A Mozart implementation of CP(BioNet)

Abstract

The analysis of biochemical networks consists in studying the interactions between biological entities cooperating in complex cellular processes. To facilitate the expression of analyses and their computation, we introduced CP(BioNet), a constraint programming framework for the analysis of biochemical networks. An Oz-Mozart prototype of CP(BioNet) is described. This prototype consists of the implementation of a new kind of domain variables, graph domain variables, and the implementation of constraint propagators for constraints over graph-domain variables. These new variables and constraints are implemented in Oz and they can then be used like other domain variables in the Oz-Mozart platform. An implementation of a path constraint propagator is described in depth and constrained path finding tests are analysed to assess the tractability of our approach. Finally, an alternative Oz-Mozart data-structure for the graph-domain variables is presented and compared to the first one. © Springer-Verlag Berlin Heidelberg 2005.