Duration
20h Th, 50h Mon. WS
Number of credits
| Master in bio-informatics and modelling (120 ECTS) | 8 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
[UPDATED IN 2019] This course teaches the Linux operating system, the command line interface, and the Perl programming language 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
- Variables (Scalars, Arrays, Hashes)
- Operators, Boolean expressions and Control flow
- Input/output
- Regular expressions
- One-liners
- Functions
- References and Nested data structures
- Modules and Unit tests
- Best of CPAN
- Idiomatic Perl - TIMTOWTDI
Learning outcomes of the learning unit
This course is the main programming course of the Master BIM. Along with other courses of this curriculum, it aims to ensure that students are able to use computers as scientific instruments. More specifically, they will have been trained for the following purposes:
1. Experimental design
- how to choose appropriate controls
- how to think in a statistical framework
- how to run large series of analyzes
- how to harness the power of grid computing
- how to automate the analysis of output files
- how to generate informative but nice looking graphs
- how to draw statistically sound conclusions
- how to document experimental protocols
- how to reorganize a series of past analyzes
- how to manage multiple versions of the data sets, of the required programs and of the generated results
Prerequisite knowledge and skills
This course requires no prior knowledge in computer programming, but it is nevertheless based on Genomics [GENE0003-1] and Bioinformatics [BIOL0008-1] courses of Master BBMC or BIM.
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.
Organisational adjustments related to the current health context
The remaining courses will be delivered online using eCampus.
Recommended or required readings
Hard copies of course materials will be distributed in class. Recommended reference books will be suggested in these course materials.
Assessment methods and criteria
Below you will find information on the evaluation methods planned for in-person and remote exams as well as those planned for hybrid sessions. Depending on how the health crisis evolves, the chosen method will be communicated to you no later than one month before the start of the exam session.
The evaluation of this course will be based both on the work done during the academic year (homework: 25%), on an open book exam where an integrative problem will have to be solved using shell commands and a Perl program (75%).
Work placement(s)
Organizational remarks
WARNING: Each M-BIM student must have a laptop on which one can install the Linux operating system (e.g., Ubuntu 18.04). 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 (with P. Tocquin).
Contacts
Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@uliege.be
Dr. Pierre Tocquin
Institut de Botanique B22 (P70)
ptocquin@uliege.be
Assistant: Dr. Damien Sirjacobs
Institut de Botanique B22 (P70)
04/366.38.54
D.Sirjacobs@uliege.be