Symbolic Methods for Chemical Reaction Networks (Dagstuhl Seminar 12462)

During 11-16 November 2012, the Dagstuhl Seminar 12462 "Symbolic Methods for Chemical Reaction Networks" was held in Schloss Dagstuhl - Leibneiz Center for Informatics. The seminar brought together researchers in symbolic computation, chemical engineering, and systems biology. During the seminar, participants presented five-minute talks introducing their research interests, five participants gave longer talks, and all participants had the opportunity to take part in various discussion groups. Abstracts of presentations and summaries of the discussion groups are compiled in this report

Structural simplification of chemical reaction networks preserving deterministic semantics

International audienceWe study the structural simplification of chemical reaction networks preserving the deterministic kinetics. We aim at finding simplification rules that can eliminate intermediate molecules while preserving the dynamics of all others. The rules should be valid even though the network is plugged into a bigger context. An example is Michaelis-Menten's simplification rule for enzymatic reactions. In this paper, we present a large class of structural simplification rules for reaction networks that can eliminate intermediate molecules at equilibrium, without assuming that all molecules are at equilibrium, i.e. in a steady state. We prove the correctness of our simplification rules for all contexts that preserve the equilibrium of the eliminated molecules. Finally, we illustrate at a concrete example network from systems biology that our simplification rules may allow to drastically reduce the size of reaction networks in practice

Inferring Reaction Models from ODEs

International audienc