Final Project

Your final project can be on anything you want that is related to this course. We want your final projects to be interesting and fun to work on, and to produce something of value beyond just satisfying an expectation of this course.

We are open to other types of projects, but are expecting most students will do one of these types of projects:

  • Systematization Projects: Start with a curious question, learn what is currently understood about it from the research literature, and produce something to explain it to computer scientists. This could be a static or interactive web page, a video, improving a Wikipedia page, or some other artifact.

  • Research Project: conduct original research on a relevant topic. This starts by understanding what is already known and identifying a question to study. Then, applying tools you learned in this class, and others you learn on your own, to make progress on answering that question.

  • Tool-Building/Improving Project: develop some tool that will be useful for computational biology research. It is probably more useful to make improvements or add a feature to a widely-used open source tool, than to build your own software from scratch.

  • Hobby Project: replicate something for fun (e.g., sequence your genome), and produce an artifact (most likely a web site) explaining your experience in a way that will be interesting and useful to others.

Your project doesn’t need to fit into any of these categories, but these should give you some ideas for the kinds of project you might do. For more ideas, you can also look at the projects from the Spring 2022 course.

Project Goals

An ideal project will satisfy these desiderata:

  • fun (for you to do, and for others to see)
  • useful (at least to yourself, but hopefully to many)
  • relevant (to the class, to yourself, to humanity)
  • technically interesting

Your project is not required to satisfy all of these, but should at least partially satisfy most of them, and fully satisfy at least one of them.


For the final project, we encourage students to work in teams of three people. This is not a strict requirement, however. You may work in a larger team if you find a project idea that benefits from a larger team and have a good plan for how to work together. You may also work alone if you prefer to work alone and make a convincing justification to me why it is better for you to work alone on this rather than as part of a team.

The impressiveness of your project should scale as at least the square root of the number of people on your team, but with a baseline expectation that everyone’s project should be at least as impressive as what would be expected of a three-person team. If your team is larger, you would expected to do something approximately sqrt(N/3) times as impressive as a three-person team (so a six-person team would be expected to do something that is approximately 1.4 times as impressive the standard three-person team project expectations).

You should not underestimate the need for management and structure as your team size grows, and even a three-person team requires some organization and leadership. If you have more than one person on your team, your project proposal should include a plan for how to manage your team and work well together.


  • Project Team and Idea, due Friday, 30 September (AoE). See the Submission Form for what is included in this.

  • Project Proposal, due Friday, 14 October (AoE): Submission Form. Your project proposal should be a single PDF file that includes:

  1. The names and email ids for all members of your team.

  2. Title of your project: short description that clearly captures your project idea.

  3. A short paragraph that describes the goal of your project.

  4. A project jusfication that explains how your planned project is likely to satisfy at least three of the goals above (fun, relevant, technically interesting, useful).

  5. State-of-the-art: your understanding of what is already available connected to the goal of your project. This could be other attempts to achieve the same goal (and why you think you can do something better), or work related to similar goals. A good state-of-the-art will include references to specific relevant work. For most types of projects, this would include research papers relevant to your topic.

  6. A project plan that explains the main tasks needed to successfully complete your project and what you will actually do.

  7. A management plan list of your team members and their roles and responsibilities. If your team has more than two people, this should also explain how you plan to coordinate and manage your team.

  • There will be project updates in classes, October 18 through end end of the semester. More information will be provided about these later, but you should expect that your project team will be ready to provide a short update about what your project is and what you are doing.

  • Project Report, due Monday, 7 November. This should be a complete project report, which will be graded. You will receive feedback on it, and have an opportunity to revise and improve.

  • Project Presentations, during the last two classes. Teams may be selected to present on their projects.

  • Revised Project Report, due Tuesday, 6 December. Final submission of the results of your project.