This course introduces students to the research fields of bioinformatics and biological modeling. Central themes are the use of data to extract underlying patterns on function and evolution, and the use of models to test hypotheses and make predictions for biological systems.
Introduction:
Biological processes are notoriously complex, and studying their dynamics through modeling and simulation is an effective way to understanding their key properties. In the first part, the students will learn to model the dynamics of biological processes such as cell signaling, gene regulation, interaction between bacteria and phages. Students will be trained to read and interpret ordinary differential equations models, as well as write such models themselves. They will analyse the models using phase spaces and stability analysis of equilibria to predict the behaviour of these dynamical systems and make use of simulation techniques. Furthermore, they learn to give a biological interpretation of the results of such analyses to answer biological questions and critically assess the model on its validity.
Large-scale data collection (omics) is ubiquitous and highly informative in the field of life sciences. To appropriately use and interpret omics data, the new wave of life scientists needs to understand bioinformatics methods. In the second part of this course, students learn about fundamental bioinformatics algorithms to study biological sequences. They will use the results to predict protein function or reconstruct the evolutionary history of genes, proteins and species. Furthermore, they will interpret high-dimensional omics-data through visualization, hierarchical clustering and machine-learning.
Set-up of this course:
The student prepares each lecture by reading the indicated parts of the syllabus. Each lecture is followed by a tutorial session to get a deeper understanding of the content and to practice the required skills. Most weeks, in an additional tutorial, students work individually or in small groups on a graded assignment (six in total). Some tutorials are on pen and paper, others require the students to bring their own laptop. Both parts of the course are concluded by a written exam.