Duration
10h Th, 40h Mon. WS
Number of credits
| Master in bio-informatics and modelling, research focus | 6 crédits |
Lecturer
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 2024] This course teaches computer programming in the context of bioinformatics applications, using the Modern Perl language as a support.
Table of Contents
- 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 in the Master BIM. Its aim is to teach the basics of programming, both theoretically and practically, using only examples and problems taken from molecular biology and bioinformatics.
Along with other courses in this curriculum, this course aims to ensure that students are able to use the computer as a scientific tool. More specifically, at the end of their program, they will have been trained in 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 requires no prior knowledge in computer programming, but it is nevertheless based on the toolbox "Nucleic acid analysis techniques" [BIOC0726-1] and the course "Command-line interfaces and tools for biologists" [INFO0960-1] of the Master BBMC and Master 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)
Face-to-face course
Further information:
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
Hard copies of course materials will be distributed in class. Recommended reference books will be suggested in these course materials.
Exam(s) in session
Any session
- In-person
oral exam
Continuous assessment
Other : Coding of a solution to a bioinformatics problem (on the day of the exam).
Further information:
The assessment of the course will be based both on the work carried out during the academic year (continuous assessment: 40%) and on an open-book test in which an integrative problem will have to be solved using shell commands and a Perl program (examination: 60%). The overall mark will be broken down as follows:
- continuous: class participation: 20%
- continuous: homework due: 20%
- exam: coding the solution: 30%
- exam: oral defence of solution coding: 30%
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 LTS). Virtual machines running in VirtualBox are not adequate solutions, but WSL2 on a recent version of Windows is possible, as is dual-boot with Windows.
https://canonical-ubuntu-wsl.readthedocs-hosted.com/en/latest/guides/install-ubuntu-wsl2/
It's also possible to use a recent Apple Mac.
Contacts
Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@uliege.be
Mrs Rosa Gago
rgago@uliege.be