Labs

Lab writeups:

  • Week 1 Lab: Pipetting

  • Week 2 Lab: Lab DNA Gel Art

    Part 1: Benchling & In-silico Gel Art Part 0a: Designing my Gel Art For this week’s lab, I aimed to create a cool shape that would be easily noticeable and bring a smile to whoever sees it. After thinking through a few ideas, I decided to try creating a rubber duck shape :)

  • Week 3: Lab Opentrons Art

    Python Script for Opentrons Artwork In this week’s lab, we used the Opentrons OT-2 pipetting robot and genetically engineered E. coli bacteria to create bio art on black (charcoal) agar plates! The bacteria were engineered to express fluorescent proteins (such as GFP – Green Fluorescent Protein), allowing them to glow in multiple colors under ultraviolet light.

Subsections of Labs

Week 1 Lab: Pipetting

cover image cover image first try first try eye_pipette eye_pipette eye eye

Week 2 Lab: Lab DNA Gel Art

Part 1: Benchling & In-silico Gel Art

Part 0a: Designing my Gel Art

For this week’s lab, I aimed to create a cool shape that would be easily noticeable and bring a smile to whoever sees it. After thinking through a few ideas, I decided to try creating a rubber duck shape :)

To start designing, I took a picture of the gel alongside the ladder from Ronan’s website and copied it into Procreate on my iPad. Then I added guiding lines in the common areas where many of the segments from the randomizing tool appeared, and sketched the overall shape of a rubber duck.

Very quickly, it became clear that a rubber duck isn’t an “easy” shape to create with this technique. Because it is full of curves and the resolution is relatively low, getting a clear shape was much harder than expected.

To make it more visible, I tried enlarging it to cover more potential segments (i.e., the image’s pixels), but it didn’t work the way I intended. After thinking it through a bit more, I decided to create a HEART! This too is a very curvy shape, but it’s definitely simpler than a duck - and it’s also Valentine’s Day in two days!

So I did the same thing and got the following basic design:

Once I was happy with my design (and honestly, while designing it), I started thinking about how I could determine which enzymes to use to make all of the DNA segments in the specific sizes I wanted. I realized the best and most efficient way for me to go about it was to use Ronan’s website again. I used the “randomize” tool again, only this time I did it for only one column at a time, to get familiar with all of the different combinations of 2-enzyme cuts I could get. It turns out that this number wasn’t very big (55 to be accurate — 45 from pairs + 10 single enzymes), and the options were limited. Since I didn’t want to use 3 or more enzymes, I had to work with this.

To be able to design through the website, I first got myself familiar with the different possible combinations of digestions, and then tried to search for the closest match to my original sketch. After a few tweaks, I created a design I was satisfied with and was ready to move on to the next step!

Part 0b: Expected Results and Walkthrough

I then moved on to Benchling to transfer my design there by uploading the Lambda DNA and adding the corresponding restriction enzymes. After a few digestions, I noticed something weird — the HindIII enzyme cutting sites on Ronan’s website didn’t match the ones on Benchling. This means that my heart design didn’t look like a heart anymore :(

So I went back to Ronan’s website and tried to find alternatives with the hope that I would find them — and I did. The new design didn’t look as rounded as I wanted, but it was certainly a heart, and I went with it! Here is the Benchling design:

And the equivalent design in Ronan’s website:

And so I moved on to the next step!

Part 2: Gel Art - Restriction Digests and Gel Electrophoresis

Part 1a: Preparing a 1% agarose electrophoresis gel

I created the gel solution and poured it into the gel tray. Weighing the agarose and measuring the TAE buffer:

Pouring the solution into the gel tray:

Then I let it set and moved on to the next step!

Part 1b: Restriction Digest

Here I again followed the protocol for digesting the Lambda DNA with my chosen enzymes: Pipetting:

And put the tubes in the 37ºC incubator for 30 minutes.

Part 2: Gel Run

Now I was finally ready to start assembling all of the components together! I took my tubes with the digested Lambda DNA and enzymes out of the incubator and prepared a new set of tubes with the right concentrations of water, loading dye, and digest solution.

I then went on and poured the TAE over the gel until fully covered and started loading it!

Then, I connected it to power and let it run:

Part 3: Imaging Your Results with a Transilluminator

After about 40 minutes, when the dye reached about 3/4 of the gel, I stopped it and carefully took it out of the tray:

Finally, we used the blue light transilluminator to see the results. We were all thrilled to see what it would look like… And here is the final result!

It may not be exactly the same as my original design, but I can still see the heart and am very proud of the final result and all of the journey there! :)

Here is the same picture but with annotations of the border of the heart, to try and help you see the shape yourself:

I don’t know about you, but I ❤️ it!

Week 3: Lab Opentrons Art

Python Script for Opentrons Artwork

In this week’s lab, we used the Opentrons OT-2 pipetting robot and genetically engineered E. coli bacteria to create bio art on black (charcoal) agar plates! The bacteria were engineered to express fluorescent proteins (such as GFP – Green Fluorescent Protein), allowing them to glow in multiple colors under ultraviolet light.

*I mainly used the GUI at opentrons-art.rcdonovan.com to produce my designs due to the short notice before the lab.

My first idea for this project was to create a picture of Earth that represents both the diverse backgrounds and countries students in the class and at MIT come from, and the global impact I hope to have through my work. I started by finding a reference photo and uploading it to the GUI. The result wasn’t very good, but I used it as a base and painted my final design over it. I would have loved to include some white (which we don’t have) for clouds, but I think it turned out amazing even without it.

The “pixelated” look of the art examples from previous years reminded both me and my mother, who, among other things, is a textile designer, of cross-stitch embroidery. I wanted to create a design inspired by the classic rose cross patterns - but using this new, cutting-edge technology. A merge between the past and the future.

Here is my design process in images:

Here is my Python script for the Earth design:

from opentrons import types

import string

metadata = {
    'protocolName': '{YOUR NAME} - Opentrons Art - HTGAA',
    'author': 'HTGAA',
    'source': 'HTGAA 2026',
    'apiLevel': '2.20'
}

Z_VALUE_AGAR = 2.0
POINT_SIZE = 0.75

venus_points = [(-9,33), (5,33), (7,33), (9,33), (11,31), (13,31), (11,29), (-19,25), (-17,25), (1,25), (3,25), (15,25), (-21,23), (-19,23), (-7,23), (-5,23), (-21,21), (-19,21), (-5,21), (-31,19), (-29,19), (-21,19), (-19,19), (-17,19), (-15,19), (-11,19), (29,19), (-31,17), (-29,17), (-13,17), (-11,17), (29,17), (-13,15), (23,15), (-13,13), (11,13), (31,13), (33,13), (11,11), (31,11), (33,11), (-23,9), (-21,9), (11,9), (-33,3), (15,3), (-33,1), (17,1), (29,-3), (27,-5), (-17,-7), (-15,-7), (-13,-7), (23,-7), (25,-7), (27,-7), (-13,-9), (-11,-9), (23,-9), (-9,-11), (-7,-11), (23,-11), (-7,-13), (27,-13), (25,-15), (-5,-17), (-5,-19), (-7,-21)]
mwasabi_points = [(-7,33), (-5,33), (-3,33), (-9,31), (-7,31), (-3,31), (-1,31), (-17,29), (-15,29), (-5,29), (-1,29), (1,29), (21,29), (-19,27), (-17,27), (-15,27), (-13,27), (-5,27), (-3,27), (-1,27), (13,27), (19,27), (-21,25), (11,25), (17,25), (23,25), (17,23), (19,23), (25,23), (27,23), (27,21), (-27,19), (-13,19), (7,19), (13,19), (15,19), (19,19), (25,19), (7,17), (11,17), (-27,15), (-25,15), (-17,15), (13,15), (15,15), (17,15), (29,15), (-27,13), (-23,13), (23,13), (25,13), (-35,11), (-31,11), (-21,11), (-15,11), (-13,11), (23,11), (-35,9), (-31,9), (-27,9), (-25,9), (-19,9), (7,9), (25,9), (27,9), (29,9), (-35,7), (-33,7), (-29,7), (-27,7), (5,7), (11,7), (13,7), (15,7), (17,7), (19,7), (21,7), (23,7), (27,7), (29,7), (31,7), (-33,5), (-29,5), (-23,5), (5,5), (11,5), (13,5), (23,5), (27,5), (33,5), (-29,3), (5,3), (19,3), (23,3), (29,3), (-31,1), (-29,1), (5,1), (11,1), (13,1), (25,1), (-31,-1), (5,-1), (15,-1), (17,-1), (25,-1), (-23,-3), (7,-3), (9,-3), (11,-3), (17,-3), (21,-3), (25,-3), (-19,-5), (19,-5), (23,-5), (25,-5), (19,-7), (-17,-9), (-15,-9), (19,-9), (-23,-11), (-21,-11), (-15,-11), (-13,-11), (-11,-11), (19,-11), (-21,-13), (19,-13), (21,-13), (23,-13), (-17,-15), (19,-15), (27,-15), (-17,-17), (-7,-17), (19,-17), (-17,-19), (-15,-19), (-11,-19), (-7,-19), (19,-19), (-13,-21), (-11,-21), (-13,-23), (-9,-23), (-7,-23), (-15,-25), (-11,-25), (-9,-25)]
azurite_points = [(-1,33), (3,33), (-15,31), (-13,31), (1,31), (7,31), (9,31), (15,31), (-11,29), (-9,29), (-7,29), (3,29), (7,29), (9,29), (-11,27), (-7,27), (1,27), (3,27), (5,27), (9,27), (11,27), (-15,25), (-3,25), (-1,25), (5,25), (7,25), (9,25), (13,25), (-17,23), (-3,23), (-1,23), (1,23), (5,23), (7,23), (11,23), (-17,21), (-15,21), (-13,21), (-11,21), (-9,21), (-7,21), (-3,21), (-1,21), (1,21), (7,21), (9,21), (11,21), (-9,19), (-7,19), (-5,19), (-1,19), (5,19), (-9,17), (-7,17), (-3,17), (-1,17), (5,17), (-11,15), (-9,15), (-1,15), (1,15), (3,15), (5,15), (7,15), (25,15), (27,15), (-11,13), (-9,13), (1,13), (5,13), (7,13), (13,13), (17,13), (19,13), (21,13), (-11,11), (-9,11), (-1,11), (3,11), (5,11), (7,11), (9,11), (13,11), (15,11), (19,11), (21,11), (-17,9), (-15,9), (-13,9), (-11,9), (-9,9), (5,9), (-21,7), (-19,7), (-17,7), (-15,7), (-3,7), (1,7), (3,7), (-21,5), (-19,5), (-17,5), (1,5), (3,5), (-25,3), (-23,3), (-21,3), (-15,3), (-3,3), (-1,3), (1,3), (3,3), (31,3), (33,3), (-35,1), (-25,1), (-23,1), (-21,1), (1,1), (3,1), (29,1), (31,1), (-35,-1), (-33,-1), (-21,-1), (-19,-1), (-17,-1), (-5,-1), (3,-1), (29,-1), (31,-1), (-35,-3), (-33,-3), (-31,-3), (-27,-3), (-21,-3), (-19,-3), (-17,-3), (-15,-3), (-11,-3), (-3,-3), (3,-3), (5,-3), (31,-3), (-35,-5), (-33,-5), (-31,-5), (-29,-5), (-27,-5), (-17,-5), (-15,-5), (-13,-5), (3,-5), (5,-5), (7,-5), (9,-5), (11,-5), (29,-5), (31,-5), (-35,-7), (-33,-7), (-25,-7), (-11,-7), (-9,-7), (-7,-7), (5,-7), (7,-7), (9,-7), (11,-7), (13,-7), (29,-7), (-35,-9), (-33,-9), (-31,-9), (-25,-9), (-23,-9), (-9,-9), (-7,-9), (-5,-9), (-3,-9), (7,-9), (11,-9), (13,-9), (25,-9), (27,-9), (-25,-11), (-5,-11), (13,-11), (15,-11), (25,-11), (27,-11), (-25,-13), (-5,-13), (-3,-13), (1,-13), (13,-13), (15,-13), (25,-13), (29,-13), (-23,-15), (-3,-15), (1,-15), (13,-15), (15,-15), (23,-15), (29,-15), (-23,-17), (-21,-17), (-19,-17), (-3,-17), (1,-17), (13,-17), (15,-17), (23,-17), (25,-17), (-19,-19), (-3,-19), (13,-19), (15,-19), (23,-19), (-19,-21), (-17,-21), (-5,-21), (-3,-21), (-1,-21), (9,-21), (13,-21), (15,-21), (17,-21), (21,-21), (23,-21), (-27,-23), (-25,-23), (-17,-23), (15,-23), (17,-23), (-23,-25), (-17,-25), (-7,-25), (-5,-25), (-21,-27), (-19,-27), (-15,-27), (-9,-27), (-7,-27), (-21,-29), (-19,-29), (-15,-29), (-13,-29), (9,-29), (-15,-31), (-13,-31), (5,-31), (9,-31)]
electra2_points = [(-7,35), (-1,35), (1,35), (3,35), (5,35), (1,33), (3,31), (5,31), (5,29), (-9,27), (7,27), (-13,25), (-11,25), (-15,23), (-13,23), (-11,23), (3,23), (9,23), (3,21), (5,21), (-3,19), (1,19), (3,19), (-5,17), (1,17), (3,17), (-7,15), (-5,15), (-3,15), (-7,13), (-5,13), (-3,13), (-1,13), (3,13), (15,13), (-7,11), (-5,11), (-3,11), (1,11), (17,11), (-7,9), (-5,9), (-3,9), (-1,9), (1,9), (3,9), (-13,7), (-11,7), (-9,7), (-7,7), (-5,7), (-1,7), (-15,5), (-13,5), (-11,5), (-9,5), (-7,5), (-5,5), (-3,5), (-1,5), (-19,3), (-17,3), (-13,3), (-11,3), (-9,3), (-7,3), (-5,3), (35,3), (-19,1), (-17,1), (-15,1), (-13,1), (-11,1), (-9,1), (-7,1), (-5,1), (-3,1), (-1,1), (33,1), (35,1), (-15,-1), (-13,-1), (-11,-1), (-9,-1), (-7,-1), (-3,-1), (-1,-1), (1,-1), (33,-1), (35,-1), (-13,-3), (-9,-3), (-7,-3), (-5,-3), (-1,-3), (1,-3), (33,-3), (35,-3), (-11,-5), (-9,-5), (-7,-5), (-5,-5), (-3,-5), (-1,-5), (1,-5), (33,-5), (35,-5), (-31,-7), (-29,-7), (-27,-7), (-5,-7), (-3,-7), (-1,-7), (1,-7), (3,-7), (31,-7), (33,-7), (35,-7), (-29,-9), (-27,-9), (-1,-9), (1,-9), (3,-9), (5,-9), (9,-9), (29,-9), (31,-9), (33,-9), (-33,-11), (-31,-11), (-29,-11), (-27,-11), (-3,-11), (-1,-11), (1,-11), (3,-11), (5,-11), (7,-11), (9,-11), (11,-11), (29,-11), (31,-11), (-33,-13), (-31,-13), (-29,-13), (-27,-13), (-1,-13), (3,-13), (5,-13), (7,-13), (9,-13), (11,-13), (31,-13), (-31,-15), (-29,-15), (-27,-15), (-25,-15), (-1,-15), (3,-15), (5,-15), (7,-15), (9,-15), (11,-15), (-31,-17), (-29,-17), (-27,-17), (-25,-17), (-1,-17), (3,-17), (5,-17), (7,-17), (9,-17), (11,-17), (27,-17), (29,-17), (-29,-19), (-27,-19), (-25,-19), (-23,-19), (-21,-19), (-1,-19), (1,-19), (3,-19), (5,-19), (7,-19), (9,-19), (11,-19), (25,-19), (27,-19), (29,-19), (-27,-21), (-25,-21), (-23,-21), (-21,-21), (1,-21), (3,-21), (5,-21), (7,-21), (11,-21), (25,-21), (27,-21), (-23,-23), (-21,-23), (-19,-23), (-5,-23), (-3,-23), (-1,-23), (1,-23), (3,-23), (5,-23), (7,-23), (9,-23), (11,-23), (13,-23), (19,-23), (21,-23), (23,-23), (25,-23), (27,-23), (-21,-25), (-19,-25), (-3,-25), (-1,-25), (1,-25), (3,-25), (5,-25), (7,-25), (9,-25), (11,-25), (13,-25), (15,-25), (17,-25), (19,-25), (21,-25), (23,-25), (-17,-27), (-11,-27), (-5,-27), (-3,-27), (-1,-27), (1,-27), (3,-27), (5,-27), (7,-27), (9,-27), (11,-27), (13,-27), (15,-27), (17,-27), (19,-27), (21,-27), (-17,-29), (-11,-29), (-9,-29), (-7,-29), (-5,-29), (-3,-29), (-1,-29), (1,-29), (3,-29), (5,-29), (7,-29), (11,-29), (13,-29), (15,-29), (17,-29), (19,-29), (21,-29), (-11,-31), (-9,-31), (-7,-31), (-5,-31), (-3,-31), (-1,-31), (1,-31), (3,-31), (7,-31), (11,-31), (13,-31), (15,-31), (-9,-33), (-7,-33), (-5,-33), (-3,-33), (-1,-33), (1,-33), (3,-33), (5,-33), (7,-33), (9,-33), (-7,-35), (-5,-35), (-3,-35), (-1,-35), (1,-35), (3,-35), (5,-35), (7,-35)]
mclover3_points = [(-5,35), (-3,35), (-11,31), (-5,31), (-21,29), (-19,29), (-13,29), (-3,29), (13,29), (15,29), (17,29), (19,29), (-21,27), (15,27), (17,27), (21,27), (-23,25), (-9,25), (-7,25), (-5,25), (19,25), (21,25), (-27,23), (-25,23), (-23,23), (-9,23), (13,23), (15,23), (21,23), (23,23), (-27,21), (-25,21), (-23,21), (13,21), (15,21), (17,21), (19,21), (21,21), (23,21), (25,21), (-25,19), (-23,19), (9,19), (11,19), (17,19), (21,19), (23,19), (27,19), (-27,17), (-25,17), (-23,17), (-21,17), (-19,17), (-17,17), (-15,17), (9,17), (13,17), (15,17), (17,17), (19,17), (21,17), (23,17), (25,17), (27,17), (-31,15), (-29,15), (-23,15), (-21,15), (-19,15), (-15,15), (9,15), (11,15), (19,15), (21,15), (-33,13), (-31,13), (-29,13), (-25,13), (-21,13), (-19,13), (-17,13), (-15,13), (9,13), (27,13), (29,13), (-33,11), (-29,11), (-27,11), (-25,11), (-23,11), (-19,11), (-17,11), (25,11), (27,11), (29,11), (-33,9), (-29,9), (9,9), (13,9), (15,9), (17,9), (19,9), (21,9), (23,9), (31,9), (33,9), (35,9), (-31,7), (-25,7), (-23,7), (7,7), (9,7), (25,7), (33,7), (35,7), (-35,5), (-31,5), (-27,5), (-25,5), (7,5), (9,5), (15,5), (17,5), (19,5), (21,5), (25,5), (29,5), (31,5), (35,5), (-35,3), (-31,3), (-27,3), (7,3), (9,3), (11,3), (13,3), (17,3), (21,3), (25,3), (27,3), (-27,1), (7,1), (9,1), (15,1), (19,1), (21,1), (23,1), (27,1), (-29,-1), (-27,-1), (-25,-1), (-23,-1), (7,-1), (9,-1), (11,-1), (13,-1), (19,-1), (21,-1), (23,-1), (27,-1), (-29,-3), (-25,-3), (13,-3), (15,-3), (19,-3), (23,-3), (27,-3), (-25,-5), (-23,-5), (-21,-5), (13,-5), (15,-5), (17,-5), (21,-5), (-23,-7), (-21,-7), (-19,-7), (15,-7), (17,-7), (21,-7), (-21,-9), (-19,-9), (15,-9), (17,-9), (21,-9), (-19,-11), (-17,-11), (17,-11), (21,-11), (-19,-13), (-17,-13), (-15,-13), (-13,-13), (-11,-13), (-9,-13), (17,-13), (-21,-15), (-19,-15), (-15,-15), (-13,-15), (-11,-15), (-9,-15), (-7,-15), (-5,-15), (17,-15), (21,-15), (-15,-17), (-13,-17), (-11,-17), (-9,-17), (17,-17), (21,-17), (-13,-19), (-9,-19), (17,-19), (21,-19), (-15,-21), (-9,-21), (19,-21), (-15,-23), (-11,-23), (-13,-25), (-13,-27)]
mjuniper_points = [(-23,-13)]

point_name_pairing = [("venus", venus_points),("mwasabi", mwasabi_points),("azurite", azurite_points),("electra2", electra2_points),("mclover3", mclover3_points),("mjuniper", mjuniper_points)]

# Robot deck setup constants
TIP_RACK_DECK_SLOT = 9
COLORS_DECK_SLOT = 6
AGAR_DECK_SLOT = 5
PIPETTE_STARTING_TIP_WELL = 'A1'

# Place the PCR tubes in this order
well_colors = {
    'A1': 'sfGFP',
    'A2': 'mRFP1',
    'A3': 'mKO2',
    'A4': 'Venus',
    'A5': 'mKate2_TF',
    'A6': 'Azurite',
    'A7': 'mCerulean3',
    'A8': 'mClover3',
    'A9': 'mJuniper',
    'A10': 'mTurquoise2',
    'A11': 'mBanana',
    'A12': 'mPlum',
    'B1': 'Electra2',
    'B2': 'mWasabi',
    'B3': 'mScarlet_I',
    'B4': 'mPapaya',
    'B5': 'eqFP578',
    'B6': 'tdTomato',
    'B7': 'DsRed',
    'B8': 'mKate2',
    'B9': 'EGFP',
    'B10': 'mRuby2',
    'B11': 'TagBFP',
    'B12': 'mChartreuse_TF',
    'C1': 'mLychee_TF',
    'C2': 'mTagBFP2',
    'C3': 'mEGFP',
    'C4': 'mNeonGreen',
    'C5': 'mAzamiGreen',
    'C6': 'mWatermelon',
    'C7': 'avGFP',
    'C8': 'mCitrine',
    'C9': 'mVenus',
    'C10': 'mCherry',
    'C11': 'mHoneydew',
    'C12': 'TagRFP',
    'D1': 'mTFP1',
    'D2': 'Ultramarine',
    'D3': 'ZsGreen1',
    'D4': 'mMiCy',
    'D5': 'mStayGold2',
    'D6': 'PA_GFP'
}

volume_used = {
    'venus': 0,
    'mwasabi': 0,
    'azurite': 0,
    'electra2': 0,
    'mclover3': 0,
    'mjuniper': 0
}

def update_volume_remaining(current_color, quantity_to_aspirate):
    rows = string.ascii_uppercase
    for well, color in list(well_colors.items()):
        if color == current_color:
            if (volume_used[current_color] + quantity_to_aspirate) > 250:
                # Move to next well horizontally by advancing row letter, keeping column number
                row = well[0]
                col = well[1:]
                
                # Find next row letter
                next_row = rows[rows.index(row) + 1]
                next_well = f"{next_row}{col}"
                
                del well_colors[well]
                well_colors[next_well] = current_color
                volume_used[current_color] = quantity_to_aspirate
            else:
                volume_used[current_color] += quantity_to_aspirate
            break

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

    # 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])

    # Deep Well Plate
    temperature_plate = protocol.load_labware('nest_96_wellplate_2ml_deep', 6)

    # Agar Plate
    agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate')
    agar_plate.set_offset(x=0.00, y=0.00, z=Z_VALUE_AGAR)

    # 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)
    
    # Helper function (dispensing)
    def dispense_and_jog(pipette, volume, location):
        assert(isinstance(volume, (int, float)))
        # Go above the location
        above_location = location.move(types.Point(z=location.point.z + 2))
        pipette.move_to(above_location)
        # Go downwards and dispense
        pipette.dispense(volume, location)
        # Go upwards to avoid smearing
        pipette.move_to(above_location)

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

    # Print pattern by iterating over lists
    for i, (current_color, point_list) in enumerate(point_name_pairing):
        # Skip the rest of the loop if the list is empty
        if not point_list:
            continue

        # Get the tip for this run, set the bacteria color, and the aspirate bacteria of choice
        pipette_20ul.pick_up_tip()
        max_aspirate = int(18 // POINT_SIZE) * POINT_SIZE
        quantity_to_aspirate = min(len(point_list)*POINT_SIZE, max_aspirate)
        update_volume_remaining(current_color, quantity_to_aspirate)
        pipette_20ul.aspirate(quantity_to_aspirate, location_of_color(current_color))

        # Iterate over the current points list and dispense them, refilling along the way
        for i in range(len(point_list)):
            x, y = point_list[i]
            adjusted_location = center_location.move(types.Point(x, y))

            dispense_and_jog(pipette_20ul, POINT_SIZE, adjusted_location)
            
            if pipette_20ul.current_volume == 0 and len(point_list[i+1:]) > 0:
                quantity_to_aspirate = min(len(point_list[i:])*POINT_SIZE, max_aspirate)
                update_volume_remaining(current_color, quantity_to_aspirate)
                pipette_20ul.aspirate(quantity_to_aspirate, location_of_color(current_color))

        # Drop tip between each color
        pipette_20ul.drop_tip()

In the lab, we uploaded the design protocol to the Opentrons, loaded the trays with the engineered E. coli, the black (charcoal) agar plate, pipette tips, and a “trash” bin. It was fascinating to watch the machine work. I was especially happy to discover that the Opentrons OT-2 operates using a 3D gantry system - very similar to 3D printers and CNC cutters - which made it very intuitive for me to use (and fun to watch).

After “the print” was finished, we placed the agar plates in the incubator overnight and photographed them under UV light the following day.

The results were AMAZING!

My Earth design:

My Cross-Stitch Rose design:

All of the amazing designs students have made:

On Saturday, I had the honor of visiting the Ginkgo Bioworks labs in Boston, where I saw how the Nebula (the RAC system at Ginkgo Bioworks) works, and even loaded another design of mine onto it. This time, I used a rectangular composition and painted the Israeli Sabra cactus - or in modern Hebrew, Tzabar - which reminds me of sweet childhood memories and my lovely country.

Here it is - My Tzabar Cactus design:

This definitely won’t be my last experiment with bio art - I’m already looking forward to bringing lab automation into my final project.

*Also, this cool idea reminded me of a game I used to play whenever I was bored. I won’t tell you anything about it —-except that it involves koalas. Here is the link to the game