QMCM paper template

This is a template that you can use for your papers.

How to use this template

1. Install quarto

2. Copy this template:

   copier copy gh:dtu-qmcm/qmcm-paper name-of-paper-folder --vcs-ref HEAD

3. Answer the questions.

4. cd name-of-paper-folder

5. Write your paper by editing the file main.md.

6. Render your paper.

   quarto render main.md

Handy links

Copier documentation

How to write your paper

Like most quarto documents, main.md is written in Pandoc flavour Markdown with a YAML front-matter section. See here for instructions on getting started with this format.

By default, the paper stores references in a BibTeX file called bibliography.bib. You can cite entries from that file using their citation key like so:

Kinetic models are great[@st.johnBayesianInferenceMetabolic2018].

You can generate an HTML preview of your paper by running the command quarto preview main.md. This will start a preview server and provide an address you can use to view your paper with your web browser. While the preview server is running, whenever you save main.md you should almost immediately be able to see the results in your browser.

The default output formats, which are created when you run quarto render main.md, are HTML, DOCX (i.e. Microsoft Word) and PDF. The PDF file is created to match the format of PLOS using this template. If you would like to use a different template, there are a lot here. In general they are quite easy to use: just run something like:

> quarto add github-username/template-repo

then follow the instructions and update the format field of the front-matter section in main.md.

If you need to submit to a journal that doesn't have a quarto template yet, you can do surgery on the file main.tex.

Don't forget to make sure that all the authors' ORCID ids and contact details are correct.