Contributed by: Jos Franssen (UB)
After having installed the free Mendeley Desktop application (http://www.mendeley.com) next to my rather old EndnoteX2 version, which the library is still supporting because of technical reasons, I was really happy that these two reference manager tools did not conflict with each other. Next, I installed Mendeley’s Word plug-in and the Web Importer tool. The latter lets you import references and documents from a wide range of academic databases with a single click, and you can save a snapshot of any webpage you are viewing. 
When I started playing around, I was really baffled by the way how PDFs, already saved on my computer, can be imported into the library by simply ‘dragging and dropping’ the file. I was even more baffled how Mendeley extracted the metadata from PDFs to create the citation details for the library record. This sophisticated feature really saves a lot of time. Another feature I like is the build-in PDF viewer which allows annotation and highlighting in PDFs. It is even possible to search your imported PDF files, full text. With the advanced collaboration options in private, public, and social network groups you are able to share these annotated documents and your collected references with peers of your choice. Besides, with uploading to the ‘cloud’, access to the library is enabled on any computer with an internet connection.
So far, I have only noticed a couple of drawbacks in Mendeley. Endnote tackles citation styles with journal title abbreviations by means of journal term lists. This works perfectly if you know how to use these. However, in Mendeley you have to create these lists yourself. First you need to create an extra ‘default.txt’ file in Mendeley’s Data Directory. Next, you will have to create a .txt-file in which for each line the full journal name (case sensitive) is followed by a TAB character, followed by the associated journal abbreviation. Another drawback is that Mendeley does not support bulk-downloads directly, as Endnote does. Importing references from Pubmed using Mendeley’s Web Importer tool only worked one by one. Selecting more references in the database and bulk importing these into Mendeley, did not work. A work around is to export an Endnote library in “XML” type and “RIS” as output style, and to import this file including the associated PDF’s in Endnote, into Mendeley with a few clicks.
In a practical way this means I will be using EndnoteX2 next to Mendeley: Mendeley when I want to collaborate and need to work on different computers and Endnote for the bulk-downloads and the more sophisticated possibilities of using and editing citation styles. Endnote’s X4 and X5 releases incorporate a lot of features I like in Mendeley, such as annotation and highlighting in PDFs and the PDF full text search capabilities. Endnote X4 already supports automated data extraction of PDFs and Endnote X5 incorporates some nice additional features which makes its use even more compelling (see http://www.endnote.com/m/video/download/x5/Whats_New-ENX5.wmv). Also the switch between EndnoteX5 and EndnoteWeb, and synchronizing the libraries including the annotated PDF’s is made quite easy. So collaborating using EndnoteWeb becomes a feasible option again and not as cumbersome as it is in combination with EndnoteX2.
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Mendeley made my life easier as Endnote did not run smoothly on my mac. What I like most of it, is to be able to work on one collection of references for an article. It makes it easier to collaborate with others.