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Resource type: Training materials 

BioData.pt | ELIXIR PT Training Data Stewards for Life Sciences - Intro Course

BioData.pt | ELIXIR Portugal, in collaboration with several other organizations has designed a program to train the first generation of Data Stewards for the life sciences, to support the implementation of data management, open science and FAIR data principles in Portuguese R&I organizations.

Scientific topics: Data management, Open science, FAIR data

Keywords: Data management plan, data-science, data-analysis, Data Integration, training, open science, data FAIRness, FAIR data, FAIR, FAIR principles, life sciences, data life cycle

Resource type: Training materials

BioData.pt | ELIXIR PT Training Data Stewards for Life Sciences - Intro Course http://tess.elixir-uk.org/materials/biodata-pt-elixir-pt-training-data-stewards-for-life-sciences-intro-course BioData.pt | ELIXIR Portugal, in collaboration with several other organizations has designed a program to train the first generation of Data Stewards for the life sciences, to support the implementation of data management, open science and FAIR data principles in Portuguese R&I organizations. Data management Open science FAIR data Data management plan, data-science, data-analysis, Data Integration, training, open science, data FAIRness, FAIR data, FAIR, FAIR principles, life sciences, data life cycle Researchers
Machine Learning & BioStatistics Hackathon 2020

Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020.

Scientific topics: Computer science, Statistics and probability, Machine learning

Keywords: machine learning, biostatistics, eLearning, EeLP

Resource type: Training materials

Machine Learning & BioStatistics Hackathon 2020 http://tess.elixir-uk.org/materials/machine-learning-biostatistics-hackathon-2020 Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020. Computer science Statistics and probability Machine learning machine learning, biostatistics, eLearning, EeLP Life Science Researchers statisticians Training Designers Training instructors Trainers
HPC Hackathon Materials

Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021.

Scientific topics: Computer science

Keywords: HPC, high-performance computing, eLearning, EeLP

Resource type: Training materials

HPC Hackathon Materials http://tess.elixir-uk.org/materials/hpc-hackathon-materials Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021. Computer science HPC, high-performance computing, eLearning, EeLP Life Science Researchers Training Designers Training instructors Trainers
Containers and Workflows training materials hackathon

Materials developed at the Containers and Workflows hackathon organised by ELIXIR-BE (VIB) in February and April 2021.

Scientific topics: Computer science

Keywords: Containers, Workflows, eLearning, EeLP

Resource type: Training materials

Containers and Workflows training materials hackathon http://tess.elixir-uk.org/materials/containers-and-workflows-training-materials-hackathon Materials developed at the Containers and Workflows hackathon organised by ELIXIR-BE (VIB) in February and April 2021. Computer science Containers, Workflows, eLearning, EeLP Life Science Researchers Training Designers Training instructors Trainers
Containers & Workflow pipelines workshop

The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify...

Keywords: Containers, Nextflow

Resource type: Training materials

Containers & Workflow pipelines workshop http://tess.elixir-uk.org/materials/containers-workflow-pipelines-workshop The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, at the end of the first day, Singularity will be highlighted as well. On the second day (27 May 2021), you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Containers, Nextflow bioinformaticians
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
GA4GH Passports and ELIXIR AAI

The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API.

Keywords: AAI , GA4GH, Passports, Auhtorisation

Resource type: Training materials, Video

GA4GH Passports and ELIXIR AAI http://tess.elixir-uk.org/materials/ga4gh-passports-and-elixir-aai The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API. Stefan Negru Teemu Kataja AAI , GA4GH, Passports, Auhtorisation software developers, bioinformaticians
FAIR principles applied to bioinformatics

Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure...

Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing

Resource type: Training materials

FAIR principles applied to bioinformatics http://tess.elixir-uk.org/materials/fair-principles-applied-to-bioinformatics Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure the traceability of analysis using Notebooks. The training material is in french Hélène Chiapello FAIR, Reproducible Science, Open science, Data analysis, Data processing bioinformaticians software developers, bioinformaticians computational scientists Researchers
Plant Phenotyping Data managment (MIAPPE)

This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners...

Scientific topics: Data management, Plant biology, Phenomics

Operations: Formatting, Annotation

Keywords: Plant Phenotyping, Data-format, data sharing

Resource type: Training materials

Plant Phenotyping Data managment (MIAPPE) http://tess.elixir-uk.org/materials/plant-phenotyping-data-managment-miappe This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners will know how to use standards and ontologies, how to describe their measurment protocole and practices how to fill a template with their data and how to apply the standards concept in some data managment tools. Data management Plant biology Phenomics Plant Phenotyping, Data-format, data sharing Biologists geneticists plant researchers software engineers database managers
Genetics education for primary care resources from the Gen-Equip project

Gen-Equip project is a project combining education, primary care and genetics. Its aim is to enable health professionals who are working in primary care to update their knowledge and skills in genetics. The aims is the long-term outcome of improvement in care of patients with genetic conditions...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Documentation, Video, Training materials, online modules, e-learning

Genetics education for primary care resources from the Gen-Equip project http://tess.elixir-uk.org/materials/genetics-education-for-primary-care-resources Gen-Equip project is a project combining education, primary care and genetics. Its aim is to enable health professionals who are working in primary care to update their knowledge and skills in genetics. The aims is the long-term outcome of improvement in care of patients with genetic conditions or concerns. They offer genetics education free of charge to those who want continuing medical or professional education in genetics. Rare diseases Rare Diseases & Research Primary care doctors health professionals
European Patients’ Academy Expert Training Course

Online course in medicines research and development. Not solely focused on rare diseases.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: online modules, e-learning, Training materials

European Patients’ Academy Expert Training Course http://tess.elixir-uk.org/materials/european-patients-academy-expert-training-course Online course in medicines research and development. Not solely focused on rare diseases. Rare diseases Rare Diseases & Research Patient Advocates rare disease patients representatives
Findacure's e-learning resources on rare diseases

Findacure’s e-learning portal is a central hub of information and training for rare disease advocates and patient groups. It contains educational materials, including written guides, animated videos, presentations and webinars, to help the establishment and growth of rare disease patient groups.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, Video, Presentation, Training materials, e-learning

Findacure's e-learning resources on rare diseases http://tess.elixir-uk.org/materials/findacure-s-e-learning-video-library Findacure’s e-learning portal is a central hub of information and training for rare disease advocates and patient groups. It contains educational materials, including written guides, animated videos, presentations and webinars, to help the establishment and growth of rare disease patient groups. Rare diseases Rare Diseases & Research Patient Advocates rare disease patients representatives
Introduction to GitHub

The aim for today is to learn the basics of GitHub so that you can use it for your own projects. - Background - What is version control? What is Git? What is GitHub? - How can you use GitHub? How can it be useful for your work? - Practical session: working with GitHub

Keywords: GitHub, Reproducibility

Resource type: Training materials

Introduction to GitHub http://tess.elixir-uk.org/materials/introduction-to-github The aim for today is to learn the basics of GitHub so that you can use it for your own projects. - Background - What is version control? What is Git? What is GitHub? - How can you use GitHub? How can it be useful for your work? - Practical session: working with GitHub Gabriella Rustici GitHub, Reproducibility Senior Managers
Beginners introduction to Git and GitHub

__Morning session__ (Sergio and Mark) https://tinyurl.com/git-intro-zoology: - Background and motivation - What is version control? What is Git? What is GitHub? - How can you use Git and GitHub? How can they be useful for you? - Practical session: working with Git and GitHub __Afternoon...

Keywords: Git, GitHub, control version, Reproducibility

Resource type: Training materials

Beginners introduction to Git and GitHub http://tess.elixir-uk.org/materials/beginners-introduction-to-git-and-github __Morning session__ (Sergio and Mark) https://tinyurl.com/git-intro-zoology: - Background and motivation - What is version control? What is Git? What is GitHub? - How can you use Git and GitHub? How can they be useful for you? - Practical session: working with Git and GitHub __Afternoon session__ (Mark and Anne) https://tinyurl.com/git-course: markdown, pages and wikis; creating good README files; issue tracking; sofware licenses Mark Fernandes pajanne Git, GitHub, control version, Reproducibility Researchers
NBIS Reproducible research course

The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers: Data management Conda Snakemake Git Jupyter R Markdown Docker

Keywords: data management, Reproducibility, Data analysis

Resource type: Training materials

NBIS Reproducible research course http://tess.elixir-uk.org/materials/nbis-reproducible-research-course The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers: Data management Conda Snakemake Git Jupyter R Markdown Docker Leif Wigge Rasmus Ågren John Sundh data management, Reproducibility, Data analysis bioinformaticians
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
Mascot training course

The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises.

Scientific topics: Proteomics

Keywords: Protein identification, Protein Mass Spectrometry

Resource type: Slides, Video, Training materials

Mascot training course http://tess.elixir-uk.org/materials/mascot-training-course The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises. Proteomics Protein identification, Protein Mass Spectrometry Biologists bioinformaticians Biochemists mass spectrometry
Essential Steps of the FAIRification Process

Since 2014, a number of FAIR Stakeholders have developed tools and methods around the FAIRifcation of typical datasets. In the last 5 years, these efforts were field tested in a series of "Bring Your Own Data" Workshops". This material documents the accumulated practical & teaching...

Keywords: FAIR, data stewardship, metadata, linked data

Resource type: Training materials

Essential Steps of the FAIRification Process http://tess.elixir-uk.org/materials/essential-steps-of-the-fairification-process Since 2014, a number of FAIR Stakeholders have developed tools and methods around the FAIRifcation of typical datasets. In the last 5 years, these efforts were field tested in a series of "Bring Your Own Data" Workshops". This material documents the accumulated practical & teaching experiences from BYODS as well as more high-level FAIR awareness trainings. This document was formerly known as the "Big Book of FAIRification". FAIR, data stewardship, metadata, linked data Researchers Support Staff data librarians software developers, bioinformaticians
FAIR Data Stewardship - Data sharing, archiving and publishing

The workshop introduces the concepts and gives hands-on experience with tools which allow safe data sharing, archiving and publishing on example services. Moreover, participants of the workshop explore together different roles which are defined around data publication and how responsibilities...

Keywords: Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication

Resource type: Slides, Training materials

FAIR Data Stewardship - Data sharing, archiving and publishing http://tess.elixir-uk.org/materials/fair-data-stewardship-data-sharing-archiving-and-publishing The workshop introduces the concepts and gives hands-on experience with tools which allow safe data sharing, archiving and publishing on example services. Moreover, participants of the workshop explore together different roles which are defined around data publication and how responsibilities towards data are distributed. The course does not require any prior knowledge. Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication General Interest Scientists Researchers data stewards
Adding schema.org to a GitHub Pages site

This guide will show you how to do add schema.org to GitHub Pages.

Scientific topics: Computer science

Keywords: Mark-up, Bioschemas, Interoperability

Resource type: Training materials

Adding schema.org to a GitHub Pages site http://tess.elixir-uk.org/materials/adding-schema-org-to-a-github-pages-site This guide will show you how to do add schema.org to GitHub Pages. Raniere Silva Computer science Mark-up, Bioschemas, Interoperability web developers System administrators
PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/)

Scientific topics: Plant biology, Functional genomics, Comparative genomics, Evolutionary biology, Phylogenomics, Genotype and phenotype

Operations: Annotation, Visualisation, Comparison

Keywords: plants, Plants bioinformatics, genomics, Visualisation, Annotation

Resource type: Training materials

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics http://tess.elixir-uk.org/materials/plaza-is-a-plant-oriented-online-resource-for-comparative-evolutionary-and-functional-genomics PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/) Plant biology Functional genomics Comparative genomics Evolutionary biology Phylogenomics Genotype and phenotype plants, Plants bioinformatics, genomics, Visualisation, Annotation Life Science Researchers plant researchers experimeintal biologist researchers postdoctoral researchers Research Assistants and Research Associates PhD
Galaxy Proteomics workshop Prague 2018

Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic

Scientific topics: Proteomics

Keywords: Galaxy, training, proteomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Galaxy Proteomics workshop Prague 2018 http://tess.elixir-uk.org/materials/galaxy-proteomics-workshop-prague-2018 Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic Andrea Argentini Frederik Coppens Pavel Dvorak Matthias Fahrner Melanie Foell Björn Grüning Martin Hubalek Hana Pergl Sustkova Marek Vrbacky Proteomics Galaxy, training, proteomics, eLearning, EeLP life scientists Researchers PhD Students
How to get the most out of your microarray experiment. A Webinar

Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017

Scientific topics: Microarray experiment

Keywords: life sciences, microarrays, eLearning, EeLP

Resource type: course materials, Training materials, Slides

How to get the most out of your microarray experiment. A Webinar http://tess.elixir-uk.org/materials/how-to-get-the-most-out-of-your-microarray-experiment-a-webinar Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017 Eva Freyhult Jessica Lindvall Mihaela Martis Microarray experiment life sciences, microarrays, eLearning, EeLP Researchers
ELIXIR eLearning definitions

Materials from the asynchronous learning course "ELIXIR eLearning definitions"

Keywords: eLearning, training, EeLP

Resource type: course materials, Training materials, Documentation

ELIXIR eLearning definitions http://tess.elixir-uk.org/materials/elixir-elearning-definitions Materials from the asynchronous learning course "ELIXIR eLearning definitions" Brane Leskosek Jure Dimec Eija Korpelainen Teresa Attwood Sarah Morgan Nicola Mulder Celia van Gelder Patricia Palagi eLearning, training, EeLP Researchers teachers Trainers
RNA-seq data analysis using Chipster

Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017

Scientific topics: Transcriptomics, Genomics

Keywords: transcriptomics, RNA-Seq, eLearning, EeLP

Resource type: course materials, Training materials, Slides, Video

RNA-seq data analysis using Chipster http://tess.elixir-uk.org/materials/rna-seq-data-analysis-using-chipster Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017 Eija Korpelainen Maria Lehtivaara Transcriptomics Genomics transcriptomics, RNA-Seq, eLearning, EeLP Researchers
ELIXIR TtR course: Basic genomics using advanced analysis tools

Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia

Scientific topics: Genomics

Keywords: Galaxy, training, Genomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

ELIXIR TtR course: Basic genomics using advanced analysis tools http://tess.elixir-uk.org/materials/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia Christophe Antoniewski Olivier Inizan Genomics Galaxy, training, Genomics, eLearning, EeLP life scientists beginner bioinformaticians Postgraduate students
Hands-on workshop in Marine Metagenomics

Materials from the ELIXIR workshop “Hands-on workshop in Marine Metagenomics”, Nov 26-30 2018 at the Arctic University of Norway, Tromso, Norway

Scientific topics: Marine biology, Metagenomics, Genomics

Keywords: Marine Metagenomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Hands-on workshop in Marine Metagenomics http://tess.elixir-uk.org/materials/hands-on-workshop-in-marine-metagenomics Materials from the ELIXIR workshop “Hands-on workshop in Marine Metagenomics”, Nov 26-30 2018 at the Arctic University of Norway, Tromso, Norway Erik Hjerde Nils Peder Willassen Espen Aberg Espen Mikal Robertsen Marine biology Metagenomics Genomics Marine Metagenomics, eLearning, EeLP Researchers Master students PhD students
ELIXIR EXCELERATE Train the Trainer

This set of course material was designed in the context of the ELIXIR EXCELERATE Train the Trainer programme. It covers four sessions: * Learning principles and how they apply to training and teaching * Teaching techniques that can be used to enhance learner engagement and participation *...

Keywords: Train the trainer, Pedagogy, Course development, Course design

Resource type: Training materials

ELIXIR EXCELERATE Train the Trainer http://tess.elixir-uk.org/materials/elixir-excelerate-train-the-trainer This set of course material was designed in the context of the ELIXIR EXCELERATE Train the Trainer programme. It covers four sessions: * Learning principles and how they apply to training and teaching * Teaching techniques that can be used to enhance learner engagement and participation * Lesson, course, and materials design * Assessment and feedback in training and teaching Train the trainer, Pedagogy, Course development, Course design Trainers Training instructors Training Designers teachers
Implementation of Data Management Plans & Data Stewardship in practice

Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece.

Scientific topics: Data submission, annotation, and curation, Data management

Keywords: data management, data stewardship, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Implementation of Data Management Plans & Data Stewardship in practice http://tess.elixir-uk.org/materials/implementation-of-data-management-plans-data-stewardship-in-practice Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece. Celia van Gelder Roland Krause Mateusz Kuzak Brane Leskosek Marko Vidak Robert Pergl Marek Suchanek Jan Slifka Vojtech Knaisl Data submission, annotation, and curation Data management data management, data stewardship, eLearning, EeLP bioinformaticians data stewards
Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R

An overview of Unix and R for bioinformatics

Keywords: Unix, R-programming

Resource type: Training materials

Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R http://tess.elixir-uk.org/materials/summer-school-2018-trainmalta-epigenomics-introduction-to-unix-and-r An overview of Unix and R for bioinformatics Luigi Grassi Unix, R-programming PhD students Life Science Researchers