Remote Lab Automation

Laura Maria Gonzalez
March 15, 2021

This week we also learned about the OpenTrons OT-2 lab automation robot. We haven't had access to the lab this year because of pandemic
protocols, but the situation gave us the opportunity to learn about lab automation. To get us familiar with the tool we underwent a short exercise
involving food dyes and pattern making on a 96-well plate. The goal was to learn commands that we could later use to execute exercises involving
enzymatic reactions like PCR.
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# First, look at the camera and see which tip is available
pipette.starting_tip = tips.well('B5')

# Plate
#laura_plate = protocol.load_labware(
#'nest_96_wellplate_200ul_flat',
#'4', # my plate
#'Destination Plate')

# Color dyes to use
dye_blue = dye_container['A1']
dye_red = dye_container['A2']
dye_orange = dye_container['A5']
dye_purple = dye_container['A7']

#Set up the wells per color
red_wells = ['B1', 'B2', 'B3', 'B4', 'C5', 'D6', 'E7', 'F8', 'G9', 'G10', 'G11', 'G12']
blue_wells = ['G1', 'G2', 'G3', 'G4', 'F5', 'E6', 'D7', 'C8', 'B9', 'B10', 'B11', 'B12']
purple_wells = ['E2', 'F2', 'C4', 'D4', 'E9', 'F9', 'C11', 'D11']
orange_wells = ['C2', 'D2', 'E4', 'F4', 'C9', 'D9', 'E11', 'F11']

#####################################
#####################################

#RED

# Aspirate Red Thick
pipette.aspirate(300, dye_red)
for well in red_wells[:6]:
# Dispense Red Thick
pipette.dispense(50, laura_plate[well]) # CHANGE ME to an ampty well!

# Aspirate Red Thick
pipette.aspirate(300, dye_red)
for well in red_wells[6:]:
# Dispense Red Thick
pipette.dispense(50, laura_plate[well]) # CHANGE ME to an ampty well!

# Throw the red tip away
pipette.drop_tip()
#####################################
#####################################

#BLUE

#pick up new tip
pipette.starting_tip = tips.well('B6')

# Aspirate Blue Thick
pipette.aspirate(300, dye_blue)
for well in blue_wells[:6]:
# Dispense Blue Thick
pipette.dispense(50, laura_plate[well]) # CHANGE ME to an ampty well!

# Aspirate Blue Thick
pipette.aspirate(300, dye_blue)
for well in blue_wells[6:]:
# Dispense Blue Thick
pipette.dispense(50, laura_plate[well]) # CHANGE ME to an ampty well!

# Throw the blue tip away
pipette.drop_tip()
#####################################
#####################################

#PURPLE

#pick up new tip
pipette.starting_tip = tips.well('B7')

# Aspirate Purple Thin
pipette.aspirate(160, dye_purple)
for well in purple_wells:
# Dispense Purple Thin
pipette.dispense(20, laura_plate[well]) # CHANGE ME to an ampty well!

# Throw the purple tip away
pipette.drop_tip()

#####################################
#####################################
#ORANGE

#pick up new tip
pipette.starting_tip = tips.well('B8')

# Aspirate Orange Thin
pipette.aspirate(160, dye_orange)
for well in orange_wells:
# Dispense Orange Thin
pipette.dispense(20, laura_plate[well]) # CHANGE ME to an ampty well!

# Throw the orange tip away
pipette.drop_tip()

CODE

OpenTrons OT-2

Next step was to plan the design of a logo. I tried to recreate the appearance of a DNA Helix. To plan what it might look like I used some graph paper and markers with the grid of the 96-well plate and the x/y numbers and letters. I wanted to test using four different colors with only four tips and vary the amount of liquid along the backbone vs the base pairs. To do this I broke the code by colors (red, blue, purple, orange). Within each color I picked a new tip, aspirated a certain amount of colored water that I would then subdivide evenly among the cells. Once the dispensing was done the pipette would be dropped and the process repeated with the next color. Because of the pattern I worked with predetermined lists, but more orderly processes can be done with more concise for loops broken apart by action instead of color.

DNA Design Sketch

Video of OpenTrons OT-2 Executing Commands

Close Up of Final Results

View from the OpenTrons OT-2 Camera

In the end I used five tips instead of four. A small error in the original code made the tip dispense into the same set of wells so I had to go back in and repeat the same color on the missing wells. I found that overall it was nice to work with the machine step by step instead of executing one big block of code. Whether or not that will be different when using the tool to perform synthetic biology tasks like PCR is unknown.

RESULTS/REFLECTION