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. Anyone that misses more than 2 class meetings without a formal excuse from a dean or health care provider will be automatically dismissed from the course.


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 master 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.


Important:

Some problems are prelab questions. They are labeled as such in the module handouts. These must be done before lab because they will help you better comprehend what you are doing during the experiment. The prelab problems are submitted both with your lab notebook at the beginning of the lab session, and also with your submitted assignment.


Assignments are due before class on the prescribed due date. 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.


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.


Lab Notebooks

Keeping an up-to-date and accurate record of your work in lab is always important. You must therefore keep a neat and thorough lab notebook. The notebook should contain below.


Already in notebook when you arrive at lab:

  • Date
  • Title of experiment
  • Purpose of experiment in one or two sentences (what you are trying to find out and how you plan to do that).
  • Methods: Bullet-point outline of what you will do in lab. This is not a detailed procedure as is laid out in the module handouts, but rather a paint-with-broad-strokes overview of what you are doing in lab.
  • Note: Answers to prelab questions in the module handouts are not on the pages of the lab notebook. Rather, they are printed on a separate sheet.

To be filled in during lab:

  • Comments on methods: Mark out any deviations from the protocols you used in the lab.
  • Observations and data: write down any observations as well as any associated data. Clearly write out any calculations you did in lab. It is important to keep it organized. For example, you could make a table that lists the amounts of solutions you used for each reaction. This is separate from data analysis activities, which are turned in separately as part of the assignment.
  • Any notes you think might be important for future reference.

Please save the first two pages of your lab notebook for a table of contents page and list all of your experiments and their page number.


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.


The grade breakdown is as follows:

  • Assignments: 70%
  • Lab performance: 17%
  • Journal club: 8%
  • Lab notebook: 5%

Lab Notebook

Your notebooks will be checked in class. Half of the credit is given for prelab on experimental information including the purpose and methods. (This is different from the prelab questions in the assignments, which count toward the assignments grade.) The other half of the credit for lab notebooks is for in-lab notes including comments on procedures, observations, data and results. Be sure your lab notebook is legible and well-organized.


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 with the lab notebook before the experiment is performed in the designated lab period.


You have a total of two "grace days" during the term for late assignments. That is, if you turn in an assigment between 0.01 and 23.99 hours after it was due, you will not lose any credit, but you will spend one of your grace days. (Grace days are not charged if you have a formal excuse from a dean or health care provider.) After you spend your grace days, late assignments without a formal excuse will have 10% credit deducted for each day that it is late (in other words, you can get up to 90% credit if one day late), up to five days late, after which the assigment will not be accepted.


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.