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Open science

Nicolas Rougier
Nicolas Rougier

This document summarizes key concepts related to open science including open access, open data, open source, open methodology, and open peer review. It provides definitions and examples for each concept. It also discusses incentives and challenges of open science as well as important figures who have advanced open science ideals through their work.

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NICOLAS P. ROUGIER, INRIA ADAWEEK, PARIS, 2016 The opposite of open isnt closed The opposite of open is broken John Wilbanks, 2007 OPENscience
OPEN ACCESS OPEN DATA OPEN SOURCE OPEN METHODOLOGY OPEN PEER-REVIEW MUCH MORE FUN PAYWALL NON-SHARED DATA CLOSED TOOLS & SOFTWARES NON-REPRODUCIBLE ANONYMOUS PEER-REVIEW PUBLISH OR PERISH Science Broken Science Open Science Science
OPENSCIENCE Open science is the movement to make scienti鍖c research, data and dissemination accessible to all levels of an inquiring society, amateur or professional.
OPENACCESS Annalen der Physik, vol.18, no13, (1905) Does the Inertia of a Body Depend upon its Energy-Content A. EINSTEIN. Journal of the Proceedings of the Linnean Society of London. Zoology, vol. 3 (1858) On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection. C. DARWIN & A. WALLACE. Nature 171 (1953) Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid J.D. WATSON & F. H. C. CRICK. Communications in Mathematical Physics 43 (1975) Particle creation by black holes S.W. HAWKING. 32$ 38$ 40$ 38$
OPENACCESS Green access / Gold access / Hybrid access Nobody pays (sort of) Author pays (a lot usually) Everybody pays (what the f?)
OPENACCESS
OPENDATA Open data may include non-textual material such as maps, genomes, connectomes, chemical compounds, mathematical and scienti鍖c formulae, medical data and practice, bioscience and biodiversity (wikipedia) Datasets are available upon request by contacting the corresponding author How long will the email address last ? Code can be found in the appendix Maybe, maybe not All data are available from my webpage 404 page not found Pseudo-code is given in table 1 And what Im supposed to do with it ?
OPENDATA
OPENDATA A second concern held by some is that a new class of research person will emerge people who had nothing to do with the design and execution of the study but use another groups data for their own ends, possibly stealing from the research productivity planned by the data gatherers, or even use the data to try to disprove what the original investigators had posited.There is concern among some front-line researchers that the system will be taken over by what some researchers have characterized as research parasites The New England Journal of Medicine (2016) Open data is the idea that some data should be freely available to everyone to use and republish as they wish, without restrictions from copyright, patents or other mechanisms of control. FAIR Data : Findable, Accessible, Interoperable, Re-Usable
OPENMETHODOLOGY
OPENMETHODOLOGY The (ugly) hacking way: p=0.052, click, click, click, p=0.049, save The (bad) excel way: click, click, select, click, click, move, del, click, re- click, save, unclick, ctrl-z, ctrl-z, click, enter, click, click, move, click, re-click, save The (good) reproducible way: >>> data = load(data.txt) >>> mean, std = data.mean(), data.std() >>> file = file.open(analysis.txt) >>> write(mean: %f, std: %f % (mean, std)) >>> exit() $ git commit -a -m Computed results from 24/11/2016 I have heard from graduate students opting out of academia, assistant professors afraid to come up for tenure, mid-career people wondering how to protect their labs, and senior faculty retiring early, all because of methodological terrorism. APS Observer (2016)
OPENMETHODOLOGY
OPENSOURCE WHAT ELSE ? I consider that the Golden Rule requires that if I like a program I must share it with other people who like it. Software sellers want to divide the users and conquer them, making each user agree not to share with others. I refuse to break solidarity with other users in this way. GNU Manifesto, Richard M. Stallman, 1985
OPENSOURCE WHAT ELSE ? github : the open-source way to host, create and curate knowledge Margaret Hamilton Director of the Software Engineering Division https://github.com/chrislgarry/Apollo-11
OPENREVIEW Nature 333 (1988) Human basophil degranulation triggered by very dilute antiserum against IgE E.DAVENAS, F.BEAUVAIS, J.AMARA, M.OBERBAUM, B.ROBINZON, A.MIADONNAI, A.TEDESCHI, B.POMERANZ, P.FORTNER, P.BELON, J.SAINTE-LAUDY, B.POITEVIN&J.BENVENISTE Social Text, 46/47 (1996) Transgressing the Boundaries: Toward a Transformative Hermeneutics of Quantum Gravity A. SOKAL International Journal of Advanced Computer Technology (2014) Get Me O鍖 Your Fucking Mailing List D. MAZIRES & E. KOHLER Unpublished (1993) The dynamics of interbeings and monological imperatives in Dick and Jane: a study in psychic translational gender modes CALVIN & HOBBES Copyright (c) 1993 Bill Waterson
OPENREVIEW
OPENREVIEW
OPENEDUCATION Open education is a collective term to describe institutional practices and programmatic initiatives that broaden access to the learning and training traditionally offered through formal education systems.
NEWPLAYERS ORCID (Open Researcher and Contributor ID) is a nonproprietary alphanumeric code to uniquely identify scienti鍖c and other academic authors and contributors Figshare is an online digital repository where researchers can preserve and share their research outputs, including 鍖gures, datasets, images, and videos. Zenodo is a research data repository created by OpenAIRE and CERN to provide a place for researchers to deposit datasets. ArXiv is a repository of electronic preprints of scienti鍖c papers in the 鍖elds of mathematics, physics, astronomy, computer science, quantitative biology, statistics, and quantitative 鍖nance, which can be accessed online. GitHub is a web-based Git repository hosting service that offers all of the distributed version control and source code management functionality of git as well as adding its own features. And many more to discover (RIO journal, F1000, The Winnover, Jupyter project, Software & Data carpentry, etc.)
successstory (SELF-ADVERTISEMENT) Measuring Reproducibility in Computer Systems Research Colbert et al. (2014)
successstory We redo Science ! ReScienceReproducible science is good. Replicated science is better. OPEN DATA OPEN SOURCE OPEN PEER-REVIEW OPEN (GREEN) ACCESS NO BUZZ BARRIER COMMUNITY SUPPORTED 0 BUDGET (SELF-ADVERTISEMENT)
successstory (SELF-ADVERTISEMENT) ReScience | | | ReScience 1 4 4 1 4 4 1 4 4 1 4 4 1 4 4 1 1 4 4 1 1 4 4 1 Vi 4 (1, i) (1, i) (i, 1) (i, 1) | | |
NEWincentives But mostly, Open Science is good for you Data citation & Software citation (recognition, collaboration, track use and re-use, etc.) Alternative metrics (Altmetrics, Depsy, PLOS ALMS, Plum analytics, etc.) New publishers (F1000, GigaScience, RIO, PeerJ, ReScience, etc.) European Open Science Agenda (foster open science, remove barriers, develop infrastructure mainstream access, embed Open Science in society) Growing concern on reproducibility (PubPeer, ReScience, p-hacking, etc.)
My work on free software is motivated by an idealistic goal: spreading freedom and cooperation GNU founder (1985) Richard M. Stallman OPEN HERO
For me, the repository was supposed to be a three-hour tour, not a life sentence ArXiv founder (1991) Paul Ginsparg OPEN HERO
Right now, copyright legislation is so complicated and varies so much from country to country that many people simply choose to ignore it European copyright reform (2015) Julia Reda OPEN HERO
Information is power. But like all power, there are those who want to keep it for themselves Guerilla Open Access Manifesto (2008) Aaron Swarzt 1986-2013 OPEN HERO
My original concept was to provide a free encyclopedia for every single person in the world Wikipedia co-founder (2001) Jimmy Wales OPEN HERO
Journalpaywallsare an example of something that works in the reverse direction, making communication less open and efficient Sci-Hub founder (2011) Alexandra Elbakyan OPEN HERO
Merck cooked up a phony, but real sounding, peer reviewed journal and published favorably looking data for its products in them. Merck paid Elsevier to publish such a tome (2003) SOME VILlAIN
The publishers Springer and IEEE are removing more than 120 papers from their subscription services after a French researcher discovered that the works were computer-generated nonsense (2014) SOME VILlAIN
Wiley is using fake DOIs to trap web crawlers and researchers. Wileys fake DOIs are not stable, and create the potential for DOI collisions, which break the system (2016) SOME VILlAIN
Quantitative metrics, grant funding, diversity challenge, gender bias, resistance to change, science careers, etc. SOME VILlAIN
DATAREVIEW SOURCEACCESSEDUCATION METHODOLOGY OPENSCIENCE Questions? COMMENTS? All ADA pictures from Lovelave & Babbage by Sydney Padua

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Open science

  • 1. NICOLAS P. ROUGIER, INRIA ADAWEEK, PARIS, 2016 The opposite of open isnt closed The opposite of open is broken John Wilbanks, 2007 OPENscience
  • 2. OPEN ACCESS OPEN DATA OPEN SOURCE OPEN METHODOLOGY OPEN PEER-REVIEW MUCH MORE FUN PAYWALL NON-SHARED DATA CLOSED TOOLS & SOFTWARES NON-REPRODUCIBLE ANONYMOUS PEER-REVIEW PUBLISH OR PERISH Science Broken Science Open Science Science
  • 3. OPENSCIENCE Open science is the movement to make scienti鍖c research, data and dissemination accessible to all levels of an inquiring society, amateur or professional.
  • 4. OPENACCESS Annalen der Physik, vol.18, no13, (1905) Does the Inertia of a Body Depend upon its Energy-Content A. EINSTEIN. Journal of the Proceedings of the Linnean Society of London. Zoology, vol. 3 (1858) On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection. C. DARWIN & A. WALLACE. Nature 171 (1953) Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid J.D. WATSON & F. H. C. CRICK. Communications in Mathematical Physics 43 (1975) Particle creation by black holes S.W. HAWKING. 32$ 38$ 40$ 38$
  • 5. OPENACCESS Green access / Gold access / Hybrid access Nobody pays (sort of) Author pays (a lot usually) Everybody pays (what the f?)
  • 7. OPENDATA Open data may include non-textual material such as maps, genomes, connectomes, chemical compounds, mathematical and scienti鍖c formulae, medical data and practice, bioscience and biodiversity (wikipedia) Datasets are available upon request by contacting the corresponding author How long will the email address last ? Code can be found in the appendix Maybe, maybe not All data are available from my webpage 404 page not found Pseudo-code is given in table 1 And what Im supposed to do with it ?
  • 9. OPENDATA A second concern held by some is that a new class of research person will emerge people who had nothing to do with the design and execution of the study but use another groups data for their own ends, possibly stealing from the research productivity planned by the data gatherers, or even use the data to try to disprove what the original investigators had posited.There is concern among some front-line researchers that the system will be taken over by what some researchers have characterized as research parasites The New England Journal of Medicine (2016) Open data is the idea that some data should be freely available to everyone to use and republish as they wish, without restrictions from copyright, patents or other mechanisms of control. FAIR Data : Findable, Accessible, Interoperable, Re-Usable
  • 11. OPENMETHODOLOGY The (ugly) hacking way: p=0.052, click, click, click, p=0.049, save The (bad) excel way: click, click, select, click, click, move, del, click, re- click, save, unclick, ctrl-z, ctrl-z, click, enter, click, click, move, click, re-click, save The (good) reproducible way: >>> data = load(data.txt) >>> mean, std = data.mean(), data.std() >>> file = file.open(analysis.txt) >>> write(mean: %f, std: %f % (mean, std)) >>> exit() $ git commit -a -m Computed results from 24/11/2016 I have heard from graduate students opting out of academia, assistant professors afraid to come up for tenure, mid-career people wondering how to protect their labs, and senior faculty retiring early, all because of methodological terrorism. APS Observer (2016)
  • 13. OPENSOURCE WHAT ELSE ? I consider that the Golden Rule requires that if I like a program I must share it with other people who like it. Software sellers want to divide the users and conquer them, making each user agree not to share with others. I refuse to break solidarity with other users in this way. GNU Manifesto, Richard M. Stallman, 1985
  • 14. OPENSOURCE WHAT ELSE ? github : the open-source way to host, create and curate knowledge Margaret Hamilton Director of the Software Engineering Division https://github.com/chrislgarry/Apollo-11
  • 15. OPENREVIEW Nature 333 (1988) Human basophil degranulation triggered by very dilute antiserum against IgE E.DAVENAS, F.BEAUVAIS, J.AMARA, M.OBERBAUM, B.ROBINZON, A.MIADONNAI, A.TEDESCHI, B.POMERANZ, P.FORTNER, P.BELON, J.SAINTE-LAUDY, B.POITEVIN&J.BENVENISTE Social Text, 46/47 (1996) Transgressing the Boundaries: Toward a Transformative Hermeneutics of Quantum Gravity A. SOKAL International Journal of Advanced Computer Technology (2014) Get Me O鍖 Your Fucking Mailing List D. MAZIRES & E. KOHLER Unpublished (1993) The dynamics of interbeings and monological imperatives in Dick and Jane: a study in psychic translational gender modes CALVIN & HOBBES Copyright (c) 1993 Bill Waterson
  • 18. OPENEDUCATION Open education is a collective term to describe institutional practices and programmatic initiatives that broaden access to the learning and training traditionally offered through formal education systems.
  • 19. NEWPLAYERS ORCID (Open Researcher and Contributor ID) is a nonproprietary alphanumeric code to uniquely identify scienti鍖c and other academic authors and contributors Figshare is an online digital repository where researchers can preserve and share their research outputs, including 鍖gures, datasets, images, and videos. Zenodo is a research data repository created by OpenAIRE and CERN to provide a place for researchers to deposit datasets. ArXiv is a repository of electronic preprints of scienti鍖c papers in the 鍖elds of mathematics, physics, astronomy, computer science, quantitative biology, statistics, and quantitative 鍖nance, which can be accessed online. GitHub is a web-based Git repository hosting service that offers all of the distributed version control and source code management functionality of git as well as adding its own features. And many more to discover (RIO journal, F1000, The Winnover, Jupyter project, Software & Data carpentry, etc.)
  • 20. successstory (SELF-ADVERTISEMENT) Measuring Reproducibility in Computer Systems Research Colbert et al. (2014)
  • 21. successstory We redo Science ! ReScienceReproducible science is good. Replicated science is better. OPEN DATA OPEN SOURCE OPEN PEER-REVIEW OPEN (GREEN) ACCESS NO BUZZ BARRIER COMMUNITY SUPPORTED 0 BUDGET (SELF-ADVERTISEMENT)
  • 22. successstory (SELF-ADVERTISEMENT) ReScience | | | ReScience 1 4 4 1 4 4 1 4 4 1 4 4 1 4 4 1 1 4 4 1 1 4 4 1 Vi 4 (1, i) (1, i) (i, 1) (i, 1) | | |
  • 23. NEWincentives But mostly, Open Science is good for you Data citation & Software citation (recognition, collaboration, track use and re-use, etc.) Alternative metrics (Altmetrics, Depsy, PLOS ALMS, Plum analytics, etc.) New publishers (F1000, GigaScience, RIO, PeerJ, ReScience, etc.) European Open Science Agenda (foster open science, remove barriers, develop infrastructure mainstream access, embed Open Science in society) Growing concern on reproducibility (PubPeer, ReScience, p-hacking, etc.)
  • 24. My work on free software is motivated by an idealistic goal: spreading freedom and cooperation GNU founder (1985) Richard M. Stallman OPEN HERO
  • 25. For me, the repository was supposed to be a three-hour tour, not a life sentence ArXiv founder (1991) Paul Ginsparg OPEN HERO
  • 26. Right now, copyright legislation is so complicated and varies so much from country to country that many people simply choose to ignore it European copyright reform (2015) Julia Reda OPEN HERO
  • 27. Information is power. But like all power, there are those who want to keep it for themselves Guerilla Open Access Manifesto (2008) Aaron Swarzt 1986-2013 OPEN HERO
  • 28. My original concept was to provide a free encyclopedia for every single person in the world Wikipedia co-founder (2001) Jimmy Wales OPEN HERO
  • 29. Journalpaywallsare an example of something that works in the reverse direction, making communication less open and efficient Sci-Hub founder (2011) Alexandra Elbakyan OPEN HERO
  • 30. Merck cooked up a phony, but real sounding, peer reviewed journal and published favorably looking data for its products in them. Merck paid Elsevier to publish such a tome (2003) SOME VILlAIN
  • 31. The publishers Springer and IEEE are removing more than 120 papers from their subscription services after a French researcher discovered that the works were computer-generated nonsense (2014) SOME VILlAIN
  • 32. Wiley is using fake DOIs to trap web crawlers and researchers. Wileys fake DOIs are not stable, and create the potential for DOI collisions, which break the system (2016) SOME VILlAIN
  • 33. Quantitative metrics, grant funding, diversity challenge, gender bias, resistance to change, science careers, etc. SOME VILlAIN