Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Biological Engineering Application Proposed application: I want to develop a computer program that helps early-stage biological research by making it easier and more responsible for researchers to analyze biological data. The tool would help organize, check, and understand biological datasets (such as genomic or protein-related data) using bioinformatics and AI-assisted methods. It would also clearly show where there is doubt and where there is a risk of misuse.

  • Week 2 HW: DNA READ, WRITE & EDIT

    Part 1: Benchling & In-silico Gel Art Simulated EcoRI Digestion Simulated HindIII Digestion Simulated BamHI Digestion Simulated KpnI Digestion Simulated EcoRV Digestion

  • Week 3 HW: Lab Automation

    Opentrons Artwork Python Script This week, I explored laboratory automation by writing and simulating a Python script for the Opentrons liquid handling robot using Google Colab. As a Committed Listener, I was not physically running the robot, but I focused on understanding the automation logic and API structure that controls robotic liquid handling.

  • Week 4 HW: Protein Design Part I

    Part A. Conceptual Questions 1. 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) Eating a 500-gram piece of meat provides you with approximately 6.62 x 10²³ molecules of amino acids. Since raw meat is roughly 22% protein, you are consuming about 110 grams of actual protein; dividing this by the average mass of 100 Daltons per amino acid tells us you have 1.1 moles of them. By multiplying that by Avogadro’s constant, we find that you are swallowing about 662 sextillion molecules, a number so large it exceeds the number of stars in the observable universe

  • Week 5 HW: Protein Design Part II

    Part A: SOD1 Binder Peptide Design Part 1: PepMLM Peptide Generation sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ SOD1 A4V mutation sequence: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ To generate candidate binders, I retrieved the human SOD1 sequence from UniProt (accession P00441) and introduced the A4V mutation at position 4. I then used the PepMLM Colab notebook to generate four 12-amino-acid peptide sequences conditioned on the mutant protein. Since only four peptides were generated, a moderate Top-K(5) ensures enough variation between candidates to evaluate different potential binding interactions with Superoxide Dismutase 1.