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Workshops and courses
Docker and Apptainer (Singularity) for reproducible and automated data analysis
14 - 15 October 2024
Face-to-face
advanced bioinformatics ELIXIR programming research data management -
Workshops and courses
Docker and Singularity (Apptainer) for reproducible and automated data analysis
14 - 15 October 2024
Face-to-face
advanced bioinformatics ELIXIR programming research data management
Showing 30 materials
out of 64
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Tutorial, Training materials, Bioinformatics
How to use REPET software for de novo annotation of transposable elements in genomes
• beginnerGenomics Structural variation Bioinformatics Genome annotation Sequence classification Transposons Annotation Pipelines Docker -
Docker for Beginners
Docker
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Docker Tutorial
Docker
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RamiKrispin/Introduction-to-Docker
Containerization Docker
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carpentries-incubator/docker-introduction
Containerization Docker
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sib-swiss/containers-introduction-training
Containerization Docker Singularity
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RamiKrispin/vscode-python
Python script Containerization Docker Python
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jsta/r-docker-tutorial
R script Containerization Docker R
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RamiKrispin/vscode-r
R script Containerization Docker R
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Bioconductor/bioconductor_docker
R script Containerization Docker R
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awesome-workshop/docker-singularity-hats
Containerization Docker Singularity
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slides
Docker and Galaxy
• beginnerGalaxy Server administration -
DataTalksClub/data-engineering-zoomcamp
Containerization Docker Data science
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ekorpela/cloud-vm-workshop
Computer science Containerization Docker Cloud computing
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BiodataAnalysisGroup/intro-to-cwl-docker
CWL Workflows Containerization Docker
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sib-swiss/containers-snakemake-training
Workflows Containerization Docker Singularity Snakemake
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PerMedCoE/mpi-in-container
Containerization Docker High performance computing Singularity
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Online material, hands-on tutorial
Introduction to Docker and Singularity
• beginnerReproducibility Container Singularity -
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 -
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
A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy
• beginnerStatistics and probability Statistics and machine learning deep-learning image-segmentation interactive-tools jupyter-lab machine-learning protein-3D-structure -
genome/bfx-workshop
Workflows Data visualisation ChIP-seq Epigenetics Genomics Metagenomics Sequencing RNA-Seq Variant pattern analysis Docker Data visualization Python R Unix/Linux ATAC-seq Next generation sequencing RNA-seq Single-cell sequencing Variant analysis Long read sequencing
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hands-on tutorial
Set up a Galaxy for Training
• beginnerTeaching and Hosting Galaxy training -
Kitematic Galaxy-RNA-Workbench
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Introduction to Containers and Snakemake for Reproducible Research
• beginnercontainer data management high-performance computing reproducibility workflows marc robinson-rechavi group training -
hands-on tutorial
Galaxy Interactive Tools
• beginnerSoftware engineering Development in Galaxy
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