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The infrastructure crisis of science

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  • 1. Björn Brembs Universität Regensburg http://brembs.net
  • 2. Institutions produce publications, data and software
  • 3. Dysfunctional scholarly literature
  • 4. • Limited access • No global search • No functional hyperlinks • No flexible data visualization • No submission standards • (Almost) no statistics • No text/data-mining • No effective way to sort, filter and discover • No scientific impact analysis • No networking feature • etc. …it’s like the web in 1995!
  • 5. Scientific data in peril
  • 6. Non-existent software archives
  • 7. • Institutional email • Institutional webspace • Institutional blog • Library access card • Open access repository • No archiving of publications • No archiving of software • No archiving of data
  • 8. How to tear down the paywalls?
  • 9. • Outside help – Funder OA mandates (enforcement!) – Removal of legislative (e.g. copyright) barriers – BUT: does not address software/data • Institutional reform – Destroy journal rank – Provide superior alternative
  • 10. • Global search for/access to ALL literature, software and data • Smart sort, filter and discover functionality • Science-based reputation system • Collaborative writing (GitHub for everything), one-click submission • Much, much cheaper: US$90/paper (e.g. SciELO) vs. US$4k/paper today Requirement: global institutional collaboration à la SciELO, LPC, SHARE…
  • 11. • No more corporate publishers – libraries archive everything and make it publicly accessible according to a world-wide standard (e.g. SciELO, SHARE, LPC) • Single semantic, decentralized database of literature, data and software Technically feasible today (almost)
  • 12. • Thomson Reuters: Impact Factor • Eigenfactor (now Thomson Reuters) • ScImago JournalRank (SJR) • Scopus: SNIP, SJR Source Normalized Impact per Paper
  • 13. • Negotiable • Irreproducible • Mathematically unsound
  • 14. • PLoS Medicine, IF 2-11 (8.4) (The PLoS Medicine Editors (2006) The Impact Factor Game. PLoS Med 3(6): e291. http://www.plosmedicine.org/article/info:doi/10.1371%2Fjournal.pmed.0030291) • Current Biology IF from 7 to 11 in 2003 – Bought by Cell Press (Elsevier) in 2001…
  • 15. • Rockefeller University Press bought their data from Thomson Reuters • Up to 19% deviation from published records • Second dataset still not correct Rossner M, van Epps H, Hill E (2007): Show me the data. The Journal of Cell Biology, Vol. 179, No. 6, 1091-1092 http://jcb.rupress.org/cgi/content/full/179/6/1091
  • 16. • Left-skewed distributions • Weak correlation of individual article citation rate with journal IF Seglen PO (1997): Why the impact factor of journals should not be used for evaluating research. BMJ 1997;314(7079):497 (15 February) http://www.bmj.com/cgi/content/full/314/7079/497
  • 17. The weakening relationship between the Impact Factor and papers' citations in the digital age (2012): George A. Lozano, Vincent Lariviere, Yves Gingras arXiv:1205.4328
  • 18. Munafò, M., Stothart, G., & Flint, J. (2009). Bias in genetic association studies and impact factor Molecular Psychiatry, 14 (2), 119-120 DOI: 10.1038/mp.2008.77
  • 19. Brembs, B., Button, K., & Munafò, M. (2013). Deep impact: unintended consequences of journal rank. Frontiers in Human Neuroscience, 7. doi:10.3389/fnhum.2013.00291
  • 20. Brown, E. N., & Ramaswamy, S. (2007). Quality of protein crystal structures. Acta Crystallographica Section D Biological Crystallography, 63(9), 941–950. doi:10.1107/S0907444907033847
  • 21. Data from: Fang, F., & Casadevall, A. (2011). RETRACTED SCIENCE AND THE RETRACTION INDEX Infection and Immunity DOI: 10.1128/IAI.05661-11
  • 22. Fang et al. (2012): Misconduct accounts for the majority of retracted scientific publications. PNAS 109 no. 42 17028-17033
  • 23. What we are doing to openly archive data and software
  • 24. Software to control the experiment and save the data
  • 25. Software to analyze and visualize the data
  • 26. However, a version is already available
  • 27. Get your API keys. Insert them in your R code
  • 28. For instance, produce an image than can be previewed (instead of a multiple page pdf)
  • 29. Same type of experiments → same script Default:→ same categories → same tags → same authors → same links → same description → One complete article, in one click. Update the figure: Higher sample size directly published while analysed, your boss may see the results before you do! (or you may see the results of your student before they do) Possibility to make it public and citable in one click or directly in the R code.
  • 30. http://dx.doi.org/10.6084/m9.figshare.97792
  • 31. One person is not an institutional infrastructure!