NFDI4Microbiota and DZIF: Linux basics and scripting for bioinformaticsIn-Person Event

25 Nov 2024, 09:00 → 27 Nov 2024, 16:05 Europe/Berlin

BRICS, Rebenring 56, Braunschweig

Cordula Almut Selma Hege, Gary Robertson, Hesham Almessady (HZI), Zhiluo Deng (Helmholtz Centre for Infection Research)

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.

Often, bioinformatics software lacks a user-friendly graphical interface. The success of programs such as BLAST or BWA shows, however, that this does not have to be an obstacle. While the use of command line tools at first sight might appear complicated, it provides excellent opportunities to automate repetitive tasks and analysis steps into pipelines. 

The aim of the workshop "Linux basics and scripting for bioinformatics" is to lay a foundation for the automated application of (bioinformatics) programs for the participants. Accordingly, interested biologists and physicians and other people interested, 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. 

The course will be held in the BRICS building (Rebenring 56, 38106 Braunschweig) between Tuesday 25^th – Thursday 27^th November 2024.

Prerequisites: 
None

 
 Language:  
English 

Tools

Bring your own laptop. 

(please get in touch, if that is a problem)

 

Contact 
bioinformatics@dzif.de  
 

Registration will be open until 8th November. Register here:

https://events.hifis.net/event/1853/registrations/1876/

The number of participants is limited, apply soon to avoid disappointment.

The workshops are in high demand, so failing to attend the course without prior cancellation, despite being admitted, may result in being unable to participate in future offerings.

The workshop will take place 25-27 November in person in the BRICS building, Braunschweig. 

Monday 25 November

NFDI4Microbiota and DZIF: Linux basics and scripting for bioinformatics: First day: * Course introduction * Introduction to Linux * Connecting to the class environment * Using the shell, navigating the filesystem, working with files, using commands * Permissions

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

Tuesday 26 November

1 Linux basics and scripting for bioinformatics: Second day

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

2 Bioinformatics Workshop “Linux basics and scripting for bioinformatics

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

Wednesday 27 November

3 Bioinformatics Workshop “Linux basics and scripting for bioinformatics: third day

• Usage of the Slurm job scheduler

• Details of HZI environment

• As time allows

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