ELIXIR node event Tools for Reproducible Research

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Description

This workshop teaches how to work reproducibly with control and structuring of project code, environment and workflow management. It focuses on giving participants hands-on experience with useful tools such as Git, Conda, Docker/Apptainer, Jupyter/Quarto and Snakemake/Nextflow through practical tutorials supplemented with short lectures.

Upcoming Training Instances

No upcoming training instances.

Details

Language
English
Licence
Creative Commons Attribution 4.0 International
Affiliations
SciLifeLab
Course Website
https://nbisweden.github.io/workshop-reproducible-research/
Last Updated
May 20, 2026 11:18

Content Providers

NBIS

https://nbis.se

Learning Outcomes

  • Organize and structure computational projects
  • Track changes and collaborate on code using Git
  • Install packages and manage software environments using Conda
  • Structure computational steps into workflows with Snakemake and Nextflow
  • Create automated reports and document their analyses with Quarto and Jupyter
  • Package and distribute computational environments using Docker and Singularity

Structure & Duration

  • Five days (Mon-Fri) from 9-17
  • Short lectures to introduce topics
  • Hands-on tutorials where participants can ask on-site teachers questions
  • The final day is devoted to "putting the pieces" together where participants have the opportunity to start implementing the tools in their own research

Prerequisites & Technical Requirements

Prior Knowledge
  • Familiarity with using the terminal (e.g. be familiar with commands such as ls, cd, touch, mkdir, pwd, wget, man, etc.).
  • Some knowledge in R and/or python is beneficial but not strictly required.
Technical Requirements
  • A laptop with access to a Linux/Unix terminal, such as Ubuntu (or similar), MacOS or Windows Subsystem for Linux.

Audience & Keywords

Target Audience
PhD Studentspostdocsgroup leadersresearchers
Keywords
reproducible researchbioinformaticsWorkflowGitGithubSnakemakeNextflowCondaQuartoPythonJupyterDockerApptainerSingularityContainersreproducibility

Course Team

Authors
Contributors
  • Mahesh Binzer-Panchal · NBIS, SciLifeLab, Uppsala University · ORCID iDORCID
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