Scientific writing in JupyterLab with MyST Markdown

MyST Markdown provides an extended Markdown syntax and toolchain for technical, scientific communications and publication (see mystmd.org/).
MyST makes it possible to write preprints, articles, papers, technical reports and even a thesis directly in markdown files and Jupyter notebooks with first class support for the things you'd expect from authoring in LaTeX; citations, reference management, equations, figures and tables with captions, numbering, cross referencing and more.
MyST Markdown is now available directly inside JupyterLab via an extension, allowing you bring your authoring work into your research environment and can be used alongside the MyST command line tools to produce PDFs or LaTeX outputs on demand, in a growing number of templates as well as creating interactive websites that can connect to computing resources via Binder or JupyterLite.
In this webinar, we'll focus on writing a paper in JupyterLab using the jupyterlab-myst extension, and taking this through to producing a submission ready PDF, as well as creating and publishing a supporting interactive website, all from the same body of markdown documents and notebooks.
During the webinar you'll learn about:
* Installing and getting started with the MyST JupyterLab extension
* How to write a paper in a Jupyter Notebook
* Key authoring features from "frontmatter" through equation numbering and citations
* Using interactive MyST features including inline execution and ipywidgets integration in markdown
* Using markdown files to create manuscripts linked to notebooks
* Creating PDF outputs using a journal template
* Building an interactive website from your publication and deploying this to the web
By the end of the webinar, you'll know setup JupyterLab with MyST, and how to start using the authoring and reproducible communication possibilities it opens up in your own work.

[@macleanarthur2058]

This is really great! Good job guys

[@rowancockett]

Thank you so much! Glad it is helpful. :)

[@macleanarthur2058]

@@rowancockettI tried to install via mamba by using “mamba install jupyter_myst” and it didn’t work :(

[@macleanarthur2058]

@@rowancockettI tried to install via mamba using “mamba install jupyter_myst” but it didn’t work :(

[@shivayshakti6575]

lovely thanks, how does it compare to quarto pandoc in terms of features and extensions and which one would you recommend for python tutoring use case?

[@kisho2679]

how can mathematical commutative diagrams be drawn?

[@curvenote]

You can use LaTeX in a math directive.

[@kisho2679]

Can JupyterLab implent a same content code snippet as reference/include input in different other documents - like as LaTex can call separate/external txt files to include in one document?

[@curvenote]

Yes it is possible to do this in a very similar way, you can include content: mystmd.org/guide/directives#directive-include As well as reuse specific parts of a document/notebook: mystmd.org/guide/reuse-jupyter-outputs

[@kisho2679]

Doesnt work yet

[@TheMlg556]

nice! using the jupyterlab extension with great success, and loving the inline execution. a question, how would I go about exporting the ipynb file to a nicely formatted pdf like you show here? I know that for jupyter tools such as nbconvert exist, but do they integrate with myst?

[@curvenote]

You can use the mystmd CLI, at mystmd.org.

[@dmnas_]

I've finally got this working in JupyterLab and I am loving it. One question I have, when exporting to PDF, is there a way to force tables and figures to appear in certain places, such as the behaviour in LaTeX when [H] is added to a figure?

[@curvenote]

We are tracking this improvement here: github.com/executablebooks/mystmd/issues/779

[@mathiaz943]

I have installed some time ago with `npm install -g myst-cli`. Will this work or is it a different tool?

[@curvenote]

See issue here: github.com/executablebooks/mystmd/issues/451 We renamed the CLI, and you will also need `pip install jupyterlab_myst` for the jupyter plugin! npm uninstall -g myst-cli npm install -g mystmd

[@kisho2679]

When use Streamlit instead Dash with Python?

[@curvenote]

Those tools are more built for dashboards, curvenote and myst are better when the main content and output is more of a document or article that wants to include some of those features. You can of course also include embedded apps if you want as well that are, e.g. hosted by streamlit.