- BBClist - maillist.psb.ugent.be

BBC12 - programme online & register now!
by Femke Francissen 16 Nov '12

16 Nov '12

*BeNeLux Bioinformatics Conference (BBC12) - programme online* The 7th edition of the BBC12 will be organized in Nijmegen, the Netherlands on 10-11 December 2012. Key theme: "Bioinformatics at the interface". You can now find the final programme on the conference website! Registration is still possible until November 26th, but the number of hotel rooms is limited, so if you would like to book a hotel room, please register a.s.a.p.! Specials for Students @ BBC12 The RSG Netherlands invites PhD-students and junior researchers for a social event on "BBC Eve", Sunday December 9th, starting from 5:30 pm in Nijmegen. The event will provide a great opportunity to explore the oldest city of the Netherlands, and to meet other (PhD-)students who will visit the BBC the next two days. You can register for the social event by sending an e-mail to rsg-netherlands(a)iscbsc.org<mailto:rsg-netherlands@iscbsc.org>. Participation of MSc and BSc students to the BBC is sponsored by the NBIC Education Programme BioWise and by CMBI (Radboud UMC Nijmegen). Students can participate by paying a reduced conference fee of 15 Euro per conference day. MSc and BSc students who want to visit the conference are requested to register themselves by sending an email to Barbara van Kampen (b.vankampen(a)cmbi.ru.nl<mailto:b.vankampen@cmbi.ru.nl>). 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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opened position: Postdoc - Bioinformatics, University of Liège
by marc.hanikenne＠ulg.ac.be 14 Nov '12

14 Nov '12

Dear all, Please find here below and in attached pdf a Bioinformatics job offer. Could you please forward this announcement to your contacts? Many thanks, With best regards, Marc Marc Hanikenne, PhD FRS-FNRS Research Associate Functional Genomics and Plant Molecular Imaging Center for Protein Engineering (CIP) Plant Biology Institute, B22 Dpt of Life Sciences University of Liège Blv du rectorat, 27 B4000 Liège Belgium Tel. +32-4-3663844 Fax. +32-4-3662960 skype: marc_hanikenne >>>>>>>>>>>>>>>>>>>> Postdoctoral position - Bioinformatician A bioinformatic postdoctoral position is available at the Unit of Functional Genomics and Plant Molecular Imaging (Dr. Marc Hanikenne) of the Centre For Protein Engineering (CIP, University of Liège, Belgium). The position is opened to non-belgian residents for an initial period of one year, with the possibility of an extension up to 2 years after positive evaluation. The start date is April 1st 2013, but is opened for discussion. Context In the course of evolution, plants adapted to widely differing metal availabilities in soils. The Brassicaceae Arabidopsis halleri is a so-called metal hyperaccumulator plant. A. halleri tolerates heavy pollution of soils by zinc and cadmium and accumulates high zinc concentrations in leaf biomass. Metal hyperaccumulators constitute fascinating models to study adaptations to hostile environments, the mechanisms of speciation and the evolution of naturally-selected complex traits. Job description The Postdoc will be involved in the analysis of NGS data (RNA-Seq, epigenome sequencing) aiming to determine the contribution of DNA methylation in gene regulation and adaptation in A. halleri. The Postdoc will also be in charge of setting-up and running the computational tools necessary for data analyses. Profile We are seeking a candidate with a degree in Biology and/or Bioinformatics with doctoral or postdoctoral experience in the analysis of NGS data. Experience with the UNIX command shell is required. Programming skills (perl, python and/or R) are a plus. The candidate should be fluent in English, have good ability to work in an interdisciplinary environment and have a demonstrable publication track record. Contact Please submit a cover letter, a full C.V., and the contact details (with name, email, address, phone number) of at least 2 reference persons to marc.hanikenne(a)ulg.ac.be. http://www.cip.ulg.ac.be/

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Invitation of Plant Genomics Minisymposium
by Yao-Cheng Lin 13 Nov '12

13 Nov '12

sorry for cross posting. --- Dear Colleagues: We would like to invite you to the "*Plant Genomics Minisymposium*" organized by Prof. Yves Van de Peer (PSB, VIB-UGent). This minisymposium is in conjunction with the ESF sponsored workshop "Generation and Analysis of Next Generation (NGS) Data<http://bioinformatics.psb.ugent.be/ngs_workshop/>". You can find the up-to-date progresses and the future perspective in the field of plant genomics during this minisymposium. *Plant Genomics Minisymposium* * * *Date*: 27th of November (Tuesday), 2012 *Location*: Jozef Schell seminar room, VIB FVMS building, Technologiepark 927 Zwijnaarde * * *Program*: 9:00 – 9:45 *Sequencing complex plant genomes : the impact of New Sequencing Technologies.* Prof. Patrick Wincker (Genoscope, France) 9:45 – 10:30 *The past, present, and future of RNA sequencing and expression quantification.* Prof. Manfred Grabherr (Uppsala University, Sweden) 10:30 - 11:00 Coffee break 11:00 – 11:45 *Journey through the past: 200 million years of plant evolution* Prof. Yves Van de Peer (Ghent University, Belgium) *Contact*: More information of this minisymposium please contact Dr. Yao-Cheng Lin (yalin(a)psb.vib-ugent.be) -- Yao-Cheng Lin Bioinformatics and Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, B-9052 Gent, Belgium TEL: +32 (0)9 33 13 821 GSM: +32 (0)472 480 968 http://bioinformatics.psb.ugent.be "Impact on farmers' fields, not learned publications, is the measure by which we will judge the value of our work." -- Norman Borlaug

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NSBM Fall Meeting November 26 2012
by Barbara van Kampen 13 Nov '12

13 Nov '12

I herewith send you the Final Programme of the NSBM Fall Meeting 2012: “Dissecting and designing interactions” 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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Workshop in Uhasselt in 13/12/2012-14/12/2012 about variable selection, model selection, model averaging , inference and prediction
by Ziv SHKEDY 09 Nov '12

09 Nov '12

Dear , Could you please forward this to the bbc list? Thanks in advance, Ziv Shkedy. Dear All, It is our pleasure to invite you to a workshop in Uhasselt in 13/12/2012-14/12/2012. This year we will focus on topics related to variable selection, model selection, model averaging, Inference and prediction. A full program of the workshop can be found in the link http://www.uhasselt.be/Documents/CENSTAT/programma.pdf As usual, the idea is to bring together statisticians, biostatisticians and bioinformaticians from both academia and industry and to discuss the theory and different areas of application. The workshop is for free but you will need to register. You can find the registration from in the following link: http://www.uhasselt.be/RegistrationForm-Variableselection Please note that the number of places in the workshop is limited so please registered as soon as possible. Best regards. Pushpike Thilakatathne, Dani Yekutieli and Ziv Shkedy.

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WORKSHOP: Statistical Methods for (post)-Genomics Data, VU Amsterdam, January 24-25
by Tim De Meyer 08 Nov '12

08 Nov '12

Could you please forward this to the bbc list? Thanks, Tim De Meyer > REMINDER: ABSTRACT DEADLINE MONDAY NOVEMBER 12. > > Dear Statistician, Bioinformatician, > > It is a pleasure to announce the 2013 meeting on Statistical Methods for (post-) Genomics Data (SMPGD), which will take place at the campus of the VU University, Amsterdam, on January 24-25, 2013. This workshop aims at gathering statisticians, bioinformaticians and biologists to discuss new statistical methodology for the analysis of genomics data and challenging, new types of genomics data requiring further development of such methodology. > We are proud that the following four invited speakers have agreed on presenting their work at SMPGD 2013: > > • Niko Beerenwinkel (ETH, Zurich, Switzerland) > • Florian Markowetz (CR UK - CRI, Cambridge, UK) > • Sylvia Richardson (MRC Biostatistics Unit, Cambridge, UK) > • Aad van der Vaart (Leiden University, Leiden, The Netherlands) > > In addition we will have three invited sessions on: > > • Metagenomics (organiser: Jean-Jacques Daudin) > • Efficient genomics studies: design, multiplicity and power (organisers: Mette Langaas, Renée de Menezes) > • Models for molecular networks (organiser: Sach Mukherjee) > > We welcome contributed talks (15 min.) and posters. Please send title and abstract of max. 1 page to info(a)smpgd2013.nl before November 12 2012, 12.00h. Please also indicate your preference: a) talk only; b) talk, poster as an alternative; c) poster. > The registration deadline is December 17 2012, 12.00h. For more information, please check: www.smpgd2013.nl > We look forward to seeing you in Amsterdam. On behalf of the scientific and organising committees, kind regards, > > > Mark van de Wiel > >

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Autumn School "Biomolecular Structure and Function - Computational Approaches"
by Barbara van Kampen 08 Nov '12

08 Nov '12

The Netherlands Society on Biomolecular Modelling (NSBM) and NBIC would like to inform you about the Autumn School "Biomolecular Structure and Function - Computational Approaches" which will be held in Essen, Germany (November 26 - 30, 2012) and in Nijmegen, the Netherlands (December 3 - 7, 2012). Overview of the programme: The autumn school will have two parts, both with a mixture of short lectures, presentations, hands-on exercises, and project work. In week 1 (26 - 30 November, 2012) one will focus on methods based on physical models of biomolecular systems. Topics of this week include molecular dynamics simulation, biomolecular electrostatics, protein-protein docking and matching, and machine learning for functional analysis. In week 2 (3 - 7 December, 2012/)/ one will deal with methods that make empirical knowledge available for modelling proteins. Topics of this week include homology modeling, ligand docking, computational solutions for structural analysis with X-ray, NMR, SAXS, or Cryo-EM. Further details are available at the websites: swift.cmbi.ru.nl/autumnschoolbioinformatics/ www.uni-due.de/autumnschoolbioinformatics/ Enclosed you will find the flyer. with kind regards, Barbara van Kampen -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl

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[Gtpb] GTPB Course announcement - IPSI12 Introduction to Population Structure Inference
by Pedro Fernandes 07 Nov '12

07 Nov '12

IGC, Oeiras, Portugal Course Announcement IPSI12 Introduction to Population Structure Inference with Lounès Chikhi and Vitor Sousa IMPORTANT DATES for this Course Deadline for applications: November 30th 2012 Latest notification of acceptance: December 5th 2012 Course date: December 17th - 19th 2012 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. http://gtpb.igc.gulbenkian.pt/bicourses/IPSI12/ Overview Genetic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic data. In this short course we shall try to take a practical approach to the analysis of genetic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix sessions where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this three-day course we will introduce the main concepts that underlie many of the population structured models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation, as they are connected to what makes landscape genetics today on the basis of multilocus data. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will (i) look at measures of genetic diversity and differentiation using GENETIX; (ii) use methods to detect population structure as implemented in the programs GENECLASS2 and STRUCTURE; (iii) use geneland to detect genetic clusters using spatial information on the sampling locations of individuals, and (iv) learn how to perform coalescent simulations of genetic data (using SPAms and ms). Thank you for your interest! (deadline for applications Nov 30th) -- ******* Upcoming Training Courses in GTPB: http://gtpb.igc.gulbenkian.pt/bicourses/BFB12 http://gtpb.igc.gulbenkian.pt/bicourses/IB12A http://gtpb.igc.gulbenkian.pt/bicourses/IPSI12 -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Annonce Poste CR (INRA)
by Didier Gonze 06 Nov '12

06 Nov '12

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[Gtpb] GTPB Course announcement - IB12A Introductory Bioinformatics (2nd course 2012)
by Pedro Fernandes 05 Nov '12

05 Nov '12

Course Announcement IB12A Introductory Bioinformatics http://gtpb.igc.gulbenkian.pt/bicourses/IB12A with David P. Judge, Phil Cunningham and Pedro Fernandes IMPORTANT DATES for this Course Deadline for applications: November 30th 2012 Latest notification of acceptance: December 3rd 2012 Course date: December 10th - 14th 2012 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview The course sets out to introduce an extensive range of computing facilities vital for molecular biological research. This will be achieved primarily through "hands on" exercises based around an investigation of a well documented human disease. How information can be obtained both by analysis of raw sequence data and by interrogation of information resources will be demonstrated. In order to enable the participants to perform sequence analysis on short read sequences, we will provide a short tutorial on NGS data analysis for beginners. Objectives The course is a user course. How to use the various tools is thus the prime objective. However, where it is useful, the operation of the programs will be discussed as far as is required. Participants will know how to set up the programs in an informed fashion, and to fully understand the output generated. On completion of this 5 day long training, they will also know how to implement this methodology elsehwere, using public domain software and data resources. The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations. Target Audience This course is intended for those wishing to investigate how they might begin to exploit the ever expanding abundance of computing resources for molecular biologists. Course Pre-requisites Basic understanding of molecular biology and no particular computing expertise will be assumed. Thank you for your interest! (deadline for applications Nov 30th) Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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