Computational modelling of mycobacterium infection and innate immune response in zebrafish

Viana de Carvalho, R. (2015)

Doctoral Thesis

In this thesis we provided a comprehensive overview on the steps that are involved in the modeling process and simulation of biological phenomena; from the choice of the method to the validation of the results. We gradually implemented a model with which we would be able to study the complex interplay of the components involved in the Mycobacterium marinum infection process and innate immune response in zebrafish embryos. In itself this process is a model for deeper understanding of tuberculosis infection in humans using zebrafish as model organism. Each chapter is a building block in the modeling process, which gradually forms a model that can represent cause-and-effect among these components involved in the biological behavior.

• Computational Modeling
• Petri nets
• 3D simulation
• Mycobacterium Infection

• All authors: Viana de Carvalho, R.
• Supervisor: Kok, J.N.
• Co-supervisor: Verbeek, F.J.
• Committee: Spaink, H.P.; Koutny, M.; Kleijn, H.C.M.
• Qualification: Doctor (dr.)
• Awarding Institution: Leiden Institute of Advanced Computer Science (LIACS), Faculty of Science, Leiden University
• Date: 2015-10-15
• ISBN (print): 9789462598812