Labs
Lab writeups:
This was a lab review week. It covered standard lab practices. There’s nothing to note here aside from that review material from source and concepts below were reviewed. Source: https://thecrashcourse.com/courses/unit-conversion-significant-figures-crash-course-chemistry-2/ Concepts: Dilution Problems, Chemistry, Molarity & Concentration Examples, Formula & Equations
This lab covered gel art through restriction digests and gel electrophoresis As a remote participant, I reviewed the material.
This lab, we were tasked with creating a design that could be generated by an OpenTrons Liquid Handling Robot. As a remote participant, I prototyped a design using the GUI at opentrons-art.rcdonovan.com. This resulted in a layered plus symbol shown below. The coordinates for generating such can be found here, courtesy of RC Donovan’s tool: sfgfp_points = [(-2.2, 6.6),(0, 6.6),(2.2, 6.6),(-2.2, 4.4),(2.2, 4.4),(-6.6, 2.2),(-4.4, 2.2),(-2.2, 2.2),(2.2, 2.2),(4.4, 2.2),(6.6, 2.2),(-6.6, 0),(6.6, 0),(-6.6, -2.2),(-4.4, -2.2),(-2.2, -2.2),(2.2, -2.2),(4.4, -2.2),(6.6, -2.2),(-2.2, -4.4),(2.2, -4.4),(-2.2, -6.6),(0, -6.6),(2.2, -6.6)] electra2_points = [(0, 4.4),(0, 2.2),(-4.4, 0),(-2.2, 0),(0, 0),(2.2, 0),(4.4, 0),(0, -2.2),(0, -4.4)] mrfp1_points = [(-4.4, 8.8),(-2.2, 8.8),(0, 8.8),(2.2, 8.8),(4.4, 8.8),(-4.4, 6.6),(4.4, 6.6),(-8.8, 4.4),(-6.6, 4.4),(-4.4, 4.4),(4.4, 4.4),(6.6, 4.4),(8.8, 4.4),(-8.8, 2.2),(8.8, 2.2),(-8.8, 0),(8.8, 0),(-8.8, -2.2),(8.8, -2.2),(-8.8, -4.4),(-6.6, -4.4),(-4.4, -4.4),(4.4, -4.4),(6.6, -4.4),(8.8, -4.4),(-4.4, -6.6),(4.4, -6.6),(-4.4, -8.8),(-2.2, -8.8),(0, -8.8),(2.2, -8.8),(4.4, -8.8)]
Week 4 Lab: Protein Design Part I
This lab was effectively part of Week4’s Homework (“This week’s Lab work is effectively part of this week’s Homework; see that assignment and document your work there.”). As follows, the assigned work was: 1.Find a group of ~3–4 students 2.Read through the Phage Reading material listed under “Reading & Resources” below. 3.Review the Bacteriophage Final Project Goals for engineering the L Protein: *Increased stability (easiest) *Higher titers (medium) *Higher toxicity of lysis protein (hard) 4.Brainstorm Session Choose one or two main goals from the list that you think you can address computationally (e.g., “We’ll try to stabilize the lysis protein,” or “We’ll attempt to disrupt its interaction with E. coli DnaJ.”). Write a 1-page proposal (bullet points or short paragraphs) describing: Which tools/approaches from recitation you propose using (e.g., “Use Protein Language Models to do in silico mutagenesis, then AlphaFold-Multimer to check complexes.”). Why do you think those tools might help solve your chosen sub-problem? Name one or two potential pitfalls (e.g., “We lack enough training data on phage–bacteria interactions.”). Include a schematic of your pipeline. 5.Each individually put your plan on your HTGAA website Include your group’s short plan for engineering a bacteriophage This can be found in Week 4’s HW Part D.
Week 5 Lab: Protein Design Part II
This week’s Lab work was effectively part of this week’s Homework. This is reflected in Part C of the week 5 homeowork.
Week 6 Lab — Genetic Circuits Part I: Assembly Technologies
This lab involved the Gibson Assembly and was in person. As an online student, this lab did not apply for me.
Week 7 — Genetic Circuits Part II: Neuromorphic Circuits
This week’s lab had a dry and wet component. The focus was the building of our own IANN. According to the lab: “IANNs are also universal function approximators–given an adequate number of intracellular artificial neurons, you can use an IANN to achieve any input/output behavior you’d like.” https://2026a.htgaa.org/2026a/course-pages/weeks/week-07/lab/index.html The Pre-lab involved us setting up and understanding Neuromorphic Wizard. We wrote instructions using this template (https://www.google.com/url?q=https://docs.google.com/spreadsheets/d/12S4Vv6e_am6U6dMgpijt1G9rtoRyfcdoKdIXvnkdGTo/edit?usp%3Dsharing&sa=D&source=editors&ust=1774224628668116&usg=AOvVaw2ayNzuuoVfm9mQYCP30sjK) and using these names (https://www.google.com/url?q=https://docs.google.com/spreadsheets/d/1cyEgmj08P40iUE5KOdvn_oaDhB7sOkQJwA7900rDqMc/edit?usp%3Dsharing&sa=D&source=editors&ust=1774224628668584&usg=AOvVaw3_lcXglYGq-h7wgkIkT-Tx). Finally we entered our circuit into a google form.