Did you ever try to scare a fish by tapping on the glass of an aquarium? What happens in the fish brain if you do that? What would happen in a fish school? In my project I tried to answer these questions via computational modelling and I will tell you how packages such as numba, pypet, and matplotlib allowed me to efficiently simulate the model and visualize results in a reproducible way.
One of the crucial tasks in the life of many animals is to escape from predators. Fish often do this with a rather stereotypical escape response that you might observe by tapping on the aquarium glass. The neurobiology behind this behavior is quite well-studied so that we wanted to find a neuronal mechanism that could explain it.
But many fish are not travelling alone and rather come together in large fish schools. How would neighbouring fish react if one of them shows the mentioned escape response? Using a model for collective behavior and combining it with the neuronal mechanism of the first part we can also look at this question.
In this talk I will sketch the computational models and their analysis and at the same time present use-cases for several python packages:
Taken together this project also shows how the python ecosystem allows to easily integrate many different packages in a project and thus enables reproducible science.
You can find all related code and material in the following github repository: https://github.com/awakenting/master-thesis