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Open Plant Pathology - BSPP Plant Health Club

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

Emerson M. Del Ponte

February 13, 2023
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  1. www.openplantpathology.org
    Valuing openness, transparency and reproducibility
    Transparency
    OpenPlant
    Pathology
    Open
    science
    Reproducibility
    Emerson Del Ponte (UFV, Brazil)
    Adam Sparks (DPIRD, Australia)

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  2. How it started?
    Crazy idea in Jan 2018 by Adam Sparks and Emerson Del Ponte

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  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

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  4. The open science ecosystem

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  5. What/how we did it?
    Communication, collaboration and structure

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  6. Communication channels
    One-to-one interactions and mass communication
    Openplantpathology.slack.com
    @[email protected]
    www.openplantpathology.org

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  7. Educational resources
    Producing and sharing openly education materials
    Workshop materials
    Slides, video lectures,
    datasets, exercises,
    reproducible examples

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  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)

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  9. Collaborative coding
    Success case 1
    https://github.com/openplantpathology/hagis

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  10. Collaborative coding
    Success case 2

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  11. Educational resources
    Producing and sharing openly education materials
    Online book
    Made with R
    R for Plant Disease
    Epidemiology

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  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.

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  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

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  14. How open/reproducible
    is Plant Pathology?

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  15. Our recent publication

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  16. Sparks et al. (2023)
    Survey in 21 plant pathology journals

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  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

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  18. What efforts are needed
    to make the
    change?

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  19. Change the mindset and framework
    Challenging!
    Knowledge
    Technology

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  20. Tools
    Workflows
    Environments
    Collaborative
    & sharing
    platforms
    Research Project
    Organized
    Documented
    Shareable
    Accessible
    Reproducible
    Learn new tools and environment

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  21. Fortunately - several open tools are available!
    BIB

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  22. Research compendium concept

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  23. Example of shared projects

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  24. A new publishing model
    Sparks et al. (2023)

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  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?

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