Theoretical Computer Science - Special issue: Computational systems biology
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Modularity - the notion that individual components can be described as self-contained units and composed in different combinations - is a concept integral to synthetic biology. In vitro, it is embodied by the notion of BioBrickTMparts: standardised DNA sequences of defined structure, function, and common interfaces that can be composed and integrated into living cells. A similar modularity in the modelling of such systems, however, has not been explored until much more recently. In the course of the 2010 International Genetically Engineered Machine (iGEM) competition, the University of Edinburgh team adopted an iterative rule-based approach to developing a BioBrick model of light-based communication in Escherichia coli. The system was modelled in the Kappa stochastic rule-based biological modelling language, allowing for the modular development and analysis of a complicated biological system. It also utilised newly developed spatial extensions to aid in the depiction of intercellular communication via light emitting and light sensing pathways, demonstrating the extensibility of the language as a whole. This paper provides a case study of modelling synthetic biology projects using the rule-based techniques outlined above, documenting the benefits of this modular iterative approach.