Computational Biology Journal Club aka

1
Computational Biology Journal Club aka Current
Topics in Computational Biologyaka 02-701

• William Cohen
• Organizational Meeting
• Sept 6, 2007

2
People Places

• Venue
• 411 Mellon Institute, CMU
• Thursdays 400-500 pm (except 11/22,
  Thanksgiving)
• William Cohen, organizer
• Office hours TBD
• http//www.cs.cmu.edu/wcohen
• Sharon Cavlovich, Williams assistant
• sharonw_at_cs.cmu.edu
• Web page
• http//www.compbio.cmu.edu/Jclub/
• Also reachable via google//William
  Cohen-gtTeaching

3
Goals for the Journal Club

• Scientists need to do much more than just do
  science
• Monitor progress in related research areas
• Critical thinking about other research
• Persuasively and clearly present their work and
  explain their ideas
• Publication
• Funding e.g. NIH grants
• Students teaching
• Scientific influence
• You need these skills to succeed in science

4
Goals for the Journal Club
But, much easier than thinking critically about
your own research ?

• Scientists need to do much more than just do
  science
• Monitor progress in related areas
• Critical thinking about other research (hard!)
• What is the potential practical benefit? How
  likely is it to pay off? How far off is the
  payoff?
• Whats the history of the subarea(s)? Who started
  it and why? What technical advances (e.g.,
  instruments, algorithms) enabled it? How does the
  history affect how people think about the
  problem?
• What are the competing techniques? What are the
  relative strengths and weaknesses?
• What are the logical next steps?
• Where could this subarea be in 3-6 months, 1
  year, 2 years, 3 years, 5 years, -?
• Persuasively and clearly present their work and
  explain their ideas
• You need these skills to succeed in science
• and you need to be able to pass them on to others

2nd year
3rd year
Start learning this as soon as possible!
5
Plan for this semester

• Eleven student-run sessions
• Two presentations and a discussion, on one paper
• Each session run by a team
• One second-year student to present the
  background and motivations
• One first-year student to present and critique
  the papers results
• One third-year student to lead a discussion on
  likely follow-up work, implications for other
  areas of success, future directions,
• Pose questions first, but have some answers ready
  to discuss
• Weaknesses are opportunities
• Strengths are opportunities
• First second years are part of one team
• Third year students will lead two teams

(some duplication expected here)
6
Responsibilities

• Team leads (3rd year students) should
• Recruit two teams
• Pick dates and papers
• in consultation with your teams William
• Supervise a dry run of both talks
• Have each speaker listen to and critique the
  others presentation
• Add any comments that you feel appropriate
• Ensure that William gets, by midnight Tuesday
• Soft copy of each draft presentation
• Email with summary of the discussion of the dry
  run the likely changes to be made
• Moderate the talks and lead the discussion
• 2-3 slides sometimes help get discussion started
• Team members should
• Commit to their topic early
• Before I get impatient and just assign you
• Prepare their talks in advance of the dry run
• You should have the slides ready, and the talk
  should be timed
• Critique their partners presentation
• Send final talk slides to Thom Gulish to put on
  the web site

7
Plan for this semester
Also, volunteer for next week?

• Eleven student-run sessions
• Each session run by a team
• One second-year student to present the
  background and motivations
• One first-year student to present and critique
  the papers results
• One third-year student to lead a discussion on
  likely follow-up work, implications for other
  areas of success, future directions,
• Pose questions first, but have some answers ready
  to discuss
• Weaknesses are opportunities
• Strengths are opportunities
• First second years are part of one team
• Third year students will lead two teams

11 1st-year 11 9 2nd-year 9 6
3rd-year 12
any volunteers to help the numbers work? (e.g.
3rd to trade one lead role for two support
roles)
8
When You Present

• Put URLs into the spreadsheet at least one week
  in advance to give your classmates time to read
  the paper
• When you give necessary background
• Whats the prior state of the art?
• What do they hope to accomplish long term?
• What did they accomplish in this paper?
• Aim for 10-20 slides for a 20-minute talk
• Aim for 20 minutes background, 20 minutes on
  paper, 15 minutes discussion, allowing time for
  questions
• This is a guideline - adjust this if appropriate
• Make the presentation clear and easy to follow
• Think about the structure of the talk
• Use informative pictures, avoid superfluous math
  or distracting graphics
• If theres math make sure you understand the main
  ideas of the proof (or algorithm) and can
  illustrate them
• Be prepared to go into more detail if you get
  questions

9
When You Dont Present

• Read the paper
• Bring copies of the paper to refer to
• Or a laptop if you must
• Be prepared with questions or comments
• Thats part of your grade!