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What's so Open about Plant Pathology?

Adam H. Sparks
February 25, 2019

What's so Open about Plant Pathology?

Adam H. Sparks

February 25, 2019

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  1. 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
  2. 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.
  3. 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
  4. 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
  5. 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.
  6. #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 [email protected] 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
  7. - 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
  8. to promote the initiative and publish community outcomes Infrastructure Community

    chat Website Directory Blog Data repository Code Files 2.
  9. 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!
  10. 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)
  11. 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/