Converting OT-2 Protocols

There are hundreds of OT-2 protocols in the Protocol Library, and you may have created your own OT-2 protocols for your lab. Opentrons Flex can perform all the basic actions that the OT-2 can, but OT-2 protocols aren't directly compatible with Flex. However, with a little effort, you can adapt an OT-2 protocol so it will run on Flex. This lets you have parity across different Opentrons robots in your lab, or you can extend older protocols to take advantage of new features only offered on Flex.

Follow the steps below. Start by making sure you're working with a Python protocol. Then, you can convert your protocol using OpentronsAI or make the changes yourself.

When you're finished, import your new protocol into the Opentrons App. Check the run preview to see that it performs the same steps as your original OT-2 protocol.

Converting to Python¶

To begin, you'll need to make sure your OT-2 protocol is a Python protocol. Older protocols created in Protocol Designer may be JSON files.

Currently, Protocol Designer can't convert an OT-2 protocol to a Flex protocol. You have to choose which robot the protocol will run on when you create it. Instead, use Protocol Designer to convert your JSON file to a Python file.

Launch Protocol Designer and import your OT-2 protocol. Protocol Designer will update your file to the latest version. Here, you can make small changes to your protocol steps, but you won't be able to change the robot type. When you're ready, export your updated protocol from Protocol Designer as a Python file.

Updating with OpentronsAI¶

OpentronsAI makes it easy to convert your OT-2 Python protocol to run on Flex.

Launch OpentronsAI and select Update an existing protocol on the home page. Upload your Python file to OpentronsAI. From the dropdown menu, choose Adapt Python protocol from OT-2 to Flex. Be sure to include details of the changes you'd like in the text field. You can request that OpentronsAI include Flex-exclusive modules and features, like a 96-channel pipette or the Flex Stacker Module, in your updated protocol.

Submit your prompt and wait for OpentronsAI to generate your updated protocol. Before downloading your new protocol, you can ask OpentronsAI to simulate for errors.

Updating with the Python Protocol API¶

Using the Python Protocol API, you can make a few changes to an OT-2 protocol for it to run on Flex.

Metadata and requirements¶

The API requires you to declare that a protocol is designed to run on Flex. Use the robotType key in the new requirements dictionary. You should also specify an apiLevel of 2.15 or higher. You can specify apiLevel either in the metadata dictionary or the requirements dictionary.

from opentrons import protocol_api
requirements = {'robotType': 'Flex', 'apiLevel': '2.15'}

Pipettes and tip racks¶

Flex uses different types of pipettes and tip racks than OT-2, which have their own load names in the API. Choose pipettes of the same capacity or larger (or whatever you've outfitted your Flex with).

For example, you could convert an OT-2 protocol that uses a P300 Single-Channel GEN2 pipette and 300 µL tips to a Flex protocol that uses a Flex 1-Channel 1000 µL pipette and 1000 µL tips:

# Original OT-2 code
def run(protocol: protocol_api.ProtocolContext):
    tips = protocol.load_labware("opentrons_96_tiprack_300ul", 1)
    left_pipette = protocol.load_instrument(
        "p300_single_gen2", "left", tip_racks=[tips]
    )

# Modified Flex code
def run(protocol: protocol_api.ProtocolContext):
    tips = protocol.load_labware("opentrons_flex_96_tiprack_1000ul", "D1")
    left_pipette = protocol.load_instrument(
        "flex_1channel_1000", "left", tip_racks[tips]
    )

The only necessary changes are the new arguments of load_labware() and load_instrument(). Keep in mind that if you use smaller capacity tips than the original protocol, you may need to make further adjustments to avoid running out of tips, and the protocol may take longer to execute.

Deck slots¶

The API accepts OT-2 and Flex deck slot names interchangeably. It's good practice to use the coordinate deck slot format in Flex protocols (as in the example in the previous subsection), but it's not required. The correspondence between deck slot numbers is as follows:

Flex	A1	A2	A3	B1	B2	B3	C1	C2	C3	D1	D2	D3
OT-2	10	11	Trash	7	8	9	4	5	6	1	2	3

A protocol that calls protocol.load_labware("opentrons_flex_96_tiprack_200ul", "1") would require you to place that tip rack in slot D1 on Flex.

Modules¶

Update module load names for the Temperature Module and Thermocycler Module to ones that are compatible with Flex, if necessary. Flex supports:

temperature module gen2
thermocycler module gen2 or thermocyclerModuleV2

The Heater-Shaker Module only has one generation, which is compatible with Flex and OT-2.

For protocols that load magnetic module, magdeck, or magnetic module gen2, see Magnetic Module Protocols below.

Magnetic Module protocols¶

Note that there is no direct analogue of the Magnetic Module on Flex. You'll have to use the Magnetic Block and Flex Gripper instead. This will require reworking some of your protocol steps, and you should verify that your new protocol design achieves similar results.