Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Chapter 1: The Idea “Are there any sterile tips left?” Most of us have asked this question at some point! It is heard dozens of times a day in labs, and followed by the sound of a plastic box opening. The issue: life sciences rely heavily on single-use materials. To maintain experimental sterility, laboratories operate within a consumption model that generates large amounts of waste (tubes,tips, etc.). For instance, Howes (2019) reported that a postgraduate student in molecular biology can produce approximately 230 g of plastic waste per day from consumables such as pipette tips and tubes, which corresponds to nearly 60 kg of plastic waste per laboratory each year.
Week 2 HW: DNA Read, Write and Edit
Part 1: Benchling & In-silico Gel Art It was definitely more difficult than I thought! First Attempt: Letter A Reference Image In-silico Gel Result Second Attempt: A Face Reference Image In-silico Gel Result Part 3: DNA Design Challenge 3.1. Choose your protein.
Homework Questions from Professor Jacobson What is the error rate of polymerase? DNA polymerase copies DNA with very high accuracy. When proofreading is active, the error rate is approximately 1 in 10⁶ base pairs, meaning one mistake per million bases added. This is much more accurate than chemical DNA synthesis, which has an error rate of about 1 in 10². DNA polymerase is also fast, adding one base roughly every 10 ms.
Part 1: Code from opentrons import types import string metadata = { ‘protocolName’: ‘{YOUR NAME} - Opentrons Art - HTGAA’, ‘author’: ‘HTGAA’, ‘source’: ‘HTGAA 2026’, ‘apiLevel’: ‘2.20’ } Z_VALUE_AGAR = 2.0 POINT_SIZE = 1 egfp_points = [(-12.65,31.05), (-10.35,31.05), (-8.05,31.05), (-5.75,31.05), (-3.45,31.05), (-1.15,31.05), (1.15,31.05), (3.45,31.05), (5.75,31.05), (8.05,31.05), (10.35,31.05), (12.65,31.05), (14.95,31.05), (-24.15,28.75), (-17.25,28.75), (-14.95,28.75), (-12.65,28.75), (-10.35,28.75), (-8.05,28.75), (-5.75,28.75), (-3.45,28.75), (-1.15,28.75), (1.15,28.75), (3.45,28.75), (5.75,28.75), (8.05,28.75), (10.35,28.75), (12.65,28.75), (14.95,28.75), (17.25,28.75), (-21.85,26.45), (-19.55,26.45), (19.55,26.45), (21.85,26.45), (33.35,17.25), (-31.05,14.95), (31.05,14.95), (-33.35,12.65), (-3.45,12.65), (-1.15,12.65), (1.15,12.65), (3.45,12.65), (31.05,12.65), (-35.65,10.35), (-5.75,10.35), (-3.45,10.35), (-1.15,10.35), (1.15,10.35), (3.45,10.35), (5.75,10.35), (31.05,10.35), (33.35,10.35), (-35.65,8.05), (35.65,8.05), (-10.35,5.75), (10.35,5.75), (37.95,5.75), (-37.95,3.45), (37.95,3.45), (-37.95,1.15), (-12.65,1.15), (14.95,1.15), (37.95,1.15), (-37.95,-1.15), (-19.55,-1.15), (-17.25,-1.15), (-14.95,-1.15), (17.25,-1.15), (19.55,-1.15), (21.85,-1.15), (37.95,-1.15), (-37.95,-3.45), (37.95,-3.45), (-37.95,-5.75), (37.95,-5.75), (-37.95,-8.05), (37.95,-8.05), (-37.95,-10.35), (37.95,-10.35), (35.65,-12.65), (-35.65,-14.95), (35.65,-14.95), (-35.65,-17.25), (35.65,-17.25)] mlychee_tf_points = [(-26.45,28.75), (26.45,28.75), (-28.75,26.45), (-26.45,26.45), (-24.15,26.45), (24.15,26.45), (26.45,26.45), (28.75,26.45), (-31.05,24.15), (24.15,24.15), (26.45,24.15), (31.05,24.15), (-33.35,21.85), (-31.05,21.85), (26.45,21.85), (31.05,21.85), (33.35,21.85), (-33.35,19.55), (-31.05,19.55), (28.75,19.55), (31.05,19.55), (33.35,19.55), (-31.05,17.25), (-14.95,17.25), (-12.65,17.25), (-10.35,17.25), (10.35,17.25), (12.65,17.25), (14.95,17.25), (31.05,17.25), (-17.25,14.95), (-14.95,14.95), (-12.65,14.95), (-10.35,14.95), (10.35,14.95), (12.65,14.95), (14.95,14.95), (17.25,14.95), (26.45,14.95), (-19.55,12.65), (-14.95,12.65), (-12.65,12.65), (-10.35,12.65), (10.35,12.65), (12.65,12.65), (14.95,12.65), (19.55,12.65), (26.45,12.65), (-26.45,10.35), (-21.85,10.35), (-12.65,10.35), (-10.35,10.35), (10.35,10.35), (12.65,10.35), (19.55,10.35), (21.85,10.35), (26.45,10.35), (28.75,10.35), (-31.05,8.05), (-28.75,8.05), (-26.45,8.05), (-21.85,8.05), (-19.55,8.05), (-12.65,8.05), (10.35,8.05), (12.65,8.05), (19.55,8.05), (21.85,8.05), (26.45,8.05), (28.75,8.05), (31.05,8.05), (-33.35,5.75), (-31.05,5.75), (-28.75,5.75), (-26.45,5.75), (-21.85,5.75), (-14.95,5.75), (-12.65,5.75), (12.65,5.75), (14.95,5.75), (17.25,5.75), (21.85,5.75), (26.45,5.75), (28.75,5.75), (31.05,5.75), (-31.05,3.45), (-28.75,3.45), (-26.45,3.45), (-19.55,3.45), (-17.25,3.45), (-14.95,3.45), (14.95,3.45), (17.25,3.45), (19.55,3.45), (26.45,3.45), (28.75,3.45), (31.05,3.45), (33.35,3.45), (-33.35,1.15), (-31.05,1.15), (-28.75,1.15), (-26.45,1.15), (26.45,1.15), (28.75,1.15), (31.05,1.15), (33.35,1.15), (-33.35,-1.15), (-31.05,-1.15), (-28.75,-1.15), (-26.45,-1.15), (26.45,-1.15), (28.75,-1.15), (31.05,-1.15), (33.35,-1.15), (-35.65,-3.45), (-33.35,-3.45), (-31.05,-3.45), (-28.75,-3.45), (-26.45,-3.45), (-24.15,-3.45), (24.15,-3.45), (26.45,-3.45), (28.75,-3.45), (31.05,-3.45), (33.35,-3.45), (-33.35,-5.75), (-31.05,-5.75), (-28.75,-5.75), (-26.45,-5.75), (-24.15,-5.75), (-21.85,-5.75), (-19.55,-5.75), (19.55,-5.75), (21.85,-5.75), (24.15,-5.75), (26.45,-5.75), (28.75,-5.75), (31.05,-5.75), (33.35,-5.75), (-33.35,-8.05), (-31.05,-8.05), (-28.75,-8.05), (-26.45,-8.05), (-24.15,-8.05), (-21.85,-8.05), (-19.55,-8.05), (-5.75,-8.05), (-3.45,-8.05), (3.45,-8.05), (5.75,-8.05), (19.55,-8.05), (21.85,-8.05), (24.15,-8.05), (26.45,-8.05), (28.75,-8.05), (31.05,-8.05), (33.35,-8.05), (-33.35,-10.35), (-31.05,-10.35), (-28.75,-10.35), (-26.45,-10.35), (-24.15,-10.35), (-21.85,-10.35), (-19.55,-10.35), (-5.75,-10.35), (-3.45,-10.35), (3.45,-10.35), (5.75,-10.35), (19.55,-10.35), (21.85,-10.35), (24.15,-10.35), (26.45,-10.35), (28.75,-10.35), (31.05,-10.35), (33.35,-10.35), (-31.05,-12.65), (-28.75,-12.65), (-26.45,-12.65), (-24.15,-12.65), (-21.85,-12.65), (-19.55,-12.65), (19.55,-12.65), (21.85,-12.65), (24.15,-12.65), (26.45,-12.65), (28.75,-12.65), (31.05,-12.65), (33.35,-12.65), (-33.35,-14.95), (-31.05,-14.95), (-28.75,-14.95), (-26.45,-14.95), (-24.15,-14.95), (-21.85,-14.95), (-19.55,-14.95), (-17.25,-14.95), (19.55,-14.95), (21.85,-14.95), (24.15,-14.95), (26.45,-14.95), (28.75,-14.95), (31.05,-14.95), (-28.75,-17.25), (-26.45,-17.25), (-24.15,-17.25), (-21.85,-17.25), (-19.55,-17.25), (-17.25,-17.25), (17.25,-17.25), (19.55,-17.25), (21.85,-17.25), (24.15,-17.25), (26.45,-17.25), (28.75,-17.25), (31.05,-17.25), (-28.75,-19.55), (-26.45,-19.55), (-24.15,-19.55), (-21.85,-19.55), (-19.55,-19.55), (-17.25,-19.55), (-14.95,-19.55), (14.95,-19.55), (17.25,-19.55), (19.55,-19.55), (21.85,-19.55), (24.15,-19.55), (26.45,-19.55), (28.75,-19.55), (-26.45,-21.85), (-24.15,-21.85), (-21.85,-21.85), (-19.55,-21.85), (-17.25,-21.85), (-14.95,-21.85), (-12.65,-21.85), (12.65,-21.85), (14.95,-21.85), (17.25,-21.85), (19.55,-21.85), (21.85,-21.85), (24.15,-21.85), (26.45,-21.85), (28.75,-21.85), (31.05,-21.85), (33.35,-21.85), (-31.05,-24.15), (-28.75,-24.15), (-26.45,-24.15), (-24.15,-24.15), (-21.85,-24.15), (-19.55,-24.15), (-17.25,-24.15), (-14.95,-24.15), (-12.65,-24.15), (-10.35,-24.15), (12.65,-24.15), (14.95,-24.15), (17.25,-24.15), (19.55,-24.15), (21.85,-24.15), (24.15,-24.15), (26.45,-24.15), (28.75,-24.15), (31.05,-24.15), (-28.75,-26.45), (-26.45,-26.45), (-24.15,-26.45), (-21.85,-26.45), (-19.55,-26.45), (-17.25,-26.45), (-14.95,-26.45), (-12.65,-26.45), (-10.35,-26.45), (-8.05,-26.45), (-5.75,-26.45), (-3.45,-26.45), (-1.15,-26.45), (1.15,-26.45), (3.45,-26.45), (5.75,-26.45), (8.05,-26.45), (10.35,-26.45), (12.65,-26.45), (14.95,-26.45), (17.25,-26.45), (19.55,-26.45), (21.85,-26.45), (24.15,-26.45), (26.45,-26.45), (28.75,-26.45), (-26.45,-28.75), (-24.15,-28.75), (-21.85,-28.75), (-19.55,-28.75), (-17.25,-28.75), (-14.95,-28.75), (-12.65,-28.75), (-10.35,-28.75), (-8.05,-28.75), (-5.75,-28.75), (-3.45,-28.75), (-1.15,-28.75), (1.15,-28.75), (3.45,-28.75), (5.75,-28.75), (8.05,-28.75), (10.35,-28.75), (12.65,-28.75), (14.95,-28.75), (17.25,-28.75), (19.55,-28.75), (21.85,-28.75), (24.15,-28.75), (26.45,-28.75), (-24.15,-31.05), (-21.85,-31.05), (-19.55,-31.05), (-17.25,-31.05), (-14.95,-31.05), (-12.65,-31.05), (-10.35,-31.05), (-8.05,-31.05), (-5.75,-31.05), (-3.45,-31.05), (-1.15,-31.05), (1.15,-31.05), (3.45,-31.05), (5.75,-31.05), (8.05,-31.05), (10.35,-31.05), (12.65,-31.05), (14.95,-31.05), (17.25,-31.05), (19.55,-31.05), (21.85,-31.05), (24.15,-31.05), (-21.85,-33.35), (-19.55,-33.35), (-17.25,-33.35), (-14.95,-33.35), (-12.65,-33.35), (-10.35,-33.35), (-8.05,-33.35), (-5.75,-33.35), (-3.45,-33.35), (-1.15,-33.35), (1.15,-33.35), (3.45,-33.35), (5.75,-33.35), (8.05,-33.35), (10.35,-33.35), (12.65,-33.35), (14.95,-33.35), (17.25,-33.35), (19.55,-33.35), (21.85,-33.35), (-17.25,-35.65), (-14.95,-35.65), (-12.65,-35.65), (-10.35,-35.65), (-8.05,-35.65), (-5.75,-35.65), (-3.45,-35.65), (-1.15,-35.65), (1.15,-35.65), (3.45,-35.65), (5.75,-35.65), (8.05,-35.65), (10.35,-35.65), (12.65,-35.65), (14.95,-35.65), (17.25,-35.65), (-10.35,-37.95), (-8.05,-37.95), (-5.75,-37.95), (-3.45,-37.95), (-1.15,-37.95), (1.15,-37.95), (3.45,-37.95), (5.75,-37.95), (8.05,-37.95), (10.35,-37.95)] tagrfp_points = [(24.15,28.75), (-14.95,26.45), (-12.65,26.45), (-10.35,26.45), (-8.05,26.45), (-5.75,26.45), (-3.45,26.45), (-1.15,26.45), (1.15,26.45), (3.45,26.45), (5.75,26.45), (8.05,26.45), (10.35,26.45), (12.65,26.45), (14.95,26.45), (17.25,26.45), (-24.15,24.15), (-21.85,24.15), (-19.55,24.15), (-17.25,24.15), (-14.95,24.15), (-8.05,24.15), (-5.75,24.15), (-3.45,24.15), (3.45,24.15), (5.75,24.15), (8.05,24.15), (14.95,24.15), (17.25,24.15), (19.55,24.15), (21.85,24.15), (-24.15,21.85), (-19.55,21.85), (-14.95,21.85), (-8.05,21.85), (-5.75,21.85), (-3.45,21.85), (1.15,21.85), (3.45,21.85), (5.75,21.85), (8.05,21.85), (10.35,21.85), (14.95,21.85), (17.25,21.85), (19.55,21.85), (24.15,21.85), (-28.75,19.55), (-26.45,19.55), (-24.15,19.55), (-21.85,19.55), (-19.55,19.55), (19.55,19.55), (21.85,19.55), (24.15,19.55), (26.45,19.55), (-26.45,17.25), (-24.15,17.25), (26.45,17.25), (28.75,17.25), (-28.75,14.95), (-26.45,14.95), (-24.15,14.95), (-28.75,12.65), (-17.25,12.65), (17.25,12.65), (-31.05,10.35), (-28.75,10.35), (-19.55,10.35), (-33.35,8.05), (-17.25,5.75), (-35.65,3.45), (35.65,3.45), (-33.35,-17.25)] mruby2_points = [(-17.25,26.45), (-12.65,24.15), (-10.35,24.15), (10.35,24.15), (12.65,24.15), (-17.25,21.85), (-12.65,21.85), (-10.35,21.85), (12.65,21.85), (-17.25,19.55), (17.25,19.55), (-33.35,17.25), (-28.75,17.25), (-21.85,17.25), (-19.55,17.25), (19.55,17.25), (21.85,17.25), (-21.85,14.95), (21.85,14.95), (-31.05,12.65), (-33.35,10.35), (33.35,8.05), (-35.65,5.75), (35.65,5.75), (-12.65,3.45), (-21.85,1.15), (-19.55,1.15), (-17.25,1.15), (-14.95,1.15), (19.55,1.15), (21.85,1.15), (-21.85,-1.15), (-35.65,-8.05), (-35.65,-10.35), (35.65,-10.35), (-35.65,-12.65), (33.35,-17.25), (-33.35,-19.55), (33.35,-19.55)] mkate2_points = [(-1.15,24.15), (1.15,24.15), (-1.15,21.85), (-5.75,19.55), (-3.45,19.55), (-1.15,19.55), (1.15,19.55), (3.45,19.55), (5.75,19.55), (-5.75,17.25), (-3.45,17.25), (-1.15,17.25), (1.15,17.25), (3.45,17.25), (5.75,17.25), (-5.75,14.95), (-3.45,14.95), (-1.15,14.95), (1.15,14.95), (3.45,14.95), (5.75,14.95), (-5.75,12.65), (5.75,12.65), (-8.05,-3.45), (-5.75,-3.45), (-3.45,-3.45), (-1.15,-3.45), (1.15,-3.45), (3.45,-3.45), (5.75,-3.45), (8.05,-3.45), (-8.05,-5.75), (-5.75,-5.75), (-3.45,-5.75), (-1.15,-5.75), (1.15,-5.75), (3.45,-5.75), (5.75,-5.75), (8.05,-5.75), (-8.05,-8.05), (-1.15,-8.05), (1.15,-8.05), (8.05,-8.05), (-8.05,-10.35), (-1.15,-10.35), (1.15,-10.35), (8.05,-10.35), (-8.05,-12.65), (-5.75,-12.65), (-3.45,-12.65), (-1.15,-12.65), (1.15,-12.65), (3.45,-12.65), (5.75,-12.65), (8.05,-12.65), (-5.75,-14.95), (-3.45,-14.95), (-1.15,-14.95), (1.15,-14.95), (3.45,-14.95), (5.75,-14.95), (-1.15,-17.25), (1.15,-17.25), (-1.15,-19.55), (1.15,-19.55), (-8.05,-21.85), (-5.75,-21.85), (-3.45,-21.85), (-1.15,-21.85), (1.15,-21.85), (3.45,-21.85), (5.75,-21.85), (8.05,-21.85)] mkate2_tf_points = [(-21.85,21.85), (21.85,21.85), (24.15,17.25), (24.15,14.95), (28.75,14.95), (-26.45,12.65), (28.75,12.65), (-10.35,8.05), (-19.55,5.75), (19.55,5.75), (33.35,5.75), (-33.35,3.45), (-21.85,3.45), (21.85,3.45), (-35.65,1.15), (17.25,1.15), (35.65,1.15), (-35.65,-1.15), (35.65,-1.15), (35.65,-3.45), (-35.65,-5.75), (35.65,-5.75), (35.65,-8.05), (-33.35,-12.65), (33.35,-14.95), (-31.05,-17.25), (-31.05,-19.55), (31.05,-19.55), (-33.35,-21.85), (-31.05,-21.85), (-28.75,-21.85)] mko2_points = [(-14.95,19.55), (-12.65,19.55), (-10.35,19.55), (-8.05,19.55), (8.05,19.55), (10.35,19.55), (12.65,19.55), (14.95,19.55), (-17.25,17.25), (-8.05,17.25), (8.05,17.25), (17.25,17.25), (-19.55,14.95), (-8.05,14.95), (8.05,14.95), (19.55,14.95), (-24.15,12.65), (-21.85,12.65), (-8.05,12.65), (8.05,12.65), (21.85,12.65), (24.15,12.65), (-24.15,10.35), (-8.05,10.35), (8.05,10.35), (24.15,10.35), (-24.15,8.05), (-8.05,8.05), (-5.75,8.05), (-3.45,8.05), (-1.15,8.05), (1.15,8.05), (3.45,8.05), (5.75,8.05), (8.05,8.05), (24.15,8.05), (-24.15,5.75), (-8.05,5.75), (-5.75,5.75), (-3.45,5.75), (-1.15,5.75), (1.15,5.75), (3.45,5.75), (5.75,5.75), (8.05,5.75), (24.15,5.75), (-24.15,3.45), (-10.35,3.45), (-8.05,3.45), (-5.75,3.45), (-3.45,3.45), (-1.15,3.45), (1.15,3.45), (3.45,3.45), (5.75,3.45), (8.05,3.45), (10.35,3.45), (12.65,3.45), (24.15,3.45), (-24.15,1.15), (-10.35,1.15), (-8.05,1.15), (-5.75,1.15), (-3.45,1.15), (-1.15,1.15), (1.15,1.15), (3.45,1.15), (5.75,1.15), (8.05,1.15), (10.35,1.15), (12.65,1.15), (24.15,1.15), (-24.15,-1.15), (-12.65,-1.15), (-10.35,-1.15), (-8.05,-1.15), (-5.75,-1.15), (-3.45,-1.15), (-1.15,-1.15), (1.15,-1.15), (3.45,-1.15), (5.75,-1.15), (8.05,-1.15), (10.35,-1.15), (12.65,-1.15), (14.95,-1.15), (24.15,-1.15), (-21.85,-3.45), (-19.55,-3.45), (-17.25,-3.45), (-14.95,-3.45), (-12.65,-3.45), (-10.35,-3.45), (10.35,-3.45), (12.65,-3.45), (14.95,-3.45), (17.25,-3.45), (19.55,-3.45), (21.85,-3.45), (-17.25,-5.75), (-14.95,-5.75), (-12.65,-5.75), (-10.35,-5.75), (10.35,-5.75), (12.65,-5.75), (14.95,-5.75), (17.25,-5.75), (-17.25,-8.05), (-14.95,-8.05), (-12.65,-8.05), (-10.35,-8.05), (10.35,-8.05), (12.65,-8.05), (14.95,-8.05), (17.25,-8.05), (-17.25,-10.35), (-14.95,-10.35), (-12.65,-10.35), (-10.35,-10.35), (10.35,-10.35), (12.65,-10.35), (14.95,-10.35), (17.25,-10.35), (-17.25,-12.65), (-14.95,-12.65), (-12.65,-12.65), (-10.35,-12.65), (10.35,-12.65), (12.65,-12.65), (14.95,-12.65), (17.25,-12.65), (-14.95,-14.95), (-12.65,-14.95), (-10.35,-14.95), (-8.05,-14.95), (8.05,-14.95), (10.35,-14.95), (12.65,-14.95), (14.95,-14.95), (17.25,-14.95), (-14.95,-17.25), (-12.65,-17.25), (-10.35,-17.25), (-8.05,-17.25), (-5.75,-17.25), (-3.45,-17.25), (3.45,-17.25), (5.75,-17.25), (8.05,-17.25), (10.35,-17.25), (12.65,-17.25), (14.95,-17.25), (-12.65,-19.55), (-10.35,-19.55), (-8.05,-19.55), (-5.75,-19.55), (-3.45,-19.55), (3.45,-19.55), (5.75,-19.55), (8.05,-19.55), (10.35,-19.55), (12.65,-19.55), (-10.35,-21.85), (10.35,-21.85), (-8.05,-24.15), (-5.75,-24.15), (-3.45,-24.15), (-1.15,-24.15), (1.15,-24.15), (3.45,-24.15), (5.75,-24.15), (8.05,-24.15), (10.35,-24.15)]