title: BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.
abstract: Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.
authors.affiliation: Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom. thomas.gorochowski@bristol.ac.uk
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Gorochowski
authors.forename: Antoni
authors.initials: A
authors.lastname: Matyjaszkiewicz
authors.forename: Thomas
authors.initials: T
authors.lastname: Todd
authors.forename: Neeraj
authors.initials: N
authors.lastname: Oak
authors.forename: Kira
authors.initials: K
authors.lastname: Kowalska
authors.forename: Stephen
authors.initials: S
authors.lastname: Reid
authors.forename: Krasimira T
authors.initials: KT
authors.lastname: Tsaneva-Atanasova
authors.forename: Nigel J
authors.initials: NJ
authors.lastname: Savery
authors.forename: Claire S
authors.initials: CS
authors.lastname: Grierson
authors.forename: Mario
authors.initials: M
authors.lastname: di Bernardo
mesh_terms: D019295:Computational Biology / Q000379:methods*; D009876:Operon; D058615:Synthetic Biology / Q000379:methods*; D049490:Systems Biology / Q000379:methods*