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What's so Open about Plant Pathology?

0da6691d49ce3e26a622158a2160514b?s=47 Adam H. Sparks
February 25, 2019

What's so Open about Plant Pathology?

0da6691d49ce3e26a622158a2160514b?s=128

Adam H. Sparks

February 25, 2019
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  1. Adam H. Sparks What’s so Open about 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 (unpublished)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. Article types Sparks et al. (unpublished)

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 (unpublished) No Upon request

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 (unpublished) No Free

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 (unpublished) No Name only Version

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 (unpublished)

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

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

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

  18. GitHub

  19. Website

  20. Member directory

  21. OPP Notes: capacity building

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