Instructors

David Bird - david_bird@ncsu.edu

Eric Stone - eric_stone@ncsu.edu

Days and Times

• Tuesday at 2:30pm - starting 25th August
• Thursday at 11:00am - starting 20th August

Place

The Journal Club meets in Room 1513 in Partners II building on Centennial Campus' Main Campus Drive.

Map of Centennial Campus

How things work

Each week, the presenter will choose a paper from the list we have provided. This list is also accessible from the "papers" tab at the top of this page. You can also look at prior journal clubs to see the types of papers we have discussed in the past. You must select a paper at least one week (ideally more) before the class. If you wish to choose your own paper, please consult either Eric or Dave to discuss the suitability of your selection. Remember, the quality of the discussion does depend to a degree on the choice of papers. Papers that use genomics to address biological questions are often good choices.

Each student is expected to read every paper, not just the one(s) you sign up for. The format of this class is a discussion of the chosen paper, and to receive credit for this course, you must contribute to the discussion on a regular basis. To do this you can:

1. Interject your interpretation/understanding of a particular point,
2. Answer questions posed by the discussion leader or other class members,
3. Ask questions of your own - especially questions like:
   • "I didn't understand the part about ..."
   • "what exactly is a ..."
   • "what does this Figure actually show?"

Each student is expected to actively participate in each class. Unfortunately, if you do not participate in the discussions, we have to assume that you have not read the papers, and you will not receive credit for the course.

On the day you've signed up as discussion leader, you are responsible for:

• Providing a brief but well-thought out background of the paper (10 minutes maximum, but ideally shorter). The purpose of this introduction is to put the paper into context (i.e., the bigger picture) and to explain aspects that may generally not be familiar to others in the class (such as specialized terminology, biology, statistics, etc.). The best way to prepare for this is to read a few background papers, possibly papers found in the references of your paper. Although you may use a computer presentation to show images that are otherwise hard to explain (such as micrographs), PowerPoint or similar presentations are strongly discouraged. It is much better to use the whiteboard to support your introduction.
• Leading the discussion. You are in charge of running the discussion for that day, and should lead the class through the paper. The discussion should address the following questions.
  
  
  1. What is the major question being asked/hypothesis being tested?
  2. What is the main research tool being used?
  3. What is the key result?
  4. What is the main conclusion of the paper. Does it answer the main question?
  5. Where to next?
• A good strategy is to go over each of the main data exhibits (figures, tables, graphs, etc.).
• Submitting a one-page written review of the paper. This review is meant to be succinct and should include a few background sentences followed by a synopsis of the five points listed under the "leading the discussion" section above. You do not need to understand your paper in perfect detail, but we do expect you to make a faithful attempt to digest its main ideas.

Course Evaluation

Online class evaluations will be available for students to complete during the last week of class:

• Fall Session: 8 a.m., Thursday, November 19th through 8 a.m., Wednesday, December 9th

Students will receive an email message directing them to a website where they can login using their Unity ID and complete evaluations. All evaluations are confidential; instructors will never know how any one student responded to any question, and students will never know the ratings for any particular instructors.

For more information see the following links:

• Evaluation website
• Information about ClassEval
• E-mail the class evaluation student help desk

Library Resources

This link takes you to the genomic data resources page at the NCSU Library. (Also linked from a tab at the top of this page.)

Hints and Tips

1. In reading a typical research paper, at a minimum you should ask the following questions:
   1. Are the questions/hypotheses clearly stated, and are they sound?
   2. Do the experiments performed address the proposed questions/hypotheses?
   3. Have sufficient data been gathered, and are the data robust (e.g., statistically validated)?
   4. Are the data properly shown (e.g., as Figures, Tables, etc)?
   5. Do the Figures make sense?
   6. Are the conclusions drawn warranted from the data?
   The focus will obviously be slightly different for a methods or a theoretical paper, but the principle is the same.
2. For some papers, there may be issues that go beyond the scientific aspects. For example, some approaches raise issues of personal privacy or have ethical ramifications. Such points are often good discussion topics.
3. As the presenter, you should pay particular attention to a) the experimental design/methods and b) the presented data. As noted above, it is useful to carefully go over the key figures in the paper.
4. As discussion leader, you should endeavor to elicit discussion. You should not use a computer to deliver a "presentation."
5. The whiteboard is a very useful tool, and students should be encouraged to draw to help explain ideas.

Finally, because the topics vary widely from week-to-week, you will find that you are very familiar with some topics (you can help explain these papers and answer questions), moderately familiar with some topics, and completely in the dark on some topics (you can ask questions about these papers).

Guides on the Web

Little and Parker: How to Read a Scientific Paper

Ashwin Ram's "How to Present a Paper"

Bob Spillman's "How to Present a Paper: A Speaker's Guide"