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 want to optimize PETase (polyethylene terephthalate hydrolase). PETase is an enzyme that can break down PET plastics, which are widely used in packaging. By optimizing PETase, we can enhance its efficiency in degrading PET and increase its stability under various conditions. This could lead to more effective recycling processes and help reduce plastic pollution.

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

    Part 0: Basics of Gel Electrophoresis I have attended the recitation. Part 1: Benchling & In-silico Gel Art I made the gel art below. It is “HT” for “How To grow almost anything”. Part 2: Gel Art - Restriction Digests and Gel Electrophoresis I worked in group with Louisa, Jasmine, and Yutong. We tried to make the cat gel art designed by Louisa, but unfortunately it was not very successful. Photo below:

  • Week 3 HW: Lab Automation

    Python Script for Opentrons Artwork I created a design using opentrons-art.rcdonovan.com Opentrons-Art Website: https://opentrons-art.rcdonovan.com/?id=80fx569l8o4tho4 Google Colab: https://colab.research.google.com/drive/1UPiCmwBP3sIFD_rNVRHeT3YhuiQQ5ZGP#scrollTo=pczDLwsq64mk&line=6&uniqifier=1 The OpentronMock gives the following output: Code:

### YOUR CODE HERE to create your design ### sfgfp_points = [(-3.3, -3.3),(-1.1, -3.3),(1.1, -3.3),(3.3, -3.3),(-3.3, -5.5),(-1.1, -5.5),(1.1, -5.5),(3.3, -5.5),(-1.1, -7.7),(1.1, -7.7),(-5.5, -9.9),(-1.1, -9.9),(1.1, -9.9),(5.5, -9.9),(-3.3, -12.1),(-1.1, -12.1),(1.1, -12.1),(3.3, -12.1)] mrfp1_points = [(-23.1, 27.5),(-20.9, 27.5),(-18.7, 27.5),(18.7, 27.5),(20.9, 27.5),(23.1, 27.5),(-23.1, 25.3),(-20.9, 25.3),(-18.7, 25.3),(-16.5, 25.3),(-14.3, 25.3),(14.3, 25.3),(16.5, 25.3),(18.7, 25.3),(20.9, 25.3),(23.1, 25.3),(-23.1, 23.1),(-20.9, 23.1),(-18.7, 23.1),(-16.5, 23.1),(-14.3, 23.1),(-12.1, 23.1),(-3.3, 23.1),(-1.1, 23.1),(1.1, 23.1),(3.3, 23.1),(12.1, 23.1),(14.3, 23.1),(16.5, 23.1),(18.7, 23.1),(20.9, 23.1),(23.1, 23.1),(-23.1, 20.9),(-20.9, 20.9),(-18.7, 20.9),(-16.5, 20.9),(-14.3, 20.9),(-12.1, 20.9),(-9.9, 20.9),(-7.7, 20.9),(-5.5, 20.9),(-3.3, 20.9),(-1.1, 20.9),(1.1, 20.9),(3.3, 20.9),(5.5, 20.9),(7.7, 20.9),(9.9, 20.9),(12.1, 20.9),(14.3, 20.9),(16.5, 20.9),(18.7, 20.9),(20.9, 20.9),(23.1, 20.9),(-23.1, 18.7),(-20.9, 18.7),(-18.7, 18.7),(-16.5, 18.7),(-14.3, 18.7),(-12.1, 18.7),(-9.9, 18.7),(-7.7, 18.7),(7.7, 18.7),(9.9, 18.7),(12.1, 18.7),(14.3, 18.7),(16.5, 18.7),(18.7, 18.7),(20.9, 18.7),(23.1, 18.7),(-23.1, 16.5),(-20.9, 16.5),(-18.7, 16.5),(-16.5, 16.5),(-14.3, 16.5),(-12.1, 16.5),(12.1, 16.5),(14.3, 16.5),(16.5, 16.5),(18.7, 16.5),(20.9, 16.5),(23.1, 16.5),(-23.1, 14.3),(-20.9, 14.3),(-18.7, 14.3),(-16.5, 14.3),(16.5, 14.3),(18.7, 14.3),(20.9, 14.3),(23.1, 14.3),(-23.1, 12.1),(-20.9, 12.1),(-18.7, 12.1),(18.7, 12.1),(20.9, 12.1),(23.1, 12.1),(-23.1, 9.9),(-20.9, 9.9),(20.9, 9.9),(23.1, 9.9),(-23.1, 7.7),(-20.9, 7.7),(20.9, 7.7),(23.1, 7.7),(-23.1, 5.5),(23.1, 5.5),(-25.3, 3.3),(-23.1, 3.3),(23.1, 3.3),(25.3, 3.3),(-25.3, 1.1),(-23.1, 1.1),(23.1, 1.1),(25.3, 1.1),(-25.3, -1.1),(-23.1, -1.1),(23.1, -1.1),(25.3, -1.1),(-25.3, -5.5),(-23.1, -5.5),(23.1, -5.5),(25.3, -5.5),(-25.3, -7.7),(25.3, -7.7),(-23.1, -9.9),(23.1, -9.9),(-23.1, -12.1),(23.1, -12.1),(-23.1, -14.3),(23.1, -14.3),(-20.9, -16.5),(20.9, -16.5),(-20.9, -18.7),(-18.7, -18.7),(18.7, -18.7),(20.9, -18.7),(-18.7, -20.9),(-16.5, -20.9),(16.5, -20.9),(18.7, -20.9),(-16.5, -23.1),(-14.3, -23.1),(-12.1, -23.1),(12.1, -23.1),(14.3, -23.1),(16.5, -23.1),(-14.3, -25.3),(-12.1, -25.3),(-9.9, -25.3),(-7.7, -25.3),(7.7, -25.3),(9.9, -25.3),(12.1, -25.3),(14.3, -25.3),(-9.9, -27.5),(-7.7, -27.5),(-5.5, -27.5),(-3.3, -27.5),(-1.1, -27.5),(1.1, -27.5),(3.3, -27.5),(5.5, -27.5),(7.7, -27.5),(9.9, -27.5),(-1.1, -29.7),(1.1, -29.7)] azurite_points = [(-9.9, 7.7),(-7.7, 7.7),(7.7, 7.7),(9.9, 7.7),(-12.1, 5.5),(-9.9, 5.5),(-7.7, 5.5),(7.7, 5.5),(9.9, 5.5),(12.1, 5.5),(-9.9, 3.3),(9.9, 3.3)] mwasabi_points = [(-27.5, -3.3),(-25.3, -3.3),(-23.1, -3.3),(-20.9, -3.3),(-18.7, -3.3),(-16.5, -3.3),(16.5, -3.3),(18.7, -3.3),(20.9, -3.3),(23.1, -3.3),(25.3, -3.3),(27.5, -3.3),(-23.1, -7.7),(-20.9, -7.7),(-18.7, -7.7),(-16.5, -7.7),(16.5, -7.7),(18.7, -7.7),(20.9, -7.7),(23.1, -7.7),(-27.5, -9.9),(-25.3, -9.9),(25.3, -9.9),(27.5, -9.9),(-16.5, -12.1),(16.5, -12.1),(-20.9, -14.3),(-18.7, -14.3),(18.7, -14.3),(20.9, -14.3),(-23.1, -16.5),(23.1, -16.5),(-25.3, -18.7),(25.3, -18.7)] scale = 1 def draw_points(points, color="Red"): segments = [] for i in range(0, len(points), 20): segments.append(points[i : i+20]) for seg in segments: pipette_20ul.pick_up_tip() pipette_20ul.aspirate(len(seg), location_of_color(color)) for x, y in seg: adjusted_location = center_location.move(types.Point(x=xscale, y=yscale)) dispense_and_detach(pipette_20ul, 1, adjusted_location) pipette_20ul.drop_tip() draw_points(sfgfp_points, "Red") draw_points(mrfp1_points, "Green") draw_points(azurite_points, "Orange") draw_points(mwasabi_points, "Orange") Result With the help of our TA Ronan, the art was printed with an Opentrons robot. The result is shown below: