Workshop open for PhD students (prioritized), postdocs, researchers and others who have previously participated in the NBIS Tools for reproducible research workshop
The workshop is organized by NBIS (ELIXIR-SE).
Responsible teachers: Verena Kutschera, Erik Fasterius, John Sundh, Per Unneberg
Contact information: firstname.lastname@example.org
Application open: September 1
Application deadline: September 18
Confirmation to accepted participants: September 25
This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 1700 SEK.
*Please note that NBIS cannot invoice individuals
As data analysis projects grow and change over time, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up, perform and monitor defined sequences of computational tasks (“workflows”), thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows.
The NBIS Tools for reproducible research workshop is held twice a year and provides an introduction into snakemake and a tutorial to learn how to use snakemake.
This snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash, R or python into a snakemake workflow, or B) apply more advanced techniques to their existing snakemake workflows.
After participation in the BYOC workshop, participants will:
1. Be able to create snakemake workflows for bioinformatics data analysis
2. Demonstrate knowledge of the structure and syntax of different types of snakemake workflows
3. Demonstrate knowledge of advanced features of the snakemake workflow language
The course can accommodate a maximum of 16 participants. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.
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.
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