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Petri Nets – A Mathematical Formalism to Analyze Chemical Reaction Networks
Author(s) -
Koch Ina
Publication year - 2010
Publication title -
molecular informatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.481
H-Index - 68
eISSN - 1868-1751
pISSN - 1868-1743
DOI - 10.1002/minf.201000086
Subject(s) - petri net , formalism (music) , computer science , cheminformatics , process architecture , concurrency , theoretical computer science , artificial intelligence , programming language , chemistry , computational chemistry , art , musical , visual arts
In this review we introduce and discuss Petri nets – a mathematical formalism to describe and analyze chemical reaction networks. Petri nets were developed to describe concurrency in general systems. We find most applications to technical and financial systems, but since about twenty years also in systems biology to model biochemical systems. This review aims to give a short informal introduction to the basic formalism illustrated by a chemical example, and to discuss possible applications to the analysis of chemical reaction networks, including cheminformatics. We give a short overview about qualitative as well as quantitative modeling Petri net techniques useful in systems biology, summarizing the state‐of‐the‐art in that field and providing the main literature references. Finally, we discuss advantages and limitations of Petri nets and give an outlook to further development.