Peer reviewed teaching notes and research resources
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OPP Notes

Open Plant Pathology accepts content to be posted to the website,, that provide examples of teaching materials, reproducible research and other materials of interest to plant pathologists. To help ensure the quality of these materials, we ask that they be peer-reviewed by qualified members of the Open Plant Pathology community.

Instructions for Use

  1. If you wish to inquire about the fit of your note first, you may open an Issue in openplantpathology/opp_notes for discussion with the OPP community. If the note is a good fit proceed to step two. Else you may start at step 2 if you wish, there is no need to first ask.

  2. Fork this repository to your own GitHub account.

  3. Rename the new_contribution folder to the first author's last name. See previous notes as examples.

  4. In the subdirectory, "1" - your first note, if there are more we increment and the second will just be placed in a subdirectory "2" - you will find five files:

    • bibliography.bib - This will hold any references you use in your note in BibTeX format. To get an easily formatted BibTeX entry, use Google Scholar to search for the article and copy the BibTeX citation from there using the "cite"" function (double quotes under the search result) or export from Mendeley or other reference managers. Insert the references in this file and when the index.Rmd is knit, it will automatically include them.

    • index.Rmd - This is the file that you will write the article in. If you are not familiar with using RMarkdown see and the cheatsheet

    • LICENSE - License file, should not be changed.

    • phytopathology.csl - Citation style used to style the citations and references in the Phytopathology format. Does not need to be changed.

    • - Update this file to introduce the note. See an example here, sparks/1/

  5. Write your note and generate a DOI using Zenodo and insert the badge in the README and index.Rmd. See sparks/1/ and sparks/1/index.Rmd for examples.

  6. Once you've completed writing your note, either open an Issue asking for peer or post in the initial Issue from step 1. emdelponte or adamhsparks will assign reviewers for your note.

  7. Once your note has been accepted, create a new release to update the DOI, and open a pull request at We will merge your repository into the OPP Notes Repository and update the OPP webpage with your new note!