A Logic Programming Approach to Reaction Systems

Reaction systems (RS) are a computational framework inspired by the functioning of living cells, suitable to model the main mechanisms of biochemical reactions. RS have shown to be useful also for computer science applications, e.g. to model circuits or transition systems. Since their introduction about 10 years ago, RS matured into a fruitful and dynamically evolving research area. They have become a popular novel model of interactive computation. RS can be seen as a rewriting system interacting with the environment represented by the context. RS pose some problems of implementation, as it is a relatively recent computation model, and several extensions of the basic model have been designed. In this paper we present some preliminary work on how to implement this formalism in a logic programming language (Prolog). To the best of our knowledge this is the first approach to RS in logic programming. Our prototypical implementation does not aim to be highly performing, but has the advantage of being high level and easily modifiable. So it is suitable as a rapid prototyping tool for implementing several extensions of reaction systems in the literature as well as new ones. We also make a preliminary implementation of a kind of memoization mechanism for stopping potentially infinite and repetitive computations. Then we show how to implement in our interpreter an extension of RS for modeling a nondeterministic context and interaction between components of a (biological) system. We then present an extension of the interpreter for implementing the recently introduced networks of RS.