Module 2: Linux

Module topics

  • Introduction to Linux, UNIX, and the command line
  • Manipulating files – useful commands and tips
  • Extracting information from files
  • Permissions, groups, and process control


SessionLecture recordingsLecture slidesPractical assignment
10. Introduction_Linux_AmelGhouila
1. Module2_Session1_Part1
2. Module2_Session1_Part2
3. Module2_Session1_Part3
4. Module2_Session1_Part4
5. Module2_Session1_part5
21. Module2_Session2_Part1
2. Module2_Session2_Part2
3. Module2_Session2_Part3
4. Module2_Session2_Part4
5. Module2_Session2_Part5
31. Module2_Session3_Part1
2. Module2_Session3_Part2
3. Module2_Session3_Part3
4. Module2_Session3_Part4
consolidation session1. Module2_Session4_part1
2. Module2_Session4_part2
3. Module2_Session4_part3
4. Module2_Session4_part4
5. Module2_Session4_part5
6. Module2_Session4_part6


You will need to have access to a Linux-based command line terminal for this module:

Linux-based operating system – terminal (built in)
MacOS – terminal (built in)
Windows operating system – install Cygwin package

The following two links explain how to install Cygwin (only applicable for Windows machines):

If you are formally enrolled in the IBT course, please consult the local staff for your IBT classroom regarding the above.





Amel Ghouila

Primary trainer

Affiliation: Institut Pasteur de Tunis; H3ABioNet

Amel Ghouila is a bioinformatician at the Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Institut Pasteur de Tunis, working mainly on the NIH-funded H3ABioNet project. She is co-chairing the research working group and also involved on education and training activities within this project. Amel has a background in Informatics and has been teaching in this field for several years at the Computer Sciences Department of the Faculty of Sciences of Bizerte, Tunisia. She then obtained a PhD in Bioinformatics from University Montpellier 2, France during which she has been working on the development of new methods for pathogens annotation. Her main research interests include pathogens functional annotation, NGS data analysis pipelines, data mining techniques and database conception and implementation.


Sumir Panji


Affiliation: University of Cape Town; H3ABioNet

Sumir obtained his PhD in Bioinformatics from the University of the Western Cape as part of the Stanford South Africa Biomedical Informatics (SSABMI) programme where he developed computational and analyses pipelines to determine the intersection between bacterial virulence and positive selection in Professor Winston Hide’s laboratory. He completed his postdoctoral studies in Professor Alan Christoffels’ laboratory at the South African National Bioinformatics Institute (SANBI) where his focus was on genome assembly, annotation, data mining, large scale statistical analysis of genomics data and development of various computational pipelines and analyses workflows for a myriad of genomics’ data types. Dr Panji’s main interests are in creating and implementing computational and analyses workflows, statistical analysis of biomedical data, biological algorithms, high performance computing and the overall application of bioinformatics and genomics methods to better understand complex biological systems. Sumir is currently a bioinformatician within the H3ABioNet consortium who is interested in genome science, data analysis workflows, statistical analyses of large ‘omics datasets, implementation and interpretation of bioinformatics solutions to diverse biological problems and providing bioinformatics support to the H3Africa projects.