From our previous work on biochemical applications, the structure of port graph (or multigraph with ports) and a rewriting calculus have proved to be well-suited formalisms for modeling interactions between proteins. Then port graphs have been proposed as a formal model for distributed resources and grid infrastructures, where each resource is modeled by a node with ports. The lack of global information and the autonomous and distributed behavior of components are modeled by a multiset of port graphs and rewrite rules which are applied locally, concurrently, and non-deterministically. Some computations take place wherever it is possible and in parallel, while others may be controlled by strategies. In this paper, we first introduce port graphs as graphs with multiple edges and loops, with nodes having explicit connection points, called ports, and edges attaching to ports of nodes. We then define an abstract biochemical calculus that instantiates to a rewrite calculus on these graphs. Rules and strategies are themselves port graphs, i.e. first-class objects of the calculus. As a consequence, they can be rewritten as well, and rules can create new rules, providing a way of modeling adaptive systems. This approach also provides a formal framework to reason about computations and to verify useful properties. We show how structural properties of a modeled system can be expressed as strategies and checked for satisfiability at each step of the computation. This provides a way to ensure invariant properties of a system. This work is a contribution to the formal specification and verification of adaptive systems and to theoretical foundations of autonomic computing.
