SIB 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.

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.
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

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

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

Resource type: Video, Training materials with mock data, 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

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

Resource type: Video, Training materials, 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

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

Resource type: Video, Training materials, Mock data, 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

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

Resource type: Video, Training materials, 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

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

Resource type: Video, Training materials, E-learning

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

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

Resource type: Video, E-learning

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

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

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

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