Invest in a good manuscript (PDF) management system

If, as starting graduate students, you are following my first key advice of reading on a regular basis scientific manuscripts related to your field of research in general and your project in particular, you’ve probably reach an obvious observation:  you are collecting a large number of PDF files very quickly.

There are, of course, a few more observations to be made:

  • Simply filing these PDF in folders is not very useful. Face it, you will have to use some (most?) of the references for your own papers that you will be writing.
  • Manually entering each manuscript information (title, authors, abstract, journal, pages, …) in a database is highly inefficient and not a very good use of time.
  • Your PDF contents is not indexed by default i.e. you can not search by key words within your documents by default.

So action must be taken; Invest in a good manuscript management system!

Myself, I have abandon the use of a citation only software a few years ago and instead opted for PDF management software. Yes their first application is to work with scientific manuscript you get online. But now most will also allow you to:

  • Grab a reference directly from a website (PubMed, Google, Amazon, …)
  • If a PDF file is involved, it will also be transferred directly to your PDF library
  • Extract the information from the metadata automatically
  • Match a document to a repository (again PubMed, Scorpus, Google, …) and filled out much more information automatically into the software database.
  • Handle also books, patents, abstracts, presentation documents and more.
  • Allow you to use this information for direct building of your reference section in WORD, PAGE, OpenOffice, LaTeX (through BibTex export) and others.

The most advanced ones, will also allow you to read, annotate, comment, rank, tag each of your manuscript, have a perfect sync with your smartphone or tablet and even  read and comments directly on your iPad and sync back with your main library afterward!. In this category, you will find Papers (Mac and Windows) and Sente (Mac). An excellent review can be found in the book Organizing Creativity (see here)

This bring another observation: At this stage of my career, time is becoming constraint and therefore expensive. Thus I do not mind investing 80$ for a state-of-the-art Mac/iPad software combination that I do not need to maintain. However, for graduate students, money is often hard to come by while time is “abundant” and cheap (at least until the last stretch before the thesis defense 😉 ).

Solution: the free Zotero software. I say free if you use it as is, without the offered cloud syncing (the annual fee alone is such that in that case, simply by one of the better app mentioned above).

I have used Zotero for over 6 months in my transition for the older Endnote and the newer Sente/Paper. It use to be only working as a plug-in for Firefox browser. Nowadays you can use Firefox, Chrome or Safari. Furthermore, Zotero now has a standalone application (displayed below)!

From the browser, you can:

  • Grab references from the PubMed website or other website directly into your Zotero database.
  • Attach PDF files to a reference entry
  • Drop PDF file and have the metadata scan to make a citable entry.
  • Index your PDF (for future search)
  • Have other file types in your database, including web pages.

An example from the PubMed website is given below (click on the figure below to get a full resolution version)

Note that support of file types, in particular for indexing anything else than PDF or RTF, is nothing like DevonThink in my experience (but DT is not free either…)

Zotero, also come with modules that allow you to tap in your database for citation when writing your own documents in various word processors and even e-mails. It also has modules for BibTex export, link to Drupal and so on. Zotero support Citation Style Language and thus any journals citation format can be built (if it does not already exist)

The complete database structure is accessible, you can even chose when you want it to reside (preference) and can be easily backed-up.

Bottom line, you have no reason to handle manuscripts and building your citation lists manually. Get a free copy of Zotero and welcome to the 21st century!


  1. Great review! I bought Papers2 this spring (and loved it), only to find that my university’s librarians were really pushing Zotero. Then I found Sente, and just could not find reviews from anyone who had actually tried all 3.

    Quick question: while your post suggests that this issue has been solved, have you experienced problems recently with annotations being lost in Papers when documents are annotated both on a computer and on an iPad/iPhone? I was excited to purchase the Papers iPad app this spring, only to see many reviewer complaints about documents stripped of annotations when opened in the iPad app!

    Finally, I wanted to share that, in my PDF annotation iPad app search, I found that GoodReader and iAnnotate seemed equally beloved for annotation ease and efficacy.


    1. Sorry, forgot to note that the GoodReader/iAnnotate recommendations were for annotator/reader use with the ZotPad app.


    1. I looked at it sometimes ago. Vey nice interface and you can now use their “online” services up to 1Gb. This is enough to get you going for a few years, depending on your reading habit. However, at some point you will break that 1Gb easily. If you can live without it, then fine. Otherwise, Zotero is also free and you can have your library on DropBox (and not using their online services).

      I really like Papers 2 implementation of citations everywhere (with hitting twice the ctrl key). Zotero might be better at extracting information from webpage though. Papers (and Sente) iPad edition is superb. With Papers now available on Windows, it is a close match-up between all of these PDF management systems. If one works for you and is low maintenance, just keep using it. If you start from scratch and are going for the free stuff, look at Zotero. If you start from scratch but are willing to buy a software, look at Papers and Sente, try them both and decide afterward.


  2. Nice post!

    I wanted to supplement your comments on Zotero.

    First, it is useful to know that you can synchronize your entire library of citations with the Zotero server or WebDav for free up to a limit (i’ve got about >2000 citations in my database so far). You can pay a premium for extra storage but I haven’t need to do so yet . You need to create an account and register on the Zotero website, then run a java script to synchronize your database with their servers, or WebDav. It works brilliantly updates instantly. I currently have it running on Firefox on my PC in my office.

    After you’ve done this, then you can explore some really fun stuff if you have a tablet, like using a 3rd party an iPad and iPhone client for Zotero, called ZotPad ( which provides a simple interface to connect to your (synchronized) Zotero database. Not only can you access your citations, but you can access your linked PDFs (i.e., read your papers!) from your ZoTero database via ZotPad. If your not into forking out the few bucks for the app, the zotero website is pretty ipad friendly so you can still access you documents from there, although it will be slow.

    With these two I have complete wireless access to my citations and associated PDF papers through my tablet. Using Zotero, along with Zotpad has significantly changed the way how and when I read papers.


    1. Great comment as I did not know about ZotPad.

      For completeness, I would point out that the free portion for automatic sync across multiple devices is only 100 Mb. I agree that this is probably fine for starting graduate students but it will quickly become insufficient.

      My own database of PDF materials in Papers 2 is above 1 Gb. For Zotero services, I would need to factor a cost of 60$/yr for 5Gb (20$/yr for 1Gb).

      Budget wise: Papers desktop is 80$ but with 40% rebate for students which means 48$. Papers for iPad/iPhone is 9.99$ (Canadian app store) exactly the same price as ZotPad. but Papers allows for full sync of annotations, notes, tags, … between the mobile and desktop version. Furthermore, the reading experience and annotation possibilities are quite different ( at least for now) and you get a few extra options with Papers.

      So my recommendation would be as follow:
      1) if you are not using Zotero sync solution (but instead the free DropBox, which is still supported by ZotPad) and you do not have money to put on software, go with Zotero. It will do a very good job and simplify your academic life.

      2) If one of the above is not true, it will be simply less expensive (and much more feature rich) in the long run to get a full blown scientific literature management system with a superb GUI such as Papers or Sente and their mobile version.

      3) If you are a PC+Android person, you might not have much choice anyhow and Zotero might be the best option in the end.


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