What's so Open about Plant Pathology?

Transcript

1. Adam H. Sparks
   What’s so
   Open about Plant Pathology?
   

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2. Science
   Collect
   Analyse
   Publish
   Write
   Ideal simplified research life-cycle
   Review
   Summarise
   Reproduce
   Re-analyse
   (meta-analysis)
   Share data
   Open repository
   Share code
   open/free
   tools
   Collaborative tools
   Citation manager
   Pre-prints
   Open Access
   

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3. Why embrace Open Practices?
   - Sponsors/journals require data (standard in molecular)
   - Allows reproducibility (data and/or methods)
   - Technology (less cumbersome) is becoming available
   - Enhanced visibility/transparency
   - Multiple citable outcomes: data, code, manuscript, etc.
   

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4. How are we plant pathologists doing?
   Sparks et al. (unpublished)
   101
   99
   Count
   

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5. Article types
   Sparks et al. (unpublished)
   

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6. Are data available?
   Sparks et al. (unpublished)
   No
   Upon request
   Paywalled
   Free
   access
   

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7. Are codes made available?
   Sparks et al. (unpublished)
   No
   Free
   access
   

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8. Software citation?
   Sparks et al. (unpublished)
   No
   Name only
   Version #
   Full citation
   

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9. Software used?
   ?
   Sparks et al. (unpublished)
   

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10. Barriers for open practices?
    - Lack of interest/knowledge (supplemental rarely posted)
    - Low incentive/pressure - that may change!
    - Takes (huge) time and effort
    - Document data and code
    - Versioning code and maintaining
    - FOBS - Fear of being scooped?
    - Not valued/taught in our graduate programs
    

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11. www.openplantpathology.org
    How can we change that?
    

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12. Open Plant Pathology (OPP) fosters
    a diverse community culture that
    values open, transparent and
    reproducible research using shared
    data and reusable software
    Vision and mission
    

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13. By creating a social network
    with a welcoming and sharing
    scientific community
    openplantpathology.slack.com
    Expanding network
    Sharing knowledge
    Brainstorming
    Building capacity
    (Hopefully!) more
    transparent, reproducible,
    efficient and reliable Plant
    Pathology research
    Social Workspace
    1.
    

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14. #general
    #welcome
    #forum
    Outcome-oriented
    #teaching
    #r_package_development
    Subject-matter
    #epidemictheory
    #genomics
    #reproducibility
    Drops us an email to get an invitation to join Slack
    openplantpathology@gmail.com
    How to join?
    Check-in at the member
    directory database
    Join channels Create public/private channels
    1
    2
    5
    4
    Introduce
    yourself !
    3
    Join other channels
    

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15. - join the conversation in #slack;
    - share your ideas!
    - ask a question or provide an answer;
    - propose workshops;
    - collaborate on a paper with others
    After joining
    

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16. to promote the initiative and publish
    community outcomes
    Infrastructure
    Community chat
    Website
    Directory
    Blog Data repository
    Code
    Files
    2.
    

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17. Twitter
    

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18. GitHub
    

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19. Website
    

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20. Member directory
    

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21. OPP Notes: capacity building
    

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22. Year 1 activities
    ICPP2018 - Workshops
    ● Network Analysis in Plant Pathology
    ● Applications of Information Theory in Plant Disease
    Management: Theory and Practice
    ● Introduction to Multivariate Statistics Using R
    ● Population Genomics in R
    useR!2018 July 13, 2018 - Talk
    ● Establishing a community for supporting and
    fostering adoption of reproducible research using R
    IEW12 June 12, 2018 - Talk
    ● Open ideas, data and code sharing: epidemiologists
    should be in front!
    

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23. Planned activities: OPP members
    Workshops
    ● Get Your Research Project Organized, Shareable, and
    Reproducible Using R (Del Ponte)
    ● Introduction to R for Plant Pathologists (Everhart)
    ● Modeling Tools and Techniques Using R (Esker)
    

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24. Data availability
    - AH Sparks, (2019). Compendium of R code and data for 'What’s so Open About
    Plant Pathology?'. Accessed 24 Feb 2019. Online at
    https://doi.org/10.5281/zenodo.2575301
    - https://github.com/openplantpathology/OPP.at.ANU/
    - Sparks, A.H., Del Ponte, E.M., Everhart, S., Foster, Z.S.L., Grünwald, N., (2019).
    Compendium of R code and data for ‘Status and Best Practices for Reproducible
    Research In Plant Pathology’. Accessed 22 Feb 2019. Online at
    https://doi.org/10.5281/zenodo.1250665
    - https://openplantpathology.github.io/Reproducibility_in_Plant_Pathology/
    

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25. OpenPlantPathology
    https://openplantpathology.org/
    @OpenPlantPathology
    OpenPlantPathology
    OpenPlantPathology@gmail.com
    https://speakerdeck.com/adamhsparks/whats-so-open-about-plant-pathology
    

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