December 2011 - 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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BBC11: Key information and updates
by Francisco Azuaje 14 Mar '12

14 Mar '12

Dear colleagues, submission of abstracts is well underway and approaching its deadline: Friday, 28 October. Also I remind you that updates on conference venue and travel are now available at: http://www.bbc11.lu/index.php?page=location We look forward to receiving your abstracts soon. All the best. Francisco Azuaje. (On behalf of the BBC11 Organisation).

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Bioinformatics PhD student job opening at Radboud University Nijmegen Medical Centre
by Sacha van Hijum 23 Dec '11

23 Dec '11

Dear all, there is a job-opening for a bioinformatics PhD student at the Radboud University Nijmegen Medical Centre. Closing date: 2nd of October 2011. For those interested, please see below for details. Best regards, Sacha van Hijum Job profile The PhD student will work in a multidisciplinary team with other scientists and medical doctors to discuss, plan and perform bioinformatics research in a highly stimulating environment. Work-place will be the Laboratory of Pediatric Infectious Diseases (Prof. dr. P. Hermans) and the Bacterial Genomics group (Dr. S. van Hijum). • Independently generate and analyze data • Present results at (inter)national scientific meetings and in international peer-reviewed journals Requirements • Msc degree in (molecular) life sciences, specializing in bioinformatics • Background in statistics and understanding of bioinformatics algorithms. Knowledge of Perl/Python and R is a plus • Preferably experience in microbiology, molecular biology and biochemistry • Fluent in English (speaking, reading and writing) • An independent and well-structured working style • Teamplayer and a strong motivation to succeed in scientific and translational research Organization unit Laboratory of Pediatric Infectious Diseases The Laboratory of Pediatric Infectious Diseases at Radboud University Nijmegen Medical Centre is an academic research lab in which scientists and medical doctors work closely together to conduct translational research on the pathogenesis, immunology, and epidemiology of pediatric respiratory tract infections. Our studies aim to increase the molecular and clinical understanding of the interactions occurring between host and pathogen during infection. This knowledge is used to design improved and novel diagnostic, therapeutic, and preventive strategies. The Laboratory of Pediatric Infectious Diseases participates in the Nijmegen Institute for Infection, Inflammation, and Immunity (N4i) and the Nijmegen Center for Molecular Life Science (NCMLS), with focus on basic science and its translation into pioneering treatments for disease. The innovations are advanced through technology platforms such as genomics, proteomics, and molecular imaging. The Laboratory of Pediatric Infectious Diseases works in close collaboration with the… Bacterial Genomics group Focus of the Bacterial Genomics group (Radboud University Nijmegen Medical Centre) is on the bioinformatics analysis of ~omics data of (consortia of) bacteria in the context of industrial fermentations, health and safety. The research involves (meta)genome sequencing and assembly, annotation, comparative genomics, RNA-seq, transcriptomics and multivariate analysis of ~omics datasets, all in relation to exploration and exploitation of the enormous microbial diversity that is found in Nature. The Bacterial Genomics group is part of the CMBI (Centre for Molecular and Biomolecular Informatics). The CMBI pursues a rigorous research program with topics ranging from computational small-molecule chemistry to bioinformatics. The CMBI is among the largest bioinformatics departments in the Netherlands producing dozens of high impact peer-reviewed publications each year. It consists of 4 research groups (Prof. Vriend, Prof. Huynen, Prof. de Vlieg and Dr. van Hijum) with strong connections with the NBiC, centre of excellence and the largest bioinformatics cluster in the Netherlands. Information Prof. dr. P.W.M. Hermans, head of the laboratory, (024) 3666406, P.Hermans(a)cukz.umcn.nl Dr. A.L. Zomer, bioinformatician, (024) 3651545, A.Zomer(a)cukz.umcn.nl Dr. S.A.F.T. van Hijum, group leader Bacterial Genomics (024) 3619389, svhijum(a)cmbi.ru.nl More information and online application via this link: http://www.umcn.nl/OverUMCstRadboud/werkenbij/Pages/Vacature.aspx?VacatureN… -- Dr. Sacha van Hijum Group leader CMBI Bacterial Genomics Group leader Bioinformatics NIZO food research B.V. Bioinformatics coordinator Top Institute Food and Nutrition T: +31(0)318 659 570 F: +31(0)318 650 400 M: +31(0)624782895 E: sacha.vanhijum(a)nizo.nl or svhijum(a)cmbi.ru.nl P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands

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molecular epidemiology course in Maastricht
by Lars Eijssen 15 Dec '11

15 Dec '11

Dear colleague, You may find the course below of interest to you or your colleagues. International course on Molecular Epidemiology of Chronic Diseases on April 23 - 27, 2012 in Maastricht, The Netherlands. The Maastricht Molecular Epidemiology Expertise group (M2E2) offers you a challenging five days course (23-27 April 2012) to grasp the essentials of molecular epidemiology. The course brings together the different fields of expertise involved in molecular epidemiological research in a comprehensive and integrated manner. Participants will be confronted with issues such as study design, challenges of incorporating omics data in population studies, statistical analysis of complex data, and interpretation of findings in the context of public health. Focus lies especially on methodological issues, with a variety of disease settings as illustration. The audience targeted is PhD students and postdoctoral fellows from epidemiology, biology, medicine, statistics, and related fields, as well as those working in public health, who want to become acquainted with this expanding research area. Please note that registration will close at 1 February 2012. The number of places is limited. For more information see our website and enclosed flyer. Register through our website: www.M2E2.nl On behalf of the course faculty, Ilja C.W. Arts, PhD and Matty P. Weijenberg, PhD Department of Epidemiology, Maastricht University, Maastricht, The Netherlands Ilja C.W. Arts, PhD Associate Professor Program Nutritional and Molecular Epidemiology ilja.arts(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.M2E2.nl Peter Debyeplein 1, 6229 HA, Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3882971 F +31 43 3884128 M + 31 6 15623990 For more information: www.M2E2.nl

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FW: job announcement
by Tim De Meyer 12 Dec '11

12 Dec '11

I am leading a small research team in Maastricht, and in co-operation with the dep. of clinical genetics, we have recently obtained a post doc position in oncogenomics (see attachment). The project will be based on the use of Next Generation Sequencing for the identification of additional genetic factors that can modify the cancer risks in carriers of Lynch syndrome mutations. Special focus will be put in Endometrial cancer. Since our expertise on database and bioinformatics analysis is poor, we are looking for candidates who may have some background and experiences in bioinformatics, biostatistics, genetics etc. Therefore, I would like to ask you whether you can let this announcement circulate at your university or if you have any candidate in mind, who may be willing to come over Maastricht for a couple of years. I thank you in advance and I am looking forward to hearing from you. Best, Andrea Romano

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NBIC PhD course Algorithms for Biological Networks
by Celia van Gelder 10 Dec '11

10 Dec '11

*NBIC PhD course Algorithms for Biological Networks* _Date:_ 16-20 January 2012 _Course coordinator_: Dick de Ridder _Location:_ Delft University of Technology, Delft, the Netherlands _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/algorithms-for-biological-networks/__ _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ *Target audience//* The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. The NBIC Technology Track course"Pattern recognition" and the ASCI course "Advanced pattern recognition" (a1) discuss many of the tools used in this course, but it is not required to have followed these. Prior knowledge of molecular biology is a bonus, but also not strictly required. / / *Course Description //* In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring these from observed measurement data. A number of alternative network models more suited for high-level simulation of cellular behaviour will also be introduced. Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed, with specific attention to the use of sequence information to refine transcription regulation networks. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks and for finding active subnetworks. *Course topics * 1. Monday 16-1-2012Networks in biology 2. Tuesday 17-1-2012Network inference 3. Wednesday 18-1-2012 Network enhancement 4. Thursday 19-1-2012 Network validation and execution 5. Friday 20-1-2012 Network mining // / / More information about the course programme can be found on: http://www.nbic.nl/education/nbic-phd-school/course-schedule/algorithms-for… . *NBIC PhD School//* This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on http://www.nbic.nl => Education => NBIC PhD School. *More information//* 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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Probabilistic Graphical Models 2012 Call for Papers
by Manuel Gómez Olmedo 02 Dec '11

02 Dec '11

Probabilistic Graphical Models (PGM2012) Workshop Granada, Spain, 19-21 September 2012 (http://leo.ugr.es/pgm2012) 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 the interactions among all participants, parallel sessions will be avoided, organizing the conference around 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 one 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 page with author instructions <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. 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 Deadline for abstract submissions April 27, 23:59 GMT, 2012 Paper submissions May 4, 23:59 GMT, 2012 Notification of acceptance June 29, 2012 Final versions due August 17, 23:59 GMT, 2012 Welcoming reception September 18, 2012 Workshop dates September 19-21, 2012 -- Manuel Gomez Olmedo e-mail: mgomez(a)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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Mathematical and Computational Evolutionary Biology (18-22/06/2012)
by Guy Baele 01 Dec '11

01 Dec '11

-------- Message original -------- Sujet: [bioinfo] Mathematical and Computational Evolutionary Biology (18-22/06/2012) Date : Wed, 23 Nov 2011 20:18:16 +0100 De : Gascuel Olivier <gascuel(a)lirmm.fr> Pour : bioinfo(a)sfbi.fr PLEASE DIFFUSE THIS ANNOUNCEMENT. THANKS! Mathematical and Computational Evolutionary Biology June 18-22, 2012, Hameau de l'Etoile (France) http://www.lirmm.fr/mceb2012/ The subject is evolution, which is considered at different scales, from genes to populations. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies. The meeting will bring together researchers originating from various disciplines: mathematics, computer science, phylogenetics and population genetics. Ten keynote speakers will introduce a field of research and discuss their own work in this field. Afternoon will be for short presentations and posters, with plenty of time for discussions, hiking and visits. The number of attendees will be limited (~60) to favor exchanges. The meeting will take place at Hameau de l'Etoile, in the Montpellier region (France). The dates are June 18-22, that is, just before SMBE 2012 that starts June 23 in the evening at Dublin (Ireland). Conference fees including accommodation (4 nights, 18 to 22), meals, coffee breaks, buses, etc., will range from ~350 EUR to ~500 EUR depending on the room type. Keynote speakers: Michael Blum (CNRS - TIMC, FR). Oliver Eulenstein (Iowa State University, US). Arnaud Estoup (INRA - CBGP, FR). Vincent Moulton (University of East Anglia, UK). Rasmus Nielsen (Berkeley, US). Noah Rosenberg (University of Michigan, US). Alexandros Stamatakis (Heidelberg, DE). Mike Steel (University of Canterbury, NZ). Edward Susko (Dalhousie University, CA). Simon Tavaré (Cambridge University, UK). Organizers: Olivier Gascuel Jean-Michel Marin See the web site for more details and pre-registration #################################################################### -- http://www.sfbi.fr Archives : http://listes.sfbi.fr/wws/arc/bioinfo ####################################################################

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