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.
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).
This course is cross-listed within Developmental Biology and Biomedical Informatics as DBIO273A and BIOMEDIN273A, respectively.
Mon Wed 1:30pm-2:50pm in Beckman B302 (Map to Beckman)
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.
Office: Beckman Center B321
Office hours: Email for appointment
Phone: (650) 723-7666
Office: Beckman Center B381
Office hours: Monday 3PM-5PM, Wednesday 3PM-5PM
Office: Beckman Center B381
Office hours: Friday 1PM-3PM
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.
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.
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.
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.
There are course schedules and materials available from the 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.
|01/10/2018||Introductory Biology Primer (!! Beckman B302 !!)||01/17/2018||Introduction to Text Processing (!! Beckman B302 !!)|
|01/24/2018||UCSC Genome Browser Tools (!! Beckman B302 !!)|
|2||1/10||Johannes: Bio Primer (CA Tutorial)|
|3||1/17||Bo: Text Processing Primer (CA Tutorial)||HW1 Due: 2/5|
|4||1/22||Gill: Protein Coding Genes|
|5||1/24||Johannes & Bo: Genome Browser Primer (CA Tutorial)|
|6||1/29||Gill: Non Coding Genes|
|7||1/31||Gill: Genes Enrichment, Gene Regulation I|
|8||2/5||Gill: Gene Regulation II||HW2 Due: 2/26|
|9||2/7||Gill: Gene Regulation III, and more?|
|10||2/12||Gill: Neutral Evolution: Repeats|
|11||2/14||Gill: Neutral evolution: repeats II|
|12||2/21||Gill: Inferring Evolution: Gene Trees|
|13||2/26||Gill: Inferring Evolution: Chains & Nets|
|14||2/28||Gill: Comparative (cross species) Genomics|
|15||3/5||Gill: From Adaptation to Disease|
|16||3/7||Gill: From Adaptation to Disease II|
|17||3/12||Gill: Mendelian Disease & Wrap Up|
|18||3/14||Final Project Presentation|