Duration
20h Th, 20h Mon. WS
Number of credits
| Master in bio-informatics and modelling, research focus | 4 crédits |
Lecturer
Coordinator
Language(s) of instruction
English language
Organisation and examination
Teaching in the first semester, review in January
Schedule
Units courses prerequisite and corequisite
Prerequisite or corequisite units are presented within each program
Learning unit contents
This course teaches the use of the Linux operating system and the command line interface (Shell), in the context of bioinformatics applications.
1. Linux
- Linux (installation, configuration and customization, tour of the GUI)
- Commande line (terminal, shell)
- Interactive shell: commands for diagnostic, browsing, file search, file processing, file input/output, string processing and permission management
- Advanced shell: process management, variables, loops, one-liners, scripts
- How to keep a tidy bioinformatics log-book
- Introduction to reproducibility in bioinformatics analyses
- Singularity/Apptainer:
- Theoretical foundations of virtualization and containerization
- Installation and configuration of a container using a sandbox
- Creation and execution of a Singularity/Apptainer container and file sharing between the host and the container
- Introduction to Nextflow and bioinformatics workflows:
- Process and channel management
- Creation and execution of simple workflows with Nextflow using DSL1
- Integration of Singularity/Apptainer containers into Nextflow
- Introduction to DSL2
Learning outcomes of the learning unit
At the end of this teaching unit, the student will be able to control a local or remote computer equipped with a UNIX-type operating system. He will be able to manage user accounts, the file system and the command line to perform basic data processing. He will be able to use the shell to set up more complex biological data analysis workflows that would implement other programs designed in different computer languages.
At the end of this teaching unit, the student will be able to understand the principles of reproducibility in bioinformatics analyses and containerization. He will be able to create, configure, and run containers using Singularity/Apptainer. He will also be able to design and execute biological data analysis workflows using Nextflow and integrate Singularity/Apptainer containers to build reproducible and portable workflows.
Prerequisite knowledge and skills
This course requires no prior knowledge in computer programming.
Planned learning activities and teaching methods
- brief theoretical lectures
- challenges to solve
- computer practicals
- self-learning (textbooks and online tutorials)
Mode of delivery (face to face, distance learning, hybrid learning)
This course is mostly face-to-face but as a problem-oriented course, it will require that students work also outside of the classroom.
Course materials and recommended or required readings
Other site(s) used for course materials
- Notes en lignes sur Gitlab (https://ptocquin.gitlabpages.uliege.be/linux-command-line/)
Further information:
Course materials are available online: https://ptocquin.gitlabpages.uliege.be/linux-command-line/
Exam(s) in session
Any session
- In-person
oral exam
Further information:
The exam will be conducted orally, with a total duration of 75 minutes per student. It will be divided into three consecutive phases: a 15-minute practical evaluation on Linux skills and command-line usage, followed by 45 minutes of preparation for the Nextflow-specific exam, and will conclude with a 15-minute oral examination to validate the knowledge acquired.
Work placement(s)
Organisational remarks and main changes to the course
PLEASE NOTE: Each M-BIM student must bring a laptop on which they must install a Linux system (such as Ubuntu 24.04). Virtual machines in VirtualBox are not a reliable solution. On recent Windows systems, it is possible to access a Linux environment using the Windows Subsystem for Linux (WSL): https://learn.microsoft.com/en-us/windows/wsl/. If necessary, assistance with installing Linux can be provided during the first class. Students who wish to benefit from this assistance should bring a USB stick with at least 12 GB of storage space on which they have burned a recent Ubuntu disk image following the instructions at: https://ubuntu.com/tutorials/install-ubuntu-desktop
Contacts
Dr. Pierre Tocquin
Institut de Botanique B22 (P70)
ptocquin@uliege.be
04/366 38 32
Dr. Luc Cornet
Institut de Botanique B22 (P70)
luc.cornet@uliege.be
04/366 22 59