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How To Get Organized With Reference Managers for Science – Mendeley

Stylized image of a laptop with drawers extending from the screen to represent the reference manager Mendeley

In this series of posts, we are discussing the features of popular reference managers.  This post covers Mendeley, one of the most established reference managers.  I have a special fondness for Mendeley as it is the software that I used to organize all my literature during my PhD.

Mendeley is a free reference manager program that can be downloaded at www.mendeley.com.  Like all reference managers, Mendeley allows you to generate and organize a library containing your favorite papers and helps generate citations and bibliographies while writing papers. In addition, Mendeley can also do most of the basics required of a reference manager, including subfolder organization and annotating and highlighting PDFs.

My favorite Mendeley feature though is the watched folders feature.  With watched folders, any PDF I download to these folders will automatically be added to my library. I even altered the setting of my browser so that all PDFs are downloaded to my watched folder, rather than opened in the browser window.  This means that my library is constantly and effortlessly maintained.

As I wrote my Thesis in LaTeX, I used BibTeX to insert citations. Mendeley is a great help with this as your whole library can be exported into one BibTeX file. As an added bonus, Mendeley can also sync with the BibTeX file constantly updating with any new PDFs added to your library. You can also export any references into EndNote, although Mendeley does not automatically update EndNote references. For those working with Microsoft Word or Open Office, Mendeley offers plug-ins for easy insertion of citations from your Mendeley library as you write.

Keeping track of your library across different computers is also made simple, as Mendeley supports cloud syncing to its own servers, which you can access through Mendeley.com. You automatically get 1GB free cloud space but be warned, this is easily filled if you have an extensive library. If having access to your library from any computer is of vital importance, Mendeley offers a range of upgrade options including an unlimited personal storage option from £11.99 a month.

Sharing papers with collaborators and co-workers is also made simple with Mendeley. Create a group folder and any notes or annotations, as well as papers, added by group members will be visible to all, meaning that you can share your opinions as well as the articles.

An iPhone and iPad App is available for this software giving you access to your library wherever you are. Sadly, for Android users, there is no official Android Mendeley app. However, several unofficial apps do exist including, Scholarley and Droideley, which are available from the Google Play store.

Mendeley was my first introduction to reference management software and I hope the features I’ve highlighted in this post have enlightened you about the wonders of this software.

And if this post got you excited about organizing your papers, then look out for my next post in this series where I’ll be introducing you to another reference manager – ReadCube.

For more tips on keeping track of the scientific literature, head over to the Bitesize Bio Managing the Scientific Literature Hub.


  1. Matthias on April 30, 2013 at 12:37 pm

    quite interesting is that all the big publishers are starting to invest/get into the Reference managment “business”.

    So – important fact for this:
    Mendeley was recently bought by Elsevier.
    Due to that there is also a “Mendelete” movement. 🙂 – quite a good article about that:
    Or a bit more rough (complaining that elsevier gets the data of scientists and intitutions):

    But Elsevier is not the only one:
    Springer bought mekentos – better known for papers.

    Thomas Reuters is behind EndNote,
    ProQuest behind RefWorks,
    Readcube already partners with Nature and Wiley& Sons,

    So the point in that is not that its bad software – i used mendeley for some time: whom do you want to know about your work? As open access starts to spread you can clearly see by my points above that the big publishers are doing some moves.

    So to complete my list (feel free to add):
    Others hat should be on the list when you search for your favourite reference/literature reader or manager are Utopia Documents (well – its a reader not a manager), Docear, Jabref and Zotero (which is my weapon of choice).

    • 5 to 16 chars on May 3, 2013 at 7:00 am

      Thanks for this post, Matthias. I was not aware that so many of the other programs were backed by publishers. (I use Jabref, so I’m in the clear.)

      I also think this article is oddly-timed to write about Mendeley without mentioning the uproar over the recent buy-out by Elsevier. I think you’ve touched on good points with this comment. As a scientist, open-source is extremely important, not only for ideology, but also full-disclosure of what the program does.

    • Nick Oswald on May 22, 2013 at 10:04 am

      Thanks Matthias – thanks for this — we had this article scheduled for a long time in advance, which is why there was no mention of the buy-out.

      You raise a very pertinent point though..thank you. We’ll put together an article on the buy-outs, and what they mean for users, in the near future.

  2. Kurt Lager on April 30, 2013 at 5:23 am

    It’s good to be able to keep local copies of PDF:s, but I would never do it for articles which I have full access to online. I only do it for articles which I have scanned paper copies of. It’s more important to also be able to attach other types of files to a reference, e.g a text file or a figure cut out from the article and attached as an image. Today many articles also contain extensive supplementary information in various file formats.

    It’s also important where references are imported from. If you import the same reference from different sites e.g. PubMed, the publisher, Google Scholar etc there are usually always some differences, some might miss some information e.g. DOI number or abstract or the format is different, therefore it’s usually best to try and import as many references as possible from the same source, and the most comprehensive source is PubMed.

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