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Research Article

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

  • Thomas E. Gorochowski mail,

    thomas.gorochowski@bristol.ac.uk

    Affiliation: Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom

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  • Antoni Matyjaszkiewicz,

    Affiliation: Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom

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  • Thomas Todd,

    Affiliation: Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom

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  • Neeraj Oak,

    Affiliation: Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom

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  • Kira Kowalska,

    Affiliation: Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom

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  • Stephen Reid,

    Affiliation: Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom

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  • Krasimira T. Tsaneva-Atanasova,

    Affiliation: Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom

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  • Nigel J. Savery equal contributor,

    equal contributor Contributed equally to this work with: Nigel J. Savery, Claire S. Grierson, Mario di Bernardo

    Affiliation: School of Biochemistry, Medical Sciences, University Walk, Bristol, United Kingdom

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  • Claire S. Grierson equal contributor,

    equal contributor Contributed equally to this work with: Nigel J. Savery, Claire S. Grierson, Mario di Bernardo

    Affiliation: School of Biological Sciences, University of Bristol, Bristol, United Kingdom

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  • Mario di Bernardo equal contributor

    equal contributor Contributed equally to this work with: Nigel J. Savery, Claire S. Grierson, Mario di Bernardo

    Affiliations: Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom, Department of Systems and Computer Engineering, University of Naples Federico II, Napoli, Italy

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  • Published: August 24, 2012
  • DOI: 10.1371/journal.pone.0042790
  • Published in PLOS ONE

About the Authors

Thomas E. Gorochowski, Antoni Matyjaszkiewicz, Thomas Todd, Neeraj Oak, Stephen Reid
Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
Kira Kowalska, Krasimira T. Tsaneva-Atanasova, Mario di Bernardo
Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
Nigel J. Savery
School of Biochemistry, Medical Sciences, University Walk, Bristol, United Kingdom
Claire S. Grierson
School of Biological Sciences, University of Bristol, Bristol, United Kingdom
Mario di Bernardo
Department of Systems and Computer Engineering, University of Naples Federico II, Napoli, Italy

Corresponding Author

Email: thomas.gorochowski@bristol.ac.uk

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: TEG AM KTT-A NJS CSG MB. Performed the experiments: TEG AM. Analyzed the data: TEG AM KTT-A NJS CSG MB. Contributed reagents/materials/analysis tools: TEG AM SR TT NO KK. Wrote the paper: TEG AM TT KTT-A NJS CSG MB.