August 2014 - BBClist - maillist.psb.ugent.be

PhD position: Haplotyping in polyploid crops
by Ridder, Dick de 28 Oct '14

28 Oct '14

We have an exciting opportunity for an enthusiastic PhD student to develop new methodology for haplotyping genomes of polyploid crops, using novel genotyping-by-sequencing approaches. We are looking for an ambitious PhD student with an MSc degree in bioinformatics, computer sciences, statistics, biotechnology, biology or plant sciences. The PhD project 'Haplotyping in polyploid crops using genetics, genomics and bioinformatics' aims at solving important questions in crops like potato, leek, rose, chrysanthemum, that have four or six copies of a genome: what is the composition (haplotype) of each of the underlying genomes, both locally (gene level) and over larger distances (chromosome level)? Can we distinguish different dosages of haplotypes? Can we characterize plants in terms of haplotype composition? Can we relate observed haplotypes to variation in phenotypic traits? In this project, the goal is to develop statistical, genetics and bioinformatics tools for novel genotyping-by-sequencing (GBS) approaches for polyploid crops. The project will deliver effective strategies for haplotyping in polyploid crops, faster discovery of candidate genes and of their allelic variants for traits of interest to plant breeders. It is a collaborative initiative of the Bioinformatics and Plant Breeding chair groups at Wageningen University. You will work in close cooperation with other PhD students and researchers involved in related projects on the development of a genetic analysis pipeline for polyploid crops and novel sequencing strategies for polyploid genomes. More information about the position, the research groups involved, and a possibility to apply for this position can be found at: http://www.wageningenur.nl/en/Education-Programmes/PhD-Programme/PhD-Vacanc… Interested candidates can apply up to September 15, 2014 through the above-mentioned website. Dr. Chris Maliepaard (Quantitative aspects of Plant Breeding) Prof. Dick de Ridder (Bioinformatics) Wageningen University The Netherlands

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CSCDA 2014
by CSCDA2014＠montefiore.ulg.ac.be 26 Aug '14

26 Aug '14

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Reminder Invitation: Bioinformatics Symposium, Utrecht Bioinformatics Center
by Breukelen, B. van (Bas) 25 Aug '14

25 Aug '14

To remind those who were on holidays or have forgotten to register: The Utrecht Bioinformatics Center (UBC) will celebrate it’s kickoff with a mini symposium at september 15th 2014. Everyone who is interested in bioinformatics and would like to hear the plans of the UBC and of course hear a few great talks is welcome to attend. There is no fee at all, we only ask you to register yourself so that we can make sure that there are enough chairs to sit on, coffee at the start and drinks afterwards. Confirmed speakers: Gerrit van Meer, Dean of the Faculty of Science Utrecht University, Utrecht Harmen Bussemaker, Columbia University , USA Edwin Cuppen, UMC Utrecht & Hubrecht Institute, Utrecht Albert Heck, Utrecht University, Utrecht Alexander van Oudenaarden, Hubrecht Institute, Utrecht The program starts at 13:00 with tea and coffee and at 13:15 the symposium will begin. Around 16:30 we will finish the scientific program with drinks and some snacks till 18:00. Everyone is welcome, See you soon, Berend Snel, Patrick Kemmeren and Bas van Breukelen to register: http://ubc.uu.nl/events/4/kickoff-mini-symposium-ubc/ our home page: http://ubc.uu.nl Bas. van Breukelen, PhD Assistant Professor, Biomolecular Mass Spectrometry and Proteomics | http://www.hecklab.com | Utrecht University Coordinator Bioinformatics | Utrecht Bioinformatics Center (UBC) | http://ubc.uu.nl | Utrecht University Hugo R. Kruytbuilding | Room O605 | Padualaan 8 | 3584 CH Utrecht | T +31(0)30253 9761 | M +31(0)6 42222520 | b.vanbreukelen(a)uu.nl<mailto:b.vanbreukelen@uu.nl> | Skype b.vanbreukelen [cid:2CDF3FE1-6FA1-40F3-A816-1D933B578100@science.uu.nl]

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Multiscale Modeling of Biomolecular Systems - 28 November 2014
by Sanne Abeln 22 Aug '14

22 Aug '14

Dear All, You are cordially invited to the Multiscale Modeling of Biomolecular Systems symposium on Friday 28 November 2014. This meeting is jointly organized by the Amsterdam Center for Multiscale Modeling (ACMM) and the Netherlands Society for Biomolecular Modeling (NSBM). The meeting aims to bridge multiple levels of modeling, from structural bioinformatics to biomolecular simulation at various scales. Please pass on this information to anyone who might be interested. See also http://www.acmm.nl and http://www.nsbm.nl Scope: The meeting will focus on multi-scale and multi-level modeling of biomolecular systems including proteins, DNA or RNA. Topics will cover (but are not limited to): bioinformatics sequence analysis, structure analysis, structure prediction methods (including docking), coarse grained simulations, full atomistic classical force field simulations, combined QM/MM, ab initio and/or DFT calculations, and enhanced sampling methods. Keynote Speakers: Prof. David Jones (UCL, UK) Prof. Ursula Roethlisberger (EPFL, Switzerland) Date: 28 November 2014 - 11:00 - 18:00 Location: VU University, De Boelelaan 1081, Amsterdam, the Netherlands Registration & posters: details will follow soon Program Committee: Jocelyne Vreede (UvA), Paola Gori-Giorgi (VU) Daan Geerke (VU), Sanne Abeln (VU) Advisory board (NSBM+ACMM): Gerry Nicolaes (UM), Gert Vriend (UMCN) Peter Bolhuis (UvA), Evert Jan Meijer (UvA) Matthias Bickelhaupt (VU), Luuk Visscher (VU) Best regards, Jocelyne Vreede, Paola Gori-Giorgi, Daan Geerke, Sanne Abeln -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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Environmental Metagenomics Symposium, 19 September 2014, Wageningen, the Netherlands
by Celia.vanGelder＠radboudumc.nl 22 Aug '14

22 Aug '14

Dear colleague, Metagenomics has quickly become one of the most important discovery tools in microbial ecology. Metagenomics is a powerful tool to study the organisms in microbial communities, that has numerous applications in many areas of biomedical science. By bypassing the need for laboratory culturing, this technology can unlock the massive uncultured microbial diversity, enabling the microbial component of specific environments to be surveyed, discover new organisms, and explore the dynamic ecology of microbial populations under changing conditions. The high throughput nature of metagenomics means that huge datasets are generated, and in order to extract biological information from these data, advanced bioinformatics and statistical tools are indispensable. On 19 September 2014, we are organizing an Environmental Metagenomics Symposium which will bring together renowned scientists in microbial ecology and bioinformatics, who will present their recent explorations of the microbiota of different environments. Moreover, we will welcome the presentations of several students of the metagenomics course held in the week leading up to this symposium. Together, this will be an exciting opportunity to see the latest advances in environmental metagenomics from young talents as well as established leaders in the field. The symposium is open for everyone interested in environmental metagenomics. Symposium website: http://nioo.knaw.nl/en/metagenomics-symposium Symposium fee: Attending the symposium is free of charge, but you have to register via the symposium website A pdf with the programme of both course and symposium is attached to this mail. The organization of course and symposium has been made possible with the generous support of AllBio.<http://www.allbioinformatics.eu/doku.php> Best regards, Bas Dutilh (Utrecht University & Radboudumc) Eiko Kuramae (NIOO-KNAW) Celia van Gelder (Radboudumc) Dr. Celia W.G. van Gelder Projectleader Education NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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FW: bioinformatics vacancies at Scientific Institute of Public Health
by Katrijn Vannerum 21 Aug '14

21 Aug '14

These vacancies reached me through the N2N (Nucleotides2Networks) network (www.nucleotides2networks.be<http://www.nucleotides2networks.be>). Enclosed the two bioinformatician profils we are recruiting in our Intitute. If you can diffuse it,… - The permanent position (statutaire) - The PhD 4 years Thanks Nancy [cid:image002.jpg@01CFBC50.BE044470]Dr Ir Nancy ROOSENS, Ph.D Head o f Division Platform Biotechnologie en Moleculaire Biologie / Plateforme Biotechnologie et Biologie Moléculaire Operationele Directie Expertise, Dienstverlening en Klantenrelaties Direction Opérationnelle Expertise, Prestations de service et relations clients Rue Juliette Wytsmanstraat 14 | 1050 Brussels T 02 642 52 58 | F 02 642 52 92 nancy.roosens(a)wiv-isp.be<mailto:nancy.roosens@wiv-isp.be> Wetenschappelijk Instituut Volksgezondheid Institut Scientifique de Santé Publique Scientific Institute of Public Health www.wiv-isp.be<http://www.wiv-isp.be> ________________________________ Checked as being free of known viruses. Scientific Institute of Public Health, Brussels, Belgium Wetenschappelijk Instituut Volksgezondheid, Brussel, België Institut scientifique de Santé Publique, Bruxelles, Belgique Visit our website: http://www.wiv-isp.be ________________________________ DISCLAIMER<http://www.iph.fgov.be/disclaimer.asp> : Please see https://www.wiv-isp.be/Pages/EmailDisclaimer.aspx ________________________________

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[Gtpb] ABSTAT14 Advanced Biostatistics training course - announcement
by Pedro Fernandes 19 Aug '14

19 Aug '14

REMINDER The Gulbenkian Training Programme in Bioinformatics is happy to announce that the ABSTAT14 - "Advanced Biostatistics for Bioinformatics Tool Users using R" training course is open for applications IMPORTANT DATES for this Course Deadline for applications: September 5th 2014 <========= Latest acceptance notification: September 6th 2014 <========= Course date: September 15th - 18th 2014 Attendance fee: Euro 320.00 Course description This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBSTAT) course that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples, worked with Bioinformatics tools. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Methodology This intensive 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. ------------------------------------------------------------ Due to the summer period, there will be little time to deal with the applications, so the sooner you apply the better and we will do our best to make the acceptance process run smoothly. Early acceptance decisions will be the rule, not the exceptions, though you can help in justifying why you need to know about it in advance (please use the appropriate space in the Application Form). More details, including APPLICATION instructions can be found under the URL: http://gtpb.igc.gulbenkian.pt/bicourses/ABSTAT14/ Thank you for your interest P. Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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Internship call for Schneider lab
by ISCBSC announcement 11 Aug '14

11 Aug '14

Dear all, The ISCB Student Council is pleased to announce a 6-month internship position with the Schneider group at Bioinformatics Core, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. The internship is expected to start in October and it is available to Masters and PhD students in computational biology or related areas from developing nations. More information can be found in the attachment. Please forward this email to all who might be interested. Best regards, Susanne Hermans ISCBSC outreach committee

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ECCB 2014 Tutorial : Analysis of Cis-Regulatory Motifs from High-Throughput
by Jacques van Helden 08 Aug '14

08 Aug '14

There are still some places available for this tutorial: ECCB Tutorial T01 Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets Date: Saturday Sept 6, 2014 Place: Forum building of the Faculty of Medicine of Strasbourg Time: 9am – 5.30pm (registration starts from 8am) Contact e-mail: mthomas(a)biologie.ens.fr More details: http://www.eccb14.org/program/tutorials/cis-r How to register: http://www.eccb14.org/registration Registration includes lunch & coffee breaks on the day of the workshop and the tutorial material (.pdf and/or print). ECCB Tutorial rates: 110 € (academic) or 60 € (student) ---------- Short description ---------- This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb). --------- Teachers ---------- - Jacques van Helden, Aix-Marseille Université (France) - Morgane Thomas-Chollier, Ecole Normale Supérieure (France) - Carl Herrmann, University Heidelberg (Germany). - Alejandra Medina-Rivera, SickKids Research Institute, Toronto (Canada) ---------- Description ---------- Next Generation Sequencing led to the development of novel methods (ChIP-seq, FAIRE-seq, clip-seq, ) to acquire massive data about diverse signals involved in genome regulation and function (cis-regulation, chromatin conformation, RNA maturation, recombination, replication, ...). Extracting relevant information from the raw data requires not only specialized software tools, but also a good understanding of their principles and parameters. In this tutorial we will demonstrate how to analyze ChIP-seq data using the Regulatory Sequence Analysis Tools (RSAT, http://www.rsat.eu/) via their different ways of access: web-interface, command-line, and web-services. This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb). ---------- Contents ---------- The tutorial will be organized in 2 half days: 1) Analysis of cis-regulatory elements with the Regulatory Sequence Analysis Tools (RSAT): methods and website utilization (http://www.rsat.eu/) 2) Using RSAT in command-line and via web services (SOAP/WSDL). Topics: - Motif discovery in NGS peak sets. - Impact of the background models. - Comparison between motifs. - Motif enrichment in peak sequences. - Evaluating the quality of motifs extracted from NGS peaks. - Building control sets to estimate the rates of false positives. ---------- Topics not covered ---------- Other steps for the analysis of ChIP-seq data (e.g. read mapping, peak calling, functional enrichment of peaks, other tools for pattern discovery and matching). ---------- Target audience ---------- The course is addressed to bioinformaticians and biologists. The afternoon will require being familiar with the Unix shell (Linux) and basic programming skills (Perl or Python) to implement clients for web services. ---------- In practice ---------- * Participants will need to bring their own laptop. * All command-line programs will be run on the IFB cloud platform (https://cloud.france-bioinformatique.fr/) managed by Christophe Blanchet (IBCP, Lyon, France). Each participant will be given a (free) account to access this cloud and thereby a fully functional virtual machine with RSAT. * Wireless internet will be available at the conference venue. * An indicative reading list will be available a few weeks before the tutorial. * The hands-on will be organized in a cookbook mode: we will distribute protocols explaining the steps to solve selected test cases. * For the practicals, we ensure that there is no need to transfer data from the conference room to the servers. ----------------------------------------------------------------

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[Gtpb] Fwd: ABSTAT14 Advanced Biostatistics training course - reminder
by Pedro Fernandes 06 Aug '14

06 Aug '14

The Gulbenkian Training Programme in Bioinformatics is happy to announce that the ABSTAT14 - "Advanced Biostatistics for Bioinformatics Tool Users using R" training course is open for applications IMPORTANT DATES for this Course Deadline for applications: September 5th 2014 <========= Latest acceptance notification: September 6th 2014 <========= Course date: September 15th - 18th 2014 Attendance fee: Euro 320.00 Course description This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBSTAT) course that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples, worked with Bioinformatics tools. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Methodology This intensive 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. ------------------------------------------------------------ Due to the summer period, there will be little time to deal with the applications, so the sooner you apply the better and we will do our best to make the acceptance process run smoothly. Early acceptance decisions will be the rule, not the exceptions, though you can help in justifying why you need to know about it in advance (please use the appropriate space in the Application Form). More details, including APPLICATION instructions can be found under the URL: http://gtpb.igc.gulbenkian.pt/bicourses/ABSTAT14/ Thank you for your interest P. Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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