Molecular Analysis of Metabolic Pathway with Graph Transformation

  • Karsten Ehrig
  • Reiko Heckel
  • Georgios Lajios
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4178)


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.


Citric Acid Cycle Graph Transformation Reaction Rule Output Agent Edge Attribute 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Karsten Ehrig
    • 1
  • Reiko Heckel
    • 1
  • Georgios Lajios
    • 1
  1. 1.Department of Computer ScienceUniversity of LeicesterUnited Kingdom

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