Friday, March 27, 2020

Recommendations needed on reference management software

A wonderful advance of the past decade for academic life (yes, there are some!) has been the availability of software to manage references and all those journal article PDFs that we download (to read later :)).

About ten years ago I started using Papers. It was brilliant. Papers 2 wasn't as good, but still did the job. And, well Papers 3 has become a burden. My version crashes continually and does not seem to have some of the features of Papers 1 that I found useful (e.g. ability to easily email a copy of an article). I am a bit slow and discovered today that it is not me (and my limited tech-savvy) that is the problem but the software itself. Online there are many negative reviews...

So I need to change to another platform. Any suggestions?
Essential requirements for the replacement include the following.

  • runs on a Mac
  • can import all my files from Papers 3 
  • is easy to install and use
Alternatives I am aware of include Mendeley and Bookends
I would particularly like to hear from anyone who has made the transition and any associated problems they have had (and solved easily :)).

7 comments:

  1. +1 for Mendeley
    too long since I switched, don't know what the export/ import game is like these days

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  2. I can recommend Zotero, it was better with the old Firefox, but I am still quite happy. Combined with the plugin `Better BibTeX` it works nicely together with Latex.

    Here you find info, how to port, but I never tried it myself: https://forums.zotero.org/discussion/34363/how-to-migrate-from-papers-3-0-to-zotero

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  3. Years ago I would have recommended Mendeley because I think Zotero was lacking in some essential ease of use features. But, I don't think that's true anymore.


    Unlike Mendeley, Zotero is open source and, most importantly, is not owned by Elsevier.

    For my use the essential features are: must have an offline application, syncing across devices, annotations of PDFs syncing across devices, ease of importing/exporting bib files for use in BibTeX, and allows tagging of keywords for easy searching.

    Zotero does all of that now. Though, the annotation features are not built into Zotero, and instead has to be annotated with an external PDF reader (it still syncs though).

    Here is a comparison list: https://www.library.yorku.ca/web/research-learn/citations/zotero-vs-mendeley-comparison/

    I personally find the 300 MB storage limit for Zotero too small, but upgrading to 2 GB for $20/yr is reasonably cheap. Unlike Mendeley, Zotero also allows you to not sync through the cloud and have everything contained locally on your computer.

    There are also plugins for Zotero, e.g., Zotfile makes annotations of PDFs easier to manage, as well as other things. Zotero also has extensions for web browsers (like Mendeley), including Safari.

    One nice feature that Mendeley has is that every week it sends a summary of papers similar to what you have been reading. Sometimes there are nice paper recommendations there.

    For reference, Papers is now ReadCube (they bought Papers and last year released a merge of ReadCube + Papers) that is supposed to be quite nice. They have a feature where it will recommend papers to you as well. It may be worth looking into if you use OSX. Definitely not open source though!

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  4. Ross, have you come to a conclusion? I have the same problem, except that I never upgraded from Papers2...

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  5. Matt, Sorry for the slow response. I downloaded ReadCube. I think UQ may have a site license since I did not pay anything. Unfortunately, it kept freezing when I transfered my 4,500 PDFs. I had to do it in about 10 runs. But finally I have it all working. It is fine. Seems stable and functional. But it seems pretty basic and does not seem to have some of the features that I liked in Papers 1. I may try something else if I find the time.

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  6. P.S. I was shocked to find I had 4,500 PDFs! I know I do download too many papers. On the other hand, I realised that if you just download one or two a day then it adds up to 4-5 K in ten years!

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