Advanced Control

As its name implies, the Python Protocol API is primarily designed for creating protocols that you upload via the Opentrons App and execute on the robot as a unit. But sometimes it’s more convenient to control the robot outside of the app. For example, you might want to have variables in your code that change based on user input or the contents of a CSV file. Or you might want to only execute part of your protocol at a time, especially when developing or debugging a new protocol.

The Python API offers two ways of issuing commands to the robot outside of the app: through Jupyter Notebook or on the command line with opentrons_execute.

Jupyter Notebook

The Flex and OT-2 run Jupyter Notebook servers on port 48888, which you can connect to with your web browser. This is a convenient environment for writing and debugging protocols, since you can define different parts of your protocol in different notebook cells and run a single cell at a time.

Access your robot’s Jupyter Notebook by either:

  • Going to the Advanced tab of Robot Settings and clicking Launch Jupyter Notebook.

  • Going directly to http://<robot-ip>:48888 in your web browser (if you know your robot’s IP address).

Once you’ve launched Jupyter Notebook, you can create a notebook file or edit an existing one. These notebook files are stored on the the robot. If you want to save code from a notebook to your computer, go to File > Download As in the notebook interface.

Protocol Structure

Jupyter Notebook is structured around cells: discrete chunks of code that can be run individually. This is nearly the opposite of Opentrons protocols, which bundle all commands into a single run function. Therefore, to take full advantage of Jupyter Notebook, you have to restructure your protocol.

Rather than writing a run function and embedding commands within it, start your notebook by importing opentrons.execute and calling opentrons.execute.get_protocol_api(). This function also replaces the metadata block of a standalone protocol by taking the minimum API version as its argument. Then you can call ProtocolContext methods in subsequent lines or cells:

import opentrons.execute
protocol = opentrons.execute.get_protocol_api("2.16")
protocol.home()

The first command you execute should always be home(). If you try to execute other commands first, you will get a MustHomeError. (When running protocols through the Opentrons App, the robot homes automatically.)

You should use the same ProtocolContext throughout your notebook, unless you need to start over from the beginning of your protocol logic. In that case, call get_protocol_api() again to get a new ProtocolContext.

Running a Previously Written Protocol

You can also use Jupyter to run a protocol that you have already written. To do so, first copy the entire text of the protocol into a cell and run that cell:

import opentrons.execute
from opentrons import protocol_api
def run(protocol: protocol_api.ProtocolContext):
    # the contents of your previously written protocol go here

Since a typical protocol only defines the run function but doesn’t call it, this won’t immediately cause the robot to move. To begin the run, instantiate a ProtocolContext and pass it to the run function you just defined:

protocol = opentrons.execute.get_protocol_api("2.16")
run(protocol)  # your protocol will now run

Setting Labware Offsets

All positions relative to labware are adjusted automatically based on labware offset data. When you’re running your code in Jupyter Notebook or with opentrons_execute, you need to set your own offsets because you can’t perform run setup and Labware Position Check in the Opentrons App or on the Flex touchscreen. For these applications, do the following to calculate and apply labware offsets:

  1. Create a “dummy” protocol that loads your labware and has each used pipette pick up a tip from a tip rack.

  2. Import the dummy protocol to the Opentrons App.

  3. Run Labware Position Check from the app or touchscreen.

  4. Add the offsets to your code with set_offset().

Creating the dummy protocol requires you to:

  1. Use the metadata or requirements dictionary to specify the API version. (See Versioning for details.) Use the same API version as you did in opentrons.execute.get_protocol_api().

  2. Define a run() function.

  3. Load all of your labware in their initial locations.

  4. Load your smallest capacity pipette and specify its tip_racks.

  5. Call pick_up_tip(). Labware Position Check can’t run if you don’t pick up a tip.

For example, the following dummy protocol will use a P300 Single-Channel GEN2 pipette to enable Labware Position Check for an OT-2 tip rack, NEST reservoir, and NEST flat well plate.

metadata = {"apiLevel": "2.13"}

 def run(protocol):
     tiprack = protocol.load_labware("opentrons_96_tiprack_300ul", 1)
     reservoir = protocol.load_labware("nest_12_reservoir_15ml", 2)
     plate = protocol.load_labware("nest_96_wellplate_200ul_flat", 3)
     p300 = protocol.load_instrument("p300_single_gen2", "left", tip_racks=[tiprack])
     p300.pick_up_tip()
     p300.return_tip()

After importing this protocol to the Opentrons App, run Labware Position Check to get the x, y, and z offsets for the tip rack and labware. When complete, you can click Get Labware Offset Data to view automatically generated code that uses set_offset() to apply the offsets to each piece of labware.

labware_1 = protocol.load_labware("opentrons_96_tiprack_300ul", location="1")
labware_1.set_offset(x=0.00, y=0.00, z=0.00)

labware_2 = protocol.load_labware("nest_12_reservoir_15ml", location="2")
labware_2.set_offset(x=0.10, y=0.20, z=0.30)

labware_3 = protocol.load_labware("nest_96_wellplate_200ul_flat", location="3")
labware_3.set_offset(x=0.10, y=0.20, z=0.30)

This automatically generated code uses generic names for the loaded labware. If you want to match the labware names already in your protocol, change the labware names to match your original code:

reservoir = protocol.load_labware("nest_12_reservoir_15ml", "2")
reservoir.set_offset(x=0.10, y=0.20, z=0.30)

New in version 2.12.

Once you’ve executed this code in Jupyter Notebook, all subsequent positional calculations for this reservoir in slot 2 will be adjusted 0.1 mm to the right, 0.2 mm to the back, and 0.3 mm up.

Remember, you should only add set_offset() commands to protocols run outside of the Opentrons App. And you should follow the behavior of Labware Position Check, i.e., do not reuse offset measurements unless they apply to the same labware in the same deck slot on the same robot.

Warning

Improperly reusing offset data may cause your robot to move to an unexpected position or crash against labware, which can lead to incorrect protocol execution or damage your equipment. The same applies when running protocols with set_offset() commands in the Opentrons App. When in doubt: run Labware Position Check again and update your code!

Using Custom Labware

If you have custom labware definitions you want to use with Jupyter, make a new directory called labware in Jupyter and put the definitions there. These definitions will be available when you call load_labware().

Using Modules

If your protocol uses modules, you need to take additional steps to make sure that Jupyter Notebook doesn’t send commands that conflict with the robot server. Sending commands to modules while the robot server is running will likely cause errors, and the module commands may not execute as expected.

To disable the robot server, open a Jupyter terminal session by going to New > Terminal and run systemctl stop opentrons-robot-server. Then you can run code from cells in your notebook as usual. When you are done using Jupyter Notebook, you should restart the robot server with systemctl start opentrons-robot-server.

Note

While the robot server is stopped, the robot will display as unavailable in the Opentrons App. If you need to control the robot or its attached modules through the app, you need to restart the robot server and wait for the robot to appear as available in the app.

Command Line

The robot’s command line is accessible either by going to New > Terminal in Jupyter or via SSH.

To execute a protocol from the robot’s command line, copy the protocol file to the robot with scp and then run the protocol with opentrons_execute:

opentrons_execute /data/my_protocol.py

By default, opentrons_execute will print out the same run log shown in the Opentrons App, as the protocol executes. It also prints out internal logs at the level warning or above. Both of these behaviors can be changed. Run opentrons_execute --help for more information.