This disclosure relates to computer systems that isolate data processing modules and methods of operating the same. In one embodiment of a method, a computer system receives a first data processing request for a first data file. The computer system may determine that a first data type of the first data file is supported by an encapsulated data processing module and determine a first communication protocol from a set of communication protocols that can be used to receive the first data file. The computer system can then receive the first data file from the first storage location in accordance with the first communication protocol and the encapsulated data processing module may be executed to convert the first data file in the first data format into second data in a second data format.