Linguistic modelling of gene regulation: Translation from the language of experiments to the language of modelling

Abstract

Understanding of gene regulation mechanisms is one of the main goals in systems biology of development. In this communication we introduce a biologically oriented approach to model gene regulation by explicitly involving all the available empirical data. The method is derived by further developing the family of diverse approaches known as fuzzy linguistic modelling (FLM) of gene action. FLM makes it possible to formulate in simple rules the known details of diverse and hierarchical gene-regulatory organization, i.e., to reword experimental conclusions formulated in the language of experimentalists into the language of model designers. Keywords: Fuzzy linguistic modelling, Language of experimentalists, Modelling language, Gene regulation, Transcriptional synergy, Binding cooperativity