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E. Bartocci, L. Bortolussi, L. Nenzi:
"A temporal logic approach to modular design of synthetic biological circuits";
Vortrag: CMSB 2013: the 11th International Conference on Computational Methods in Systems Biology, Klosterneuburg, Austria; 23.09.2013 - 25.09.2013; in: "Proc. of CMSB 2013: the 11th International Conference on Computational Methods in Systems Biology", LNCS/Springer, vol. 8130 (2013), ISBN: 978-3-642-40707-9; S. 164 - 178.

We present a new approach for the design of a synthetic biological circuit whose behaviour is specified in terms of signal temporal logic (STL) formulae. We first show how to characterise with STL formulae the input/output behaviour of biological modules miming the classical logical gates (AND, NOT, OR). Hence, we provide the regions of the parameter space for which these specifications are satisfied. Given a STL specification of the target circuit to be designed and the networks of its constituent components, we propose a methodology to constrain the behaviour of each module, then identifying the subset of the parameter space in which those constraints are satisfied, providing also a measure of the robustness for the target circuit design. This approach, which leverages recent results on the quantitative semantics of Signal Temporal Logic, is illustrated by synthesising a biological implementation of an half-adder.

Synthetic Biology, Computational Systems Biology

http://dx.doi.org/10.1007/978-3-642-40708-6_13