Modelling Course in Population and Evolutionary Biology

Practical information

The course runs between 4-15 June 2012, every workday between 8.30am-5.30pm (the Vorlesungsverzeichnis shows 7-19, but this is just to allow flexibility). Place: HG G 26.5 (see the HG building on the map; and the location of the room within the building). The first class starts 4 June, 9am. If you have questions, contact Viktor Müller.

There is also a possibility for people from outside the ETH and the UZH to register for the course. For details, click here.

General description

This block course can be attended by masters students of biology and environmental science and by doctoral students of ecology and evolution..

In 2012, the course is going to take place between 4-15 June, every workday, all day. During the course, students work in small teams on two modules chosen from the list below (one first and one second level module). The models are developed in the open source software R (see R resource page) by modifying and adding to existing example programs. Previous experience with R is helpful, but not required for this course.

The goal of this course is (i) to get familiar with basic approaches in the modelling of biological processes, (ii) to obtain a conceptual insight into interesting biological questions, (iii) to learn to appreciate the excitement and utility of computional modelling in biology.

Organization of the course

The course starts with an introduction to R and the available modules. Teams of 2-3 students are formed and choose a first and a second level module. The majority of the time involves supervised group work in which the student teams work out the solutions to their chosen modules. Dual-boot (Mac/Windows) MacBook Pro laptops can be provided to all students; alternatively, students may use their own laptops. Instructors are present in the classroom to help when needed and to monitor progress. Selected problems may be discussed with the whole group during the afternoon breaks. The first half of the course will be devoted to the completion of a Level 1 module, the second half to the completion of a Level 2 module. The course concludes with the last half day devoted to presentations, in which each team present their results on their Level 2 module.

Evaluation

The final mark is composed as the average of four marks awarded for the following tasks: 1) The implementation of the first module, 2) The technical implementation of the second module, 3) Biological analysis and interpretation of the second module and 4) the final presentation. The instructors are constantly monitoring progress during the course, and judge understanding of concepts, creativity, the functionality of implemented code and, ultimately, the scientific answers to the questions in the modules. To enable the evaluation of individuals, each team member should be responsible for well-defined tasks within the student projects, and also take part in the presentation. Importantly, criteria are defined such that students with no prior knowledge of R should also be able to achieve the highest mark.

First Level Modules

• The logistic difference equation and the route to chaotic behaviour
  
• SIR models of epidemics
  
• Stochastic effects on the genetic structure of populations
  
• Within-host HIV dynamics: estimation of parameters
  
• Within-host HIV dynamics: the emergence of drug resistance
  

Second Level Modules

• Discrete vs. continuous time models of malaria infections
  
• Evolution of the sex ratio
• Network models of epidemics
  
• Rock-paper-scissors dynamics in space
  
• Spatial cooperation games
  
• Stability and complexity of model ecosystems: Are large ecosystems more stable than small ones?
  
• Stochastic simulation of epidemics
  
• Unstable oscillations and spatial structure: The Nicholson-Bailey model of host-parasitoid dynamics

Background information

Additional background information (biology and modelling techniques) can be found for several modules in the reader of the course "Ecology and Evolution II: Populations" (701-0273-00l WS) by Prof. Sebastian Bonhoeffer. Look for references in the readers provided for the modules.

The course in the Vorlesungsverzeichnis.

Powerpoint file of introductory presentation

R sample files:

• sample.r
• distance.r
• reaction.r

Other resources

A collection of research papers on spatial dynamics