Delivering and Supporting open science practices through Open Plant Pathology

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

Transcript

1. Adam H. Sparks
   Delivering and
   Supporting
   open science practices through Open Plant
   Pathology
   

   View Slide

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
   

   View Slide

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.
   

   View Slide

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 (unpublished)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

   View Slide

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 (unpublished)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

   View Slide

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 (unpublished)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

   View Slide

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 (unpublished)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

   View Slide

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 (unpublished)
   

   View Slide

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
   

   View Slide

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

    View Slide

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
    

    View Slide

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.
    

    View Slide

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
    

    View Slide

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
    

    View Slide

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

    View Slide

16. Twitter
    

    View Slide

17. GitHub
    

    View Slide

18. Website
    

    View Slide

19. Member directory
    

    View Slide

20. OPP Notes: capacity building
    

    View Slide

21. R package: hagis
    

    View Slide

22. Reproducibility survey
    

    View Slide

23. 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!
    

    View Slide

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

    View Slide

25. 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/
    

    View Slide

26. OpenPlantPathology
    https://openplantpathology.org/
    @OpenPlantPath
    OpenPlantPathology
    OpenPlantPathology@gmail.com
    hhttps://speakerdeck.com/adamhsparks/delivering-and-supporting-open-scienc
    e-practices-through-open-plant-pathology
    

    View Slide