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Online Journal of Bioinformatics©
Volume 20(2):144-165, 2019.
A Fuzzy petri net model for Lac Operon regulation in E. coli.
RI Hamed1, SI Ahson2 and R Parveen1
1Department of Computer Science, Jamie M.I., New Delhi-110025, 2Bioinformatics and Computational Biology, Patna University - 800005, India.
Hamed RI, Ahson SI, Parveen R., A Fuzzy petri net model for Lac Operon regulation in E coli, Onl J Bioinform., 20(2):144-165, 2019. Current approaches in modeling dynamic biological systems often lack comprehension especially for users without a mathematical background. We propose using a graphical representation of Petri nets (PN) with fuzzy logic systems to construct a genetic regulatory network of the lac operon. The fuzzy Petri Net (FRPN) avoids use of differential equation models that require kinetic parameter values and Boolean Formalism which sets regulation as on or off. The lac operon is a model for understanding gene expression and its regulation. We validated the FRPN model by automatically checking regulation of lactose in E coli. The proposed algorithm adopts a matrix equation similar to ordinary PNs but because FRPN is a graphical tool, we can describe, visualize and construct fuzzy reasoning for genetic regulation of the lac operon in E. coli (catabolite repression and induction) and validate the FRPN model. Our results suggest that FRPN was more suitable than Boolean logic because FRPN infers gene expression of appropriate enzymes in response to changes in concentrations of activators and/or repressors. The regulatory genes are considered either on or off in Boolean logic, therefore, the adaptation of regulatory structure to changes in substrate concentration in the medium cannot be reflected as it actually happens.
Keywords: Fuzzy reasoning Petri net; Lac operon; fuzzy system; Modeling and simulation.