Utilizing Signal Temporal Logic to Characterize and Compose Modules in Synthetic Biology

Madsen Curtis, Vaidyanathan Prashant, Vasile Cristian Ioan, Ivison Rachael, Wang Junmin, Belta Calin, and Densmore Douglas. Utilizing Signal Temporal Logic to Characterize and Compose Modules in Synthetic Biology. In International Workshop on Biodesign Automation (IWBDA), pages 25–26, Newcastle University, Newcastle upon Tyne, UK, August 2016. link.

Published date: 
Wednesday, August 17, 2016
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Abstract

Designing systems in synthetic biology typically involves composing pieces of DNA to achieve a desired behavior. In order to accomplish this goal, methods for specifying the function realized by genetic modules are necessary. Additionally, it is often difficult to efficiently explore the design space of genetic circuits while taking into account various biological constraints. In this work, we propose a methodology for automatically characterizing genetic constructs using signal temporal logic (STL) specifications. These specifications allow for composition using an extension to STL that adds the notion of input, output, and internal signals. Furthermore, we have devised a procedure that employs tree-based searching and pruning techniques to explore the design space of a genetic circuit given a library of modules and a desired specification.