Academic reading without paper: the BibDesk & Skim duo

Most academics will recognize the problem: how to properly manage the abundance of articles, book chapters, and papers that our work is based on. How do we store them, and more importantly, how do we retrieve them after a while? Personally, I very much like to write on the papers I read, indicating and coding important sections. This generally means printing, while I also want to bring the papers I read along, facing me with the impossibility of lugging hundreds of articles around. So what to do? Some papers I only use for quick reference I don’t print, but those meant for close reading, I did. I’ve always been looking for a method to read digitally while allowing me to take notes.

Until recently, that is. I think that I may have found a good combination of two software packages that allow me to orderly store my loads of articles, and to read and annotate them digitally. Ladies and gentlemen: I present you BibDesk and Skim!


BibDesk is a little piece of software meant for bibliography management focused on the BibTex format. It is thereby specifically focused on integration with LaTeX, but that happens to the way I prefer to write my papers. However, even if you don’t work with LaTeX, it is still suited to work with. It automatically stores files to a given location and shows the bibliographic information in a nice overview. It also allows the user to search in repositories as PubMed and Web of Science, including the ability to download the references to articles of interest. In the sidebar a preview of the article is shown.
I’ve been able to find only a single drawback to BibDesk: it allows the user to create folders and store articles in these folders, thereby keeping your bibliography in an orerly fashion. However, it is not possible to create such folders within folders. Thereby, it is not possible to create a folder for a specific topic or paper you’re presently working on, including some sub-topics.



When it comes to reading the nicely stored papers in BibDesk, it works together in an integrated manner with Skim. Skim allows you to read papers stored in .PDF and, more importantly, to take notes! Just clicking in the text creates a yellow field in which some text can be typed. These fields can be adjusted in size, color, and position. Many more different types of markers are available as well, such as underlining text (just select and click the icon), arrows, and boxes / circles. Also, you can make longer notes which just have an ‘anchor’ in the text which reveal the note when clicked on. Again, these anchors can have a variety of icons. All in all, this allows the user to develop his or her own coding-system. Most interestingly, in the right-sidebar a list of all comments is shown, which can be searched independently of the text. When in full-screen reading mode, this sidebar can be called forward by simply moving the mouse-pointer to the right edge of the screen.

The integration between the storing in BibDesk and the reading in Skim is strong. Skim can easily be called forward from within BibDesk. Both being very light-weight software packages, this works very fast and smoothly. Moreover, the notes you make in Skim can be directly read from within BibDesk. It is also possible to export your notes exclusively, thereby allowing the usage of these notes in other software.

What we thus have here is a system that allows the easy on-screen reading of papers, while taking notes in the actual paper itself. It surely requires some getting used to, but soon it seems to work nicely and speedily. I can surely see how Skim would into my workflow.


Both BibDesk and Skim are freeware and open-source, a software philosophy I gladly adhere to. Designed for MacOSX, they both run perfectly on my operating system of choice. The only drawback is that since both are far ahead of the competition, some compatibility issues might arise. This is especially clear when using Skim: it stores the comments in an ‘additional pocket’ to the actual .PDF files, a feature not yet supported by all file systems. So, for instance, when e-mailing the .PDF or when storing it on an old USB-disk, the comments may be lost. It is however possible to export a .PDF document with the comments stored inside, so that other people still can read your thoughts. But then again, all software has some compatibility issues.

To conclude, I must say that I’m already looking forward to go reading again using BibDesk and Skim. To all mac-based researchers I would like to suggest to give it a try. Please report back your own experiences!

UPDATE: I wrote a how-to on syncing your BibDesk library to your MobileMe iDisk.

6 comment on “Academic reading without paper: the BibDesk & Skim duo

  • Hi, nice writeup. I’m glad BD and Skim fit so well. (I’ve been a developer on both)

    If you want subfolders to keep track of the papers being used for a current article you’re writing, I suggest instead using keywords. You can set the sidebar on the left to show keywords instead of folders, and then organize papers by assigning keywords. I use keywords for permanent organization by categories, like “compilers” and “performance”, and folders to keep track of papers in progress.

    Since a paper can have any number of keywords and be in any number of groups, it works fine (for me) without needing a hierarchy of groups.


  • Dear Michael,

    thanks for the compliment!

    I agree that using keywords to organize papers does help to some extent, but I must say that I would still love to be able to apply some ‘nesting’ to my categories / keywords. On that account I must admit I prefer the way ‘Papers’ handles it. Perhaps some future version will allow it …

  • Great write up! I agree with you, the duo is quite nice! I’ve even taken to reading ebooks in pdf in the full-screen mode in Skim. You can even use BibDesk as a sort of book-case for your ebooks. :)

    Good write-up!

  • Well, thank you! Indeed, even reading complete books becomes a possibility with the increasing quality of both software and computer screens. I sometimes wonder what in a few years I will find myself reading from screen, and what from paper.

    For now, I think there’s nothing better than a beautifully printed book, especially when I want to read it carefully. For reference, I don’t mind digital.

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