Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Describe a biological engineering application or tool you want to develop and why. One application that might be worth exploring would be in the realm of data storage for an imagined, hypothetical semi-exposed media. For this context special proteins could be designed in applications that bind to sequences that code for hidden malware or faulty sequences and or act for preserving media. I imagine that both this media design and this protein use would be niche but nonetheless fun to design for. Modalities could be as a gentle spray or as a settled solution that could be extracted.
Week 2 HW: DNA Read, Write, and Edit
Part 0: Basics of Gel Electrophoresis [This was a pure watch session. Thus there’s nothing to add here.] Part 1: Benchling & In-silico Gel Art Restriction Enzymes Simulated on Lambda_NEB: EcoRI, HindIII, BamHI, KpnI, EcoRV, SacI, and SalI Simple Art produced by way of Paul Vanouse’s Latent Figure Protocol artworks through the use of RC Donovan’s Gel Art Iteration Tool (https://rcdonovan.com/gel-art): “4 corners”, using EcoRI and SalI in Lanes 1 and 10.
Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. DeRoo, J.B., Jones, A.A., Slaughter, C.K., Ahr, T.W., Stroup, S.M., Thompson, G.B. and Snow, C.D., 2025. Automation of protein crystallization scaleup via Opentrons-2 liquid handling. SLAS technology, 32, p.100268. https://doi.org/10.1016/j.slast.2025.100268 This work describes an approach by which an Opentrons-2 liquid handling robot was used for automating sitting drop protein crystallization trials. This ability also improve comparability of products produced, improving studies that depend on their proper manufacture. An important detail is how the Opentrons-2 can prove a cost-effective option for laboratory operations. For example, at the time of writing, the Opentrons-2 can be purchased for around 13.5K USD vs that of a Gryphon machine at around 65K USD.