Integrative Analysis of Gene Networks Using Dynamic Process Pattern Modelling

Abstract

In this article, a novel object-oriented modeling approach in the field of biochemical network modeling is presented. Molecular objects are modeled conceptually using object classes, internally based on the standard object models Java and ODMG. Objects and object networks are composed automatically using data integration. In combination with that, a specific view concept based on access paths has been implemented to model biochemical processes from integrated databases directly. Together with the application of graphical methods, networks are computed by the system. Each step of the workflow can be executed using a server and a graphical interface implemented with Java.