3 events found

Node: France 

  • ELIXIR TtR course: Basic genomics using advanced analysis tools

    20 - 21 December 2018

    Ljubljana, Slovenia

    Elixir node event
    ELIXIR TtR course: Basic genomics using advanced analysis tools https://tess.elixir-europe.org/events/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools **NEW DATE FOR THE COURSE HAS BEEN SET: Dec. 20-21** **ELIXIR TtR course: Basic genomics using advanced analysis tools Genomic Data Science with Galaxy** **December 20-21, 2018**, Faculty of Medicine, Vrazov trg 2, Ljubljana (Slovenia) Galaxy is an open source, web-based platform for data intensive biomedical research. The Galaxy Platform provides user friendly software for producing reproducible genomic pipelines for data analysis. This workshop will provide a 2 day introductory session to Galaxy software system. The course will be in English. The course will take place in the computer classroom at the Institute of Biostatistics and Medical Informatics (IBMI), Faculty of Medicine, Vrazov trg 2, Ljubljana. **The limit of participants is 20**. This course will focus on introducing the Galaxy user interface and how it can be used for basic genomic analyses. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Community. We will cover the basic features of Galaxy, including where to find tools, how to import and use your data, and an introduction to workflows. This session is recommended for anyone who has not used, or only rarely uses Galaxy. **Program topics:** Quick introduction to Galaxy UI (20.12. morning) From peaks to genes (20.12. morning) Reference-based RNA-seq - Quality control (20.12. afternoon) Reference-based RNA-seq - Sequencing (21.12. morning) Lecturers will be **Christophe Antoniewski** and **Olivier Inizan** from ELIXIR France. Course is organised by **ELIXIR Slovenia** in collaboration with **ELIXIR France**. ELIXIR is an European ESFRI priority research infrastructure for bioinformatics that provides databases, (software) tools, services and training (including training materials) for information, cloud storage and supercomputers in the area of life sciences. It coordinates, develops, integrates and sustains life science (bioinformatics) resources across Europe. **Prerequisites:** Wi-Fi enabled laptop with a modern web browser. Latest versions of Google Chrome, Firefox, Safari and Opera will work best. **Location: Faculty of Medicine, University of Ljubljana** If you have any questions about this course, please contact ELIXIR-SI 2018-12-20 09:00:00 UTC 2018-12-21 12:00:00 UTC ELIXIR Slovenia and Faculty of Medicine, University of Ljubljana University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia University of Ljubljana, Faculty of Medicine Ljubljana Central Slovenia Slovenia SI-1000 Genomics University of Ljubljana, Faculty of Medicine elixir@mf.uni-lj.si [] life scientistsPostgraduate studentsbeginner bioinformaticians 20 workshops_and_courses registration_of_interest galaxygenomicstrainingeLearningEeLP
  • Course single-cell transcriptomics and epigenomics 2019

    3 - 8 February 2019

    Roscoff, France

    Course single-cell transcriptomics and epigenomics 2019 https://tess.elixir-europe.org/events/course-single-cell-transcriptomics-and-epigenomics-2019 Duration The workshop will take place 3 - 8 February 2019 at Station Biologique de Roscoff, France Objectives This workshop focuses on the large-scale study of heterogeneity across individual cells from a genomic, transcriptomic and epigenomic point of view. New technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce come with novel methodological challenges for the analysis. In this regard, specific bioinformatics and statistical methods have been developed in order to extract robust information. The workshop aims to provide such methods for engineers and researchers directly involved in functional genomics project making use of single-cell. A wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. Audience This course is directed towards engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD Student and Post Doc in computational biology or bioinformatics that are interested in the development of methods and pipelines for highly dimensional single-cell data analysis. Working environment Unix command will be used for bioinformatic analysis, and R programming language for statistical analysis. Requirements Understanding of bioinformatics tools and pipelines for next generation sequencing data (RNA-seq or Hi-C or ATAC-seq bulk). Participants must have prior experience on NGS data analysis with R and basic Unix command line skills. Registration Deadline : 15th novembre 2018 (participants selection: end of November 2018). As the number of participants is limited (30 participants), the steering committee will retain candidates on the basis of the information inquired on the registration form. Frais d’inscription pour les personnels académiques Registration fees. A) Academy/University: 600€HT=720€TTC ; B) Private sector: 1.750€HT=2.100€TTC. The registration fee includes accommodation and meals. Scientific coordination:​ ​ Marc Deloger (Institut Curie, INSERM U900, Mines ParisTech), Marie-Agnès Dillies, C3BI (USR 3756 IP CNRS), Agnès Paquet, UCAGenomiX (IPMC CNRS), Antonio Rausell (Institut Imagine, INSERM UMR-1163), Nicolas Servant (Institut Curie, INSERM U900, Mines ParisTech), Morgane Thomas-Chollier, IBENS (CNRS UMR8197, ENS, INSERM U1024). Technical coordination :​ ​ Erwan Corre (ABIMS FR2424 CNRS-UPMC, Station Biologique de Roscoff) Administrative management​ :​ ​ C3BI (Institut Pasteur) 2019-02-03 09:00:00 UTC 2019-02-08 17:00:00 UTC Marc Deloger, Marie-Agnès Dillies, Agnès Paquet, Antonio Rausell, Nicolas Servant, Morgane Thomas-Chollier Station Biological De Roscoff, Place Georges Teissier, Roscoff, France Station Biological De Roscoff, Place Georges Teissier Roscoff Finistère France 29680 Epigenomics Transcriptomics [] inceptionifbfrance genomique [] 30 workshops_and_courses registration_of_interest []
  • Manual curation of Transposable element annotation

    4 - 6 February 2019

    Versailles, France

    Manual curation of Transposable element annotation https://tess.elixir-europe.org/events/manual-curation-of-transposable-element-annotation URGI organizes a BYOD-­style (Bring Your Own Data) training course on manual curation of transposable elements reference sequences obtained with REPET pipelines. For pre-registration, please fill the form before December 26, 2018, we will answer you before January 3rd, 2019: https://goo.gl/forms/ordIgogDuQffuQbZ2 Preliminary program Day 1: - Presentation of REPET outputs of TEdenovo and TEannot pipelines needed to curate the consensus library - Presentation of tools used to assist curation/validation of TE consensus - Presentation of use cases Day 2 and 3 -Practice on your data or a set of precomputed data Prerequesite You have already launched TEdenovo and TEannot pipelines using REPET version 2.5 The MySQL database is still alive OR You have already participated to a TE annotation training (@URGI or in the frame of an Elixir Genome assembly and annotation Course)In this case we’ll provide you a precomputed dataset for the training Fees : 150 € (Payment modalities will be sent once registration accepted) 2019-02-04 09:00:00 UTC 2019-02-06 17:00:00 UTC INRA, URGI platform INRA, URGI, Bat 18 ­ Route de Saint­Cyr ­ RD10, Versailles, France INRA, URGI, Bat 18 ­ Route de Saint­Cyr ­ RD10 Versailles France 78000 Bioinformatics Genomics INRA urgi-contact@inra.fr [] Bioinformatician, Bioanalysts 10 workshops_and_courses registration_of_interest Transposable elementsManual curationGenome sequence analysis
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