Huynh Linh, Tsoukalas Athanasios, Köppe Matthias, Tagkopoulos Ilias
Department of Computer Science and UC Davis Genome Center, University of California-Davis, CA 95616, United States.
ACS Synth Biol. 2013 May 17;2(5):263-73. doi: 10.1021/sb300095m. Epub 2013 Mar 11.
The development of a scalable framework for biodesign automation is a formidable challenge given the expected increase in part availability and the ever-growing complexity of synthetic circuits. To allow for (a) the use of previously constructed and characterized circuits or modules and (b) the implementation of designs that can scale up to hundreds of nodes, we here propose a divide-and-conquer Synthetic Biology Reusable Optimization Methodology (SBROME). An abstract user-defined circuit is first transformed and matched against a module database that incorporates circuits that have previously been experimentally characterized. Then the resulting circuit is decomposed to subcircuits that are populated with the set of parts that best approximate the desired function. Finally, all subcircuits are subsequently characterized and deposited back to the module database for future reuse. We successfully applied SBROME toward two alternative designs of a modular 3-input multiplexer that utilize pre-existing logic gates and characterized biological parts.
鉴于合成电路中预期的部件可用性增加以及日益增长的复杂性，开发用于生物设计自动化的可扩展框架是一项艰巨的挑战。为了实现（a）使用先前构建和表征的电路或模块，以及（b）实现可扩展到数百个节点的设计，我们在此提出一种分治式合成生物学可重复使用优化方法（SBROME）。首先将抽象的用户定义电路进行转换，并与包含先前已通过实验表征的电路的模块数据库进行匹配。然后将所得电路分解为子电路，并用最接近所需功能的部件集填充这些子电路。最后，对所有子电路进行表征，并将其存回模块数据库以供将来重用。我们成功地将SBROME应用于模块化三输入多路复用器的两种替代设计，该设计利用了预先存在的逻辑门和已表征的生物部件。
