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OJBTM
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.
ABSTRACT
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.
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