A Qualitative Biochemistry and Its Application to the Regulation of the Tryptophan Operon

This article is concerned with the general question of how to represent biological knowledge in computers such that it may be used in multiple problem solving tasks. In particular, I present a model of a bacterial gene regulation system that is used by a program that simulates gene regulation experiments, and by a second program that formulates hypotheses to account for errors in predicted experiment outcomes. This article focuses on the issues of representation and simulation; for more information on the hypothesis formation task see (Karp, 1989; Karp, 1990). The bacterial gene regulation system of interest is the tryptophan (trp) operon of E. coli (Yanofsky, 1981). The genes that it contains code for enzymes that synthesize the amino acid tryptophan.