Practical Modelling for Biologists

Faculteit Science and Engineering
Jaar 2021/22
Vakcode WMBY009-05
Vaknaam Practical Modelling for Biologists
Niveau(s) master
Voertaal Engels
Periode semester I b (10-01-2022 till 28-01-2022)

Uitgebreide vaknaam Practical Modelling for Biologists
Leerdoelen This course aims to teach the topic and the tools involved in the modelling of ecosystems, using marine systems as focus area. Different from many other courses, it takes a multidisciplinary approach, and introduces the student to the modelling of interactions of the biological components with their abiotic environment. The course moreover focuses on computational (i.e. computer calculations) rather then on mathematical (i.e. symbol manipulation) techniques.

This course will provide an introduction into numerical modelling for marine Biologists. After following the course, the student will be able to:

1.Identify whether a scientific or societal problem can be addressed with models;

2.Recognize several types of models used in marine sciences (e.g. models using 0D, 1D and 2D spatial setting);

3.Develop and code a model in R based on underlying processes and relations concerning the system at study;

4.Analyse the model to study the effect of changing conditions on species interactions and ecosystem functioning;

5.Formulate and evaluate scientific or managerial conclusions from the model analysis.
Omschrijving Mathematical modelling has become an important tool throughout the natural sciences. Especially when the dynamics of natural populations, being molecules within the cell, a population of seals in an estuary, or the global importance of termites are concerned, modelling is an indispensible tool, as it can help in understanding how species interaction can cause unexpected, nonlinear dynamics in ecosystems. Particularly when modelling marine systems, this often involves not only biological interactions, but also interactions with the physical and chemical environment.

In the course, the following subjects will be treated:
-Marine resource modelling
-Modelling ecosystem engineering and positive feedback
-Spatial modelling: Advection/Diffusion
-Simple 1D depth models
-Self organization
-Modelling water flow: Navier Stokes & shallow water equations
-Cellular automata: (wave) disturbance modelling
-Individual-based modelling
-Movement & search of animals.

The course will consist of three parts. The first part will be a series of lectures that will provide an introduction into the most important topics within marine modelling. Using practical exercises, the student will get acquainted with the basic modelling techniques, and learn how to use the models to answer ecological and environmental problems. In the last 2 weeks of the course, the students will do a modelling assignment where they independently develop (e.g., not provided by the lecturer) a model to answer a scientific question, as group work. At the last day of the course, the students will report on their work in a poster presentation.

The course is part of the Marine Biology Master’s curriculum, and therefore strongly builds on examples from the Marine realm. The techniques that are taught are general, and the course is therefore open to all biology students.
Uren per week 40
Onderwijsvorm Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC)
(The students are expected to make the practical assignments. If they do not show up, they will not get the associated points.)
Toetsvorm Presentatie (P), Verslag (R)
(Evaluation weight (EW): 20% Practical reports + 20% Practical Planning* + 20% Group modelling* + 40% Interpretation & Presentation. If the end grade is higher then 5.5, the student passes. The grade is computed as: 1+9*EW)
Vaksoort master
Coördinator prof. dr. J. van de Koppel
Docent(en) prof. dr. C.K. Hemelrijk ,dr. ir. D. van Oevelen
Verplichte literatuur
Titel Auteur ISBN Prijs
Handout (web-based)
A Practical Guide to Ecological Modelling
Soetaert and Herman 978-90-481-7936-7 ca. €  60,00
Entreevoorwaarden The course unit assumes no prior knowledge but the course ‘Practical Bioinformatics for Biologists’ is advisable.
Opmerkingen max 15 students
Opgenomen in
Opleiding Jaar Periode Type
MSc Biology: Modelling in the Life Sciences  (Electives/Optional modules) - semester I b keuze
MSc Biology: Research  (Compulsory master courses) - semester I b keuze
MSc Biology: Science, Business and Policy  (Compulsory master courses) - semester I b keuze
MSc Biomolecular Sciences  (Electives/Optional modules) - semester I b keuze
MSc Courses for Exchange Students: Biology - semester I b
MSc Ecology and Evolution: Ecology and Conservation  (Electives/optional modules) - semester I b keuze
MSc Ecology and Evolution: Evolutionary Biology  (Electives/optional modules) - semester I b keuze
MSc Marine Biology: Research  (Compulsory master courses) - semester I b keuze