Linux basics and scripting for bioinformatics

Increasingly, physicians and biologists are facing large amounts of data that can no longer be analyzed "by hand." In many research fields bioinformatics contributes both general and specific algorithms implemented in software packages that simplify the interpretation of the data or allow a deeper analysis.

Bioinformatics software often lacks a user-friendly graphical interface. However, the success of programs such as BLAST or BWA shows that this need not be an obstacle. Although working with command-line tools may seem complicated at first, these tools offer excellent opportunities to combine repetitive tasks and analysis steps into automated pipelines..

The aim of the workshop "Linux basics and scripting for bioinformatics" is to lay a foundation for this automated application of (bioinformatics) programs for the participants. Accordingly, interested biologists and physicians are invited to participate in a hands-on, in-person workshop, where they can become familiar with the Linux environment and its associated landscape, using common bioinformatics tools as examples for creating shell scripts. 

The final day of the workshop will cover the basics of the Slurm job scheduler, with a particular focus on its use on the cluster at the Helmholtz Centre for Infection Research (HZI). The content is also applicable to other Slurm-based systems. Participants will also have the opportunity to bring and discuss their own bioinformatics questions.

Note that the aim of the course is to build computing skills, and to use bioinformatics tools as a vehicle for this with a worked exercise, but teaching the use of specific bioinformatics tools and methods is not a goal.

No prior knowledge of Linux is required.

All participants will receive a certificate of attendance together with the course material. Participants would ideally bring their own laptop, but this is not an absolute requirement.

Language
English

Registration
Deadline: October 28, 2026
Register

Scientific organization
Gary Robertson
Sama Goliaei
Zhi-Luo Deng

Contact
Carmen Paulmann
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