An Introduction to Open Science

This presentation is an introduction to open science. It focuses mainly on the principles of open science and it includes a few tools as well.
This presentation would not have been possible without the 2017 Open Science for Synthesis Training at NCEAS (https://www.nceas.ucsb.edu/OSS2017) where I learned about many of the topics presented here.
References to products in this presentation are not endorsements or recommendations.

Transcript

1. Open Science Vanessa Tobias October 18, 2017 @marshprincess An Introduction to
2. What is Open Science?
3. Open science is a movement Figure:http://ec.europa.eu/research/openscience/
4. 1. Open Data Principles of Open Science Graph: Piwowar & Vision 2013 Big increases in data publishing and reuse https://peerj.com/
5. Citations were 9% higher for papers with available data Piwowar & Vision 2013 independent of other variables (p < 0.01, 95% confidence intervals [5%to13%]).
6. 2. Open, Versioned Code & Documents Principles of Open Science Key Concepts: Code your Analyses (R, Python, etc.) Use Version Control Open to feedback image: http://thepilcrow.net/explaining-basic-concepts-git-and-github/
7. Automating repetitive tasks frees up time https://nceas.github.io/oss-lessons/spatial-data-gis-law/1-mon-spatial-data-intro.html
8. 3. Open Publishing Principles of Open Science Laasko & Björk 2012 https://doi.org/10.1186/1741-7015-10-124
9. Open articles are cited more “It is in authors’ best interest to create a more open environment. Given the evidence that any embargo reduces citations, the ideal would be no time at all.” Ottaviani 2016 https://doi.org/10.1016/j.respol.2011.05.025 Gaule & Maystre 2011
10. 4. Open Minds Principles of Open Science Lowndes et al. 2017 https://www.nature.com/articles/s41559-017-0160 Tools evolve but the principals of open science are the same
11. Example: An Open Science Philosophy https://github.com/BahlaiLab/Policies/blob/master/general_guidelines.md#open-philosophy
12. Lowndes et al. 2017 https://www.nature.com/articles/s41559-017-0160 Open science is a process
13. 1) 2) 3) not open research product Legend Paths to Open Science Hampton et al. 2015 http://onlinelibrary.wiley.com/doi/10.1890/ES14-00402.1/epdf
14. New Concept of a Scientific Product images: http://www.christopherlortie.info/the-revolution-will-not-be-televised-the-end-of-papers-the-rise-of-data/ Also R code – functions, packages, reproducible reports
15. image: http://blogs.agu.org/geospace/2016/05/05/changing-science-culture-contributing-open-science/ Open science is a community #openscience #opendata #rstats
16. Data & Informatics Science Communication Synthesis Data Science Science Communication Data Documentation Open science is a foundation for synthesis
17. Making New Connections Structure of synthesis teams at NIMBioS Baron et al. 2017 https://www.sciencebase.gov/catalog/item/594800f9e4b062508e3442f7
18. Tools for Open Science
19. Some open tools for each step Michener 2015 http://dx.doi.org/10.1016/j.ecoinf.2015.06.010 Also has a list of data repositories
20. GitHub – Community Coding https://guides.github.com/activities/hello-world/
21. GitHub – Project Management https://github.com/utn100/NCEAS-OSS2017-Project2/projects/1?fullscreen=true
22. More open publishing http://www.sherpa.ac.uk/ Check copyrights before selecting a journal - open access options - preprints & postprints Find legal open copies of papers you need http://unpaywall.org/
23. Example Hosts: https://youtu.be/2zMgY8Dx9co How Preprints Work: List of Preprint Servers: McKiernan et al. 2016 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973366/ asapbio.org
24. Giving Credit Identifying people & products http://www.doi.org Dataset Manuscript Figure Researcher https://orcid.org/ Preprint
25. Citation Tracking Tools - Examples Software or Code: Manuscripts: www.depsy.org www.impactstory.org www.scholar.google.com
26. What do you think?
27. Questions for Discussion • How open is our current process? • Which parts could be more open? • Which parts do we want or need to keep closed? • What benefits do you see from doing more open science? • What are the barriers to doing more open science? • How do we encourage open science practices? • Which tools would help? • What do you want to do as an individual? • What do you think we can do as a group?
28. References & Resources
29. Open Science Articles • Hampton et al. 2015: http://onlinelibrary.wiley.com/doi/10.1890/ES14-00402.1/epdf • Piwowar & Vision 2013: https://peerj.com/articles/175/?utm_content=buffer9059d&utm_so urce=buffer&utm_medium=twitter&utm_campaign=Buffer • Reichman et al. 2011: http://science.sciencemag.org/content/331/6018/703.full?rss=1 • Ottaviani 2016: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.01 59614
30. Open Computing & Software Articles • Best Practices for Scientific Computing: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio. 1001745 • Wilson: Good Enough Practices in Scientific Computing: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcb i.1005510 • DataOne Open Data Education https://www.dataone.org/education- modules
31. Synthesis Centers – Articles • Full list of international synthesis centers: http://synthesis-consortium.org/ • Baron et al. 2016: Synthesis centers as critical research infrastructure: • Summary: https://i2insights.org/2017/08/22/synthesis-centers-as-infrastructure/ • Article: https://www.sciencebase.gov/catalog/item/594800f9e4b062508e3442f7 • Palmer et al. 2016: Practices for facilitating interdisciplinary synthetic research: the National Socio-Environmental Synthesis Center (SESYNC) • Summary: https://i2insights.org/2016/05/31/institutional-practices-for- interdisciplinarity/ • Article: https://doi.org/10.1016/j.cosust.2016.01.002
32. Resources TRACKING TOOLS • ImpactStory (impactstory.org) • Depsy (depsy.org) • Nature article: http://www.nature.com/news/the-unsung-heroes-of-scientific- software-1.19100 • OrcID (orcid.org) FIND OPEN ARTICLES • Unpaywall (unpaywall.org) CODING • Software Carpentry http://software-carpentry.org