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24 materials found

Node: Switzerland 


SPHN/BioMedIT Data Privacy and IT Security Training

No description provided.

SPHN/BioMedIT Data Privacy and IT Security Training http://tess.elixir-uk.org/materials/sphn-biomedit-data-privacy-and-it-security-training No description provided.
Cellosaurus : A resource on cell lines

No description provided.

Cellosaurus : A resource on cell lines http://tess.elixir-uk.org/materials/cellosaurus-a-resource-on-cell-lines No description provided.
Querying Data with SPARQL

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

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

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

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

Querying Data with SPARQL http://tess.elixir-uk.org/materials/querying-data-with-sparql This training module will provide researcher with an introduction to SPARQL queries for health-related data. Philip Krauss Sabine Österle Computer science Data management FAIR data Medical informatics Clinical data, SPARQL, Query data, RDF, Knowledge graph, SNOMED CT, LOINC Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
SARS-CoV-2 : Studying a new virus

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...

SARS-CoV-2 : Studying a new virus http://tess.elixir-uk.org/materials/sars-cov-2-studying-a-new-virus 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 viruses is presumed.
Explore and visualize your data with Python

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.

Explore and visualize your data with Python http://tess.elixir-uk.org/materials/explore-and-visualize-your-data-with-python 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.
Cybersecurity Quiz for SIB employees only (internal use)

No description provided.

Cybersecurity Quiz for SIB employees only (internal use) http://tess.elixir-uk.org/materials/cybersecurity-quiz-for-sib-employees-only-internal-use No description provided.
neXtProt : Exploring human proteins

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.

neXtProt : Exploring human proteins http://tess.elixir-uk.org/materials/nextprot 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.
Information Security Awareness (BioMedIT)

No description provided.

Information Security Awareness (BioMedIT) http://tess.elixir-uk.org/materials/demo-cyber-security-awareness-biomedit No description provided.
Course design: Considerations for trainers – a Professional Guide

This Professional Guide in the Resources for Training Trainers series introduces a structured approach to course design, highlighting the importance of articulating learning outcomes commensurate with the cognitive complexity of the target learning, prior to devising learning experiences and...

Keywords: Curriculum development, course design, learning outcomes, Bloom's Taxonomy, assessment, course evaluation, training trainers, training material

Course design: Considerations for trainers – a Professional Guide http://tess.elixir-uk.org/materials/course-design-considerations-for-trainers-a-professional-guide This Professional Guide in the Resources for Training Trainers series introduces a structured approach to course design, highlighting the importance of articulating learning outcomes commensurate with the cognitive complexity of the target learning, prior to devising learning experiences and course content. The specific focus here is on face-to-face activities, but the guidance is also relevant for those designing online courses. Curriculum development, course design, learning outcomes, Bloom's Taxonomy, assessment, course evaluation, training trainers, training material Training instructors Trainers Training Designers Anyone who wants to become a good trainer or teacher teachers
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

Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide http://tess.elixir-uk.org/materials/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, its proteins, its origins and its evolution are explored. Bioinformatics for schools, basic bioinformatics, SARS-CoV-2 pandemic, genome analysis, protein sequence analysis, protein structure analysis, virus variants, spike protein, training material Trainers Training instructors Training Designers PhD students post-docs Life Science Researchers
IFB Shiny training

Shiny package training (in french)

Keywords: R-programming, Reproducible Science

IFB Shiny training http://tess.elixir-uk.org/materials/ifb-shiny-training Shiny package training (in french) Hélène Chiapello Jacques van Helden R-programming, Reproducible Science bioinformaticians statisticians
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

Operations: Read pre-processing, Alignment, Variant calling

Keywords: coronavirus, NGS bioinformatics, Variant-calling

Resource type: Computer Software, workflow

How to use V-pipe (SARS-CoV-2 data) http://tess.elixir-uk.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
Querying SIB resources with SPARQL



Querying SIB resources with SPARQL http://tess.elixir-uk.org/materials/sparql 
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 http://tess.elixir-uk.org/materials/blast-and-multiple-sequence-alignment-msa-programs-0b2b34d0-a157-49d4-a065-3dcad67ff99d 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
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

Phylogenetics of animal viral pathogens http://tess.elixir-uk.org/materials/phylogenetics-of-animal-viral-pathogens-428432a3-67ca-4284-8962-fefc2ade75db 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
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

High Performance Computing (HPC) in Life Sciences http://tess.elixir-uk.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. Biology Bioinformatics Computer science High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
High Performance Computing in Life Sciences

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.

High Performance Computing in Life Sciences http://tess.elixir-uk.org/materials/high-performance-computing-in-life-sciences 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.
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 http://tess.elixir-uk.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 Vassilios Ioannidis Grégoire Rossier Volker Flegel Heinz Stockinger Frédéric Schütz Problem based learning, Programming, Unix Bench biologists Clinical Scientists Graduate Students beginner bioinformaticians biocurators 2014-01-13 2017-10-09
R Basics Quiz

How to learn R basics

R Basics Quiz http://tess.elixir-uk.org/materials/r-basics How to learn R basics
Vital-IT Infrastructure Usage

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

Vital-IT Infrastructure Usage http://tess.elixir-uk.org/materials/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...

Introduction to 3D-Structure Visualization and Homology Modeling using the Swiss-Model Workspace http://tess.elixir-uk.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.
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 http://tess.elixir-uk.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
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 http://tess.elixir-uk.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 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.

UNIX Fundamentals http://tess.elixir-uk.org/materials/unix-fundamentals 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. 2014-01-13