The following topics and tools are covered in the course:
- Data management
- Project organisation
- Git
- Conda
- Snakemake
- Nextflow
- Quarto
- Jupyter
- Docker
- Apptainer
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 and develop workflows with Snakemake and Nextflow
- Use Quarto and Jupyter Notebooks to document and generate automated reports for their analyses
- Use Docker and Apptainer to distribute containerized computational environments
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.
By accepting to participate in the course, you agree to follow the NBIS Training Code of Conduct.
Training is one of the core values of NBIS, and benefits from the contributions of the entire scientific community. We value the involvement of everyone in the community. We are committed to creating a friendly and respectful place for learning, teaching and contributing. All participants in our events and communications are expected to show respect and courtesy to others.
To make clear what is expected, everyone participating in NBIS/ELIXIR courses is required to conform to the Code of Conduct. This Code of Conduct applies to all spaces managed by NBIS including, but not limited to, courses, email lists, and online forums such as Studium, GitHub, Slack, Twitter and LinkedIn. Course organisers and teachers are expected to assist with the enforcement of the Code of Conduct.
We are dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. By participating in this event, participants accept to abide by the NBIS Code of Conduct and accept the procedures by which any Code of Conduct incidents are resolved. Any form of behaviour to exclude, intimidate, or cause discomfort is a violation of the Code of Conduct. In order to foster a positive and professional learning environment we encourage the following kinds of behaviours in all platforms and training events:
- Use welcoming and inclusive language
- Be respectful of different viewpoints and experiences
- Gracefully accept constructive criticism
- Focus on what is best to all those involved in this training event
- Show courtesy and respect towards everyone involved in this training event
The NBIS Training Coordinator is responsible for enforcing the Code of Conduct, and may be contacted by emailing education@nbis.se. All reports will be reviewed and will be kept confidential. If you believe someone is violating the Code of Conduct, we ask that you report it to the NBIS Training coordinator, who will take the appropriate action to address the situation.
For an extended description please see the ELIXIR Code of Conduct.