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For anyone who is interested in the different options for reference management, I've been sporadically maintaining a webpage about the various options since 2015: https://maxmasnick.com/projects/reference-managers/

I re-un-recommended Mendeley back in June 2018 when this news first broke. (I was initially too sketched out by Elsevier to recommend Mendeley, and this just confirms these suspicions.)

tl;dr Zotero is a pretty good bet for most people, especially since they added support for citation management in Google Docs at the end of last year (very important for academic writers). PaperPile (https://paperpile.com) and Papers (https://www.papersapp.com) are also worth checking out.




Which one gives the best seamless mobile integration experience? Papers for iOS wasn't bad (if you let it finish syncing with Dropbox ) but curious about this!


Probably Papers is your best bet at this point.

Zotero will let you send PDFs to/from a tablet with the ZotFile (http://zotfile.com) plugin. This works well if your workflow is (1) find PDF on your computer; (2) read on tablet. But if you want to do anything else -- even choosing a PDF to read from your tablet without touching your computer -- then Zotero won't work. With that said, I know Zotero is working on mobile apps...not sure how far they have come though.

If you're Mac/iOS only, also check out https://www.sonnysoftware.com/bookends/bookends.html.


Do you have any experience with bookends?


Yes, it's got some really nice features but it is a little clunky/complex compared to Zotero. I would try out Papers first before looking at Bookends...Bookends can work great, but it does take some work to set up.

Also, Bookends annoyingly checks to see if you are running the same license on multiple devices on your network, and if you have more than once instance running it forces you to close it down. This may seem superficially reasonable, but for someone with both a desktop and a laptop it's quite annoying. I emailed the developer about it and they didn't seem to get why this was a problem.


I'm using Papers 3 right now, and it is fairly buggy. I'm not a fan of switching to a subscription model (especially as I'm not an academic, which makes it too expensive), so I was looking for something else.

I like Zotero, but the lack of an ipad client is annoying. The file plugin requires more forethought than I really like. Bookends having a mobile client was one of the attractive features.

What is the work that it takes to get set up?


Very informative post, thanks. I’d love to hear your impression of Citationsy (closer to CiteThisForMe or RefMe in functionality than Zotero it EndNote).


Never heard of it before!

Looking at their website, it does seem like Citationsy is somewhere in-between a full-blown reference management application and one-off bibliography creation applications.

What Citationsy does not appear to do is manage inline citations within a Word or Google Docs document. Zotero will let you hit a keyboard shortcut, search for a reference, and insert a citation right in a paragraph (e.g. "(Smith, 2001)") . It then takes care of also adding that citation to the bibliography at the bottom of the document, and keeping the numbering in sync (if your citation style uses numbering).

I would only use a reference manager that has a word processor plugin for inline citation management -- and it doesn't look like Citationsy does.

To quickly build a bibliography, or just get a properly formatted citation for a single paper, I like https://zbib.org (also from Zotero).

Edit: clever, clever, parent poster is the creator of Citationsy. Hello! For more backstory on Citationsy see https://blog.prototypr.io/on-citationsy-4e143bbafc04. Sounds like Cenk has good taste (mentions iA Writer as inspiration). I'll be exploring Citationsy more.


Have you looked at Citavi? It's the software many German universities offer. While it's PDF annotation system/knowledge database is awesome (elements of different types linked to locations in the PDF, categorizable and taggable) and the Add-Ins are very fast and bug-free (compared to Zotero), collaboration is cumbersome and its focus on "projects" instead of one overarching "library" is annoying


This is new to me too. Thanks, I'll take a look.


I don’t remember ever visiting your site but it’s great. Thanks!




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