Modular composition of synthetic biology designs using rule-based models

As the complexity of engineered biological systems increases, computational approaches become ever more important to identify biologically feasible solutions. Computational modelling and simulation is crucial to design and verify genetic circuits in an efficient manner. The availability of modular and reusable models is desirable to automate this process. Here, we provide a modelling approach to automate the design of genetic circuits using rule-based models, extending previously defined Standard Virtual Parts and Kappa BioBrick Framework. We have defined abstract templates that can be instantiated, and are annotated, in order to automate composition for rule-based models and produce executable composite rule-based models.