Computer Science 663
Algorithms in Structural Biology

Highly Recommended Textbooks

    Introduction to Protein Structure [Paperback] 
    Carl Branden (Author), John Tooze (Author) 
    Publication Date: January 3, 1999 | ISBN-10: 0815323050 | ISBN-13: 978-0815323051 | Edition: 2
    Available on Amazon

    Biochemistry by Lubert Stryer - Hardcover - 1064 pages 4th Bk&cdr
    edition (March 1995) W H Freeman and Co; ISBN: 071673687X ; Dimensions
    (in inches): 1.76 x 11.30 x 8.79. More recent editions are also fine. 

Here is a list of other recommended textbooks.

Projects

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

Final projects are due on Wednesday, 05/01/2013.

• Example Final Project #1
• Example Final Project #2

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.

Notes:

• (1) and (2) can be the same document.
• Put your webpage in the following place. If your username is "erdmann", then put it at "http://www.cs.duke.edu/~erdmann/cps296_4/index.html".
• If your report contains embargoed or unpublished work then either (a) use .htaccess to limit access to your report to The Duke Network or (b) I will excuse you from the Webpage requirement if you bring a copy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 Circulate." A typical .htaccess file is available here: 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!!

Your reports should:

• 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.

You must

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

Notes:

• (1) and (2) can be the same document.
• Email me the URL for the webpage for your critique. E.g., "http://www.cs.duke.edu/~hood/compbio/critique.html".
• Your critique can be in PDF, html, PostScript from LaTeX, or PDF from LaTeX. If you want to use another format, ask me first.

Acknowledgments: Some of the discussion of how to give talks and reports was borrowed, with thanks, from Greg Gangor's description of the reviews used in his class at CMU.

• Presentations:

  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.

• Assignments:

  All students are required to give feedback on a student's notes. Give your feedback to the TA physically or digitally before the following Monday.

  Several assignments may 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.

• Scribe:

  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. An example for the notes is here.

  Use this Latex package as a starting point for your notes. [example-for-class.zip]
  Do not change the title: your notes should be a chapter, so that there are many chapters but the title page stays the same.

  While you are encouraged to use images in your notes, please cite the source of the images in the captions like this: "Reprinted from [3]" where [3] is given in the References. Scribes of notes from previous classes are encouraged to update reference information for their images.

  Your scribed lecture notes are due the Monday after your presentation, no extensions. Email them to the TA, after which I will give you comments and ask you to revise them at least twice. Revisions are due in a week, after which the rest of the class will give comments and feedback. Commends and feedback are required and considered assignments for this class. They are due a week after the notes have been uploaded. You may choose to compose email comments and email them to the TA or annotate the physical paper and turn it in via hardcopy or digital scans. Please use PDFLaTeX instead of other forms of LaTeX.. Example comments can be found here:
  

  • Substantive Comments.
  • Detailed Annotation.
  • Detailed Annotation (Instructor's comments).

• Research Project:
  See above