The following topics and tools are covered in the course:
- Data management
- Project organisation
- Git
- Conda
- Docker
- Apptainer
- Quarto
- Jupyter
- Snakemake
- Nextflow
- Documentation
At the end of the course, students should be able to:
- Use good practices for data analysis and management
- Clearly organise their bioinformatic projects
- Use the version control system Git to track and collaborate on code
- Use the package and environment manager Conda
- Use Docker and Apptainer to distribute containerized computational environments
- Use Quarto and Jupyter Notebooks to document and generate automated reports for their analyses
- Use and develop workflows with Snakemake and Nextflow
- Write and maintain good project documentation
This is an NBIS / Elixir course. The course is open for PhD students, postdocs, group leaders and core facility staff. International applications are welcome, but we will give approximately half of the participant slots to applicants from Swedish universities, due to the national role NBIS plays in Sweden.
The only entry requirements for this course is a basic knowledge of Unix systems (i.e. being able to work on the command line) as well as at least a basic knowledge of either R or Python.
Due to limited space the course can accommodate maximum of 20 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.
Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.