Parts & Pools: a framework for modular design of synthetic gene circuits

• Main Author: Mario Andrea Marchisio
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2014-10-01
• Series: Frontiers in Bioengineering and Biotechnology
• Subjects: Synthetic Biology; modeling; parts; gene circuits; Pools; Boolean gates
• Online Access: http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00042/full

Published in 2008, Parts & Pools represents one of the □first attempts to conceptualizethe modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNAsegments) and Pools of molecules referred to as common signal carriers (e.g. RNA polymerasesand ribosomes). The original framework for modeling bacterial components and designingprokaryotic circuits evolved over the last years and brought, fi□rst, to the development of analgorithm for the automatic design of Boolean gene circuits. This is a remarkable achievementsince gene digital circuits have a broad range of applications that goes from biosensors forhealth and environment care to computational devices. More recently, Parts & Pools wasenabled to give a proper formal description of eukaryotic biological circuit components. Thiswas possible by employing a rule-based modeling approach, a technique that permits a faithfulcalculation of all the species and reactions involved in complex systems such as eukaryoticcells and compartments. In this way, Parts & Pools is currently suitable for the visual andmodular design of synthetic gene circuits in yeast and mammalian cells too.