Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class assignment 1. First, describe a biological engineering application or tool you want to develop and why. My brother has autism, which is why this area is personal for me. As a CS/AI master’s student, I find it exciting that I can use AI protein design tools like AlphaFold to work on something that actually matters to me and my family.
Week 2 HW: DNA Read, Write and Edit
Part 1: Benchling & In-silico Gel Art For this exercise, the full genome of Bacteriophage Lambda (GenBank accession J02459.1, 48,502 bp) was imported into Benchling from NCBI. A virtual restriction enzyme digestion was performed using seven enzymes: EcoRI, HindIII, BamHI, KpnI, EcoRV, SacI, and SalI. Each enzyme was applied individually to identify its recognition sites across the Lambda genome. The digest results were visualized using Benchling’s simulated gel electrophoresis tool. To get a nice visual, I tried different ladders and different lane orderings. The final output consisting of for each enzyme’s fragment pattern is below.
Part 1: Python Script Opentron Artwork Opentrons Colab for Source Code My Jelly Smiley Design Part 2: Post-Lab Questions Question 1: Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.