Optimal Part and Module Selection for Synthetic Gene Circuit Design Automation

• Published in: ACS synthetic biology Vol. 3; no. 8; pp. 556 - 564
• Main Authors: Huynh, Linh, Tagkopoulos, Ilias
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 15.08.2014
• Subjects: Algorithms; Databases, Factual; Escherichia coli - genetics; Gene Library; Gene Regulatory Networks; Plasmids - genetics; Synthetic Biology - methods; computer-aided design; module matching; CAD tool; biodesign automation; module library; part selection
• ISSN: 2161-5063; 2161-5063
• DOI: 10.1021/sb400139h

An integral challenge in synthetic circuit design is the selection of optimal parts to populate a given circuit topology, so that the resulting circuit behavior best approximates the desired one. In some cases, it is also possible to reuse multipart constructs or modules that have been already built and experimentally characterized. Efficient part and module selection algorithms are essential to systematically search the solution space, and their significance will only increase in the following years due to the projected explosion in part libraries and circuit complexity. Here, we address this problem by introducing a structured abstraction methodology and a dynamic programming-based algorithm that guaranties optimal part selection. In addition, we provide three extensions that are based on symmetry check, information look-ahead and branch-and-bound techniques, to reduce the running time and space requirements. We have evaluated the proposed methodology with a benchmark of 11 circuits, a database of 73 parts and 304 experimentally constructed modules with encouraging results. This work represents a fundamental departure from traditional heuristic-based methods for part and module selection and is a step toward maximizing efficiency in synthetic circuit design and construction.