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Workshops and courses
Docker and Singularity (Apptainer) for reproducible and automated data analysis
12 - 13 October 2023
Brussel, Belgium
Face-to-face
advanced bioinformatics research data management programming ELIXIR -
Docker and Singularity for Reproducible Research: Getting Started with Containers
13 October 2023
Online
reproducibility training container data management data security high-performance computing rémy bruggmann group
Showing 30 materials
out of 47
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Docker for Beginners
Docker
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Docker Tutorial
Docker
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Online material, hands-on tutorial
Introduction to Docker and Singularity
• beginnerReproducibility Container Singularity -
slides
Slides for 'Docker and Galaxy' tutorial
admin
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Slides
Galaxy Server administration - Docker and Galaxy
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Docker version of Welsh Gene Park NGS course
• beginnerNGS IFR Institute of Food Research Quadram Institute -
Introduction to using containers - OpenShift, Kubernetes and Docker oriented view
• beginnerContainers Kubernetes Cloud computing -
Docker and Singularity for Reproducible Research: Getting Started with Containers
• beginnerreproducibility container data management data security high-performance computing -
IFR Dockerised version of the EBI's Introduction to RNA-seq course
• beginnerRNA-Seq IFR Institute of Food Research Quadram Institute -
IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis
• beginnerNGS Command line IFR Institute of Food Research Quadram Institute -
Slides, course materials
Introduction to using cloud and containers for training - OpenStack and Docker oriented view
Cloud computing Containers
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hands-on tutorial
Hands-on for 'A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy' tutorial
statistics interactive-tools machine-learning deep-learning jupyter-lab image-segmentation protein-3D-structure
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Kitematic Galaxy-RNA-Workbench
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hands-on tutorial
Hands-on for 'Set up a Galaxy for Training' tutorial
teaching
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hands-on tutorial
Hands-on for 'Tools, Data, and Workflows for tutorials' tutorial
contributing
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Training materials
Containers & Workflow pipelines workshop
•• intermediateContainers Nextflow -
Tutorial
Contributing to the Galaxy Training Material - Creating a new tutorial - Defining the technical infrastructure
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Training materials
NBIS Reproducible research course
data management Reproducibility Data analysis
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The IFB cloud for bioinformatics
Cloud computing Virtual machine
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Presentation, course materials
Introduction to Nextflow workshop
• beginnerWorkflows Nextflow DSL2 -
Tutorial
How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene
Genetic variation Genomics ELIXIR RIR, BridgeDb
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Multiple testing
Statistics and probability
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Working with DNA Sequences
Data Representation
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Talk
Discussion: Guidelines for submitting data to ExperimentHub
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Talk
HCA Data Access
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Talk
Introduction to DataFrames and the impact of recent changes
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Talk
Pitfalls and best practices for serializing Bioconductor objects
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Lab 9-1: Efficient and Parallel Evaluation
Big data
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Lecture 19: Gene Set Enrichment Analysis
GSEA
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Lecture 20-1: Working with Large Data
Big data
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