Duration
10h Th, 10h Pr
Number of credits
| Master in bio-informatics and modelling (120 ECTS) | 2 crédits |
Lecturer
Language(s) of instruction
English language
Organisation and examination
Teaching in the second semester
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
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.
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.
Recommended or required readings
Course materials are available online: https://ptocquin.gitlabpages.uliege.be/info0960/
Exam(s) in session
Any session
- In-person
written exam ( open-ended questions )
Work placement(s)
Organisational remarks and main changes to the course
WARNING: Each M-BIM student must have a laptop on which one can install the Linux operating system (e.g., Ubuntu 20.04). Virtual machines running in VirtualBox are not adequate solutions. However, dual-boot with Windows is possible. Linux install will be one topic of the first course. For this first session, each student will have a USB key (minimum 4GB) that can be completely erased.
Contacts
Dr. Pierre Tocquin
Institut de Botanique B22 (P70)
ptocquin@uliege.be
04/366 38 32