Computer Science 590 / CBB 590
Topics in Computational Structural Biology

• Projects

  Students will be required to do a project. Pick something in the field of algorithms for structural molecular biology, or computational structural biology and biophysics, or structural biology, that you are interested in, and (a) implement it, (b) analyze it, (c) improve it, (d) extend it, or (e) apply it.
  
  A one-page written project proposal is due on Feb 18.
  We will meet with you in recitation to discuss possible projects and give you advice in defining a project to propose.
  You are welcome to talk to us or come to office hours to discuss.
  Final projects are due on the last day of class. You must:
  • Turn in a written report, using Sakai.
  • Your final report can be in html or PDF from Latex. If you want to use another format, ask me first.
  • If you wrote code, I would like to see it. Please include the code with your final project. Specifically:
  • Turn in all Code, Data, PDB files, analyses... -- everything needed to replicate and understand your results.
  
  I suggest your final report should contain many illustrative pictures and figures.
  
  Here are some examples. These 3 projects resulted in publications for the students. Obviously, this might not happen for every project.... but why not try? Do your best!
  • Example Final Project #1
  • Example Final Project #2
  • Example Final Project #3
  
  

  Due Dates
  Your final project is due on the last day of class, April 21.

  On April 30, everyone will give a short presentation on their project. You will have 4 minutes to present, plus 2 minutes for questions, and can have a max of 4-5 slides. You must send your slides, exported as a PDF, to Andy no later than 10 AM April 27 so he can put them together on his computer in case there are Zoom questions. Please be sure to show your results and conslusions - it's fine to define the problem but we want to see what you did! To ensure everyone has time to present, the time limits will be enforced; to avoid getting cut off by the timer, please rehearse your short talk a couple times prior to giving your presentation.

  If you need it, we can grant you an extension until noon, April 27th on the final report. In order to get an extension you must email us by 23:59 on April 18, after which no extension will be granted. These due dates for the final project and limit on extensions are determined by Duke, and we're giving you the maximum allowed. And while we're happy to grant you an extension, we strongly encourage you to do your best to complete your project by April 21 because our ability to meet with and advise you on your final project will be truncated after April 21st. The optimal strategy for you is to: 1) target April 20th/21st for completing your project, 2) request an extension until April 27th (even if you don't use it), and 3) run into snags (which past experience has taught is a common occurrence) in your project prior to the 20th, so you can ask us for help.

  There will be no extensions granted for project presentations on April 30. This is a Duke rule!

• 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.

• Course Notes:

  Paper presentations have two main components, the presentation itself and scribing notes about the papers you've read. The notes are due on the Thursday (two days) after your presentation. There are a few requirements that your notes must meet:

  • You must use the LateX template we provide. We won't accept anything that isn't using the template, be it a Word Document, PDF, or LaTeX with a different template. Do not change the title: your notes should be a chapter, so that there are many chapters but the title page stays the same.
  • It has to compile. Non-compiling LaTeX will be "returned to sender."
  • At least 3-4 pages with references. Longer is perfectly fine and may be appropriate based on the papers you presented.
  • The notes should not be copies of your powerpoint presentation. There should be additional content in your notes.
  • You must have credits for the figures you include.
  • Must must have a reference list.

  You might be wondering "how should I go about writing these notes?" Well, one way you might get an intuition for what we're expecting is to pick fifteen chapters from ASMB (you've already read many) and read them. They're all examples of good course notes. Of course, they're all a bit different, so consider them a distribution over the set of ideal course notes. Chapter 11 in ASMB on Mayo is a perfect example of what we're expecting. Writing something short and insightful is better than copying figures and text like a content farm. It's okay to include some figures, but everything included must be explained. For example, it's not okay to copy a picture of an algorithm or a graph of results without explaining the algorithm or analyzing the results in the text. Engage in some discussion; analyze the papers. Evaluate the ideas presented within; offer some suggestions or critiques where possible. You should ask yourself how your notes can augment the papers, or act as a complete stand-in in cases where someone has access to your notes but not to the paper.

  An example for the notes is here.

  Email the TA your notes 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. Comments 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. Example comments can be found here:
  

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

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 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.