Best Practices for Publishing

Peer reviewed manuscript are one of the major products from our efforts.

In the collaborative writing phase please check with your respective PI for guidance. In many instances Google Docs works well (and works with a popular citation software PaperPile) to create manuscripts paired with GitHub for data analysis. Rstudio (Rmarkdown) also has some advantages.

For any manuscript that includes code there should be a complementary GitHub repository. At publication the repository should be archived with a doi. This can be done with services such as Zenodo or Figshare. Open Science Framework (OSF) can also be used and integrates with GitHub. One advantage of OSF is larger files can be stored.

The code in the repository should be written in a manner where someone else can reproduce analysis that takes data through to figures in a manuscript. All GitHub repositories should contain a README file that contains a "guidebook" for any user to navigate the project code and analyses.

When ready to submit the manuscript for peer review please consider an open-access model. At the time you submit a manuscript for peer-review you can also publish as a pre-print on platforms such as bioRxiv to facilitate open access.

For all products (i.e., papers, code repositories) please acknowledge our funding source. Here is an example:

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To better document, collaborate, share, promote and quantify manuscripts (and related products) please add information to this spreadsheet. We will use our own internal ID system for easy reference.