Algebraic approach to single-pushout graph transformation
Theoretical Computer Science - Special issue on selected papers of the International Workshop on Computing by Graph Transformation, Bordeaux, France, March 21–23, 1991
Graph Replacement Chemistry for DNA Processing
DNA '00 Revised Papers from the 6th International Workshop on DNA-Based Computers: DNA Computing
Graph transformation in molecular biology
Formal Methods in Software and Systems Modeling
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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.