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Facilitating the Spread of Scientific
Knowledge via Open Science
IDWeek 2013
October 3, 2013
Jonathan A. Eisen
University o...
Disclosures

Thursday, October 3, 13
My “Conversion”

Thursday, October 3, 13
Public Library of Science (PLoS)
• Started in 2000 by
•Harold Varmus
•Pat Brown
•Michael Eisen
• First action was to circu...
JCan you get people to sign this and FAX it to me.
1-786-549-0137. Craig and
Claire’s sigs would be greatly appreciated.
I...
Me and PLoS

User agrees to
not publish
genome level
analyses

Thursday, October 3, 13

• Joined founding
Editorial Board ...
Open Data Experiment
• Unrestricted data
access policy on
Tetrahymena thermophila
• First time done at
TIGR
• Many people
...
Open Access Experiment

WMD - the
Wolbachia of
Male
Destruction

Thursday, October 3, 13

• Had published one paper in an
...
Brotherly Love

Thursday, October 3, 13
Wolbachia in PLoS Biology

Thursday, October 3, 13
Wolbachia in PLoS Biology

• But still unclear to me whether this
Open Access thing was a good idea or
not
Thursday, Octob...
Thursday, October 3, 13
RhoGam

• Supplier
• RhoGAM should be administered within 72 hours of
known or suspected exposure to Rh-positive red
blood...
Thursday, October 3, 13
Thursday, October 3, 13
You can purchase online access to this
article (and all its versions) for a 24hour period. Articles are US $  29.95,
with ...
Access Blocked - What Next?

• Bought lots of articles
• Tried to contact experts
• Got friends to get some articles from ...
Medical Guesswork

• Wife got Rhogam 11 days after blood exposure
• Other treatments became in part guesswork as
well
• No...
Baby Lost

• Benjamin Augustin Eisen stillborn August
29, 2003

Thursday, October 3, 13
Disclosures

Thursday, October 3, 13
A Few Other Stories

Thursday, October 3, 13
Father’s Day

Thursday, October 3, 13
Thursday, October 3, 13
Thursday, October 3, 13
Thursday, October 3, 13
Thursday, October 3, 13
What is Open Science?

Thursday, October 3, 13
Open Access

• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Pap...
Open Access

• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Pap...
Open Science

• Papers and presentations
• Data
• Protocols
• Samples
• Software
• Hardware
• Classes and teaching materia...
Open vs. Free

Thursday, October 3, 13
Citizen Science

Thursday, October 3, 13
Crowdfunding/Crowdsourcing

Thursday, October 3, 13
What Can You Do?

Thursday, October 3, 13
1. Make your public material open
• Making something public? Make it open
• Papers
• Data
• Software

Thursday, October 3,...
• 2. Participate in open discussions
post publication
• Post publication review
• Blogs
• Twitter
• Meetings

Thursday, Oc...
3. Consider being more open
pre-publication
• Data
• Papers
• Talks
• Software
• Ideas
• Noteboook

Thursday, October 3, 1...
4. Judge people by their
contributions not surrogates
• Hiring
• Promotion
• Students

Thursday, October 3, 13
5. Embrace and use open material

• CC licensed figures for talks
• Give credit
• Remix and repurpose

Thursday, October 3...
6. Work for entities that are open

Thursday, October 3, 13
7. Do not support closed science

Thursday, October 3, 13
Many Exiting Barriers

• Impact factor
• Money raising efforts
• Conservative behaviors
• Red herrings
• Lack of peer revi...
Genbank

Thursday, October 3, 13
Search BRCA1 human

Thursday, October 3, 13
Search BRCA1 human

Thursday, October 3, 13
Search BRCA1 human

You can purchase online access to this
article (and all its versions) for a 24hour period. Articles ar...
Paid

Thursday, October 3, 13
BLAST Result

Thursday, October 3, 13
Blast Result

You can purchase online access to this
article (and all its versions) for a 24hour period. Articles are US $...
Blast Result

Plus - you are not allowed to share your
alignments with anyone

Thursday, October 3, 13
A network of literature and data

Thursday, October 3, 13
A network of literature and data

Free = you can read all the papers

Thursday, October 3, 13
A network of literature and data

Open = Repurpose and share any
part of your analysis w/ no
restrictions. No lawyers. No ...
Educational Benefits of OA

• No debate about “fair use”
• No need for password’s or logins for
course web sites
• No lawy...
Disclosures

Thursday, October 3, 13
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Jonathan Eisen talk for #IDWeek: Facilitating the Spread of Scientific Knowledge via Open Science

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Jonathan Eisen talk for #IDWeek: Facilitating the Spread of Scientific Knowledge via Open Science

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Jonathan Eisen talk for #IDWeek: Facilitating the Spread of Scientific Knowledge via Open Science

  1. 1. Facilitating the Spread of Scientific Knowledge via Open Science IDWeek 2013 October 3, 2013 Jonathan A. Eisen University of California, Davis @phylogenomics Thursday, October 3, 13
  2. 2. Disclosures Thursday, October 3, 13
  3. 3. My “Conversion” Thursday, October 3, 13
  4. 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 Thursday, October 3, 13
  5. 5. JCan you get people to sign this and FAX it to me. 1-786-549-0137. Craig and Claire’s 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 Thursday, October 3, 13
  6. 6. Me and PLoS User agrees to not publish genome level analyses Thursday, October 3, 13 • Joined founding Editorial Board of PLoS Biology • Still not fully convinced about need for OA • Worried more about push for full “Open Science”
  7. 7. 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 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, 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, 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 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 Thursday, October 3, 13 Thanks for the message about the genome, that is a nice surprise. Lots of Bacillus DNA in there unfortunately but we are going to go wild looking in it. Patrick
  8. 8. Open Access Experiment WMD - the Wolbachia of Male Destruction Thursday, October 3, 13 • Had published one paper in an Open Access journal (Genome Biology) • We were working on a paper on the first Wolbachia genome • Wolbachia are maternally transmitted parasites that target males in many species • In filarial nematodes appear to be mutualistic symbionts • Our paper was being recruited by Nature and Science
  9. 9. Brotherly Love Thursday, October 3, 13
  10. 10. Wolbachia in PLoS Biology Thursday, October 3, 13
  11. 11. Wolbachia in PLoS Biology • But still unclear to me whether this Open Access thing was a good idea or not Thursday, October 3, 13
  12. 12. Thursday, October 3, 13
  13. 13. RhoGam • Supplier • RhoGAM should be administered within 72 hours of known or suspected exposure to Rh-positive red blood cells. • Wikipedia • It is given by intramuscular injection as part of modern routine antenatal care at about 28 weeks of pregnancy, and within 72 hours after childbirth.[5] It is also given after antenatal pathological events that are likely to cause a feto-maternal hemorrhage.[6] • Question • What happens if you do it even later? Thursday, October 3, 13
  14. 14. Thursday, October 3, 13
  15. 15. Thursday, October 3, 13
  16. 16. You can purchase online access to this article (and all its versions) for a 24hour period. Articles are US $  29.95, with some exceptions where prices may vary. Click "Buy Now" to display the price Thursday, October 3, 13
  17. 17. Access Blocked - What Next? • Bought lots of articles • Tried to contact experts • Got friends to get some articles from libraries • Got more and more pissed off Thursday, October 3, 13
  18. 18. Medical Guesswork • Wife got Rhogam 11 days after blood exposure • Other treatments became in part guesswork as well • Note, doctors at this time were spectacular • They even asked for assistance in finding out answers to some treatment questions • In theory, the scientific / medical literature could help .... Thursday, October 3, 13
  19. 19. Baby Lost • Benjamin Augustin Eisen stillborn August 29, 2003 Thursday, October 3, 13
  20. 20. Disclosures Thursday, October 3, 13
  21. 21. A Few Other Stories Thursday, October 3, 13
  22. 22. Father’s Day Thursday, October 3, 13
  23. 23. Thursday, October 3, 13
  24. 24. Thursday, October 3, 13
  25. 25. Thursday, October 3, 13
  26. 26. Thursday, October 3, 13
  27. 27. What is Open Science? Thursday, October 3, 13
  28. 28. 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 Thursday, October 3, 13
  29. 29. 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 Thursday, October 3, 13
  30. 30. Open Science • Papers and presentations • Data • Protocols • Samples • Software • Hardware • Classes and teaching materials • Communications Thursday, October 3, 13
  31. 31. Open vs. Free Thursday, October 3, 13
  32. 32. Citizen Science Thursday, October 3, 13
  33. 33. Crowdfunding/Crowdsourcing Thursday, October 3, 13
  34. 34. What Can You Do? Thursday, October 3, 13
  35. 35. 1. Make your public material open • Making something public? Make it open • Papers • Data • Software Thursday, October 3, 13
  36. 36. • 2. Participate in open discussions post publication • Post publication review • Blogs • Twitter • Meetings Thursday, October 3, 13
  37. 37. 3. Consider being more open pre-publication • Data • Papers • Talks • Software • Ideas • Noteboook Thursday, October 3, 13
  38. 38. 4. Judge people by their contributions not surrogates • Hiring • Promotion • Students Thursday, October 3, 13
  39. 39. 5. Embrace and use open material • CC licensed figures for talks • Give credit • Remix and repurpose Thursday, October 3, 13
  40. 40. 6. Work for entities that are open Thursday, October 3, 13
  41. 41. 7. Do not support closed science Thursday, October 3, 13
  42. 42. Many Exiting Barriers • Impact factor • Money raising efforts • Conservative behaviors • Red herrings • Lack of peer review • Cost of publishing • Journal copyright protects authors • Lobbyists Thursday, October 3, 13
  43. 43. Genbank Thursday, October 3, 13
  44. 44. Search BRCA1 human Thursday, October 3, 13
  45. 45. Search BRCA1 human Thursday, October 3, 13
  46. 46. Search BRCA1 human You can purchase online access to this article (and all its versions) for a 24hour period. Articles are US $  29.95, with some exceptions where prices may vary. Click "Buy Now" to display the price Thursday, October 3, 13
  47. 47. Paid Thursday, October 3, 13
  48. 48. BLAST Result Thursday, October 3, 13
  49. 49. Blast Result You can purchase online access to this article (and all its versions) for a 24hour period. Articles are US $  29.95, with some exceptions where prices may vary. Click "Buy Now" to display the price Thursday, October 3, 13
  50. 50. Blast Result Plus - you are not allowed to share your alignments with anyone Thursday, October 3, 13
  51. 51. A network of literature and data Thursday, October 3, 13
  52. 52. A network of literature and data Free = you can read all the papers Thursday, October 3, 13
  53. 53. A network of literature and data Open = Repurpose and share any part of your analysis w/ no restrictions. No lawyers. No fear. Thursday, October 3, 13
  54. 54. 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 Thursday, October 3, 13
  55. 55. Disclosures Thursday, October 3, 13

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