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)
   

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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
   @openplantpathology@scicom.xyz
   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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