Referencing Software

Ooh, Bookends looks interesting, thanks for the link! I use Papers, but it’s rather crash-prone in recent times. Bookends looks like it has all the features I’ve come to rely on, and imports from Papers libraries…

In significant chunks of the academic world — especially those sympathetic toward the idea of open access — Elsevier are thought of as bad actors, and highly predatory (excessive journal costs, plus excessive profit margins).

There’s a really lengthy blog post on it here. Thousands of researchers have pledged to boycott Elsevier at The Cost of Knowledge, and Science published a post with more information here.

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Just a little plug for Bookends again.

This thread over at the Bookends forum, sees a user make reference on 1 July 2018 to a very useful Alfred worklfow that was developed by a fellow-user. By 7 July 2018, the developer invites users to sign up to test a modified version of the workflow, now being built-in to Bookends…

Don’t think there are many referencing products out there that could see something similar happening, never mind at this speed!

I used BibDesk for all of this, not sure if it links well into word but works realy well if your using latex! My uni were able to give my a bibtec stylefile so i knew 100% my reference style would comply (very useful when ones thesis has over 300 references)

Hi, new here and given the topic thought I’d post. I’m a UK academic who publishes quite a bit. I almost exclusively use Zotero.

Endnote is a dreadful piece of software, particularly on the Mac (they took a year to have a version that worked with office 365). The MAC app feels like an afterthought and you can’t share full PDFs

Papers is good but doesnt offer me anything over Zotero.

Zotero is free (paid for larger shared libraries) but the sharing is one of the best things about it. I’ve published multiple systematic reviews with my postgrads (who may be in another country) but with the whole shebang managed via Zotero. If my post grad highlights a pdf I see the highlight instantly.

The word integration is awesome, with keyboard shortcuts to bring up the picker making citation entry really fast (triple tab and space to enter just the date).

Sorry if this sounds like a fan! I’m not affiliated at all but it’s one piece of software I genuinely cannot do without. When you have to reformat citations and references to meet differences journal requirements it’s invaluable.

Oh, hi all… :slight_smile:


Thanks for this perspective. I’m also a UK academic and therefore especially interested in your ideas. I use Papers and generally like it, but interested in alternative approaches.

What do you do with Zotero on a phone or iPad?

Used to use Endnote, but even in its current versions it always feels like a Mac afterthought to me. I still recommend it to students because its free at our Uni. I have used Papers since 1.0, which initially was a pdf organiser but couldn’t cite. I moved to Sente then, it worked well but the sync was awful. It died in 2016 so I moved back to Papers. Papers 3 is a fully functional citation manager with cross device sync, and I like the fact that the developers are/were research students themselves.

.@philmor’s question is a good one. What are people doing for reference management on iOS?
There’s an app called Papership that works with both Mendeley and Zotero. I’ve used it a little with Zotero, but not enough to have a useful opinion about it. Mendeley has its own iOS app, but it’s nothing to get excited about.

I use Bookends on macOS primarily. They also have an iOS app that has most of the desktop functionality.
I highlight and make notes in PDF Expert, export annotations to Markdown, then paste in the Notes field in Bookends. At that point I can condense them into meaningful notes.
Bookends has a pretty cool feature called Autocomplete Paper. If you drop in a pdf, it looks for refs online. If it can’t find it, you can click Autocomplete and it opens a window where you can search Google Scholar and other sources for the metadata for the paper. So it’s not so much Autocomplete, but I guess ‘click here to find the metadata for this paper’ was too long for the menu item.

For context, I have about 1500 Papers in my library, and am working on my PhD in Applied Physiology (essentially the motor control, neuroscience aspects).

Bookends has just released a major update, with a “Floating Citations” window workflow.

This was originally inspired by one of the BE users developing a very useful Alfred workflow, and is making for a very useful addition. Figured I would pop this up here, since I’m also curious to hear if other Reference Managers offer something similar?

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I think I first saw that in Papers3.
Just tried to check their website, but their site seems mostly broken, save for the landing pages.

They (Papers) are preparing for a major relaunch, I think in the next few weeks.

I’ve done the same thing for BibDesk with an Alfred snippet that calls a BibDesk script filter .

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I was also looking for a suitable reference manager for my Bachelor thesis but was only partially successful.

I tried Mendeley for an essay we wrote as a group (the collaboration features sounded useful to us) but I was disappointed by its capability to produce an accurate literature list. Somehow, even though I‘m pretty sure that my settings were correct, the style did not match the guidelines. But, more importantly, when importing sources, it seemed that Mendeley could not process all information and left some fields blank (which also lead to problems in the literature list).

I then downloaded the free Endnote trial because it is the only reference manager I know that integrates with Pages. Unfortunately, it crashed about 80% of the time I opened it. I couldn‘t figure out why this happened and since Endnote is really expensive, I did not want to spend the money.

In the end, I settled for Citavi, which is only available for Windows. I run it in Parallels which is fine but not really ideal. But the app itself workes great - I never had problems with information missing or literature lists not being accure. And that‘s the most important thing, after all.

Late to the party here.

I use Mendeley to collaborate with my research group. I appreciate that it provides a way to share publications for free. Some of my research group also use Windows, and Mendeley is cross-platform. I agree with @rgilmour … the Mendeley iOS app is nothing exciting.

I use Papers3 to maintain all of my citations. I do not share anything from Papers3 directly on its cloud. My library is too large. I am exploring the options to export collections to Dropbox, annotate from my iPad in PDFExpert, and re-import. Why not just use Papers3 annotation tools? Because my library is too big to sync with my iPad and because I know and like the annotation tools in PDFExpert. How far this will go is yet to be determined (it is a work in progress).

I use BibDesk to manage the BibTex files that are merged with my LaTeX documents. I generate the BibTex files directly from Papers3.

I took a brief look at Bookends. The ability of Papers3 to find comparable citations to a given article far surpassed what was possible in Bookends. I also have high hopes for the Papers3 -> Papers/Readcube transition as a way to replace Mendeley to collaborate with my research group.

I took a brief look at ReadCube. I am in the physical sciences, not the medical science. ReadCube does the latter well, whereas Papers3 does the former well.

Endnote was just too expensive and too ugly for my tastes. As noted by @Coulmac, Endnote on a Mac is an afterthought.

I tried Zotero once some time ago.It does not allow me to find similar reference articles as with Papers3. I may try Zotero again just to see what is new.

In the end, I recommend that you find one citation manage that you understand and stay with it. Nothing is perfect and you can spend forever trying to find something better rather than just doing your work.

And Word for an MS Thesis? Dare I say UGH! But that is a whole topic to itself.


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Same here. Could you see DevonThink somewhere in there?


I am using DTPro to compile a list of documents from over three decades of teaching a certain topic at undergrad and grad levels. The documents are lecture notes, exams, homework, study guides, and study problems. They are mostly in tex and pdf format. The goal is to assemble the content into a textbook.

For various reasons, I do not see that I will ever bring DTPro into my workflow to process my journal articles. To make a long story short, I am rather unconvinced at this stage in my career that I would see a significant enough net positive return on the investment in time that I will need to figure out how to integrate DTPro and concurrently that I would avoid being constantly frustrated by what I see as the general cumbersomeness in using DTPro (and that was the short answer to your question :slight_smile:).


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My recommendation for those using LaTeX is to collect references with Zotero. They can then be exported with the bibTeX format, which is the easiest way to include references in a LaTeX document.

I’ve been doing the same in Scrivener, also for a textbook project.