Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Project Proposal: I am interested in the applications synthetic biology could have on the people staying in the Saharawi refugee camps in Tindouf, Algeria. I would like to explore the possibilities of a lowcost fermentation system specifically designed to reduce irondeficiency anemia, which is a big problem there because the intertwining of various circumstances has caused the community to rely almost exclusively on humantiarian aid, which consists mostly of long shelf life products like rice, lentils, and cereals.
- Reflections for Week 2 Homework Questions from Professor Jacobson: Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy?
Week 2 HW: DNA Read, Write, and Edit
Part 1: Benchling & In-silico Gel Art I created a Benchling account, imported the Lambda phage genome (GenBank J02459, ~48.5 kb), and ran restriction simulations for all seven enzymes. Benchling calculates cut sites and spits out the expected fragment sizes for each digest, which is really all you need to start planning a gel layout. The design side is where it gets interesting. Paul Vanouse’s Latent Figure Protocol uses the natural variation in fragment sizes across different enzyme digests to compose images — the biology does the art. I used Ronan’s gel simulation tool to quickly preview different lane arrangements without re-running everything in Benchling each time, which saved a lot of back-and-forth. The goal was to pick an enzyme combination and lane order where the resulting band pattern, viewed across lanes, suggests a recognizable shape.
Python Script for Opentrons Artwork I started off drawing my picture here, with lots of different colors and going through quite a few iterations. Once I exported my python code and imported it into the colab notebook, I worked through a few debugging problems, and also realized that the colors were didfferent than the ones I had chosen on the opentron simulator. This group of purple, for example, I wanted to change, so I moved the coordinates to the section that coded for red dots.