Bio331: Computational Systems Biology

In the era of high-throughput genomics, proteomics, and transcriptomics, we can now computationally explore biological processes at a systems level. Networks, or graphs, have become a dominant mathematical representation in this area of research. We will draw on the vast amount of established graph theory to learn about network models currently applied to biological systems.

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 Bio331 - 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.
  • Types of Work: an explanation of how components in this course are evaluated and contribute to the final course grade.
  • Support: the support systems offered in the course.
  • Policies: policies surrounding attendance, deadlines, collaboration, and online resources.
  • Learning Environment: my commitment to making the classroom an inclusive learning environment.
  • Keys for Success: tips for succeeding in the course.

The final version of this syllabus will be set by the first day of class. Any modifications during the semester will be noted in the change log and will be communicated to the class via Moodle.

Course details

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

Lecture: MWF 10-10:50am in ETC 211

Lab: M 1:10-4:00 in ETC 208

Materials: All reading, videos, and other materials will be freely available via Moodle. A week-by-week schedule is available on Moodle as well.

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 for the programming assignments.
  • We will use Moodle for written assignment submissions.
  • We will use other technologies (like Padlet or ImageJ/FIJI) for class activities.
  • If you have a question, others likely have the same question. Reach out at any time to me at aritz@reed.edu.

The Honor Principle is in effect at all times. This includes our work and interactions in class as well as our work done outside of class. We will have a discussion at the beginning of the semester about how the honor principle might be relevant in Bio131.