BioSim: A New Qualitative Simulation Environment for Molecular Biology

Traditionally, biochemical systems are modelled usingkinetics anddifferential equationsin a quantitative simulator. However,for manybiological processes detailed quantitative informationis not available, only qualitative or fuzzystatements about the nature of interactions. In a previous paper wehave shownthe applicability of qualitative reasoning methodsfor molecularbiological regulatory processes. Now,wepresent a newlydeveloped simulation environment, BioSim,that is written in Prolog using constraint logic programmingtechniques. Thesimulator combinesthe basic ideas of two mainapproaches to qualitative reasoning and integrates the contents of a molecular biology knowledge base, EcoCyc. Weshow that qualitative reasoning can be combinedwith automatic transformation of contents of genomic databases into simulation modelsto give an interactive modellingsystemthat reasons about the relations andinteractions of biologicalentities. This is demonstratedon the glycolytic pathway.

• Type: Conference
• Year: 1998
• Where: ISMB
• Authors: Karsten R. Heidtke, Steffen Schulze-Kremer
• Keywords: Computational Biology, ISMB 1998, Molecularbiological Regulatory Processes, Qualitative Reasoning, Quantitative Simulator