Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  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.

• Week 2 HW: DNA Read, Write, & Edit

  Part 1: Benchling & In-silico Gel Art After locating the E. coli phage Lambda genome in the NCBI database, I loaded the sequence into my Benchling project by searching for the GenBank accession number (GenBank: J02459.1): I then went to the DNA Gel Art Interface (https://rcdonovan.com/gel-art) and went through the gallery for inspiration and to observe what bands looked like for the digestion enzymes listed both individually and in combination with one another, taking screenshots of these images to determine which of these I could use as “building blocks” for my image.

• Week 3 HW: Lab Automation

  1. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. I came across the following paper, Brown DM, Phillips DA, Garcia DC, Arce A, Lucci T, Davies JP Jr, Mangini JT, Rhea KA, Bernhards CB, Biondo JR, Blum SM, Cole SD, Lee JA, Lee MS, McDonald ND, Wang B, Perdue DL, Bower XS, Thavarajah W, Karim AS, Lux MW, Jewett MC, Miklos AE, Lucks JB. Semiautomated Production of Cell-Free Biosensors. ACS Synth Biol. 2025 Mar 21;14(3):979-986. doi: 10.1021/acssynbio.4c00703. Epub 2025 Mar 12. PMID: 40073441., that compares the semi-automated production of cell-feee biosensors against manual production, utilizing the Opentron OT-2 liquid handler. I hope to use this and similar papers (I believe Opentron has prepared Python scripts for applications like this that I could modify as needed) as a basis for my final project.

• Week 4 HW: Protein Design Part I

  Coming soon!

• Week 5 HW: Protein Design Part II

  Coming soon!

• Week 6 HW: Genetic Circuits Part I: Assembly Technologies

  Coming soon!

• Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits

  Coming soon!

• Week 9 HW: Cell-Free Systems

  Coming soon!

• Week 10 HW: Advanced Imaging & Measurement Technology

  Coming soon!

• Week 11 HW: Bioproduction & Cloud Labs

  Coming soon!

• Week 12 HW: Building Genomes

  Coming soon!

• Week 13 HW: Biodesign & Engineered Living Materials

  Coming soon!

• Week 14 HW: Bio Design & Bio Fabrication

  Coming soon!