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re: I've been using Emacs for a long time, but only recently began to use org-mode, and I plan to write my biology thesis in it with org-ref. Do you ...

Will you be using LaTeX? I would advise that you invest in making LaTeX work rather than worrying about Org. That said, I didn't really invest in Emacs and Org until after graduate school, so I've never used them for writing papers or theses.

My only advice is that writing a thesis is hard enough already, don't try to wedge your workflow into using org just for the sake of using org. I know that org is particularly good at organizing (and re-organizing) documents, which would be helpful in the theses writing process... I'm just not sure how it all fits together.

Now if you're using org-ref as a stand alone (while writing your document in LaTeX) that may work. Bibtex is hard to get right so any tool that helps there is good.

I'm happy to chat more about writing theses and/or using LaTeX, just let me know!


Thank you, it is a great help.

My case is a bit tricky, because of the regulations of the biology faculty, the thesis must be provided in ".docx" :( . However, I am so comfortable with Emacs, since I use it every day to work, and so alien to any kind of office app, that writing my thesis in org mode, then formatting it in some office app on completion will be more efficient than using an office app from the beginning. It will also have some code in it, so I can use babel to make it reproductible. However, during the org-mode phase it would be nice to export it to .pdf, and when all is finished I will able to publish it to GitHub.

I use org-latex-export-to-pdf, and you as you said it gave me a hard time with a 'undefined citation' error, it has a strange solution: one should use texi2dvi as a .pdf exporter:

(setq org-latex-pdf-process (list "texi2dvi -p -b -V %f"))

then it works perfectly with one call.

I export the .bib file from Zotero.

and you are totally right I should not overkill this one, since this will be my first thesis.

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