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.
How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data)
Scientific topics: Workflows, Genetic variation, Virology
Keywords: coronavirus, NGS bioinformatics, Variant-calling
Resource type: Computer Software, workflow
This training module will provide researcher with an introduction to SPARQL queries for health-related data.
Scientific topics: Computer science, Data management, FAIR data, Medical informatics
Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, SNOMED CT, LOINC
Resource type: Video, Training materials with mock data, E-learning
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
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
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
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
No description provided.
No description provided.
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
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
How to efficiently use Vital-IT hardware and software infrastructure.
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...
In this 2-hour e-learning course, you will learn about the main operations of compute clusters, how to correctly submit jobs, and the most common commands and parameters in job scheduling software. Basic knowledge of UNIX is required.
How to learn R basics
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
No description provided.
In this 1-hour e-learning course, you will learn what type of information on human proteins is found in neXtProt, where it comes from and how it is organized in topic-specific entry views. Basic knowledge of biology and proteins is required.
No description provided.
This 3-hour e-learning course presents the UNIX environment and the most basic commands. Examples are taken from various fields of biology and have been carefully chosen to be accessible to a wide audience. No knowledge of UNIX is required.
In this e-learning course, you will reproduce a typical analysis pipeline using Python, an open-source and general-purpose scripting language which runs on all major operating systems. Basic knowledge of Python programming is required.
In December 2019, a new type of virus of the family Coronaviridae called SARS-CoV-2 (formerly 2019-nCoV) was identified as the cause of an outbreak. In this e-learning course, you will learn to find, use or interpret information about a new virus. Knowledge of the basic molecular biology of...
-
Summer School on Genetic Epidemiology
29 June - 2 July 2022
Davos, Switzerland
Summer School on Genetic Epidemiology https://www.sib.swiss/training/course/20220629_SSGEP http://tess.elixir-uk.org/events/summer-school-on-genetic-epidemiology Overview This summer school aims at providing guidelines on optimal practice in designing, analyzing, and interpreting genetic epidemiological studies, for those who would like to actively analyze DNA sequencing from whole genome sequencing or whole 2022-06-29 09:00:00 UTC 2022-07-02 00:00:00 UTC SIB, Davos, Switzerland SIB Davos Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Introduction to high-performance computing (sciCORE cluster)
14 September 2022
Streamed from Basel, Switzerland
Introduction to high-performance computing (sciCORE cluster) https://www.sib.swiss/training/course/20220914_IHPC http://tess.elixir-uk.org/events/introduction-to-high-performance-computing-scicore-cluster-73ca4b1c-7185-4a0a-9ea7-17be4fe5f45b This course is susceptible to be streamed to the registered participants, depending on the evolution of the sanitary situation Overview This full-day course has a practical focus, where participants will learn how to use the Linux command line and 2022-09-14 09:00:00 UTC 2022-09-14 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Research Data Management and Data Management Plan
30 June - 1 July 2022
Bern or Lausanne, Switzerland
Research Data Management and Data Management Plan https://www.sib.swiss/training/course/20220630_RDMP http://tess.elixir-uk.org/events/research-data-management-and-data-management-plan Overview Recent studies have shown that worldwide, between 51% and 89% of published life sciences research is not reproducible, with consequent losses estimated at around $100 billions/year in biomedical research (Chalmers et al., 2009; Freedman 2022-06-30 09:00:00 UTC 2022-07-01 00:00:00 UTC SIB, Bern or Lausanne, Switzerland SIB Bern or Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Good practice in high-throughput experiments
21 - 22 September 2022
Zurich or streamed, Switzerland
Good practice in high-throughput experiments https://www.sib.swiss/training/course/20220921_GPHTE http://tess.elixir-uk.org/events/good-practice-in-high-throughput-experiments-b5752b6c-f7ee-4865-8875-ff2ee12485eb Overview This course offers an overview of good practice in high-throughput experiments (e.g. next-generation sequencing or compound screening). Particularly we focus on pitfalls in the design of projects (e.g. 2022-09-21 09:00:00 UTC 2022-09-22 00:00:00 UTC SIB, Zurich or streamed, Switzerland SIB Zurich or streamed Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
First Steps with UNIX for Life Scientists
26 September 2022
Zurich, Switzerland
First Steps with UNIX for Life Scientists https://www.sib.swiss/training/course/20220926_FSWU http://tess.elixir-uk.org/events/first-steps-with-unix-for-life-scientists Overview With a constant evolution of technologies, life scientists (such as laboratory biologists) are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis. 2022-09-26 09:00:00 UTC 2022-09-26 00:00:00 UTC SIB, Zurich, Switzerland SIB Zurich Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Comparative Genomics
12 - 14 September 2022
Streamed or Lausanne, Switzerland
Comparative Genomics https://www.sib.swiss/training/course/20220912_COMGE http://tess.elixir-uk.org/events/comparative-genomics-d3e772d0-ca37-4239-8d74-2ac20f260036 Overview The aims of this course are to (i) explore key evolutionary concepts, (ii) examine different methodological approaches, and (iii) gain hands-on experience in eukaryotic comparative genomic analyses. 2022-09-12 09:00:00 UTC 2022-09-14 00:00:00 UTC SIB, Streamed or Lausanne, Switzerland SIB Streamed or Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Advanced Programming with R
29 - 31 August 2022
Lausanne, Switzerland
Advanced Programming with R https://www.sib.swiss/training/course/20220831_APRWR http://tess.elixir-uk.org/events/advanced-programming-with-r Overview This 3-day advanced course is targeted at life scientists or bioinformaticians using the R statistical software who want to extend their knowledge. Lectures will be conducted in the morning, with practicals in the afternoon. 2022-08-29 09:00:00 UTC 2022-08-31 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Single-cell Transcriptomics
4 - 6 July 2022
Bern, Switzerland
Single-cell Transcriptomics https://www.sib.swiss/training/course/20220704_ISCTR http://tess.elixir-uk.org/events/single-cell-transcriptomics-be70d45c-e4dd-4319-866d-d0c192c60ccf Overview In contrast to the Bulk RNA sequencing used to quantify the abundance of gene and transcript expression at a whole population level, single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression profile at a single cell 2022-07-04 09:00:00 UTC 2022-07-06 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Research Data Management and Data Management Plan
27 - 28 October 2022
Bern or Lausanne, Switzerland
Research Data Management and Data Management Plan https://www.sib.swiss/training/course/20221027_RDMP http://tess.elixir-uk.org/events/research-data-management-and-data-management-plan-feebe9bb-fbe8-4a5b-b317-77b82083ff31 Overview Recent studies have shown that worldwide, between 51% and 89% of published life sciences research is not reproducible, with consequent losses estimated at around $100 billions/year in biomedical research (Chalmers et al., 2009; Freedman 2022-10-27 09:00:00 UTC 2022-10-28 00:00:00 UTC SIB, Bern or Lausanne, Switzerland SIB Bern or Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
First Steps with Python in Life Sciences
28 - 30 September 2022
Lausanne, Switzerland
First Steps with Python in Life Sciences https://www.sib.swiss/training/course/20220928_PYTFS http://tess.elixir-uk.org/events/first-steps-with-python-in-life-sciences-05751ded-3ccd-4325-a3bf-7fd378452f09 Overview Have you ever been stuck with a file format that doesn't precisely conform to your needs, found yourself doing annoyingly repetitive data manipulations, or struggled to efficiently manage and explore your data? Python to the rescue! 2022-09-28 09:00:00 UTC 2022-09-30 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
First Steps in Parallelization with OpenMP
23 November 2022
Basel or streamed, Switzerland
First Steps in Parallelization with OpenMP https://www.sib.swiss/training/course/20221123_OPEMP http://tess.elixir-uk.org/events/first-steps-in-parallelization-with-openmp-e78a74a8-b0da-4972-94c8-b58a9b5062e6 Overview We currently live in the era of multicore computers, where almost every computing machine has many CPUs. In order to benefit from this computational power, we need to devise programs explicitly written for parallel machines. 2022-11-23 09:00:00 UTC 2022-11-23 00:00:00 UTC SIB, Basel or streamed, Switzerland SIB Basel or streamed Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Advanced Statistics: Statistical Modelling
22 - 25 August 2022
Lausanne, Switzerland
Advanced Statistics: Statistical Modelling https://www.sib.swiss/training/course/20220822_ASSM http://tess.elixir-uk.org/events/advanced-statistics-statistical-modelling-dc58174b-c34c-468a-a484-1fa4c7ed7957 Overview While the statistical models and tools presented in an introductory statistics course (such as linear regression) can be used to answer a wide range of questions in life sciences, many types of data can not be analyzed using these simple 2022-08-22 09:00:00 UTC 2022-08-25 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Introduction to RNA-Seq: From quality control to pathway analysis
1 - 2 September 2022
Basel, Switzerland
Introduction to RNA-Seq: From quality control to pathway analysis https://www.sib.swiss/training/course/20220901_IRNAS http://tess.elixir-uk.org/events/introduction-to-rna-seq-from-quality-control-to-pathway-analysis-d8c6ae2e-37f6-44fe-826e-a3348db94bd4 Overview This two-day course will present the theory and bioinformatics tools required to analyze RNA-seq gene expression data, The course will present the theory and bioinformatics tools required to analyse RNA-seq gene expression data, from the 2022-09-01 09:00:00 UTC 2022-09-02 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] [] -
Introduction to high-performance computing (sciCORE cluster)
7 December 2022
Streamed from Basel, Switzerland
Introduction to high-performance computing (sciCORE cluster) https://www.sib.swiss/training/course/20221207_IHPC http://tess.elixir-uk.org/events/introduction-to-high-performance-computing-scicore-cluster-e05b9960-7646-4eb2-aaca-3e9204da4a82 This course is susceptible to be streamed to the registered participants, depending on the evolution of the sanitary situation Overview This full-day course has a practical focus, where participants will learn how to use the Linux command line and 2022-12-07 09:00:00 UTC 2022-12-07 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
