Abstract
Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components—Standard Biological Parts and Pools of molecules—on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.
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Acknowledgment
This work was partially supported by the EU FP7 project ST-FLOW (contract 289326).
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Marchisio, M.A. (2015). Modular Design of Synthetic Gene Circuits with Biological Parts and Pools. In: Marchisio, M. (eds) Computational Methods in Synthetic Biology. Methods in Molecular Biology, vol 1244. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1878-2_7
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DOI: https://doi.org/10.1007/978-1-4939-1878-2_7
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