Heidtke K R, Schulze-Kremer S
Max-Planck-Institute for Molecular Genetics, Department Lehrach, Berlin, Germany.
Proc Int Conf Intell Syst Mol Biol. 1998;6:85-94.
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.
传统上，生化系统是在定量模拟器中使用动力学和微分方程进行建模的。然而，对于许多生物过程来说，详细的定量信息并不存在，只有关于相互作用性质的定性或模糊描述。在之前的一篇论文中，我们已经展示了定性推理方法在分子生物学调控过程中的适用性。现在，我们展示一个新开发的模拟环境BioSim，它是使用约束逻辑编程技术用Prolog编写的。该模拟器结合了定性推理的两种主要方法的基本思想，并整合了分子生物学知识库EcoCyc的内容。我们表明，定性推理可以与将基因组数据库内容自动转化为模拟模型相结合，从而得到一个能够对生物实体的关系和相互作用进行推理的交互式建模系统。这在糖酵解途径上得到了证明。
