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Guillaume Lobet |
A VIEW FROM THE BENCH
@guillaumelobet
www.guillaumelobet.be
bit.ly/lobet-open-be
my own views,
as a scientist,
about the importance
of open science
Guillaume Lobet | 2
WHO I AM ?2 0 0 3
2 0 0 8
2 0 1 3
M AST ER IN BIO - ENGINEERING
PHD AGRONO M IC AL S CIENCE S
P O ST- DOC TOR AL F EL L OW
UNI VER SI T É C AT HOL IQUE DE
L O UVAIN
UNI VER SI T É C AT HOL IQUE DE
L O UVAIN
UNI VER SI T É DE L IÈ GE
2 0 1 6 VI SI T ING S CIEN T I ST
F OR S CH UNG S Z EN T RU M
J UL ICH
FNRS
BELSPO
FNRS
YOU
YOU
YOU
THANK YOU
Guillaume Lobet | 3
SCIENTIFIC PIPELINE
PA P E R SD ATA A N A LY S I SE X P E R I M E N T
Guillaume Lobet | 4
THE JIF
CHURCH
Illustration from John R. McKiernan http://whyopenresearch.org/ bit.ly/academic_days_talk_2015@
Guillaume Lobet | 5
Nature
Science
Cell
0 105
40
1 2 3 4 6 7 8 9 11 12
IF
https://quantixed.wordpress.com/2015/05/05/wrong-number-a-closer-look-at-impact-factors/
I F = # C I TAT I O N S / # PA P E R S
[ D U R I N G T H E PA S T 2 Y E A R S ]
IF = 42.352
…not representative…
Guillaume Lobet | 6
SCIENTIFIC PIPELINE
P O S T E R S
P R E S E N TAT I O N S
PA P E R S
L A B L I F E
R E A D PA P E R S
D ATA S E T S
C O D E
D ATA A N A LY S I SE X P E R I M E N T
R E V I E W I N G
Guillaume Lobet | 7
OPEN
PAPERS
Illustration from John R. McKiernan
1
http://whyopenresearch.org/
Guillaume Lobet |
R E V I E W E R S
R E A DP U B L I S H
R E J E C T
8
PUBLISHING PIPELINE
M E
E D I T O R
Guillaume Lobet |
0$ 0$
$ 0$
$$$ 0$
0$ $$$
$$$ $$$
R E V I E W E R S
R E A DP U B L I S H
9
M E
Figure from Richard Sever (@cshperspectives), with data from Steve Royle (@clathrin)
REDUCED ACCESS
6 MONTHS
Guillaume Lobet | 10
PREPRINT SERVERS
• archive while submitting
• directly available
• freely available
• check specific journal policy…
http://www.sherpa.ac.uk/romeo/search.php
R E V I E W E R S
R E A DP U B L I S HM E
…
Guillaume Lobet | 11
OPEN
DATA2
Guillaume Lobet | 12
LETS TALK ABOUT YOUR DATA
EXPENSIVE TIME
CONSUMING
CONTAINS
MISTAKES
Ɲ
ARE NOT 100%
EXPLOITED
Guillaume Lobet | 13
DATA REPOSITORIES / JOURNALS
• Decrease the cost of data
• Increase reproducibility
• Allow new findings
• Get more citations for your work
…
Guillaume Lobet | 14
https://opennessinitiative.org/
1. Data should be made publicly available.
2. Stimuli and materials should be made publicly available.
3. In case some data or materials are not open, clear
reasons should be given why.
4. Documents containing details for interpreting any files or
code, and how to compile and run any so ware programs
should be made available with the above items.
5. The location of all of these files should be advertised in
the manuscript, and all files should be hosted by a reliable
third party.
“We will not offer
comprehensive review for,
nor recommend the
publication of, any
manuscript that does not
meet the following minimum
requirements.“
Guillaume Lobet | 15
RESEARCH PARASITES
Data Sharing. Longo and Drazen
N Engl J Med 2016; 374:276-277
“people who had nothing to do with the design and execution of the study
but use another group’s 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”
#RESEARCHPARASITES
Illustration from @redpenblackpen
Guillaume Lobet | 16
OPEN
CODE3
"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com
Guillaume Lobet | 17
THE FAITH OF ACADEMIC SOFTWARES
tool development
funding for an in-house specialist
manual
publication
use ????
no funding
no publication
no incentives
Guillaume Lobet | 18
NOBODY LIKES BLACKBOXES
Illustration from John R. McKiernan http://whyopenresearch.org/
Guillaume Lobet | 19
REPRODUCIBILITY IS CRITICAL
Estimating the reproducibility of psychological science
Open Science Collaboration
Science 28 Aug 2015:Vol. 349, Issue 6251, pp.
$$$
Guillaume Lobet | 20
CODE REPOSITORIES
• Collaboration -> long term maintenance
• Open source -> better debugging
• Version control -> archiving
Guillaume Lobet | 21
OPEN
EVERYTHING4
Picture from Pedro Albuquerque
Guillaume Lobet | 22
R E AD PAPE R S
EVERY STEP CAN BE OPEN
L AB L I F ER E V I E W I N G
Guillaume Lobet | 23
WRAPPING UP
GOOD FOR SCIENCE GOOD FOR YOU GOOD FOR THE PUBLIC
Reproducibility
Long term vision
Error proofing
Visibility
Valorise everything
More citations
Better use of
public money
Access
Everything can be shared!
“The internet was built
in the first place to
share scientific data”
Presentation on figshare
bit.ly/lobet-open-be
Mark Hahnel
figshare founder

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OpenAire Sessions - Open Science - A view from the bench

  • 1. Guillaume Lobet | A VIEW FROM THE BENCH @guillaumelobet www.guillaumelobet.be bit.ly/lobet-open-be my own views, as a scientist, about the importance of open science
  • 2. Guillaume Lobet | 2 WHO I AM ?2 0 0 3 2 0 0 8 2 0 1 3 M AST ER IN BIO - ENGINEERING PHD AGRONO M IC AL S CIENCE S P O ST- DOC TOR AL F EL L OW UNI VER SI T É C AT HOL IQUE DE L O UVAIN UNI VER SI T É C AT HOL IQUE DE L O UVAIN UNI VER SI T É DE L IÈ GE 2 0 1 6 VI SI T ING S CIEN T I ST F OR S CH UNG S Z EN T RU M J UL ICH FNRS BELSPO FNRS YOU YOU YOU THANK YOU
  • 3. Guillaume Lobet | 3 SCIENTIFIC PIPELINE PA P E R SD ATA A N A LY S I SE X P E R I M E N T
  • 4. Guillaume Lobet | 4 THE JIF CHURCH Illustration from John R. McKiernan http://whyopenresearch.org/ bit.ly/academic_days_talk_2015@
  • 5. Guillaume Lobet | 5 Nature Science Cell 0 105 40 1 2 3 4 6 7 8 9 11 12 IF https://quantixed.wordpress.com/2015/05/05/wrong-number-a-closer-look-at-impact-factors/ I F = # C I TAT I O N S / # PA P E R S [ D U R I N G T H E PA S T 2 Y E A R S ] IF = 42.352 …not representative…
  • 6. Guillaume Lobet | 6 SCIENTIFIC PIPELINE P O S T E R S P R E S E N TAT I O N S PA P E R S L A B L I F E R E A D PA P E R S D ATA S E T S C O D E D ATA A N A LY S I SE X P E R I M E N T R E V I E W I N G
  • 7. Guillaume Lobet | 7 OPEN PAPERS Illustration from John R. McKiernan 1 http://whyopenresearch.org/
  • 8. Guillaume Lobet | R E V I E W E R S R E A DP U B L I S H R E J E C T 8 PUBLISHING PIPELINE M E E D I T O R
  • 9. Guillaume Lobet | 0$ 0$ $ 0$ $$$ 0$ 0$ $$$ $$$ $$$ R E V I E W E R S R E A DP U B L I S H 9 M E Figure from Richard Sever (@cshperspectives), with data from Steve Royle (@clathrin) REDUCED ACCESS 6 MONTHS
  • 10. Guillaume Lobet | 10 PREPRINT SERVERS • archive while submitting • directly available • freely available • check specific journal policy… http://www.sherpa.ac.uk/romeo/search.php R E V I E W E R S R E A DP U B L I S HM E …
  • 11. Guillaume Lobet | 11 OPEN DATA2
  • 12. Guillaume Lobet | 12 LETS TALK ABOUT YOUR DATA EXPENSIVE TIME CONSUMING CONTAINS MISTAKES Ɲ ARE NOT 100% EXPLOITED
  • 13. Guillaume Lobet | 13 DATA REPOSITORIES / JOURNALS • Decrease the cost of data • Increase reproducibility • Allow new findings • Get more citations for your work …
  • 14. Guillaume Lobet | 14 https://opennessinitiative.org/ 1. Data should be made publicly available. 2. Stimuli and materials should be made publicly available. 3. In case some data or materials are not open, clear reasons should be given why. 4. Documents containing details for interpreting any files or code, and how to compile and run any so ware programs should be made available with the above items. 5. The location of all of these files should be advertised in the manuscript, and all files should be hosted by a reliable third party. “We will not offer comprehensive review for, nor recommend the publication of, any manuscript that does not meet the following minimum requirements.“
  • 15. Guillaume Lobet | 15 RESEARCH PARASITES Data Sharing. Longo and Drazen N Engl J Med 2016; 374:276-277 “people who had nothing to do with the design and execution of the study but use another group’s 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” #RESEARCHPARASITES Illustration from @redpenblackpen
  • 16. Guillaume Lobet | 16 OPEN CODE3 "Piled Higher and Deeper" by Jorge Cham www.phdcomics.com
  • 17. Guillaume Lobet | 17 THE FAITH OF ACADEMIC SOFTWARES tool development funding for an in-house specialist manual publication use ???? no funding no publication no incentives
  • 18. Guillaume Lobet | 18 NOBODY LIKES BLACKBOXES Illustration from John R. McKiernan http://whyopenresearch.org/
  • 19. Guillaume Lobet | 19 REPRODUCIBILITY IS CRITICAL Estimating the reproducibility of psychological science Open Science Collaboration Science 28 Aug 2015:Vol. 349, Issue 6251, pp. $$$
  • 20. Guillaume Lobet | 20 CODE REPOSITORIES • Collaboration -> long term maintenance • Open source -> better debugging • Version control -> archiving
  • 21. Guillaume Lobet | 21 OPEN EVERYTHING4 Picture from Pedro Albuquerque
  • 22. Guillaume Lobet | 22 R E AD PAPE R S EVERY STEP CAN BE OPEN L AB L I F ER E V I E W I N G
  • 23. Guillaume Lobet | 23 WRAPPING UP GOOD FOR SCIENCE GOOD FOR YOU GOOD FOR THE PUBLIC Reproducibility Long term vision Error proofing Visibility Valorise everything More citations Better use of public money Access Everything can be shared!
  • 24. “The internet was built in the first place to share scientific data” Presentation on figshare bit.ly/lobet-open-be Mark Hahnel figshare founder