This submission template is for a markdown-based publication with additional supporting notebook and markdown files, as well as supporting data, bibliography, and MyST build configuration.

The primary source file for this template is a MyST markdown article. This file may reference notebook cells from other sub-articles to use the output of these cells as figures. It may also reference content from other markdown sub-articles. All of these supplementary source notebooks/articles should be saved in the notebooks/ folder. It also contains MyST blocks tagged in their metadata as "part": "abstract", or "part": "availability" - these cells will be extracted from the document and included as the specified part in the built output.

By convention, all data should be saved in data/ directory. There is nothing magic about this directory; references to your data from your notebook must still specify the correct relative path.

Similar to the data/ directory, images for figures should be specified in images/ directory.

Bibliography entries may be specified two ways, both described in the MyST docs. They may be listed explicitly in BibTeX format, by convention in the file references.bib, and referenced by key using a cite MyST role. They may also be specified as inline DOI links. These do not require full bibliographic information; the data is fetched implicitly on build from the DOI.

A myst.yml file must be provided to configure notebook metadata and exports. This includes authors, affiliations, licenses, keywords, and much more.

To build PDF/JATS output from your source data, you must have the MyST Markdown CLI installed

npm install -g mystmd

Then build all exports defined in the myst.yml file:

myst build --all