Section: Other Grants and Activities
“Equipe associée” PORGY
Participants : Daniel Archambault, Hélène Kirchner, Guy Melançon, Bruno Pinaud.
Project: PORGY (Interactive Analysis and Visualisation of Port Graph Rewriting Systems)
Call: INRIA Equipe associée call
start/end January 2009 – December2010
Budget: 20 000 euros (grant for all partners)
PORGY aims at designing genuine techniques to support the visual exploration and analysis of graph rewriting systems. A graph rewrite system is a set of rewrite rules of the form AB where A and B are graphs with variables. Such a rule applies to a graph G if G contains at least one instance of the left-hand side A , i.e. a subgraph isomorphic to A . Then G rewrites to a new graph G' obtained by replacing the instance of A by an instance of B where variables have been instantiated as in A . This induces a transitive relation on graphs. Each rule application is a rewriting step and a derivation is a sequence of rewriting steps, that we will sometimes call a computation, referring to application of rewriting to programming languages.
From a visualization perspective, dealing with graph rewriting systems boils down to dealing with dynamic graphs – although the dynamic aspects here are not given as time-stamped evolution of a graph but rather are consequences of the non-deterministic applications of rewriting rules. indeed, rewriting is intrinsically non-deterministic since it may be possible to rewrite several subgraphs of a graph at the same time with different rules or the same one, possibly getting different results.
Rewriting systems have been studied as theoretical apparatus in computer science, as a rewriting system can be considered as a “program”, in a sense. These formal objects however have interesting potential applications.
A port graph is a graph where nodes have explicit connection points called ports and the edges are attached to specific ports of nodes. This type of graph was identified from an abstract view of proteins and the molecular complexes resulted from the protein-protein interactions in a biochemical network. From a biochemical perspective, a protein is characterized by a collection of small patches on its surface, called functional domains or sites, and one kind of protein-protein interaction results in the two proteins binding on some particular sites. Then a protein, viewed as a named collection of sites, is graphically modeled by a node with ports, and a bond between two proteins by an edge in a port graph. Graphically, a node in a port graph is represented as an empty box having the identifier placed at the exterior and the ports as small points on the surface of the box. The rewriting of subgraphs correspond here to a change of states of bio-molecules. The study of the rewriting systems becomes critical to gain a better understanding of the biochemical mechanism driving interactinos between molecules.
The PORGY project gathers researchers from GRAVITÉ(The PORGY “Equipe associée” also includes Hélène Kirchner, although Hélène is not a permanent member of GRAVITÉ.) and King's college London(See the URL http://gravite.labri.fr/porgy/Soumission09.html .).
After designing a software architecture allowing the interactive manipulation and visualization of graph rewriting systems, efforts have been devoted to the development of an editor easing the generation of all necessary components (see Fig. 9 ). All graphs produced along the application of rules are stored into a tree of graph instances thus relying on a node/metanode approach. Rules are themselves considered as graphs. The visual representations of all these components raise a number of graph drawing and graph visualization issues we are currently studying.