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# Writing academic papers in Org-Roam
Vincent Conus (he/him) - Pronunciation: vɪnsᵊnt koʊnᵊs, IRC: sunoc, Mastodon: @sunoc@social.linux.pizza, <mailto:vincent.conus@pm.me>
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Org-mode and more so org-roam are making for a fantastic note-taking system
inside Emacs. Combining the note-taking of org-mode, the capability to export
a note to LaTeX and PDF directly, the spectacular org-roam-bibtex package
and the flexibility of the elisp configuration of Emacs, it become possible
to use a org-roam note as the main document for write academic papers, even
when exotic templates are provided.
In this presentation, I want to talk about the way I am using org-roam to write
LaTeX documents, the benefits of it but also the various pitfalls and
difficulties encountered in this journey.
The key benefits being:
- The integration with other org-roam notes.
- Bibliography integration and links directly to PDF.
- Org-mode literate programming capabilities.
- Direct export to PDF.
The main challenges are:
- Dealing with strangely formatted LaTeX templates.
- Related, having to use other LaTeX compilers.
- These two points can make citation of references, in particular, challenging.
About the speaker:
A PhD student in robotics at
Nanzan University, Japan. I have been using Linux for around 10 years at that
point, eventually moving many of my work and personal stuff to Emacs over the
years, including academic writing.
See also:
[[!taglink CategoryOrgMode]]
[[!taglink CategoryRoam]]
# Discussion
## Questions and answers
- Q: how do you convince your coauthors to use emacs?
- (not yet answered)
- Q: I'd be interested how to start this journey of writing academic papers in Org-Roam when not having used Emacs Org-Mode yet? Thanks!
- A: I saw this one before and I guess it would be possible to do that, to use Org documents only as the way that you are writing papers. Maybe you can just use that as a template that you're going to export. If you are familiar with LaTeX, it's going to be more useful, and maybe more convenient to work with inside of Emacs. But then I'm not 100% sure if that's... How do you say that? Maybe, in my opinion, the benefits of using org-roam in that setup is that you can link the things. For me, I'm using the search function for org-roam to just navigate between the files. So that's really some, a good advantage, but like, yeah, that could be, like Leo said in the presentation, that's some, maybe that's something you can start using org-mode with to write papers. So yeah.
- Agreed on opinion of working in org vs LaTeX
- Q: How about connecting Emacs Org-Roam to Zotero? Is that something you have experience with?
- A: You could export your bibliography from Zotero to bibtex.
- Tip: check out the Better Bibtex plugin and its handly \"Keep
updated\" option - I do this selecting biblio.bib file in roam
folder as target
- Q: Out of curiosity, how do you manage your bibliography? Do you do it from inside Emacs, or using a separate program like Zotero?
Because personally, I have struggled to do it from Emacs, although I
have wanted to for sometime. I see, then I am just lazy and don\'t
want to do it by hand -_-
- A: So the way I manage that is I just have a couple of .bib files that I edit by hand, where I put the reference when I find them. And yeah, I just showed very briefly in the presentation, but the way. One of the great thing with the org reference system is that if you have your bibliographic files that are connected to that system, you can just like, you can put the link, the reference to the paper, like click on it from your org note, and then you can open the PDF. You can open the DOI link to open the whatever publisher page. So no, I don't use Zotero and I just edit bib or bib files by hand in Emacs.
- I understand the appeal for having it integrated in the browser. Maybe that's something I should look up, actually, because right now I just like doing it very much by hand, like going on the publisher page and copying the bibtex block and just using putting that in my file. Yes, it can be not a very efficient workflow on that side. But after that, you're having the PDF and having it inside the note.
- Q: How do you start a new document? There are a lot of headers you
have to setup! Do you use a template? I'm curious if they use
yasnippets to deal with all of those latex/org meta commands? (IRC:
gringo)
- A: At present, not using snippets (but considering). Currently
re-uses previous doc as template. There's reconciling template
received from the journal/publisher.
- Q: What do you think of using citar with org-roam-bibtex? It seems
that bibtex-completion is tied to org-roam-bibtex.
- A: Has not explored citar. I am pretty sure org-roam-bibtex
works with citar.
- Q: Most academic journals insist that papers are formatted in their
own custom LaTeX documentclass. Does org-roam make it easy to do
that? (jmd)
- A: No. Makes a custom org latex class, to the import the cls;
then putting the template provided in the headers of the
document, or as needed in the body block. Then there\'s manual
adaption. When using LaTeX, you care much about the output of
the document; each domain/field of research has its own flavour
of expectations.
- Q: Are you using zotra
([https://github.com/mpedramfar/zotra](https://github.com/mpedramfar/zotra))
or org-ref ?
- Never heard of it. That's something I'm going to have to look into.
- Q: How much of this is tied to org-roam specifically?
- Not that much
## Notes
- Presentation org notes formatted for org-present: [https://gitlab.com/sunoc/emacsconf-2024-presentation](https://gitlab.com/sunoc/emacsconf-2024-presentation)
- Thank you for this! I am using org to export my CV, and had to
figure out a few of these things. Lots of new bits for me to
explore.
- Thanks, good presentation.
- Those exports look awesome
- Nice demo, thanks!
- How'd he get that image on the right page? ;-)
- I wonder if work has been done to export an ODT document with citations in zotero's format
- Yeah, that's what I enjoy about citations, It's a sort of universal link.
- I wonder how much LaTeX experience is wrapped up in that export
process
- The problem-solving aspect of tinkering with Emacs is a boon.
- The reference management that Vincent demo'd comes from org
integration. You wouldn't have that functionality with bare
LaTeX/Typst, etc.
- Org to typst converstion:
[https://github.com/jmpunkt/ox-typst](https://github.com/jmpunkt/ox-typst)
- One way I've seen to go about headers is having a template file:
[https://www.youtube.com/watch?v=0qHloGTT8XE](https://www.youtube.com/watch?v=0qHloGTT8XE) that you can import with a "#+SETUPFILE:" line
- Then you just override the document specific stuff right gs-101? In that case a snippet would come in handy
- Yes, for packages not featured in the template I just add them to the file with "#+latex_header:"
- Maybe down the line we can make ties with LLMs to translate styles
- IIRC pandoc also now has tools to do the conversion. I don't know how good that is though.
- It's a good point. I think a lot of people use org mode as their default document editing syntax, so being able to use the same syntax for your papers instead of switching contexts to latex is helpful
- The reference management that Vincent demo'd comes from org integration. You wouldn't have that functionality with bare LaTeX/Typst, etc.
- AFAIK, pandoc converts everything to an intermediate format, so you do lose some information.
- i come from latex originally, before i started trying to do everything from org, so i recognize how powerful latex is. typst is just not there yet at all.
- mainly started learning typst as i orginally started with latex but got overwealmed
- as long as you don't have typesetting software specific code in your org file, sure
- I learned LaTeX just to write good looking math in Org notes lol
- for journals, you usually need appropriate documentclass. That does not require org-roam. Just Org itself
- Thanks Vincent! work in progress
- just got this in mind when reading here about typst ;-) https://xkcd.com/927/
- I also have the video saved in the bibliography, so I can go to the file by just opening the citation link.
- I'll check out Zotra now, seems really interesting. better.
- Thanks for sharing your techniques Vincent!
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