PPS-21306 Modelling Biological Systems


Studiepunten 6.00

Practical extensively supervised18
Course coordinator(s)dr. ir. PA Leffelaar
Lecturer(s)dr. ir. PA Leffelaar
dr. L Hemerik
prof. dr. ir. JL van Leeuwen
prof. dr. BM Mulder
dr. ir. S Kranenbarg
prof. dr. ir. MCM de Jong
Examiner(s)dr. ir. PA Leffelaar
dr. L Hemerik
prof. dr. ir. JL van Leeuwen
prof. dr. BM Mulder
prof. dr. M Scheffer
dr. ir. S Kranenbarg
dr. ir. EH van Nes
prof. dr. ir. MCM de Jong

Language of instruction:

Lectures in Dutch; written materials in English

Assumed knowledge on:

First year courses in biology, including MAT-14803 and MAT-14903 + MAT-15303

Continuation courses:

BSc Minor Life Science Modelling (Depending on approval of the Educational Institute), PPS-20306, FTE-23306, CSA-20806


This introductory course takes fascinating biological phenomena as starting point to develop models of the underlying mechanisms. Biological phenomena dealt with in the course are for instance equilibria (including stability and attractors) and the possibility of alternative equilibria (bifurcation), cycles and chaos, pattern formation in ecology and development, and emergence of complexity. Important steps required in model development will be discussed. First and foremost the reasoning is addressed of how to come from a biological system to a simplified representation: a model. Furthermore, model quantification, verification, simplification, simulation and validation are discussed. For validation experimental data can be gathered from research papers and the internet. The differences and possibilities of analytical and numerical models will be addressed. Finally, attention will be paid to order of magnitude calculations and to the design and interpretation of graphical representations of model simulations and experiments, and especially to the biological significance of models and their relation with reality.

Learning outcomes:

After thoroughly studying the written materials, preparing and critically following the lectures and performing the practicals, the student should be able to:
- demonstrate and motivate how a model for a biological system can be derived, given a specific objective;
- recognize phenomena in a biological system;
- formulate the underlying assumptions of the discussed mathematical formulae;
- estimate orders of magnitude and to have an understanding of time constants and scaling problems;
- explain the advantages of combining experiments and models;
- distinguish between different types of models;
- design graphical representations of systems and their associated models and interpret numerical and graphical model results;
- explain that the same model can often be used at different temporal and spatial scales, and why this strongly enhances the insight at and links between different levels such as from the cell to the ecosystem;
- indicate that the same biological phenomenon can be represented by different models, because research questions and objectives can differ.


Each week introductory lectures will be given on a biological phenomenon and on how to come from its characteristics to a model. The topics addressed in the lectures will be trained in practical assignments and supervised tutorials. Formulating the coherence between the week phenomena and answering (former) exam questions form part of the course.


The examination is based on the phenomena reports and a written examination with open questions.


Lecture notes and a selection of scientific papers and chapters.

Verplicht voor: BBIBiologyBSc2MO
Keuze voor: WUSYBBSc Minor Systems Biology2MO