Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Concept Create new BioArt experiences for members of a community MakerSpace where our stated goal is to Make, Learn, and Share. The MakerSpace has recently opened a BioArt Studio, led by Karen Ingram, co-author of “BioBuilder - Synthetic Biology in the Lab” (ISBN 978-1-491-90429-9). My applications are inspired by the innovative use of living systems to create art & design. Concepts incorporate digital imaging, interactive 3d and microprocessing to create algorithmic artwork, influenced and driven by the biological science found in the collection of experimental solutions described below: (Click to expand each item)
Week 2 HW: DNA Read-Write-Edit
Checklist Part 0: Basics of Gel Electrophoresis Attend Lecture (2 of 3) Attend Recitation Review 2025 recording (3 of 3) Part 1: Benchling & In-silico Gel Art Part 2: Gel Art - Restriction Digests and Gel Electrophoresis (Optional- for those with Lab access) Design Simulation Part 3: DNA Design Challenge 3.1 Choose your Protein 3.2 Reverse Translate: Protein (amino acid) sequence to DNA (nucleotide) sequence. 3.3 Codon optimization 3.4. You have a sequence! Now what? 3.5. [Optional] How does it work in nature/biological systems? Part 4: Prepare a Twist DNA Synthesis Order 4.1. Create a Twist account and a Benchling account 4.2. Build Your DNA Insert Sequence 4.3. On Twist, Select The “Genes” Option 4.4. Select “Clonal Genes” option 4.5. Import your sequence 4.6. Choose Your Vector Part 5: DNA Read/Write/Edit 5.1 DNA Read (i) What DNA would you want to sequence (e.g., read) and why? (ii) In lecture, a variety of sequencing technologies were mentioned. What technology or technologies would you use to perform sequencing on your DNA and why? 5.2 DNA Write (i) What DNA would you want to synthesize (e.g., write) and why? (ii) What technology or technologies would you use to perform this DNA synthesis and why? 5.3 DNA Edit (i) What DNA would you want to edit and why? (ii) What technology or technologies would you use to perform these DNA edits and why? Part 1: Benchling & In-silico Gel Art In this section, I was able to successfully sign up for Benchling, request to join HTGAA (pending), and create a new project. I was able to find the Lambda DNA sequence in the FASTA database, which I copied and pasted. I then found the downloadable file in GenBank, which I imported into Benchling. It took me a few tries to get multiple Digests to appear, once I selected multiple restriction enzymes and ordered the tabs before Virtual Digest. I exported the resulting image as a .PNG as well as my NC_001416 Project “Linear Map” and “Sequence Map” as well as the Lambda Map from GenBank, as PDFs for future reference.
Focus on Lab Automation research, with creative examples of OpenTrans instruction sets using Python. Final project slide to be included in Node deck. Opentrons Art This week started witn an exploration of the Opentrons Art web app found at https://opentrons-art.rcdonovan.com I was able to quickly upload an image and randomize the colors, to generate a point paired data set. I really like the bitmap rasterization and creative expression found in the gallery.
Week 4 HW: Protein Design Part I
This week focuses on how sequence, structure, and energetics can be modeled and manipulated to create or optimize proteins with specified functions. Part A - Conceptual Questions For my homework, I initated a conversation with Claude Ai using Sonnet v4.6. My prompts use a method I use to start with a question, allow me to provide my answer, and receive an evaluation of my response with reinforcing key learning concepts. (Expand to see detailed responses to my answers.). I find this approach to be more interactive and leads to better knowledge retention.
Week 5 HW: Protein Design Part II
This week we learned how cutting-edge AI and protein language models are used to design functional proteins and peptides “in silico”. Part A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
This week we learn core molecular biology tools and techniques for processing and assembling DNA, including PCR and Gibson Assembly. Assignment: DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The mix contains DNA Polymerase, known for thermostable accuracy. Used to amplify fragments used in PCR for Gibson Assembly. What are some factors that determine primer annealing temperature during PCR?
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
This week covers neuromorphic genetic circuits, showing how engineered gene networks can implement neural-network “perceptron”-like computation and learning. Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) Q1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Answer: IANNs have many possible responses, reflecting more of a gaussian distribution rather than binary ON/OFF outputs. This allows for gradiated, continuous range or responses versus the step-function behavior of Boolean genetic circuits, making them well-suited for environments with high levels of variability such as changing temperatures, pH, or time.
This week introduces synthesis of proteins using cellular machinery outside of a cell. Section 1: General Homework Questions Question 1 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.
Week 10 HW: Advanced Imaging and Measurement Technology
This week’s lecture presents a range of advanced technologies to do precision measurement of proteins at atomic scales, characterizing chemical composition, and detecting protein sequence and structure. Question 1 — What aspects of your project will you measure? Validity and viability of the pBioLight-1B-eLightOn-v1 plasmid obtained from Twist, confirmed through gel electrophoresis and successful colony growth in E. coli.
Week 11 HW: Bioproduction and Cloud Labs
HTGAA 2026 — Week 11: Bioproduction & Cloud Labs Hypothesis — Version 2.1 This is a hypothesis on the design of a variable luminosity construct based on cell-free protein synthesis. By adding independent reagent modifications to a fixed cell-free DNA and master mix, we hypothesize a measurable delta in sfGFP luminosity relative to the unmodified control, operating on a single mechanistic axis — free Mg2+ availability:
HTGAA Week 12 Homework Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Item 1: Pixel Contribution I contributed to plate #G3, initiating a rose design on April 15. I seeded the concept on Discourse: "#G3 - Starting to build a rose… let’s see what grows!"