Duration
10h Th, 30h Mon. WS
Number of credits
| Master in bio-informatics and modelling (120 ECTS) | 4 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 2021] High throughput sequencing technologies have revolutionized Biology. Analyzing the data they generate requires the implementation of bioinformatic tools and the use of high-performance computers.
This course provides a practical approach to illustrate concepts and tools for analyzing genomic data. It is composed of different modules:
- Module 1. Assembling a genome
- Module 2. Introduction to the use of high performance computers (HPC)
- Module 3. Introduction to Markdown reporting
- Module 4. RNA-Seq data analysis
- Module 5. Analysis of genomic sequence variants
Learning outcomes of the learning unit
By the end of the course, students will have acquired basic practical knowledge for the analysis of high throughput sequencing data. The course involves intense use of the command line, interaction with a computing cluster, and the use of popular analysis pipelines.
Prerequisite knowledge and skills
Genomics (GENE0003-1) and bioinformatics (BIOL0008-1) concepts acquired at the end of block 1 of the Master BBMC or BIM are required to take the course. Similarly, the practical skills of the courses INFO0960-1 (Command-line interfaces and tools for biologists) and INFO0953-1 (Scripting interfaces for biological software and databases) are also required.
Planned learning activities and teaching methods
Each module starts with a brief theoretical introduction, before moving to computer practicals in a dedicated computer room.
Mode of delivery (face to face, distance learning, hybrid learning)
Blended learning
Additional information:
Modules 1 to 3 are organized face-to-face. For modules 4 and 5, students work independently and a meeting of 1 hour per week is scheduled with the teachers to discuss the progress of the work and problems encountered.
Recommended or required readings
Course notes, PowerPoint slides and datasets to be analyzed are made available to students through myULiège.
Written work / report
Additional information:
The analyses conducted in modules 4 and 5 are the subject of a written report summarizing the objectives, the analyses implemented and the results, using Markdown technologies.
The Professors will only consider the reports for which material proof of the realization of the analyses is available and/or if the student attended more than 50% of the weekly progress discussions.
Reports will have to be submitted by the end of February at the latest. If not, the evaluation will take place during the second exam session as an exercise to perform during the exam.
Work placement(s)
Organisational remarks and main changes to the course
The course is taught in English. The material is written in English.
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. For PhD students, a VirtualBox is acceptable, though.
Contacts
Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@uliege.be
Prof. Marc Hanikenne
Institut de Botanique B22 (P70)
marc.hanikenne@uliege.be