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PLoS One. 2013 Oct 17;8(10):e78011. doi: 10.1371/journal.pone.0078011. eCollection 2013.

Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation.

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Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America.


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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