50 Shades of Rule Composition: From Chemical Reactions to Higher Levels of Abstraction

Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

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Abstrakt

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.
OriginalsprogEngelsk
TitelFormal Methods in Macro-Biology : Proceedings of the First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014
RedaktørerFrançois Fages, Carla Piazza
ForlagSpringer
Publikationsdato2014
Sider117-135
ISBN (Trykt)978-3-319-10397-6
ISBN (Elektronisk)978-3-319-10398-3
DOI
StatusUdgivet - 2014
Begivenhed1st International Conference on Formal Methods in Macro-Biology - Nouméa, Ny Kaledonien
Varighed: 22. sep. 201424. sep. 2014
Konferencens nummer: 1

Konference

Konference1st International Conference on Formal Methods in Macro-Biology
Nummer1
LandNy Kaledonien
ByNouméa
Periode22/09/201424/09/2014
NavnLecture Notes in Computer Science
Vol/bind8738
ISSN0302-9743

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