1 . 2 . Model Building in Systems Biology

An important aspect of systems biology is the concept of modeling the dynamics of biochemical networks where molecules are the nodes and the molecular interactions are the edges. Due to the size and complexity of these networks, intuition alone is not sufficient to fully grasp their dynamical behavior. Instead an explicit mathematical description of the network and its interaction dynamics is used, which allows for testing and predicting the behavior in computer simulations. This text starts with an introduction to dynamical systems. It then describes buildingblocks used when modeling molecular interactions, and introduces how these ’bricks’ are combined into models of large biochemical networks. Then different parameter estimation and analysis methods are discussed. In the end there is a discussion on diffusion and the combination of reactions and diffusion into one model. The text is very sparse and it is meant to be used as lecture notes for both teacher(!) and students.