title: SBROME: a scalable optimization and module matching framework for automated biosystems design.
abstract: 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.
authors: Department of Computer Science and UC Davis Genome Center, University of California-Davis, CA 95616, United States.
authors: Linh
authors: L
authors: Huynh
authors: Athanasios
authors: A
authors: Tsoukalas
authors: Matthias
authors: M
authors: Köppe
authors: Ilias
authors: I
authors: Tagkopoulos
mesh_terms: D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D008954:Models, Biological; D011381:Programming Languages; D012984:Software; D058615:Synthetic Biology / Q000379:methods*; D018511:Systems Integration