Abstract: An automated system is provided for carrying out nucleic acid based assays on a plurality of liquid samples with little or no intervention by a human operator. The system includes at least one reaction station adapted to hold and apply controlled amounts of heat to a plurality of reaction devices in which the liquid samples are receivable. Each of the reaction devices includes a sample area for receiving a liquid sample, a reaction area into which the liquid sample is movable to carry out a nucleic acid decontamination or amplification reaction on the sample, and a pneumatic port for allowing air to be aspirated from and dispensed into the reaction device to move the sample between the sample area and the reaction area.