GADY algorithm: Towards an evolutionary protocol for bottom-up design of synthetic bacteria

Abstract

Synthetic biology applications are currently based on the programming of bacteria with tailor-made circuits designedad hocby applying a top-down strategy. We introduce a novel algorithm oriented to design synthetic bacteria according to a bottom-up approach, i.e. via an ‘evolutionary programming’ algorithm. The proposed algorithm has been referred to as GADY: an acronym forGet signal,Antidote,Die when a killer gene is expressed, emitsYellow fluorescence. We include in this technical note a script of the algorithm in Gro cellular programming language, programming a colony of synthetic bacteria and illustrating its usefulness in a case of bioremediation or elimination of a strain of pathogenic bacteria.