Download - The infrastructure crisis of science
![Page 1: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/1.jpg)
The infrastructure crisis of science
Björn BrembsUniversität Regensburg
http://brembs.net
![Page 2: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/2.jpg)
SCHOLARSHIP
Institutions produce publications, data and software
![Page 3: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/3.jpg)
CRISIS I
Dysfunctional scholarly literature
![Page 4: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/4.jpg)
Literature
• 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!
![Page 5: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/5.jpg)
CRISIS II
Scientific data in peril
![Page 6: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/6.jpg)
![Page 7: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/7.jpg)
![Page 8: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/8.jpg)
![Page 9: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/9.jpg)
CRISIS III
Non-existent software archives
![Page 10: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/10.jpg)
![Page 11: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/11.jpg)
![Page 12: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/12.jpg)
Today‘s Digital Dystopia
• Institutional email• Institutional
webspace• Institutional blog• Library access card• Open access
repository
• No archiving of publications
• No archiving of software
• No archiving of data
![Page 13: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/13.jpg)
WHAT NOW?
How to tear down the paywalls?
![Page 14: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/14.jpg)
Potential Solutions
• 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
![Page 15: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/15.jpg)
Superior alternative
• 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…
![Page 16: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/16.jpg)
My Digital Utopia
• 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)
![Page 17: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/17.jpg)
![Page 18: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/18.jpg)
![Page 19: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/19.jpg)
JournalRank
• Thomson Reuters: Impact Factor• Eigenfactor (now Thomson Reuters)• ScImago JournalRank (SJR)• Scopus: SNIP, SJR
Source Normalized Impact per Paper
![Page 20: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/20.jpg)
Main Problems with the IF
• Negotiable
• Irreproducible
• Mathematically
unsound
![Page 21: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/21.jpg)
Negotiable
• 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…
![Page 22: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/22.jpg)
![Page 23: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/23.jpg)
![Page 24: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/24.jpg)
Not Reproducible
• 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
![Page 25: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/25.jpg)
Not Mathematically Sound
• 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
![Page 26: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/26.jpg)
Journal rank and citations
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
![Page 27: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/27.jpg)
Journal rank and unreliability
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
![Page 28: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/28.jpg)
Journal rank and methodology
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
![Page 29: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/29.jpg)
Journal rank and quality
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
![Page 30: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/30.jpg)
Journal rank and retractions
Data from: Fang, F., & Casadevall, A. (2011). RETRACTED SCIENCE AND THE RETRACTION INDEX Infection and Immunity DOI: 10.1128/IAI.05661-11
![Page 31: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/31.jpg)
Journal rank and fraud/error
Fang et al. (2012): Misconduct accounts for the majority of retracted scientific publications. PNAS 109 no. 42 17028-17033
![Page 32: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/32.jpg)
OUR LAB
What we are doing to openly archive data and software
![Page 33: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/33.jpg)
![Page 34: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/34.jpg)
Software to control the experiment and save the data
![Page 35: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/35.jpg)
Software to analyze and visualize the data
![Page 36: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/36.jpg)
![Page 37: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/37.jpg)
buridan.sourceforge.net
![Page 38: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/38.jpg)
![Page 39: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/39.jpg)
![Page 40: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/40.jpg)
![Page 41: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/41.jpg)
However, a version is already available
![Page 42: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/42.jpg)
Get your API keys.Insert them in your R code
![Page 43: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/43.jpg)
Add the variables to your code
![Page 44: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/44.jpg)
What to publish on figshare
For instance, produce an image than can be previewed (instead of a multiple page pdf)
![Page 45: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/45.jpg)
Add new, or update an existing article
![Page 46: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/46.jpg)
Run your script and...
Same type of experiments → same scriptDefault: → 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.
![Page 48: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/48.jpg)
Citable!
![Page 49: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/49.jpg)
![Page 50: The infrastructure crisis of science](https://reader036.vdocuments.net/reader036/viewer/2022062512/5549ef06b4c90512488b5214/html5/thumbnails/50.jpg)
JULIEN COLOMB
One person is not an institutional infrastructure!