Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment — DUE BY START OF FEB 10 LECTURE Question 01 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. According to the well-regarded popular science writer Matthew Cobb (2022), since the Asilomar conference in 1975, molecular biologists have been the vanguard in self-regulating when playing God. This means we refrain from conducting our research irresponsibly by deploying unnecessarily hazardous experimental methods. Alas, this also means that some of the most exciting genetic engineering is no longer done. Consider Dr. Oswald Avery’s transforming principle experiment. Blindly take a population of virulent pneumonia bacteria and feed them harmless kin until they lose their aggressive function and magically adapt into weak and indifferent pneumonia. Since Asilomar, this is indeed one kind of experiment that trustworthy principal investigators must abstain from. I get it, and still I contemplate. Wasn’t Avery the best of us, though? Between Schrodinger and Watson, Crick, and Franklin – Dr. Avery intuited DNA into existence with his transforming principle and used it effectively. Surely I didn’t name my oldest son after this man for nothing?
Week 2 HW: DNA Read Write and Edit
Table of contents Software used: Terminal, git, xcode, hugo, benchling, rcdonovan website, twist website. Objective: This week explores the read–write–edit toolkit: sequencing and synthesis workflows, restriction digests and gel electrophoresis, and early genome-editing frameworks.
Homework for HTGAA 2026 (Week 03): Lab Automation Table of contents Software used: Terminal, git, Opentrons, rcdonovan website, Google Colab. Objective: This week we get hands-on (or at least code-on) with pipetting robots.
Week 4 HW: Protein Design Part I
Homework: Protein Design I Assignment Objective: Learn basic concepts: amino acid structure, 3D protein visualization, and the variety of ML-based design tools. Brainstorm as a group how to apply these tools to engineer a better bacteriophage (setting the stage for the final project).