So much of research tends to be a sort of chaotic self-directed learning experience, little nuggets of information coming from many different resources,  sometimes with no way to tie them all together. Our lives today are much improved by utility tools and software that go some way in alleviating this problem. One quintessential tool that we will all use at some point in our graduate studies is a reference management software. I use three. Let me tell you why.

I used some downtime at work (read: while training animals for months and months that disappeared into one another) to look at all the major reference management players. I prepared a chart comparing their various features.

Reference Management Software

Many before me have prepared more exhaustive charts and lists . Reference management systems try to accomplish more than just managing references, so the most important thing to consider before using these helpful charts is which of the many available functions you are likely to use. Ask yourself these helpful questions:

  • Do you work on multiple computers/operating systems?
  • Do you want to pay for one?
  • Do you need it to organize your library and/or citations?
    • What software do you use to write?
  • Do you need to share your now extensively curated library or citations with others?

The major functions can thus be reduced to reference manager, reference searcher, citation manager, and life easy-maker. I regret to inform you that I have yet to find the one software to rule them all, but I have found a system that works. I found that Mendeley takes care of many of these functions the best. It starts with being available as a stand-alone app for many platforms. This is helpful because I have a Windows PC at work, a Macbook for personal use, an Android tablet and an iPhone. I have Mendeley on all of them and can take any of my portable devices on my travels, to lab meetings, or conferences and have my library on hand. It is free, with some extra features for paying users. The free features are entirely sufficient for my personal use and allow me to have a shared folder with two lab colleagues. Mendeley has a browser bookmarklet that allows me to save PDFs directly to Mendeley’s free 2GB web storage option or my unlimited device storage. I ask it to kindly rename my PDF files when it stores them so that they all look neat and tidy and not ‘sss9320495-4jfkmd-fk-off.pdf’. I use Microsoft Word to do most of my writing, but Mendeley offers support for Open Office and LaTex and where it does not, it offers flexible ways to add citations in a few clicks. Mendeley has a web version as well, where you can search for papers in other members’ libraries and follow other members to get your social media fix. It does not quite hit the spot with free features for collaborations, but this is precisely how they draw in entire labs to pay for the premium features. Mendeley has a decent PDF viewer that allows you to annotate and star while reading. You can search for words, authors, titles, and journals to find the papers you want. It also has a superb indexing system, can extract meta data, finds duplicates to clear, and offers a vast library of citation styles you can personalize or edit.

Another program named Zotero is very similar to Mendeley in all these features (although it only offers 300MB of free web storage) and is open source. I cannot speak for the stability of the standalone app as I have not used it for an extended time but I hear good things. If Mendeley, which has recently been acquired by Elsevier, goes over to the dark side and makes everything premium moving to Zotero would be an almost seamless switch. I did not start with Zotero as they did not have a standalone app at the time I started using reference management software, but they have come a long way since then.

Features I didn’t know I missed in Mendeley, I found in Readcube. If you’ve read a Nature paper, you have at least seen this combination of letters in this context. Nature, and more recently other journals, offer the Readcube PDF viewer, which is the winning feature of this system. Readcube is now a full-fledged reference management software available as a standalone application with beta features being developed as I write this. The PDF viewer has inline references and an automatic supplemental information download. My PDF reading experience has been vastly improved. Now, while reading a paper, I know which article is citation number 30 by letting my mouse hover over it. I also don’t have to find the buried supplementary files on the journal websites; instead, I just click on the ‘Enhance’ button. Readcube is, quite simply, beautiful. Another feature I have advertised regularly is the ‘Recommendations’ feature, which allows Readcube to look through your library and find you relevant literature you may have missed. It has such an impressive algorithm that it beats Pubmed, ScienceDirect and feedly hands down. It has a wonderful citation editor and plugs into Word flawlessly. Its Pro version, however, does not come cheap and offers a lot of the features that Mendeley does for free, like syncing across multiple devices or watching a folder for automatic imports. The way I get around this is by using my third system.

Dropbox. Dropbox is where I store my references. I do a minimum amount of Dropbox gardening by putting all my PDFs in a folder there and asking Mendeley to watch this folder. I also do semi-regular imports on Readcube from the same folder, which Mendeley has helped me keep tidy and organised. Readcube helpfully adds supplemental materials to this folder and Mendeley renames them. Readcube helps me read them and sometimes download more related papers to the same folder. Dropbox makes sure Mendeley watches them on all my devices and so the trapeze act continues. I still continue to check on updates and new software (currently frowning at Paperpile and Flow) because I’ll jump ship the minute something better comes around. That’s how I convince myself I’m still young. Either way, it’s a helpful world out there and you really don’t have to use Endnote.

Pooja Viswanathan is a graduate student at the Institute of Neurobiology and the Graduate Training Centre for Neuroscience in Tübingen, Germany.


sarahaenzi · 18th January 2016 at 2:33 pm

Hey Pooja, thanks for sharing:-) I have been using Mendeley, but was also tempted by ReadCube’s pdf reader… but never got started because I didn’t know how to combine the two. So I was wondering whether you could give a bit more detail of how you integrate the two (/three)?
-What do you allow Mendeley sync to synchronise?
-do you have ReadCube pro? if yes, again, what do you sync?
-It sounds as if you use ReadCube to find new literature – which you then save in a folder which Mendeley watches, is that correct?
-do you also google for new literature? if yes, what is your workflow for that?
-which of the two do you use when you write? or in other words, do you regard one of the two as the ‘master’ where everything comes together?

    majorpooper · 18th January 2016 at 4:17 pm

    Hey Sara!
    1) Mendeley sync uploads all the files to Mendeley Cloud (free 2GB) with the synchronize function and thus allows you to access your library from all devices. If you were to go above that limit, I would suggest using Dropbox to house your library so that even if you don’t have the file on the Mendeley cloud, you can access it through the Dropbox cloud.
    2) I don’t have Readcube Pro but did get to try it out for a few months thanks to an SFN offer. Now, I only have Readcube free and import my library periodically from the same Dropbox folder which Mendeley uses.
    3) I use the Readcube ‘Recommendations’ feature and the ‘Enhance’ feature to download new literature. It does also have integrated PubMed search, which Mendeley still doesn’t but I don’t tend to use that much. To download new literature, I use the Mendeley browser bookmarklet most often.
    Note: both Readcube and Mendeley use the same folder for these downloads, which is housed within my Dropbox.
    4) Do you mean Google Scholar? I also use the Mendeley browser bookmarklet to save new literature I find. It works on every website with a link to PDF.
    5) I have used both to add citations when writing but find Mendeley to be more equipped at the moment.
    Hope this is helpful!

      sarahaenzi · 21st January 2016 at 5:51 pm

      hey, cool thanks:-) a few more detailed questions though: when you import into readcube, do you import pdfs or citations? do you have a ‘watched folder’ in Mendeley? I am asking the second question because I am not sure whether I should put the watched folder or the Mendeley ‘output’ folder on Dropbox… thanks!

        majorpooper · 21st January 2016 at 6:13 pm

        Readcube, I import the whole Dropbox folder that I call ‘References’. It is also my watched folder on Mendeley, my download folder on Readcube and my Mendeley output folder (which Mendeley routinely checks with me about doing).

Torben · 19th January 2016 at 3:50 pm

I also use Mendeley to manage my references on several devices. To keep track of new stuff, however, I use mostly RSS via feedly (eg TOCs of journals and keyword RSS from pubmed). How do you keep track of new literature? I mean except for the recommendation/enhance feature that you mentioned, which I guess is not enough?

I didn’t find a way that worked for me with Readcube. Maybe I missed something, but that’s why Readcube wasn’t really interesting for me so far. Or I need at least 3 pieces of software, Mendeley for managing, feedly for keeping up with literature, and Readcube for reading only 😀

What I like about the feedly/Mendeley combo is that I can import new literature I found in the RSS/eTOCs at my feedly in chrome with one (or two, technically) clicks to Mendeley by using a nice script I found here: and then manage/read in Mendeley

    majorpooper · 20th January 2016 at 8:01 pm

    Cool! Thanks for the feedly-Mendeley tip, Torben!
    I have to admit I have no super system to look at new literature. I use eAlerts for major journals and journals I like, Pubmed alerts for keywords and labs, feedly, and Readcube ‘Recommended’ (Mendeley JUST launched a similar feature). I also follow popular science magazines and websites on Facebook and check Scientific American, New Scientist at a regular frequency. People (mainly Scott) tell me I should get on reddit but I haven’t yet. Also, another friend recommended Utopia ( to me two days ago and I’m just starting to check it out.

    sarahaenzi · 21st January 2016 at 5:52 pm

    Hey Torben 🙂
    For keeping up with literature, I do the old-fashioned getting eTOCs to my inbox… which I then wade through from time to time. What I found useful as well is following ‘interesting’ people on ResearchGate, which then tells me when they add new publications. (I don’t think googlescholar profiles have this feature, but am not quite sure)

Anonymous · 3rd May 2017 at 11:47 am

how can I use mendeley for citation?

majorpooper · 6th July 2018 at 5:09 pm

Update: Mendeley has made an awful move to encrypt their database with version 1.19, thus making a move to open-source platforms like Zotero that much harder.
Zotero offers possible solutions, the first of which is to avoid updating to version 1.19, so if you can, please cancel that update.

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