Types of Work
There are three types of work that will be done outside of class: work on biology and computational thinking concepts, work on programming skills, and work on biology and society. In addition to these three themes, there is also some required programming lab work and optional choose-your-own (CYO) assignments that will count towards your grade.
All work will be assessed as “complete,” “partially complete,” or “missing” according to the criteria below.
As stated in the deadline policy, all work for the course must be completed by the last day of finals at 5pm.
1. Biology and Computational Thinking
In Bio131, you will learn about biological sequences (DNA, RNA, and protein), the relationships among these molecules, and some biological questions that researchers study. You will also learn how to take these biological questions and turn them into a form that can we can solve with computation.
The work for this theme consists of two take-home exams (E1 and E2). The purpose of the exams is to demonstrate your knowledge about the concepts from lectures, so the exams must be done individually (except for the in-class opportunity described below). The exams consist of multiple questions. To pass a question, you will have to follow all directions and get the majority of the question correct. The criteria for success for each question will be clearly described on the exam. You will be able to revise the questions after receiving feedback.
Additionally, there is an opportunity to work on a subset of the questions from E1 and E2 in class the day that the exam is released. The purpose of the in-class opportunity is to practice answering exam questions and get clarifying questions answered, either on your own or with other students. Working with other students in class is also a way for you to learn about how others approach the exam questions. The in-class opportunity is completely optional - students can choose to skip this day and complete the entire exam individually if they choose.
| Complete | Partially Complete | Missing | |
|---|---|---|---|
| E1: Exam 1 | You pass all 5 questions | You pass 3-4 questions | You pass fewer than 3 of the questions or you do not submit the exam |
| E2: Exam 2 | You pass all X questions | You pass X-X questions | You pass fewer than X of the questions or you do not submit the exam |
Note: the number of questions will be updated when the exams are finalized.
2. Programming Skills
Bio131 is designed to introduce Python programming as a way to implement solutions to computational problems. There is no expectation of programming knowledge prior to this course - everything you need will be taught and practiced in lectures and labs. We also have lots of built-in support for the class - see the support page for some resources.
The work for this theme consists of four programming assignments (P1-P4), some of which are multi-week assignments. The purpose of these assignments is to demonstrate your knowledge of Python programming and your understanding of how biological questions can be posed and answered using computers. Collaboration is highly encouraged for this type of outside work - refer to the collaboration policy for more information.
Each programming assignment has multiple tests that check the outputs of your programs - these are called unit tests and they are automatically run when you submit your assignment in GitHub Classroom. The criteria for success corresponds to how many tests your code passes. You can resubmit any of the programming assignments at any time, including after getting feedback. It is important that your code runs without errors - note that if your code does not run because of one or more errors it does not pass any tests and will be considered Missing.
| Complete | Partially Complete | Missing | |
|---|---|---|---|
| P1: Python Practice | 11 or more out of 13 tests pass | 7-10 tests pass | Fewer than 7 tests pass or you do not submit the assignment |
| P2: Central Dogma | 11 or more out of 13 tests pass | 6-10 tests pass | Fewer than 6 tests pass or you do not submit the assignment |
| P3: Motif Finding | X or more out of X tests pass | X-X tests pass | Fewer than X tests pass or you do not submit the assignment |
| P4: Alignment | X or more out of X tests pass | X-X tests pass | Fewer than X tests pass or you do not submit the assignment |
Note: The number of tests will be updated when the assignments are finalized.
3. Biology and Society
We will read about and discuss aspects of molecular and cell biology and its influence on society and culture (and vice versa). You will read excerpts from three books and discuss these readings with your lab section.
The work for this theme consists of three written reflections (B1-B3) followed by three discussions during class (lecture time). The purpose of the written reflection is to take some time to think about the book and prepare for the in-lab discussion.
- If you do not submit the reflection before the discussion, you will need to incorporate the summary of the discussion in your reflection for it to be considered complete.
- If you cannot make the in-class discussion (for example due to illness or other circumstances), you must let Anna know before class. In that case, you will write a longer-form reflection that may include an additional prompt based on the in-class discussion.
The following table is used for all book reflections:
| Complete | Partially Complete | Missing | |
|---|---|---|---|
| Reflection & Discussion | You write 250 or more words in response to the writing prompt before class and you attend the discussion | You attend the discussion but you do not submit a reflection | You do not attend the discussion and do not submit a reflection |
| Discussion only (if you did not submit the reflection before class) | You attend the discussion and write 750 or more words that summarizes the discussion and provides your personal reflection to the writing prompt | You attend the discussion but you do not submit a reflection | You do not attend the discussion and do not submit a reflection |
| Reflection only (you must notify Anna if you miss the discussion) | You write 1,000 or more words in response to the writing prompt and any other in-class prompts | You write a reflection but it is less than 1,000 words | You do not attend the discussion and do not submit a reflection |
4.Programming Labs
Programming labs are an opportunity to work on shorter pieces of code that help you prepare for the programming assignments. The purpose of these labs are to prepare you for the programming assignments and give you additional insight into the lecture content. In many cases, the labs are components of the programming assignments. Lab time is also a place where I will be available to help with any programming issues you face.
There are eight programming labs (L1-L8), which are assessed as “submitted” (rather than complete) or “missing.” By “submitted” I mean that you turn in whatever you have by the time lab is done (or that you have worked on it for about 1.5-2 hours). Note that you can submit labs that are not completely finished - the goal here is that you have spent time working on the programming skills for the later assignments.