PCR can be carried out by hand or by machine.

process is what happens to matter, energy, and information

a step is a mechanism ("the technical aspects of doing something")

a step can be a machine, OEM part, or parameters to a process
(different mechanisms that satisfy the same parameters to a process
might be interchangeable and could be evaluated)

sequence is a set of steps that are performed by (or contained within)
a machine (or multiple machines) in order to carry out a process

an assembly of a sequence tells you how to put the mechanisms together

the intent of PCR is to amplify a section of DNA; this is the 
functionality of the PCR process

a different sequence of steps are performed by a thermocycler versus a 
human with water baths, but they result in the same process, as long as 
the process parameters are the same (temperatures, primers, dwell time)

the parameters to the process are read by some computer aided 
manufacturing software (CAM) and transformed into a protocol, which, 
depending on the target (human assisted or pure automation) are written 
as a sequence of steps in either natural language (english) or some 
specific machine control language.