The Opentrons Magnetic Module is designed to automate magnetic bead based protocols on the OT-2. The magnetic module (sometimes referred to as the "magdeck") is compatible with most magnetic bead kits on the market, allowing biologists to automate nucleic acid purification protocols including PCR clean-up, genomic DNA extraction, plasmid purification, RNA extraction, and more. 

This article goes through:

  1. Compatible labware 
  2. Installing the magnetic module on the OT-2
  3. Creating a protocol using the magnetic module
  4. Calibrating a protocol using the magnetic module

Compatible Labware

See: What labware can I use with my modules?

Installing the Magnetic Module on the OT-2

1. Place module on the deck. 

The magnetic module fits directly on the OT-2 robot. You can place it into any of the side slots, with the cable sockets facing outwards towards the acrylic panels of the robot. 

Note: Putting the magnet module into one of the center slots (2, 5, or 8) will cause the power and control cables to cross over other slots on the deck, and is not advised. 

The Magnetic Module requires two different connections, one to the power source and one to the OT-2 for control by the robot. The pronged jack is the power cable and the USB Type-A goes into the USB port in the back of the robot. 

The power cable connects directly to a large power supply brick that plugs into the wall power outlet. The control cable goes to the USB sockets in the top left corner of the OT-2

Use the cable holders on the side of the robot to keep the USB cable out of the way. 


3. Power On & Check Connection

Press the small black button to power-on the magnetic module. You should hear some small motor noises as the module homes itself on boot. 

Now your robot should be able to see that it has a magdeck connected to it. Open the OT App and connect to your robot over USB or WiFi. Then you can click on the "Pipettes & Modules" tab below the name of your robot. You should see the pipettes and modules connected to your robot, as in the screenshot below:

Creating a Protocol with the Magdeck 

There are currently two ways to create a protocol that uses the magdeck:

You can also find some protocols using the magdeck on our Protocol Library. Support for modules is not currently included in our Protocol Designer, but will be soon! 

Writing a Python Protocol

There are a three things you need to include in your python protocol to be able to use the magnetic module. 

  1. Include the modules package from the Opentrons library: 
from opentrons import modules


2. Instantiate your magdeck in a deck slot (in this case, slot 1):
magdeck = modules.load('magdeck', '1')  

3. Put a PCR plate on top of the magdeck:
plate = labware.load('96-PCR', '1', share = True)
Note the "share = True" that indicates this plate is on top of the magdeck, sharing the deck slot with it.

If you include those three things, you can feel free to use the magdeck in your protocol. You can transfer, distribute, etc into the plate on top of the magdeck. You can engage and disengage the magnets using magdeck.engage() and magdeck.disengage() .  

Calibrating a Protocol with the Magnetic Module

When you have completed your protocol using the magdeck, it is time to load it into the Opentrons App and run it. 

The robot will be able to see that your protocol includes a MagDeck and will check to make sure that it is connected. It will then display the module in the deck slot the protocol you assigned to the MagDeck (Slot 1 in the example below). You can then proceed through labware calibration in the same way you normally would. The robot will move to the A1 location of the plate on top of the MagDeck for you to save the position in the same way as it does for every other labware.

Once you have completed your calibration, you can run your protocol! 

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