Choose-Your-Own (CYO) Assignments

Choose-Your-Own (CYO) Assignments are optional assignments that can be done to improve your grade beyond a B. You can complete one or more of the CYO assignments throughout the semester, and there is time near the end of the semester (no outside additional work and free lab time) to work on them. The number of CYO assignments you complete determines your final grade, which is described in the grading contract.

CYO Assessment & Deadlines

Before you begin a CYO, you will submit a form that describes the assignment, your criteria for success, and any internal deadlines you plan to have. For the CYOs with written deliverables, you may instead choose to give a short presentation in class on the topic during the final presentation slot. See Moodle for more details.

CYO assignments are assessed as “complete” or “not complete” - there is no partially complete option, and they are not missing since they are all optional.

As stated in the deadline policy, all CYO Assignments must be submitted by the last day of finals at 5pm. If you want a chance to revise your CYO assignments, you must submit them earlier; talk with Anna to determine internal deadlines.

1. Biology and Computational Thinking – Example CYOs

  • Pass additional take-home questions on the biology topics presented in the last week(s) of the semester. I will provide 2-3 questions in the same format as E1 and E2.
  • Write your own exam questions (& solutions) on the course content. Aim for two multi-part questions and detailed solution keys.
  • Read an additional chapter of the textbook and describe the biological question, why it’s important, and how people have solved it as a computational question (750-1000 words suggested).
  • Write a mini-chapter about a new topic related to biological sequence analysis that is not covered by the textbook (750-1000 words suggested).
  • Draw detailed illustrations about biology concepts that we have learned in class (or new topics related to biological sequence analysis).
  • Other proposals welcome; see the Moodle page for more specifics.

2. Programming Skills – Example CYOs

  • Design an algorithm to identify multiple origins of replication (Lab extension)
  • Implement a greedy motif finder or other motif finders (P3 extension)
  • Implement local alignment and global protein alignment (P4 extension)
  • Implement affine gap alignment (P4 extension)
  • Implement one or more other bioinformatics problems from the textbook, which are offered through the Rosalind website.
  • Other proposals welcome; see the Moodle page for more specifics.

3. Biology and Society – Example CYOs

CYOs based on the books

  • Choose one of the books we discuss in class, read the entire book, and write a letter to an interested person (real or imaginary) about what you liked about the book, what challenged you about the book, and why the topic is important (750-1000 words suggested).
  • Imagine the authors from the books (Kim Tallbear, Alondra Nelson, and Rebecca Skloot) in conversation. What would they say to each other? Where would they agree and where would they disagree? (750-1000 words suggested).
  • Learn more about the authors from the books (and/or other scholars that the authors draw heavily from). What is their scholarly discipline and areas of research? (750-1000 words suggested).
  • Other proposals welcome; see the Moodle page for more specifics.
  • Write an essay about how computational biology might influence or shape genetics & identity or ownership over our bodies in medical procedures (750-1000 words suggested).
  • Dig into how commercial DNA testing companies (e.g., AncestryDNA) explains how to interpret results, especially in the context of Native American or Black ancestry. What do they tell their consumers? (750-1000 words suggested).
  • Have you been thinking about another topic that intersects with biology and society? Write about it! It’s OK to focus on biology other than molecular biology here, though you might have to write a bit more in that case.