Week 3: Lab Automation

Python Script for Opentrons Artwork

Using the GUI at opentrons-art.rcdonovan.com I was able to generate a pattern to simulate the skyline at night in a desert (see Figure 1). LifeFabs Opentrons only has access to Blue, Pink, and Purple pigment which is why I decided to use these 3 colors only.

Figure 1. Night sky in a desert (Automation Art Interference GUI).

The colors were achieved using eqFP578 (blue), TagRFP (pink), and mCherry (purple.)

Then, using the coordinates from the GUI, I followed the instructions in the HTGAA26 Opentrons Colab to write my own Python script with the assistance of Claude (Anthropic) which helped me structure the pipetting logic. This is the code:

from opentrons import types

metadata = {    # see https://docs.opentrons.com/v2/tutorial.html#tutorial-metadata
    'author': 'Karol Duque',
    'protocolName': 'Fluorescent Protein Scene',
    'description': 'Three-color artistic scene using fluorescent bacteria: '
                   'mCherry (purple under UV) in A1, '
                   'TagRFP (pink under UV) in B1, '
                   'EqFP578 (blue under UV) in C1. '
                   'Coordinates generated at opentrons-art.rcdonovan.com. '
                   'AI assistance: Claude (Anthropic) helped structure the pipetting logic.',
    'source': 'HTGAA 2026 Opentrons Lab',
    'apiLevel': '2.20'
}

##############################################################################
###   Robot deck setup constants - don't change these
##############################################################################

TIP_RACK_DECK_SLOT = 9
COLORS_DECK_SLOT = 6
AGAR_DECK_SLOT = 5
PIPETTE_STARTING_TIP_WELL = 'A1'

# Using CSS color names that closely match actual fluorescence appearance:
#   mCherry  → 'darkorchid'  (fluoresces purple)
#   TagRFP   → 'hotpink'       (fluoresces pink)
#   EqFP578  → 'dodgerblue'    (fluoresces blue)
#
# Confirm physical well positions with your TA before running!
well_colors = {
    'A1' : 'darkorchid',  # mCherry
    'B1' : 'hotpink',       # TagRFP
    'C1' : 'navy',    # EqFP578
}


def run(protocol):
  ##############################################################################
  ###   Load labware, modules and pipettes
  ##############################################################################

  tips_20ul = protocol.load_labware('opentrons_96_tiprack_20ul', TIP_RACK_DECK_SLOT, 'Opentrons 20uL Tips')
  pipette_20ul = protocol.load_instrument("p20_single_gen2", "right", [tips_20ul])
  temperature_module = protocol.load_module('temperature module gen2', COLORS_DECK_SLOT)
  temperature_plate = temperature_module.load_labware('opentrons_96_aluminumblock_generic_pcr_strip_200ul', 'Cold Plate')
  color_plate = temperature_plate
  agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate')  ## TA MUST CALIBRATE EACH PLATE!
  center_location = agar_plate['A1'].top()
  pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL)

  ##############################################################################
  ###   Patterning
  ##############################################################################

  def location_of_color(color_string):
    for well, color in well_colors.items():
      if color.lower() == color_string.lower():
        return color_plate[well]
    raise ValueError(f"No well found with color {color_string}")

  def dispense_and_detach(pipette, volume, location):
      assert(isinstance(volume, (int, float)))
      above_location = location.move(types.Point(z=location.point.z + 5))
      pipette.move_to(above_location)
      pipette.dispense(volume, location)
      pipette.move_to(above_location)

  ###
  ### YOUR CODE HERE to create your design
  ###

  # Coordinates from opentrons-art.rcdonovan.com
  # mCherry  → 'darkorchid'  well A1  (fluoresces purple)
  # TagRFP   → 'hotpink'       well B1  (fluoresces pink)
  # EqFP578  → 'navy'    well C1  (fluoresces blue)

  mcherry_points = [(-5, 25),(5, 25),(-20, 20),(10, 20),(-12.5, 17.5),(-27.5, 15),(-25, 15),(-30, 12.5),(-27.5, 12.5),(-25, 12.5),(-22.5, 12.5),(27.5, 12.5),(-30, 10),(-27.5, 10),(-25, 10),(-22.5, 10),(-20, 10),(-17.5, 10),(-15, 10),(25, 10),(27.5, 10),(-32.5, 7.5),(-30, 7.5),(-27.5, 7.5),(-25, 7.5),(-22.5, 7.5),(-17.5, 7.5),(-15, 7.5),(-12.5, 7.5),(-10, 7.5),(0, 7.5),(2.5, 7.5),(5, 7.5),(7.5, 7.5),(10, 7.5),(12.5, 7.5),(22.5, 7.5),(25, 7.5),(27.5, 7.5),(30, 7.5),(-32.5, 5),(-27.5, 5),(-25, 5),(-22.5, 5),(-20, 5),(-17.5, 5),(-15, 5),(-12.5, 5),(-10, 5),(-5, 5),(-2.5, 5),(0, 5),(2.5, 5),(10, 5),(12.5, 5),(15, 5),(17.5, 5),(20, 5),(22.5, 5),(27.5, 5),(30, 5),(-32.5, 2.5),(-30, 2.5),(-27.5, 2.5),(-25, 2.5),(-22.5, 2.5),(-17.5, 2.5),(-15, 2.5),(-12.5, 2.5),(-10, 2.5),(-7.5, 2.5),(-5, 2.5),(-2.5, 2.5),(2.5, 2.5),(12.5, 2.5),(15, 2.5),(17.5, 2.5),(20, 2.5),(22.5, 2.5),(25, 2.5),(27.5, 2.5),(30, 2.5),(-32.5, 0),(-30, 0),(-27.5, 0),(-25, 0),(-22.5, 0),(-20, 0),(-17.5, 0),(-15, 0),(-12.5, 0),(-10, 0),(-5, 0),(-2.5, 0),(2.5, 0),(10, 0),(15, 0),(17.5, 0),(20, 0),(22.5, 0),(25, 0),(-20, -2.5),(-17.5, -2.5),(-12.5, -2.5),(-10, -2.5),(-7.5, -2.5),(-5, -2.5),(-2.5, -2.5),(2.5, -2.5),(17.5, -2.5),(-7.5, -5),(-5, -5)]

  tagrfp_points = [(-10, 15),(10, 15),(-7.5, 12.5),(12.5, 12.5),(-20, 7.5),(-30, 5),(25, 5),(-20, 2.5),(10, 2.5),(-7.5, 0),(27.5, 0),(30, 0),(-32.5, -2.5),(-30, -2.5),(-27.5, -2.5),(-25, -2.5),(-22.5, -2.5),(-15, -2.5),(10, -2.5),(15, -2.5),(20, -2.5),(22.5, -2.5),(25, -2.5),(27.5, -2.5),(30, -2.5),(-32.5, -5),(-30, -5),(-27.5, -5),(-25, -5),(-22.5, -5),(-20, -5),(-17.5, -5),(-15, -5),(-12.5, -5),(-10, -5),(-2.5, -5),(10, -5),(15, -5),(17.5, -5),(22.5, -5),(25, -5),(27.5, -5),(30, -5),(-32.5, -7.5),(-30, -7.5),(-27.5, -7.5),(-22.5, -7.5),(-20, -7.5),(-17.5, -7.5),(-12.5, -7.5),(-10, -7.5),(-7.5, -7.5),(-5, -7.5),(-2.5, -7.5),(15, -7.5),(17.5, -7.5),(25, -7.5),(27.5, -7.5),(30, -7.5),(-32.5, -10),(-30, -10),(-20, -10),(-17.5, -10),(-12.5, -10),(-7.5, -10),(-5, -10),(-2.5, -10),(0, -10),(2.5, -10),(15, -10),(22.5, -10),(25, -10),(27.5, -10),(30, -10),(-30, -12.5),(-20, -12.5),(-12.5, -12.5),(-7.5, -12.5),(-5, -12.5),(-2.5, -12.5),(0, -12.5),(2.5, -12.5),(12.5, -12.5),(15, -12.5),(17.5, -12.5),(22.5, -12.5),(27.5, -12.5),(-30, -15),(-27.5, -15),(-22.5, -15),(-20, -15),(-17.5, -15),(-7.5, -15),(-5, -15),(-2.5, -15),(0, -15),(2.5, -15),(10, -15),(12.5, -15),(15, -15),(17.5, -15),(-20, -17.5),(-17.5, -17.5),(-10, -17.5),(-7.5, -17.5),(-5, -17.5),(0, -17.5),(2.5, -17.5),(10, -17.5),(-17.5, -20),(-12.5, -20),(-10, -20),(-7.5, -20),(-10, -22.5)]

  eqfp578_points = [(-10, 30),(-7.5, 30),(-5, 30),(-2.5, 30),(0, 30),(2.5, 30),(5, 30),(7.5, 30),(-15, 27.5),(-12.5, 27.5),(-10, 27.5),(-7.5, 27.5),(-5, 27.5),(-2.5, 27.5),(0, 27.5),(2.5, 27.5),(5, 27.5),(7.5, 27.5),(10, 27.5),(12.5, 27.5),(-20, 25),(-17.5, 25),(-15, 25),(-12.5, 25),(-10, 25),(-7.5, 25),(-2.5, 25),(0, 25),(2.5, 25),(7.5, 25),(10, 25),(12.5, 25),(15, 25),(17.5, 25),(-22.5, 22.5),(-20, 22.5),(-17.5, 22.5),(-15, 22.5),(-12.5, 22.5),(-10, 22.5),(-7.5, 22.5),(-5, 22.5),(-2.5, 22.5),(0, 22.5),(2.5, 22.5),(5, 22.5),(7.5, 22.5),(10, 22.5),(12.5, 22.5),(15, 22.5),(17.5, 22.5),(20, 22.5),(-25, 20),(-22.5, 20),(-17.5, 20),(-15, 20),(-12.5, 20),(-10, 20),(-7.5, 20),(-5, 20),(-2.5, 20),(0, 20),(2.5, 20),(5, 20),(7.5, 20),(12.5, 20),(15, 20),(17.5, 20),(20, 20),(22.5, 20),(-27.5, 17.5),(-25, 17.5),(-22.5, 17.5),(-20, 17.5),(-17.5, 17.5),(-15, 17.5),(-10, 17.5),(-7.5, 17.5),(-5, 17.5),(-2.5, 17.5),(0, 17.5),(2.5, 17.5),(5, 17.5),(7.5, 17.5),(10, 17.5),(12.5, 17.5),(15, 17.5),(17.5, 17.5),(20, 17.5),(22.5, 17.5),(25, 17.5),(-22.5, 15),(-20, 15),(-17.5, 15),(-15, 15),(-12.5, 15),(-7.5, 15),(-5, 15),(-2.5, 15),(0, 15),(2.5, 15),(5, 15),(7.5, 15),(12.5, 15),(15, 15),(17.5, 15),(20, 15),(22.5, 15),(25, 15),(-20, 12.5),(-17.5, 12.5),(-15, 12.5),(-12.5, 12.5),(-10, 12.5),(-5, 12.5),(-2.5, 12.5),(0, 12.5),(2.5, 12.5),(5, 12.5),(7.5, 12.5),(10, 12.5),(15, 12.5),(17.5, 12.5),(20, 12.5),(22.5, 12.5),(25, 12.5),(-12.5, 10),(-10, 10),(-7.5, 10),(-5, 10),(-2.5, 10),(0, 10),(2.5, 10),(5, 10),(7.5, 10),(10, 10),(12.5, 10),(15, 10),(17.5, 10),(20, 10),(22.5, 10),(-7.5, 7.5),(-5, 7.5),(-2.5, 7.5),(15, 7.5),(17.5, 7.5),(20, 7.5),(-7.5, 5),(5, 5),(7.5, 5),(0, 2.5),(5, 2.5),(7.5, 2.5),(0, 0),(5, 0),(7.5, 0),(12.5, 0),(0, -2.5),(5, -2.5),(7.5, -2.5),(12.5, -2.5),(0, -5),(2.5, -5),(5, -5),(7.5, -5),(12.5, -5),(20, -5),(-25, -7.5),(-15, -7.5),(0, -7.5),(2.5, -7.5),(5, -7.5),(7.5, -7.5),(10, -7.5),(12.5, -7.5),(20, -7.5),(22.5, -7.5),(-27.5, -10),(-25, -10),(-22.5, -10),(-15, -10),(-10, -10),(5, -10),(7.5, -10),(10, -10),(12.5, -10),(17.5, -10),(20, -10),(-27.5, -12.5),(-25, -12.5),(-22.5, -12.5),(-17.5, -12.5),(-15, -12.5),(-10, -12.5),(5, -12.5),(7.5, -12.5),(10, -12.5),(20, -12.5),(25, -12.5),(-25, -15),(-15, -15),(-12.5, -15),(-10, -15),(5, -15),(7.5, -15),(20, -15),(22.5, -15),(25, -15),(27.5, -15),(-27.5, -17.5),(-25, -17.5),(-22.5, -17.5),(-15, -17.5),(-12.5, -17.5),(-2.5, -17.5),(5, -17.5),(7.5, -17.5),(12.5, -17.5),(15, -17.5),(17.5, -17.5),(20, -17.5),(22.5, -17.5),(25, -17.5),(-27.5, -20),(-25, -20),(-22.5, -20),(-20, -20),(-15, -20),(-5, -20),(-2.5, -20),(0, -20),(2.5, -20),(5, -20),(7.5, -20),(10, -20),(12.5, -20),(15, -20),(17.5, -20),(20, -20),(22.5, -20),(25, -20),(-25, -22.5),(-22.5, -22.5),(-20, -22.5),(-17.5, -22.5),(-15, -22.5),(-12.5, -22.5),(-7.5, -22.5),(-5, -22.5),(-2.5, -22.5),(0, -22.5),(2.5, -22.5),(5, -22.5),(7.5, -22.5),(10, -22.5),(12.5, -22.5),(15, -22.5),(17.5, -22.5),(20, -22.5),(22.5, -22.5),(-22.5, -25),(-20, -25),(-17.5, -25),(-15, -25),(-12.5, -25),(-10, -25),(-7.5, -25),(-5, -25),(-2.5, -25),(0, -25),(2.5, -25),(5, -25),(7.5, -25),(10, -25),(12.5, -25),(15, -25),(17.5, -25),(20, -25),(-20, -27.5),(-17.5, -27.5),(-15, -27.5),(-12.5, -27.5),(-10, -27.5),(-7.5, -27.5),(-5, -27.5),(-2.5, -27.5),(0, -27.5),(2.5, -27.5),(5, -27.5),(7.5, -27.5),(10, -27.5),(12.5, -27.5),(15, -27.5),(17.5, -27.5),(-15, -30),(-12.5, -30),(-10, -30),(-7.5, -30),(-5, -30),(-2.5, -30),(0, -30),(2.5, -30),(5, -30),(7.5, -30),(10, -30),(12.5, -30),(-10, -32.5),(-7.5, -32.5),(-5, -32.5),(-2.5, -32.5),(0, -32.5),(2.5, -32.5),(5, -32.5),(7.5, -32.5)]

  def draw_points(points, color_string):
      """One tip per color. Aspirates in batches of 20uL, dispenses 1uL per dot."""
      pipette_20ul.pick_up_tip()
      i = 0
      while i < len(points):
          batch = min(20, len(points) - i)
          pipette_20ul.aspirate(batch, location_of_color(color_string))
          for _ in range(batch):
              x, y = points[i]
              loc = center_location.move(types.Point(x=x, y=y))
              dispense_and_detach(pipette_20ul, 1, loc)
              i += 1
      pipette_20ul.drop_tip()

  # Draw order: blue background first, then purple (mCherry), then pink (TagRFP) on top
  draw_points(eqfp578_points, 'navy')   # EqFP578 → blue 
  draw_points(mcherry_points,  'darkorchid') # mCherry → purple
  draw_points(tagrfp_points,   'hotpink')      # TagRFP  → pink

  # drop_tip() is called inside draw_points() for each color

The output is the following:

Figure 2. Night sky in a desert (Opentrons Colab).

Post-Lab Questions

Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details.

Final Project Ideas

This idea is ba continuation on the research I did for the homework in Weeks 1 and 2.

This idea came about after reading about the recent wildfires in Patagonia, Argentina and further researching recent wildfires across the world including Chile, Spain and Portugal. I started thinking about the ways that already exist to prevent wildfires and thought if there were any methods that use modified living organisms.

Because my background is in biomedical engineering I thought I should have at least one project idea that was related healthcare. Before starting my degree I did some research into bandaids made with hydrogels which act like stitches and prevent infection. Last summer, I did an internship which used microfluidics for blood glucose monitoring which made me think if there was any way I could combine microfluidics and something to improve wound care. That led me to chronic wounds and I began researching monitoring methods for these wounds that led me to biosensors for chronic wound management.