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Keywords: service descriptions  or Open Targets  or Unix/Linux  or Population Genomics 

  • Unix/Linux Tutorial for beginners

    28 - 30 March 2017

    Elixir node event
    Unix/Linux Tutorial for beginners NBIS (the Swedish node of Elixir) and Elixir Slovenia are offering an "Introduction to Linux" course targeted at life scientists to extend their skills and knowledge. The course is delivered via classroom training and via an e-learning platform, thus offering the participants the possibility of attending the course either by traveling to Linköping, Umea (Sweden) or Ljubljana (Slovenia), or by connecting remotely via the Elixir Slovenia e-learning platform. The number of remote students is limited to 10. The course will be broad-casted from Sweden, Linköping. NGS technologies generate vast amount of data, usually in the form of very large text files. Trying to handle this data with applications like Word or Excel is difficult or impossible, while using the Linux command line can drastically simplify your work and improve your efficiency. Linux/Unix provides an excellent computing environment for bioinformatics and the command line interpreter (shell) serves as an interface to a large amount of bioinformatics programs. The course provides a basic introduction to Unix/Linux commands for bioinformatics and covers how Unix/Linux commands can be used to manage and inspect your data and results, and how to generate and run bioinformatics pipelines and work-flows using basic shell scripting. Apply here: 2017-03-28 09:00:00 UTC 2017-03-30 17:00:00 UTC Elixir Sweden, Elixir Slovenia NBIS Mihaela Martis [] Life Science Researchers workshops_and_courses first_come_first_served Unix/Linux
  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1

    20 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1 #### Computational requirements for running the H3ABioNet GWAS workflows The first of a series of seven online lectures for Genome Wide Association Studies (GWAS) will cover the technical requirements for setting up a your computational environment for running the H3ABioNet GWAS workflows. In this inaugural lecture of the series, Prof. Hazelhurst will cover the the following topics: Installing and using Nextflow Installing and using Github Use of containers for packaging and running tools Pulling the GWAS pipeline from Github and running it As this lecture aims to provide attendees with an environment to the run the H3ABioNet GWAS workflow at their own pace, there are some preliminary software requirements: Either a Linux machine or an Apple running macOS Ideally you should have machine with at least 2-4 cores and 8GB of RAM. Java 8 Nextflow installed (see installation instructions at Python 3 Please also install either Docker OR the following dependencies using pip3: Pandas, Matplotlib, Openpyxl, SciPy, NumPy PLINK 1.9 [Please also refer to the following documentation to obtain the H3ABioNet GWAS workflow]: 2018-08-20 15:00:00 UTC 2018-08-20 16:30:00 UTC H3ABioNet Population genomics Genotyping experiment Computational biology Workflows GWAS study Bioinformatics H3ABioNet H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chipAnyone who wants to learn more about GWAS workshops_and_courses [] NextflowDockerH3ABioNetGWASWorkflowsGenotyping array analysis bioinformaticsAfricaPopulation GenomicsReproducible ScienceH3Africa genotyping arrayHigh performance computingCloud computingGWAS workflowH3ABioNet GWAS 2018 Lecture Series
  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 4

    29 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 4 ### Quality control and its importance in GWAS In the fourth of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS), the importance of doing good quality control for a GWAS will be discussed. The lecture will cover the types of errors one should control for, the specific bioinformatics tools used for quality control. Specific sample and SNP quality control steps that should be undertaken in a GWAS will be explored using specific examples. 2018-08-29 15:00:00 UTC 2018-08-29 16:30:00 UTC H3ABioNet Genotyping experiment GWAS study Computational biology Bioinformatics Population genomics Population genetics H3ABioNet H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 workshops_and_courses [] Genome Wide Association StudiesGenotype callingH3Africa genotyping arrayAfrican populationsQuality Control for GWASSample Quality ControlSNP Quality ControlPopulation GenomicsGenotypingPLINK formatPrincipal Component AnalysisLow minor allele frequencyMissingnessGWAS workflowDiscordant Sex informationNextflowGenotyping rate callHeterozygosity rateRelated and duplicate individualsIdentity by DescentHardy Weinberg EquilibriumBioinformaticsH3ABioNet GWAS 2018 Lecture Series
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