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. I’m heavily inspired by Professor Jacobson’s call for a “bio-FPGA” tool, as well as his lecture about cellular automata. I’d like to develop a bio-FPGA that can be programmed to grow into arbitrary 2D patterns on a petri dish, using the machine learning technique mentioned in the lecture to reverse learn the cellular automata rules for growing a specific pattern. The learned CA rules can be encoded by genetically programming the bio-FPGA then using bacteria with the genes to grow an actual cell culture into the pattern, like the butterfly wing letter patterns in the lecture. If this is feasible, 3D patterns would be the next step, and one might even imagine a wild future of programmable plants that grow into the shapes of houses and furniture.

• Week 2 HW: DNA Read, Write, and Edit

  Part 0: Basics of Gel Electrophoresis I watched the lecture, recitation, and read the lab. Essentially, we use the negative charge of DNA to pull DNA fragments towards a positive anode in a porous agarose gel. Larger DNA fragments move slower in the agarose gel. Part 1: Benchling & In-silico Gel Art I spent some time playing around with Ronan’s gel art site to make a pattern (below on the left). I noticed that some of the restriction enzymes in the gel art tool weren’t on the HTGAA enzyme list, so I didn’t use them.

• Week 3 HW: Lab Automation

  Opentrons Artwork My artwork is here: https://rcdonovan.com/?id=vmns94wqt45wpqc I used Ronan’s tool to make this. I uploaded an image of tomatoes but it didn’t render well, so I modified it significantly by hand with the editor. Then, I attended the Saturday session on Zoom with Ronan, Michelle, and Ice at Ginkgo Bioworks. Here’s the end result:

• Week 4 HW: Protein Design, Part I

  Part A: Conceptual questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) A dalton is 1.66053906892(52)*10−23 g, so 500g = 500 / 1.66053906892(52)*10−23 = 3.0110704e+25 daltons.