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  • Metagenomic Bioinformatics Analysis

    18 - 19 February 2020

    Heidelberg, Germany

    Metagenomic Bioinformatics Analysis https://tess.elixir-europe.org/events/metagenomic-bioinformatics-analysis Educators: Laura Carroll, Nicolai Karcher, Alessio Milanese, Jakob Wirbel, Georg Zeller (HD-HuB) Date: 18/02/2020 - 19/02/2020 09:00 - 17:00 Location: ATC Computer Training Lab, European Molecular Biology Laboratory (EMBL) Contents: Shotgun metagenomic sequencing approaches are being increasingly employed to characterize the human microbiome. Such complex metagenomics data sets are a rich source for generating functional hypotheses about the roles that gut microbiota play in human health and disease. In this bioinformatics course, participants will be exposed to computational and statistical approaches for the analysis of shotgun metagenomic data. Through a combination of theory-centric lectures and hands-on, practical exercises, the course will cover topics such as taxonomic profiling (i.e., determining “who’s there” in a microbial community), functional analysis (i.e., broadly assessing the functional and metabolic potential of a microbial community, and also mining for specific gene families such as toxins), and comparative metagenomics (i.e., identifying taxa or microbial functions associated with a disease of interest). Learning goals: - Pre-processing and quality control of Illumina metagenomic data - Taxonomic profiling - Exploratory analyses and visualization methods for metagenomic data - Functional metagenomic profiling (using both general purpose databases and targeted approaches) - Comparative analysis of metagenomic data Prerequisites: - Familiarity with the Linux command line interface (e.g., running programs from the command line, creating and moving between directories, accessing a remote host via SSH) - Basic knowledge of the R programming language (e.g., loading data into R, manipulating data frames, creating basic plots) Keywords: Metagenomics 2020-02-18 09:00:00 UTC 2020-02-19 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • CABANA Workshop: Analysis of Crop Genomics Data

    16 - 20 March 2020

    Bogota, Colombia

    Elixir node event
    CABANA Workshop: Analysis of Crop Genomics Data https://tess.elixir-europe.org/events/cabana-workshop-analysis-of-crop-genomics-data-0d1c7271-613b-4672-bac5-19f641f9be70 This course will introduce crop biologists to methods and approaches for analysing crop genomics data. 2020-03-16 08:30:00 UTC 2020-03-20 12:30:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Marco Cristancho [] [] [] [] HDRUK
  • Introduction to Regular Expressions

    18 March 2020

    Heidelberg, Germany

    Introduction to Regular Expressions https://tess.elixir-europe.org/events/introduction-to-regular-expressions Educators: Supriya Khedkar, Toby Hodges (HD-HuB) Date: 18/03/2020 09:30 - 16:00 Location: EMBL Heidelberg; Room 202 Contents: Do you often work with lots of data files on the computer, are you often trying to spot particular files or lines of text in them that are important for you? If so, then using regular expressions could save you a lot of time and frustration! Regular expressions (regex/REs) are a language designed to describe patterns of characters that you want to match in a body of text. For example, if you want to extract every Ensembl Gene ID in a GFF file, find tandem repeats in a large set of sequences, or extract every email address in a large document, regular expressions are the perfect tool. Regular expressions are incorporated into a wide range of software and programming languages, and the workshop will include examples of their use on the UNIX command line and in R and Python. Learning goals: This workshop will provide an introduction to REs and cover some of the simple but powerful ways that these can be used to find patterns in large volumes of text data. The workshop will be interactive and driven by examples to demonstrate how you might use regular expressions in your work. Prerequisites: Participants are required to bring their own laptop to the workshop, with a text editor suitable for programming (e.g. Atom, Sublime Text, VSCode, Notepad++) installed. Keywords: UNIX command line, R, Python Tools: UNIX command line, R, Python 2020-03-18 09:00:00 UTC 2020-03-18 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Innovation and SME Forum: Data Driven Innovation in the Agritech Sector

    24 - 25 March 2020

    Lyon, France

    Innovation and SME Forum: Data Driven Innovation in the Agritech Sector https://tess.elixir-europe.org/events/innovation-and-sme-forum-data-driven-innovation-in-the-agritech-sector The Innovation and SME Forum on Data Driven Innovation in the Agritech Sector will take place 24-25 March in Lyon, France. This event aims to inform participants about ELIXIR resources and create a space for networking between industry and academia. What can attendees expect? Attendees at this event will be immersed in a world of data-driven innovation, with a mix of high-level keynote presentations and hands-on sessions to discuss and interact with other companies, academics and ELIXIR partners.  A dedicated session with Flash Talks, will give SMEs and Start-Ups the chance to introduce their work to a broad audience (see registration form).  Who should attend? This event is open to anyone interested in the data driven life sciences sector, for example: Researchers in academia and industry Large and small companies that develop services for data management and analysis Policy makers and funders Organisers  This event is a collaborative effort, organised by ELIXIR France, ELIXIR Belgium, EMPHASIS and the Bayer Life Hub Lyon. 2020-03-24 12:00:00 UTC 2020-03-25 14:00:00 UTC Bayer Life Hub Lyon, Lyon, France Bayer Life Hub Lyon Lyon France 69009 [] [] [] meetings_and_conferences [] []
  • Ensembl Browser Workshop, DKFZ, 5 May 2020

    5 May 2020

    Heidelberg, Germany

    Elixir node event
    Ensembl Browser Workshop, DKFZ, 5 May 2020 https://tess.elixir-europe.org/events/ensembl-browser-workshop-dkfz-5-may-2020 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2020-05-05 09:00:00 UTC 2020-05-05 09:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl REST API Workshop, DKFZ, 6 May 2020

    6 May 2020

    Heidelberg, Germany

    Elixir node event
    Ensembl REST API Workshop, DKFZ, 6 May 2020 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-dkfz-6-may-2020 Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2020-05-06 09:00:00 UTC 2020-05-06 09:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • 9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis

    26 - 29 May 2020

    České Budějovice, Czechia

    9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis https://tess.elixir-europe.org/events/7th-repeatexplorer-workshop-on-the-application-of-next-generation-sequencing-to-repetitive-dna-analysis The workshop will focus on theoretical and practical aspects of using next generation sequencing (NGS) data for analyzing repeat composition of plant genomes. Special emphasis will be given to repeat characterization methods implemented in the RepeatExplorer pipeline, including practical training in using the pipeline. The workshop should also serve as a platform for exchange of ideas and latest results with ample time dedicated to open discussions. Participants are encouraged to make short presentations of their research related to the workshop topic and/or bring their own data for practical training. The workshop is organized by the Laboratory of Molecular Cytogenetics of the Biology Centre AS CR. It will take place at the Academy of Sciences / University campus in Ceske Budejovice, Czech Republic. The meeting programme will include theoretical lectures and research reports combined with hands-on training (no programming skills required). Registration if open till 5th May. In case of any questions or comments please contact Jiri Macas. 2020-05-26 09:00:00 UTC 2020-05-29 00:00:00 UTC Institute of Plant Molecular Biology, České Budějovice, Czech Republic Branišovská 1160/31, 31, Branišovská, České Budějovice, Czechia Branišovská 1160/31, 31, Branišovská České Budějovice České Budějovice Czechia [] Jiri Macas ELIXIR: The Czech Republic Node PhD StudentspostdocsResearchers workshops_and_courses first_come_first_served []
  • 9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis

    26 - 29 May 2020

    České Budějovice, Czechia

    9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis https://tess.elixir-europe.org/events/repeatexplorer-workshop The workshop will focus on theoretical and practical aspects of using next generation sequencing (NGS) data for analyzing repeat composition of plant genomes. Special emphasis will be given to repeat characterization methods implemented in the RepeatExplorer pipeline, including practical training in using the pipeline. The workshop should also serve as a platform for exchange of ideas and latest results with ample time dedicated to open discussions. Participants are encouraged to make short presentations of their research related to the workshop topic and/or bring their own data for practical training. The workshop is organized by the Laboratory of Molecular Cytogenetics of the Biology Centre AS CR. It will take place at the Academy of Sciences / University campus in Ceske Budejovice, Czech Republic. The meeting programme will include theoretical lectures and research reports combined with hands-on training (no programming skills required). In case of any questions or comments please contact Jiri Macas. 2020-05-26 09:00:00 UTC 2020-05-29 00:00:00 UTC Institute of Plant Molecular Biology building at the Academy of Sciences and University campus in České Budějovice Branišovská 1160/31, 31, Branišovská, České Budějovice, Czechia Branišovská 1160/31, 31, Branišovská České Budějovice České Budějovice Czechia [] Jiri Macas [] Life Science Researchersbioinformaticians workshops_and_courses first_come_first_served []
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