Improve your citations in 5 easy steps!

Oh clickbait. You are my fave. But seriously, because I've started to get to the writing phase of research (as opposed to the how-long-can-I-keep-doing-econometrics-without-putting-any-words-on-the-page phase), I've put some time into figuring out how to best manage my bibliographies. What I really want in a citation system is the ability to auto-generate a citation, without me having to type things in by hand wherever possible; to export to BibLaTeX; to attach PDFs to my citation library; and to store these citations and PDFs in the cloud somewhere. After searching far and wide and being given a recommendation by my much-more-tech-savvy-than-I colleague Kenny Bell, I've arrived at a solution that I really like:

Zotero + Zotero browser plugin + Better Bibtex plugin + Zotfile + Dropbox!

It takes a little while to set up, but trust me, it's worth it

No more of this with my bibliographies! 

No more of this with my bibliographies! 

The installation process is a little bit of a pain, and I couldn't find a single guide that gave me all of the steps in one place, so I'll try to lay it out here. The basic idea is that I'm going to install and use Zotero to organize citations; the Zotero chrome plugin to auto-generate new ones; the Better Bibtex plugin to export things to BibLaTeX and auto update citations (bonus points for syncing with ShareLaTeX - more on that later); the Zotfile plugin to move/rename files (we'll see why in a second); and Dropbox to actually store the PDFs associated with the Zotero citations. I'm doing things this convoluted way because Zotero, while otherwise great, gives you almost no free storage space, and their own cloud storage is expensive. I have ample (okay I'm actually almost out of my 1TB allocation but SHH) space on Dropbox, and it syncs to the cloud, so that's the ideal place for me to keep my PDFs. 

Edit: Note that you can even do this on multiple computers. Make sure you do the below steps on all of your computers that you'd like to sync, and just make sure that your filepaths lead to the same Dropbox folder. Thanks, Matt!  New request: If anyone knows how all of this works with multiple authored Zotero folders, let me know. I was under the impression that it wouldn't, but as with all things, I might be mistaken. If you're better than me at Zotero, feel free to write in a comment or shoot me an email!)

(Step 0: Install Dropbox. If you don't already have a Dropbox account, I don't really know how you're running your life. Go. Run. Download. Change your world.) 

Step 1: Install Zotero and make an account. I prefer Zotero standalone, but you're welcome to also give the Firefox version a try (I haven't been using it, so no promises).

Step 2: Install the Zotero plugin for your favorite browser. Now when you go to a page with a paper (here, for example), you should see a little paper icon in your web address bar. If you click on it, it will auto-download the citation, and if you've got permission, the PDF, to Zotero. Sweet. (One quirk, at least of the Mac version - Zotero will let you set up folders for different projects. You need to make sure you have the right project folder open when you auto-generate a citation in this way, otherwise Zotero will file your citation in a different place.)

Step 3: Install the Better Bibtex plugin for Zotero. (Scroll down to Installation (one-time)), and click on the ``latest version'' link. There are now instructions on the Github page, but in case you missed them, open Zotero, go to Tools>Add-ons; click on Extensions; click on the gear and click 'Install Add-on from File...', navigate to the .xpi file you just downloaded, click 'Install', and restart Zotero. Now you should be able to export your bibliography to BibLaTeX (you can even auto-export. Cool.). To export a bibliography, open Zotero, click on the gear icon, and scroll to 'Export Library'. (I like to export with Better BibLaTeX, and to keep 'auto-update' checked, but more on that in a bit.)

Step 4: Install the Zotfile plugin for Zotero. Download the .xpi file, and follow the same steps as above to install it.

Step 5: Set Zotero up to store things in your Dropbox folder. This is where things get a little bit complicated, but bear with me.

5A - Syncing: Unsync your PDFs from the Zotero server. To do this: go to your Zotero preferences (File>Preferences or the gear). Click on Sync. Under File Syncing, uncheck both of the boxes ('Sync attachment files ...') This will stop your PDFs from uploading to the Zotero server (but only your PDFs. Your citations will still sync). 

5B - Zotero file path: Tell Zotero to keep your PDFs in your Dropbox folder. Go back to Zotero preferences, and this time, go to the Advanced tab. Where it says 'Base directory', click Choose. Change your file path to a folder inside your Dropbox. (Mine is just /Dropbox/Zotero). This is the first step in getting your PDFs to save into Dropbox.

5C - Zotfile file path: Tell Zotfile where you're keeping your PDFs, and move things if necessary. Click on the gear icon, and go to the Zotfile preferences. Under the General Settings tab, change your Location of Files path to Custom Location, and choose the same filepath as you had above (/Dropbox/Zotero). Check the 'Use subfolder defined by...' box if you'd like your PDFs not all to be in the same folder. I've set mine up as /%c, which puts each project (Zotero folder)'s papers in their own folder. If you're picky about how your PDFs are named, go to the Renaming Rules tab, and play around. 

5D - Move existing files: Finally! If you've downloaded any PDFs at this point, select all of your citations that have attachments, right click on them, and pick Manage Attachments>Rename Attachments. Zotfile will now move these guys to your Dropbox folder. Any new citations you download will be put into Dropbox automatically. YES.

Done. Enjoy your new awesome citation manager.

Bonus step: ShareLaTeX. I've also gotten on the ShareLaTeX bandwagon. I've actually been using ShareLaTeX since I was in college, but it's way bigger and better now. The basic upshot is it's GoogleDocs for LaTeX - so you can share with your co-workers, etc. I've upgraded to the paid version, because it's cheap for students; it allows track changes (how can you write a paper with someone else without???); and it allows syncing with Dropbox. Every time you compile, ShareLaTeX will sync the .tex file to my Dropbox. I can also upload images/tables/etc to ShareLaTeX / Dropbox and have them upload in the other. Awesome. Bonus points for doing this with Zotero/Better BibLaTeX - remember how BBL lets you automatically update your bibliography? I've set my bibliography file to be in my ShareLaTeX folder - so any time I make a change to my Zotero collection for a given paper, the .bib file updates by itself and gets added to my ShareLaTeX repository. Yes please.


Any really good productivity tools I missed? Let me know.