BSim 2.0: An Advanced Agent-Based Cell Simulator

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

Date Published: 2017

DOI: 10.1021/acssynbio.7b00121

Sponsors: No sponsors listed

Platforms: Java

Model Documentation: Other Narrative

Model Code URLs: https://github.com/bsim-bristol/bsim

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 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.

Tags

agent-based simulation cell populations synthetic biology Microbial communities Gene regulatory network Microbial consortia Consortium