Duration
30h Th, 30h Mon. WS
Number of credits
| Master in biochemistry and molecular and cell biology (120 ECTS) | 6 crédits |
Lecturer
Coordinator
Language(s) of instruction
French language
Organisation and examination
Teaching in the first semester, review in January
Units courses prerequisite and corequisite
Prerequisite or corequisite units are presented within each program
Learning unit contents
1. Linux
- UNIX environment (Bio-Linux)
- text files and file formats
- CLI features (jokers, variables, loops, history...)
- bash shell
- Perl basics and Modern Perl
- Perl Object-Oriented Programming using Moose
- Markdown / pandoc / LaTeX (XeTeX) / Zotero
- version control with git
- WWW programming (HTML/CSS/JS/PHP)
Learning outcomes of the learning unit
This course is the first of three courses -- "Introduction to linux programming" [INFO0097-2], "Introduction to databases for biology" [INFO0099-2], "Introduction to algorithms in bioinformatics" [INFO0094-3] -- taught by the same teacher in the context of the specialized approach in bioinformatics of M2-BBMC. The course "Introduction to biological data analysis" [INFO0115-2] by Prof. Patrick Meyer shares the same goals.
At the end of this series of courses, students will be able to use the computer as a scientific instrument. More specifically, they will have been trained towards the following objectives:
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 is part of a specialized approach in bioinformatics. Even if it requires no special knowledge in computer science, it is nevertheless based on the Genomics [GENE0003-1] and Bioinformatics [BIOL0008-1] courses of the M1-BBMC.
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)
This course is partly face-to-face but as a problem-oriented course, it will require that students work also outside of the classroom.
Recommended or required readings
Assessment methods and criteria
Course assessment will be based on both the work carried out during the academic year and the development of a personal project, in principle distinct from the Master's thesis.
Work placement(s)
Organizational remarks
Taking notes on a laptop or tablet is allowed. However, students are expected not to surf or chat in the classroom.
Contacts
Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@ulg.ac.be
Dr. Pierre Tocquin
Institut de Botanique B22 (P70)
ptocquin@ulg.ac.be
Assistant: Dr. Damien Sirjacobs
Institut de Botanique B22 (P70)
04/366.38.54
D.Sirjacobs@ulg.ac.be