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Spatio-Temporal Modelling in Biology
Last Updated: 2026-02-05 15:48:38
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. Morphogen Gradients 3. Dynamical Systems 4. Cell-cell Signalling (Dr Boareto) 5. Travelling Waves 6. Turing Patterns 7. Chemotaxis 8. Mathematical Description of Growing Biological Systems 9. Image-Based Modelling 10. Tissue Mechanics 11. Cell-based Tissue Simulation Frameworks 12. Plant Development (Dr Dumont) 13. Growth Control 14. Summary
Resources
Lecture Notes
All lecture material will be made available onlineLink
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)
- Main link
- Lecture Material
General Information
- Language
- English
- Levels
- BSC , MSC
- Frequency
- Yearly recurring
Examination
- Type
- session examination
- Mode
- oral 20 minutes
Course Components
| Type | Title | Time & Place | Hours |
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| lecture with exercise |
Spatio-Temporal Modelling in Biology
The lecture course will be offered as “inverted classroom”. Lecture videos, slides, and scripts will be made available via Moodle, and students are expected to watch the videos ahead of the lecture. The 45-minute in person lecture time serves to answer student question where necessary, and to discuss application examples with students to deepen their understanding of the material. Similarly, problem sheets and solutions will be made available ahead of the tutorial. The tutorials serve to address further questions. Remote participation is always possible. It is a new form of teaching. Feedback will be most welcome.
Friday 11-12 Q&A Lecture (ZH)
Friday 12-13 Tutorial (ZH)
Course starts: Friday, Sept. 24 in ZH
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3 h weekly |
Offered In
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Computational Biology and Bioinformatics Master (More information at: )
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Core Courses (Please note that the list of core courses is a closed list. Other courses cannot be added to the core course category in the study plan. Also the assignments of courses to core subcategories cannot be changed. Students need to pass at least one course in each core subcategory. A total of 40 ECTS needs to be acquired in the core course category.)
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Electives (The electives list in the ETH course catalogue is an open list, and the courses listed in the ETH course catalogue provide just examples for possible elective courses, e.g. a selection of eligible courses. Students are expected to look for relevant courses in the ETH and University of Basel course catalogue and ask their mentor for approval. Courses from the advanced course category may also be taken as electives. We particularly recommend browsing the University of Basel course catalogue for elective courses of relevant master's degree programes (using the filter "programe structure" on the course catalogue website), such as for example: Biomedical Engineering, Chemistry, Drug Sciences, Epidemiology, Infection Biology, Molecular Biology, Nanosciences.)
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