Each module consists of lectures, written problem sets, and a final, graduate level written project that is half the length of the full course's final project.
Discussion Section / Readings
Papers will be assigned throughout the course. These papers will be presented and discussed in weekly 60-minute sections with the TFs. A brief summary (a half-page per article) should be submitted at the beginning of the discussion session.
Bioinformatics quizzes
There will be four short quizzes (25 minutes) in class comprising SIMPLE questions that you should be able to answer from the lectures plus the main readings.
Answer keys to Quizzes 1-4 in the fall of 2012 can be found here
Programming Assignments (CBB and CS) and Programming issues
There will be several short programming assignments required for CBB and CS students taking this course. Acceptable languages and submission requirements will be discussed prior to the first assignment. These assignments are NOT required for students not taking the CBB or CS sections of the course.
These are the programming languages that we permit in the programming assignments and final project: Perl, Python, C, C++, MATLAB and R. If you really feel more comfortable with other languages, please email the TFs to discuss. Also, packages such as BioPerl and BioPython are not allowed in the assignments and final project. If in doubt, please consult the TFs.
We recommend the use of PERL for most of the programming. A useful resource is the following book: Programming Perl, 3rd Edition in the O' Reilly series, by Larry Wall, Tom Christiansen, Jon Orwan. The Yale Library has also older editions, which would work too. We would also recommend the following online resources: http://www.perlmonks.org and http://stackoverflow.com/. Otherwise, Google is your best friend.