Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

被引：56

作者：

Biggs, Matthew B. ^{[1
]}

Papin, Jason A. ^{[1
]}

机构：

[1] Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22903 USA

来源：

PLOS ONE | 2013年 / 8卷 / 10期

基金：

美国国家卫生研究院;

关键词：

METABOLIC NETWORK ANALYSIS; FLUX BALANCE ANALYSIS; ADAPTATION; GROWTH;

D O I：

10.1371/journal.pone.0078011

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Multiscale modeling is used to represent biological systems with increasing frequency and success. Multiscale models are often hybrids of different modeling frameworks and programming languages. We present the MATLAB-NetLogo extension (MatNet) as a novel tool for multiscale modeling. We demonstrate the utility of the tool with a multiscale model of Pseudomonas aeruginosa biofilm formation that incorporates both an agent-based model (ABM) and constraint-based metabolic modeling. The hybrid model correctly recapitulates oxygen-limited biofilm metabolic activity and predicts increased growth rate via anaerobic respiration with the addition of nitrate to the growth media. In addition, a genome-wide survey of metabolic mutants and biofilm formation exemplifies the powerful analyses that are enabled by this computational modeling tool.

引用

页数：8

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