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  • Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl

    22 - 23 November 2016

    Edinburgh, United Kingdom

    Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl https://tess.elixir-europe.org/events/introduction-to-chip-seq-data-analysis-and-visualisation-using-ensembl ChIP-seq (Chromatin ImmunoPrecipitation followed by Sequencing) is a popular high-throughput sequencing assay to identify binding sites of DNA-associated proteins and histone modifications. Determining how proteins interact with DNA and the epigenetic landscape is essential for elucidating the regulation of gene expression. The aim of this workshop is to familiarise the participants with the primary analysis of ChIP-seq data sets by providing a balanced set of lectures and practicals on analysis methodologies. Practicals include publicly available ChIP-seq datasets, processed using widely used and open-source software programs (e.g. FASTQC, BWA, samtools, bedtools, wiggletools, MACS2, MEME, TOMTOM, ngsplot) and visualised on the Ensembl genome browser. 2016-11-22 00:00:00 UTC 2016-11-23 00:00:00 UTC Edinburgh Genomics The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom ChIP-seq Bioinformatics [] [] [] workshops_and_courses [] BioinformaticsChIP-seq
  • Introduction to RAD-seq Data Analysis

    29 - 30 November 2016

    Edinburgh, United Kingdom

    Introduction to RAD-seq Data Analysis https://tess.elixir-europe.org/events/introduction-to-rad-seq-data-analysis-f4a75354-b605-4b30-ad75-60967b8a06f4 using next generation DNA sequencing. The principal advantage of RAD-seq is the ability to simultaneously examine tens of thousands of genetic loci with vastly reduced sequencing costs versus whole genome approaches. RAD-seq can be used on crosses of any design as well as wild populations and organisms with and without a reference genome. Applications include SNP discovery, linkage mapping and QTL mapping, but also more complex analyses such as population genomic and phylogeographic studies. The aim of this workshop is to familiarise researchers with RAD-seq data and to initiate them in the analysis by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs (e.g. FastQC, BWA, samtools, IGV, Stacks) will be used. In the last section of this workshop we will focus on linkage analysis and population genomics. 2016-11-29 00:00:00 UTC 2016-11-30 00:00:00 UTC Edinburgh Genomics The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom Bioinformatics [] [] [] workshops_and_courses [] BioinformaticsRAD-seq
  • Introduction to Python for Biologists

    12 - 16 December 2016

    Edinburgh, United Kingdom

    Introduction to Python for Biologists https://tess.elixir-europe.org/events/introduction-to-python-for-biologists-d358d018-fabc-4a90-9b9c-cfd4475411f5 Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way. 2016-12-12 00:00:00 UTC 2016-12-16 00:00:00 UTC Edinburgh Genomics The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom Software engineering Bioinformatics [] [] [] workshops_and_courses [] BioinformaticsComputerprogrammingPython
  • Linux for Genomics

    20 January 2017

    Edinburgh, United Kingdom

    Linux for Genomics https://tess.elixir-europe.org/events/linux-for-genomics-04835f08-3c91-4dc6-be5c-9ccb661c495e Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician’s toolkit. The Linux command-line enables one to view, filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to perform certain tasks, and run bioinformatics software for which no web interface is available. In this workshop we will first cover the most used Linux commands, followed by a short introduction to several popular command-line tools that were especially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF). 2017-01-20 00:00:00 UTC 2017-01-20 00:00:00 UTC Edinburgh Genomics The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom Bioinformatics [] [] [] workshops_and_courses [] BioinformaticsLinux
  • Introduction to Linux and Workflows for Biologists

    24 - 28 April 2017

    Edinburgh, United Kingdom

    Introduction to Linux and Workflows for Biologists https://tess.elixir-europe.org/events/introduction-to-linux-and-workflows-for-biologists Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customise their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. 2017-04-24 00:00:00 UTC 2017-04-28 00:00:00 UTC Edinburgh Genomics The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom Bioinformatics [] [] [] workshops_and_courses [] BioinformaticsLinuxWorkflows
  • Think Tank Hackathon

    6 - 7 February 2018

    Ljubljana, Slovenia

    Elixir node event
    Think Tank Hackathon https://tess.elixir-europe.org/events/think-tank-hackathon CHARME Think Tank Hackathon, Feb 6-7, 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia 2018-02-06 09:00:00 UTC 2018-02-07 17:00:00 UTC CHARME, ELIXIR Slovenia, NIB University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia University of Ljubljana, Faculty of Medicine Ljubljana Slovenia Computer science University of Ljubljana, Faculty of Medicine [] life scientistsResearchersPhD students 20 workshops_and_courses registration_of_interest Computer sciencelife sciencestrainingeLearningEeLP
  • 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

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