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 2023] This course teaches programming in the Perl language and the creation and use of relational databases, in the context of bioinformatics applications.
1. Modern Perl
- 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
General concepts and benefits of structuring data
Database structure modelling
- The Entity-Association Model
- The relational model
- Normalization
- Generation of a relational diagram
- From the model to the physical structure, the Data Definition Language (DDL)
- Manipulate and query the database, the Data Modification Language (DML)
- Simple queries
- Complex queries
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 the courses in Genomics [GENE0003-1], Bioinformatics [BIOL0008-1] and the introduction to the Linux environment and the command line [INFO0960] 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)
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
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
written exam ( open-ended questions )
Additional information:
The deux parts of the course, Perl and Databases, are evaluated separately, each by a written exam, face-to-face. The Perl and Databases grades represent 70% and 30% of the final grade, respectively.
1.Perl
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%).
2. Databases
The evaluation will consist of the realization of an integrative problem. The exam will be open book.
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://ubuntu.com/tutorials/install-ubuntu-on-wsl2-on-windows-11-with-gui-support
Contacts
Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@uliege.be
Dr. Pierre Tocquin
Institut de Botanique B22 (P70)
ptocquin@uliege.be
Mrs Rosa Gago
rgago@uliege.be