How to write a paper using myst markdown

Abstract

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In this paper we are describing how to write a paper using myst markdown.

Introduction¶

Myst markdown or Curvenote markdown is a tool where you can use markdown and jupyter notebooks together to weave codes, figures, and data to tell a story. You can add a jupyter notebook for generating figures and tables, and use the markdown to write the narrative. As we know writing any academic or scholarly document requires the writer to provide the following structure (this can vary but generally this is true of most structures):

• An Abstract
• An Introduction or the background
• A section on methods etc
• A set of results if that is applicable
• A discussion section
• Tables
• Figures
• Citations throughout the paper
• A list of references at the end of the paper appended to it

The above list in myst markdown can be conveniently converted to a table Let's copy paste and add what we want by way of describing each one.

This list table now becomes table one if you want to refer to it as Table 1 where the name of the table is what you write within a pair of parentheses after a pair of square brackets.

How to add tables¶

• Add tables as list tables
• Convert a list to a table
• Use a markdown table as a list table

Cross-reference a table¶

If you want to cross-reference a table, use [](#table_name). Doing this will produce a highlighted table number that will be automatically updated. Example: As seen in Table 2, this is a thing blah blah.

We can also write a markdown table and then use it as a list table.

In this case Table 3 is a list table

Figures and images can be added¶

I can refer to the image as Figure 1

I could also save this image of the cat to the local folder where I have the paper and then replace the rest of the url with ./, it would have the same effect. Later on in this document I will write how you can intereface a jupyter notebook with all these elements with cross-referencing, but for now pretend we are writing using nothing but markdown syntax.

Citations¶

Citations are important and there are a few ways to insert citations in myst markdown formatted papers. The easiest way is to locate the DOI of the paper say from crossref.org and insert the DOI. Like this [](doi url) will produce something like as follows: a statement by if it is a valid DOI, it will parse the DOI, add a citation and add a reference item when it produces the formatted page.

A second method of producing the same content using the DOI and nothing else is to use doi:10.53731/r294649-6f79289-8cw1c ; this will also produce something similar. In this case start with cite code and then add the doi: doi next to it.

A third method, if you do not have a valid DOI, is to use a bibtex file and then do as follows:

1. First add the bibtex file to the frontmatter
2. Then add the reference to the bibtex file
3. Then source the bibtext file id in the text of the paper

The following citation was posted this way. White has written an article on how to write scholarly documents (White, 2022 ). There are other ways of writing this as well, such as White (2022) has proposed ways of writing scholarly document and so on. The idea here is you put together a bibtex file, add it to the folder where you keep your markdown file and then when you want to cite it, use this syntax of {cite} followed by doi written between backticks. The doi could be raw doi taken off from crossref or from anywhere or you can use the citation id of the citation that you want to add to your paper.