Homework

Weekly homework submissions:

  1. First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. For HTGAA 2026, I’d like to propose the design and development of a synthetic biology based microbial system for the improvement of agricultural productivity in saline soils of the Bolivian Altiplano. This is because oil salinization is continuing to progress in the high-altitude areas of Bolivia as a consequence of climate change, water shortage and historical land use (Andrade, 2025). According to the Food and Agriculture Organization (n.d.), already a considerable fraction of irrigated and arid agricultural lands worldwide face the challenge of soil salinity. Scientific studies have shown that soil salinity significantly reduces crop yields, alters soil biological functions, and directly threatens food security, particularly in smallholder farming systems (Farooq et al., 2021). In the same way, the majority of smallholder farmers in the Altiplano rely on marginal soils, often where conventional fertilizers cannot be used effectively or are economically unaffordable and are a direct threat to local food security and livelihoods from salinization. This is why my proposed project aims to investigate the conceptual design for soil microorganisms that can sense such high salinity and improve soil structure and plant stress tolerance. However, beyond its technical feasibility, this application raises relevant ethical, environmental and governance issues surrounding environmental release and biosafety and also equitable access to biotechnology. Finally, as a Bolivian, I see this work as an opportunity to link cutting edge biological engineering with locally anchored solutions that address real challenges faced by vulnerable agricultural communities in my country.

  • Week 2 HW: DNA Read, Write, & Edit

    HOMEWORK 2 Part 1: Benchling & In-silico Gel Art See this week’s lab protocol “Gel Art: Restriction Digests and Gel Electrophoresis” for details. Overview: Make a free account at benchling.com Import the Lambda DNA. Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. You might find Ronan’s website a helpful tool for quickly iterating on designs! HOMEWORK RESULTS :)

  • Week 3 HW: Lab Automation

    Assignment: Python Script for Opentrons Artwork Link: https://colab.research.google.com/drive/1G9DLa7Y6og9m0Ik8HrF0KU1YG555WzoK?usp=sharing MY CODE: import math ################################ GREEN SECTION (Body + Flagella) ################################ pipette_20ul.pick_up_tip() center = center_location Oval body: a = 16 b = 8 points = 40 for i in range(points): if i % 8 == 0: pipette_20ul.aspirate(8, location_of_color('Green')) angle = 2 * math.pi * i / points x = a * math.cos(angle) y = b * math.sin(angle) loc = center.move(types.Point(x=x, y=y, z=0)) dispense_and_detach(pipette_20ul, 1, loc) Flagella: