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50 shades of rule composition

From chemical reactions to higher levels of abstraction
: Andersen, J.L.; Flamm, C.; Merkle, D.; Stadler, P.F.


Fages, F.:
Formal methods in macro-biology. First international conference, FMMB 2014 : Nouméa, New Caledonia, September 22 - 24, 2014; Proceedings
Cham: Springer International Publishing, 2014 (Lecture Notes in Computer Science 8738)
ISBN: 978-3-319-10397-6 (Print)
ISBN: 978-3-319-10398-3 (Online)
International Conference on Formal Methods in Macro-Biology (FMMB) <1, 2014, Nouméa>
Conference Paper
Fraunhofer IZI ()

Graph rewriting has been applied quite successfully to model chemical and biological systems at different levels of abstraction. A particularly powerful feature of rule-based models that are rigorously grounded in category theory, is, that they admit a well-defined notion of rule composition, hence, provide their users with an intrinsic mechanism for compressing trajectories and coarse grained representations of dynamical aspects. The same formal framework, however, also allows the detailed analysis of transitions in which the final and initial states are known, but the detailed stepwise mechanism remains hidden. To demonstrate the general principle we consider here how rule composition is used to determine accurate atom maps for complex enzyme reactions. This problem not only exemplifies the paradigm but is also of considerable practical importance for many down-stream analyses of metabolic networks and it is a necessary prerequisite for predicting atom traces for the analysis of isotope labelling experiments.