BGC modeling

Main content

701-1338-00 G Biogeochemical Modelling of Sediments, Lakes and Oceans

Lecturers: M. Schmid (33%), A. Brand (33%), M. Vogt (33%)

Study area: MSc Environmental Systems Sciences

Course Type: Methodological Tools: Modelling course

Dates and Times:

Lectures: Spring semester 2016, Friday 8-10, ML J 37.1;

Dates: 26.02.; 04.03.; 11.03.; 18.03.; 08.04.; 15.04.; 22.04.; 29.04.; 06.05.; 13.05.; 20.05.; 27.05.; 03.06.

Short description

Numerical models are useful tools for the evaluation of biogeochemical processes in complex natural systems, for the interpretation of observational data, and for the prediction of the reaction of a system to disturbance or natural changes. In this course, the students acquire the skills to implement basic numerical models for the simulation of biogeochemistry in aquatic systems using Matlab. The focus of the course is on the practical application of modeling tools, and the scientific evaluation and validation of the results. Students taking part in this course will be able to apply the learned concepts to many real-world problems in natural systems, and to better understand the relative importance of different process for the behavior of the system and its response to change.

Course aim

The aim of this course is to encourage and enable students to develop and apply basic numerical models for their own real-world applications.

Course content     

  • Formulation of transport and reaction equations describing aquatic systems
  • Numerical recipes (discretization in time and space, finite differences, finite volumes, boundary conditions)
  • Implementation of simple models in Matlab (box models, 1D-models, with applications from sediments, lakes, and oceans)
  • Techniques for applied modelling (sensitivity analysis, parameter estimation)
  • Applications of modelling in current research (examples from scientific literature)

Practical work

All modelling techniques taught in class will be practised in exercises.

Semester project

During the course, students develop and implement a numerical model for a topical application (case study) in groups of two. Applications are based on published results in peer-reviewed papers, and deal with hot topics in limnology, oceanography and sediment studies. At the end of the course, students present their project to the class, and explain, discuss and evaluate their results in a report. The semester project will be graded.

Course material

All course material (lectures, exercises, and material for case studies) will be published on the courses’ ILIAS web repository

Literature recommendation

  • E Holzbecher, 2012, Environmental Modeling Using MATLAB, 2nd edition, Springer.
  • DM Glover, WJ Jenkins, SC Doney, 2011. Modeling Methods for Marine Science, Cambridge University Press.
  • K Soetaert, PMJ Herman, 2009. A Practical Guide to Ecological Modelling, Springer.


The following course or equivalent knowledge is required:

  • Mathematics III: Systems Analysis (701-0071-00L, autumn semester)
  • Basic programming knowledge in Matlab is required, e.g. the following course:
    Anwendungsnahes Programmieren mit MATLAB (252-0840-01L, spring semester, German)

The following course is useful but not required:

Modellierung aquatischer Ökosysteme (701-0426-00L, spring semester

Modelling Platform

The students are expected to work with their own Laptop where Matlab should be installed prior to the course (available for free from Stud-IDES). Template codes will be provided for lectures and exercises.


The number of participants is limited to 18. Selection of the students: order of registration.

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