June 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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MacBrain symposium: first announcement
by E.Marchiori＠cs.ru.nl 27 Jun '12

27 Jun '12

*** MacBrain Symposium *** http://macbrain2012.cs.ru.nl/ 6 September 2012; Nijmegen, The Netherlands A one day international symposium on the integrative analysis of brain diseases: brain banks, machine learning, clinical and pathological studies. Speakers * Jean-Paul Vonsattel Director of the New York Brain Bank at Columbia University, USA * Daniel Lightfoot Director of the Autism Tissue Program, USA * Sophia Ananiadou Director of the National Centre for Text Mining, UK * Yves Moreau Program director of POC Bioinformatics Department of Bio-Engineering sciences, KU Leuven, Belgium * Amanda Kiliaan Department of Anatomy/Cognitive Neurosciences, Radboud University, NL * John C. van Swieten Erasmus MC, NL * Inge Huitinga Netherlands Brain Bank, NL * Elena Marchiori Radboud University, NL Overview The goal of this symposium is to provide researchers and practitioners an overview of the cutting edge research on core aspects of integrative research of brain diseases, combining data management, machine learning and clinical and pathological studies. The lectures from worldwide domain experts will describe state-of-the-art research and discuss innovative directions aiming at optimizing knowledge discovery processes, from data collection in brain banks through machine learning to integrative clinical and pathological studies. The symposium will provide a multi-disciplinary forum for discussing issues and achievements in research on brain diseases. It will stimulate and strengthen synergy and collaboration among researchers from different disciplines, such as brain bankers, data managers, IT specialists, pathologists and clinicians, in order to improve the efficiency and effectiveness the integrative study of brain diseases. Registration Registration is on a first-come first-serve basis, so register as soon as possible at http://macbrain2012.cs.ru.nl/registration. The registration fee for the MacBrain 2012 symposium is 50. It includes coffee/drinks and lunch.

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NGS workshop Ghent
by Michiel Van Bel 26 Jun '12

26 Jun '12

Dear, can the following message be forwarded to colleagues from Eastern European countries? 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. In this workshop, two innovative and complementary schemes will address the issue of introducing advanced plant genomics to Eastern European countries. We believe these initiatives could have the potential to achieve a step-change in plant genomics in Eastern European countries. _The initiative will fund the generation of up to 5 Next Generation Sequencing datasets, specifically resutling from invited proposals from Eastern European countries._ This will be followed up by a dedicated sequence analysis workshop, which will be open to participants across Europe, but at which the Next Generation Sequencing data obtained will be analysed. Collaborative projects are welcome, but the projects must be led by a group from an Eastern European country. Applicants will need to ensure that their one page proposal identifies an individual with suitable bioinformatics experience to qualify them for the subsequent NGS workshop. The deadline for project submission is July 15. Please visit http://bioinformatics.psb.ugent.be/ngs_workshop/ for more information. kind regards, The organizing commitee

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Course on 3DM/Yasara/Utopia applied to biocatalysis and drug design
by Joosten, Henk-Jan 20 Jun '12

20 Jun '12

Dear BBC members, Bio-Prodict is proud to present the first 3DM/Yasara/Utopia course. In the course participants will learn how to apply the protein superfamily analysis tool 3DM, the state of the art protein structure visualisation tool Yasara, and the literature analysis tool Utopia, to protein engineering and drug design. Besides presentations from well established scientists the participants will solve real life problems from these scientific fields using the tools themselves. Anyone interested in the course can get more information and register using the Bio-Prodict website: www.bio-prodict.nl<http://www.bio-prodict.nl>. Please note, there will be room only for a limited number of participants. Best regards, Henk-Jan Joosten

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PhD position in evolutionary genomics at Utrecht University
by Berend Snel 19 Jun '12

19 Jun '12

Dear all, we have an open PhD position in my group for a project on "Evolutionary cell biology of signal transduction networks from primitive eukaryotes to higher plants" sponsored by the NWO TOP-GO program. see below or here: http://www-binf.bio.uu.nl/snel/group.html#jobs sincerely yours, Berend Snel, PhD *PhD position in Evolutionary cell biology of signal transduction networks from primitive eukaryotes to higher plants (NWO TOP-GO)* Snel Lab, Theoretical Biology and Bioinformatics, Utrecht University Utrecht University is inviting applications for a PhD position in the bioinformatic investigation of evolution and functioning of the molecular signaling networks that regulate plant growth. Plants have complicated signaling networks to regulate growth. Preliminary results suggest that these systems are the result of a combination of the emergence of novel pathways and adaptation of pre-existing pathways. The aim is reconstruct the evolution of these systems, first from the common eukaryotic ancestor to animals, fungi and primitive algae and secondly from algae to primitive plants (such as mosses and ferns) and higher plants (such as the plant model organism Arabidopsis thaliana). The methods for this reconstruction are comparative genomics to study the gene loss, gain and duplication of the core pathway components as well as integrative bioinformatics to study the rewiring of the network. The results of the research should provide fundamental insights into evolution as well as predictions on signaling interactions in plants, which will be tested within the framework of existing collaborations with experimental labs of Utrecht University. The candidates are offered a full-time position for four years. *Qualifications* We are looking for highly motivated individuals with experience, or an interest, in biology and training in bioinformatic analysis. Applicants should possess hands on experience with sequence analysis or expression data analysis, as well as experience with a scripting language (such as perl or python). The persons to be hired should communicate easily in English, both verbally and in writing. *How to apply* Please send your CV, along with a cover letter outlining your specific qualifications for the preferred positions including contact information for at least two references to Dr. Berend Snel, B.Snel(a)uu.nl.

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vacatures voor docenten en analisten op Hogeschool Leiden
by Marja Krosenbrink-Gruijters 19 Jun '12

19 Jun '12

Hoi, is het mogelijk om onderstaande tekst onder de BBC-leden te verspreiden? Alvast bedankt, Marja Beste collega's, De opleidingen Bio-informatica, Biologie en medisch laboratoriumonderzoek en Chemie van Hogeschool Leiden zijn op zoek naar 5 enthousiaste docenten (Bio-informatica, Moleculaire Biologie, Histologie/cytologie, Organische chemie en Chemie/Analytische chemie). Daarnaast zijn we op zoek naar een Chemisch analist voor de functie hoofd chemisch laboratorium en een biomedisch analist voor de functie onderwijsassistent. De bijlagen bevatten de vacatureteksten. Mocht u iemand kennen die mogelijk interesse heeft voor een van de functies, zou u deze dan onder zijn/haar aandacht willen brengen? Bedankt voor uw hulp, Marja Krosenbrink dr. M.J.G. Krosenbrink-Gruijters onderwijsmanager cluster Techniek, opleidingen Bio-informatica en Chemie werkdagen: maandag, dinsdag, woensdag, donderdag, vrijdag Hogeschool Leiden Cluster Techniek Zernikedreef 11, kamer G3.052 Postbus 382, 2300 AJ Leiden Telefoon: 06 - 48133954 Website: www.hsleiden.nl/bioinformatica Op deze e-mail zijn de voorwaarden van toepassing als vermeld op: The following conditions apply to this e-mail: http://www.hsleiden.nl/disclaimer-email

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Job opening for Computational Biologist at Janssen R&D
by Casneuf, Tineke [JRDBE] 18 Jun '12

18 Jun '12

Dear all, We have an open position for a Computational Biologist in the Oncology Biomarker group at Janssen R&D, located in Beerse, Belgium. More information can be found at: https://Computational Biologist in Oncology Biomarker group=000005PZ <https://jnjc.taleo.net/careersection/2/jobdetail.ftl?&lang=en&job=000005PZ&…> . If you are interested, please apply online. Best, Tine ************************************************** Tine Casneuf, PhD Senior Scientist Janssen Research & Development Oncology Biomarkers Turnhoutseweg 30 2340 Beerse Tel: +32 14 607814 tcasneu1(a)its.jnj.com ************************************************** Confidentiality Notice: This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that Johnson & Johnson can arrange for proper delivery, and then please delete the message from your inbox. Thank you.  Please consider the environment before printing this email

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MacBrain symposium
by E.Marchiori＠cs.ru.nl 17 Jun '12

17 Jun '12

[Please distribute to colleagues potentially interested, thanks.] *** MacBrain Symposium *** http://macbrain2012.cs.ru.nl/ 6 September 2012; Nijmegen, The Netherlands A one day international symposium on the integrative analysis of brain diseases: brain banks, machine learning, clinical and pathological studies. Speakers * Jean-Paul Vonsattel Director of the New York Brain Bank at Columbia University, USA * Daniel Lightfoot Director of the Autism Tissue Program, USA * Sophia Ananiadou Director of the National Centre for Text Mining, UK * Yves Moreau Program director of POC Bioinformatics Department of Bio-Engineering sciences, KU Leuven, Belgium * Amanda Kiliaan Department of Anatomy/Cognitive Neurosciences, Radboud University, NL * John C. van Swieten Erasmus MC, NL * Inge Huitinga Netherlands Brain Bank, NL * Elena Marchiori Radboud University, NL Overview The goal of this symposium is to provide researchers and practitioners an overview of the cutting edge research on core aspects of integrative research of brain diseases, combining data management, machine learning and clinical and pathological studies. The lectures from worldwide domain experts will describe state-of-the-art research and discuss innovative directions aiming at optimizing knowledge discovery processes, from data collection in brain banks through machine learning to integrative clinical and pathological studies. The symposium will provide a multi-disciplinary forum for discussing issues and achievements in research on brain diseases. It will stimulate and strengthen synergy and collaboration among researchers from different disciplines, such as brain bankers, data managers, IT specialists, pathologists and clinicians, in order to improve the efficiency and effectiveness the integrative study of brain diseases. Registration Registration is on a first-come first-serve basis, so register as soon as possible at http://macbrain2012.cs.ru.nl/registration. The registration fee for the MacBrain 2012 symposium is 50. It includes coffee/drinks and lunch.

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