EvanKirshenbaum
commented
9 months ago It should run a relatively complicated pipelined protocol that uses the pipettor a lot. If you leave off the --pipettor ot2 argument, it will just run on the display, printing out messages about what the pipettor would be doing. (This is equivalent to running with --pipettor dummy.) With --pipettor ot2, the robot should actually perform the requested aspirations and dispensing. The display will also show up, so you can follow along with what's going on.
Basically,
- Pull in a bunch of "fragment reagents" to the top right extraction point, and mix them together. Keep one drop and send the rest to waste. Thermocycle the drop.
- Dilute the drop 8x with Dilution Buffer, then mix in Master Mix and PM Primers. Keep one drop and send the rest to waste. Thermocycle the drop.
- Dilute 5x with Prep Mixture. Keep one drop and send the rest to waste. Thermocycle the drop.
- Dilute 5x with Prep Mixture and mix with Master Mix. Keep one drop and send the rest to waste. Thermocycle the drop.
- Mix with PF Primers, brought in via middle extraction point. Keep one drop and send the other to waste. Thermocycle the drop.
- Remove the drop as a product via the lower extraction point.
This is run as a pipeline, with up to eleven drops in progress at any time, each starting with a different random combination of fragments.
What happens when you run it?
To run a simpler script, the easiest thing is to create your own Task and create a script along the lines of interactive.
The Task is straightforward, something like (warning: I'm typing on the fly, so there are probably errors):
class TestTransfer(Task):
def __init__(self) -> None:
super().__init__(name="test-transfer", description="Simple pipettor transfer test")
def run(self, board: Board, system: System, args: Namespace) -> None:
r = Reagent.find("R")
in_ep = board.extraction_points[0]
out_ep = board.extraction_points[1]
path = Path.teleport_into(in_ep, reagent=reagent).to_pad(out_ep.pad).teleport_out()
path.schedule()Then in your script (see interactive.py), you can do something like
exerciser = PlatormChoiceExerciser.for_task(TestTransfer,
platforms=(joey.PlatformTask,),
pipettors=(opentrons.PipettorConfig,))
exerciser.parse_args_and_run()If you just run this, you'll get it simulated on the display. If you run it with --pipettor ot2 and the other ot2 params, it will drive the robot.
Finally, you need to create a reagents JSON file to pass as the --ot-reagents parameter to tell the robot where reagent R is stored, something like
{
"reagents": [
{
"name": "R",
"wells": [
{ "plate": 0, "well": "A1", "quantity": 200, "use": "input" }
]
}
]
}
To run the opentrons with our own scripts:
@EvanKirshenbaum:
Migrated from internal repository. Originally created by Mark Huber on Sep 14, 2022 at 4:25 PM PDT.