Abstract: Systems, methods and algorithms for automatically performing optimization of an electroporation system. A system according to the present invention typically includes a cuvette holding assembly configured to hold a plurality of electroporation cuvettes, wherein each cuvette includes a first and second electrode, and a shocking chamber configured to hold the cuvette holding assembly, the chamber having a commutator assembly configured to provide an electrical contact to the first electrode of each of the plurality of cuvettes in turn. The system also typically includes a control system communicably coupled to the shocking chamber, wherein the control system controls the commutator to automatically contact the first electrode of each cuvette in an order and to provide a potential across the cuvette electrodes when contact is made.