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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


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

    Open Plant Pathology
  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
  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.
  4. How are we plant pathologists doing? Sparks et al. (unpublished)

    101 99 Count
  5. Are data available? Sparks et al. (unpublished) No Upon request

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 (unpublished) No Free

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 (unpublished) No Name only Version

    # Full citation
  8. Software used? ? Sparks et al. (unpublished)

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

  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
  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.
  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
  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
  15. to promote the initiative and publish community outcomes Infrastructure Community

    chat Website Directory Blog Data repository Code Files 2.
  16. Twitter

  17. GitHub

  18. Website

  19. Member directory

  20. OPP Notes: capacity building

  21. R package: hagis

  22. Reproducibility survey

  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!
  24. Planned activities Workshop • “R Markdown for Scientists” (Sparks, Melloy,

    Tierney, Weerarathnee)
  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/
  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