期刊
ACS SYNTHETIC BIOLOGY
卷 2, 期 5, 页码 263-273出版社
AMER CHEMICAL SOC
DOI: 10.1021/sb300095m
关键词
biodesign automation; CAD tool; computer-aided design; modular design; module matching; part selection; multiplexer
资金
- NSF [0941360, 1146926]
- Direct For Computer & Info Scie & Enginr [1146926, 941360] Funding Source: National Science Foundation
- Division of Computing and Communication Foundations [1146926] Funding Source: National Science Foundation
- Division of Computing and Communication Foundations
- Direct For Computer & Info Scie & Enginr [1254205] Funding Source: National Science Foundation
- Office of Advanced Cyberinfrastructure (OAC) [941360] Funding Source: National Science Foundation
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.
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