CS273a

Course Description

A computational introduction to the most amazing programming language on the planet: your genome. Topics include genome sequencing (assembling source code from code fragments); the human genome functional landscape: variable assignments (genes), control-flow logic (gene regulation) and run-time stack (epigenomics); human disease and personalized genomics (as a hunt for bugs in the human code); genome editing (code injection) to cure the incurable; and the source code behind amazing animal adaptations. Algorithmic approaches will introduce ideas from computational genomics, machine learning and natural language processing.

Prerequisites

There are no biological or computational prerequisites for CS273a. While there are no official prerequisites, a background in programming is strongly encouraged. Introductory sections on molecular biology, text processing in UNIX, and the UCSC Genome Browser will be given early in the quarter (see schedule below).

Cross-listings

This course is cross-listed within Developmental Biology and Biomedical Informatics as DBIO273A and BIOMEDIN273A, respectively.

Class Schedule

Tues Thurs 1:30PM-2:50PM in Alway M114

Bibliography
The course is mostly based on current or very recent literature. As such, it does not follow any textbook. Please use the papers mentioned at each lecture as pointers into the relevant literature (for more material, you can look at the papers' references, or at more recent publications that cite those papers). The easiest way to find a paper would be to search for its title and/or authors on Google Scholar or vanilla Google.

As a Stanford student you also have free access to many biomedical journals. In order to be granted access to them while you are off-campus you simply need to add https://lane.stanford.edu/help/searchtools.html to the main URL and enter your Stanford credentials upon request (for example http://www.somejournal.com/other/stuff would become http://www.somejournal.com.laneproxy.stanford.edu/other/stuff).

The following book can be used as a general reference to the biological topics discussed in class: Human Molecular Genetics, 4th edition. The course may also use material from Genomes, Browsers and Databases: Data-Mining Tools for Integrated Genomic Databases.

Communication

All course communication will be handled via Piazza. Find our class page at Piazza and enroll to receive announcements and access to other private course resources.

Instructor

Gill Bejerano
Office: Beckman Center B321
Office hours: Email for appointment
Phone: (650) 723-7666
Email:

Teaching Assistants

Bo Yoo
Office: Beckman Center B381
Office hours: TBD
Email:

Yatish Turakhia
Office: TBD
Office hours: TBD
Email:

Course Requirements
There are three course requirements:
  1. Homeworks. Throughout the class there will be two homework assignments. Three late days are awarded for the quarter. Once these late days are used up, homework turned in late will be penalized 20% per late day. The number of late days used is rounded up to the nearest day, so assignments turned in one hour late use one full late day. Late days cannot be applied to the project milestone or final project presentation.

    All codes must be executable on stanford student machines (i.e. cardinal, myth, or rice). No Jupyter notebooks will be allowed. Include how to run your code in your README, and all your codes must be able to run without user modification (e.g. if the code takes in a file as an input the path or the file name should not be hard coded but should be passed in through command line. All files must be named appropriately and your submitted zipped file must include your name. Be as detailed as possible to ensure that you get all the points.

    Because we reuse some problem set questions from previous years' homeworks, looking at previous years' solution sets is not permitted and is an honor code violation.

    Students may discuss homework problems in groups. However, each student must write down the solutions independently, and without referring to written notes from the joint session. In other words, each student must understand the solution well enough in order to reconstruct it by him/herself. In addition, each student should write on the problem set the set of people with whom s/he collaborated.

  2. Project. Students will form groups, and each group will be assigned an individual project. Instead of a final exam, at the end of the class there will be a poster session where the groups will present their work.

  3. Attendance. For this class, attendance is mandatory. You may miss up to 2 lectures without affecting your grade, with consideration given if you are not feeling well.

Grades will be determined by roughly the following breakdown: 30% HW1, 30% HW2, 5% Attendance, 35% Final Project.
Course Tools

The base course directory is located at /afs/ir.stanford.edu/class/cs273a, and is reachable from the cardinal and corn machines. Source tree executables are available within the bin directory, and are machine-dependent. If you add "/afs/ir.stanford.edu/class/cs273a/bin/@sys" to your PATH variable, the correct version of the executable will be executed.

Previous CS273A Materials

There are course schedules and materials available from the Winter 2017/2018, Autumn 2016/2017, Autumn 2015/2016, Autumn 2014/2015, Autumn 2013/2014, Autumn 2011/2012, Autumn 2010/2011, Autumn 2009/2010, Autumn 2008/2009, Autumn 2007/2008, and Spring 2006/2007 versions of the course. Also see the Winter 2012/13 class of CS173.


Introductory Bio and CS Sessions
The following is a list of introductory sessions for students unfamiliar with (or just wanting a refresher lecture on) biology and computer science to the depth necessary to make the course enjoyable. Details about these sessions will be announced soon .

Date Subject
TBD Introductory Biology Primer
TBD Introduction to Text Processing
TBD UCSC Genome Browser

Schedule

 DateTitleHW
11/08  
21/10  
31/15 HW1 Due: January 31, 2019
41/17  
51/22  
61/25  
71/29  
81/31 HW2 Due: February 19, 2019
91/17  
102/5  
112/7  
122/12  
132/14  
142/19 Final Project Released
152/21  
162/26  
172/28  
183/5  
193/7  
203/12  
213/14Final Project Presentation (3 hours)