Preface: Petri nets for Systems and Synthetic Biology

Abstract

This special issue Petri Nets for Systems and Synthetic Biology presents selected highlights of a challenging and highly active research field. It consists of two parts, the former ‘‘Part 1: Bridging Gaps’’ and the current ‘‘Part 2: Unifying Diversity’’. Systems Biology is the biology-based interdisciplinary research area that focuses on complex interactions between the components of biological systems, and how these interactions give rise to function and behavior of these systems. One of the ambitions of Systems Biology is to discover the outcome of organic evolution and to describe this acquired knowledge in models, which are explanatory of the biological mechanisms as well as suitable for reliable prediction of behaviour when the system is perturbed by, e.g., mutations, chemical interventions or changes in the environment. In the emerging discipline Synthetic Biology, the very same kind of models are taken as design templates for novel synthetic biological systems, i.e., to design and construct new biological functions and systems not found in nature. Here, model verification and validation turn out to be crucial for reliable system design as models may serve as blueprints. One of the core issues in Systems and Synthetic Biology is the construction of biomolecular networks; either the reconstruction of networks which have been designed—as opposed to technical systems—by the organic evolution of living organisms, or the variation and/or design of novel networks, respectively. This kind of networks are most naturally described by bipartite graphs, e.g., Petri nets (PN), to distinguish between passive system components (such as chemical compounds, proteins, genes, etc.) and active system components (such as chemical reactions, complexation/decomplexation, activation/deactivation, etc.). Petri Nets have a well-defined semantics, which can either be an interleaving semantics captured in Labeled Transition Systems (LTS) to describe all possible behaviour by all interleaving sequences in the style of transition-labelled automata, or a partial order