Types of Work

Bio331 involves learning about two distinct themes - biological networks at different scales and graph algorithms - and how they can be combined to answer new biological questions. The work is graded on Missing/Partially Complete/Complete (M/P/C), Submitted/Not Submitted, or Present/Absent. Nearly all work may be submitted for an improved grade. Each assignment will clearly describe the criteria for success according to these assessment types.

In an advanced course such as Bio331, I believe it is important for students to know if their efforts exceed my expectations. For some types of assignments, there is a possibility of receiving an Excellent (M/P/C/E). Only truly exceptional work is marked as excellent, and it is not intended for a student to achieve an E for all eligible assignments. All assignments are initially graded as M/P/C; in order to get an “Excellent,” students must do additional work after receiving feedback. More details will be provided with each eligible assignment.

Initial Survey

The first assignment is a brief survey to better understand your motivations for taking the course, and what you hope to gain from it. It is graded as Submitted / Not Submitted.

Programming Assignments

There are four programming assignments to be done outside of class. The programming labs are designed to help you start on these assignments (lab solutions will be released on Wednesdays), and the assignments can be collaborative. You will complete these programming assignments in the first half of the semester. These are graded as M/P/C/E, and you may resubmit work. “Excellent” assignments require a reflection on the changes that were made.

Exams

There will be three exams that review and expand upon the lecture content of the course; they are not collaborative. They will be assigned at approximately the 5-week, 10-week, and 13-week mark. These are graded as M/P/C/E, and you may resubmit work. “Excellent” assignments require a deeper dive into one of the exam questions by investigating current research or alternative approaches.

Lab Engagement

There are 6 programming labs and 7 lab-time opportunities for research project work. Attendance (or otherwise participating) in these activities is important for the class’s learning goals. There will be ways to make up these components of the class if you miss them (see the attendance policy). These are graded as Present/Absent.

Research Deliverables

You will work on a research project in the second half of the semester (either individually or in small groups). There are two types of deliverables for the research project: well-documented and correct code and a structured write-up describing your project. There are three deliverables graded as Submitted / Not Submitted, five deliverables graded as M/P/C, and the final research project deliverable is graded as M/P/C/E. The final deliverable is “excellent” if all feedback for both the code and the write-up have been addressed.

Deliverable	Description	Assessment Type	Feedback
Preference Form	Brief survey of research project and group preferences	Submitted / Not Submitted	N/A
R1: Question, Data, & Roles	A concise research question, a description of your data, and group roles (if applicable)	M/P/C	Lab Check-In
R2: Code Draft 1	Documented code base and a summary of in-progress work	M/P/C	Code Review
R3: Document Draft 1	Full draft of your write-up, including preliminary results	M/P/C	Write-Up Review
Pivot Plan	Brief description of your plans for the rest of the semester	Submitted / Not Submitted	Lab Check-In
R4: Code Draft 2	Documented code base	M/P/C	Written feedback
R5: Document Draft 2	Updated draft of your write-up	M/P/C	Written feedback
R6: Research Project Deliverables	Final versions of your code base and write-up	M/P/C/E	Written Feedback
Final Presentations	Low-stakes presentation during finals week to share your research project	Submitted / Not Submitted	Written feedback