Lectures and readings
Lecture attendance and required reading are mandatory. The lecture/reading schedule is on the course website.
Grading
80% of the grade is determined from problem sets and quizzes, reading memos, and discussions about the reading.
20% of the grade is determined from the News and Views final project (see below).
Honor Code
Unless otherwise noted on a particular problem set, you may discuss assignments and your final project with other students. The work, however, should be substantially your own. It is a violation of the Honor Code to copy solutions from classmates or to refer to course materials from previous years.
Homework
Homework and News and Views due dates are listed on the course website. All assignments are due at 1 pm on the stated dates (before class starts). All homework must be completed as Jupyter notebooks (See "Computing," below.) Email completed work to caltech.chebe163@gmail.com. Each student is allocated six "late days" which can be allocated to any assignments with no deduction (e.g., turn in Homework 1 two days late, and Homework 3 four days late with no deduction). After the six late days have been used up for the term, late assignments will not be accepted. Late work submitted with a note from a dean (e.g., for medical reasons) does not count against your six late days. Please note that no assignment can be turned in after Friday, March 16, due to the term ending.
Final project
An article in the News and Views section of Nature typically describes a current research paper to a non-expert audience. The articles are between 1.5 and 2 pages in length, typically have a single figure, and usually have about eight references. They provide a basic contextual background for the highlighted paper, describe its major findings, and pose open questions in the field. Check out Nature’s website for examples of recent News and Views articles.
Your final project is to select a current research paper (no more than three years old) and write a News and Views piece. The paper can be in any journal, but the News and Views should be written in the style of Nature. It should be no more than two single-spaced pages in length (11 pt font, 1 inch margins), including a figure that you create (i.e., not taken from the original paper, but designed to tell the story for your piece) and 5 to 10 references.
Your News and Views article must be submitted as a hard copy and emailed to caltech.chebe163@gmail.com by 5 pm on Friday, March 16. You can submit the hard copies in Justin's mailbox in the administration office on the first floor of Broad (his mailbox is in the lower left corner). At the top of your article, indicate whether the it covers rational design or directed evolution methods.
Computing
Homework is completed as Jupyter notebooks, which allow mixing executable code and its output with text and images, including equations. The equations are rendered using LaTeX. Please consult tutorials on using Jupyter notebooks and LaTex.
This course requires use of NUPACK, a growing software suite for the analysis and design of nucleic acid structures, devices, and systems. Additionally, you will need to use other Python-based software, such as NumPy. You can use a computing resource on Amazon Web Services (AWS) that we set up for you. This already has NUPACK installed, along with Python wrappers to aid in its use, and other Python packages you will need. For instructions on how to launch and use an AWS instance, see the tutorial.
Alternatively (though not officially supported for this class), you can install NUPACK locally on your machine by registering on the NUPACK Downloads page and following the installation instructions in the documentation. You can install Python-based tools you need by downloading and installing the Anaconda Python Distribution. Be sure to install the Python 3.6 version. Finally, you can download the NUPACK Python wrappers here.
Reading memos and in-class discussion
In the directed evolution portion of the class, you will read papers each week, and we will discuss them in class. Reading should be an active process. To help you with the reading and to help us assess how well you are understanding the material, you are required to complete reading memos (based on the idea by Edwin Taylor) for select reading assignments. To construct a reading memo, sit with the paper and your computer with blank email message to compose. As you read through the paper, if something is unclear, including equations, immediately write it down. If the issue becomes clear later on as you're reading the paper or background material, go back to your original note and write down how it was clarified. At the end of the paper, write down any general difficulties or questions you have. Do not delete anything you write. It should be spontaneous. After reading the paper, go back to the top of your email message and write a two or three sentence summary of the paper. Finally, send the reading memo to caltech.chebe163@gmail.com with subject line
your_lastname: paper_1st_aut_lastname, paper_pub_year.
This email must be sent by noon on the day of the assigned reading. The reading memos comprise 10% of your final grade, and no late submissions are accepted.
We will discuss the papers in class. Come prepared to discuss the major points of the papers and any questions you may have. Some papers have "questions to consider" that accompany them to help you think about some pertinent questions. The discussions are done in small groups, and the groups will share their thoughts with the rest of the class. This means that lecture attendance is imperative. One percent of your final grade will be subtracted for each unexcused lecture.