Modelling Life

Faculteit Science and Engineering
Jaar 2020/21
Vakcode WBBY024-05
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) Analyse differential-equation models by a variety of techniques, including elementary analytical solution methods,
qualitative analysis and numerical simulation.
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 necessary baseline skills in an e-learning environment (SOWISO), where
students are able to select personalised practice material based on the results of self-evaluation tests.
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 and chaos’, ‘Linear algebra’ 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 working-group
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 14 hrs, Problem-solving in working groups 30 hrs, Math self-evaluation test 3 hrs, hand-in excercises 3 hrs, Computer practical 20 hrs, Pen-and-paper exercises 20 hrs, Self study 47 hrs)
Toetsvorm Opdracht (AST), Schriftelijk tentamen (WE), Tussentoets (IT)
(Students need to obtain at least a 50% score on the online math test and the working-group assignments. The weighted average of the grades for the online math tests, the working-group assignments and the final exam has to be at least 6.0.)
Vaksoort bachelor
Coördinator dr. G.S. van Doorn
Docent(en) dr. A. Milias Argeitis ,dr. G.S. van Doorn
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 €  5,00
SageMath v8.6 or later SageMath Project
Entreevoorwaarden 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)

Biology and Life Science & Technology (old curriculum) course units are only accessible for students of those degree programmes. Students from other degree programmes who would like to participate in Biology course units are obliged to contact one of the academic advisors before registration. After this contact, students have to request admission from the Board of Examiners Biology/Life Science & Technology. Failing to follow this procedure results in immediate unenrollment without prior notification.
Opmerkingen The course provides students with broadly applicable quantitative and mathematical analytical skills; in particular, it prepares, for
the courses Mathematics in the Life Sciences, Biostatistics II and Self-Organisation.

Dit vak had vorig jaar vakcode WBLS19014
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