Welcome to the Protocol Designer 

Onboarding Protocol Tutorial

Try this simple plate duplication protocol to get started with your OT-2.

Moving forward, you can use Protocol Designer to design your own custom protocols to run on the OT-2.

Step 1: Create a protocol

Select your pipettes and assign a tip rack type to each pipette. 

Step 2: Define liquids

Head to the liquids tab. 

Add 2 liquids you want to use for a test run on your robot.

Step 3: Add labware

Now go to the design tab.

When you first go to the design tab, you will see the starting deck state. Hover over empty slots to add labware.

 Add one source labware and one destination labware. Leave both empty. 

Choose whatever labware you have on hand that is both in the Protocol Designer labware library and compatible with your pipettes.  

This example will use 96 well plates. 

Step 4: Add liquids to their starting places

Hover over your first labware and click “Name & Liquids”. 

Click and drag to select all the wells in column 1 and fill them with your first liquid. 

Select all the wells in column 2 and fill them with your second liquid. 

Hit the “Deck” button in the title bar at the top to return to your deck view.

Step 5: Add a transfer

Once your selected labware is on the deck and liquids are in their starting location, it’s time to add steps.  

You can hover on each of the step types to get a description of what they do. 

Let’s start with a Transfer step

Step 6: Make your step

Fill out the required fields in your step form. 

Aspirate from the wells in the first 2 columns of your source labware.

Dispense into the wells of the first 2 columns of your destination labware. 

Step 7: Customize your step

Each step allows you to customize how the pipette aspirates and dispenses. To see aspirate and dispense advanced settings click the cog. 

Feel free to explore some of the available settings. 

… now hit save at the bottom of your form!

Step 8: Keep track of your steps

When you hover on a step, a blue highlight will appear on the 

  • source and destination labware
  • source and destination wells
  • tips used in the step

If you hover on a specific well in the sidebar, you will see

  • source & destination well highlighted
  • tip used highlighted
  • contents of the well 

….When you’re done looking, collapse your step by clicking on the arrow next to the title!

Step 9: Check your work

When you’re done, click on the Final Deck State step. 

Now, when you click on labware and hover on wells, you can see the final state of your wells at the end of your protocol. 

Step 10: Export your protocol

In the File tab, select Export. Your protocol will be downloaded to your computer as a .json file.

Step 11: Upload your protocol to your OT-2

Open the Opentrons App and connect to your OT-2:


In the Protocol tab, select Open. Select the .json file that was exported from Protocol Designer:

It will take a moment for your protocol to upload to your OT-2.

Next Steps

Click Proceed to calibrate to move on to pipette and labware calibration.

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