jabref VS zotero-better-bibtex

JabRef might work for you. Website link and GitHub link.

This issue https://github.com/JabRef/jabref/issues/5867 hints at JavaFX issue with the potential workaround of running with the environment variable GDK_DISPLAY=1.

I use JabRef for managing references, which allows you to generate entries via a DOI and saves to a local .bib file.

JabRef

If the town is "online reference managers," you are probably right, but I would argue that reference managers are one of those areas where you really want something offline:

- Offline ensures that you do not suffer an externally caused downtime just before a deadline

- Offline ensures that you have a path for keeping your database throughout your research career, and to do system updates when _you_ want to.

- Offline ensures that if you leave academia, you will always have access to local copies of the academic papers you have referenced.

My favorite offline/local reference manager is `jabRef` [0] which stores all metadata directly in a bibtex-file. The GUI has an excellent pdf-integration, and everything is local and super fast.

Case in point: after a decade in industry, I am looking to get back into my academic fief. All the papers I ever read are in my Dropbox, and all I had to do to pick up where I left was download a current version jabRef and point it to my database which it read without any issues.

[0]: https://www.jabref.org/

I used JabRef throughout my work. It's indeed too late for my PhD work, but Zotero does indeed look very nice.

There a zotero plugin that stores the entire contents of your zotero db as an auto-updated bibtex file too.

https://github.com/retorquere/zotero-better-bibtex

Thanks for sharing these. I already use a number of these on your list. Though I don't use copy-by-link for files. For me one of the key purposes of zotero is that its the place where I keep these files so I don't have to keep them elsewhere where they aren't as easily searchable.

I'm excited to try the duplicates merger tool, I've been forever putting off this because the normal way is such a slog. The Tag one also looks good.

To add to the list, my key add-ons are:

- better bibtex, this one is essential for me as a latex user

- zotfile. This one is cool because if you add annotations to a pdf, like highlighting or comments while you read it, then zotfile will pull those out into notes in the zotero entry. This makes it really easy to see both that I've read this document, and what parts I thought were important.

[1] https://retorque.re/zotero-better-bibtex/)

I was going to suggest that you ask the BBT dev about it as I had no idea why that didn't work, then I saw this bug from 3 days ago: Bug: citekey formula does not update. That might be the issue!

Another problem is that no matter how much I tried, the two available Zotero plugins for Obsidian do not work for me (this https://github.com/mgmeyers/obsidian-zotero-integration and this https://github.com/hans/obsidian-citation-plugin). I am not sure if that is because I'm on Linux, but they just don't work. However, RStudio on Linux works great with Zotero, and I can easily add citations using the Better BibTeX for Zotero plugin (https://github.com/retorquere/zotero-better-bibtex) to create citation keys. That way, I can simply copy/paste the citation key (e.g. '@lastname2020') in the text and have it render into the citation when I render the file in Rstudio. I sometimes write documents with > 300 references, and Zotero running in a Windows VM, trying to refresh a huge word document would take a long time, and would lead to corrupt citations. That's no problem with a markdown/Rmarkdown document.

I have the Better BibTeX plugin in Zotero installed, which keeps ~/Research/refs.bib up-to-date with my entire Zotero library.

P.S. Better BibTeX addon grants even more luxurious experience.

I've been using the Better Bibtex plugin for zotero for a couple months now, and so far it seems to work flawlessly. You can export a .bib file attached to a zotero collection or library and it will automatically update it as you add things to the collection.

I use Zotero with the better bibtex addon. Works great. When I first started using zotero, I imported my existing bibtex library, so all my existing bibtex keys all worked. I use zotero as my library for everything and add bibtex keys to things I cite.

https://retorque.re/zotero-better-bibtex/

Better bibtex