Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Scale-up of nanocapsules for drug delivery using bacteria as ferritin manufacturers 1. Describe a biological engineering application or tool you want to develop and why. Biologics are drugs synthesized by living organisms, which have gained more notoriety throughout the years (Walsh, 2018). Cancer drugs and vaccines are some of the achievements scientists have accomplished with biotechnology. This is a novel area with increasing knowledge and endless applications. Currently, iron deficiency is one of the main global issues affecting overall health (Lee et al., 2025). This project aims to develop a drug delivery system using bacteria-made ferritin, given the popularity and extended use of these microorganisms over the years for drug manufacturing (Kulkarni, 2026).
Week 2 HW: DNA Read, Write, and Edit
HOMEWORK Part 1: Benchling & In-silico Gel Art Below are some screenshots from the steps followed to create a basic pattern: Step 1: The sequence is imported from the webpage to Benchling. Figures 1 and 2. Lambda DNA import process. Step 2: The digest function is shown as a test with EcoRI as the chosen restriction enzyme.
Assignment no. 1: Python Script for Opentrons Artwork The code used was the following to create a simple swirl pattenr with four different colors: from opentrons import types import math metadata = { 'author': 'Jean Colmenares', 'protocolName': 'Agar Swirl Pattern - 4 Colors', 'description': 'Swirl pattern with four colors per branch', 'source': 'HTGAA 2026 Opentrons Lab', 'apiLevel': '2.20' } TIP_RACK_DECK_SLOT = 9 COLORS_DECK_SLOT = 6 AGAR_DECK_SLOT = 5 PIPETTE_STARTING_TIP_WELL = 'A1' well_colors = { 'A1': 'Red', 'B1': 'Green', 'C1': 'Orange', 'D1': 'Blue' } def run(protocol): tips_20ul = protocol.load_labware( 'opentrons_96_tiprack_20ul', TIP_RACK_DECK_SLOT, 'Opentrons 20uL Tips' ) pipette_20ul = protocol.load_instrument( "p20_single_gen2", "right", [tips_20ul] ) temperature_module = protocol.load_module( 'temperature module gen2', COLORS_DECK_SLOT ) temperature_plate = temperature_module.load_labware( 'opentrons_96_aluminumblock_generic_pcr_strip_200ul', 'Cold Plate' ) color_plate = temperature_plate agar_plate = protocol.load_labware( 'htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate' ) center_location = agar_plate['A1'].top() pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL) # —————————————————————— # Helper functions # —————————————————————— def location_of_color(color_string): for well, color in well_colors.items(): if color.lower() == color_string.lower(): return color_plate[well] raise ValueError(f"No well found with color {color_string}") def dispense_and_detach(pipette, volume, location): above_location = location.move(types.Point(z=location.point.z + 5)) pipette.move_to(above_location) pipette.dispense(volume, location) pipette.move_to(above_location) # —————————————————————— # SWIRL PATTERN — BIG + FIXED COLOR PER BRANCH (P20 SAFE) # —————————————————————— DROP_VOLUME = 3 branches = 4 points_per_branch = 24 radius_start = 3 radius_step = 1.6 angle_step = math.pi/9 branch_colors = ['Red', 'Green', 'Orange', 'Blue'] for branch in range(branches): base_angle = branch * (2*math.pi/branches) color = branch_colors[branch] source = location_of_color(color) for i in range(points_per_branch): pipette_20ul.pick_up_tip() pipette_20ul.aspirate(DROP_VOLUME, source.bottom(1)) angle = base_angle + i * angle_step radius = radius_start + i * radius_step x = radius * math.cos(angle) y = radius * math.sin(angle) loc = center_location.move(types.Point(x=x, y=y, z=0)) dispense_and_detach(pipette_20ul, DROP_VOLUME, loc) pipette_20ul.drop_tip() The pattern is shown below: