Biological Modelling and Model Analysis

Faculteit Science and Engineering
Jaar 2017/18
Vakcode WBLS16001
Vaknaam Biological Modelling and Model Analysis
Niveau(s) bachelor
Voertaal Engels
Periode semester I a
ECTS 10
Rooster rooster.rug.nl

Uitgebreide vaknaam Biological Modelling and Model Analysis
Leerdoelen The student is able to:
1. Construct a quantitative model to address a biological research question
2. Analyse a model with the help of mathematical techniques and computer simulation
3. Derive biological insights from model analysis and communicate these to a broad audience
4. Confront models with data and choose among models on the basis of empirical evidence
5. Apply modelling strategies from a range of biological disciplines, and assess their strengths and weaknesses for addressing a given research question

The first half of the course (week 1-3) will focus on the modelling cycle. Students will first choose a topic from a list of project ideas collected from a range of life-science disciplines. They will receive relevant literature, an empirical data set and other relevant background information, and will then develop their own modelling project step-by-step (from model building, analysis, interpretation and validation to communication of the results), following all phases of the modelling cycle that are introduced in the first three weeks of the course. The work on the projects is documented in a written report and summarized in an oral presentation at the end of the third week.

The second part of the course (week 4-6) provides an in-depth overview of a spectrum of modelling approaches (e.g. stochastic models, spatial models, self-organisation, adaptive dynamics) used in various disciplines of the life sciences. Every week, students submit one of the exercises for evaluation.
Omschrijving In this course, students are made familiar with all phases of the modelling cycle: the translation of biological questions into formal models; the simplification of models to manageable complexity; the analysis of models with the help of mathematical, numerical and simulation techniques; the presentation of the conclusions obtained from the model analysis; the estimation of model parameters and model validation; the comparison of models and the choice of most-supported model on the basis of empirical data; the refinement of models on the basis of the interplay between modelling and model-based data analysis.
Throughout the course, students will apply modelling and model analysis to research questions from various disciplines (e.g., systems biology, neurobiology, bioinformatics, phylogenetics, behavioural and social sciences, community ecology, evolutionary biology). The emphasis of the course will not only be on the technical aspects, but also on the biological conclusions that can be drawn from a modelling approach. The course is taught by theoreticians working in different areas of biology, who are using a broad variety of modelling techniques. In this way, students gain an overview of the theoretical research done in the life sciences at the University of Groningen, as well as an understanding of the strength and weaknesses of different modelling strategies for addressing particular kinds of research questions.
The first half of the course (week 1-3) will focus on the modelling cycle, while the second part of the course (week 4-6) provides an in-depth overview of a spectrum of modelling approaches (e.g. stochastic models, spatial models, self-organisation, adaptive dynamics) used in various disciplines of the life sciences. During the course, students develop their own modelling project step-by-step, following all phases of the modelling cycle, and submit dedicated exercises for evaluation and feedback.
Uren per week
Onderwijsvorm Hoorcollege (LC), Practisch werk (PRC)
(Lecture (100 h), computer practical (180 h))
Toetsvorm Opdracht (AST), Practisch werk (PR)
(The final grade of the course is based on a mark for the modelling project with associated report and presentation (40% of the final grade) and the grades for the 6 weekly assignments (each determining 10% of the final grade).)
Vaksoort bachelor
Coördinator dr. G.S. van Doorn
Docent(en) prof. dr. R.S. Etienne , Gastdocent(en) ,prof. dr. C.K. Hemelrijk ,prof. dr. I.R. Pen ,prof. dr. J. van de Koppel ,dr. G.S. van Doorn ,prof. dr. F.J. Weissing
Verplichte literatuur
Titel Auteur ISBN Prijs
Course manual with study material, exercises and solutions.
Entreevoorwaarden This course is a compulsory element of the minor Modelling in the Life Sciences, and is also open to students outside the minor programme. Entry requirements are: sufficient background in mathematics and working knowledge of the computer algebra program Mathematica. These requirements can be met by completing the course Mathematics in the Life Sciences or an equivalent course.
Opmerkingen Other lecturers: A. Milias Argeitis.

Maximum capacity: 24 students.

Active participation in the computer practicals, the project and the weekly assignments are a precondition for obtaining a final mark.

Maximum capacity: 24 students.
Opgenomen in
Opleiding Jaar Periode Type
FSE Minor Modelling in the Life Sciences 3 semester I a verplicht