Modelling Life

Faculteit Science and Engineering
Jaar 2021/22
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 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. On the basis of 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. Qualitative (graphical) analysis of the vector field and simulated system trajectories 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.
Modelling Life is a high-pace three-week block course with a full-time schedule. Following other courses in parallel is not recommended.
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)
(WE-40%, IT-30%, AST-30%. Students need to obtain at least a 50% score on the online math test and 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. The partial exam grade for the SOWISO math test remains valid for students who need to retake the course; other partial grades lapse at the end of the academic year.)
Vaksoort bachelor
Coördinator prof. dr. G.S. van Doorn
Docent(en) dr. A. Milias Argeitis ,prof. 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
SageMath v8.6 or later SageMath Project
Modelling Life – Course syllabus G.S. van Doorn, A. Milias €  5,00
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)

Students from degree programmes other than Biology/Life Science & Technology who would like to participate in this course unit need to be available full-time during the course. The course is a three-week block course with a full schedule. It is not possible to follow another course next to this course.

Students from the Bachelor's degree programmes Biology and Life Science & Technology take priority over students from other degree programmes when the course has a maximum capacity.
Opmerkingen Regular attendance at the working groups is necessary to satisfy the 50% score requirement for the working group hand-in assignments
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 Physics  (Track: Biophysics and Medical Physics ) 3 semester I b verplicht