Resource type: hackathon or Training materials
Expanding the SPHN RDF Schema is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...
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
The RDF and SPARQL training primer was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...
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
This video was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and serves as an introduction to the main standards used within the [SPHN Interoperability...
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
RDF Schema and Data Visualization is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...
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
Validate Graph Data with SHACL is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...
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
How to use Python and R with RDF Data is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centred around the [SPHN Interoperability...
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
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
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
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
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
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
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
The training (delivered 23 June 2021) consisted of one hour of presentations (recorded stream), followed by a hands-on exercise with a Virtual Machine. In the hands-on part the trainees integrate their VM to ELIXIR AAI as an OpenID Connect client to...
Keywords: AAI , GA4GH, Passports, Auhtorisation
Resource type: Training materials, Video
Under the subtitle “Getting into using ELNs for experimental and computational workflows”, participants learned how to establish a workflow using Scinote-based electronic lab notebooks. It started with an introduction to the Scinote inventory and continues with hands-on instructions on how to...
Resource type: Presentation, hackathon
The French Institute of Bioinformatics (IFB) has organised in partnership with the Institute of Integrative Biology (I2BC) a training course for bioinformaticians and biostatisticians wishing to implement the "FAIR" principles (Findable, Accessible, Interoperable, Reusable) in their analysis and...
Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing
Resource type: Training materials
This training material has been used in a two-day training workshop on data management organized by Elixir and the Wheat Initiative.
It provides an overview of current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity...
Scientific topics: Data management, Plant biology, Phenomics
Operations: Formatting, Annotation
Keywords: Plant Phenotyping, Data-format, data sharing
Resource type: Training materials
GEN-EQUIP project combine education, primary care and genetics. Each module is based on a case and covers a different type of genetic condition you might see in primary care. Through its website, it offers genetics education free of charge to those who want continuing medical or professional...
Scientific topics: Rare diseases
Keywords: Rare Diseases & Research
Resource type: Documentation, Video, Training materials, online modules, e-learning
The portal is aimed at rare disease advocates, patient groups and charities, though anyone with an interest in rare diseases or advocacy is welcome to sign-up. It is completely free to use, and users are encouraged to contact Findacure with suggestions for new content.
The portal shares ‘how to’...
Scientific topics: Rare diseases
Keywords: Rare Diseases & Research
Resource type: Webinar, Video, Presentation, Training materials, e-learning
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
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
This course introduces single cell RNA-seq data analysis methods, tools and file formats. 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...
Keywords: scRNA-seq
Resource type: Slides, Training materials
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
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" (https://www.dtls.nl/fair-data/byod/).
This document records the...
Keywords: FAIR, data stewardship, metadata, linked data
Resource type: Training materials
In this workshop we focus on three aspects of FAIR data stewardship: Data sharing, publishing and archiving. Many scientists have an insufficient overview over data services, roles and their responsibilities towards safe data sharing, archiving and publishing. Shedding light on these roles helps...
Keywords: Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication
Resource type: Slides, Training materials
GitHub Pages are an excellent platform for creating informative websites. The hosting is (currently) free which is a huge plus; the collaborative tools allow teams (that may be widely distributed, fluctuating, and/or voluntary) to contribute in a well-structured, verifiable, and open manner; and...
Scientific topics: Computer science
Keywords: Mark-up, Bioschemas, Interoperability
Resource type: Training materials
PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. It allows querying and visualising structural and functional annotations, gene families, protein domains, phylogenetic trees, and genome organization. PLAZA 4.0 is the latest iteration of the PLAZA...
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
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
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
Materials from the asynchronous learning course "ELIXIR eLearning definitions"
Keywords: eLearning, training, EeLP
Resource type: course materials, Training materials, Documentation
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