home_syllabus.qmd

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title: "Syllabus"
subtitle: "Syllabus, learning outcomes, entry requirements and code of conduct"
pagetitle: "Syllabus | Tools for Reproducible Research"
date: ""
toc: false
number-sections: false
sidebar: false
format: html
---

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## Syllabus

The following topics and tools are covered in the course:

 - Data management
 - Project organisation
 - Git
 - Conda
 - Snakemake
 - Nextflow
 - Quarto
 - Jupyter
 - Docker
 - Apptainer

## Learning outcomes

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

## Entry requirements

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.

## Code of Conduct

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](mailto: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](https://elixir-europe.org/events/code-of-conduct).

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