WEEK 03

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(c) Flo Razoux, AI generated

Subsections of WEEK 03

Lab Automation

1.Python Script for Opentrons Artwork

Generation of a glowing uterus in GUI

HOW IT STARTED cover image cover image

HOW IT’S GOING cover image cover image


DOCUMENTATION

(1) Searching for “uterus image vector” on the web (2) Loading best image (simple graphic design and good color contrast) in Automation Art Interface (3) Adjusting Zoom (0.9), Brightness (70%), Contrast (110%) Pixelation (-10%) and Saturation (300%) (4) Refining design manually (incl. testing different colorations) (5) Exporting coordinates: mscarlet_i_points = [(-7.7, 20.9),(-5.5, 20.9),(-3.3, 20.9),(-1.1, 20.9),(1.1, 20.9),(3.3, 20.9),(5.5, 20.9),(7.7, 20.9),(-14.3, 18.7),(-12.1, 18.7),>(-9.9, 18.7),(-7.7, 18.7),(7.7, 18.7),(9.9, 18.7),(12.1, 18.7),(14.3, 18.7),(-29.7, 16.5),(-27.5, 16.5),(-25.3, 16.5),(-23.1, 16.5),(-20.9, 16.5),(-18.7, 16.5),(-16.5, 16.5),(-14.3, 16.5),(-12.1, 16.5),(-5.5, 16.5),(-3.3, 16.5),(-1.1, 16.5),(1.1, 16.5),(3.3, 16.5),(5.5, 16.5),(12.1, 16.5),(14.3, 16.5),(16.5, 16.5),(18.7, 16.5),(20.9, 16.5),(23.1, 16.5),(25.3, 16.5),(27.5, 16.5),(29.7, 16.5),(-31.9, 14.3),(-29.7, 14.3),(-27.5, 14.3),(-25.3, 14.3),(-23.1, 14.3),(-20.9, 14.3),(-18.7, 14.3),(-16.5, 14.3),(-9.9, 14.3),(-7.7, 14.3),(-5.5, 14.3),(-3.3, 14.3),(-1.1, 14.3),(1.1, 14.3),(3.3, 14.3),(5.5, 14.3),(7.7, 14.3),(9.9, 14.3),(16.5, 14.3),(18.7, 14.3),(20.9, 14.3),(23.1, 14.3),(25.3, 14.3),(27.5, 14.3),(29.7, 14.3),(31.9, 14.3),(-34.1, 12.1),(-31.9, 12.1),(-29.7, 12.1),(-16.5, 12.1),(-14.3, 12.1),(-12.1, 12.1),(-9.9, 12.1),(-7.7, 12.1),(-5.5, 12.1),(-3.3, 12.1),(-1.1, 12.1),(1.1, 12.1),(3.3, 12.1),(5.5, 12.1),(7.7, 12.1),(9.9, 12.1),(12.1, 12.1),(16.5, 12.1),(29.7, 12.1),(31.9, 12.1),(34.1, 12.1),(-34.1, 9.9),(-29.7, 9.9),(-14.3, 9.9),(-12.1, 9.9),(-9.9, 9.9),(-7.7, 9.9),(-5.5, 9.9),(-3.3, 9.9),(-1.1, 9.9),(1.1, 9.9),(3.3, 9.9),(5.5, 9.9),(7.7, 9.9),(9.9, 9.9),(14.3, 9.9),(29.7, 9.9),(34.1, 9.9),(-34.1, 7.7),(-29.7, 7.7),(-27.5, 7.7),(-25.3, 7.7),(-14.3, 7.7),(-12.1, 7.7),(-9.9, 7.7),(-7.7, 7.7),(-5.5, 7.7),(-3.3, 7.7),(-1.1, 7.7),(1.1, 7.7),(3.3, 7.7),(5.5, 7.7),(7.7, 7.7),(12.1, 7.7),(14.3, 7.7),(25.3, 7.7),(27.5, 7.7),(34.1, 7.7),(-34.1, 5.5),(-23.1, 5.5),(-12.1, 5.5),(-9.9, 5.5),(-7.7, 5.5),(-5.5, 5.5),(-3.3, 5.5),(-1.1, 5.5),(1.1, 5.5),(3.3, 5.5),(5.5, 5.5),(7.7, 5.5),(12.1, 5.5),(23.1, 5.5),(34.1, 5.5),(-34.1, 3.3),(-23.1, 3.3),(-20.9, 3.3),(-12.1, 3.3),(-9.9, 3.3),(-7.7, 3.3),(-5.5, 3.3),(-3.3, 3.3),(-1.1, 3.3),(1.1, 3.3),(3.3, 3.3),(5.5, 3.3),(12.1, 3.3),(20.9, 3.3),(23.1, 3.3),(34.1, 3.3),(-31.9, 1.1),(-18.7, 1.1),(-12.1, 1.1),(-9.9, 1.1),(-7.7, 1.1),(-5.5, 1.1),(-3.3, 1.1),(-1.1, 1.1),(1.1, 1.1),(3.3, 1.1),(5.5, 1.1),(9.9, 1.1),(12.1, 1.1),(18.7, 1.1),(31.9, 1.1),(-31.9, -1.1),(-18.7, -1.1),(-9.9, -1.1),(-7.7, -1.1),(-5.5, -1.1),(-3.3, -1.1),(-1.1, -1.1),(1.1, -1.1),(3.3, -1.1),(9.9, -1.1),(18.7, -1.1),(31.9, -1.1),(-29.7, -3.3),(-27.5, -3.3),(-20.9, -3.3),(-9.9, -3.3),(-7.7, -3.3),(-5.5, -3.3),(-3.3, -3.3),(-1.1, -3.3),(1.1, -3.3),(3.3, -3.3),(7.7, -3.3),(9.9, -3.3),(20.9, -3.3),(27.5, -3.3),(29.7, -3.3),(-25.3, -5.5),(-23.1, -5.5),(-7.7, -5.5),(-5.5, -5.5),(-3.3, -5.5),(-1.1, -5.5),(1.1, -5.5),(3.3, -5.5),(7.7, -5.5),(23.1, -5.5),(25.3, -5.5),(-7.7, -7.7),(-5.5, -7.7),(-3.3, -7.7),(-1.1, -7.7),(1.1, -7.7),(7.7, -7.7),(-7.7, -9.9),(-3.3, -9.9),(-1.1, -9.9),(1.1, -9.9),(7.7, -9.9),(-7.7, -12.1),(-3.3, -12.1),(-1.1, -12.1),(1.1, -12.1),(3.3, -12.1),(7.7, -12.1),(-7.7, -14.3),(-5.5, -14.3),(5.5, -14.3),(7.7, -14.3),(-5.5, -16.5),(5.5, -16.5),(-5.5, -18.7),(-3.3, -18.7),(3.3, -18.7),(5.5, -18.7),(-5.5, -20.9),(-3.3, -20.9),(3.3, -20.9),(5.5, -20.9),(-5.5, -23.1),(-3.3, -23.1),(3.3, -23.1),(5.5, -23.1),(-5.5, -25.3),(-3.3, -25.3),(3.3, -25.3),(5.5, -25.3),(-5.5, -27.5),(-3.3, -27.5),(3.3, -27.5),(5.5, -27.5),(-5.5, -29.7),(-3.3, -29.7),(3.3, -29.7),(5.5, -29.7)] mko2_points = [(14.3, 12.1),(12.1, 9.9),(-31.9, 7.7),(9.9, 7.7),(31.9, 7.7),(-29.7, 5.5),(9.9, 5.5),(29.7, 5.5),(-29.7, 3.3),(-27.5, 3.3),(-25.3, 3.3),(7.7, 3.3),(9.9, 3.3),(25.3, 3.3),(27.5, 3.3),(29.7, 3.3),(-29.7, 1.1),(-27.5, 1.1),(-25.3, 1.1),(-23.1, 1.1),(-20.9, 1.1),(7.7, 1.1),(20.9, 1.1),(23.1, 1.1),(25.3, 1.1),(27.5, 1.1),(29.7, 1.1),(-27.5, -1.1),(-25.3, -1.1),(-23.1, -1.1),(5.5, -1.1),(7.7, -1.1),(23.1, -1.1),(25.3, -1.1),(27.5, -1.1),(5.5, -3.3),(5.5, -5.5),(3.3, -7.7),(5.5, -7.7),(3.3, -9.9)] mrfp1_points = [(-5.5, 18.7),(-3.3, 18.7),(-1.1, 18.7),(1.1, 18.7),(3.3, 18.7),(5.5, 18.7),(-9.9, 16.5),(-7.7, 16.5),(7.7, 16.5),(9.9, 16.5),(-14.3, 14.3),(-12.1, 14.3),(12.1, 14.3),(14.3, 14.3),(-31.9, 9.9),(31.9, 9.9),(29.7, 7.7),(-31.9, 5.5),(-27.5, 5.5),(-25.3, 5.5),(25.3, 5.5),(27.5, 5.5),(31.9, 5.5),(-31.9, 3.3),(31.9, 3.3),(-29.7, -1.1),(-20.9, -1.1),(20.9, -1.1),(29.7, -1.1),(-25.3, -3.3),(-23.1, -3.3),(23.1, -3.3),(25.3, -3.3),(-5.5, -9.9),(5.5, -9.9),(-5.5, -12.1),(5.5, -12.1),(-3.3, -14.3),(-1.1, -14.3),(1.1, -14.3),(3.3, -14.3),(-3.3, -16.5),(-1.1, -16.5),(1.1, -16.5),(3.3, -16.5),(-1.1, -18.7),(1.1, -18.7),(-1.1, -20.9),(1.1, -20.9),(-1.1, -23.1),(1.1, -23.1),(-1.1, -25.3),(1.1, -25.3),(-1.1, -27.5),(1.1, -27.5)]

(6) Laptop/internet crashed before submission for publication in the gallery 😢

HTGAA26 Opentrons Colab Textbook

HOW IT STARTED cover image cover image

HOW IT’S GOING cover image cover image


DOCUMENTATION ChatGPT was used to (1) understand code lines from the CoLab examples, (2) understand and fix errors when trying to write my own code from the CoLab examples, (3) and later when trying to adapt the code downloaded from Ronan Donovan’s AAI. Step (2) and (3) were not successful despite many attempts. At last, documentation of other students were checked and the code of the design Golden Lyre by Katherine Kolin was used as a base. The code was easily adapted and the first test images were generated in Colab quickly after.

Glowing Uterus Colab Code

Finally, coloring tests were made to get as close as possible of the fluorescent images published in the gallery

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2.Post-Lab Questions

To be updated on March 10th

Final project ideas

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FINAL PROJECT IDEA 01 | BIOLUMINESCENT MENSTRUAL BLOOD (BIOART INSTALLATION)

Fields: Bioart, menstrual health, microbiota medicine.

Main goal: Raise awareness of the societal impact of scientific bias and the urgent need to invest in neglected research fields + potential of synthetic biology for bringing insights into menstrual health.

Methods: Option 01 Change the genome of bioluminescent marine microorganisms to help them adapt to a liquid culture made of menstrual blood serum and elicit a photonic response under specific stimuli (biosensor approach) Option 02 Insert luciferase/luciferin genes into vaginal microbiota to monitor early “cellular ecosystem” biomarkers (biosensor approach) Option 03 Create a protein ressembling hemoglobin with luciferase properties that produce light when binding to dioxygen (design approach)

Documentation: https://pages.htgaa.org/2026a/flo-razoux/homework/week-01-hw-principles-and-practices/hw-governance/index.html

FINAL PROJECT IDEA 02 | GROWING AN EGGPLANT

Fields: Trans health & medicine, organoids, regenerative medicine.

Main goal: Inducing extended clitoral growth in FTM transgender patients to avoid or optimize phalloplasty/metoidioplasty surgical procedures (hybrid methods), which are currently heavy and often yield suboptimal outcomes in terms of sensation and function.

Methods: Gene-circuit strategy applied locally (corpora cavernosa) to reopen or bypass embryonic gene programs that locked the penile or/and clitoral architecture. Reactivation of the expression of the genes involved in tissue growth such as androgens receptors or SRY downstream targets.

Documentation: What is Bottom Growth? A trans perspective: https://www.tiktok.com/@bugandalex/video/7287946425164434720 ChatGPT, prompt: “What are the biological mechanisms underlying bottom-growth, and why does growth stops at the some point?” https://chatgpt.com/s/t_699c7b5178e48191aa41ad42cddf2e9b ChatGPT, prompt: “According to previous discussion, how could synthetic biology be implemented to “unlock” the bottom-growth ceiling?” https://chatgpt.com/s/t_699c7c245f1081919576d9e7d082bc98

FINAL PROJECT IDEA 03 | ENGINEERED SPERMATOZOA AS PRECISION MICRO-CARRIERS

Fields: Reproductive medicine, targeted drug delivery.

Main goal: Use of engineered spermatozoa as micro-carriers for localized drug delivery in the reproductive tract (and in a second step, possibly via blood stream).

Methods: This would depend on the application: targeted uterine/ovarian cancer, anti-proliferative therapy in endometriosis, or contraceptive innovation.

Documentation: ChatGPT, prompt: “Write a list of applications on how sperm cells could be used to deliver drugs locally, with a focus on reproductive health” https://chatgpt.com/s/t_699c7e1d63f88191a129fdab9c3b69a4

FINAL PROJECT IDEA 04 | SENSE 8

Fields: Neuroscience, human augmentation.

Main goal: Restore, enhance and expand human sensory capacity by modulating the expression of genes involved in sensory processing: increase sensory sensitivity, discrimination, and even enable detection of novel chemical/physical stimuli.

Documentation: ChatGPT, prompt: “How would you pitch a project on using synthetic biology to enhance senses (especially the olfaction). Please suggest different directions to explore” https://chatgpt.com/s/t_699e3902307c8191bb9abf5aa7add2d7

FINAL PROJECT IDEA 05 | MAJOR TOM

Fields: Neuroengineering, haptics, mental health.

Main goal: Create bio-integrated, programmable mechanosensory systems that replicate natural touch perception at the cellular level. Applications: immersive VR experiences and therapeutic solutions for touch deprivation in isolation or long-duration space travel.

Documentation: ChatGPT, prompt: “How would you pitch a project on using synthetic biology to mimic the sense of touch to be implemented for instance in VR, or to avoid touch deprivation in case of isolation or during long-duration spaceflight. Please include biology background (mecano receptors in the skin specific to different types of touch)” https://chatgpt.com/s/t_699e3ad59224819180390539c385bc9e

FINAL PROJECT IDEA 06 | CHILDREN OF THE MOON

Fields: Radiation physics, cellular stress biology.

Main goal: Engineering gene circuits that detect ionizing radiation–induced molecular damage and trigger a visible alert (e.g. reversible pigmentation change) and possibly a rapid cellular protective response. Applications: acute radiation syndrom, high-risk occupational exposure, Xeroderma Pigmentosum.

Documentation: ChatGPT, prompt: “How would you pitch a project on using synthetic biology to insert a biosensing mechanism in skin cells that could trigger either an alarm (change of skin pigmentation for instance) or a protective cellular response to an immediate risk of acute irradiation exposure? Please include physics background of radiation contamination monitoring devices, biology background on the effects of radiation exposure at the cellular and molecular levels as well as possible protective strategies, if any.” https://chatgpt.com/s/t_699e4925d558819181d04229c849199b