Course Organization

The class website is the central location for information about Bi 1x. Contact information for the course instructors and TAs may be found here, as well as a schedule of all activities. Each activity has a link to an associated document. For experiments, the document provides background on the experiment, protocols, and assignments. Documents for tutorials and journal clubs are also linked to from the schedule page.

Attendance

Bi 1x is focused on projects that depend on protocols carried out during class time. Thus, attendance is 100% mandatory. Tardiness is unacceptable and will affect your grade.

Journal Club

During the course, we will read various articles and discuss them in class. The journal club articles may be downloaded from the class website, along with talking points to get you thinking about pertinent questions ahead of the in-class discussion. You should have answers ready ahead of time from the talking points to share with the class.

Assignments

Assignments are found in the document for each of the experiments in the course. They are designed to help step you through the data analysis and to help you understand the experiment in greater depth. They consist of n+1 problems pertaining to the respective lab module. Problems 0 and n+1 are always the same. Problem 0 asks you to write a summary of the lab module. Problem n+1 asks you to show any data or code. Problems 1 through n help take you through the data analysis and ask you to think about conclusions.

Assignments are due at a specified date and time. They must be submitted electronically via Canvas. All assignments must be submitted as a Jupyter notebook and also an HTML conversion of the notebook. You may hand-write and scan portions of these assignments and include the scans in your Jupyter notebook. Naturally, everything must be legible. You may also need to submit image files, for example if you scan hand-written notes (see the into to Jupyter tutorial). All files must be submitted as a single ZIP file. The name of the document must be lastname_firstname_#.zip, where # is the number of the module as shown on the schedule page. The name of the Jupyter notebook must be lastname_firstname_#.ipynb and the HTML document must be lastname_firstname_#.html. You should also name the folder your zip as lastname_firstname_#.

All code must be submitted with your assignment. Using Jupyter notebooks makes this seamless. They allow you to include comments, code, and graphics together in the same document, and also allow TAs to run your code to make sure everything works properly.

You are encouraged to discuss your experiments and assignments with your classmates and to work together. However, all submitted materials must be your own. For computer code, the 50 foot rule applies. Obviously, you may not refer to work other students have done from previous editions of the course.

You may not use any large language models (LLMs; examples include ChatGPT and Clause) or any other code or prose generating software.

Grading

Lab Performance

Your lab performance is based on attendance, attitude, and and how carefully you work. First and foremost, you must work safely. You are also expected to take care with all equipment and to keep it clean. Your lab area must also be clean and tidy. Your lab performance score will be lowered by tardiness.

Assignments

See the description above for assignment format. The assignments are due by the beginning of class on the due date specified on the class website. The exceptions are the prelab questions for the assignment, which must be handed in on paper before the experiment is performed in the designated lab period and also electronically with your assignment submission via Canvas.

You are expected to turn assignments in on time. There are no extensions. This is not meant to be cruel. It is meant to prevent students from falling behind the pace. Late assignments are eligible for up to 50% credit up to three days late. All assignments have to be turned in to pass the class (even if more than 3 days late). If you have a CASS accommodation, you need to communicate it to the instructors within the first week of class, or within the first week after the accommodation is issued if issued during the term. If your accommodation allows for extra time on coursework, you need to let course staff know you will be exercising that accommodation at least 24 hours before the homework is due or as soon as reasonably practicable. No assignments will be accepted after June 12.

Journal Club

You will receive credit for contributions to journal club discussions. Therefore, you should come to journal club prepared to discuss the talking points.