Practical Modelling for Marine Biologists

Organizer

Prof. Dr. Johan van de Koppel (Royal Netherlands Institute for Sea; Conservation Ecology, UG)

Course information

See the course flyer for more information

Aim of the course

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.

Contents & Structure

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.

General Information