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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.

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.png?1469458452
Showing 12 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

BLAST and multiple sequence alignment (MSA) programs https://tess.elixir-europe.org/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 new data is very useful to the research field through the development of bioinformatics tools and databases that deal with large amount of sequences. Among them, BLAST (Basic Local Alignment Search Tool) and MSA () programs are very efficient for protein or nucleotide sequence similarity search. The present course introduces the main biological databases, alignment tool BLAST and Multiple sequence alignments (MSA) programs, and interpretation of results. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-zone, Swiss-Prot group at the SIB Swiss Institute of Bioinformatics   Blast, E learning, Multiple sequence alignment Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28 2017-10-09
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

UNIX Fundamentals https://tess.elixir-europe.org/materials/unix-fundamentals-35adf82d-ae32-449d-9627-43b5d18da8cc 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 the course, participants are expected to be able to: Have some understanding on UNIX systems Navigate through the UNIX filesystem Execute and understand some UNIX process commands Correctly set file permissions Perform basic file management Participants are encouraged to follow the tutorial sections sequentially. The tutorial content is sometimes an oversimplification of the Truth - yes, we know! Due to the diversity of computer systems, we will just assume that participants do have access to a terminal. For help, please contact your IT support - or a good friend!Authors are affiliated to the SIB Swiss Institute of Bioinformatics: Vassilios IoannidisWith some content provided by Frédéric Schütz, Volker Flegel and Heinz StockingerContent integration by Grégoire Rossier and Vassilios Ioannidis Problem based learning, Programming, Unix Bench biologists Clinical Scientists Graduate Students beginner bioinformaticians biocurators 2014-01-13 2017-10-09
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: Computer science, Bioinformatics, Biology

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences https://tess.elixir-europe.org/materials/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 either as the electronic component of a blended training format or as a self-running learning product. Computer science Bioinformatics Biology High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
Vital-IT Infrastructure Usage

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

Vital-IT Infrastructure Usage https://tess.elixir-europe.org/materials/vital-it-infrastructure-usage How to efficiently use Vital-IT hardware and software infrastructure.
SPARQL



SPARQL https://tess.elixir-europe.org/materials/sparql 
How to use V-pipe (SARS-CoV-2 data)

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

How to use V-pipe (SARS-CoV-2 data) https://tess.elixir-europe.org/materials/how-to-use-v-pipe-sars-cov-2-data How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data) Workflows Genetic variation Virology coronavirus, NGS bioinformatics, Variant-calling bioinformaticians Biologists, Genomicists, Computer Scientists
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...

Introduction to 3D-Structure Visualization and Homology Modeling using the Swiss-Model Workspace https://tess.elixir-europe.org/materials/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 using the Swiss-Model expert system for homology modeling.
High Performance Computing in Life Sciences

No description provided.

High Performance Computing in Life Sciences https://tess.elixir-europe.org/materials/high-performance-computing-in-life-sciences No description provided.
R basics

How to learn R basics

R basics https://tess.elixir-europe.org/materials/r-basics How to learn R basics
Cybersecurity Quiz for SIB employees only (internal use)

No description provided.

Cybersecurity Quiz for SIB employees only (internal use) https://tess.elixir-europe.org/materials/test-sib-security-quiz No description provided.
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

Phylogenetics of animal viral pathogens https://tess.elixir-europe.org/materials/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 useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases. The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-Zone, Swiss-Prot Group at SIB Swiss Institute of Bioinformatics   Animal pathogens, E learning, Phylogenetics Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28 2017-10-09
UNIX Fundamentals

This 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.

UNIX Fundamentals https://tess.elixir-europe.org/materials/unix-fundamentals This 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. 2014-01-13
Showing 14 upcoming events. Found 204 past events. View all results.

  • Metagenome-atlas: Three commands to start analysing your metagenome data

    7 December 2020

    Streamed from Geneva, Switzerland

    Elixir node event
    Metagenome-atlas: Three commands to start analysing your metagenome data https://tess.elixir-europe.org/events/metagenome-atlas-three-commands-to-start-analysing-your-metagenome-data Overview Metagenomics is transforming how we study microbiomes by enabling the analysis of entire microbial communities from diverse environments, without the need for culturing. 2020-12-07 09:00:00 UTC 2020-12-07 00:00:00 UTC SIB, Streamed from Geneva, Switzerland SIB Streamed from Geneva Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • UNIX scripting for Life Scientists

    1 - 2 October 2020

    Lausanne, Switzerland

    Elixir node event
    UNIX scripting for Life Scientists https://tess.elixir-europe.org/events/unix-scripting-for-life-scientists More information on due time... 2020-10-01 09:00:00 UTC 2020-10-02 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First steps with R in Life Sciences

    27 - 28 October 2020

    Lausanne, Switzerland

    Elixir node event
    First steps with R in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-009cd52b-e152-423a-8888-02c096d98fc5 This course will take place in Lausanne with rules complying to COVID situation (distances and hygiene). 2020-10-27 09:00:00 UTC 2020-10-28 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First Steps with UNIX in Life Sciences

    12 January 2021

    Lausanne, Switzerland

    Elixir node event
    First Steps with UNIX in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-unix-in-life-sciences-2ff593cf-d240-4e36-900e-7fcfe3dbbd4f More information soon... 2021-01-12 09:00:00 UTC 2021-01-12 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 - streamed

    25 November 2020

    Streamed from Basel, Switzerland

    Elixir node event
    First Steps in Parallelization with OpenMP - streamed https://tess.elixir-europe.org/events/first-steps-in-parallelization-with-openmp-streamed This course will be streamed only for the registered participants. Registered participants will receive specific information directly from the respective course’s organizers. 2020-11-25 09:00:00 UTC 2020-11-25 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • NGS - Quality control, Alignment, Visualisation

    4 - 6 November 2020

    Bern, Switzerland

    Elixir node event
    NGS - Quality control, Alignment, Visualisation https://tess.elixir-europe.org/events/ngs-quality-control-alignment-visualisation-812c2b46-ad83-4afa-973b-991d91edf93f This course will take place in Bern with rules complying to COVID situation (distances and hygiene). 2020-11-04 09:00:00 UTC 2020-11-06 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • NGS - Genome variant analysis

    8 - 9 December 2020

    Bern, Switzerland

    Elixir node event
    NGS - Genome variant analysis https://tess.elixir-europe.org/events/ngs-genome-variant-analysis-3c6175a8-5953-4030-8caf-ebc32ee36273 Overview The detection of genetic variation is of major interest in various disciplines spanning from ecology and evolution research to inherited disease discovery and precision oncology. 2020-12-08 09:00:00 UTC 2020-12-09 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • UNIX scripting for Life Scientists

    1 - 2 October 2020

    Lausanne, Switzerland

    Elixir node event
    UNIX scripting for Life Scientists https://tess.elixir-europe.org/events/unix-scripting-for-life-scientists-ef67aec8-cc7b-4010-8668-fe9d5ba9091d This course will take place in Lausanne with rules complying to COVID situation (distances and hygiene). 2020-10-01 09:00:00 UTC 2020-10-02 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First Steps with Python in Life Sciences

    1 - 3 December 2020

    Lausanne, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences More information on due time... 2020-12-01 09:00:00 UTC 2020-12-03 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 - streamed

    5 - 6 October 2020

    Streamed from Basel, Switzerland

    Elixir node event
    Introduction to RNA-Seq: From quality control to pathway analysis - streamed https://tess.elixir-europe.org/events/introduction-to-rna-seq-from-quality-control-to-pathway-analysis-a2df060f-df2e-499e-be62-1f68e7b8cb91 This course is over-subscribed with a very long waiting list. We are not accepting applications any more. 2020-10-05 09:00:00 UTC 2020-10-06 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Protein Bioinformatics: Sequence-Structure-Function - streamed

    18 - 20 November 2020

    streamed from multiple locations, Switzerland

    Elixir node event
    Protein Bioinformatics: Sequence-Structure-Function - streamed https://tess.elixir-europe.org/events/protein-bioinformatics-sequence-structure-function-dates-to-be-confirmed This course will be streamed for the registered participants. Overview Sequence-structure-function relationships of proteins are central to a comprehensive understanding of cellular biology. 2020-11-18 09:00:00 UTC 2020-11-20 00:00:00 UTC SIB, streamed from multiple locations, Switzerland SIB streamed from multiple locations Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Introduction to high-performance computing (sciCORE cluster) - streamed

    11 November 2020

    Streamed from Basel, Switzerland

    Elixir node event
    Introduction to high-performance computing (sciCORE cluster) - streamed https://tess.elixir-europe.org/events/introduction-to-high-performance-computing-scicore-cluster-streamed This course will be streamed only for the registered participants. Registered participants will receive specific information directly from the respective course’s organizers. This course is currently over-subscribed with a waiting list. 2020-11-11 09:00:00 UTC 2020-11-11 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Ligand-protein docking, and computer-aided drug design

    3 - 5 November 2020

    Lausanne, Switzerland

    Elixir node event
    Ligand-protein docking, and computer-aided drug design https://tess.elixir-europe.org/events/ligand-protein-docking-and-computer-aided-drug-design-a6576d32-6b99-4155-a68c-d273db65592a This course will take place in Lausanne with rules complying to COVID situation (distances and hygiene). 2020-11-03 09:00:00 UTC 2020-11-05 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Enrichment Analysis - streamed

    4 December 2020

    Streamed from Lausanne, Switzerland

    Elixir node event
    Enrichment Analysis - streamed https://tess.elixir-europe.org/events/enrichment-analysis-streamed-e34c9070-8d06-485b-9a92-2fdcd0b9385a Overview Experiments designed to quantify gene expression often yield hundreds of genes that show statistically significant differences between two classes (two biological states, two phenotype states, two experimental conditions, etc). 2020-12-04 09:00:00 UTC 2020-12-04 00:00:00 UTC SIB, Streamed from Lausanne, Switzerland SIB Streamed from Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []