Logo Logo
  • Home
  • Publications
  • Meet Our Team
  • Contact

More Info

  • Email [email protected]
  • Phone Office: (434) 924-8195 Computational lab: (434) 982-6267 Wet lab: (434) 924-8640
  • Location 415 Lane Road, Room 2041 Charlottesville, VA 22903

Related Links

  • PubMed
  • Undergraduate Opportunities
  • Graduate Opportunities
  • UVA Engineering

Connect With Us

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

  • Home
  • Blog Details
October 17 2013
  • Published Works

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.

Biggs-and-Papin-Novel-Multiscale-Modeling-Tool-Applied-to-Pseudomonas-aeruginosa-PLoS-ONE-2013Download
Previous Post Next Post

Recent Posts

  • Fecal sphingolipids predict parenteral nutrition associated cholestasis in the neonatal intensive care unit
  • Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models
  • Comparative analyses of parasites with a comprehensive database of geno-scale metabolic models
  • Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions
  • Computational approaches to understanding Clostridioides difficile metabolism and virulence
Logo

Computational Systems Biology Laboratory; The research group of Dr. Jason Papin in the Department of Biomedical Engineering at the University of Virginia. Dedicated to discovering revolutionary advancements.

Related Links

  • PubMed
  • Undergraduate Opportunities
  • Graduate Opportunities
  • UVA Engineering

Contact Info

The research group of Dr. Jason Papin in the Department of Biomedical Engineering at the University of Virginia

  • Email: [email protected]
  • Phone (434) 924-8195

© Copyright 2021 Papin Lab. Designed by Sabres Media LLC

  • Home
  • Publications
  • Meet Our Team
  • Contact