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37 materials found

Content provider: CSC - IT Center for Science  or Swiss Institute of Bioinfor... 


Introduction to using containers - OpenShift, Kubernetes and Docker oriented view

This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez

Keywords: Containers, Kubernetes, Cloud computing

Introduction to using containers - OpenShift, Kubernetes and Docker oriented view http://tess.elixir-uk.org/materials/introduction-to-using-containers-openshift-kubernetes-and-docker-oriented-view This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez Containers, Kubernetes, Cloud computing Cloud users
Expanding the SPHN RDF Schema

This training module will provide researchers with an introduction on how to expand the SPHN RDF Schema using an ontology editor.

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

Operations: Editing, Ontology visualisation, Visualisation, Data handling

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

Resource type: Video, Training materials, E-learning

Expanding the SPHN RDF Schema http://tess.elixir-uk.org/materials/expanding-the-sphn-rdf-schema This training module will provide researchers with an introduction on how to expand the SPHN RDF Schema using an ontology editor. Kristin Gnodke Sabine Österle Ontology and terminology Medical informatics FAIR data Data management Computer science Clinical data, Data semantics, FAIR, Ontology editing, Protegé, RDF, OWL Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Training Primer (RDF and SPARQL)

This training provides a first introduction to RDF and SPARQL.

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

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

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

Resource type: Video, Training materials, E-learning

Training Primer (RDF and SPARQL) http://tess.elixir-uk.org/materials/training-primer-rdf-and-sparql This training provides a first introduction to RDF and SPARQL. Sabine Österle Computer science Data management FAIR data Medical informatics Ontology and terminology Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Semantic Standards

This training module provides an introduction on the key semantic standards used within SPHN.

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

Resource type: Video, Training materials, E-learning

Semantic Standards http://tess.elixir-uk.org/materials/semantic-standards This training module provides an introduction on the key semantic standards used within SPHN. Sabine Österle Ontology and terminology Medical informatics FAIR data Data management Computer science Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
RDF Schema and Data Visualization

This training module will provide researchers with an introduction on how to explore and visualize the SPHN ontology and mock data.

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

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

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

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

RDF Schema and Data Visualization http://tess.elixir-uk.org/materials/rdf-schema-and-data-visualization This training module will provide researchers with an introduction on how to explore and visualize the SPHN ontology and mock data. Vasundra Touré Sabine Österle Data visualisation Medical informatics FAIR data Data management Computer science Clinical data, SPARQL, Data visualization, RDF, Knowledge graph, GraphDB, Mock data Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Validate Graph Data with SHACL

This training module will provide researchers with an introduction on SHACL for RDF graphs validation.

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

Validate Graph Data with SHACL http://tess.elixir-uk.org/materials/validate-graph-data-with-shacl This training module will provide researchers with an introduction on SHACL for RDF graphs validation. Sabine Österle Vasundra Touré Computer science Data management FAIR data Medical informatics Clinical data, SHACL, Data validation, RDF, Knowledge graph, GraphDB, RDF, RDF graph validation Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
How to use Python and R with RDF Data

This training module will provide researchers with an introduction on how use R and Python in combination with SPARQL to query RDF data.

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 Python and R with RDF Data http://tess.elixir-uk.org/materials/how-to-use-python-and-r-with-rdf-data This training module will provide researchers with an introduction on how use R and Python in combination with SPARQL to query RDF data. Sabine Österle Vasundra Touré Medical informatics FAIR data Data management Computer science Clinical data, SPARQL, Query data, RDF, Knowledge graph, Python, R, GraphDB Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
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

No description provided.

SARS-CoV-2 : Studying a new virus http://tess.elixir-uk.org/materials/sars-cov-2-studying-a-new-virus No description provided.
Explore and visualize your data with Python

No description provided.

Explore and visualize your data with Python http://tess.elixir-uk.org/materials/explore-and-visualize-your-data-with-python No description provided.
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

No description provided.

neXtProt : Exploring human proteins http://tess.elixir-uk.org/materials/nextprot No description provided.
BioMedIT: Information Security Awareness Training

No description provided.

BioMedIT: Information Security Awareness Training http://tess.elixir-uk.org/materials/demo-cyber-security-awareness-biomedit No description provided.
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
Introduction to research data management, data management planning and services provided by CSC – IT Center for Science

Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project.

Keywords: DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE

Resource type: Series of videos, Video, youtube video

Introduction to research data management, data management planning and services provided by CSC – IT Center for Science http://tess.elixir-uk.org/materials/introduction-to-research-data-management-data-management-planning-and-services-provided-by-csc-it-center-for-science Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project. Maria Lehtivaara DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE Researchers Life Science Researchers Undergraduate students Master students PhD candidates postdoctoral researchers Senior Researchers, Lab Managers, Postdocs and PhD Students with basic knowledge of DMPs. Participants in the "Introduction to Data Management Plans" workshop.
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

No description provided.

Querying SIB resources with SPARQL http://tess.elixir-uk.org/materials/sparql No description provided.
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
Detecting differentially expressed genes with RNA-seq 11.9.2019

This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and...

Scientific topics: RNA-Seq

Detecting differentially expressed genes with RNA-seq 11.9.2019 http://tess.elixir-uk.org/materials/detecting-differentially-expressed-genes-with-rna-seq This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the workshop is thus suitable for everybody. RNA-Seq
Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Single cell RNA-seq data analysis using Chipster http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-using-chipster This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3 tools embedded in the user-friendly Chipster software. scRNA-seq Biologists bioinformaticians
Introduction to using cloud and containers for training - OpenStack and Docker oriented view

This material is based on CSC's Pouta cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenStack (VM, volumes, networks, security Groups, VM snapshots, etc). It also covers topics like orchestration with Heat and accessing Pouta Object...

Keywords: Cloud computing, Containers

Resource type: Slides, course materials

Introduction to using cloud and containers for training - OpenStack and Docker oriented view http://tess.elixir-uk.org/materials/introduction-to-using-cloud-and-containers-for-training-openstack-and-docker-oriented-view This material is based on CSC's Pouta cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenStack (VM, volumes, networks, security Groups, VM snapshots, etc). It also covers topics like orchestration with Heat and accessing Pouta Object storage. The original material was produced by Shubham Kapoor and Johan Guldmyr, and it was tailored for trainers by Jarno Laitinen. Eija Korpelainen Cloud computing, Containers Trainers
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
Single cell RNA-seq data analysis with R

This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with R http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-r This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists
Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

Single cell RNA-seq data analysis with Chipster http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
High Performance Computing in Life Sciences

No description provided.

High Performance Computing in Life Sciences http://tess.elixir-uk.org/materials/high-performance-computing-in-life-sciences No description provided.
Community analysis of amplicon sequencing data (16S rRNA)

This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...

Resource type: course materials, Video

Community analysis of amplicon sequencing data (16S rRNA) http://tess.elixir-uk.org/materials/community-analysis-of-amplicon-sequencing-data-16s-rrna This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....

Scientific topics: RNA-Seq

Resource type: course materials, Video

Virus detection using small RNA-seq http://tess.elixir-uk.org/materials/virus-detection-using-small-rna-seq This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq