3 ECTS credits
80 h study time
Offer 1 with catalog number 4019308FNR for all students in the 1st semester at a (F) Master - specialised level.
The partim 'Bioinformatics' starts with an introduction to the most common biological databanks, including the discussion of the most common data formats in bioinformatics and databank types, followed by the discussion of strategies to search those databanks based on text information. Next, principles will be discussed to search the databanks with DNA and protein sequences using specific programs (e.g., BLAST). Hereto, focus will be on the principles of sequence alignments (scoring of alignments, global versus local alignments). Next, methods for multiple sequence alignments will be discussed (ClustalW, T-Coffee, Muscle, etc.) including their use in phylogenetic analysis. Finally, genome annotation: (gene and function prediction, genome annotation and genome information platforms) as well as metagenomic sequence data analysis (ecocsystem composition, functional analysis) will be discussed. In the WPO-sessions, the students will solve exercises on biological databases, sequence alignment, etc. For the genome and metagenome sequence data analysis, the scientific workflow Galaxy will be used.
The partim 'Industrial Systems Biology' consists of an introduction to systems biology, industrial systems biology, as well as to the principles of flux balance analysis, after which several cases will be discussed, such as the production of lysin, succinic acid, biofuels, and 1,3-propanediol, showing how bioinformatics and omics can be used to optimise processes in industrial biotechnology.
Attending the WPO-sessions is compulsory. In the event of absence, an alternative assignment will be provided in consultation with the titular.
The power point presentations used during classes as well as the hand-outs for the practical hands-on sessions will be available on the learning platform Canvas.
Upon completion of the partim ‘Bioinformatics’ of this course, the students should be able to:
- Discuss which information is stored in the most common biological databanks.
- Search and retrieve information from the most common biological databanks and platforms using text and sequence data.
- Explain the principles of and compare the bioinformatics programs for sequence alignment, genome annotation and metagenome sequence data analysis discussed.
- Use the bioinformatics programs discussed to solve (own) research questions.
Upon completion of the partim ‘Industrial Systems Biology’ of this course, the students should be able to:
- Discuss the principles of industrial systems biology.
- Demonstrate, based on the cases discussed, how industrial biotechnological processes can be better understood and improved applying an industrial systems biology approach.
The final grade is composed based on the following categories:
Oral Exam determines 100% of the final mark.
Within the Oral Exam category, the following assignments need to be completed:
Partim 'Bioinformatics': Oral exam after written preparation
Partim 'Industrial Systems Biology': Oral exam after written preparation
Each partim has a weight of 50% in the final mark on condition that the partial mark on each partim is at least 10/20. If the partial mark on at least one of the partims is lower than 10/20, the final mark will be equal to the lowest partial mark. The partial mark of the partim for which the student has passed is transferred to the second session. The student can relinquish the partial mark for the partim for which he has passed, provided that he notifies the titular by e-mail no later than August 15 (2nd session). Once the student has indicated that he will abandon his partial mark, he will irrevocably lose the partial mark.
This offer is part of the following study plans:
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Medical Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Molecular Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Agrobiotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Food Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Chemical Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Biochemical Biotechnology (only offered in Dutch)