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Agent-based modelling in synthetic biology

Research output: Contribution to journalReview article

Original languageEnglish
Pages (from-to)325-336
Number of pages12
JournalEssays in Biochemistry
Issue number4
DateAccepted/In press - 8 Sep 2016
DatePublished (current) - 30 Nov 2016


Biological systems exhibit complex behaviors that merge at many different levels of organization; from the regulation of gene expression within single cells, to the use of quorum sensing to coordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviors. However, in many cases it is not understood how individual cells should be programmed to ensure the emergence of a required collective behavior. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. Here, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions.

    Structured keywords

  • Bristol BioDesign Institute
  • BrisSynBio

    Research areas

  • agent-based modelling, cell populations, synthetic biology, collective behaviors

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  • Full-text PDF (final published version)

    Rights statement: This is the final published version of the article (version of record). It first appeared online via Portland Press at DOI: 10.1042/EBC20160037 . Please refer to any applicable terms of use of the publisher.

    Final published version, 824 KB, PDF document

    Licence: CC BY


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