes being sequenced by that group. The second year of the project will involve interaction with iPlant to install the TriAnnot-VM within the iPlant cyber infrastructure in US. The successful candidate will also assist with writing and preparation of manuscripts for publication. Qualifications Required The candidate must have a minimum of a Master's degree in computer science or a related field with at least three years of bioinformatics experience. The candidate should have a good knowledge in Perl, python and Object Programming. Previous experience of Perl Object Oriented Programming is recommended. Candidate has to be familiar with parallel programming (Cluster) and Cloud computing. Research experience in plant genomics is desirable. Applicant must have a clear evidence of productivity, creativity and independence; excellent communication skills, and must be proficient in both reading and writing in the English language and an ability to work both independently and within a team. Candidates must have demonstrated report writing and publication capabilities. Salary: A competitive salary is available with full benefits (pension, health & dental, life insurance). Salary will be commensurate with experience. The University of Saskatchewan is committed to employment equity and applications from women, aboriginal peoples, visible minorities and persons with disabilities are encouraged. All qualified individuals are invited to apply, but Canadian citizens and permanent residents will be given priority. Contacts Parties interested in the position should provide by email a letter of application, Curriculum Vitae with a publication list, a brief statement of research and interests, and the names and contact information for at least three references, to: Chris Barker Genome Prairie Senior Project Manager Room 2E80, Agriculture Building Department of Plant Sciences University of Saskatchewan Saskatoon, Saskatchewan S7N 5A8 cbarker(a)genomeprairie.ca Review of applications will begin September 15th, 2012 and continue until the position is filled. All applicants will be notified shortly thereafter. The preferred start date for the position is November 1st, 2012. -- UMR 1095 INRA/UBP - Génétique, Diversité et Ecophysiologie des Céréales Group "Structure, Fonction & Evolution des Génomes de Blé" Philippe LEROY 234 Avenue du Brèzet 63100 CLERMONT-FERRAND - FRANCE Tel: +33 (0)4.73.62.43.37 Fax: +33 (0)4.73.62.44.53 Cellular : +33 (0)6.72.62.76.06 UMR 1095 : http://www.clermont.inra.fr/umr1095/ TriAnnot : http://www.clermont.inra.fr/triannot/ DE^CODAGE : http://www.inra.fr/decodage Curriculum Vitae : http://www.phleroy.fr/CV_PL.html

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maillist status
by Luc Van Wiemeersch 17 Oct '12

17 Oct '12

This maillist was unavailable due to maintenance, from 16 October till 17 October , 11h. Sorry for any inconvenience --

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