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636-0706-00L 4 Credits BSC , DR , MSC D-BSSE , D-INFK , D-BIOL , D-MATH
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Spatio-Temporal Modelling in Biology

Lecturers & Examiners: Prof. Dr. Dagmar Iber
VVZ CR n/a

Last Updated: 2026-06-01 11:30:43

Abstract

This course focuses on modeling spatio-temporal problems in biology, in particular on the cell and tissue level. The main focus is on mechanisms and concepts, but mathematical and numerical techniques are introduced as required. Biological examples discussed in the course provide an introduction to key concepts in developmental biology.

Objective

Students will learn state-of-the-art approaches to modelling spatial effects in dynamical biological systems. The course provides an introduction to dynamical system, and covers the mathematical analysis of pattern formation in growing, developing systems, as well as the description of mechanical effects at the cell and tissue level. The course also provides an introduction to image-based modelling, i.e. the use of microscopy data for model development and testing. The course covers classic as well as current approaches and exposes students to open problems in the field. In this way, the course seeks to prepare students to conduct research in the field. The course prepares students for research in developmental biology, as well as for applications in tissue engineering, and for biomedical research.

Content

1. Introduction to Modelling in Biology 2. Bioimage Analysis 3. Morphogen Gradients 4. Precision & Robustness of Patterning 5. Mathematical Description of Growing Biological Systems 6. Travelling Waves & Wave Pinning 7. Turing Patterns 8. Chemotaxis 9. Epithelial Organisation 10. Tissue Simulation Frameworks 11. Tissue Mechanics & Fluid Dynamics 12. Growth Control 13. Image-Based Modelling 14. Summary

Resources

Lecture Notes

All lecture material will be made available online via Moodle.

Literature

The lecture course is not based on any textbook. The following textbooks are related to some of its content. The textbooks may be of interest for further reading, but are not necessary to follow the course: Murray, Mathematical Biology, Springer Forgacs and Newman, Biological Physics of the Developing Embryo, CUP Keener and Sneyd, Mathematical Physiology, Springer Fall et al, Computational Cell Biology, Springer Szallasi et al, System Modeling in Cellular Biology, MIT Press Wolkenhauer, Systems Biology Kreyszig, Engineering Mathematics, Wiley

Learning Materials (Links)

General Information

Language
English
Levels
BSC , DR , MSC
Frequency
Yearly recurring

Examination

Type
session examination
Mode
written 120 minutes
Aids
None
Die Prüfung wird als Multiple-Choice durchgeführt, wenn möglich über Computer. Die Prüfung kann prinzipiell simultan in Basel und Zürich gestellt werden.Teilnehmer des Tutoriums, die in jedem Tutorium die Übungen bearbeitet und vorführen können, bekommen eine Notenerhöhung von 0.25 in der Endnote (Lernelement).

Course Components

Type Title Time & Place Hours
lecture with exercise Spatio-Temporal Modelling in Biology
Thursday 1:15-2 pm Tutorial Thursday 2:15-3 pm Inverted classroom, maybe extended to 90 minutes in case of live recordings of new lectures The course starts in the second week of the semester. The first tutorial will offer an introduction to solving PDEs with Matlab. Online course: rooms on campus are reserved for students wishing to follow the course from there.
  • Thu 13:15-15:00 (HG D 7.1)
  • Thu 13:15-16:00 (BSS E 44)
  • Thu 15:15-16:00 (HG D 7.1)
3 h weekly

Offered In