The Open Science Workshop at PSB 2009




        A recap by Shirley Wu
          BMIR RIP 1/15/09
2 hours of talks + 1 hour discussion

                  Phil Bourne
                  Drew Endy
                 Larry Hun...
If you couldn’t make it...
If you couldn’t make it...

              Microblogging
                    Slides
                 Webcasts
       http:/...
“Open Science?”

                                                 What is it?

                                           ...
“Open Science?”
                                         The movement that advocates making
                              ...
If a million
post-docs
repeat a
million
experiments...

http://flickr.com/photos/heymans/480396810/
... and 25% of
those don’t
work...



http://flickr.com/photos/cliche/120070310/
... how much
taxpayers’
money is that?



http://flickr.com/photos/luismimunoznajar/2093185804/
Make research
more...

     efficient
     effective
     accessible

http://flickr.com/photos/luismimunoznajar/2093185804/
“We argue in good faith
from shared evidence to
shared conclusions.”

           - Lee Smolin
“I never had an idea that
couldn’t be improved by
sharing it with as many
people as possible…”
           - Bill Hooker
Idea

                          Develop
          Read




Publish                           Fund




      Process       ...
Idea

                          Develop
          Read




Publish                           Fund




      Process       ...
D
               ev
                 elo
                   p
        Fu




                        Id
        nd




   ...
ad
               D
               ev




                                                                   Re
          ...
ad
               D
               ev




                                                                   Re
          ...
Protocols
Experimental record
Data
Literature




                      http://flickr.com/photos/virtualsugar/316200555/
http://flickr.com/photos/65068167@N00/158070855
http://flickr.com/photos/zanotti/314391903/
http://flickr.com/photos/65068167@N00/158070855
Workshop agenda

• Identify challenges and next steps for
 Open Science

• Discuss:
   • Current approaches and practice
 ...
Keynote: Phil Bourne
                Open Science:
          One Person’s View and What
            We Are Doing About It
...
Keynote: Phil Bourne
                  Open Science:
            One Person’s View and What
              We Are Doing Abo...
Keynote: Phil Bourne
        Open Science:
  One Person’s View and What
    We Are Doing About It
Keynote: Phil Bourne
        Open Science:
  One Person’s View and What
    We Are Doing About It
Tool development
      David de Roure
The myExperiment approach
   towards open science
Tool development
                   Nigam Shah
            How bio-ontologies enable
                  open science
Open s...
Social issues
                        CF Quo
               Community annotation in
             translational bioinformat...
Social issues
                        CF Quo
               Community annotation in
             translational bioinformat...
Social issues
                        CF Quo
               Community annotation in
             translational bioinformat...
Social issues
                        CF Quo
               Community annotation in
             translational bioinformat...
Social issues
                        CF Quo
               Community annotation in
             translational bioinformat...
Social issues
      Heather Piwowar
  Measuring the adoption of
  open science sharing data


How much is shared, not shar...
Social issues
              Heather Piwowar
          Measuring the adoption of
          open science sharing data

40% s...
Social issues
               Heather Piwowar
           Measuring the adoption of
           open science sharing data

Be...
Main themes
          “If you build it, they won’t come.”
                               - Sean Mooney

The design of tool...
Main themes
 “You cannot manage what you cannot measure.”
                                 - Lord Kelvin


Does any of thi...
Tools?

Specific tools are required
  (persistent identity, good
  repository systems)

Build the service and the
 communit...
Policy?
Standards and methods of
  citation are at the core of
  good science

Focus on specific actions
  with measurable
...
Funding?


 Infrastructure

 Research on research




http://flickr.com/photos/luismimunoznajar/2093185804/
Improving the research process
is an area for (experimental) research
        that requires the same
     rigour, standard...
http://tinyurl.com/psb09-openscience
Upcoming SlideShare
Loading in …5
×

Open science workshop recap - BMIR research colloquium

931 views

Published on

Recap of the PSB 2009 Open Science workshop, given at the Biomedical Informatics Research group weekly colloquium, 1/15/2009

Published in: Education, Technology, Sports
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
931
On SlideShare
0
From Embeds
0
Number of Embeds
13
Actions
Shares
0
Downloads
19
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Open science workshop recap - BMIR research colloquium

  1. 1. The Open Science Workshop at PSB 2009 A recap by Shirley Wu BMIR RIP 1/15/09
  2. 2. 2 hours of talks + 1 hour discussion Phil Bourne Drew Endy Larry Hunter Russ Altman Steven Brenner Style, text, photos borrowed from Cameron Neylon
  3. 3. If you couldn’t make it...
  4. 4. If you couldn’t make it... Microblogging Slides Webcasts http://tinyurl.com/psb09-openscience
  5. 5. “Open Science?” What is it? Why should I care? http://flickr.com/photos/good-karma/710068054/
  6. 6. “Open Science?” The movement that advocates making changes to the research process that make more of the outputs of research accessible in an effective and timely way more stuff, more available, more quickly http://flickr.com/photos/good-karma/710068054/
  7. 7. If a million post-docs repeat a million experiments... http://flickr.com/photos/heymans/480396810/
  8. 8. ... and 25% of those don’t work... http://flickr.com/photos/cliche/120070310/
  9. 9. ... how much taxpayers’ money is that? http://flickr.com/photos/luismimunoznajar/2093185804/
  10. 10. Make research more... efficient effective accessible http://flickr.com/photos/luismimunoznajar/2093185804/
  11. 11. “We argue in good faith from shared evidence to shared conclusions.” - Lee Smolin
  12. 12. “I never had an idea that couldn’t be improved by sharing it with as many people as possible…” - Bill Hooker
  13. 13. Idea Develop Read Publish Fund Process Plan Record
  14. 14. Idea Develop Read Publish Fund Process Plan Record
  15. 15. D ev elo p Fu Id nd ea Idea D Develop Read Pl ev an elo p Re Publish Fund Fu co nd rd Pr oc e ss Process Plan Record
  16. 16. ad D ev Re elo sh p bli Fu ea Id Pu nd Id ea Idea s es p D oc elo Develop Read Pl ev Pr an elo ev D p rd Re co nd Publish Fund Fu co Re Fu nd rd Pr an oc Pl e ss Process Plan Record
  17. 17. ad D ev Re elo sh p bli Fu ea Id Pu nd Id ea Idea s es p D oc elo Develop Read Pl ev Pr an elo ev D p rd Re co nd Publish Fund Fu co Re Fu nd rd Pr an oc Pl e ss Process Plan Record Web 2.0
  18. 18. Protocols Experimental record Data Literature http://flickr.com/photos/virtualsugar/316200555/
  19. 19. http://flickr.com/photos/65068167@N00/158070855
  20. 20. http://flickr.com/photos/zanotti/314391903/ http://flickr.com/photos/65068167@N00/158070855
  21. 21. Workshop agenda • Identify challenges and next steps for Open Science • Discuss: • Current approaches and practice • Development of tools • Socio-cultural issues
  22. 22. Keynote: Phil Bourne Open Science: One Person’s View and What We Are Doing About It The research contract is changing The relationship between scientist and publisher will be different
  23. 23. Keynote: Phil Bourne Open Science: One Person’s View and What We Are Doing About It What’s missing? • Seamless integration between data and publications • Seamless integration of the authoring and publishing process • Association of publications with multimedia • Professional networking akin to social networking
  24. 24. Keynote: Phil Bourne Open Science: One Person’s View and What We Are Doing About It
  25. 25. Keynote: Phil Bourne Open Science: One Person’s View and What We Are Doing About It
  26. 26. Tool development David de Roure The myExperiment approach towards open science
  27. 27. Tool development Nigam Shah How bio-ontologies enable open science Open science requires structured content Generation of structured content requires automated and collaborative curation NCBO provides services that address these needs: Ontology services Annotator services Data services
  28. 28. Social issues CF Quo Community annotation in translational bioinformatics: lessons from Wikipedia Picture by Hay Kranen
  29. 29. Social issues CF Quo Community annotation in translational bioinformatics: lessons from Wikipedia Few users, many edits Many users, few edits Picture by Hay Kranen
  30. 30. Social issues CF Quo Community annotation in translational bioinformatics: lessons from Wikipedia If 0.01% of users contribute... Picture by Hay Kranen
  31. 31. Social issues CF Quo Community annotation in translational bioinformatics: lessons from Wikipedia Picture by Hay Kranen
  32. 32. Social issues CF Quo Community annotation in translational bioinformatics: lessons from Wikipedia ... you need millions of users Picture by Hay Kranen
  33. 33. Social issues Heather Piwowar Measuring the adoption of open science sharing data How much is shared, not shared? Who is sharing and who isn’t? Why do people share or not share?
  34. 34. Social issues Heather Piwowar Measuring the adoption of open science sharing data 40% said data sharing was discouraged during their training 80% said sharing was too much effort Obstacles are publishing, control, and cost
  35. 35. Social issues Heather Piwowar Measuring the adoption of open science sharing data Benefits are personal as well as societal People will share if they think it really helps others It would be easier if there was more help, better tools and guidelines
  36. 36. Main themes “If you build it, they won’t come.” - Sean Mooney The design of tools cannot be divorced from the cultural and social issues that surround them Community building is just as important as tool building Need active conversation between users and builders
  37. 37. Main themes “You cannot manage what you cannot measure.” - Lord Kelvin Does any of this actually provide benefits, and if so, to whom? What is the return on investment? Without this it is difficult to convince anyone of anything
  38. 38. Tools? Specific tools are required (persistent identity, good repository systems) Build the service and the community http://www.flickr.com/photos/gaetanlee/2792436526/
  39. 39. Policy? Standards and methods of citation are at the core of good science Focus on specific actions with measurable outcomes Identify successes (and celebrate), identify failures (and learn) http://flickr.com/photos/amrufm/2351316712/
  40. 40. Funding? Infrastructure Research on research http://flickr.com/photos/luismimunoznajar/2093185804/
  41. 41. Improving the research process is an area for (experimental) research that requires the same rigour, standards, and funding as anything else that we do
  42. 42. http://tinyurl.com/psb09-openscience

×