生物與醫學資訊專論
Biomedical Informatics Paper Reading

* Greetings
   - We will spend some of our lives together in this class
   - Let's learn and have fun!


* Paper Presentation

** One paper/person ~20-40 min
*** Take turns presenting
*** One presentation (later in the course) should be an "encore" paper,
    presenting a paper already presented by someone else earlier.
*** I might prepare a list of papers I would like to see presented.
*** Describe
    - Background
    - Motivation
    - Each Figure/Table
    - Conclusions
    - Positioning (relationship to previous work)
    - Criticism (positive or negative)
*** Summarized what *you* learned from the paper
    - 1-3 points from the paper


** Practice technical communication
   - Present to everyone (not just to the Prof)
   - Check if the audience seems to understand your main points.
       - Make eye contact
       - Pause occassionally
   - When the audience get's lost (will happen a lot)
       - Restate, reword as necessary.
       - Maybe even draw an impromptu picture.
       - Or let another who understands try to help explain
   - Pause occasionally and check if 
   - English preferred, Mandarin OK (emphasis on communication)


* Paper Selection Suggestions
** Look at papers presented in previous years see =paulhorton.gitlab.io= web site.  Papers listed there.
***  Gray color means, was not interesting or off topic paper
***  Blue color means a good discussion provoking paper
** Journal Suggestions
*** Bioinformatics Journals
   - Bioinformatics
   - PLoS Computational Biology
   - Briefings in Bioinformatics
*** Other journals including bioinfo articles
   - Nucleic Acids Research
   - Genome Research
   - Genome Biology
   - BMC Journals (lower average quality?)
** Start Early
   - Scan/skim several papers first, before picking one
   - Pick a paper that you think is good work, and/or one that teaches you something.
   - Tell me the title of the paper(s) you select one week in advance (starting week 2)


* Presentation Preparation
   - Expect to spend at least 6 hours in preparation
     -  Sorry, but it really takes this much time!
     -  Includes reading background material (Wikipedia etc)
   - Prepare a slide or two (or even just a paper drawing) to summarize what you want to present
   - Use your own laptop / or upload your presentation to somewhere on the internet
   - You may find some pdf editing software useful, e.g. Okular
   - Share what you learned from the paper
   - Focus on methods or principles involved
   - You may want to highlight parts of the paper pdf, using software such as Xournal.


* 看不懂怎麼辦?
   - Don't worry!  That's normal.  Reading papers takes practice, and some papers are hard for anyone to read.
   - If you think it is the way the paper is written, drop it an select another (many fish in the sea!)
   - Otherwise, maybe you need to first present background material (maybe a review paper or tutorial)
     and come back to the main paper later.

* Class Participation
   - Communication is a two way street  Presentor <==> Audience
   - For this class, being understood is more important than being complete,
     share with us what you understood from the paper.
   - When listening, make eye contact.  Let the presentor know you care ♥