Creating metabolic and regulatory network models using fuzzy cognitive maps

This paper describes a model of metabolic networks that uses fuzzy cognitive maps. Nodes of the map represent specific biochemicals such as proteins, RNA, and small molecules, or stimuli, such as light, heat, or nutrients. Edges of the map capture regulatory and metabolic relationships found in biological systems. These relationships are established by a domain expert, the biological literature, and extracted from RNA microarray data. This work is part of the development of a software tool, FCModeler, which models and visualizes metabolic networks. A model of the metabolism of the plant hormone gibberellin in Arabidopsis is used to show the capabilities of the fuzzy model.