Meetings and Recitations

Lecture occurs twice a week (Tuesdays and Thursdays) from 1:00 - 2:25 pm in the Baxter lecture hall. These sessions will involve lecture and in-class participation including back-of-the-envelope estimations, derivations, and natural philosophy. This course is designed to serve as an overview of some of the overarching principles of biological inquiry and address how biology fits in along physics, chemistry, mathematics, and engineering.

Recitation sessions are held once a week. These occur in the evening on Mondays through Thursdays and on Friday afternoons. These sessions are held with graduate and undergraduate teaching assistants and are designed to aid you on problem sets and further explain the topics covered in class.

Computational prowess is an incredibly useful skill in the modern biological era. Many homework problems will require you to write computer programs to execute calculations, analyze experimental data, perform simulations, and more. No prior computer programming experience is required for this course. The TA’s will host computational tutorial sessions five times during the course and will take place during normal recitation times and locations. While many programming languages are used in biology (R, C++, Java, Matlab, etc), Python will be the language of instruction for this course. Please see the programming page for instructions on setting up a scientific Python computing environment.

Homework and Regrading

Homework will be assigned on Thursdays will be due the following Thursday at the beginning of class. All homework submissions are electronic and must be in PDF (text) or .ipynb (code) format within a .zip file. Formats such as .docx and .pages will not be accepted. If you are writing your entire homework in the Jupyter notebook, you may submit it as a .ipynb file only. You do not need to convert it to PDF.

To ensure proper grading, all homework must be submitted via email to bi1.caltech [at] gmail [dot] com with the following filename:

• lastname_firstname_hw#.zip containing the files lastname_firstname_hw#.pdf or lastname_firstname_hw#.ipynb for problems requiring code along with any images used in the .ipynb file.

The subject line of your submission email must have the following format:

• [Homework #] Submission of HW# for Firstname Lastname

For example, a submission for the first homework set would be submitted by email with the subject line [Homework 1] Submission of HW1 for Barbara McClintock. The attachment would be McClintock_Barbara_hw1.zip containing the files McClintock_Barbara_hw1.pdf and McClintock_Barbara_hw1.ipynb and any image files used in the .ipynb document.

Any submission not abiding by this format will not be graded!

If you are interested in challenging the way your homework was graded, you are limited to 2 challenges total over the term. If you ask for a regrade, your entire homework will be subjected to the same high level of scrutiny you have requested for the problem you feel has not been graded properly. This could result in a net reduction in your grade on that particular homework if your previous graded version on other problems gets “overturned”. Your regrades may also be used for grading of improperly submitted homework.

To submit a regrade, email the name of the assignment you would like regraded to bi1.caltech [at] gmail [dot] com with the following subject line:

[Homework #] Homework Regrade Request for Firstname Lastname

Collaboration Policy and the Honor Code

Collaboration is imperative to scientific discovery. You may work with others on your homework assignments, however all work handed in must be your own. This means that you are not allowed to hand in work copy pasted from those you worked with.

For programming, please follow the 50 foot rule from CS11 which reads

[…] If you help another student with their programming problems (including debugging), you must not consult your own code while doing so. Specifically, we ask that your own code be at least 50 feet away i.e. not visible to you or the person you are helping while you are helping them. This means that you may work with each other on programming problems but you may not copy others code directly. […] Help them with your brain, not with your code.

You may use resources on the internet, primary literature, or textbooks to help you answer the questions, although you must provide a reference. You may not use previous homework questions or solutions from previous years of this course or other courses like it.

Finally, you must follow the Caltech honor code which states

No member of the Caltech community shall take unfair advantage of any other member of the Caltech community.

We have designed the computational sections to provide you with all of the information you need to complete the problems described in the homework. While you may use any of the code provided in the tutorials verbatim to solve your homework, please do not “copy-and-paste” it directly into your notebook. We will often use different variable names and some hard-coded numbers in the tutorials than you will use in your homework. To make sure you understand what each line of the code is actually doing, you should type it out by hand.

Grading, Attendance, and Electronic Devices

There will be no exams, quizzes, reports, or research proposals. The entirety of your grade comes from completing the homework. Late homework submissions (submitted after 1:00 pm on the due date) will not be accepted without penalty. For each day a homework assignment is late, a 10% deduction will be made from the maximum possible score, beginning immediately after the homework is due. This means that if your homework is handed at 2:00 on the day it is due, the maximum possible score is 90%. If a homework is received four days late will maximally earn 50%. Attendance is expected of all students in the class. As a general rule “on time” means that you are sitting in the class room five minutes early.

You may use an electronic device (e.g., tablet, laptop) to take notes during class only if you use it for this purpose. We will ask you to turn off your electronic devices or ask you to leave, if their use is off-topic or distracting to others.

Communication

You may contact the course TAs through email at any time, but please do not unnecessarily ‘spam’ them with emails.

The course Piazza can be used for general questions. You may discuss homework and post public questions about problems, topics, or things of general interest to the Bi1 students and course staff. You may also post questions anonymously. The course TAs will monitor this page with regularity and will respond to valid inquiries.

Absences, Extensions, and Ditch Day

No absence or extension on homework will be granted without an adequate and compelling reason. All extensions require a note from a doctor or a dean

In the event that Ditch Day falls on the day that an assignment is due, the deadline will be extended to two calendar days later (i.e., if Ditch Day is on a Thursday when a problem set is due, then the revised due date will be Saturday at 1:00 pm). Any course meetings affected by Ditch Day will be resecheduled and posted on the website home page.