Open Plant Pathology - BSPP Plant Health Club

Presentation given to the Plant Health Club of the British Society of Plant Pathology on 14 April 2023

Transcript

1. www.openplantpathology.org Valuing openness, transparency and reproducibility Transparency OpenPlant Pathology Open science Reproducibility Emerson Del Ponte (UFV, Brazil) Adam Sparks (DPIRD, Australia)
2. How it started? Crazy idea in Jan 2018 by Adam Sparks and Emerson Del Ponte
3. Our vision Open Plant Pathology (OPP) fosters a diverse community culture that values openness, transparency and reproducibility of scientific research data and methods applied to plant pathological research and education
4. The open science ecosystem
5. What/how we did it? Communication, collaboration and structure
6. Communication channels One-to-one interactions and mass communication Openplantpathology.slack.com @openplantpathology@scicom.xyz www.openplantpathology.org
7. Educational resources Producing and sharing openly education materials Workshop materials Slides, video lectures, datasets, exercises, reproducible examples
8. Collaborative coding Coding together and developing new open source tools https://github.com/openplantpathology - R Packages (hagis, epifitter) - Research compendia (HTML Webpage RStudio project and R Package Templates) - Interactive databases (FGSCdb)
9. Collaborative coding Success case 1 https://github.com/openplantpathology/hagis
10. Collaborative coding Success case 2
11. Educational resources Producing and sharing openly education materials Online book Made with R R for Plant Disease Epidemiology
12. Science dissemination (during quarantine) Scheduling of FREE online scientific talks Virtual Seminars Live broadcast + video recording of scientific seminars in the field of Plant Pathology. Interaction with the speakers via live chat and in a Slack channel for 24 h after the talk.
13. Reproducibility Editorship Supporting journals to promote adoption of open practices Brazilian Phytopathological Society Journal In 2020, a Reproducibility Team was created to support authors, reviews and editors to value data and code sharing for review and public release in permanent repositories
14. How open/reproducible is Plant Pathology?
15. Our recent publication
16. Sparks et al. (2023) Survey in 21 plant pathology journals
17. Sparks et al. (2023) No data Upon request Paywalled Free access ~ 10% share data openly (most molecular) How are data/codes shared? Computational methods
18. What efforts are needed to make the change?
19. Change the mindset and framework Challenging! Knowledge Technology
20. Tools Workflows Environments Collaborative & sharing platforms Research Project Organized Documented Shareable Accessible Reproducible Learn new tools and environment
21. Fortunately - several open tools are available! BIB
22. Research compendium concept
23. Example of shared projects
24. A new publishing model Sparks et al. (2023)
25. For group discussion … 1. Why (benefits) embrace open science practices? 2. What are the barriers for adopting open science? 3. What has helped you to make your research more open? 4. What should OPP/plant pathology community do to help accelerate the change?