April 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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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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International Chemical Discovery and Design Course, 18-22 June 2012, Nijmegen, the Netherlands
by Celia van Gelder 08 May '12

08 May '12

International Chemical Discovery and Design Course June 18th-22nd 2012, the Computational Drug Discovery (CDD) Group of the Radboud University Nijmegen organizes a course about Chemical Design and Discovery, in cooperation with NBIC and the Netherlands eScience Center. This course covers the recent advances in discovery informatics, with a focus on the application of e-science to real life problems. Different scientific concepts and programs will be introduced and discussed, which are part of the modern drug, food supplement and ingredient discovery pipeline from target discovery & validation to lead discovery & optimization. The morning sessions will introduce key concepts related to the use of computers for chemical discovery in the pharmaceutical industry and other life science pursuits and will be of general interest to anybody in these or other chemistry fields. For the first time we were able to invite keynote speakers from the Netherlands and abroad. As experts in their field of research they will summarize the core message of the course in their presentations. The following speakers have accepted their invitation to give a keynote lecture: ·Dr. John Overington, Computational Chemical Biology, EMBL-EBI, Hinxton, UK ·Prof. Dr. Hugo Kubinyi, Former Head of Drug Design &Combinatorial Chemistry and Molecular Modelling, BASF AG, Ludwigshafen, Germany ·Dr. Ir. Fred van de Velde, NIZO food research BV, The Netherlands ·Prof. Dr. Peter Murray-Rust, Unilever Centre for Molecular Science Informatics, University of Cambridge, UK In the afternoon the hand-ons are targeted at fourth-year university students, PhD students and postdocs, that are interested in the field of computational target and drug discovery. A basic background in bioinformatics or computational chemistry is a prerequisite for attendance. Read more on the course website: http://www.cmbi.ru.nl/ICDD2012. You can also find registration information here. See the course flyer: http://www2.cmbi.ru.nl/site_media/CDD_course2012_flyer2_A4.pdf -- 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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Galaxy Tour de France 2012
by Dave Clements 30 Apr '12

30 Apr '12

Galaxy Tour de France 2012 Galaxy is going on tour in France during the last week of May. We will be holding workshops in Perpignan, Lyon, and Paris. Details are below. Galaxy is an open-source web-based framework for data integration and analysis in the life sciences (http://galaxyproject.org/) Galaxy is available as a free public web site, or as software that can be installed and run locally, or on the cloud. Workshop registration is free, but space is limited and registration for each workshop will be closed as each fills up. http://wiki.g2.bx.psu.edu/**Events/GalaxyTourDeFrance2012<http://wiki.g2.bx.psu.edu/Events/GalaxyTourDeFrance2012> 28 mai : Perpignan 30 Mai : Lyon 1 juin : Institut Curie Amphithéatre Constant Burg, 12 rue Lhomond, 75005 Paris, France Galaxy for Biologists 9:00-12:00 Basic concepts: interface, histories, workflows Analysis of NGS data: polymorphism discovery, ChIP-seq. RNA-seq Using your own instance on the Cloud Publishing supplemental results with Galaxy Pages Galaxy for Developers 14:00-17:00 Galaxy architecture Wrapping tools for Galaxy system, Galaxy Toolshed API Running Production Galaxy sites: Infrastructure, Job Scheduling, Data and User management -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Call for Registration: BeneLearn 2012
by Michael Rademaker 27 Apr '12

27 Apr '12

(Apologies for multiple postings) ------------------------------------------------------------------------ CALL FOR PARTICIPATION BENELEARN 2012 The 21st annual machine learning conference of Belgium and The Netherlands in combination with the PMLS (Predictive Modelling for the Life Sciences) workshop. http://www.benelearn2012.ugent.be May 24 and 25, 2012 Universiteit Gent, Belgium ------------------------------------------------------------------------ Scope BeneLearn is the annual machine learning conference of Belgium and The Netherlands. It serves as a forum for researchers to exchange ideas, present recent work, and foster collaboration in the broad field of Machine Learning and its applications. BeneLearn 2012 is organised by the KERMIT research unit at the Department of Mathematical Modelling, Statistics and Bioinformatics of Universiteit Gent (Ghent University). The conference and its satellite workshop will take place on May 24 and 25, 2012 in Ghent, Belgium. Program The two day program will include invited talks by Ricardo Silva (Department of Statistical Science/CSML, UCL (UK)), Peter Challenor (National Oceanography Centre (UK)) and Tijl De Bie (University of Bristol (UK)) and a satellite workshop on applications of predictive modelling in the life sciences. Next to the invited speakers, we have scheduled about 20 talks on recent machine learning research and applications, as well as a poster session presenting another 15 or so theoretical or practical achievements. Important dates Early bird registration deadline: May 8th Electronic registration deadline: May 21st Conference: May 24th - 25th, 2012 Information about registration costs, the venue, specific program details etc. can be found at: http://www.benelearn2012.ugent.be <http://www.benelearn2012.ugent.be/> Organising Committee Bernard De Baets, KERMIT UGent Bernard Manderick, VUB Willem Waegeman, KERMIT UGent Michael Rademaker, KERMIT UGent Contact: benelearn2012(a)ugent.be

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Postdoctoral position Australian National University
by Conrad Burden 26 Apr '12

26 Apr '12

Postdoctoral Fellow/ Research Fellow in Statistical and Mathematical Analyses of Biological Sequence Data. Australian National University, Canberra The Centre for Mathematics and its Applications at ANU is seeking to appoint a Postdoctoral Fellow (Level A) or Research Fellow (Level B). The successful applicant will have strong research interests and activities in Statistical and Mathematical Analyses of Sequence Data. The appointment will be located in the Bioinformation Science program of the Mathematical Sciences Institute and is solely a research position. The Australian Research Council under a grant awarded to Dr Conrad Burden will fund the position. This position is a fixed term appointment at either Academic Level A or Academic Level B. Appointment at Academic Level A will be for two (2) years and three (3) months. Appointment at Academic Level B will be for one (1) year and ten (10) months. Applicants should address the selection criteria found within the position description, in their online application. Details at http://jobs.anu.edu.au/PositionDetail.aspx?p=2676 For enquiries regarding this position please email conrad.burden(a)anu.edu.au or telephone 61-2-6125 0730. Note that the closing date for applications is 14 May 2012.

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Probabilistic Graphical Models (PGM2012) Third Call for Papers and deadline extension
by Manuel Gómez Olmedo 24 Apr '12

24 Apr '12

Probabilistic Graphical Models (PGM2012) Workshop Granada, Spain, 19-21 September 2012 (http://leo.ugr.es/pgm2012) The submission deadline has been extended to June 4th (abstract) and June 8th (full paper) (see list of important dates below) *Call for papers:* The aim of the workshop is to bring together people interested in probabilistic graphical models and provide a forum for discussion of the latest research developments in this field. The workshop is organized so as to facilitate discussions and collaboration among the participants also outside the workshop sessions. To facilitate the spreading of research results and promote interactions among the participants, parallel sessions will be avoided and the workshop will be organized around a single thread of plenary and posters sessions. We welcome theoretical and applied contributions related to the following topics: - Principles of Bayesian (belief) networks, chain graphs, decision networks, influence diagrams, and other probabilistic graphical models (PGMs). - Information processing in PGMs (exact and approximate inference). - Learning and data mining in the context of PGMs: machine learning approaches, statistical testing and search methods, MCMC simulation. - Exploitation of results from related disciplines for the construction of PGMs, e.g., statistics, information theory, optimization, decision making under uncertainty, multivariate statistical analysis. - Software systems based on PGMs. - Application of PGMs to real-world problems. We invite submissions that concern oneCHANGED or more of the above topics, or any other aspects related to probabilistic graphical models. Papers submitted for review should report on original, previously unpublished work. Each submitted paper will be reviewed by at least two reviewers. Submission procedure PGM 2012 requires electronic submission of papers according to the instructions found on the web page http://leo.ugr.es/pgm2012/author-instructions.php. The authors must prepare their papers according to the PGM proceedings format, and submit the full version of the papers by the deadline found below. The page limit is 8 pages, including figures and bibliography. The page for author instructions contains format information and provides access to style files and templates. Paper presentation Papers will be accepted for plenary or poster presentation. All accepted papers will be included in the proceedings (with ISBN), which will be made available at the workshop reception. At least one author of accepted papers is expected to attend the workshop. After the workshop, authors of selected papers will be invited to submit an extended version of their paper to appear in a special issue of a high quality journal. All of the submitted papers will undergo a full reviewing process. Important Dates Call for papers opened November 2011 *CHANGED*: Deadline for abstract submissions June 4, 23:59 GMT, 2012 *CHANGED*: Paper submissions June 8, 23:59 GMT, 2012 *CHANGED*: Notification of acceptance July 20, 2012 *CHANGED*: Final versions due August 24, 23:59 GMT, 2012 Welcoming reception September 18, 2012 Workshop dates September 19-21, 2012 -- Manuel Gomez Olmedo e-mail:mgomez@decsai.ugr.es Dpto. de Ciencias de la Computacion e Inteligencia Artificial E.T.S. Ingenierias Informatica y de Telecomunicacion Universidad de Granada Tel.: +34 958 246143 18071 - GRANADA (Spain) Fax: +34 958 243317

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Job openings for a bioinformatician and data manager at the University of Antwerp
by Anthony Liekens 24 Apr '12

24 Apr '12

Dear colleagues, We have two openings for support functions, a bioinformatician and a data manager, at the VIB Department of Molecular Genetics at the University of Antwerp. Please find the vacancies at the following URLs: http://www.vib.be/en/jobs/Pages/Bioinformaticus.aspx http://www.vib.be/en/jobs/Pages/Data-Manager.aspx Please be warned that applications close 30 April 2012! Sincerely, Anthony Liekens,- -- The contents of this email may be confidential and may be privileged. They are intended for the named addressee(s) only. If you are not the addressee, nor a person authorised to receive for the addressee, please do not copy, use or disclose the contents of this message. Kindly notify me immediately of this erroneous reception, and destroy the message.

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Postdoctoral Position in Computational Protein Design (Brussels/Belgium)
by Yves Dehouck 23 Apr '12

23 Apr '12

Postdoctoral Position in Computational Protein Design (Brussels/Belgium) A two-year Postdoctoral Position is available in the Genomic and Structural BioInformatics Unit of the Université Libre de Bruxelles (Brussels, Belgium), to work on the development of computational tools for the rational design of proteins with modified (thermal) stability, solubility, or activity. The position is open immediately. The starting date should be no later than October 2012. Competitive salary commensurate with experience is offered. The candidate should hold a PhD degree in bioinformatics, computational biology or in a related field, have an extensive experience in programming (preferably in C), a strong publication record, and a high motivation to carry out research in this area. The candidate should not have been domiciled in Belgium during the last two years. Candidates with a background in physics, mathematics, statistics, computer science or engineering, and with a strong desire to develop and apply rational and computational tools to problems of biological or medical interest are also encouraged to apply. Interested individuals should send an e-mail to Marianne Rooman (mrooman(a)ulb.ac.be) containing their CV, a cover letter, and contact information to two references. Review of the applications will start immediately, and continue until the position is filled.

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