Attractor Equivalence: An Observational Semantics for Reaction Networks

International audienceWe study observational semantics for networks of chemical reactions as used in systems biology. Reaction networks without kinetic information, as we consider, can be identified with Petri nets. We present a new observational semantics for reaction networks that we call the attractor equivalence. The main idea of the attractor equivalence is to observe reachable attractors and reachability of an attractor divergence in all possible contexts. The attractor equivalence can support powerful simplifications for reaction networks as we illustrate at the example of the Tet-On system. Alternative semantics based on bisimulations or traces, in contrast, do not support all needed simplifications

Stochastically timed predicate-based communication primitives for autonomic computing

Predicate-based communication allows components of a system to send messages and requests to ensembles of components that are determined at execution time through the evaluation of a predicate, in a multicast fashion. Predicate-based communication can greatly simplify the programming of autonomous and adaptive systems. We present a stochastically timed extension of the Software Component Ensemble Language (SCEL) that was introduced in previous work. Such an extension raises a number of non-trivial design and formal semantics issues with different options as possible solutions at different levels of abstraction. We discuss four of these options. We provide formal semantics and an illustration of the use of the language modeling a variant of a bike sharing system, together with some preliminary analysis of the system performance