Thesis Logistics & Support

Meetings

Constant communication is crucial for both student and advisors to be on the same page. Therefore, we have organized weekly meetings to stay up to date on progress.

Weekly Group Meetings. We will have weekly group meetings in the computational biology lab (B203). Group meetings include thesis students and other researchers in the CompBio lab, and are an opportunity to provide updates and solicit advice about your project at different stages throughout the year.

Weekly Individual Meetings. We will also have time set aside for individual meetings with each thesis student (ideally with any co-advisors). These individual meetings are your time to get guidance on any aspect of the thesis project. Before the meeting, spend some time organizing your thoughts about (a) what you have accomplished since the last meeting, (b) any obstacles that you have come across, and (c) what your next steps could be. Individual meetings may need to be postponed due to other conflicts, and can also be replaced by written communication about the three items above if you have a good sense about where to go next.

Communication & Technology

Official communications about thesis deadlines and oral examinations will come from the Office of the Registrar and the Biology Department emails. These will also be posted on the Dept Moodle Page.

All thesis students will join the CompBio Slack channel, and we will have informal communication through Slack. The required logistics for a thesis project are that:

  1. You use the Reed Thesis template.
  2. You decide on a way to back up your work (for your thesis document and any datasets/analyses).
  3. You keep track of your daily and weekly work towards your thesis, in any format you choose.
  4. You communicate consistently with me and other co-advisors throughout the entire process.

When considering other technology you will use, my rule of thumb is to follow a path of least resistance. This may mean writing programs in a language you are familiar with (e.g. R, Python,…), generating figures with software that you are familiar with (e.g., R, Python, JMP, Excel,…), and using a text editor that you are familiar with (e.g. Word, LaTeX,…). This is a great time to learn something new, and if you explicitly want to learn a new technology or programming language, we will work that into the goals of your thesis. Keep in mind, though, that if you deviate far from your advisors’ expertise, we have limited means to help you.

I strongly suggest using GitHub to maintain any code you will write as part of your thesis. You can make a private repository and add me as a collaborator - this will help with code reviews and helping with bugs.

Use of generative AI

Generative AI is technology that is trained to generate text, images, or code from natural language prompts. Two examples of generative AI that you might have seen before are ChatGPT (which returns text based on prompts) and GitHub Copilot (which returns code based on prompts).

Everyone must write a thesis document. This document represents your work, your results, and your conclusions. Further, it can be written in your style, which might be as formal as a scientific paper. When you write papers, you are claiming the words and the ideas within them as your own. In order to demonstrate the learning objective that you have writen a coherent document, it needs to be in your words. As a result, you may not use generative AI to compose all or part of your thesis document. Generative AI is acceptable to use to help organize your thoughts in the planning/outlining phase (you will need to acknowledge this in the thesis). You should also be using spellcheck software, though this doesn’t need to be ChatGPT.

If you use generative AI for any part of your thesis (even for planning/organization), this needs to be clearly acknowledged in the thesis document.

Using others’ code and tools

If you use any code you found online in your own programs (such as from StackOverflow, or other sites), you must acknowledge this in your code - include the author, a brief description, and the URL.

If you use tools from other groups, you will also acknowledge these in your thesis. Typically, tools have an accompanying paper that you should cite.

If you have any questions, ask me.

Thesis Support

As your thesis advisor, one of my jobs is also to put you in touch with others who can support you through the thesis process. One of the most important groups are your peers doing thesis alongside you! The other computational biology thesis students (and other thesis students in general) can be a wonderful resource.

Thesis Funding and Borrowing Equipment

Computational thesis projects rarely need a budget for supplies. However, several possible sources of funding exist for thesis project supplies, the main mechanism being the Biology Undergraduate Research Project (BURP) grants to support thesis work offered through the Biology Department. BURP grants may fund licenses for software (e.g. Matlab) or access to databases if they are not publicly available.

There is also a Student Technology Equipment Program (STEP) program where seniors doing thesis can apply to borrow equipment from Computer User Services.

Thesis Formatting

The Help Desk will hold drop-in thesis formatting hours, resources for templates, etc. - check out their page.

Academic Accommodations

Thesis is a course, and like all Reed courses I have a commitment to accommodating any documented needs you may have. Please discuss any documented accommodations with me, especially those that affect one or more of the three-part evaluation for thesis. Please let me know if there are useful supplements to thesis meetings (videos, large-font texts, captioning, etc.). Disability Accommodation Notification Letters can be obtained from Disability & Accessibility Resources (DAR). All discussions will remain confidential.

Disruptions to the Academic Year

Many students will have personal circumstances that may affect their performance this year. In fact, it is likely that we all have been and will be deeply affected by events locally, nationally, and globally.

  1. You are encouraged to seek guidance from me and your co-advisors on any anticipated or realized issues. We will work with you to make adjustments to milestones as needed.
  2. Mental and physical health is more important than your thesis project, though it may not always feel that way. If you miss multiple meetings, I will reach out to make sure you are okay.

Diversity and Inclusion

Historically, biological discoveries and advances in computer science have been dominated by privileged voices, namely those of white men. Computational biology, while a more recent field, also lacks diversity along many important axes (including race, gender, nationality, class, sexuality, religion, ability, etc.). As we proceed with thesis, I acknowledge my own bias that stems from systemic privilege in academia, and will aim to make the resources I offer more inclusive. I welcome any other suggestions to make thesis a more inclusive learning process for Reed students.

Land Acknowledgement

As we come together to learn at Reed College, we acknowledge that the territory on which Reed stands is that of Indigenous and Native peoples. The Portland Metro area rests on traditional village sites of the Multnomah, Wasco, Cowlitz, Kathlamet, Clackamas, Bands of Chinook, Tualatin, Kalapuya, Molalla, and many other tribes who made their homes along the Columbia River (Portland Indian Leaders Roundtable, 2018). Native lands have been taken through hundreds of breaches of treaty laws, and in 1953 more then sixty tribes in Oregon were terminated by the federal government which removed millions of acres of land from Indigenous stewardship (The Native American Community in Multnomah County: An Unsettling Profile). This statement is one small step in acknowledging the history that brought us to reside on this land. Portland also has a vibrant and diverse Indigenous community and has the ninth largest urban Native American population in the US. We honor the present Indigenous communities in the area. Visit native-land.ca to explore an interactive map of Indigenous lands.