www.openplantpathology.org
Valuing openness, transparency and reproducibility
Transparency
OpenPlant
Pathology
Open
science
Reproducibility
Emerson Del Ponte (UFV, Brazil)
Adam Sparks (DPIRD, Australia)
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How it started?
Crazy idea in Jan 2018 by Adam Sparks and Emerson Del Ponte
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Our vision
Open Plant Pathology (OPP) fosters a
diverse community culture that values
openness, transparency and
reproducibility of scientific research
data and methods applied to plant
pathological research and education
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The open science ecosystem
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What/how we did it?
Communication, collaboration and structure
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Communication channels
One-to-one interactions and mass communication
Openplantpathology.slack.com
@openplantpathology@scicom.xyz
www.openplantpathology.org
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Educational resources
Producing and sharing openly education materials
Workshop materials
Slides, video lectures,
datasets, exercises,
reproducible examples
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Collaborative coding
Coding together and developing new open source tools
https://github.com/openplantpathology
- R Packages
(hagis, epifitter)
- Research compendia
(HTML Webpage RStudio project and R Package Templates)
- Interactive databases
(FGSCdb)
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Collaborative coding
Success case 1
https://github.com/openplantpathology/hagis
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Collaborative coding
Success case 2
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Educational resources
Producing and sharing openly education materials
Online book
Made with R
R for Plant Disease
Epidemiology
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Science dissemination (during quarantine)
Scheduling of FREE online scientific talks
Virtual Seminars
Live broadcast + video recording of
scientific seminars in the field of Plant
Pathology. Interaction with the speakers
via live chat and in a Slack channel for 24
h after the talk.
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Reproducibility Editorship
Supporting journals to promote adoption of open practices
Brazilian Phytopathological Society Journal
In 2020, a Reproducibility Team was created to support authors, reviews and
editors to value data and code sharing for review and public release in
permanent repositories
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How open/reproducible
is Plant Pathology?
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Our recent publication
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Sparks et al. (2023)
Survey in 21 plant pathology journals
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Sparks et al. (2023)
No data
Upon request
Paywalled
Free access ~ 10% share
data openly
(most molecular)
How are data/codes shared?
Computational methods
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What efforts are needed
to make the
change?
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Change the mindset and framework
Challenging!
Knowledge
Technology
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Tools
Workflows
Environments
Collaborative
& sharing
platforms
Research Project
Organized
Documented
Shareable
Accessible
Reproducible
Learn new tools and environment
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Fortunately - several open tools are available!
BIB
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Research compendium concept
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Example of shared projects
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A new publishing model
Sparks et al. (2023)
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For group discussion …
1. Why (benefits) embrace open science practices?
2. What are the barriers for adopting open science?
3. What has helped you to make your research
more open?
4. What should OPP/plant pathology community do
to help accelerate the change?