Bio131: Introduction to Computational Biology

High-throughput technologies produce massive amounts of data, much too large to analyze by hand. The goal of this course is to learn how to analyze DNA, RNA, and protein sequences using computers. Through a combination of foundational examples and current research questions, this course aims to demystify computer science, molecular biology, and some of the ways they intersect.

Who this class is for

This class is for anyone who wants to learn about biological questions that can be addressed with computation and gain insight into how these computational problems are solved. This class is also for students who want to explore how biological advances might affect or reflect societal values. Bio131 is an introductory course, assumes at least one semester of Topics in Biology (Bio101/102) concepts, and has no prerequisite programming knowledge. Students from all years and many different majors come together in this class to collectively learn about computational biology.

About this syllabus

This syllabus is a public, searchable document that contains all of the details for this iteration of the course. It serves as a contract for the students taking Bio131 - if you take this course, you agree to abide by the policies described here. As the instructor, I commit to following this syllabus and administering it fairly and equitably. The main parts of the syllabus are:

• Goals: the course goals and learning objectives.
• Support: the support systems offered in the course.
• Policies: policies surrounding attendance, deadlines, collaboration, and generative AI (e.g., ChatGPT).
• Schedule: an overview of the course topics and assignments.
• Assessment: a detailed explanation of the contract grading in the course.
• Learning Environment: my commitment to making the classroom an inclusive learning environment.
• Land Acknowledgement: an acknowledgement that Reed College rests on territory belonging to Indigenous peoples.
• Keys for Success: tips for succeeding in the course.

Any modifications to the syllabus during the semester will be noted in the change log and will be communicated to the class via Moodle. We will discuss any major changes to the assessment and grading contract in class before the syllabus is altered.

Course details

Instructor: Anna Ritz (Biology 200B, see the support page for student hours)

Lecture: MWF 10-10:50am in Chem 301

Labs: M 1:10-3:00 in ETC 208 and Tu 9-10:50 in ETC208

Materials:

• Textbook: Bioinformatics Algorithms by Pavel Pevzner and Philip Compeau. The chapters we will cover in class are freely available online. The textbook is also available at the library and in the bookstore.
• We will read excerpts of these three books (PDFs will be provided, books also available in the library):
  • The Social Life of DNA: Race, Reparations, and Reconciliation After the Genome by Alondra Nelson
  • Native American DNA: Tribal Belonging and the False Promise of Genetic Science by Kim TallBear
  • The Immortal Life of Henrietta Lacks by Rebecca Skloot

Communication & Technology

Official communications about all course materials and assignments will be done through the Moodle page.

• Check your email every day to stay updated.
• We will use GitHub and GitHub Codespaces for the programming assignments (you will be taught how to use it).
• We will use Moodle for some assignments (e.g., the starter assignment and the book reflections).
• If you have a question, others likely have the same question. Reach out at any time to me at aritz@reed.edu.