Theoretical Biology & Bioinformatics

tree of life

Bachelor program

Within the bachelor program of the department of biology we give five introducing modeling and bioinformatics to students in biology and the sciences in general. These courses run for 10 weeks, half-time, and each course is 7.5 EC-points. Courses typically involve lectures in the morning and paper-and-pen and/or computer practicals in the afternoon. As a preparation for a master track in our group you should have completed at least the Bioinformatic processes course, but we recommend that you attend all of our bachelor courses. Courses can be attended by students from all over the world, and will be given in English whenever required. Students preparing for a master in Theoretical Biology and Bioinformatics are advised to attend the bachelor courses listed here and supplement that with biological courses in their field of interest.

Systems biology

Because modern biology is accumulating enormous amounts of information about complex regulatory systems in very rich data bases, we aim to introduce at least the basics of bioinformatic pattern recognition and the basic of mathematical modeling to all students in biology. The first part of this course is an introduction to mathematics of non-linear differential equations (ODEs). Students learn to analyze models by phase plane methods (i.e., nullclines and local stability analysis). After mastering these mathematical skills, the second part of the course focuses on interpreting results from mathematical models in biological terms. Reviewing classical modeling examples from a variety of biological disciplines, students learn to translate between mathematical models and biological insight. The third part of the course is an introduction in bioinformatic methods (like clustering, phylogeny, sequence alignment and blast). We aim to explain how these methods work and how they have contributed to biological research. This is a level-1 course given to a large (>200) group of students. For practical information (in Dutch) please read more.

Theoretical Ecology

Mathematical modeling plays an important role in ecological research. This has a strong emphasis on model development. We aim to derive models from first principles rather than copy them from the textbooks such that students no longer view models as a "black box". The first part of the course re-derives most of the classical models in theoretical ecology, and students use steady state analysis and phase plane analysis to study the properties of the models and interpret them biologically. We cover Lotka-Volterra models, predator-prey models with non-linear functional responses, and meta-population models. We work with paper-and-pencil exercises and a computer program (GRIND) that is good at phase plane analysis. The second part of the course is about game theory. Our aim is to students learn so much about model development and analysis that they can judge the quality and usefulness of models in their future career. This is a level-2 course given to groups of 30-40 students, and we assume that students master the skills we teach in the level-1 Bioinformatics course. For practical information (in Dutch) please read more.

Computational Biology (Bioinformatic processes)

The emphasis of this course is on composing exact models, based on specific hypotheses, in different formalisms (ODEs, cellular automata, agent based models). The models are analyzed, the results yielding insights in the original biological system. The models that are studied address fundamental questions from a variety of biological fields like evolution, development, and behavior. This is a level-3 course given at two levels for bachelor and master students. For practical information please read more.

ImmunoBiology

The immune system comprises innate and acquired defense mechanisms against (pathogenic) microorganisms. Immunology has traditionally been a qualitative science describing the cellular and molecular components of the immune system and their functions. In the last twenty years this traditional approach is being replaced by a systems biology approach, where theoretical studies helps to interpret experimental data, to resolve controversies, and --most importantly-- to suggest novel experiments allowing for more conclusive and more quantitative interpretations. This course is planned to give an overview of wet and theoretical immunological research. We aim to provide insight into the function of the immune system in health and disease and to give an introduction to the use of mathematical models and bioinformatics in immunological research. For practical information please read more.

Genome Biology

Biology is increasingly being performed at the genome-wide level and this level 3 course deals with various aspects of this research. The first three weeks of this course are focusing on genome-organisation, the second three weeks centre around genome evolution, and the third week deals with the steps from the genome to the phenotype. Altough this course is coordinated by Guido van den Ackerveken, our department is heavily involved in this course because of the importance of bioinformatics in genome-wide analyses and our knowledge of genome evolution.