BE/CS/CNS/Bi 191ab:  Biomolecular Computation
Professor: Erik Winfree
Winter term teaching assistants: Robert Johnson, Andrés Ortiz-Muñoz, and Tyler Ross


This page is under development for Winter 2018. The previous incarnation was Winter 2017.

Description from the course catalog:
BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units (3-0-6) second term; (2-4-3) third term. Prerequisite: none. Recommended: ChE/BE 163, CS 21, CS 129 ab, or equivalent. This course investigates computation by molecular systems, emphasizing models of computation based on the underlying physics, chemistry, and organization of biological cells. We will explore programmability, complexity, simulation of and reasoning about abstract models of chemical reaction networks, molecular folding, molecular self-assembly, and molecular motors, with an emphasis on universal architectures for computation, control, and construction within molecular systems. If time permits, we will also discuss biological example systems such as signal transduction, genetic regulatory networks, and the cytoskeleton; physical limits of computation, reversibility, reliability, and the role of noise, DNA-based computers and DNA nanotechnology. Part a develops fundamental results; part b is a reading and research course: classic and current papers will be discussed, and students will do projects on current research topics. Instructor: Winfree.

Time & Place: 
BE/CS 191a: Winter 2018, Moore B270, Tu & Th 10:30am-11:55am

Office hours:
Please start your homework set early, and come to the first relevant TA session. The homework will usually be too much to do at the last minute, and planning for this is your responsibility.
TAs (191a only): Annenberg 107 Mondays at 7pm and Annenberg 243 Tuesdays at 4pm. Note that different days have different rooms.
For simple and quick questions, TAs can also be reached by email at cs191_ta * dna.caltech.edu, but may not be available to answer substantial questions in a timely manner. Non-trivial questions should be deferred to and answered at the office hours. Even if you know them, please do not use the TAs' personal email addresses; it is important that all TAs be kept in the loop on class-related issues.
Professor (Winter term only): Tuesdays 1-2pm in Moore 204. This is only for things that can't be handled by the TAs, such as administrative issues. Email is answered, though often not quickly, at winfree * caltech.edu.

Textbook:
None. Everything you need to know will be presented in class. The references suggested in the syllabus are optional further reading, but neither sufficient nor necessary.

Lectures:
Attending lectures is mandatory. There may be an in-class quiz from time to time.

Syllabus for 191a:
The syllabus as presented gives you a rough idea of what will be in the class, but it is subject to change in detail. The topics and references should be considered final only on the day of the lecture, and after. Prior to that, the topics and links may be revised.

Note: reference links may require a Caltech IP address.

Homeworks
The expectation is that homework will be handed out in class every other Thursday, and due by email as a single PDF file before 11:59pm on Wednesday 13 days thereafter. I expect to assign six homework sets.

Grading Policy for 191a:
There will be roughly one problem per class lecture, with homework sets due roughly every other week. There is no midterm or final exam per se.
Homeworks: Homeworks will be graded on a 0-10 scale for each problem.
Late policy: Late homework will be penalized by 10% per day, e.g. if turned in 24 hours late, the score will be multiplied by 0.9 after grading, and if turned in 48 hours late, the penalty will be 20%. The penalty increases linearly per hour, accumulating 10% per day, until a 9 day late homework's score is multiplied by 0.1, and a 10 day late homework gets no credit. The homework sets are hard, but ample time is given. Start as soon as they are handed out.
Extension policy: Extensions may be granted by the professor only, at his discretion, for interfering situations that cannot be planned for, e.g. a health problem with a doctor's note, last-minute travel for interviews, etc. Travel that can be planned well in advance (e.g. a sports competition) is less likely to merit an extension, since starting and completing homework early should be an option.
Grade composition: Your class grade will be based on homeworks only.
Collaboration policy: For all problem sets, you may discuss problems with other students prior to writing anything down, but what you turn in must be entirely written by you, by yourself, including any program code. That is to say, the "50 foot rule" applies here explicitly for both program code and mathematical derivations, and in spirit applies to other aspects of your class work. For more detail and discussion, see the nice write-up for CS11 or this more recent flier .

Accompanying Notes and Files for Homework:
For homework 1: AnnotatedExamples.nb provides some useful hints for how to use the CRN Simulator package in Mathematica. Note that some browsers will download the package as AnnotatedExamples.nb.txt, in which case you will need to rename it after download. Homework 1 will be accepted with no late penalty if submitted before midnight Friday, January 12.

Helpful background:



Description for 191b:
In the spring term, I have sometimes taught a class that begins by reading and discussing classic and contemporary research papers on biomolecular computation, and also includes a mini research project. This second term will be taught in 2018 by demand only, by at least 5 students. UPDATE: Part b *will* be taught in 2018.