Ecosystem Modelling

Course code:
Period 1
Language of tuition:
Fac. der Aard- en Levenswetenschappen
dr. ir. S. Luyssaert
dr. ir. S. Luyssaert
dr. ir. S. Luyssaert
Teaching method(s):
Lecture, Computer lab

Course objective

Students will be able to:
- Write, run and validate a simple computer program
- Select whether a modelling-approach is valid for answering the
ecological or environmental research question at hand
- Critically investigate and evaluate the assumptions underlying
numerical models
- Apply different techniques used in numerical modelling for answering
ecological and environmental questions.

Course content

Where science unravels more and more physiological, physical and
ecological processes, models can help to synthesise this knowledge in a
consistent numerical framework. Also, when field experiments are
impossible, unethical or excessively expensive, simulation experiments
can be used to forecast the outcome of different treatments or climate
scenarios. This course will introduce the different usages of numerical
models. The basic tools of the trade will be introduced and implemented
during computer-based exercises. Moreover, two challenging models will
be built; one simulating carbon allocation in trees, the other
simulating growth of coral reefs, self-organisation of vegetation in
arid regions or flocking of birds and fish. The course builds on
ecological, physical and mathematical knowledge and skills obtained
during the BSc years to construct new skills: basic computer
programming, numerical modelling and critical thinking in the context of
numerical models.

Form of tuition

The course consists of 7 hours of lectures and 52 hours of supervised
computer-based exercise classes. An additional 100 hours of unsupervised
study is required to complete the exercises. The course Ecological
Modelling accounts for 6ECTS.
The lectures address:
Measure or model – Overview of the main ecosystem models (week 1)
Tools of the trade – Basics of computer programming (week 1)
Tools of the trade – Developing a carbon allocation model for forests
(week 2 – 4)
Measure or model – Numerical issues in ecological models (week 5)
Tools of the trade – Developing a spatially explicit ecological model
(week 5-8)

Type of assessment

During the course, three individual exercises and a presentation will be
graded to make up the final grade:
Exercise 1: The basics of computer programming (1 point)
Exercise 2: A carbon allocation model (3 points)
Exercise 3: A spatially explicit ecological model, i.e.,
self-organisation of vegetation in drylands OR flocking of birds and
fish OR growth of coral reefs (5 points).
Presentation of the model and results (1 point).

Exercise 1, 2 and 3 should be handed in respectively in week 2 the day
before the first class, week 5 the day before the first class and week 8
the day before the last class. All three exercises should be handed in
before 13.00 am (sharp) the day of the deadline. Exercises handed in
after 17.00 the day of the deadline are not corrected. Exercises handed
in between 13.00 and 17.00 have a reduced maximum score @ minus 1 point
per hour. Students will receive their grade and feedback the day
following the deadline. If your score is between 1 and 6 you get another
week to revise the exercise based on the feedback and aim for a 6 max.

Course reading

The exercise are based on:
Allocation - Naudts, K., et al (2015). A vertically discretised canopy
description for ORCHIDEE (SVN r2290) and the modifications to the
energy, water and carbon fluxes, Geosci. Model Dev., 8, 2035-2065,
Vegetation patterns - HillerisLambers et al. (2001). Vegetation pattern
formation in semi-arid grazing systems. Ecology, 82, 1, 50–61, doi:
Flocking - Reynolds , C.W. (1987). Flocks, Herds, and Schools: A
Distributed Behavioral Model. Computer Graphics, 21, 4, 25-34.
Coral reefs - Nakamura, T. and Nakamori, T. (2007). A geochemical model
for coral reef formation. Coral Reefs, 26, 741–755, doi:

During the computer practica at the VU, Matlab will be used. Students
who want to do the unspurvised work at home are recommended to use
OCTAVE which is a free open-source initiative that is almost fully
compatible with Matlab.

The ecology underlying the exercises is largely described in Chapin,
F.S., Matson, P., and Vitousek, P.M. 2011. Principles of Terrestrial
Ecosystem Ecology, Second Edition, Springer. This book is the course
material for ‘’Ecologie, mens en natuur’’. Ecological modeling is
introduced in Smith, J., and Smith, P. 2007. Environmental Modelling,
Oxford University Press. The tools of the trade (including exercises)
are explained in Harte, J. 1988. Consider a Spherical Cow, University
Science Books and Harte, J. 2001. Consider a Cylindrical Cow, University
Science Books. A detailed description of one type of environmental
models, i.e., land surface models is given by Bonan, G., 2015.
Ecological Climatology, Third Edition, Cambridge University Press. These
books are not essential to follow the course. Following an appointment
with the lecturer, a copy of these books can be consulted at the
Department of Ecological Science.

Recommended background knowledge

Ecologie, mens en natuur I (AB_1001)
Ecologie, mens en natuur II (AB_1002)
Levensgemeenschappen en ecosystemen (AB_1208)

Target audience

MSc Third year BSc students in Biology and Minor Evolutionary Biology
and Ecology with an interest in quantitative (large-scale) ecology

© Copyright VU University Amsterdam
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