Paper Management Tools: What are they? Why use them? and which one to use?

If you’ve been doing any research, be it for an assignment, a report or your dissertation, you will have read at least a few papers or articles or books. While researching for reports during undergrad I used to have a lot of problems frequently :

1. I lost papers or articles that I had read

2. Even in cases where I actually I had papers, I more often than not, forgot what I had read in it and why that particular paper was important.

3. Even if i remembered  a paper and what was in it, it was impossible to find it.

4. For citing the papers in my report, I had to manually enter all the metadata (author name, article, journal, publication date, etc. ) which I could often not find on my printed copy of the paper.

5. I’ve seen huge piles of papers spread across the tables of PhD students. In fact, when I came to my lab for the first time as a PhD student, the size of the stack of papers next to the student indicated how long they had been a research student there.

6. I couldn’t carry all my papers with me.

7. There was also the standard problem of trying to highlight stuff not the paper. Beyond a point, my whole paper would end up highlighted or underlined to show interesting parts.

All these problems can be easily overcome by using online personal digital libraries. The simpler older ones are simply reference managers, like EndNote, Bibdesk, Jabref, etc. The newer ones like Mendeley, wizfolio and Papers are not only reference managers but much more capable pdf organizers as well and for all practical purposes they can be thought of as your own personal library. I’ve tried all these things to different extents over the last two years and I’ll first try to convince you about why it’s really important to use some software like this and also some of the differences that i’ve found between them and why I would recommend some and not the others.

Firstly lets get the simple reference managers out of the way. They are without a doubt extremely nifty tools for paper writing and until recently, it was impossible to work without them. They keep a track of all the papers you’ve read and their metadata. And through plugins and other stuff allow you to easily cite these works in your document. I’ve not really used EndNote much even though that’s the one that I’ve seen most advertised in my university. My supervisor and others who had  used it started cursing the moment I mentioned it, so truthfully, I never gave it a try. But common complaints I’ve heard is that it’s not particularly intuitive. JabRef is a java based (hence cross platform) client for handling your document references provided you use latex. BibDesk is much more powerful but as far as i know exists for mac only. Bibdesk is a seriously good reference manager and allows you to write notes about the paper, store the actual files and other related files and is very stable. I would recommend it to anyone using a mac if it weren’t for software like papers, mendeley, etc.

Zotero is a similar tool which is available as a plugin for firefox.  It can store al sorts of documents with there metadata. The best thing about Zotero is that it can detect some metadata automatically, and that you can organize your papers to categories, give them tags and most importantly, you can directly download them to your database from the internet. Sadly, even though it’s a firefox plugin, the data is stored on your computer itself so unless you find some innovative way to use dropbox there isn’t really anyway you can get your library across computers. And it’s ugly. It takes up a lot of space on your firefox screen and it generally doesn’t look good and isn’t good to use. I gave up on it within a week.

Papers, mendeley and wizfolio are three software that take this to a whole different level. These software in a way are very similar to Bibdesk and zotero, they store documents and metadata and notes about the file and like zotero they have plugins (very buggy ones) that help you import files from websites directly into your database. However, the way the information is presented and the way we interact with the system changes the entire equation.  They have much cleaner, better , more intuitive interfaces, they can most often guess the metadata from the file, they provide you with a facility to read within the app itself and highlight and take notes there itself.  you generally have 3 columns. One with  list of your papers organized in a way you want. Another column shows the paper that you’ve currently selected or the results of the search that you’re currently doing. And the last one is generally the notes you’ve taken down about the particular paper. Besides organizing them in hierarchies you can generally add your own tags. Also they have in built searches that search the document’s text, and metadata and notes for the keyword that you searched. So it becomes a lot easier to find that paper you read three years back which you remember was written by a chap from Cornel and which mentioned a crystal ball in the second page….

Wizfolio is the youngest of the lot and the one I’ve used the least. It’ s very intuitive. It is supported by a lot of online repositories which makes it good at getting metadata. It allows you group into categories and allows you to store all kinds of documents ranging form videos, pictures to website and books.. In fact it even provides a built in youtube search engine. For existing mendeley users it also provides an import from mendeley option the imports all the papers and their metadata without any problems. I’ve also heard they have a very awesome iPad app. The only reasons I don’t use it is because it only there on the cloud and that mostly makes it a pain because i don’t always have internet connection and quite frankly I’d prefer switching of the distraction of the internet when working towards my final deadlines.

Mendeley is perhaps the most popular of the lot. Like Wizfolio your documents are stored on the cloud. Mendeley also tries to advertise itself as the Facebook for academics through their social networking site. In fact, that is the main feature they advertised initially : the ability to collaborate with others. I’ve not really seen much activity on mendeley in my field, so I’ve found this aspect of it quite pointless. The best thing about mendeley is that they have desktop clients for mac and windows ( I think linux too, though I’m not entirely sure) and it is free as long as you have less than 500 GB of papers and documents. Beyond this, you start having to pay a monthly fee. The data being stored on the cloud allows the desktop clients to be synchronized across different computers; Including all the metadata. I’ve sometimes found problems with this syncing though but most of these issues are in some of the notes and similar metadata and mendeley gives a warning when there are conflicts.  It is extremely good at extracting metadata automatically. It allows you to highlight text and add notes and annotations to the papers besides notes about the paper itself. Another useful feature is the ability to create groups in which all the users get to see papers together. This is an invaluable tool for collaboration or for discussing things with your PhD supervisor and/or other colleagues. The interface is neat and keeps improving though it doesn’t look half as good as papers. Mendeley also provides plugins to import directly from the web ;which only downloads the metadata (and not the pdf) , that too to your cloud database. So I found this feature useless.  They also provide plugins for word and open office to cite in word directly. Since I’ve stopped using word for a while now, I’m not entirely sure how good these plugins are. It also has mobiles apps for iPhone, iPad and the android OS. It’s been at least a year since I tried the app out. I initially found it pointless because it would only store references on the mobile by default. Overall, Mendely is amazing and if you use multiple platforms, if you want something that’s free (till 500GB) and if you’re one of the lucky ppl with an actual mendeley community in your area of research, then go ahead and use mendeley.

Finally lets get to Papers which is my favorite. Unlike the previous two, this stores all the data on your hard disk. But by storing the library in your dropbox folder this problem can be easily overcome. As in mendeley, they also have an iPhone version (no android version) and a really really good iPad app which is beautiful and allows to make notes and stuff on the paper. Papers for the mac does not allow you to make annotations directly, though you can open PDFs directly in 3rd party PDF readers like skim which does allow you to annotate. Some of the key advantages of papers over mendeley is it’s beautiful interface. Reading a bunch of dreary papers, this actual does matter quite a bit to me. I love good design. Papers2 allows you to specify as much , if not more, metadata than mendeley. It is also slightly better at grabbing metadata from files than before (though I think mendeley’s is still better). It has an in built search engine for searching multiple databases like google scholar, scopes, web of science, etc.. You can also put in your libary’s proxy so that you get to access this papers and download them directly. They’ve recently included a social element called live to it because of the competition, but I haven’t tried this much and I’m not sure how much it’ll work considering they don’t have a website. It only a free trial for a 30 days, beyond this it is paid software and expensive enough to discourage most students. However, there is one killer feature because of which I willingly paid the registration fee: Papers manuscripts. Generally when we’re citing papers in latex,  we export a .bib file containing all this metadata and use the generated or pre specified ‘cite keys’ to refer to each document to cite. This can invariably be a pain, having to look up the cite key for each paper. Simlarly for word, there are two ways to specify references, either use the in built reference manager provided by Word or use plugins provided by endnote or mendeley. If you had to refer to some paper or citation in something totally different, like a powerpoint presentation or an email you’re sending someone, you were on your own. Papers2 changes all that. Wherever you are, you press ctrl key twice and a small search box opens up, you type a word or a phrase that you remember from that paper (author, title, journal, year, your notes, affiliated university or content or anything else) and the paper is shown to you; you can then insert it as a cite command on papers or as a formatted reference as per your need. So you can literally have all your papers at your fingertips!( I think for citations in word you might have to export to endnote and then use their plugin).

Awesome, eh?

One formatted reference has been inserted. The pop up box appears on pressing ctrl twice. And entering RV returns all the papers with RVO model being used in them and you can choose one to cite or enter a formatted reference

Oh and one last thing, all these softwares being new are being constantly updated and new features are coming at a very frequent rate, so I’m sure this post will be outdated pretty soon. But as of now, I see mendeley updating a lot more frequently than papers. Papers has recently started stating what all they are working on on their forums and this is i believe an extremely good idea.

Addressing some general issues-

The first and most common complaint that I’ve heard is that reading on a screen is a pain. This shouldn’t discourage you from using one of these softwares because, firstly, there is nothing preventing you form actually printing the paper out and reading and just using the software to note down important points. In fact, papers even allows you to keep a track of which papers you have already printed. Besides, I think this problem will be overcome over the next few years by a better kindle or a more widespread use of the e-ink technology.

Entering metadata is a pain; but a lot of these apps get information automatically. However, they’re not really good at it and more often than not you’ll have to enter the metadata in yourself. But this is anyway, necessary since you would need references.

Most of them are free and very intuitive to use. So there is practically no learning curve to start using. In the unlikely case that you do need help, they have good forums.

What if you already have a lot of papers? If you already have soft copies of files you can just drag and drop them inside these. If you have hard copies, papers allows you to directly scan in papers and the others can store images in their library so you could just scan and store in the library. It’s definitely worth the hassle if you’re likely to read a lot more papers over the rest of your career or even just for the next few years.

I can’t think of any other issues, but if you do have any please don’t hesitate to voice it in the comments.

Concluding remarks :

I don’t think a research student should be without a paper management tool like Papers or mendeley. It keeps you organized and it saves all those trees and prevents global warming and helps make the world a better place for you and for me and the entire human race (

Some other (slightly dated) links : : tabular comparison of zotero, mendeley and papers …most of the ‘no’s for papers are ‘yes’s now. I wanted to make something like this. But feels like too much effort for now. I will make one later and edit this post. : Old but interesting nonetheless. Most of the disadvantages mentioned here have been overcome  : Papers creator in defense of why papers and bid desk have different clientele. Again, this is old, with Papers2 they’ve just taken over bib desk’s clientele too…

If you know any more links for good reviews/ comparison of these software, please do post below and I shall post it here for anyone’s reference.


5 thoughts on “Paper Management Tools: What are they? Why use them? and which one to use?

  1. Man, if only I had something like this before I did my FYP! Phew, would’ve saved me so much trouble. But nice detail there 🙂
    – Vivek

  2. Hi
    Thanks for this interesting post
    I think that you can give a new try to Zotero (I’m a great fan of this software) because they are developping a standalone version (today in beta) with it you are not forced to use Firefox



  3. @Vivek … I know, sadly even I got to know about all these after FYP only. and thanks for the comment 🙂

    @François … Thanks for your comment too. Didn’t know about the standalone version of Zotero. That does make it more enticing. Shall give it a try at some point of time. 🙂

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s