As I have recommenced study at university, I have a renewed interest in software and systems that facilitate good research habits and consistently reliable access that research in a way that doesn't interfere with me getting my thoughts and ideas committed to paper. I think I have landed on a great setup that makes research fun again. Maybe this could help you too?

Even though my university has made EndNote freely available to students, and and the proliferation of EndNote "integration" in library searches, the reality of actually using this system is something akin to torture. EndNote routinely crashes, looses my annotations, notes and musings, incorrectly stores files against the wrong references, and is generally a giant pain in the arse!

Thankfully, a friend of mine (ex-academic, and all round nice guy, Dr K. Diment) put me onto Zotero a while ago! This is an open-source, free alternative that actually delivers on all the promises of EndNote, but without the headaches, and is supported on Windows, Mac and Linux. After installing Zotero and spinning up the integration for my preferred word processor, and adding the browser plugin too, out of the box I have:

The ability to create hierarchical research folders in Zotero to structure my work based on a subject, topic, or whatever seems most appropriate.
Searching the university's library and hunting down a journal article or thesis only requires a single click on the Zotero browser plugin and it is inserted into the folder of my choosing, or defaults to the last one I specified.
If a full-text PDF etc was available in #2, it gets downloaded and linked to the article I now have referenced in my Zotero library.
Now that I have a full-text PDF, I can open that and make annotations, take notes, etc, and these are added to the article in Zotero (see 'Zotfile' extension below)
When writing my papers and assignments I can now easily insert citations in practically any format (APA6, Harvard, etc) AND get a reference list that is correctly sorted.

Not bad for something that's FREE. However, we can make it better :)

Zotero has a rich plugin ecosystem too so you can add additional conveniences such as DOI verification/shortening, duplicate file detection (same article, different reference etc) and a number of other interesting workflow enhancements. Three of my must-have extension for anyone getting started are:

Zotfile: automatically rename, move, and attach PDFs (or other files) to Zotero items.
- It also can scan your annotated PDFs and add those as notes. I can't emphasise enough this one feature, it's what makes my entire workflow, well, "work".
DOI Manager: a one-stop manager for all thing DOI related!
- Look up DOI names from CrossRef
- Automatically retrieve shortDOI names from http://shortdoi.org and replace them in the Zotero DOI field.
- Check DOI validity and mark items with invalid DOIs.
- Clean the DOI field (e.g., to remove http://doi.org/).
Storage Scanner: Scan your Zotero storage folder for missing attachments and possible duplicates

With that trio, you are now blitzing past EndNote's clunky interface, sketchy workflow, and research starts becoming FUN! Have I mentioned Zotero is free?

Need to work on multiple machines or platforms? Zotero has you covered. If you create a Zotero account you can synchronise your research to their cloud infrastructure which will allow you to use Zotero anywhere you have a web browser, Zotero installed or a compatible mobile app! Free accounts come with 300MB of storage, or for a paltry USD$20/yr you get 2GB (keep in mind we're dealing with usually small PDFs etc). If you want the full "unlimited" experience you're up for USD$120/yr. There are ways roll-your-own synchronisation with OneDrive/Dropbox/Google Drive etc, but the ability to use anything other than a native Zotero application will be limited.

For instance, I use a program called Papership for iOS to access all my research and notes/annotations etc on my iPad. I find it a great platform to read and take notes whilst away from "home base". Your mileage may vary, but it works really well for me.

"Zotero" is a trademark of the Corporation for Digital Scholarship.

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