Computer Science 296.4
Algorithms in Structural Biology

Overview | Syllabus | Schedule | Topics | How to give a good talk
Supplemental Materials | Some Relevant WWW Links


Students will be required to do a project. Pick something in computational biology you are interested in, and (a) implement it, (b) analyze it, (c) improve it, (d) extend it, or (e) apply it.

A 4-5 page written project proposal is due on (February 12).

Final projects are due on the last day of class.

You must
  1. Turn in a written report,
  2. Make a web page about your project, and
  3. Prepare a short presentation for the class on what you did. Make slides for your presentation.


You may be assigned one or more reports to do during this class. This section discusses what is entailed in a report.

Your reports should:

We do not want a book report or a repeat of the paper's abstract. Rather, we want your considered opinions about the key points indicated above. Of course, if you have an insight that doesn't fit the above format, please include it as well. Your reports will be graded on content, not length. For most of the papers we read, one or two well thought-out paragraphs should be sufficient. You are, of course, welcome to write as much as you want.
If you were not assigned to do an in-class presentation, you must, in addition to the project, write a critique (report) on one of the papers we read. Your critique should be a detailed analysis of the methods presented, their flaws, strengths, and weaknesses. You should consider improvements and extensions in your critique. Reports should be about 10 pages single-spaced.

You must

  1. Turn in a written critique, and
  2. Make a web page about your critique.

Recommended Textbooks

Here is a list of recommended textbooks.

How to Exchange Files

We share a common file system so it is criminal for CS students to send enclosures. Never send enclosures for anything related to this course. If you have an account on the CS Unix Filesystems, send a pointer to the filename. Or, put it on the web and send the URL.


Grading: Grades will be based upon (a) your presentations in class, (b) your project, (c) class participation/discussion, (d) assigned homework exercises, and (e) scribing approximately two lectures. If you are not giving a presentation, "(a)" will be graded based on your report.