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BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology

Research output: Contribution to journalArticle

Original languageEnglish
Article numbere42790
Number of pages9
JournalPLoS ONE
Issue number8
DateAccepted/In press - 10 Jul 2012
DatePublished (current) - 24 Aug 2012


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 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.

    Research areas

  • synthetic biology

    Structured keywords

  • Bristol BioDesign Institute

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  • journal.pone.0042790

    Rights statement: This is the final published version of the article (version of record). It first appeared online via PLOS at Please refer to any applicable terms of use of the publisher.

    Final published version, 461 KB, PDF document

    Licence: CC BY


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