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.