BioSim--a new qualitative simulation environment for molecular biology

Traditionally, biochemical systems are modelled using kinetics and differential equations in a quantitative simulator. However, for many biological processes detailed quantitative information is not available, only qualitative or fuzzy statements about the nature of interactions. In a previous paper we have shown the applicability of qualitative reasoning methods for molecular biological regulatory processes. Now, we present a newly developed simulation environment, BioSim, that is written in Prolog using constraint logic programming techniques. The simulator combines the basic ideas of two main approaches to qualitative reasoning and integrates the contents of a molecular biology knowledge base, EcoCyc. We show that qualitative reasoning can be combined with automatic transformation of contents of genomic databases into simulation models to give an interactive modelling system that reasons about the relations and interactions of biological entities. This is demonstrated on the glycolytic pathway.