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Abstract. Metabolic pathway analysis is one of the tools used in biology and medicine in order to understand reaction cycles in living cells. A shortcoming of the approach, however, is that reactions are analysed only at a level corresponding to what is known as the 'collective token view' in Petri nets, i.e., summarising the number of atoms of certain types in a compound, but not keeping track of their identity. In this paper we propose a refinement of pathway analysis based on hypergraph grammars, modelling reactions at a molecular level. We consider as an example the citric acid cycle, a classical, but non-trivial reaction for energy utilisation in living cells. Our approach allows the molecular analysis of the cycle, tracing the flow of individual carbon atoms based on a simulation using the graph transformation tool AGG.

Stochastic Graph Transformation combines graphical modelling of various software artefacts with stochastic analysis techniques. Existing approaches are restricted to processes with exponential time distribution. Such processes are sufficient for modelling a significant class of stochastic systems, however there are interesting systems which cannot be specified appropriately in such a framework. In several cases one needs to consider non-exponential time distributions. This paper proposes a stochastic model based on graph transformation with general probability distributions. This model is well suited to represent concurrency and performance aspects of architecture reconfiguration. It is also possible to apply Monte Carlo simulation techniques in order to analyse behaviour of complex stochastic systems. The new model is implemented and used to simulate simple networks.

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