Computational Biology Journal Club
aka “Current Topics in Computational Biology”
aka “02-701”
William Cohen
Organizational Meeting
Sept 6, 2007
People & Places
• Venue:
– 411 Mellon Institute, CMU
– Thursdays 4:00-5:00 pm (except 11/22, Thanksgiving)
• William Cohen, organizer
– Office hours TBD
– http://www.cs.cmu.edu/~wcohen
– Sharon Cavlovich, William’s assistant
• sharonw+@cs.cmu.edu
• Web page:
– http://www.compbio.cmu.edu/Jclub/
• Also reachable via google://”William Cohen”->”Teaching”
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
Goals for the Journal Club
•
But, much easier than
Scientists need to do much more than just “dothinking
science”
critically about
your own research 
– Monitor progress in related areas
– Critical thinking about other research (hard!)
2nd year
3rd year
• What is the potential practical benefit? How likely is it to “pay off”? How
far off is the payoff?
• What’s 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
• … Start learning this as soon as possible!
• You need these skills to succeed in science
– and you need to be able to pass them on to others
Plan for this semester
• Eleven student-run sessions
– Two presentations and a discussion, on one paper
• Each session run by a team:
(some duplication expected here)
– One second-year student: to present the background and
motivations
– One first-year student: to present and critique the paper’s 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
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 other’s 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 partner’s presentation
– Send final talk slides to Thom Gulish to put on the web site
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 paper’s 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
st
First & second years are part of one team 11 1 -year = 11
•
• Third year students will lead two teams
any volunteers to help the numbers work?
(e.g. 3rd to trade one “lead” role” for two
“support roles”)
9
2nd-year = 9
6
3rd-year = 12
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
– What’s 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 there’s 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
When You Don’t Present
• Read the paper
• Bring copies of the paper to refer to
– Or a laptop if you must
• Be prepared with questions or
comments
– That’s part of your grade!