NBIS/ELIXIR-SE Tools for Reproducible Research


Air&Fire, SciLifeLab Stockholm
Tomtebodavägen 23A
Solna, Sweden

NBIS/ELIXIR-SE Tools for Reproducible Research

April 22, 2024 @ 08:00 April 26, 2024 @ 17:00 CEST

NBIS / ELIXIR-SE course open for PhD students, postdocs, group leaders and core facility staff at all Swedish universities interested in making their computational analysis more reproducible.

Important dates and information

Application opens: 2024-02-19

Application closes: 2024-03-18

Confirmation to accepted students: 2024-03-22

Course Leader and teachers:

  • John Sundh (CL)
  • Erik Fasterius (CL)
  • Estelle Proux-Wéra
  • Lokeshwaran Manoharan
  • Tomas Larsson
  • Cormac Kinsella
  • Mahesh Binzer-Panchal

In case you miss information on any of the above dates, please contact:  edu.trr@nbis.se

Course fee

A course fee* of 3000 SEK will be invoiced to accepted participants. The fee includes lunches, coffee/tea and snacks as well as a course dinner.

*Please note that NBIS cannot invoice individuals

Course content

This course will introduce best practices in making research reproducible – from code tracking to software packaging and documentation – via short lectures and hands-on tutorials.

Topics covered will include:

  • Good practices for data analysis
  • Version control and collaborative code development
  • Package and environment management
  • Workflow management
  • Documentation and reporting
  • Containerized computational environments

Learning Outcomes

Upon completion of this course, you will be able to:

  • 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

Entry requirements

The following is a list of skills required for being able to follow the course and complete the exercises:

  • 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

Due to limited space the course can accommodate a maximum of 20 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.

Contact information: edu.trr@nbis.se

Tomtebodavägen 23A
Solna, Sweden
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Last updated: 2024-02-20

Content Responsible: Hampus Persson(hampus.persson@scilifelab.uu.se)