Week 3 HW: Lab Automation

from opentrons import types
import math

metadata = {    # see https://docs.opentrons.com/v2/tutorial.html#tutorial-metadata
    'author': 'Elsa Donovan',
    'protocolName': 'HGTAA Opentrons Lab',
    'description': 'The protocol will pipette 4 different types of genetically engineered e. coli bacteia into a rainbow design.',
    'source': 'HTGAA 2025 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'

well_colors = {
    'A1' : 'Red',
    'B1' : 'Yellow',
    'C1' : 'Green',
    'D1' : 'Cyan',
    'E1' : 'Blue'       # if in a 24-well plate, this needs to be moved to e.g. D2
}


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

  # Tips
  tips_20ul = protocol.load_labware('opentrons_96_tiprack_20ul', TIP_RACK_DECK_SLOT, 'Opentrons 20uL Tips')

  # Pipettes
  pipette_20ul = protocol.load_instrument("p20_single_gen2", "right", [tips_20ul])

  # Modules
  temperature_module = protocol.load_module('temperature module gen2', COLORS_DECK_SLOT)

  # Temperature Module Plate
  temperature_plate = temperature_module.load_labware('opentrons_96_aluminumblock_generic_pcr_strip_200ul',
                                                      'Cold Plate')
  # Choose where to take the colors from
  color_plate = temperature_plate

  # Agar Plate
  agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate')  ## TA MUST CALIBRATE EACH PLATE!
  # Get the top-center of the plate, make sure the plate was calibrated before running this
  center_location = agar_plate['A1'].top()

  pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL)

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

  ###
  ### Helper functions for this lab
  ###

  # pass this e.g. 'Red' and get back a Location which can be passed to aspirate()
  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}")

  # For this lab, instead of calling pipette.dispense(1, loc) use this: dispense_and_jog(pipette, 1, loc)
  def dispense_and_jog(pipette, volume, location):
      """
      Dispense and then move up 5mm to shake all dispensed fluid off the tip;
      move back down to touch the agar to try to make sure the drop adheres;
      then go back up 5mm to avoid smearing the drop before moving laterally.
      """
      assert(isinstance(volume, (int, float)))
      pipette.dispense(volume, location)
      currLoc = pipette._get_last_location_by_api_version()
      pipette.move_to(currLoc.move(types.Point(z=5)))
      pipette.move_to(currLoc)
      pipette.move_to(currLoc.move(types.Point(z=5)))

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

  radius_step = 3  # Distance between concentric circles within a color layer
  color_layer_spacing = 6  # Distance between different color layers
  num_layers = 2
  base_drops_per_circle = 4  # Drops in the first circle
  color_layer = 1

  for color_name in well_colors.values():
    pipette_20ul.pick_up_tip()
        
    for layer in range(num_layers):
      radius = (layer + 1 + color_layer) * radius_step
      drops_per_circle = base_drops_per_circle * (color_layer + layer + 1) 
      angle_step = math.pi / drops_per_circle  # only cover the top half
      pipette_20ul.aspirate(10, location_of_color(color_name))
            
      for i in range(drops_per_circle+1):
        if pipette_20ul.current_volume < 1:
          pipette_20ul.aspirate(10, location_of_color(color_name))
                
        angle = i * angle_step  # restrict angle to top half (0 to pi)
        x_offset = radius * math.cos(angle)
        y_offset = radius * math.sin(angle) - 10
        drop_location = center_location.move(types.Point(x=x_offset, y=y_offset))
        dispense_and_jog(pipette_20ul, 1, drop_location)
        
    pipette_20ul.drop_tip()
    color_layer += num_layers

Paper:
Jun, J.S. et al. (2025). Automated and Programmable Cell-Free Systems for Scalable Synthetic Biology with a Focus on Biofoundry Integration. Journal of Microbiology and Biotechnology, 35, e2507019.