title: Modular design of synthetic gene circuits with biological parts and pools.
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.
authors.affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland, marchisio@hit.edu.cn.
authors.forename: Mario Andrea
authors.initials: MA
authors.lastname: Marchisio
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005813:Genes, Synthetic; D012333:RNA, Messenger / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger