Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

Authored by Matthew B. Biggs, Jason A. Papin

Date Published: 2013-10-17

DOI: 10.1371/journal.pone.0078011

Sponsors: Commonwealth Fellowship in Engineering from the University of Virginia United States National Institutes of Health (NIH)

Platforms: NetLogo MATLAB

Model Documentation: Other Narrative

Model Code URLs: http://bme.virginia.edu/csbl/downloads-matnet.php

Abstract

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.

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