TY  - JOUR
TI  - Constructing and visualizing chemical reaction networks from pi-calculus models
AU  - John, Mathias
AU  - Schulz, Hans-Jörg
AU  - Schumann, Heidrun
AU  - Uhrmacher, Adelinde M.
AU  - Unger, Andrea
T2  - Formal Aspects of Computing
AB  - The pi-calculus, in particular its stochastic version the stochastic pi-calculus, is a common modeling formalism to concisely describe the chemical reactions occurring in biochemical systems. However, it remains largely unexplored how to transform a biochemical model expressed in the stochastic pi-calculus back into a set of meaningful reactions. To this end, we present a two step approach of first translating model states to reaction sets and then visualizing sequences of reaction sets, which are obtained from state trajectories, in terms of reaction networks. Our translation from model states to reaction sets is formally defined and shown to be correct, in the sense that it reflects the states and transitions as they are derived from the continuous time Markov chain-semantics of the stochastic pi-calculus. Our visualization concept combines high level measures of network complexity with interactive, table-based network visualizations. It directly reflects the structures introduced in the first step and allows modelers to explore the resulting simulation traces by providing both: an overview of a network’s evolution and a detail inspection on demand.
DA  - 2013///
PY  - 2013
DO  - 10.1007/s00165-011-0209-0
VL  - 25
IS  - 5
SP  - 723
EP  - 742
SN  - 0934-5043
ER  -