Seminar on Mathematical Modelling in Biology (WS 23/24)
Here you find information about the seminar on Mathematical Modelling in Biology in the winter semester 2023/24.
2024-02-05
General Information
- Organizers
Please contact Hridya Varma if you have questions regarding this seminar.
- Meetings
- We will meet in person on Mondays 14:15 - 15:45 in SR 1 (INF 205)
- The kick-off meeting will be on October 16, 2023 in room 1/414 (INF 205)
- Level:
- Master students, advanced Bachelor students
- Language
- English
- Recommended Background
- You should have some experience with the following topics:
- Analysis
- Linear Algebra
- Ordinary Differential Equations
- Partial Differential Equations
You can get a feeling whether you have the necessary background for the seminar by skimming through the given topics and literature. It is important that you are able to understand the topics very well in order to explain them to your peers. So if you are able to read and understand the given literature, you should be good to go :)
- Registration
- To participate in the seminar, please register on MÜSLI. If the registration is full on MÜSLI, you can send an e-mail to Hridya Varma to be added to the waiting list.
Kick-Off Meeting
The kick-off meeting will take place on October 16, 2023. Here, we will explain the seminar format, our goals and expectations, discuss organizational matters and present the planned schedule for the seminar.
Topics
Below you can find a tentative list of the topics that we offer along with some literature suggestions. We plan to have 8 presentations on 8 different topics.
- Single-species and interacting population models in ecology
- Integro-difference equations in spatial ecology
- Delay differential equations and their applications in biology
- Compartmental models in mathematical epidemiology
- Modelling chemical reactions and gene regulatory networks
- Reaction-diffusion models for biological pattern formation
- Cellular automata approach to biological modelling
- Evolutionary game theory
After the kick-off meeting on October 16, 2023, you will have one week to look into the offered topics and send your top 3 preferred topics along with a short note on your mathematical background to Hridya Varma. Please send the e-mail by 10:00 on Monday October 23, 2023. We will then try to distribute the topics according to your preferences keeping in mind your mathematical background. You will be assigned a topic by October 25, 2023.
Goals of the Seminar
- Explore the world of mathematical modelling in biology
- Share your knowledge with your peers by presenting your topic in an engaging and understandable way
- Learn how to present a complex topic in any length of time
Expectations
In order to complete the seminar successfully, you have to:
- attend the weekly meetings
- present your topic in 5 minutes at the pitch session
- present your topic in 45 minutes (+ 15 minutes discussion)
- actively participate in the discussion and give constructive feedback to your peers
- provide a 1-2 page handout for the 45-minute talk
Schedule
| Date | Topic | Speaker(s) |
|---|---|---|
| October 16, 2023 | Kick-off meeting | |
| October 23, 2023 | Deadline to send your topic preferences | |
| October 25, 2023 | Distribution of the topics | |
| November 27, 2023 | 5-minute pitch session | everyone |
| December 4, 2023 | Single-species and interacting population models in ecology | - |
January 22, 2024 | Integro-difference equations in spatial ecology | Nico Haaf |
| December 18, 2023 | Delay differential equations in biology | - |
| January 8, 2024 | Compartmental models in mathematical epidemiology | Julian Trebels |
January 29, 2024 | Modelling chemical reactions and gene regulatory networks | Cicely Nguyen |
| January 22, 2024 | Reaction-diffusion models for biological pattern formation | - |
| January 29, 2024 | Cellular automata approach to biological modelling | - |
February 12, 2024 | Evolutionary game theory | Timo Weber |
Grading
We primarly rate your talks based on this rubric.
Literature
Here you will find some literature suggestions. These are only meant to be used as a starting point. We expect you to identify further literature as necessary on your own.
You can find all the following literature online when you are connected to the university network. Alternatively, you can also find them in this heiBOX folder. The password for this folder will be shared at the kick-off meeting.
- Single-species and interacting population models in ecology
- Müller, Johannes, and Christina Kuttler. “Methods and models in mathematical biology.” Lecture Notes on Mathematical Modelling in Life Sciences, Springer, Berlin (2015) - Chapter 2 (Mathematical Ecology)
- Integro-difference equations in spatial ecology
- Lutscher, Frithjof. Integrodifference equations in spatial ecology. Cham, Switzerland: Springer International Publishing, 2019 - Chapters 2, 3, 4, 5.
- Delay differential equations and their applications in biology
- Hadeler, K. P. “Delay equations in biology.” Functional Differential Equations and Approximation of Fixed Points: Proceedings, Bonn, July 1978. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. 136-156.
- Ruan, Shigui. “Delay differential equations in single species dynamics.” Delay differential equations and applications 205 (2006): 477-517.
- Compartmental models in mathematical epidemiology
- Brauer, Fred. “Compartmental models in epidemiology.” Mathematical epidemiology (2008): 19-79.
- Hadeler, Karl Peter, Michael C. Mackey, and Angela Stevens. Topics in mathematical biology. Berlin: Springer, 2017 - Chapter 6 (Epidemic models)
- Modelling chemical reactions and gene regulatory networks
- Müller, Johannes, and Christina Kuttler. “Methods and models in mathematical biology.” Lecture Notes on Mathematical Modelling in Life Sciences, Springer, Berlin (2015) - Sections 5.1 and 5.2 in Chapter 5 (Reaction Kinetics).
- Edelstein-Keshet, Leah. Mathematical models in biology. Society for Industrial and Applied Mathematics, 2005 - Chapter 7 (Models for Molecular Events).
- Reaction-diffusion models for biological pattern formation
- Maini, Philip K., and Thomas E. Woolley. “The Turing model for biological pattern formation.” The dynamics of biological systems (2019): 189-204.
- Kondo, Shigeru, and Takashi Miura. “Reaction-diffusion model as a framework for understanding biological pattern formation.” Science 329.5999 (2010): 1616-1620.
- Edelstein-Keshet, Leah. Mathematical models in biology. Society for Industrial and Applied Mathematics, 2005 - Chapter 11 (Models for Development and Pattern Formation in Biological Systems).
- Cellular automata approach to biological modelling
- Ermentrout, G. Bard, and Leah Edelstein-Keshet. “Cellular automata approaches to biological modelling.” Journal of theoretical biology 160.1 (1993): 97-133.
- Hadeler, Karl-Peter, and Johannes Müller. Cellular automata: analysis and applications. Heidelberg: Springer, 2017.
- Deutsch, Andreas, and Sabine Dormann. Cellular Automaton Modeling of Biological Pattern Formation. Birkhäuser Boston, 2005.
- Evolutionary game theory
- Sigmund, Karl. “Introduction to evolutionary game theory.” Evolutionary game dynamics 69 (2011): 1-26.
- Hammerstein, Peter, and Reinhard Selten. “Game theory and evolutionary biology.” Handbook of game theory with economic applications 2 (1994): 929-993.
Please remember that the goal of this seminar is not to present all the contents of the literature. This is unrealistic and will make it difficult for your audience to understand your talk. The literature is meant to help you get a good understanding of the topic, so that you can summarize your learnings and present it to your peers in a way they can understand.
