Admission requirements
N/a.
Description
This elective aims to provide a foundation in bioinformatics. In this introduction, the emphasis is on applying basic Linux/Python to understand and analyze various concepts in sequence analysis.
The course is largely based on the integration courses “Orientation Bioinformatics” and “Sequence Analysis” of the specialization Bioinformatics
In addition to basics skills programming skills bash (Linux) and Python, attention is paid to various topics such as sequence alignments, file formats, phylogenetics and microbiome analysis.
Course objectives
After completing the course, students are able to:
Understand and apply basics of Linux programming
Understand and apply basics of Python programming
Analyze simple (DNA sequence) data set
Choose basic bioinformatics tools for sequence analysis based on the problem at hand
Interpretation of results from microbiome analysis
Compare different methods or strategies for sequence alignment
Create a simple pipeline to predict and annotate genes
Discuss results from phylogenetics analysis
Report in scientific poster
Timetable
Mode of instruction
Small practicals: BLAST, genome assembly, gene prediction, gene expression
Graded assignments: individual report, group assignment (presentations/poster)
Using online data sources, e.g. basics of programming, simple (online) exercises to practice Python coding, e.g. linked to motif search, visualizing omics data. And Bioinformatics textbook: Concepts in Bioinformatics and Genomics - Jamil Momand and Eliot Bush, 2025.
Assessment Method
You will be evaluated by completing 3 practical assignments and by participating in the lectures and practical classes in the course.
Assignment 1 and 2 consists of a written (individual) assignment and assignment 3 is a poster (group) presentation.
Grading of the course:
Assignment 1 is worth 30% of your grade
Assignemtn 2 is worth 40% of your grade
Assignment 3 (the poster presentation) is worth 20%.
Participation in practical exercises in class is required for the final 10%
Minimum grade:
Second and third year courses require a minimum, unrounded 5.5 grade to complete.
If a course has 2 or more written partial exams, the minimum grade only applies to the weighted average of the exams.
For partial grades from components other than exams (e.g. practicals, seminars, writing assignments), the bottom grade does apply to the individual components.
Please refer to the Student Charter for an overview of regulations.
Reading list
Sterk aanbevolen: Bioinformatics textbook: Concepts in Bioinformatics and Genomics - Jamil Momand and Eliot Bush, 2025