A Process-Oriented Model of Bacterial Gene Regulation

Reference: Karp, P. D. A Process-Oriented Model of Bacterial Gene Regulation. June 1988, 1988.

Abstract: We descibe a working program which embodies a theory of bacterial gene regulation. Its components include a knowledge base of the objects in this domain, a knowledge base of processes which describe interactions between these objects, and procedures for applying processes to objects to predict the behavior of the biological system. The contributions of this paper include methods for representing and instantiating objects with complex component part structures, and a language for defining processes which utilizes inheritance to construct process descriptions from general templates. In addition, we propose and justify an approach to managing the existence and properties of objects during a simulation. Several methods for increasing the efficiency of this approach are discussed including a novel use of the ATMS: it can reduce the space required to represent similar objects within a simulation by sharing their common features.

Notes: 14 pages.

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