Computer Science 296.4
Algorithms in Structural Biology
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.
in a written report,
- Make a web page about your project, and
Prepare a short presentation for the class on what you did. Make
slides for your presentation.
- (1) and (2) can be the same document.
- Put your webpage in the following place. If your username is
"erdmann", then put it at
- If your report contains embargoed or unpublished work
then either (a) use .htaccess to limit access to your report to The
Duke Network or (b) I will excuse you from the Webpage requirement if
you bring a copy (including color figures) of the equivalent material to class, by the due date,
for others to read (please mark it "Draft: Please Do Not Photocopy Or
A typical .htaccess file is available here:
- Your final report can be in html or PDF from pdflatex. If you
want to use another format, ask me first.
- I suggest your final report (and slides) should contain
illustrative pictures and figures.
- If you wrote code, I would like to see it. Please include the
code with your writeup, and link to it from your webpage.
- Some students will want to do projects close their thesis
area. If your thesis area is not molecular or structural
biological, there is a danger here:
- If your thesis area is not molecular or structural
biological, to make sure your project proposal is acceptable -- make
sure that in the proposal/project what you *mostly* write about are
the computational biology algorithms you invent, use, and implement
and how they worked -- what we don't want is a really long description
that's 90 percent about your (non-biology) research area, and only 10
percent about the important stuff: the computational biology
algorithms, how they work, what you did that is innovative etc. It
should be more like 5% -background vs. 95% - computational biology
algorithms and systems.
- It is important that this project exercise the kind of techniques
we're studying in this course. I would not want to see a project that
was essentially and exclusively on your (non-biological) thesis, that
did not use and explore algorithms from computational biology and
chemistry with some extensiveness.
- If your thesis is on a topic in computational molecular
biology, then I expect that your project would extend or innovate in
some way at an appropriate scale for one term -- for example I don't
want a project that is simply your last paper, written up for this
class. However, the project could be on your next paper -- and in the
past, several class projects for this class have turned into papers
that were published at prestigious conferences and journals in
computational biology and chemistry!!
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.
- State at least three important things the paper says. These could
be some combination of their motivations, observations, interesting
parts of the design, or clever parts of their implementation.
- Describe at least one deficiency in the paper. Every paper has
some fault. Perhaps an experiment was poorly designed or the main idea
had a narrow scope or applicability. Being able to assess weaknesses
as well as strengths is an important skill for this course and beyond.
- Describe what conclusion(s) you draw from the paper as to
how to build and analyze computational biology algorithms and systems
in the future. Most of the assigned papers are have been significant
to the computational biology and/or computer science community and
have had some lasting impact on the area.
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.
- Turn in a written critique, and
- Make a web page about
- (1) and (2) can be the same document.
- Email me the URL for the webpage for your critique. E.g.,
- Your critique can be in PDF, html, PostScript from LaTeX, or
PDF from LaTeX. If you want to use another format, ask me first.
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.
You may be assigned one or more papers to present in class.
See guidelines for how to give a good talk.
Aim for your presentation (with questions) to be approximately 1 hour long
and prepare for discussion afterwards.
Several assignments will be given during the
semester. You may work in pairs to do these assignments. Working in
pairs is especially recommended to form teams of computer scientists
and life scientists.
Each student has
to scribe roughly two lectures. Scribed notes can be done by
teams. You should certainly ask your peers to clarify any point that
your notes leave unclear.
Use this Latex package as a starting point for your notes.
While you are encouraged to use images in your notes, please
cite the source of the images in the captions like this:
"Reprinted from " where  is given in the
References. Scribes of notes from previous classes are
encouraged to update reference information for their images.
- Research Project: