| Titel |
Modeling of biological systems 
|
| Title |
Modeling of biological systems |
| Schwerpunkt/Focus |
|
| Sprache/Language |
englisch |
| VV-Nr./Course No. |
134187 |
| Modulverantwortlich/Responsible |
Dr. Bharat Ravi |
| Vertreter/Co-responsible |
|
| Anbieter/Teachers |
Dr. B. Ravi, Dr. C. Kemena, Dr. M. Merski, Dr. R. Abdilzahdeh, Dr. Bornberg-Bauer |
| Typ/Type |
Lectures, Tutorials, Coding sessions |
| SWS/Semerster periods per week |
|
| Arbeitslast(h)/Work load |
150 h |
| KP/Credit points |
5 KP |
| Zuordnung/Classification |
Fortgeschrittenen-Modul |
| Semester/Semester |
SoSe |
| Studierende/Students |
MSc Biowissenschaften
MSc Biotechnologie
MSc Molekulare Biomedizin |
| Corona-Informationen/Corona-Information |
|
| Zeit/Date |
Block II, 01.06.26-26.06.26 |
| Ort/Location |
tba |
| Beginn/Start |
|
| Vorbesprechung/Obligatory pre-meeting |
keine / none |
| Voraussetzung/Prerequisite |
keine / none |
| Anmeldung/Registration |
Online-Anmeldung |
| Leistungskontrollen/Performance assessments |
homeworks, active participation in tutorials |
| Termine f. Leistungskontrollen/Date for performance assessments |
|
| max. NP/Max. grade points |
|
| Ziele/Aims |
Design of a theoretical model that describes a biological phenomenon; theoretical analysis of a mathematical model; implementation and simulation of a model in julia |
| Inhalte/Content |
Biology is full of complex systems where different components interact with each other — biomolecules in a cell, cells in an organism, organisms in an ecosystem etc. Complex systems such as these cannot usually be understood using simple intuition. Representing them in the form of mathematical equations helps describing them precisely using a defined set of rules and formal logic. These representations (mathematical models) can be solved using formal analysis (pen and paper) or computational methods to understand the behavior of the biological systems they represent.
This module follows a problem based learning approach where students would learn modeling by working on a modeling project of their choice. The project starts from the beginning of the module, with the identification of a biological problem. At every step of the project, the students will be assisted on scientific, logical and technical aspects. At the end of the module, the students will briefly present their projects. It is important to note that the project does not have a fixed goal and is intended only as a learning exercise.
In parallel to the projects, students will learn about modeling principles and techniques through lectures.
Computational analysis of the models (and simulations) would be done using the Julia programming language (easy syntax like python but is much faster and is widely used for mathematical modeling). No prior experience on mathematical and computational methods is necessary. However, a basic (high school level) understanding of algebra and calculus is essential, and some experience with programming (any language) would be a benefit. |
| Methoden/Methods |
1. Identification of a biological question
2. Representing the biological system in a mathematical form
3. Solving the mathematical model using formal analysis for simple models (e.g. Michaelis-Menten enzyme kinetics)
4. Performing numerical simulations/solutions for complex models using Julia
5. Understanding transient versus steady-states of the system
6. Understanding how parameters affect the system's behavior (stability analysis) |
| Berufsrelevante und interdisziplinäre Komponenten/Occupational and interdisciplinary skills |
|
| Voraussetzung für/Prerequisite for |
|
| Präsenzpflicht/Compulsory presence |
ja |
| Plätze/Number of participants |
12 |
| Gruppengröße/Group size |
|
| Materialien/Materials |
|
| Literatur/Literature |
Die Literatur wird in der ersten Vorlesung bekannt gegeben.
--
Relevant literature will be announced in the first lecture. |
| Links |
|
| Sonstiges/Further information |
|
= Modul gehört zum SPP Imoplant / Module is part of the SSP Imoplant
= Modul gehört zum SPP Evolution /Module is part of the SSP Evolution
= Modul gehört zum SPP Bioanalytics and Biochemistry /Module is part of the SSP Bioanalytics and Biochemistry
= Modul gehört zum SPP Neuroscience and Behaviour /Module is part of the SSP Neuroscience and Behaviour
= Modul gehört zum SPP Quantitative Cell Biology /Module is part of the SSP Quantitative Cell Biology