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
https://nextflow-workshop.readthedocs.io/en/latest/
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.
Alexander Botzki
Tuur Muyldermans
Containers, Nextflow
bioinformaticians
Introduction to Nextflow workshop
workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available...
Scientific topics: Workflows
Keywords: Nextflow, DSL2
Resource type: Presentation, course materials
Introduction to Nextflow workshop
https://github.com/vibbits/nextflow-jnj
http://tess.elixir-uk.org/materials/introduction-to-nextflow-workshop
workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available [here](https://github.com/vibbits/nextflow-jnj/blob/master/presentation/slidedeck.pdf)
Tuur Muyldermans
Workflows
Nextflow, DSL2
bioinformaticians
Reproducible data analysis with RStudio, github and Rmarkdown
Best practices for writing reproducible data-analysis
Creating a reproducible and re-usable data-analysis environment with Rstudio
Input: https://github.com/vibbits/RDM-LS
Output: https://github.com/vibbits/RDM-LS-solution
Scientific topics: Data management, Data architecture, analysis and design
Keywords: Data analysis
Resource type: Presentation
Reproducible data analysis with RStudio, github and Rmarkdown
https://osf.io/qrt95/
http://tess.elixir-uk.org/materials/reproducible-data-analysis-with-rstudio-github-and-rmarkdown
Best practices for writing reproducible data-analysis
Creating a reproducible and re-usable data-analysis environment with Rstudio
Input: https://github.com/vibbits/RDM-LS
Output: https://github.com/vibbits/RDM-LS-solution
Tuur Muyldermans
Data management
Data architecture, analysis and design
Data analysis
life scientists
Research Data Management in Life Sciences
The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.
Scientific topics: Data management
Resource type: Presentation, Vignette, Video
Research Data Management in Life Sciences
https://osf.io/fpvgy/
http://tess.elixir-uk.org/materials/research-data-management-in-life-sciences
The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.
Alexander Botzki
Laura Standaert
Tuur Muyldermans
Hanne Elsen
Paula Oset
Thomas Van de Velde
Flora D'Anna
Nele Pauwels
Griet Den Herder
Jan Lammertyn
Data management
Life Science Researchers
Pathways and Network Analysis of -Omics data 2018 Module 3-Network Visualization and Analysis with Cytoscape
Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information.
Pathways and Network Analysis of -Omics data 2018 Module 3-Network Visualization and Analysis with Cytoscape
https://bioinformaticsdotca.github.io/pathways_2018
http://tess.elixir-uk.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-3-network-visualization-and-analysis-with-cytoscape
Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information.
Gary Bader
Researchers
Graduate students
Post-Doctoral Fellows
Biologists, Genomicists, Computer Scientists
Pathways and Network Analysis of -Omics Data 2018 Module 1-Introduction to Pathway and Network Analysis
Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information.
Pathways and Network Analysis of -Omics Data 2018 Module 1-Introduction to Pathway and Network Analysis
https://bioinformaticsdotca.github.io/pathways_2018
http://tess.elixir-uk.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-1-introduction-to-pathway-and-network-analysis
Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information.
Gary Bader
Researchers
Post-Doctoral Fellows
Biologists, Genomicists, Computer Scientists
Graduate Students
Pathways and Network Analysis of -Omics Data 2017 Module 3-Network Visualization and Analysis with Cytoscape
Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Pathways and Network Analysis of -Omics Data 2017 Module 3-Network Visualization and Analysis with Cytoscape
https://bioinformaticsdotca.github.io/pathways_2017
http://tess.elixir-uk.org/materials/pathways-and-network-analysis-of-omics-data-2017-module-3-network-visualization-and-analysis-with-cytoscape
Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Gary Bader
Pathways and Network Analysis 2017 Module 2-Finding Over-Represented Pathways
Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Pathways and Network Analysis 2017 Module 2-Finding Over-Represented Pathways
https://bioinformaticsdotca.github.io/pathways_2017
http://tess.elixir-uk.org/materials/pathways-and-network-analysis-2017-module-2-finding-over-represented-pathways
Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Gary Bader
Pathways and Network Analysis of -Omics Data 2017 Module 1-Introduction to Pathway and Network Analysis
Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Pathways and Network Analysis of -Omics Data 2017 Module 1-Introduction to Pathway and Network Analysis
https://bioinformaticsdotca.github.io/pathways_2017
http://tess.elixir-uk.org/materials/pathways-and-network-analysis-of-omics-data-2017-module-1-introduction-to-pathway-and-network-analysis
Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Gary Bader
Researchers
Biologists, Genomicists, Computer Scientists
Graduate Students
Post-Doctoral Fellows
