BSim 2.0: An Advanced Agent-Based Cell Simulator

Antoni W Matyjaszkiewicz, Gianfranco Fiore, Fabio Annunziata, Claire S Grierson, Nigel J Savery, Lucia Marucci, Mario di Bernardo

Research output: Contribution to journalArticle (Academic Journal)

8 Citations (Scopus)
260 Downloads (Pure)

Abstract

Agent-based models (ABMs) provide a number of advantages relative to traditional continuum modeling approaches, permitting incorporation of great detail and realism into simulations, allowing in silico tracking of single-cell behaviors and correlation of these with emergent effects at the macroscopic level. In this study we present BSim 2.0, a radically new version of BSim, a computational ABM framework for modeling dynamics of bacteria in typical experimental environments including microfluidic chemostats. This is facilitated through the implementation of new methods including cells with capsular geometry that are able to physically and chemically interact with one another, a realistic model of cellular growth, a delay differential equation solver, and realistic environmental geometries.

Original languageEnglish
Pages (from-to)1969-1972
Number of pages4
JournalACS Synthetic Biology
Volume6
Issue number10
Early online date6 Jun 2017
DOIs
Publication statusPublished - 20 Oct 2017

Structured keywords

  • BrisSynBio
  • Bristol BioDesign Institute

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