The work of our group is revolving around the general question how computers can be used to support modeling and simulation in the scientific process. From a computer science and philosophy of science point of view not only results from experiments and imulations but also the scientific models themselves that connect these results as well as the computational tools that are used to analyse and communicate these models in the scientific cycle are data. In order for computers to help make sense of these data the corresponding algorithms must handle it in a way that is compatible with the knowledge that is represented by those models. With a focus on dynamic models in systems biology we therefore ask: what are adequate computer “understandable” formal representations 1) of this knowledge, 2) of the role of the models in simulations and 3) of the results produced by these simulations, i.e. of the structure, function and behaviour of these models?