Markdown/reStructuredText to write a PhD thesis in STEM fields?

You need to look carefully into your institution's dissertation formatting requirements. I've not gone through the process myself, but have heard of people having to reformat their dissertation after not following the University's specific requirements.

While these can all be addressed through styling, you'll end up doing a lot of this styling yourself. Most people use Word or LaTex because they can start with an existing template from an earlier student, or ones provided by your institution.

The formatting details are tricky enough that some universities provide, for example, weekly free walk-in group sessions - https://gradschool.wsu.edu/pdi/submitting-thesis-dissertatio... . The people who provide the help are more likely to be able to help with Word and LaTeX problems than a less common system.

Look at Thesisdown[0] which is a modified bookdown[1] template for a thesis. It’s based on R Markdown[2], so you get R (or other programming languages) in your document that is run when the document is processed.

The authors of R Markdown/Bookdown are working on a newer tool, Quarto[3].

[0] https://github.com/ismayc/thesisdown [1] https://bookdown.org/ [2] https://rmarkdown.rstudio.com/ [3] https://quarto.org/

I wrote my PhD in TeXmacs: https://www.texmacs.org

Advantages:

- It's the fastest environment for me to type mathematical manuscripts.

- If you are familiar with LaTeX, you can backlash your way in immediately.

- If you are familiar with Word, you can use the dropdowns as you would use the Equation editor.

- The typesetting is great.

- It has great LaTeX export (there are a few things to clean up, but that time is in the single percent digits compared to the time savings).

- It has .bib support for citations.

(Working with exported LaTeX code seems ugly, because of the pretty-printing though)

Disadvantages:

- It crashes. Nowadays much less, but that's still a hassle. Splitting your work in multiple files helps (especially for a PhD-sized document).

- Five years ago, it was difficult for me to figure out how to use macros, customize the layout, so I mostly gave up. If you have to automate a lot of custom type-setting, LaTeX is probably still king. I haven't skimmed through the new book, I would do it if you plan to use TeXmacs: https://www.scypress.com/book_info.html

- Fiddling with bibliography formatting wasn't fun, it is not fun either with LaTeX, but LaTeX often has a StackOverflow answer for you.

I'd give it a try, absolutely. You'll need to decide pretty quickly if you want your workflow to go TeXmacs->LaTeX->PDF or TeXmacs->PDF.

In the first case, you'll process the pain points in LaTeX, but there'll be people around you to help you.

In the second case, you'll have to dig into TeXmacs styles if the default options do not suit you.

I also use TeXmacs to prepare slides, because that's the most efficient workflow I have. Though I have to route my intent around the software limitations, I find it quite worth it.

I use Zettlr (https://www.zettlr.com) for all my academic writing. It's a Markdown editor that also supports Latex and exports to various file formats including Latex PDF using pandoc.

You can add custom Latex templates (https://docs.zettlr.com/de/academic/custom-templates/) and then compile to PDF. I'm also using Zotero as my citation engine that is supported natively by Zettlr.

Can only recommend it.

I wrote my thesis (not PhD) with Pandoc, Zotero, and the Better BibTeX Zotero extension, and found it very enjoyable. Pandoc lets you use Markdown for content and a LaTeX template for styling.

Use Asciidoc. It's better for books and long docs.

I wrote parts of it in markdown and then used pandoc to convert it into LaTeX. I still did the template and all the tricky bits in LaTeX though.

I had a friend that tried to do it entirely in Rmarkdown and it seemed to work well until they had to format it for submission and nearly had a nervous breakdown. It's a stressful time and I'm not sure I'd want that uncertainty.

No, but I would caution you to look at it pragmatically instead: 1. What requirements does you university have for formatting and file formats 2. What format are your advisor and anyone else you want to edit/give feedback on most likely to use.

Back when I was doing this, it only made sense to use Latex because the conferences all had Latex templates, so whenever I had to publish part of my dissertation I could easily copy+paste+adapt the Latex source without having to reformat everything.

In my part of STEM - the S part - no one knows about LaTeX. It's MS Word or bust.

try emacs org-mode... some one did it before.

I use org-mode all the time, I don't even know why it didn't occur to me when writing my PhD dissertation.