Lectures and readings
Lecture attendance and required reading are mandatory. The lecture/reading schedule are on the course website. In-class quizzes will be given over the reading.
Grading
60% of the grade is determined from problem sets and quizzes over the reading.
40% of the grade is determined from the final projects (20% each, 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 final project due dates are listed on the course website. All assignments are due at 1pm on the stated dates (before class starts). Email completed work to caltech.chebe163@gmail.com. Work can be submitted up to three days late, with a 10% deduction taken per day (e.g., for a problem set that is two days late, the maximum score will be 80%).
Final projects
There are two written final projects, a "News and Views" piece about a current research paper and a "miniproposal" for an original research project. One of these two will be for directed evolution and the other for rational design; you are free to choose which is the miniproposal and which is the News and Views.
You may find this list of research groups working on rational nucleic acid design useful.
For both the News and Views and Miniproposal, we strongly advise consulting with the course instructors and TAs as early as possible. We will provide valuable guidance in picking topics and in writing.
Both projects must be submitted as hard copies and emailed to caltech.chebe163@gmail.com by 5 pm on Friday, December 9. 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 News and Views and your miniproposal, indicate whether the document is being submitted as a rational design project or a directed evolution project.
Following is a summary of what we are expecting for the respective projects.
News and Views
An article in the News and Views section of the journal Nature typically describes a current research paper to a non-expert audience. The articles are between 1.5 and 2 pages in length (this is two pages in magazine-style font), 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 for it. 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, including a figure and references (do not include too many references; somewhere between 5 and 7 is typical in Nature).
Miniproposal
You will write an abbreviated version of an NIH-style proposal for original research inspired by the material presented in the course. Your miniproposal will essentially consist of the Specific Aims and Significance sections of NIH proposals. Here are descriptions of these sections, taken from NIH document SF424, which is the application guide for NIH grants. The proposal should be no more than two single-spaced pages in length including a figure, but exclusive of references.
Specific Aims
- State precisely the goals of the proposed research and summarize the expected outcome(s) including the impact that the results of the proposed research will exert on the research field(s) involved.
- List succinctly the specific objectives of the research proposed, e.g., to test a stated hypothesis, create a novel design, solve a specific problem, challenge an existing paradigm or clinical practice, address a critical barrier to progress in the field, or develop new technology.
Significance
- Explain the importance of the problem or critical barrier to progress in the field that the proposed project addresses.
- Explain how the proposed project will improve scientific knowledge, technical capability, and/or clinical practice in one or more broad fields.
- Describe how the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field will be changed if the proposed aims are achieved.