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  • 9th Galaxy workshop on HTS data analysis

    17 - 21 February 2020

    Freiburg im Breisgau, Germany

    9th Galaxy workshop on HTS data analysis https://tess.elixir-europe.org/events/9th-galaxy-workshop-on-hts-data-analysis Educators: RBC Freiburg Date: 17.-21.02.2020 Location: Uni Freiburg Contents: 1-week full-day hands-on workshop in Freiburg. Topics: - Galaxy Introduction - Data analysis of RNA-seq, ChIP-seq, Exome-seq, MethylC-seq data Learning goals: Using Galaxy for data analysis of HTS data. Topics: - Quality control - Mapping - Differential expression analysis - Workflow design - Statistics - Visualization. Prerequisites: No. Beginner training course! Keywords: Galaxy, NGS, HTS, RNA-seq, ChIP-seq, Exome-seq, MethylC-seq Tools: Galaxy 2020-02-17 09:00:00 UTC 2020-02-21 17:00:00 UTC de.NBI Freiburg im Breisgau, Freiburg im Breisgau, Germany Freiburg im Breisgau Freiburg im Breisgau Freiburg Germany [] [] [] workshops_and_courses [] []
  • 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 [] []
  • Automated Workflow Composition in the Life Sciences

    9 - 13 March 2020

    Leiden, Netherlands

    Automated Workflow Composition in the Life Sciences https://tess.elixir-europe.org/events/automated-workflow-composition-in-the-life-sciences In the age of computational science, researchers in the life sciences – just as in other domains – regularly face the need of composing several individual software tools into pipelines or workflows that perform the specific data analysis processes that they need in their research. For over 20 years now, dedicated scientific workflow management systems have been supporting scientists in this task, and they continue to gain popularity. In fact, recent years have seen significant progress in the functional annotation of bioinformatics software tools, as well as their virtualization, containerization and assembly into workflows for automatically executing the processes. At least since the rise of the Semantic Web in the early 2000s, also the idea of semantics-based automated composition of workflows has been around to simplify the work with scientific workflows further and free life science researchers from having to deal with the technicalities of software composition. This would not only save valuable research time, but also reduce errors, allow benchmarking of data analysis pipelines and enable new scientific findings by discovering workflows that researchers would not have thought of themselves. However, despite its obvious potential and appeal, the need for optimizing data analysis workflows, and despite different research groups working on the topic, automated workflow composition has not yet arrived in the daily practice of life science researchers. The reasons for this are manifold. Some are more practical (for example the lack of automatic composition tools in the commonly used software frameworks), others are of more fundamental nature (such as questions on specification languages, composition algorithms, formal semantics and workflows representations). On one important aspect, namely the semantic annotation of tools on a large scale, the life science community has made significant progress in the last years: The EDAM ontology provides a controlled vocabulary of bioinformatics operations, data types and formats, and the bio.tools registry has become a large collection of bioinformatics tools that are semantically annotated with terms from the EDAM ontology. As demonstrated in a recent Bioinformatics publication (https://academic.oup.com/bioinformatics/article/35/4/656/5060940), this forms a solid basis for performing automated workflow composition in the life sciences domain. Nevertheless, it is still a long way to its use in daily scientific practice. This workshop will bring together researchers and practitioners who have been working on different aspects related to automated workflow composition in the life sciences. These include life science researchers, tool providers, infrastructure developers, ontologists, algorithmics researchers and many more. They do not normally come together as a group at the regular scientific events, so a Lorentz workshop devoted to this topic provides a unique opportunity to join forces and together significantly advance the field. 2020-03-09 09:00:00 UTC 2020-03-13 17:00:00 UTC Jon Ison, Anna-Lena Lamprecht, Magnus Palmblad and Veit Schwämmle Lorentz Center Oort, Leiden, Netherlands Lorentz Center Oort Leiden Netherlands 2333 Omics Workflows Leiden University reinards@lorentzcenter.nl ELIXIRLorentz CenterLUMC software developers, bioinformaticiansbiocurators 50 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 [] []
  • Workshop Metagenomics

    1 May 2020

    Leiden, Netherlands

    Elixir node event
    Workshop Metagenomics https://tess.elixir-europe.org/events/workshop-metagenomics-50fa03ae-bc84-447a-92fe-b353cea33030 In deze cursus wordt een algemene achtergrond van metagenomics gegeven. Hands-on data-analyse is een belangrijk onderdeel: tijdens computer practica kan je 16S- en metagenoom datasets analyseren. De workflow van monstervoorbereiding, DNA-isolatie, selectie van platform, read mapping, annotatie en metagenoomassemblage wordt behandeld.… The post Workshop Metagenomics appeared first on Dutch Techcentre for Life Sciences. 2020-05-01 09:00:00 UTC 2020-05-01 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
  • 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
  • Analyse Next Generation Sequencing (NGS) data

    8 June 2020

    Leiden, Netherlands

    Elixir node event
    Analyse Next Generation Sequencing (NGS) data https://tess.elixir-europe.org/events/analyse-next-generation-sequencing-ngs-data Deze tweedaagse workshop geeft toepasbare up to date informatie over NGS. Verschillende platforms, de werking van sequencers en nucleïnezuur isolatie komen uitvoerig aan bod. De analyse van NGS data bij DNA en RNA sequencing wordt geïntroduceerd. Verschillende toepassingen zoals genoom… The post Analyse Next Generation Sequencing (NGS) data appeared first on Dutch Techcentre for Life Sciences. 2020-06-08 09:00:00 UTC 2020-06-08 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
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