Opentrons OT-2/Flex SOP


This document describes onboarding the Opentrons OT-2 and Flex instruments into Genie’s LabOS.


  • Functional, calibrated, network connected OT-2 or Flex. Must be possible to run a simple protocol from the Opentrons App.
  • Genie LabOS Account
  • Network connected Windows PC


Instrument Connector

You only need to install a single Instrument Connector per network, even if you are managing multiple instruments.
  • From the Windows PC, log in to Genie’s LabOS.
  • Click on your name in the top right corner of the screen and select Connectors
  • Click on the + icon to add a new Connector
    • Download the Windows Connector
    • Generate a Registration Code (be sure to copy and save it) and click Claim
  • Install the Windows Connector on the PC, entering the registration code when prompted
  • A few seconds after the installation finishes, refresh the Connector screen. The installed connector will be listed in the Connectors table. By default its name will be set to the registration code. You can click on the name to change it to something more user friendly.

OT-2/Flex Modules

Plug all modules, such as the OT-2 or Flex Magnetic Module, into the Desktop PC instead of plugging them into the OT-2/Flex. The Instrument Connector will communicate directly with the accessories, bypassing the OT-2/Flex.


Perform the steps below from LabOS.

Add Instrument

  • Navigate to the Virtual Lab page
  • Click on the + icon to add a new Instrument
    • Select the previously installed Instrument Connector and click Continue
    • Enter a user friendly name for the instrument, such as “My OT-2“ or “My Flex”
    • Set the Type to Liquid Handler
    • Set the Model to Opentrons OT-2 or Flex
    • Set the URL to http://{IP}:31950 where {IP} is the OT-2’s IP address
    • Click on Add Instrument

Configure Heads

  • Navigate to the Virtual Lab page
  • Open the OT-2 or Flex Instrument
  • Select the Configuration tab
  • Change the Head configuration(s) to match the pipettes on the OT-2 or Flex
  • Click Save
  • Select the Actions tab
  • Run the Home command to verify the LabOS is able to communicate with the instrument

Configure Modules

  • Navigate to the Virtual Lab page
  • Onboard Opentrons Modules into LabOS
    • For example, add a new instrument of type Magnet and model Opentrons Magnetic Module
  • Open the OT-2 or Flex Instrument
  • Select the Deck tab
  • Select the onboarded instrument for the deck slot (e.g. B3) where the instrument is located
  • Click Save


Use the Opentrons Native UI to replace pipettes and thereafter re-calibrate the instrument and power cycle it. Once calibrated, login to LabOS, select the OT-2 or Flex instrument, click on the Configuration tab, modify the Heads and click Save.

Changing the pipettes on the OT-2 or Flex (e.g. P20 to P1000) will invalidate the previously generated settings, since the settings were generated for different pipettes. Simply re-generate the settings to bind your protocol to the new OT-2 or Flex configuration.

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