Modeling and Simulating Biological Processes as Logical Enterprises1

Understanding and improving the biological machines responsible for very complex phenomena would be greatly speeded by a computational tool which simulates the outcome of laboratory manipulations. These processes are extremely diicult to think about because they involve literally hundreds of interacting parts. For modeling to be realistic enough to be useful, the model must include detailed information on both the structure of the molecular parts and their functions in biochemical reactions. Representing and using this information in databases to simulate even simple processes is the rst step to achieving larger, more comprehensive models. We are studying how the molecules, reactions and constraints on their interactions can be represented in the computer. A key requirement is that facts, ideas and questions all be represented in the same language and using the same fundamental approach, while still permitting scientists to describe and manipulate ideas in the language they nd most natural. We have achieved this goal by using declarative database technology and by expressing molecules, reactions and constraints in a formal grammar. The grammar allows one to pick the most congenial way to describe and model the biochemistry in a detailed and comprehensive manner.