Software for research and study - apps that keep me sane

I've been studying for an awfully long time. The studying life can be hard, but since it allows me to wake up at noon and work while watching cricket, I don't see myself toddling off to contribute to the nation's GDP anytime soon.

It's only recently, though, that I've started to clever software from the internets to help organise and keep safe my literature collections, citations, and documents. I used to do all my referencing manually all through undergrad and much of postgrad, but there comes a time when you realise it's time to use the tools that are out there to save more time for drinking and catching up on Gossip Girl. Here are my top five favourite applications to help me with my work - hopefully they might help others too.


Zotero
Zotero is a reference management application (like Endnote, sort of). Unlike Endnote, however, it's free and open source. Zotero has cite while you write plug-ins for Word and Open Office, which I find somewhat better than Endnote's as they allow easy editing of citation name display without using the 'exclude author' option [e.g. changing from '(Johnson & Wills, 2005)' to 'Johnson and Wills (2005)']. It's also not nearly as prone to destroying pieces of work when you do terrible things like, say, copying and pasting a reference from one paragraph to another. The real benefit of Zotero, though, is its capabilities in terms of saving and organising literature and citation data - when looking at an article or abstract from an online database, one click will save both the literature and its citation data. You can then organise literature into collections, apply tabs, attach rich text notes to articles, and annotate (html) documents. Zotero actually works as an add-on to Mozilla Firefox, which means no problems with cross-platform work, and has a very active forum-based support community.

Dropbox
Dropbox is a very simple online sync/save app that means you can stop worrying about emailing documents to yourself or using a flash drive if you're working across multiple computers. Dropbox works very simply: a "My Dropbox" folder is installed wherever you want it in your computer, and you put your important docs/literature etc. into this folder. Dropbox then continuously syncs whatever's in your My Dropbox folder to their online server. You can then install Dropbox on another computer, and data in the My Dropbox folders on each computer will be kept synchronised! You can also log on to the Dropbox website to access and download your documents (and revert recent deletions) when you're on a computer where installing the Dropbox app isn't practicable. Dropbox is free for the first 2GB of storage, with paid options for more space, and 250MB extra if you invite friends/accept an invite to start with. The link below is an invite from me and will give both thee this extra 250 megs:
https://www.getdropbox.com/referrals/NTE1MjU0MzE5

Do be aware that there is the possibility that DropBox employees could look at what you have in your storage - so for sensitive information (e.g. participant data) I'd suggest encryption (e.g. via TrueCrypt).

Syncback
While DropBox is great, I don't use it as my primary storage point for my main project (MA thesis) at the moment because of the quantity of literature and documents I have and the fact that I do most of my work at home and only a little at uni - i.e., getting the My Dropbox folder at uni up to date means waiting a fair while for stuff to download each time I do use the uni labs. So I still use a flash drive for my main collection, with backups to My DropBox on my laptop hard drive (you can't install a My Dropbox folder on a flash drive without mounting trickery and risking deletion when you remove the drive). To backup the data on my flash drive I use Synback, a really nice and easy to use backup/synchronisation utility. Synback allows both manually run and scheduled backup and synchronisation tasks - it's pretty much as simple as choosing a source (the folder/s you want to backup) and a destination (where to back up to), and you're away. Synback uses incremental backups, so it can backup only data that has been changed since the last backup - making it a very quick process usually.

The only sticking point for me is that Syncback requires administrator privileges for installation, meaning I can't install it on my network drive at university. I've tried a few different other backup utilities that don't require admin privileges, but without much joy. Suggestions welcome.

Pdfxchange Viewer
In the past, if I wanted to make notes and annotations to a journal article in pdf format, I'd either print it or create a new Word document with notes about the article. Both of these options are a massive pain. Pdfxchange is a pdf viewer (much like Adobe Reader), but unlike Reader, it allows highlighting and annotations (except where these options have been specifically deactivated by the document author). Being able to highlight and add text notes to articles in pdf format is just fantastic. Of course, when working at uni you usually have access to the full (expensive) Adobe Acrobat, so making annotations is easy enough - if you do most of your work at uni, changing file associations so Adobe Acrobat (rather than Reader) is the default application for pdf files is a good alternative to pdfxchange.

Pdfxchange is Windows-based, but can be run via Wine in Linux - I haven't figured out how to make pdfxchange work as the default file association for pdf files in Linux though (you need to use a script apparently - just changing the file association in the usual way opens pdfxchange in Wine but doesn't open the document, strangely).

PDFill PDF Tools and PDF Writer
Aside from annotations and highlighting, I often need to save Word documents in pdf format or remove unnecessary pages from a pdf document (e.g. scanned cover pages from interloaned documents which waste space). These two utilities from PDFill are great for this. To use the writer you just go to print your Word document and select PDFill write from the printer options, whereas PDF Tools is a standalone app with easy to use options. I actually think the writer was automatically installed when I installed the tools app, so you might not need to download both.


Thoughts on these applications and the apps that help you with your research very welcome!