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Delivering and Supporting open science practices through Open Plant Pathology

Delivering and Supporting open science practices through Open Plant Pathology

Presentation on the Open Plant Pathology community for the Queensland APPS Seminar Series

Adam H. Sparks

October 21, 2019
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  1. Adam H. Sparks
    Delivering and
    Supporting
    open science practices through Open 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 (unpublished)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. Are data available?
    Sparks et al. (unpublished)
    No
    Upon request
    Paywalled
    Free access

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 (unpublished)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

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 (unpublished)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

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 (unpublished)

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  9. 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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  10. www.openplantpathology.org
    How can we change that?

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  11. 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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  12. 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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  13. #general
    #welcome
    #forum
    Outcome-oriented
    #teaching
    #r_package_development
    Subject-matter
    #epidemictheory
    #genomics
    #reproducibility
    Visit https://openplantpathology.org and click on:
    “Not part of our Slack? Sign up Here!”
    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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  14. - 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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  15. to promote the initiative and publish
    community outcomes
    Infrastructure
    Community chat
    Website
    Directory
    Blog Data repository
    Code
    Files
    2.

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  16. Member directory

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  17. OPP Notes: capacity building

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  18. R package: hagis

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  19. Reproducibility survey

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  20. Previous 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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  21. Planned activities
    Workshop
    ● “R Markdown for Scientists” (Sparks, Melloy, Tierney,
    Weerarathnee)

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  22. 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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  23. OpenPlantPathology
    https://openplantpathology.org/
    @OpenPlantPath
    OpenPlantPathology
    [email protected]
    hhttps://speakerdeck.com/adamhsparks/delivering-and-supporting-open-scienc
    e-practices-through-open-plant-pathology

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