Modelling Life

Faculteit Science and Engineering
Jaar 2019/20
Vakcode WBLS19014
Vaknaam Modelling Life
Niveau(s) bachelor
Voertaal Engels
Periode semester I b

Uitgebreide vaknaam Modelling Life
Leerdoelen At the end of the course, the student is able to:
1. Apply elementary methods from algebra and calculus (e.g., solving equations,
operations on vectors and matrices, differentiation and integration) in a biological context, and derive biological insight from the resulting outcomes.
2. Simplify complex biological systems by means of approximation methods,
separation of time- or length-scales or by evaluating relevant limits.
3. Construct mathematical models to describe basic biological processes, and interpret the quantitative and qualitative behaviour of these models from a biological perspective.
4. Analyse dynamical models of biological systems, based on a study of their
associated vector fields, in order to infer equilibrium states and long-term and transient dynamical behaviours.
5. Infer how the stability of equilibrium states and long-term system behaviour is affected by (externally imposed) changes to system parameters
Omschrijving This course introduces students to the mathematical modelling of biological systems, and covers model development, analysis and interpretation. In order to deal with variation in prior knowledge, students will have an opportunity to identify potential weak spots in their understanding of mathematics, and develop essential baseline skills in a personalized e-learning environment. In the first week of the course, students complete two interim self-evaluation tests, and are assigned to working groups based on their score, to promote effective peer learning.
The new material covered in this course introduces mathematical tools to describe and analyse dynamical interactions and feedback mechanisms in a wide variety of biological systems, including gene-regulation networks, nerve cells, hormonal control mechanism, epidemics of infectious diseases and ecological interactions. Here, we will follow the textbook Modeling Life – The Mathematics of Biological Systems (Garfinkel et al., 2017). Students learn how to develop dynamical models of biological systems and how to determine their dynamical behaviour and equilibrium states, based on an analysis of system trajectories and the underlying vector field. Qualitative (graphical) analysis and simulation are the main tools for generating biological insight; analytical methods are introduced on a need-to-know basis.
Topics covered in this course include: ‘Dynamical modelling and simulation’, ‘Equilibrium behaviour’, ‘Non-equilibrium dynamics: oscillations’, ‘Chaos’ and ‘Multi-variable systems’.
Students prepare for each topic by reading sections of the book, and are introduced to the new material in a lecture. Next, they develop an active understanding of each topic by working on pen-and-paper and computer exercises, both individually and in a working-group setting. For each topic, one of the practical assignments has to be handed in for evaluation. The course is concluded with a written exam.
Uren per week
Onderwijsvorm Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC), Werkcollege (T)
(Traditional lecture 22 hrs, Problem-solving in working groups 20 hrs, Math self-evaluation test 6 hrs, hand-in excercises 10 hrs, Computer practical 10 hrs, Pen-and-paper exercises 20 hrs, Self study 52 hrs)
Toetsvorm Opdracht (AST), Schriftelijk tentamen (WE), Tussentoets (IT)
(Final written exam 60%, Math self-evaluation test 10%, Hand-in exercises 30%. The weighted average of the grades for the math self-evaluation tests, the practical assignments and the final exam has to be at least 6.0)
Vaksoort bachelor
Coƶrdinator dr. G.S. van Doorn
Docent(en) prof. dr. B.M. Bakker ,dr. J. Bakker ,dr. A. Milias Argeitis ,prof. dr. F.J. Weissing
Verplichte literatuur
Titel Auteur ISBN Prijs
Modeling Life – The Mathematics of Biological Systems, year 2017 Alan Garfinkel, Jane Shevtsov and Yina Guo 978-3-319-59730-0 €  60,00
Modelling Life – Course syllabus G.S. van Doorn, A. Milias, F.J. Weissing €  5,00
SageMath v8.6 or later SageMath Project
Opmerkingen The course units assumes prior knowledge and skills, acquired from the following other course units and/or degree programmes : High-school mathematics (equivalent to VWO wiskunde A and/or B)

The course provides students with broadly applicable quantitative and mathematical analytical skills.
Opgenomen in
Opleiding Jaar Periode Type
BSc Biology: major Behaviour and Neurosciences 2 semester I b verplicht
BSc Biology: major Biomedical Sciences 2 semester I b verplicht
BSc Biology: major Ecology and Evolution 2 semester I b verplicht
BSc Biology: major Integrative Biology 2 semester I b verplicht
BSc Biology: major Molecular Life Sciences 2 semester I b verplicht
BSc LS&T: major Behaviour and Neurosciences (cohort 2018 and 2019) 2 semester I b verplicht
BSc LS&T: major Biomedical Sciences (cohort 2018 and 2019) 2 semester I b verplicht
BSc LS&T: major Molecular Life Sciences (cohort 2018 and 2019) 2 semester I b verplicht
BSc Physics  (Track: Biophysics and Medical Physics ) 3 semester I b verplicht