Open science in Natural Sciences: Workflows and Tools

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The document discusses open science workflows and tools for natural sciences. It presents how the traditional closed research cycle can be transformed into a more open model through practices like gold and green open access publishing, open notebooks, research data management and archiving, and open peer review. Examples are given of open data repositories and journals as well as open source software tools that can help make individual research more transparent, efficient, and reusable as part of the wider scientific process. The presenters advocate for education and community engagement to establish open science as the new norm in research.

Sciences

● Marine Scientist by training
● Currently Fundraiser for
research, and an
● Open Science enthusiast
● Paleontologist by training
● ScienceOpen
● PaleorXiv
● SciComm
● Open Science

http://www.g7italy.it/sites/default/files/documents/G7%20Science%20Communiqu%C3%A9_1.pdf

… to enhance YOUR
Research Workflow
from this …

IDEA &
PROPOSAL
TEST
DATA
MODEL
CODE
PUBLISHEDUCATE
& TRAIN
RESEARCH
LIFECYCLE
Peer-
review
Impact Factor
(IF)
“Research Cycle” adapted from Tenopir et al., (2011) doi:10.1371/journal.pone.0021101
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021101
Standard Research Workflow in Natural Science

IDEA &
PROPOSAL
TEST
DATA
MODEL
CODE
Gold &
Green OA
EDUCATE
& TRAIN
REF Evaluation,
Societal Impact,
Open Innovation,
CO-CREATION
Open
Notebook
Science
RDM,
Archive &
Publish
Curate &
Publish
OS key part
of concept
Open
Educational
Resources
RESEARCH
LIFECYCLE
DOI: 10.5281/zenodo.49960
PUBLISH
● Transparency
● Efficiency
● Sustainability
● Rigour
● Re-usability

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0669-2
@BioMickWatson

Open Data needs RESEARCH DATA MANAGEMENT:
Two upcoming webinars on the topic

Open Data:
https://peerj.com/articles/175/
Find more Data Repositories at re3data.org
Find more Data Journals at www.doaj.org

Open Data: Just one example of a pipeline
Find more Data Repositories at re3data.org
Find more Data Journals at www.doaj.org

Example: Dinosaurs
https://github.com/ropensci/paleobioDB
https://paleobiodb.org/navigator/
https://www.nature.com/articles/ncomms12737/

Open Access to ALL your research papers:
http://whyopenresearch.org/costs
https://figshare.com/articles/How_to_m
ake_your_research_open_access_For_fr
ee_and_legally_/5285512

It’s your work. Publish where you want.
But don’t lock it up.

And what about Open Peer Review?
Disclaimer: These are NOT the best, but just our publications!
Try #openpeerreview hashtag on SM for the full breadth of the discussion

Absolutely whoppingly 10000% essential:
https://elifesciences.org/articles/16800

How do we make open science the norm?
• Education and training for our students
• Learn skills for new, better ways of doing
research
• Empowerment and leadership for the next
generation
• Shifting power dynamics to reduce bias and abuse
• Building a global community based on sharing and collaboration
• Massive-scale engagement to re-align Open Science with current
incentive structures

https://opensciencemooc.eu/ https://github.com/OpenScienceMOOC
… want to take part?

Good Luck with
Open Science!
https://www.slideshare.net/ivogrigorov/open-science-in-natural-sciences/

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Open science in Natural Sciences: Workflows and Tools

1. Natural Sciences & Open Science: Workflows & Tools Presenters: Jon Tennant (ScienceOpen, @Protohedgehog) Ivo Grigorov (FOSTER+, @OAforClimate) OAW2017 https://www.slideshare.net/ivogrigorov/open-science-in-natural-sciences/

2. ● Marine Scientist by training ● Currently Fundraiser for research, and an ● Open Science enthusiast ● Paleontologist by training ● ScienceOpen ● PaleorXiv ● SciComm ● Open Science

3. http://www.g7italy.it/sites/default/files/documents/G7%20Science%20Communiqu%C3%A9_1.pdf

4. … to enhance YOUR Research Workflow from this …

5. IDEA & PROPOSAL TEST DATA MODEL CODE PUBLISHEDUCATE & TRAIN RESEARCH LIFECYCLE Peer- review Impact Factor (IF) “Research Cycle” adapted from Tenopir et al., (2011) doi:10.1371/journal.pone.0021101 http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021101 Standard Research Workflow in Natural Science

6. … into something like this …

7. IDEA & PROPOSAL TEST DATA MODEL CODE Gold & Green OA EDUCATE & TRAIN REF Evaluation, Societal Impact, Open Innovation, CO-CREATION Open Notebook Science RDM, Archive & Publish Curate & Publish OS key part of concept Open Educational Resources RESEARCH LIFECYCLE DOI: 10.5281/zenodo.49960 PUBLISH ● Transparency ● Efficiency ● Sustainability ● Rigour ● Re-usability

8. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0669-2 @BioMickWatson

9. Open Data needs RESEARCH DATA MANAGEMENT: Two upcoming webinars on the topic

10. Open Data: https://peerj.com/articles/175/ Find more Data Repositories at re3data.org Find more Data Journals at www.doaj.org

11. Open Data: Just one example of a pipeline Find more Data Repositories at re3data.org Find more Data Journals at www.doaj.org

12. Example: Dinosaurs https://github.com/ropensci/paleobioDB https://paleobiodb.org/navigator/ https://www.nature.com/articles/ncomms12737/

13. Open Software: Publish as Peer-Reviewed

14. Open Access to ALL your research papers: http://whyopenresearch.org/costs https://figshare.com/articles/How_to_m ake_your_research_open_access_For_fr ee_and_legally_/5285512

15. It’s your work. Publish where you want. But don’t lock it up.

16. And what about Open Peer Review? Disclaimer: These are NOT the best, but just our publications! Try #openpeerreview hashtag on SM for the full breadth of the discussion

17. Some of our favourite tools:

18. Absolutely whoppingly 10000% essential: https://elifesciences.org/articles/16800

19. How do we make open science the norm? • Education and training for our students • Learn skills for new, better ways of doing research • Empowerment and leadership for the next generation • Shifting power dynamics to reduce bias and abuse • Building a global community based on sharing and collaboration • Massive-scale engagement to re-align Open Science with current incentive structures

20. https://opensciencemooc.eu/ https://github.com/OpenScienceMOOC … want to take part?

21. Good Luck with Open Science! https://www.slideshare.net/ivogrigorov/open-science-in-natural-sciences/

22. Natural Sciences & Open Science: Workflows & Tools Presenters: Jon Tennant (ScienceOpen, @Protohedgehog) Ivo Grigorov (FOSTER+, @OAforClimate) OAW2017 https://www.slideshare.net/ivogrigorov/open-science-in-natural-sciences/

Open science in Natural Sciences: Workflows and Tools

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