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/~wcohenhttp://www.cs.cmu.edu/~wcohen –Sharon Cavlovich, William’s assistant sharonw+@cs.cmu.edu Web page: –http://www.compbio.cmu.edu/Jclub/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 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 But, much easier than thinking critically about your own research 2 nd year 3 rd 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 (3 rd 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 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 1 st -year = 11 9 2 nd -year = 9 6 3 rd -year = 12 any volunteers to help the numbers work? (e.g. 3 rd to trade one “lead” role” for two “support roles”) Also, volunteer for next week?

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!