Emerson M. Del Ponte Adam H. Sparks Open ideas, data and code sharing: epidemiologists should be in front! OpenPlantPathology

Science Collect Analyze Publish Write Simplified research life-cycle Review Summarize Reproduce Re-analyze (meta-analysis) Share data Open repository Share code open/free tools Collaborative tools Citation manager Pre-prints Open Access

Why to 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.

How are we plant pathologists doing? Sparks et al (unpublished)

Article types Sparks et al (unpublished)

Are data available? Sparks et al (unpublished) 0 - Not available 1 - Upon request to authors 2 - Online behind paywall 3 - Free access

Are codes made available? Sparks et al (unpublished) 0 - Not available 1 - Upon request to authors 2 - Online behind paywall 3 - Free archive

Software used? Sparks et al (unpublished)

Software citation? Sparks et al (unpublished) 0 - not mentioned 1 - mentioned by name only 2 - cited with version number 3 - full citation (procs, package, etc)

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

www.openplantpathology.org How can we change that?

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

Epidemiologists in front!

By creating a social network with a welcoming and sharing scientific community openplantpathology.slack.com Expanding network Sharing knowledge Brainstorming Building capacity More transparent, reproducible, efficient and reliable Plant Pathology research Social Workspace 1.

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

Website and Twitter

#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

Member directory

- join the conversation in #slack - share your ideas! - ask a question or provide an answer - write an OPP Note; - propose workshops - collaborate on a paper with others After joining

Collaborative coding: GitHub https://github.com/openplantpathology

OPP Notes: capacity building

Planned activities: OPP members Population Genomics in R Introduction to R for Plant Pathologists Introduction to Multivariate Statistics Using R

Data availability - EM Del Ponte, AH Sparks, (2018). Compendium of R code and data for 'Open ideas, data and code sharing: epidemiologists should be in front!'. Accessed 09 Jun 2018. Online at https://doi.org/10.5281/zenodo.1286101 - https://openplantpathology.github.io/OPP.at.IEW12/ - Sparks, A.H., Del Ponte, E.M., Everhart, S., Foster, Z.S.L., Grünwald, N., (2018). Compendium of R code and data for ‘Status and Best Practices for Reproducible Research In Plant Pathology’. Accessed 08 Jun 2018. Online at https://doi.org/10.5281/zenodo.1250665 - https://openplantpathology.github.io/Reproducibility_in_Plant_Pathology/

Thank you! Help to promote OPP!