Development of a software tool for in silico simulation of Escherichia coli using a visual programming environment.
This study describes the development of a software tool, EcoSim, to assist users in implementing quantitative in silico simulation easily. It consists of four parts: extracellular environment and constraints setting mode, table for optimal metabolic flux distribution and chart for changes of substrate concentration, dynamic flux distribution viewer and dynamic hierarchical regulatory network viewer. Representation of a hierarchical regulatory network was constructed with defined modeling symbols and weight in the central Escherichia coli metabolism. All programming procedures for EcoSim were accomplished in a visual programming environment (LabVIEW). To illustrate quantitative in silico simulation with EcoSim, this program was performed on E. coli using glucose and acetate as carbon sources. The simulation results were in agreement with the experimental data obtained from the literature. EcoSim can be used to assist biologists and engineers in predicting and interpreting dynamic behaviors of E. coli under a variety of environmental conditions.
Lee
Sung Gun
SG
Department of Chemical Engineering, College of Engineering, Pusan National University, 30 Jangjeon-dong, Geumjeong-gu, Busan 609-735, South Korea.
Kim
Cheol Min
CM
Hwang
Kyu Suk
KS
D000085:Acetates / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins; D015964:Gene Expression Regulation, Bacterial; D005947:Glucose / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
D000085:Acetates; D029968:Escherichia coli Proteins; D005947:Glucose