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
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
- Module 6. Analysis of metagenetic data
- Module 7. Phylogenetic analyses
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 course 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)
Modules 1 to 3 are organized face-to-face. For modules 4 to 7, 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.
Assessment methods and criteria
The analyses conducted in modules 4 to 7 are the subject of a written report summarizing the objectives, the analyses implemented and the results, using Markdown technologies.
Work placement(s)
Organizational remarks
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
Dr. Marc Hanikenne
Institut de Botanique B22 (P70)
marc.hanikenne@uliege.be
Assistant: Dr. Damien Sirjacobs
Institut de Botanique B22 (P70)
04/366.38.54
D.Sirjacobs@uliege.be
Adaptation of teaching commitments following the COVID-19 pandemic for the May-June 2020 session
Teaching methods implemented : distance-learning
Assessment subjects
Assessment methods
Contacts
Adaptation of teaching commitments following the COVID-19 pandemic for the Aug-Sept 2020 session
Assessment subjects
Assessment methods
Students who have not submitted their reports (see above) on time for the first session will have to submit them by email by the end of August.