Talk on Open Science at ISMB / BOSC2012 session

1. Science Wants to Be Open:
If Only We Could Get Out of Its Way
BOSC2012
July 12, 2012
Jonathan A. Eisen
University of California, Davis
@phylogenomics
Friday, July 13, 12

2. Disclosures
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3. My “Conversion”
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4. Public Library of Science (PLoS)
• Started in 2000 by
•Harold Varmus
•Pat Brown
•Michael Eisen
• First action was to circulate an
open letter on publishing
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5. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and scholarly
discourse in medicine and the life sciences in a freely accessible, fully
searchable, interlinked form. Establishment of this public library would vastly
increase the accessibility and utility of the scientific literature, enhance
scientific productivity, and catalyze integration of the disparate communities of
knowledge and ideas in biomedical sciences.We recognize that the publishers
of our scientific journals have a legitimate right to a fair financial return for
their role in scientific communication. We believe, however, that the
permanent, archival record of scientific research and ideas should neither be
owned nor controlled by publishers, but should belong to the public and should
be freely available through an international online public library.To encourage
the publishers of our journals to support this endeavor, we pledge that,
beginning in September 2001, we will publish in, edit or review for, and
personally subscribe to only those scholarly and scientific journals
that have agreed to grant unrestricted free distribution rights to any
and all original research reports that they have published, through PubMed
Central and similar online public resources, within 6 months of their initial
publication date.
Friday, July 13, 12

6. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and scholarly
discourse in medicine and the life sciences in a freely accessible, fully
searchable, interlinked form. Establishment of this public library would vastly
increase the accessibility and utility of the scientific literature, enhance
scientific productivity, and catalyze integration of the disparate communities of
knowledge and ideas in biomedical sciences.We recognize that the publishers
of our scientific journals have a legitimate right to a fair financial return for
their role in scientific communication. We believe, however, that the
permanent, archival record of scientific research and ideas should neither be
owned nor controlled by publishers, but should belong to the public and should
be freely available through an international online public library.To encourage
the publishers of our journals to support this endeavor, we pledge that,
beginning in September 2001, we will publish in, edit or review for, and
personally subscribe to only those scholarly and scientific journals
that have agreed to grant unrestricted free distribution rights to any
and all original research reports that they have published, through PubMed
Central and similar online public resources, within 6 months of their initial
publication date.
Friday, July 13, 12

7. Friday, July 13, 12

8. Friday, July 13, 12

9. J-
Can you get people to sign this and FAX it to me.
1-786-549-0137. Craig and
Claires sigs would be greatly appreciated.
I assume I can put your name on it, no?
I set up a site http://www.publiclibraryofscience.org
to keep lists of
people who have signed.
-M
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10. PLoS After the Letter (2003)
• > 25,000 people signed the letter
• Small increase in open access
support
• But not enough
• So PLoS announced the launch of
their own journals
•PLoS Biology
•PLoS Medicine
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11. Me and PLoS
• Joined founding
Editorial Board of
PLoS Biology
• Still not fully
convinced about
need for OA
• Worried more about
User agrees to push for full “Open
not publish Science”
genome level
analyses
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12. Ft. Lauderdale Agreement
• Feb 2003 meeting in Ft. Lauderdale on “Genome
Sequencing Data Release Policies”
• Follow up to the “Bermuda Accord”
• Debate about how open to be with data
• NHGRI had supported a similar policy to TIGRs
(see http://www.genome.gov/10506537)
• Sean Eddy gave a talk that convinced me that
these restrictions we in direct conflict with the
whole point of giving money to places to generate
the data
• So I did what any scientist should do - some
experiments
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13. Open Data Experiment
• Unrestricted data
access policy on
Tetrahymena thermophila
• First time done at
TIGR
• Many people
published papers
before we did
• But many more helped
with our paper
1 The Institute for Genomic Research, Rockville, Maryland, United States of America, 2 Department
of Biology, York University, Toronto, Ontario, Canada, 3 Centre for Research in Mass Spectrometry,
York University, Toronto, Ontario, Canada, 4 Department of Biological Sciences, Marquette
University, Milwaukee, Wisconsin, United States of America, 5 Razavi-Newman Center for
Thanks for the message about the
Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of
America, 6 Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago,
Illinois, United States of America, 7 Department of Biology, Harvey Mudd College, Claremont,
genome, that is a nice surprise. Lots of
California, United States of America, 8 Department of Biology, University of Texas at San Antonio,
San Antonio, Texas, United States of America, 9 Department of Electrical Engineering, University of
Texas at San Antonio, San Antonio, Texas, United States of America, 10 Department of Molecular
and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America,
Bacillus DNA in there unfortunately but
11 Department of Computer Science and Engineering, University of Washington, Seattle,
Washington, United States of America, 12 Department of Cellular Biology, University of Georgia,
Athens, Georgia, United States of America, 13 Department of Biological Sciences, University of
we are going to go wild looking in it.
Iowa, Iowa City, Iowa, United States of America, 14 Department of Biology, University of Rochester,
Rochester, New York, United States of America, 15 Canadian Institute for Advanced Research,
Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, 16
Department of Genetics, Stanford University, Stanford, California, United States of America, 17
Department of Molecular, Cellular, and Developmental Biology, University of California Santa
Barbara, Santa Barbara, California, United States of America Patrick
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14. Open Access Experiment
• Had published one paper in an
Open Access journal (Genome
Biology)
• We were working on a paper on
WMD - the the first Wolbachia genome
Wolbachia of
Male • Wolbachia are maternally
transmitted parasites that target
Destruction males in many species
• In filarial nematodes appear to
be mutualistic symbionts
• Our paper was being recruited
by Nature and Science
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15. Brotherly Love
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16. Wolbachia in PLoS Biology
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17. Experiments in Progress …
• But still unclear to me whether this Open
Access thing was a good idea or not
• Then real life intervened
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18. Friday, July 13, 12

19. Lack of Access
• Scientist without access
• Would access have helped?
• Is limiting access useful or needed?
• Goal of much of scientific and medical
research is to spread knowledge
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20. Father’s Day
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21. Friday, July 13, 12

22. OA Publishing
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23. Open Access
• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Papers are immediately deposited in a
public online archive, such as PubMed Central
Bethesda Principles, April 2003
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24. Open Access
• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Papers are immediately deposited in a
public online archive, such as PubMed Central
Bethesda Principles, April 2003
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25. Friday, July 13, 12

26. Open vs. Free
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27. Search BRCA1 human
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28. Search BRCA1 human
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29. Search BRCA1 human
You can purchase online access to this
article (and all its versions) for a 24-
hour period. Articles are US $ 29.95,
with some exceptions where prices may
vary. Click "Buy Now" to display the
price
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30. Paid
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31. BLAST
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32. BLAST
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33. BLAST Result
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34. Blast Result
You can purchase online access to this
article (and all its versions) for a 24-
hour period. Articles are US $ 29.95,
with some exceptions where prices may
vary. Click "Buy Now" to display the
price
Friday, July 13, 12

35. Blast Result
Plus - you are not allowed to share your
alignments with anyone
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36. A network of literature
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37. A network of literature and data
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38. A network of literature and data
Free = you can read all the papers
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39. A network of literature and data
Open = Repurpose and share any
part of your analysis w/ no
restrictions. No lawyers. No fear.
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40. Educational Benefits of OA
• No debate about “fair use”
• No need for password’s or logins for
course web sites
• No lawyers have to be involved
• Material from OA publications can be
repackaged for any purpose
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41. Many Exiting Barriers
• Impact factor
• Money raising efforts
• Conservative behaviors
• Red herrings
• Lack of peer review
• Cost of publishing
• Journal copyright protects authors
• Lobbyists
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42. Other Areas of Open Science
• Open data
• Open source software
• Open discussion
• Open resources
• Open review
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43. Why Can You Do?
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44. 1. Make your public material open
• Making something public? Make it open
• Papers
• Data
• Software
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45. • 2. Participate in open discussions
post publication
• Post publication review
• Blogs
• Twitter
• Meetings
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46. 3. Consider being more open
pre-publication
• Data
• Papers
• Talks
• Software
• Ideas
• Noteboook
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47. 4. Judge people by their
contributions not surrogates
• Hiring
• Promotion
• Students
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48. 5. Embrace and use open material
• CC licensed figures for talks
• Give credit
• Remix and repurpose
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49. 6. Work for entities that are open
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50. 7. Do not support closed science
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51. Disclosures
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