Calibrate the Deck
Now that you've downloaded your protocol, you need to calibrate the deck so your robot can run it for you!
First, make sure you have your labware placed on the deck, and that you select the correct deck size from the dropdown menu in the app.
Next, load your protocol file into the OT app by dragging it into the appropriate spot in the interface.
When your protocol has been successfully uploaded, you'll notice a list of labware populate the "Positions" box. (This list is defined by the protocol.) You simply need to save the A1 position for each piece of labware in the protocol -- your robot can take care of the rest!
These jog buttons allow you to move the robot into the correct position. You can change the distance the robot moves with each jog command using the row of numerical buttons under "Select Increment".
The first position you should save is the tip rack. Jog the robot so that the pipette shaft is hovering directly above the first tip in the rack. Here's a good rule of thumb: if you put an imaginary piece of paper on the tip you would want the pipette to touch the paper, but not depress it into the tip.
When you think the pipette is in the proper position, flip to the "Pipette" tab on the app interface, select the correct pipette, and hit "pick up tip." The robot will jog up and down three times on the Z axis in an attempt to pick up the tip. If the tip does not seat correctly onto the pipette shaft, no worries - just position your pipette a little lower on the Z axis and try again!
If the robot seems to be putting too much force on the pipette when it picks up the tip, reposition the pipette a little higher on the Z axis, eject the tip, and try picking it up again. Save the position that will consistently pick up the tip without applying too much force.
**Pro tip: The distance the machine moves on the Z axis to pick up the tip is defined in the "tip plunge" field, which is nested within the pipette definition in the "Head" section of the JSON protocol file. This value is always noted in millimeters. Instead of repositioning your pipette, you can change this number and reload your protocol.**
Each time you've calibrated the A1 position for a particular piece of labware, you should always hit the 'Save' button next that labware. Once you've saved a position for a piece of labware, a 'move-to' button will appear by it. This allows you to go back to that position directly with a single click of the button - no need to jog there again!
When you save a tip-rack, an orange "reset" button also appears next to that position. This is for you to use when you "crash" the robot. This is a "when" and not an "if" because everyone will eventually press the jog button too many times, causing the robot to try to go too far down one axis and crash into itself -- it's part of the learning process!
When this happens, don't panic -- just hit "Home All" to re-establish the zero point for your robot. Your saved positions might still be slightly off because of the crash, so to determine whether this is the case, you can hit the "move-to" button next to the tip rack. If the robot moves back to the correct position, you're all good! However, if it moves to a position that's slightly off the mark, every position you saved is now off by the same amount. To correct this, you simply need to adjust to the correct tip-rack position, save it, and hit "Reset." That will correct all of the saved labware positions for that pipette according to the adjustment you made for the tip rack. It's an easy fix that keeps you from having to calibrate your containers again!
Now that your deck is set up, you're ready to calibrate the volume for your pipettes!