1. Home
  2. Materials
Register training material
9 materials found

Authors: Manuel Corpas  or Tuur Muyldermans 

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
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 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) 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 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 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 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. Data management Life Science Researchers
BioJS

Introduction to BioJS a standard for visualisation of biological data in JavaScript

Keywords: Biojs, Javascript, Software, Standards

BioJS http://tess.elixir-uk.org/materials/biojs-1ff5ad84-3b06-4997-bba6-e18a4dcf32c0 Introduction to BioJS a standard for visualisation of biological data in JavaScript Biojs, Javascript, Software, Standards software developers, bioinformaticians 2014-02-27 2017-10-09
GOBLET Training portal

Presention

Keywords: Goblet

GOBLET Training portal http://tess.elixir-uk.org/materials/goblet-training-portal Presention Goblet 2015-07-01 2017-10-09
Presentation About GOBLET Portal

This is a presentation I gave at the Jornadas de Bioinformática in Seville, Spain (24/09/14)

Keywords: Goblet, Training portal

Presentation About GOBLET Portal http://tess.elixir-uk.org/materials/presentation-about-goblet-portal This is a presentation I gave at the Jornadas de Bioinformática in Seville, Spain (24/09/14) Goblet, Training portal Bioinformatics General Interest Trainers Users 2014-09-26 2017-10-09
Training Bioinformatics in the Cloud

I present the points of view, the challenges and advantages of developing training materials through the cloud.

Keywords: Advanced bioinformatics training, Cloud computing, Training

Training Bioinformatics in the Cloud http://tess.elixir-uk.org/materials/training-bioinformatics-in-the-cloud I present the points of view, the challenges and advantages of developing training materials through the cloud. Advanced bioinformatics training, Cloud computing, Training Bench biologists beginner bioinformaticians 2014-05-20 2017-10-09
RNA-seq analysis

I give an overview of the analysis of gene expression in plants using RNA-seq data. This course provides a foundation on the tuxedo software suite: TopHat, Cufflinks, CummeRbund.

RNA-seq analysis http://tess.elixir-uk.org/materials/rna-seq-analysis I give an overview of the analysis of gene expression in plants using RNA-seq data. This course provides a foundation on the tuxedo software suite: TopHat, Cufflinks, CummeRbund. 2013-06-28 2017-10-09