2020 remark: This article was first published in 2011 under the name A little guide to Reference Manager application.
No one can say that they never use PDF files nowadays. It’s fast, easier, and reliable file format for storing any documents. I myself also need to read lots of PDFs research papers. At first it seems much easier than go to library and look for some books. However, when all the PDF files came together in your computer, a nightmare begins! Now all these PDFs are all over your computer that you have to look for it everywhere even in the deepest corner (err.. actually folder) of your computer. It’s now take a lot of effort just to find which PDF contains the content you’re looking for, not even think about writing the bibliography! You may try to manage them into order manually, but it’ll surely turn into a painful experience. When it came to this, a good Reference Manager application can save your life ( and lots of time, of course).
There are many reference managers nowadays. Some of them only be able to manage the reference data in BibTeX format (a global standard script for bibliography) which are not so useful compare to the other mentioned here. These are the list of renown reference manager applications your should check them out;
1. EndNote
One of the most widely used reference manager among the professionals and researchers. Many institution have it available for their member. However, its price is quite expensive as almost $300, thus, make me to look for its alternatives. (Its website also not so attractive, though.)
2. Papers
http://www.mekentosj.com/papers/
I never uses this application myself. Many of my friends told me this is one of the very good reference manager available on Apple Mac. However, it’s ONLY available for Mac. So sad for Linux and Windows user like me. Its price is about $79 and it seems to have a good Apple style. Also available on iOS as well. The good thing I saw for this application is its ability to search the research papers directly in its application.
3. PDF Stacks
A good and easy to use reference manager. Actually it works well to organise the PDFs all over the computer into one place. Its disadvantage is that good thing is the only thing it can do. No cloud service or sync system at all. Its price is not so expansive about $40.
4. Zotero
Zotero is a FREE reference manager which is a Firefox extension. The best thing is that it integrates itself into browser and, therefore, have the ability to store and manage the reference sources during visited their site. It’s also provide online sync system to sync across the computers. The disadvantages of it are, firstly, it is the Firefox extension which means you’re required to use Firefox in order to use it. Secondly, I found it’s not so easy to use compare to other applications. Lastly, if its online storage (which is quite small) is not sufficient, you have to upgrade its size with a monthly charge.
5. Mendeley
This application is quite interesting because it’s FREE. Easy to use, full feature reference manager with ability to organise the PDF libraries, read, highlight and put a note into PDFs. It has a cloud service to sync entire library to other computers as well as iOS devices. Moreover, it can work well on both Windows/Mac/Linux desktop and on website. It also has the online community and database which can search for articles’ data and provide the related articles. Its drawback is that it only provides 500MB free online storage. To use more than this quota, you need to pay for it monthly at least $5 a month. I personally recommend this application over the others because of its full functionality and its price.
6. Qiqqa
This application is also FREE! Full feature reference manager with online sync service. It’s also very good compare to other applications discussed so far. It lacks of the online database of Mendeley but, however, it has the better PDF viewing, highlighting, Adding note than Mendeley. It’s also have the brainstorm system to help the collaborating work. However, I found that its interface is a little bit confuse and hard to use. It provides 200MB free online storage for storing and syncing the documents which is quite small, however the expansion price is quite cheap less than $1. Even though its online service is cheap, I found that its web library really lacks of useful functions. No mobile devices platform also, which they suggest to use the web library (which lacks of functionality) instead. Also, its online service requires users to top-up their account in order to store and sync files if free space is not sufficient, which is not quite so comfortable compares to a normal subscription methods.