Content Providers

  • SIB Swiss Institute of Bioinformatics

    The SIB Swiss Institute of Bioinformatics is an academic, non-profit foundation recognised of...

    18 training materials
    5 upcoming events (354 past events)
    SIB Swiss Institute of Bioinformatics https://tess.elixir-europe.org/content_providers/swiss-institute-of-bioinformatics The SIB Swiss Institute of Bioinformatics is an academic, non-profit foundation recognised of public utility and established in 1998. SIB coordinates research and education in bioinformatics throughout Switzerland and provides high quality bioinformatics services to the national and international research community. /system/content_providers/images/000/000/011/original/sib_logo_medium.jpg?1662299701
  • Showing 18 materials.
    How to use Python and R with RDF Data

    How to use Python and R with RDF Data is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centred around the [SPHN Interoperability...

    Scientific topics: Medical informatics, FAIR data, Data management, Computer science

    Operations: Data retrieval, Data handling, Query and retrieval

    Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, Python, R, GraphDB

    Resource type: Video, Training materials, Mock data, E-learning

    How to use V-pipe (SARS-CoV-2 data)

    This tutorial demonstrate how to use V-pipe - Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.

    For the purpose of this toturial, we use the sars-cov2 branch of V-pipe and analyse SARS-CoV-2 runs downloaded from NCBI SRA.

    Scientific topics: Workflows, Genetic variation, Virology

    Operations: Read pre-processing, Alignment, Variant calling

    Keywords: coronavirus, NGS bioinformatics, Variant-calling

    Resource type: Computer Software, workflow

    Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide

    This Practical Guide outlines basic bioinformatics approaches for exploring the SARS-CoV-2 genome and its corresponding proteins, focusing on the protein exposed on the viral particle surface: the spike protein. The ways in which bioinformatics can be harnessed to study a new virus, its genome,...

    Keywords: Bioinformatics for schools, basic bioinformatics, SARS-CoV-2 pandemic, genome analysis, protein sequence analysis, protein structure analysis, virus variants, spike protein, training material

    Resource type: Training materials

    BLAST and multiple sequence alignment (MSA) programs

    Background
    The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

    Keywords: Blast, E learning, Multiple sequence alignment

    Resource type: e-learning

    BLAST and multiple sequence alignment (MSA) programs

    Background
    The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

    Keywords: Blast, E learning, Multiple sequence alignment

    UNIX Fundamentals

    This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge.
    The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience.
    At the end of...

    Keywords: Problem based learning, Programming, Unix

    Resource type: e-learning

    High Performance Computing (HPC) in Life Sciences

    High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

    Scientific topics: Biology, Bioinformatics, Computer science

    Keywords: High performance computing, high-performance computing

    Resource type: Tutorial, Slideshow, e-learning

    Phylogenetics of animal viral pathogens

    Background
    The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

    Keywords: Animal pathogens, E learning, Phylogenetics

    Resource type: e-learning

    Vital-IT Infrastructure Usage

    How to efficiently use Vital-IT hardware and software infrastructure.

    Introduction to 3D-Structure Visualization and Homology Modeling using the Swiss-Model Workspace

    The goal of this course is to expose the participants to 3-dimensional structures of proteins. Analysis and visualization software (DeepView) will be used to display, analyze, compare and interpret protein structures. The second part of the course is dedicated to protein structure prediction...

    Phylogenetics of animal viral pathogens

    Background
    The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

    Keywords: Animal pathogens, E learning, Phylogenetics

    Resource type: ViralZone

    FAIR principles in practice for health data

    FAIR principles in practice for health data was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

    Scientific topics: Medical informatics, FAIR data, Data management, Computer science

    Operations: Design, Standardisation and normalisation

    Keywords: Clinical data, RDF, Knowledge graph, Semantic framework, FAIR, Findability, Accessibility, Interoperability, Reusability

    Resource type: Video, E-learning

    RDF Schema and Data Visualization

    RDF Schema and Data Visualization is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

    Scientific topics: Computer science, Data management, FAIR data, Medical informatics, Data visualisation

    Operations: Query and retrieval, Data handling, Data retrieval, Visualisation, Ontology visualisation

    Keywords: Clinical data, SPARQL, Data visualization, RDF, Knowledge graph, GraphDB, Mock data

    Resource type: Video, Training materials, Mock data, E-learning

    Validate Graph Data with SHACL

    Validate Graph Data with SHACL is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

    Scientific topics: Computer science, Data management, FAIR data, Medical informatics

    Operations: Data handling, Validation

    Keywords: Clinical data, SHACL, Data validation, RDF, Knowledge graph, GraphDB, RDF, RDF graph validation

    Resource type: Video, Training materials, E-learning

    Semantic Standards

    This video was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and serves as an introduction to the main standards used within the [SPHN Interoperability...

    Scientific topics: Ontology and terminology, Medical informatics, FAIR data, Data management, Computer science

    Operations: Standardisation and normalisation, Data handling

    Keywords: Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD, Interoperability

    Resource type: Video, Training materials, E-learning

    Expanding the SPHN RDF Schema

    Expanding the SPHN RDF Schema is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

    Scientific topics: Computer science, Data management, FAIR data, Medical informatics, Ontology and terminology

    Operations: Data handling, Visualisation, Ontology visualisation, Editing

    Keywords: Clinical data, Data semantics, FAIR, Ontology editing, Protegé, RDF, OWL

    Resource type: Video, Training materials, E-learning

    Training Primer (RDF and SPARQL)

    The RDF and SPARQL training primer was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

    Scientific topics: Ontology and terminology, Medical informatics, FAIR data, Data management, Computer science

    Operations: Data retrieval, Data handling, Database search, Query and retrieval

    Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology

    Resource type: Video, Training materials, E-learning

    Querying Data with SPARQL

    Querying Data with SPARQL is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

    Scientific topics: Computer science, Data management, FAIR data, Medical informatics

    Operations: Query and retrieval, Database search, Data handling, Data retrieval

    Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, SNOMED CT, LOINC, Interoperability

    Resource type: Video, Training materials with mock data, E-learning

    Showing 5 upcoming events. Found 354 past events. View all results.
    • First Steps with UNIX for Life Scientists

      26 September 2022

      Zurich, Switzerland

      ELIXIR node event
    • Research Data Management and Data Management Plan

      27 - 28 October 2022

      Bern or Lausanne, Switzerland

      ELIXIR node event
    • First Steps with Python in Life Sciences

      28 - 30 September 2022

      Lausanne, Switzerland

      ELIXIR node event
    • First Steps in Parallelization with OpenMP

      23 November 2022

      Basel or streamed, Switzerland

      ELIXIR node event
    • Introduction to high-performance computing (sciCORE cluster)

      7 December 2022

      Streamed from Basel, Switzerland

      ELIXIR node event