An interesting aricle on visualising running code, with imortant insights on models in general:
Validating Dynamic Systems - Enterprise Integration Patterns
One of the key messages we are trying to highlight during our talk is the importance of mapping the captured data to a model that is suited to answering the questions you are interested in. This model can be a graph, a process or any other abstract representation of your system.
Not getting too pedantic on the exact form of model seems like good advice - what type of model answers the questions that need to be asked?