Publishing pipeline

This is the sequence of steps that our group follows when completing a scientific project/manuscript.

This is not designed to be onerous, but rather to ensure that we are following best practice in our research, and that we are able to share our research with the broader community. It is also a chance for you to develop broader skills in reproducible science, coding, and the ability to communication clearly to diverse audiences (all of these skills are critical to being able to do science at a high level).

Stage 1: Finalizing the manuscript

  • Finalize the paper and ensure all coauthors are happy for it to be submitted (and discuss potential journals that are appropriate).
  • Code Review: Prepare your code in an open repository on our GitHub organizational site and complete a basic code review (request from another student in the lab who is able to verify the sequence in steps outlined in your code). That is, they should aim to be able to reproduce the outputs from the inputs that you have provided. You may see some prior examples from the group for a template to model.
    • A deeper code review (actually checking for bugs) is best practice, and should be considered where possible.
    • You should submit a GitHub tag (and release with version number) to ensure that the code is snapshotted at the time of submission.
    • You may also submit a Zenodo DOI for the code, which will be archived and provide a citable reference for the code (that can also be used in the manuscript).
    • Zenodo should also be used for any data associated with the project (do not keep data in the GitHub repository).

Stage 2: Submitting to a journal for peer-review

  • Submit the paper to a preprint server (e.g., arXiv, bioRxiv, …).
  • Submit the paper to a journal for peer-review.
  • Once it appears on the preprint server, communicate this with relevant researchers, e.g., on social media (mastodon, X, LinkedIn), and/or via email to any interested people.

Stage 3: Acceptance to a journal

  • After peer-review and acceptance, you should be ready to produce a brief video (around 1-5 min) summarizing for a general audience the problem and main findings of the paper.
    • This could be a minimal and casual description working through the key figures of the paper (in slides of a presentation) on a zoom recording, say.
    • It could also be more creative and refined, if you have the time and interest.
  • You should write a short post about the paper (~1-2 paragraphs) as a blog entry to place on the group’s website.
  • You should update any public posts you’ve made (e.g., on social media) to include a link to the published paper.
  • Consider whether or not to contact the University media department, or whether to pitch an article to be published in The Conversation.