Computational Biology Journal Club aka “Current Topics in Computational Biology” aka “02-701”

1. Computational Biology Journal Club aka “Current Topics in Computational Biology”aka “02-701” William Cohen Organizational Meeting Sept 6, 2007

2. 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”

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? • 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 • … • 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 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 (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 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

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 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 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 • 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

9. 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!