Jonathan Eisen talk on "Open Science" at #BOSC2012 #ISMB

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 @phylogenomicsFriday, July 13, 12

DisclosuresFriday, July 13, 12

My “Conversion”Friday, July 13, 12

Public Library of Science (PLoS) • Started in 2000 by •Harold Varmus •Pat Brown •Michael Eisen • First action was to circulate an open letter on publishingFriday, July 13, 12

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

Friday, July 13, 12

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. -MFriday, July 13, 12

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 MedicineFriday, July 13, 12

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 analysesFriday, July 13, 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 experimentsFriday, July 13, 12

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 PatrickFriday, July 13, 12

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 ScienceFriday, July 13, 12

Brotherly LoveFriday, July 13, 12

Wolbachia in PLoS BiologyFriday, July 13, 12

Experiments in Progress … • But still unclear to me whether this Open Access thing was a good idea or not • Then real life intervenedFriday, July 13, 12

Friday, July 13, 12

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 knowledgeFriday, July 13, 12

Father’s DayFriday, July 13, 12

Friday, July 13, 12

OA PublishingFriday, July 13, 12

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 2003Friday, July 13, 12

Friday, July 13, 12

Open vs. FreeFriday, July 13, 12

Search BRCA1 humanFriday, July 13, 12

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 priceFriday, July 13, 12

PaidFriday, July 13, 12

BLASTFriday, July 13, 12

BLAST ResultFriday, July 13, 12

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 priceFriday, July 13, 12

Blast Result Plus - you are not allowed to share your alignments with anyoneFriday, July 13, 12

A network of literatureFriday, July 13, 12

A network of literature and dataFriday, July 13, 12

A network of literature and data Free = you can read all the papersFriday, July 13, 12

A network of literature and data Open = Repurpose and share any part of your analysis w/ no restrictions. No lawyers. No fear.Friday, July 13, 12

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 purposeFriday, July 13, 12

Many Exiting Barriers • Impact factor • Money raising efforts • Conservative behaviors • Red herrings • Lack of peer review • Cost of publishing • Journal copyright protects authors • LobbyistsFriday, July 13, 12

Other Areas of Open Science • Open data • Open source software • Open discussion • Open resources • Open reviewFriday, July 13, 12

Why Can You Do?Friday, July 13, 12

1. Make your public material open • Making something public? Make it open • Papers • Data • SoftwareFriday, July 13, 12

• 2. Participate in open discussions post publication • Post publication review • Blogs • Twitter • MeetingsFriday, July 13, 12

3. Consider being more open pre-publication • Data • Papers • Talks • Software • Ideas • NoteboookFriday, July 13, 12

4. Judge people by their contributions not surrogates • Hiring • Promotion • StudentsFriday, July 13, 12

5. Embrace and use open material • CC licensed figures for talks • Give credit • Remix and repurposeFriday, July 13, 12

6. Work for entities that are openFriday, July 13, 12

7. Do not support closed scienceFriday, July 13, 12

DisclosuresFriday, July 13, 12

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Jonathan Eisen talk on "Open Science" at #BOSC2012 #ISMB

by Jonathan Eisen on Jul 13, 2012

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Jonathan Eisen talk on "Open Science" at #BOSC2012 #ISMB Presentation Transcript