Workshop

Linux basics and scripting for bioinformatics

Braunschweig
26.11.24 - 28.11.24
Scientific
BRICS

We, the department of “Computational Biology for Infection Research” at HZI, are pleased to announce our next bioinformatics workshop: “Linux basics and scripting for bioinformatics”. The course will be held in the BRICS building (Rebenring 56, 38106 Braunschweig) between Tuesday 26th – Thursday 28th November 2024. The workshop’s language is English.

The goal of the course is to lay a foundation for this automated application of (bioinformatics) programs for the participants. Accordingly, interested biologists, bioformaticians and physicians and other interested individuals 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 last day of the workshop will cover the fundamentals of the Slurm job scheduler, specifically as used in the HZI cluster, although this material is generally applicable. There will also be time available to allow participants to discuss their own bioinformatics problems.

The course assumes no Linux knowledge, and will be taught in English. All participants will receive a certificate of attendance.

Agenda

Day 1

  • Course introduction
  • Introduction to Linux
  • Connecting to the class environment
  • Using the shell, navigating the filesystem, working with files, using commands
  • Permissions

Day 2

  • Scripting constructs / pipelines
  • Installing software
  • Working on bioinformatics exercise

Day 3

  • Usage of the Slurm job scheduler
  • Details of HZI environment

 As time allows

  • Associated themes (scripting options, Git)
  • Discussion of individual problems

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-on exercise, but teaching the use of specific bioinformatics tools and methods is not a goal.

Requirements

The course assumes no Linux knowledge, and will be taught in English. All participants will receive a certificate of attendance.

Tools

Laptop (if that poses a problem get in touch) 

Further information

Event location: BRICS building (Rebenring 56, 38106 Braunschweig)

Find more information here.

To register for the workshop, please fill out the application form at the following link.
The deadline for applications is 15th November.

The number of places will be limited! Shortly after the registration deadline, we will provide you with further details. 

If you have any questions regarding the workshop, please do not hesitate to email us.

Portrait Cordula Hege

Press contact

Dr Cordula Hege
Project Management