The Opentrons app allows the user to execute protocols untethered to the USB by using the shift key and run button within the platform. Unfortunately, Jupyter without the following code you would be unable to disconnect the robot during a protocol.
Post the following code within your Jupyter cells, ( [ln i] represents the cell).
!pip install "git+https://github.com/OpenTrons/opentrons.git@develop#egg=opentrons&subdirectory=api"
from opentrons import robot
# PART ONE
from opentrons.drivers.smoothie_drivers.v2_0_0 import player
p = player.SmoothiePlayer_2_0_0() # the Player will save the GCode commmands
robot.set_connection('simulate_switches') # set the Robot to simulate your commands
robot._driver.record_start(p) # start recording to the Player
# PART TWO
protocol commands go here
from opentrons import containers, instruments
robot._driver.record_stop() # stop recording
robot.set_connection('live') # set the connection to be the physical OT-One
robot._driver.play(p) # save the GCode commands to the a file on the OT-One and start