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

Synthetic biology applications are currently based on the programming of bacteria with tailor-made circuits designed ad hoc by 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 for Get signal, Antidote, Die when a killer gene is expressed, emits Yellow 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.