STAT598N •  Statistics in Systems Biology
Overview | Course Requirements | Schedule of Readings

Reading papers 

    In order for you to participate in the class discussions it is essential that you've actually read the papers. While you don't necessarily have to understand all of them, you should have at least attempted to get through the paper, at least looking at all of it.

Writing evaluations

    To help motivate the class discussion, everyone enrolled in the class is required to submit a short (1/2 page, no more than 1 page; single-spaced, 12pt font) evaluation of the papers being discussed. These evaluations should briefly summarize the main contributions of each paper, as well as your assessment of its main strengths and weaknesses. In particular, you should highlight what you believe to be the novel insight or approach, and how it might be useful outside the scope of the paper. These evaluations should be submitted via email the evening before class. Since I realize many of you may prefer to work while others of us sleep, the "evening before class" will be construed to end at 6am, EST, on the morning of class. Those students presenting the paper are excused from submitting an evaluation.

      You may elect to skip three classes' worth of reviews, in addition to presentation days, without penalty.

Participating classes

    The most important requirement is active participation in class discussions. The evaluations should provide ample topics for discussion, but don't feel constrained to limit your comments to those expressed in your evaluations. Questions or clarifications about confusing parts of the papers are entirely appropriate. Thoughtful criticism or extension of the work presented in the paper is highly encouraged. We've all read the papers---it's your new insight we're interested in!

Presentating papers

    Everyone enrolled in the class will be asked to present at least one paper during the quarter (the more folks enrolled, the fewer papers you'll need to present, so encourage your friends to sign up!). This doesn't need to be a conference-quality talk, so don't worry too much about it. The basic idea is to present to the class a brief summary of the paper (what problem does it attempt to tackle, why is that problem interesting, what is the approach, how effective was it, etc.) for the benefit of those sitting in (there will usually be several), and to present your evaluation of the strengths and weaknesses of the paper, as well as any interesting next steps or related issues. Think of it as an oral presentation of what you would have written down. You should also prepare a short list of discussion topics to help get the class started. Slides are encouraged but not required. In many cases, it might be possible to google for slides either on the webpages of the first authors or elsewhere.

Project

    A list of potential topics will be posted to here or discussed in class, but feel free to suggest your own. Some projects might be preliminary investigations of something that could turn into conference submissions. That level of originality is encouraged but not required. I'd be happy to discuss such prospects with you during or after the term. You may work on this project individually or in small groups (no more than ). A group's project is expected to be larger in scope than an individual's project, and will be graded on that assumption.

Preliminary report: Due Mar 10

    The preliminary report should be a 3-4 page report that includes:

Presentation: Due Apr 28-30

    The oral presentation to the class should provide an overview of the project's goals, necessary background information (including work done by others), a description of any experiments, and a summary of your results and findings.

Final report: Due May 5

    The final project report should be a 8-15 page, single column report.  Please use  12-point font with standard margins.  Here are some useful links:

"How to write a good research paper", Simon Peyton Jones, [pdf]
"The Science of Scientific Writing", George D. Gopen and Judith A. Swan,  American Scientist 78(6) 550-558, November-December 1990. [pdf]
 Local resources: The Writing Lab at Purdue

Collaboration policy

    Each paper evaluation must be completed individually; you must write everything that you submit. You may (and, in fact, are encouraged) to discuss the papers with others, but you may not copy evaluations from someone else or make your writeups available to others.

    You are expected to be aware of the Department's academic honesty guidelines. Any violation of the course or institute policies will be treated very seriously, and could lead to severe repercussions, up to, and including, expulsion. Don't cheat. It's not worth it. For a quick summary of department and university policies, please refer to Prof. Spafford's webpage here.