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Standard operating procedure for robot cellpainter

Standard operating procedure for robot cellpainter.

Access gui on http://cellpainter:5000

From the windows computer use http://cellpainter:5000. From other computers on the network use http://10.10.0.55:5000.

This can fail if the windows nuc has been the restarted and the labrobots server is not running. Check if http://10.10.0.56:5050 can be reached. If not, run labrobots on the windows computer. The icon looks like this and it starts a terminal with this kind of output. Minimize the terminal and keep it running.

If still unavailable the process on the ubuntu nuc might be down if that computer has been restarted. Here are detailed instructions how to start it (for system administrators).

The gui runs on the NUC running ubuntu which has hostname NUC-robotlab.

It runs in a screen named painter in the ~/painter-robotlab checkout of the repo.

ssh pharmbio@10.10.0.55
screen -x painter

If the screen is not running, start it with:

ssh pharmbio@10.10.0.55
pharmbio@NUC-robotlab:~$ screen -S painter
pharmbio@NUC-robotlab:~$ cd painter-robotlab/
pharmbio@NUC-robotlab:~/painter-robotlab$ source painter-venv/bin/activate
(painter-venv) pharmbio@NUC-robotlab:~/painter-robotlab$ cd cellpainter/
(painter-venv) pharmbio@NUC-robotlab:~/painter-robotlab/cellpainter$ cellpainter-gui --live
Running with config.name='live'
 * Env(VIABLE_DEV=True, VIABLE_RUN=True, VIABLE_HOST=None, VIABLE_PORT=None)
 * Serving Flask app 'cellpainter.gui.main'
 * Debug mode: off

Incubator preparation

  1. Turn on incubator.

Washer preparation

  1. Turn on washer.

  2. Attach pump D. (For dry runs: attach water from the green tap.)

  3. Attach the waste bottle.

Dispenser preparation

  1. Turn on dispenser.

  2. Attach the casettes to the peristaltic pumps.

  3. For dry runs: you may run with air (do nothing more) or with water for the green tap.

  4. Attach a waste bottle. For dry runs: pick one used only with water and ethanol.

Robot arm preparation

Use the teach pendant (the handheld touchpad tablet).

  1. Power on the robotarm.

  2. Move the robot arm to the neutral position (in front of the B21 hotel rack.)

    With the teach pendant, hold down the freedrive button on the back side.

  3. Put the robot in remote mode (upper-right corner).

  4. Put the teach pendant close to the keyboard so you can reach the emergency button.

Test communications

  1. Use the windows computer and go to the gui at http://cellpainter:5000.

  2. Run the test communications protocol, test-comm to verify that all machines can be communicated with.

    Common ways this can fail:

    • Robotarm might be in local mode. Change it to remote mode on the teach pendant.

    • The incubator communication program STX Driver must be running. Run it on the windows computer. The icon and the program looks like this. Press the Run button. Minimize the program and keep it running.

    • Incubator communication might not be activated. Run the incu-reset-and-activate protocol.

Run test circuit

  1. Run the test circuit protocol, test-circuit, to see that everything is in the correct place. This is optional if you know everything is in order.

    Start with one plate with lid in the incubator transfer door.

    If moves fail: move the instruments to their correct locations.

    If that is not possible ask Dan to update the locations under More: edit moves.

Loading the incubator

For dry runs: make sure the plates are decontaminated since they are going into the incubator.

  1. Place the plates in A1, A2, A3, ... They will be moved to L1, L2, L3, ... inside the incubator. L1 is the first plate to be painted, L2 the second, and so on.

  2. Make sure the robot is in neutral position (in front of the B21 hotel rack).

    Use the teach pendant and its freedrive button.

  3. Use the windows computer and go to the gui at http://cellpainter:5000.

  4. Use the load incubator protocol, incu-load, and enter the number of plates. Press start!

Painting

  1. Make sure the robot is in neutral position (in front of the B21 hotel rack)

    Use the teach pendant and its freedrive button.

  2. Use the windows computer and go to the gui at http://cellpainter:5000.

  3. Select the cell-paint protocol and enter the desired settings.

    The fields description and operators are informal. They are saved convenience and may be edited later.

    To run multiple batches in a row enter them with a comma: 6,6. The second batch will start right after the first.

    If running with more than 9 plates you might need to increase the incubation time (depending on the protocol directory.)

    The protocol directory contains the protocol files for the washer and dispenser. These need to be named according to the schema in protocol_paths.py.

    For 7 and more plates use two final wash rounds.

    Press start or press simulate.

    Recovering from a crash

    Use start from stage to recover from a crash. Start from the stage you want to continue from. Press simulate and rewind the time to the start to see what the locations of every plate should be when starting.

    If a plate needs some extra dispense or wash step run these before starting the robotarm again.

    If a plate has been damaged and cannot be used further in the experiment, decrease the number of plates under batch sizes. This will make the starting positions change so simulate and check what the starting locations are.

    An example. Consider this batch of 6 plates where plate 4 is damaged during the Triton step. Plates 1, 2 and 3 have had their Triton applied. Plate 5 and 6 have not yet had their Triton. An illustration:

    plate 1 plate 2 plate 3 plate 4 plate 5 plate 6

    Remove plate 4. The batch size is now 5. The batch looks like this:

    plate 1 plate 2 plate 3 plate 4
    (previously plate 5)     		plate 5
    (previously plate 6)

    Change the batch size to 5 and start from the stage Triton, plate 4. The robot will start with the plate now called 4, which previously was plate 5.

    In simulation, with time set to the beginning, the initial locations can be read off from the loc-plate table. Place the plates correctly before restarting the robot. This is a screenshot of the simulation:

After painting: saving the log file

  1. Use the windows computer and go to the gui at http://cellpainter:5000.

  2. Go to the show logs section.

  3. Check the boxes for the new log files, press add to git and follow the pop-ups.

After painting: rewinding the lab

  1. For dry run: Prime the washer tubes to empty them.

  2. For dry run: Detach the washer waste bottle. If it is only water: dispose it.

  3. For dry run: If dispenser was run with water: Prime to empty tubes and dispose the waste water.

  4. Detach the dispenser cassettes around the peristaltic pumps.

  5. Incubator:

    • For dry runs when the incubator is not set up for experiments: turn off and have it slightly open for a while to let it cool down.

    • When the incubator is set up for experiment: ask Polina. The procedure will include removing the water with a suction pump.

Configure BioTek and blue washer protocols and add time estimates for them

  1. Make a new directory in the protocols root on the windows computer. You could copy an existing one, automation_v5.0/ might be a good start.

  2. Modify the LHC files as you please and give their names prefixes according to the documentation of ProtocolPaths and template_protocol_paths in cellpainter/protocol_paths.py.

  3. Put one plate without lid in the washer and connect it to water. Run the dispenser on air, a plate is optional. Using liquids and a plate will not work, the plate will overflow.

  4. Use the windows computer and go to the gui at http://cellpainter:5000.

  5. Select time-protocols and enter the protocol directory name. Start!

  6. After success, press store timings.

The remaining steps save the timings to version control. They are not strictly required to start using the protocol directory.

  1. Use pharmbio@NUC-robotlab in the directory for the repo, ~/painter-robotlab/.

  2. Use git status and git diff to see that cellpainter/estimates.json and cellpainter/protocol_paths.json are correctly updated.

  3. Commit and push the changes:

    git add cellpainter/estimates.json cellpainter/protocol_paths.json
git commit -m 'Add time estimates for a new protocol directory'
git push

Update robotarm timings

  1. Run a protocol containing the missing moves.

  2. After success, press store timings.

Test plate decontamination

The purpose of this step is to make the test plates safe and clean to be used inside the incubator. If they have any dirt the incubator quickly gets contaminated. If the clean plate are touched by hand without gloves they are not considered clean any more and must not enter the incubator.

  1. Put test plates in Virkon for a few hours

  2. Prepare for --wash-plates-clean:

    2.1 Put plates in A1, A2, ....

    2.2 Attach washer pump D to water from green tap.

    2.3 Attach washer pump C to ethanol.

    2.4 Attach washer waste bottle, preferably an empty one or one just used with water and ethanol.

  3. Use the windows computer and go to the gui at http://cellpainter:5000.

  4. Select wash-plates-clean and enter the number of plates. Press start!

  5. After wash-plates-clean:

    4.1 Prime the washer tubes empty.

    4.2 Detach the washer waste bottle. If it contains only water and ethanol: empty it in the sink.

    4.3 Your plates are now safe! Safe plates may enter the incubator. They must not be touched without gloves.