A temperature control device and method are provided for an analytical system for performing laboratory protocols. The device includes a well within a housing configured to receive a biological specimen according to a predetermined sample process. The specimen is suspended by a holding device in the well. A thermal element is provided in heat exchange communication with fluid in the well. A temperature sensor is located in the well at a location to be covered and uncovered by rocking motion of fluid in the well. A controller, in communication with the thermal element, the temperature sensor, and an agitation system, is operative to control the thermal element in correlation with temperature data, for example, peak temperature data, from the temperature sensor.