The RI performs I/O through a socket interface, simulating the interaction with a card reader implementing T=1, T=CL, or T=0 communications with the card reader.
Use apdutool to read script files and send APDUs through a socket to the RI. See apdutool Examples for details. Note that you can have the Java Card RI running on one workstation and run apdutool on another workstation.