Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class assignment – designing policy frameworks around bioengineering tools ⭐⭐ Web app with policy homework content ⭐⭐ (external link) 🔗✏️ Proof-of-work links (drafts, AI conversations/prompts used to brainstorm, generate the web app, and other sections) ✏️🔗 HTGAA 2026: Week 1 Governance Framework Project: DIY Aging Biomarkers Kit for Community Labs Objective: To lower the single biggest barrier to longevity research (cost) through an affordable, open-source testing kit.
Week 2 HW: DNA Sequencing and Synthesis
PART 2 path to image: 2026a-zoe-isabel-senon/webpages/src/branch/main/assets/images/heartsim.jpg (I tried to recreate a heart shape…) I did the digest simulation in Benchling and checked the virtual gel simulation result: image in: 2026a-zoe-isabel-senon/webpages/src/branch/main/assets/images/benchlingdigest1.jpg image in: 2026a-zoe-isabel-senon/webpages/src/branch/main/assets/images/benchlingdigest2.jpg 3.1 PICK A PROTEIN & Find the protein sequence: I picked SIRT1
Week 3 HW: Lab Automation 🎨 Assignment: Python Script for Opentrons Artwork Link: https://colab.research.google.com/drive/1Yw0ZrnxIz1kG73b_9PcuZNgXGv6uQy9s?usp=sharing mscarlet_i_points = [(-17.6, 17.6),(-15.4, 17.6),(-13.2, 17.6),(-11, 17.6),(-8.8, 17.6),(-6.6, 17.6),(-4.4, 17.6),(-2.2, 17.6),(0, 17.6),(2.2, 17.6),(4.4, 17.6),(6.6, 17.6),(8.8, 17.6),(11, 17.6),(13.2, 17.6),(15.4, 17.6),(17.6, 17.6),(19.8, 17.6),(-17.6, 15.4),(-15.4, 15.4),(-13.2, 15.4),(-11, 15.4),(-8.8, 15.4),(-6.6, 15.4),(-4.4, 15.4),(-2.2, 15.4),(0, 15.4),(2.2, 15.4),(4.4, 15.4),(6.6, 15.4),(8.8, 15.4),(11, 15.4),(13.2, 15.4),(15.4, 15.4),(17.6, 15.4),(19.8, 15.4),(-17.6, 13.2),(-15.4, 13.2),(-13.2, 13.2),(-11, 13.2),(-8.8, 13.2),(-6.6, 13.2),(-4.4, 13.2),(-2.2, 13.2),(0, 13.2),(2.2, 13.2),(4.4, 13.2),(6.6, 13.2),(8.8, 13.2),(11, 13.2),(13.2, 13.2),(15.4, 13.2),(17.6, 13.2),(19.8, 13.2),(-17.6, 11),(-15.4, 11),(-13.2, 11),(-11, 11),(-8.8, 11),(-6.6, 11),(-4.4, 11),(-2.2, 11),(0, 11),(2.2, 11),(4.4, 11),(6.6, 11),(8.8, 11),(11, 11),(13.2, 11),(15.4, 11),(17.6, 11),(19.8, 11),(-17.6, 8.8),(-15.4, 8.8),(-13.2, 8.8),(-11, 8.8),(-6.6, 8.8),(-4.4, 8.8),(-2.2, 8.8),(0, 8.8),(2.2, 8.8),(4.4, 8.8),(6.6, 8.8),(8.8, 8.8),(13.2, 8.8),(15.4, 8.8),(17.6, 8.8),(19.8, 8.8),(-17.6, 6.6),(-15.4, 6.6),(-13.2, 6.6),(-11, 6.6),(-6.6, 6.6),(-4.4, 6.6),(-2.2, 6.6),(0, 6.6),(2.2, 6.6),(4.4, 6.6),(6.6, 6.6),(8.8, 6.6),(13.2, 6.6),(15.4, 6.6),(17.6, 6.6),(19.8, 6.6),(-17.6, 4.4),(-15.4, 4.4),(-13.2, 4.4),(-11, 4.4),(-6.6, 4.4),(-4.4, 4.4),(-2.2, 4.4),(0, 4.4),(2.2, 4.4),(4.4, 4.4),(6.6, 4.4),(8.8, 4.4),(13.2, 4.4),(15.4, 4.4),(17.6, 4.4),(19.8, 4.4),(-17.6, 2.2),(-15.4, 2.2),(-13.2, 2.2),(-11, 2.2),(-8.8, 2.2),(-6.6, 2.2),(-4.4, 2.2),(-2.2, 2.2),(0, 2.2),(2.2, 2.2),(4.4, 2.2),(6.6, 2.2),(8.8, 2.2),(11, 2.2),(13.2, 2.2),(15.4, 2.2),(17.6, 2.2),(19.8, 2.2),(-24.2, 0),(-22, 0),(-19.8, 0),(-17.6, 0),(-15.4, 0),(-13.2, 0),(-11, 0),(-8.8, 0),(-6.6, 0),(-4.4, 0),(-2.2, 0),(0, 0),(2.2, 0),(4.4, 0),(6.6, 0),(8.8, 0),(11, 0),(13.2, 0),(15.4, 0),(17.6, 0),(19.8, 0),(22, 0),(24.2, 0),(26.4, 0),(-24.2, -2.2),(-22, -2.2),(-19.8, -2.2),(-17.6, -2.2),(-15.4, -2.2),(-13.2, -2.2),(-11, -2.2),(-8.8, -2.2),(-6.6, -2.2),(-4.4, -2.2),(-2.2, -2.2),(0, -2.2),(2.2, -2.2),(4.4, -2.2),(6.6, -2.2),(8.8, -2.2),(11, -2.2),(13.2, -2.2),(15.4, -2.2),(17.6, -2.2),(19.8, -2.2),(22, -2.2),(24.2, -2.2),(26.4, -2.2),(-24.2, -4.4),(-22, -4.4),(-19.8, -4.4),(-17.6, -4.4),(-15.4, -4.4),(-13.2, -4.4),(-11, -4.4),(-8.8, -4.4),(-6.6, -4.4),(-4.4, -4.4),(-2.2, -4.4),(0, -4.4),(2.2, -4.4),(4.4, -4.4),(6.6, -4.4),(8.8, -4.4),(11, -4.4),(13.2, -4.4),(15.4, -4.4),(17.6, -4.4),(19.8, -4.4),(22, -4.4),(24.2, -4.4),(26.4, -4.4),(-17.6, -6.6),(-15.4, -6.6),(-13.2, -6.6),(-11, -6.6),(-8.8, -6.6),(-6.6, -6.6),(-4.4, -6.6),(-2.2, -6.6),(0, -6.6),(2.2, -6.6),(4.4, -6.6),(6.6, -6.6),(8.8, -6.6),(11, -6.6),(13.2, -6.6),(15.4, -6.6),(17.6, -6.6),(19.8, -6.6),(-17.6, -8.8),(-15.4, -8.8),(-13.2, -8.8),(-11, -8.8),(-8.8, -8.8),(-6.6, -8.8),(-4.4, -8.8),(-2.2, -8.8),(0, -8.8),(2.2, -8.8),(4.4, -8.8),(6.6, -8.8),(8.8, -8.8),(11, -8.8),(13.2, -8.8),(15.4, -8.8),(17.6, -8.8),(19.8, -8.8),(-17.6, -11),(-15.4, -11),(-13.2, -11),(-11, -11),(-8.8, -11),(-6.6, -11),(-4.4, -11),(-2.2, -11),(0, -11),(2.2, -11),(4.4, -11),(6.6, -11),(8.8, -11),(11, -11),(13.2, -11),(15.4, -11),(17.6, -11),(19.8, -11),(-13.2, -13.2),(-11, -13.2),(-6.6, -13.2),(-4.4, -13.2),(6.6, -13.2),(8.8, -13.2),(13.2, -13.2),(15.4, -13.2),(-13.2, -15.4),(-11, -15.4),(-6.6, -15.4),(-4.4, -15.4),(6.6, -15.4),(8.8, -15.4),(13.2, -15.4),(15.4, -15.4),(-13.2, -17.6),(-11, -17.6),(-6.6, -17.6),(-4.4, -17.6),(6.6, -17.6),(8.8, -17.6),(13.2, -17.6),(15.4, -17.6),(-13.2, -19.8),(-11, -19.8),(-6.6, -19.8),(-4.4, -19.8),(6.6, -19.8),(8.8, -19.8),(13.2, -19.8),(15.4, -19.8)] mjuniper_points = [(-4.4, 28.6),(-2.2, 28.6),(0, 28.6),(2.2, 28.6),(4.4, 28.6),(-4.4, 26.4),(-2.2, 26.4),(2.2, 26.4),(4.4, 26.4),(-4.4, 24.2),(-2.2, 24.2),(2.2, 24.2),(4.4, 24.2),(-6.6, 22),(-4.4, 22),(-2.2, 22),(2.2, 22),(4.4, 22),(6.6, 22),(-6.6, 19.8),(-4.4, 19.8),(-2.2, 19.8),(0, 19.8),(2.2, 19.8),(4.4, 19.8),(6.6, 19.8)] mturquoise2_points = [(0, 26.4),(0, 24.2),(0, 22)] 📖 Assigment: Automation paper “Automated Cell Culture Splitter (ACCS): An open-source benchtop system for cell passaging with integrated cell counting” — PNAS Nexus, December 2025
Week 4 HW: Protein Design Part I
⛓️ Collab Notebook Link ⛓️ Link to the Colab for the chosen protein (FOXO3): Collab notebook 💡 PART A - CONCEPTUAL QUESTIONS How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons)
Week 5 HW: Protein Design Part II
🔎 Part 1: Generate Binders with PepMLM Sequence with mutation: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ ![[htgaa-hw5-pt1-binders.png]] In text, the generated ones (plus the one provided to compare) were: 0 WRYYAAALRHKX 9.957530 1 WRYYAVAARHKK 13.948671 2 WRSYVVVLELGX 18.185468 3 HHYPAVAVALKX 7.987091 4 FLYRWLPSRRGG 20.635231 AlphaFold however was throwing errors with these sequences, so I asked Claude to check: ![[Screenshot 2026-03-08 at 17.05.41.png]]
Week 6 HW: Genetic Circuits Part I
SECTION 1: PCR & GIBSON ASSEMBLY “What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? It is composed of 3 essential components: 1. Phusion DNA Polymerase: a high-fidelity enzyme with low error rates (50x higher fidelity than Taq) and fast extension speeds (15-30sec/kilobase) 2. dNTPs (deoxynucleotide triphosates) (dATP, dCTP,dGTP, dTTP): the nucleotide building blocks the polymerase incorporates into the DNA starnd it builds 3. An optimized reaction buffer containing Mg(^2+) ions (polymerase cofactor that also stabilizes annealing) and KCl, which promotes specific primer binding while suppressing non-specific interactions. The Green Master Mix also contains other reagents (green dye, density reagents) so the reaction can be directly loaded into an agarose gel.
Week 7 HW: Genetic Circuits Part II
PART 0 1. How do ERNs work + how this differs from proteases They cleave mRNA transcripts before they can be translated into proteins, so the mRNA is not processed by the ribosomes and gets degraded quickly by cellular exonucleases. They work directly at the RNA level, unlike proteases which work on the final translated proteins. This means that they prevent new proteins from being produced, but they do not affect the existing pool of proteins.
Week 9 Homework: Cell-Free Systems [WIP!] Homework Part A: General and Lecturer-Specific Questions General homework questions Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production. The benefit can be summarized as “it removes the constraints we usually face for protein synthesis when working with live cells”. For example, working with live cells requires culturing cells throughout the whole cell lifecycle, with all the possibilities for error that this implies (mistakes, unexpected cell behavior due to their non-deterministic nature, etc), as well as the required timelines (speed is limited by the fundamental speed constraints from the cell growth cycle), and costs. Cell-free systems also allow for much greater control, as the main system is boiled down to its most basic functional components, removing a lot of complexity (variables outside of our control), and therefore allowing the possibility of producing much more homogeneous products.
Week 10 Homework: Mass Spectrometry