Handbook of graph grammars and computing by graph transformation: volume I. foundations
Handbook of graph grammars and computing by graph transformation: volume I. foundations
Programmed graph replacement systems
Handbook of graph grammars and computing by graph transformation
Proceedings of the 10th International Conference on Rewriting Techniques and Applications
RtA '99 Proceedings of the 10th International Conference on Rewriting Techniques and Applications
Tutorial introduction to the algebraic approach of graph grammars
Proceedings of the 3rd International Workshop on Graph-Grammars and Their Application to Computer Science
Explicit collision simulation of chemical reactions in a graph based artificial chemistry
ECAL'05 Proceedings of the 8th European conference on Advances in Artificial Life
Graph transformation in molecular biology
Formal Methods in Software and Systems Modeling
Molecular analysis of metabolic pathway with graph transformation
ICGT'06 Proceedings of the Third international conference on Graph Transformations
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The processing of nucleic acids is abstracted using operators on directed and labeled graphs. This provides a computational framework for predicting complex libraries of DNA/RNA arising from sequences of reactions involving hybridisation intermediates with significant combinatorial complexity. It also provides a detailed functional classification scheme for the reactions and side-reactions of DNA processing enzymes. It is complementary to the conventional string-based DNA Computing grammars such as splicing systems, in that the graph-based structure of enzyme-nucleic acid complexes is the fundamental object of combinatorial manipulation and in that the allowed reactions are specified by local graph replacement operators (i.e. catalysts for structural transitions) associated with enzymes. The focus of the work is to present a calculus for the compact specification and evaluation of the combined action of multiple DNA-processing reactions. Each enzyme and its side-reactions may be classified by a small set of small graph replacement operators. Complex replication and computation schemes may be computed with the formalism.