November 2012 - BBClist - maillist.psb.ugent.be

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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[Gtpb] GTPB Course announcement - BFB12 Biostatistical Foundations in Bioinformatics
by Pedro Fernandes 02 Nov '12

02 Nov '12

BFB12 Biostatistical Foundations in Bioinformatics IMPORTANT DATES for BFB12 Deadline for applications: November 17th 2012 <------------- Latest Notification of Acceptance: November 18th 2012 Course date: December 3rd - December 7th 2012 With Lisete Sousa and Carina Silva-Fortes We are proud to annouce the third edition of our Foundations course in BioStatistics. Led by the firm hand of two Statisticians that have their research work centered in the Life Sciences, participants go through a comprehensive set of short lectures and guided hands-on exercises. The course revisits concepts bottom-up from probability to classification, using an exclusive set of bioinformatics examples. It is a five day opportunity to put statistics back in shape, to acquire confidence in methods and to learn how to write small scripts using open source software (R). *Course description:* This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques used in Bioinformatics. Many analytical and inferential methods, regardless of their novelty, have their niches of application all over the place in Bioinformatics. Newer techniques such as the ones employed in high throughput data analysis are not different in this respect. We will be looking at statistical methods, digging into their inner workings, wearing the skins of professional statisticians. Attendees can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods, and extensive hands-on practice, exclusively based on biological examples. *Target Audience* Everybody using Bioinformatics methods is implicitly using statistical methods. Most people have had one or more semester courses in Statistics in their graduate education. For many, Statistics happened in their lives a long a time ago, and that makes it difficult to go back and manipulate the concepts with full confidence. Moreover, proper judgement of the results often calls for a deeper level of understanding than what is required to solve scholarly exercises. Attending this course is a chance of revisiting subjects like experimental design, hypothesis testing, inference and prediction in an intensive and systematic way. We will look into particular areas such as Bayesian Inference, Hidden Markov Chains and Multivariate methods with the attitude, eyes and brains of a statistician that wants to understand how the methods work. Methodology The course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. For more information, application procedures, etc. please visit http://gtpb.igc.gulbenkian.pt/bicourses/BFB12 Thank you for your interest! (deadlinefor applications Nov 17th) Pedro Fernandes GTPB Coordinator -- 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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